miR-25 Regulates Gastric Cancer Cell Growth and Apoptosis by Targeting EGR2

Sensitive detection of miR-21 and miR-25 in gastric adenocarcinoma patient serum using a SERS sensor based on AuNT and enzyme cleavage strategy

MicroRNA (miRNA) detection has significant application value for early cancer diagnosis. In this study, a surface-enhanced Raman scattering (SERS) sensor was developed for detecting miR-21 and miR-25 in the serum of Gastric adenocarcinoma (GAC) patients. The sensor was constructed using arrays of Au trioctahedral nanoparticles (AuNT) and enzyme cleavage techniques. The AuNT was obtained by self-assembly at the oil-water interface, and the Cy5-labeled miR-21 and 5-FAM-labeled miR-25 complementary single-stranded ssDNA-21 and ssDNA-25 were connected with the AuNT to form the SERS sensor. When miR-21 and miR-25 were present, ssDNA-21 and ssDNA-25 were paired and hybridized to form miR-21-ssDNA-21 and miR-25-ssDNA-25 double strands. Duplex-specific nuclease (DSN) could act on the DNA phosphodiester bond in the double strand, causing Cy5 and 5-FAM to be far away from the AuNT, which resulted in a reduction of the SERS signal. In the range of 10 aM to 1 pM, the logarithm of miR-25 concentration was linearly related to the intensity of the characteristic peak of 5-FAM at 1178 cm-1, and the limit of detection (LOD) was determined to be 8.12 aM. The logarithm of miR-21 concentration was linearly related to the characteristic peak intensity of Cy5 at 1367 cm-1, and the LOD was determined to be 4.29 aM. Furthermore, the accuracy of the SERS sensor for the detection of miR-21 and miR-25 in clinical serum samples was evaluated using real-time quantitative polynucleotide chain reaction (qRT-PCR) technology as the gold standard. The relative errors of the two methods miR-21 in healthy people and gastric adenocarcinoma patients were 1.71% and -2.40%. The relative errors of miR-25 were 2.74% and -2.67%. There was no significant difference between the two methods, and the expression levels of miR-21 and miR-25 in the serum of GAC patients were found to be higher than those in healthy individuals. Consequently, this method offers a reliable solution for the early diagnosis of gastric cancer.

STLBRF: an improved random forest algorithm based on standardized-threshold for feature screening of gene expression data

When the traditional random forest (RF) algorithm is used to select feature elements in biostatistical data, a large amount of noise data and parameters can affect the importance of the selected feature elements, making the control of feature selection difficult. Therefore, it is a challenge for the traditional RF algorithm to preserve the accuracy of algorithm results in the presence of noise data. Generally, directly removing noise data can result in significant bias in the results. In this study, we develop a new algorithm, standardized threshold, and loops based random forest (STLBRF), and apply it to the field of gene expression data for feature gene selection. This algorithm, based on the traditional RF algorithm, combines backward elimination and K-fold cross-validation to construct a cyclic system and set a standardized threshold: error increment. The algorithm overcomes the shortcomings of existing gene selection methods. We compare ridge regression, lasso regression, elastic net regression, the traditional RF algorithm, and our improved RF algorithm using three real gene expression datasets and conducting a quantitative analysis. To ensure the reliability of the results, we validate the effectiveness of the genes selected by these methods using the Random Forest classifier. The results indicate that, compared to other methods, the STLBRF algorithm achieves not only higher effectiveness in feature gene selection but also better control over the number of selected genes. Our method offers reliable technical support for feature expression analysis and research on biomarker selection.

miR‑25‑3p serves as an oncogenic in colorectal cancer cells by regulating the ubiquitin ligase FBXW7 function

