Single-cell RNA sequencing analysis of baicalein’s immunomodulatory effects in lung graft ischemia-reperfusion injury
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE285146 | GEO | 2025/03/25
REPOSITORIES: GEO
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Project description:Background: Hepatic ischemia reperfusion injury (IRI) is a complex clinical complication during surgery and often leads to cell damage and dysfunction. N6-Methyladenosine (m6A) is an emerging epigenetic modification that plays key roles in the regulation of biological functions and cellular mechanisms in IR injury in different organs. However, the understanding of m6A-modified mRNAs in hepatic IRI is limited. Methods: Methylated RNA immunoprecipitation with high-throughput sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were used to profile the transcriptome-wide distribution of m6A methylation for hepatic IRI in mice. Results: In this study, there were 2061 nonoverlapping m6A peaks within 22471 coding gene transcripts (mRNAs) in the sham group and 2669 nonoverlapping m6A peaks within 22766 coding gene transcripts in the hepatic IR group. The distribution of m6A peaks was especially enriched in the coding sequence (CDS) and 3'UTR. Moreover, functional enrichment analysis demonstrated that the significantly enriched terms of genes with upmethylated m6A sites were the mRNA surveillance pathway, purine metabolism and metabolic pathways, and the significantly enriched terms of genes with downmethylated m6A sites were the Rap1 signaling pathway, sphingolipid signaling pathway, platelet activation, Wnt signaling pathway, chemokine signaling pathway and focal adhesion. Furthermore, we identified a relationship between differentially methylated genes and differentially expressed genes to obtain the three overlapping predicted target genes (Fnip2, Phldb2, and Pcf11). Conclusions: Our study first identified a transcriptome-wide map of m6A mRNAs in hepatic IRI. An in-depth analysis according to methylation modifications will provide effective treatment strategies and a theoretical basis for future research in terms of molecular mechanisms.
2023-05-12 | GSE190216 | GEO
Project description:Purpose: Cyclic mechanical stretch (CMS) promoted proliferation of serum starved mesenchymal stem cells (MSCs) by inhibiting miR-337 expression, similar to FBS. In order to reveal the underlying mechanisms of both CMS and FBS on MSC activation, as well as the regulatory role of miR-337, this research performed high-throughput RNA sequencing (RNA-seq) on MSCs isolated from both wild-type (ET)- and miR-337 knockout- (miR-337-/-) rats. Methods: MSCs isolated form 2-month-old wild-type (WT) and miR-337 knockout (-/-) rats and cultured in vitro to passage 3. After serum starvation for 8h, MSCs were treated with FBS or 10% CMS for another 24h before deep sequencing in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level. Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample. We identified 2472 differentially expressed genes (DEGs) between CMS-stimulated vs. SSt conditions, 2468 DEGs FBS-treated vs. SSt groups. However, only 97 DEGs were identified between CMS and FBS groups, indicating that CMS and FBS groups are more similar to each other and both CMS and FBS groups are quite different from the SSt group. Analysis of DEGs between CMS- or FBS-treated and SSt -treated group revealed that CMS and FBS stimulation activated similar biological processes, of which, PI3K-Akt-mTOR pathway was highly enriched. However, PI3K-Akt-mTOR pathway was not enriched in miR-337-/- MSCs, indicating constitutive activation of this pathway. Conclusions: Our RNA-seq data revealed that both CMS and FBS activates quiescent MSCs through regulating similar genes and pathways. miR-337 is one of the main factors that regulate MSC activation by targeting PI3K-Akt pathway.
2021-12-02 | GSE189845 | GEO
Project description:Background and Aims: Liver transplantation is a successful treatment for patients with liver failure. However, organ shortage results in over 11% of patients loosing their chance of a transplant due to worsening of their liver disease. Ischemia/reperfusion injury (IRI) is the major cause leading to graft loss after liver transplantation. Therefore, novel methods of organ-preservation have been developed in recent years to minimize IRI. One such device is the OrganOx metra, a normothermic machine perfusion (NMP) device providing oxygen and nutrition to allow aerobic metabolism and minimizing IRI. OrganOx metra has presented with several advantages compared to conventional cold storage (CS). We aimed to confirm the impact of NMP on reducing IRI and to define the underling mechanisms. Methods: We compared 12 NMP with 27 CS-preserved livers by performing gene microarray, immunoprofiling of hepatic lymphocytes and immunochemistry staining of liver tissues for assessing necrosis, platelet deposition and neutrophil infiltration, and the status of steatosis after NMP or CS pre- and post-reperfusion. Results: Recipients receiving NMP grafts showed significantly lower peak AST levels than those receiving CS grafts. NMP altered gene-expression profiles of liver tissue from pro-inflammation to pro-healing and regeneration. NMP also reduced the number of IFN- and IL-17 producing T cells and enlarged CD4posCD25highCD127negFOXP3pos Treg pool. NMP liver tissues showed less necrosis and apoptosis in the parenchyma and fewer neutrophils and platelet infiltration compared to CS liver tissues. Conclusion: Reduced IRI in NMP recipients was the consequence of the combination of inhibiting inflammation and promoting graft regeneration.
