The expression of oxidative stress genes related to myocardial ischemia reperfusion injury in patients with ST-elevation myocardial infarction

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

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.

The heat shock protein DNAJB2 as a novel biomarker for essential thrombocythemia diagnosis associated with immune infiltration

BACKGROUND AND OBJECTIVE

Essential thrombocythemia (ET) is a rare myeloproliferative malignancy which may lead to severe thrombohemorrhagic complications. The diagnosis of ET is primarily based on bone marrow morphology and exclusion of other possibilities of myeloproliferative neoplastic diseases; the lack of gene biomarkers fails to provide a prompt diagnosis of ET. Therefore, this study was designed to identify biomarkers for early ET diagnosis, especially that associated with immune cell infiltration, by using the Gene Expression Omnibus (GEO) database and machine-learning algorithms.

METHODS

Two publicly available gene expression profiles (GSE9827 and GSE123732) from the GEO database were used to identify the differentially expressed genes (DEGs) between bone marrow samples of ET patients and healthy individuals, and functional enrichment analyses were conducted. The least absolute shrinkage and selection operator (LASSO) regression model and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) machine-learning algorithm were performed to select the candidate gene biomarker. The expression level and diagnostic effectiveness of the identified gene biomarker were further validated using GSE567 and GSE2006 datasets. The involvement of infiltrating immune cells and their correlations with the gene biomarker were examined using cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm.

RESULTS

There were 105 DEGs identified between ET and healthy control samples. Disease Ontology (DO) analysis showed that the diseases enriched by those DEGs were mainly human cancers, neurological diseases and inflammation while Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that pathways related to immune responses were primarily involved. The heat shock protein, DNAJB2, was identified as the potential biomarker for ET diagnosis with high effectiveness, with the area under the receiver operating characteristic (ROC) curve (AUC) equals to 0.905 in the validation cohort. The expression level of DNAJB2 in ET samples was indeed significantly higher than that in healthy control ones. The immune cell infiltration analysis showed that DNAJB2 was positively correlated with CD8+ T cells in ET with the proportion significantly higher than that in normal controls.

CONCLUSION

The present study identified DNAJB2 as a novel diagnostic biomarker for ET with high effectiveness based on ET and normal samples from the GEO database, which provides new insights into predicting ET with accuracy and promptness in clinical practice.