Accumulating evidence indicates that the dysregulation of microRNAs (miRNAs or miRs), is associated with human malignancies and suggests a casual role of miRNAs in tumor initiation and progression. Even though it has been discovered that a number of miRNAs play significant parts in the development of colorectal cancer (CRC), it is crucial to comprehend the regulatory functions that other miRNAs play in CRC. Based on GSE183437 and GSE156719 microarray data that were obtained from Gene Expression Omnibus database, candidate miRNAs were researched. The oncogenic effects of miR‑25‑3p in different malignancies have led to its selection for additional investigation in the present study. The expression of miR‑25‑3p was verified by reverse transcription‑quantitative PCR, and its correlation with clinicopathological characteristics in patients with CRC was then investigated. In vitro assays were conducted to investigate the influence of miR‑25‑3p on the proliferative and apoptotic behaviors of HCT116 and Caco‑2 cells. The present data revealed that miR‑25‑3p exhibited one of the most significant upregulations in CRC tissues and cell lines. The expression levels of miR‑25‑3p were found to be intimately correlated with tumor size, distant metastasis, tumor‑node‑metastasis stage, and shorter overall survival rate. In terms of functionality, the downregulation of miR‑25‑3p led to the inhibition of cellular proliferation and the enhancement of apoptosis in both HCT116 and Caco‑2 cell lines. The critical tumor suppressor F‑box and WD repeat containing domain 7 (FBXW7) was identified as a direct molecular target for miR‑25‑3p, with an inverse relationship observed between the two in neoplastic tissues. Subsequent studies demonstrated that the tumor suppressive effects of miR‑25‑3p inhibitor were effectively negated by the silencing of FBXW7. Moreover, the ability of FBXW7 to inhibit the expression of several oncogenes was deemed essential for countering the anticancer effects mediated by miR‑25‑3p downregulation. These findings posit miR‑25‑3p as a promising therapeutic target and prognostic indicator for CRC.

Investigating the clinical role and prognostic value of genes related to insulin-like growth factor signaling pathway in thyroid cancer

BACKGROUND

Thyroid cancer (THCA) is the most common endocrine malignancy having a female predominance. The insulin-like growth factor (IGF) pathway contributed to the unregulated cell proliferation in multiple malignancies. We aimed to explore the IGF-related signature for THCA prognosis.

METHOD

The TCGA-THCA dataset was collected from the Cancer Genome Atlas (TCGA) for screening of key prognostic genes. The limma R package was applied for differentially expressed genes (DEGs) and the clusterProfiler R package was used for the Gene Ontology (GO) and KEGG analysis of DEGs. Then, the un/multivariate and least absolute shrinkage and selection operator (Lasso) Cox regression analysis was used for the establishment of RiskScore model. Receiver Operating Characteristic (ROC) analysis was used to verify the model's predictive performance. CIBERSORT and MCP-counter algorithms were applied for immune infiltration analysis. Finally, we analyzed the mutation features and the correlation between the RiskScore and cancer hallmark pathway by using the GSEA.

RESULT

We obtained 5 key RiskScore model genes for patient's risk stratification from the 721 DEGs. ROC analysis indicated that our model is an ideal classifier, the high-risk patients are associated with the poor prognosis, immune infiltration, high tumor mutation burden (TMB), stronger cancer stemness and stronger correlation with the typical cancer-activation pathways. A nomogram combined with multiple clinical features was developed and exhibited excellent performance upon long-term survival quantitative prediction.

CONCLUSIONS

We constructed an excellent prognostic model RiskScore based on IGF-related signature and concluded that the IGF signal pathway may become a reliable prognostic phenotype in THCA intervention.

To identify biomarkers associated with the transfer of diabetes combined with cancer in human genes using bioinformatics analysis

Currently, the incidence of diabetes mellitus is increasing rapidly, particularly in China, and its pathogenesis is still unclear. The goal of this study was to find meaningful biomarkers of metastasis in patients with diabetes and cancer using bioinformatic analysis in order to predict gene expression and prognostic importance for survival. We used the Differentially Expressed Gene, Database for Annotation Visualization and Integrated Discovery, and Gene Set Enrichment Analyses databases, as well as several bioinformatics tools, to explore the key genes in diabetes. Based on the above database, we ended up with 10 hub genes (FOS, ATF3, JUN, EGR1, FOSB, JUNB, BTG2, EGR2, ZFP36, and NR4A2). A discussion of the 10 critical genes, with extensive literature mentioned to validate the association between the 10 key genes and patients with diabetes and cancer, to demonstrate the importance of gene expression and survival prognosis. This study identifies several biomarkers associated with diabetes and cancer development and metastasis that may provide novel therapeutic targets for diabetes combined with cancer patients.

An emphasis on the interaction of signaling pathways highlights the role of miRNAs in the etiology and treatment resistance of gastric cancer

Gastric cancer (GC) is 4th in incidence and mortality rates globally. Several genetic and epigenetic factors, including microRNAs (miRNAs), affect its initiation and progression. miRNAs are short chains of nucleic acids that can regulate several cellular processes by controlling their gene expression. So, dysregulation of miRNAs expressions is associated with GC initiation, progression, invasion capacity, apoptosis evasions, angiogenesis, promotion and EMT enhancement. Of important pathways in GC and controlled by miRNAs are Wnt/β-catenin signaling, HMGA2/mTOR/P-gp, PI3K/AKT/c-Myc, VEGFR and TGFb signaling. Hence, this review was conducted to review an updated view of the role of miRNAs in GC pathogenesis and their modulatory effects on responses to different GC treatment modalities.