2019-04-10 | GSE112713 | GEO
Project description:The identification of the expression patterns of long non‑coding RNAs (lncRNAs) and mRNAs in the kidney under normal and renal ischemia/reperfusion (IR) conditions is essential for understanding the genetic mechanisms underlying the pathogenesis of renal IR injury. Here, we have carried out a genome-wide long non-coding RNA and mRNA microarray analysis in mice kidneys with IR. The data revealed that the expression profiles of lncRNAs and mRNAs in the kidneys differed markedly between the Sham group and IR group, and in total 276 differentially expressed (>2‑fold) lncRNAs (201 upregulated, 75 downregulated) and 267 mRNAs (192 upregulated, 75 downregulated) were identified. qRT-PCR analysis was performed to verify the expression patterns of several lncRNAs and mRNAs.We found a specific and strongly differentially expressed lncRNA, an renal ischemia-reperfusion (IR) injury associated RNA, termed lncRNA-IRAR, which was mainly located in tubular epithelia cells. In vitro and in vivo gain- or loss-of-function studies were performed to investigate the role of lncRNA-IRAR during renal IRI. Moreover, an expression volcano map of the differentially expressed mRNAs showed that UCP1 was the most dramatically downregulated gene, and its role in oxidative stress and apoptosis was assessed both in vitro and in vivo. Genetic deletion of UCP1 was used to investigate the effects of UCP1 on ischemia -indued acute kidney injury in mice.
2019-05-21 | GSE131454 | GEO
Project description:Ischemia reperfusion injury (IRI) in organ transplantation remains a significant problem with limited alternative therapeutic options. Organs that undergo significant damage during IRI, particularly those enduring long warm ischemia times, undergo significant delayed graft function (DGF) after reperfusion and tend to have greater complications long term with the onset of chronic rejection. The gas molecule carbon monoxide (CO) has emerged as an agent that can suppress IRI in rodent models of solid organ transplantation. Since the use of CO is a potential therapeutic modality in humans, we tested if CO can prevent DGF in a pig model of kidney transplantation Keywords: stress response, treatment response 18 Samples from pig kidneys, two naïve controls, two timepoints, two conditions, 4 replicates
2009-01-20 | E-GEOD-14373 | biostudies-arrayexpress
Project description:Baicalein is a bioactive compound that is found in an herbal plant, Oroxylum indicum, grown in Southeast Asia including Thailand. There are several reports investigating on the bioactivities of baicalein including an anticancer activity. However, there is no report on the anticancer activity of the baicalein in nasopharyngeal carcinoma. Thus, the aim of this study is to identify differentially expressed genes (DEGs) that are targets of baicalein in order to reveal cellular pathways and molecular mechanisms of the baicalein in nasopharyngeal carcinoma. In this study, NPC HK-1 cells were used as an NPC representative and treated with 10 and 20 µM baicalein for 24 hours before collecting cells for whole transcriptome profiles. The results revealed that a number of cellular pathways, based on KEGG enrichment analysis, are affected baicalein treatment such as focal adhesion and PI3K-Akt signaling pathway which were also phenotypically related to cell migration and invasion assays. Changes in transcriptome profiles of baicalein-treated HK-1 cells would provide insight on baicalein activity in NPC.
2022-01-26 | GSE127765 | GEO
Project description:Due to organ shortage, the transplantation community are increasingly using kidney from deceased donors such as donation after circulatory death (DCD) and donation after brain death (DBD). However, DCD donation have increased delayed graft function compared to DBD, an underline mechanism is still not well defied at the molecular level. In this study, we employed a rat model to mimic warm ischemia (45 mins) and reperfusion injury (IRI) for 4h and 24h. Apoptotic and tissue histological staining confirmed apoptosis and necrosis occurred at 4h and 24h post IRI respectively. Tissue proteome study revealed acute phase response, coagulation and complement activation and lipid X receptor activation as major pathway altered in intervention kidneys. Metabolomics follow up disclosed an increased level of lipids and fatty acids (FA). Mitochondrial function analysed by mitochondrial complex I activity and oxygen consumption and ATP levels in intervention kidney tissues were maintained 4h post IRI, but was significantly reduced 24h post IRI. Integrated proteo-metabolome analysis discovered an increased FA beta-oxidation 4h post IRI to sustain energy production. Kidney function were declined 24h post IRI indicated by increased blood creatinine and lactate levels. This study provides the frame work for the design of future metabolic intervention strategies to minimize kidney injury.
