Bioinformatics analysis of genes related to ferroptosis in hepatic ischemia-reperfusion injury

Sun, Shuo; Xue, Jianming; Guo, Yunfei; Li, Jianling

doi:10.3389/fgene.2022.1072544

Cited by 4 publications

(4 citation statements)

References 44 publications

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“…The pathophysiology of IRI remained elusive, and bioinformatics became an essential tool for discovering novel genes of IRI, such as renal IRI [37], cardiac IRI [38], hepatic IRI [39], and intestinal IRI [40]. In this study, we identified five CR-associated DEGs, including DUSP1, GADD45A, GADD45B, GADD45G, and HSPA1A, which were upregulated in human renal IRI tissues after kidney transplantation.…”

Section: Discussionmentioning

confidence: 93%

GADD45A and GADD45B as Novel Biomarkers Associated with Chromatin Regulators in Renal Ischemia-Reperfusion Injury

Xie

Huang

et al. 2023

IJMS

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Chromatin regulators (CRs) are essential upstream regulatory factors of epigenetic modification. The role of CRs in the pathogenesis of renal ischemia-reperfusion injury (IRI) remains unclear. We analyzed a bioinformatic analysis on the differentially expressed chromatin regulator genes in renal IRI patients using data from public domains. The hub CRs identified were used to develop a risk prediction model for renal IRI, and their expressions were also validated using Western blot, qRT-PCR, and immunohistochemistry in a murine renal IRI model. We also examined the relationships between hub CRs and infiltrating immune cells in renal IRI and used network analysis to explore drugs that target hub CRs and their relevant downstream microRNAs. The results of machine learning methods showed that five genes (DUSP1, GADD45A, GADD45B, GADD45G, HSPA1A) were upregulated in renal IRI, with key roles in the cell cycle, p38 MAPK signaling pathway, p53 signaling pathway, FoxO signaling pathway, and NF-κB signaling pathway. Two genes from the network, GADD45A and GADD45B (growth arrest and DNA damage-inducible protein 45 alpha and beta), were chosen for the renal IRI risk prediction model. They all showed good performance in the testing and validation cohorts. Mice with renal IRI showed significantly upregulated GADD45A and GADD45B expression within kidneys compared to sham-operated mice. GADD45A and GADD45B showed correlations with plasmacytoid dendritic cells (pDCs) in infiltrating immune cell analysis and enrichment in the MAPK pathway based on the weighted gene co-expression network analysis (WGCNA) method. Candidate drugs that target GADD45A and GADD45B include beta-escin, sertraline, primaquine, pimozide, and azacyclonol. The dysregulation of GADD45A and GADD45B is related to renal IRI and the infiltration of pDCs, and drugs that target GADD45A and GADD45B may have therapeutic potential for renal IRI.

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Section: Discussionmentioning

confidence: 93%

GADD45A and GADD45B as Novel Biomarkers Associated with Chromatin Regulators in Renal Ischemia-Reperfusion Injury

Xie

Huang

et al. 2023

IJMS

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“…Five genes (ATF3, IL6, IL1B, CDKN1A, and PTGS2) and several miRNAs (miR-128-3p and miR-24-3p) were identified[ 54 ]. Subsequently, Maresin conjugate in tissue regeneration 1 ameliorated ferroptosis-induced HIRI by promoting nuclear factor erythroid-derived 2-like 2 expression[ 55 ]. However, μ opioid receptor alleviated ferroptosis in HIRI via the HIF-1α/ axis[ 56 ].…”

Section: Hiri and The Underlying Mechanismsmentioning

confidence: 99%

“…Acidic microenvironment has been reported to be a key factor affecting HIRI through the regulation of PPAR-γ[ 26 ]. Besides, lipid metabolites[ 57 , 58 ], calcium overload[ 56 ], adenosine triphosphate depletion[ 55 ], gap junctions[ 6 ], dysfunctional microcirculation[ 5 , 53 ], and endoplasmic reticulum stress[ 26 , 29 ] can affect the development of HIRI.…”

Section: Hiri and The Underlying Mechanismsmentioning

confidence: 99%

Non-coding RNAs: The potential biomarker or therapeutic target in hepatic ischemia-reperfusion injury

Shao,

Wang,

Xiao

et al. 2023

World J Gastroenterol

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Delayed passage of meconium or constipation during the perinatal period is traditionally regarded as a signal to initiate further work up to evaluate for serious diagnoses such as Hirschsprung’s disease (HD), meconium ileus due to Cystic Fibrosis, etc. The diagnosis of HD particularly warrants invasive testing to confirm the diagnosis, such as anorectal manometry or rectal suction biopsy. What if there was another etiology of perinatal constipation, that is far lesser known? Cow’s milk protein allergy (CMPA) is often diagnosed in infants within the first few weeks of life, however, there are studies that show that the CMPA allergen can be passed from mother to an infant in-utero, therefore allowing symptoms to show as early as day one of life. The presentation is more atypical, with perinatal constipation rather than with bloody stools, diarrhea, and vomiting. The diagnosis and management would be avoidance of cow's milk protein within the diet, with results and symptom improvement in patients immediately. Therefore, we discuss whether an alternative pathway to address perinatal constipation should be further discussed and implemented to potentially avoid invasive techniques in patients. This entails first ruling out CMPA with safe, noninvasive techniques with diet modification, and if unsuccessful, then moving forward with further diagnostic modalities.

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“…Hepatectomy and liver transplantation are the two major surgical procedures for the treatment of primary liver cancer, which is the sixth most common cancer in the world ( Sung et al, 2021 ; Maki and Hasegawa, 2022 ). HIRI is generally unavoidable during both operations ( Sun et al, 2022 ). HIRI is the most common cause of hepatic dysfunction or functional failure after liver surgery and can even be life-threatening ( Lentsch et al, 2000 ).…”

Section: Introductionmentioning

confidence: 99%

The application of optical technology in the diagnosis and therapy of oxidative stress-mediated hepatic ischemia-reperfusion injury

Wang

Shao²,

Chen³

et al. 2023

Front. Bioeng. Biotechnol.

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Hepatic ischemia-reperfusion injury (HIRI) is defined as liver tissue damage and cell death caused by reperfusion during liver transplantation or hepatectomy. Oxidative stress is one of the important mechanisms of HIRI. Studies have shown that the incidence of HIRI is very high, however, the number of patients who can get timely and efficient treatment is small. The reason is not hard to explain that invasive ways of detection and lack of timely of diagnostic methods. Hence, a new detection method is urgently needed in clinic application. Reactive oxygen species (ROS), which are markers of oxidative stress in the liver, could be detected by optical imaging and offer timely and effective non-invasive diagnosis and monitoring. Optical imaging could become the most potential tool of diagnosis of HIRI in the future. In addition, optical technology can also be used in disease treatment. It found that optical therapy has the function of anti-oxidative stress. Consequently, it has possibility to treat HIRI caused by oxidative stress. In this review, we mainly summarized the application and prospect of optical techniques in oxidative stress-induced by HIRI.

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Bioinformatics analysis of genes related to ferroptosis in hepatic ischemia-reperfusion injury

Cited by 4 publications

References 44 publications

GADD45A and GADD45B as Novel Biomarkers Associated with Chromatin Regulators in Renal Ischemia-Reperfusion Injury

GADD45A and GADD45B as Novel Biomarkers Associated with Chromatin Regulators in Renal Ischemia-Reperfusion Injury

Non-coding RNAs: The potential biomarker or therapeutic target in hepatic ischemia-reperfusion injury

The application of optical technology in the diagnosis and therapy of oxidative stress-mediated hepatic ischemia-reperfusion injury

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