Comparison of Oncogenes, Tumor Suppressors, and MicroRNAs Between Schizophrenia and Glioma: The Balance of Power

The risk of cancer in schizophrenia has been controversial. Confounders of the issue are cigarette smoking in schizophrenia, and antiproliferative effects of antipsychotic medications. The author has previously suggested comparison of a specific cancer like glioma to schizophrenia might help determine a more accurate relationship between cancer and schizophrenia. To accomplish this goal, the author performed three comparisons of data; the first a comparison of conventional tumor suppressors and oncogenes between schizophrenia and cancer including glioma. This comparison determined schizophrenia has both tumor-suppressive and tumor-promoting characteristics. A second, larger comparison between brain-expressed microRNAs in schizophrenia with their expression in glioma was then performed. This identified a core carcinogenic group of miRNAs in schizophrenia offset by a larger group of tumor-suppressive miRNAs. This proposed "balance of power" between oncogenes and tumor suppressors could cause neuroinflammation. This was assessed by a third comparison between schizophrenia, glioma and inflammation in asbestos-related lung cancer and mesothelioma (ALRCM). This revealed that schizophrenia shares more oncogenic similarity to ALRCM than glioma.

Pre-clinical and clinical importance of miR-21 in human cancers: Tumorigenesis, therapy response, delivery approaches and targeting agents

The field of non-coding RNA (ncRNA) has made significant progress in understanding the pathogenesis of diseases and has broadened our knowledge towards their targeting, especially in cancer therapy. ncRNAs are a large family of RNAs with microRNAs (miRNAs) being one kind of endogenous RNA which lack encoded proteins. By now, miRNAs have been well-coined in pathogenesis and development of cancer. The current review focuses on the role of miR-21 in cancers and its association with tumor progression. miR-21 has both oncogenic and onco-suppressor functions and most of the experiments are in agreement with the tumor-promoting function of this miRNA. miR-21 primarily decreases PTEN expression to induce PI3K/Akt signaling in cancer progression. Overexpression of miR-21 inhibits apoptosis and is vital for inducing pro-survival autophagy. miR-21 is vital for metabolic reprogramming and can induce glycolysis to enhance tumor progression. miR-21 stimulates EMT mechanisms and increases expression of MMP-2 and MMP-9 thereby elevating tumor metastasis. miR-21 is a target of anti-cancer agents such as curcumin and curcumol and its down-regulation impairs tumor progression. Upregulation of miR-21 results in cancer resistance to chemotherapy and radiotherapy. Increasing evidence has revealed the role of miR-21 as a biomarker as it is present in both the serum and exosomes making them beneficial biomarkers for non-invasive diagnosis of cancer.

EGR2 is a hub-gene in myocardial infarction and aggravates inflammation and apoptosis in hypoxia-induced cardiomyocytes

Background

Myocardial infarction (MI) is characterized by coronary artery occlusion, ischemia and hypoxia of myocardial cells, leading to irreversible myocardial damage. Therefore, it is urgent to explore the potential mechanism of myocardial injury during the MI process to develop effective therapies for myocardial cell rescue.

Methods

We downloaded the GSE71906 dataset from GEO DataSets, and the R software was used to identify the differentially expressed genes (DEGs) in mouse heart tissues of MI and sham controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were performed to understand the significantly activated signaling pathways in MI. Protein–protein interaction (PPI) network was constructed to highlight the hub genes in DEGs. The Western Blot, qRT-PCR and TUNEL staining were used to explore the function of hub gene in hypoxia-induced cardiomyocytes in vitro.

Results

A total of 235 DEGs were identified in GSE71906 dataset. Functional enrichment analysis revealed that the upregulated genes were primarily associated with the inflammatory response and apoptosis. 20 hub genes were identified in PPI network, and the early growth response 2 (EGR2) was highlighted. In vitro. We confirmed the EGR2 was upregulated induced by hypoxia and revealed the upregulated EGR2 aggravates pro-inflammation and pro-apoptotic genes expression. In addition, EGR2 knockout mitigates hypoxia-induced inflammation and apoptosis in cardiomyocytes.

Conclusion

The present study identified the EGR2 was a hub gene in myocardial damage during MI process, the excessive EGR2 aggravates hypoxia-induced myocardial damage by accelerating inflammation and apoptosis in vitro. Therefore, targeting EGR2 offers a potential pharmacological strategy for myocardial cell rescue in MI.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12872-022-02814-3.