2020-07-06 | PXD005101 | Pride
Project description:INTRODUCTION Ischemia and reperfusion injury (IRI)-elicited tissue injury contributes to morbidity and mortality in a wide range of pathologies, including myocardial infarction, ischemic stroke, acute kidney injury, trauma, circulatory arrest 1. Ischemia-reperfusion injury is also a major challenge during organ transplantation and cardiothoracic, vascular and general surgery 1. IRI, one of the biggest challenges for organ transplantation, continues to be a vital source of morbidity among recipients, especially in liver transplantation 2. With the enlarging shortage of available donor livers, the increased use of extended criteria donor grafts further increases IRI, adversely affecting both short-term and long-term outcomes of graft and patient survival 3. Numerous studies have investigated the benefits of pharmacological, heat shock, and ischemic preconditioning interventions aimed at decreasing liver IRI 4. However, the benefit was limited. Our center has been making great effort in conquering IRI and have developed a novel surgical technique called ischemia-free liver transplantation 5. It is an ultimate method to overcome IRI in liver transplantation, but there is still a long way to popularize it. As a result, it is still of great significance to study IRI and identify the core genes in the process and the underlying mechanism. Comprehensive bioinformatics analysis has been increasingly important as a method to study various pathological and physiological condition 6. By enrolling multiple omics or combining different types of omics, comprehensive bioinformatics analysis was able to recognize key factors that could have potentially pathogenic impact such as gene expression, protein function, and downstream pathways. With the rapid development of high-throughput sequencing technologies, several transcriptomic datasets on IRI of liver transplantation have become available in the Gene Expression Omnibus (GEO) database. Herein, we recruited 3 GEO datasets to conduct comprehensive analysis with the GEO dataset from our center. Moreover, we performed the first proteome of liver tissues to study liver IRI. Then the transcriptome and proteome were used for combined analysis to reveal key factors in liver IRI.
2022-02-23 | PXD010812 | Pride
Project description:Ischemia/reperfusion injury (IRI) has a major impact on the long-term outcome of renal allografts. However, the mechanisms of IRI related to chronic allograft nephropathy (CAN) are still poorly understood. To address this issue, in a F344 to Lewis transplantation model of the rat, kidneys were either subjected to 20 min. or 24 hours of cold ischemia. A customized cDNA microarray representing 737 immune related genes was used for gene expression analysis after 12 hours and 6 months of engraftment. Thereby showing the 6-month graft function and histology were only moderately deteriorated following short cold ischemic time (20 min.), while prolonged ischemia (24 hrs) accelerated CAN development. Following prolonged cold ischemia already 12 hrs after engraftment about 30 genes were differentially expressed up to >20-fold. This included adhesion molecules, heat shock proteins, transcription factors and chemokines (CXCL10) associated with a strong CD68+ macrophage infiltration. Furthermore we observed a remarkable up-regulation of immunoproteasomes implying a re-organisation of the proteasome complex. This data might explain the higher incidence of alloreactivity following enhanced IRI. After 6 months, the prolonged cold ischemia of 24 hours revealed the significant induction of 4 genes: clusterin, C4, and the CCR7 ligands CCL19/21. This supported the observation of enhanced vasculopathy, humoral alloreactivity and increased tracking of MHC-II+ antigen presenting cells during CAN suggesting them as suitable novel targets for combating IRI. Keywords: transplantation, cold ischemia, inflammation, gene expression profiling Renal allografts from F344 donors were transplanted into unmodified LEW recipients. Before harvesting, grafts were perfused with University of Wisconsin solution at 4°C undergoing 20 min. (group A) or 24 hrs (group B) cold ischemia. Engrafted organs were either removed after 12 hrs (group I-A (n=3) and I-B (n=2)) or after 6 months (group II-A (n=3) and II-B (n=2)). Recipient animals of the group II received CyA treatment for 10 days at a dosage of 1.5 mg/kg. Untreated normal kidneys from F344 rats served as control. RNA from transplanted and untreated (control) rat kidneys were labeled by reverse transcription with Cy5 and Cy3 fluorescence, respectively.
2010-06-25 | E-GEOD-4441 | biostudies-arrayexpress
Project description:Background Immunosuppressants and renal ischemia-reperfusion injury (IRI) are risk factors for BK polyomavirus infection after kidney transplantation. However, the mechanism remains unclear. Methods We used a model of mouse polyomavirus (MPyV) infection to investigate the mechanism of IRI and immunosuppressants to promote polyomavirus replication. Results After primary infection, MPyV established persistent infection in the kidneys until week 9 and subsequently were significantly increased by IRI or immunosuppressants treatment individually. In IRI group, viral loads peaked on day 3 in the left kidney, which were significantly higher than that in the right kidney and the control group, and then gradually decreased. In immunosuppressants group, viral loads increased on day 3 without significant difference between left and right kidney, which were significantly higher than that in the control group, and then maintained at high levels. Protein-protein interaction network analysis screened complement C3, EGFR, and FN1 as core genes. Pathway enrichment analysis based on the IRI or immunosuppressants related genes selected by WGCNA indicated that NF-?B signaling pathway was the main pathway involved in promoting MPyV replication. We further confirmed our findings using published datasets GSE47199 and GSE75693. Conclusions Our study demonstrated that IRI and immunosuppressants promote polyomavirus replication through common molecular mechanisms.
2021-12-27 | GSE192576 | GEO