In silico analysis revealed the potential circRNA-miRNA-mRNA regulative network of non-small cell lung cancer (NSCLC)

Identification of circRNA-miRNA-mRNA networks to explore underlying mechanism in lung cancer

Background

Circular RNAs (circRNAs) are involved in the occurrence and development of various tumors. CircRNAs can act as competing endogenous RNAs (ceRNAs), which are important regulatory networks, by regulating microRNAs (miRNAs). However, the effects of ceRNA networks on lung cancer (LC), especially the circRNA-miRNA-mRNA regulatory network, remain incompletely understood. Therefore, the aim of this study was to explore novel ceRNA networks and their function and underlying mechanisms in LC.

Methods

Six RNA expression datasets were obtained from the Gene Expression Omnibus microarray datasets (circRNA: GSE158695, GSE101684, GSE112214, and GSE101586; miRNA: GSE135918; mRNA: GSE98929). First, we constructed a circRNA-miRNA-mRNA ceRNA network in LC using Cytoscape. Second, we constructed a protein-protein interaction network using STRING and identified hub genes using CytoHubba. Functional analysis was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to predict the potential function of the hub genes. Third, expression and survival analysis of the hub genes were performed to identify prognostic genes.

Results

We constructed a ceRNA network including 18 circRNAs, 32 miRNAs, and 135 mRNAs, and identified 10 hub genes (VEGFA, FOS, MAD2L1, CREBBP, TYMS, EDN1, RFC5, KIF11, SLC2A1, and TOP2A). Both GO and KEGG analyses revealed that the 10 hub genes were associated with several cancer‑related biological functions and pathways, including "oxygen levels", "nuclear division", and "HIF-1 signaling pathway". Five genes (MAD2L1, TYMS, KIF11, SLC2A1, and TOP2A) were associated with the prognosis of lung adenocarcinoma (LUAD), the most common histological type of LC.

Conclusion

Our study provides novel insights into the pathogenesis and therapy of LC from a ceRNA network perspective.

Targeting Kinesins for Therapeutic Exploitation of Chromosomal Instability in Lung Cancer

New therapeutic approaches that antagonize tumour-promoting phenotypes in lung cancer are needed to improve patient outcomes. Chromosomal instability (CIN) is a hallmark of lung cancer characterized by the ongoing acquisition of genetic alterations that include the gain and loss of whole chromosomes or segments of chromosomes as well as chromosomal rearrangements during cell division. Although it provides genetic diversity that fuels tumour evolution and enables the acquisition of aggressive phenotypes like immune evasion, metastasis, and drug resistance, too much CIN can be lethal because it creates genetic imbalances that disrupt essential genes and induce severe proteotoxic and metabolic stress. As such, sustaining advantageous levels of CIN that are compatible with survival is a fine balance in cancer cells, and potentiating CIN to levels that exceed a tolerable threshold is a promising treatment strategy for inherently unstable tumours like lung cancer. Kinesins are a superfamily of motor proteins with many members having functions in mitosis that are critical for the correct segregation of chromosomes and, consequently, maintaining genomic integrity. Accordingly, inhibition of such kinesins has been shown to exacerbate CIN. Therefore, inhibiting mitotic kinesins represents a promising strategy for amplifying CIN to lethal levels in vulnerable cancer cells. In this review, we describe the concept of CIN as a therapeutic vulnerability and comprehensively summarize studies reporting the clinical and functional relevance of kinesins in lung cancer, with the goal of outlining how kinesin inhibition, or "targeting kinesins", holds great potential as an effective strategy for treating lung cancer.

An integrative analysis of GEO data to identify possible therapeutic biomarkers of prostate cancer and targeting potential protein through Zea mays phytochemicals by virtual screening approaches

Prostate cancer (PC) is a prevalent type of cancer among men. Delaying the treatment of patients with upgraded or upstaged cancer may lead to unmanageable circumstances. The aim of this study is to contribute to the finding of biomarkers that are specific to PC and identify drug candidates derived from plants. The information about cancer is critical for clinicians to make decisions about patient treatment in the era of precision medicine. Advances in genomics technology have opened up new possibilities for identifying genes that are associated with cancer, including PC. This study identifies novel differentially expressed genes for PC. The seven PC microarray datasets were selected from the National Center for Biotechnology Information (NCBI)/Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) were found based on a fold change of |logFC| ≥ 1 and an adjusted p-value of <0.05. The DEGs were further studied using several bioinformatics tools, including STRING, CytoHubba, SRplot, Coremine Medical database, FunRich and GeneMANIA, cBioPortal. The six new potential biomarkers, GAGE2A, GAGE12G, GAGE2E, GAGE13, GAGE12F and CSAG1 were identified. These biomarkers are associated with biological processes (BPs) such as cell division, and gene expression regulation, so these genes may have a crucial role in PC progression and may serve as potential biomarkers for PC. A total of 497 phytochemicals from corn plants have been screened against the target protein and found LTS0176591 as the best lead molecule with docking score of -6.31 kcal/mol. Further, molecular mechanics-generalized born surface area (MM-GBSA), molecular dynamics simulation, principal component analysis (PCA), free energy landscape (FEL) and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) were carried out to validate the findings.Communicated by Ramaswamy H. Sarma.

Construction of a potentially functional long noncoding RNA-microRNA-mRNA network in diabetic cardiomyopathy

Background

Diabetic cardiomyopathy (DCM) is a severe complication among patients with Type 2 diabetes, significantly increasing heart failure risk and mortality. Despite various implicated mechanisms, effective DCM treatments remain elusive. This study aimed to construct a comprehensive competing endogenous RNA (ceRNA) network in DCM using bioinformatics analysis.

Materials and Methods

Three expression profiles datasets (GSE161827, GSE161931, and GSE241166) were collected from gene expression omnibus database and then integrated for the identification of differentially expressed genes (DEGs). Gene Ontology, Kyoto Encyclopedia of Gene and Genome pathway analysis, and Gene set enrichment analysis (GSEA) were employed for functional analysis. Protein-protein interaction (PPI) network and hub genes were also identified. The ceRNA regulatory networks were constructed based on interaction between long noncoding RNA (lncRNA) and DEGs, microRNA (miRNA) and DEGs, as predicted by public available databases.

Results

A total of 105 DEGs, including 44 upregulated and 61 downregulated genes were identified to be associated with DCM. Functional enrichment analysis showed that fatty acid metabolism pathway and inflammatory responses were significantly enriched in DCM. A total of 56 interactions between miRNA with DEGs, and 27 interactions between lncRNA with miRNA was predicted. Besides, a ceRNA network includes 9 mRNA, 17 miRNA and 10 lncRNA was constructed, among which Cdh20 and Cacna2d2 were hub genes in PPI network.

Conclusion

The identified hub genes and ceRNA network components provide valuable insights into DCM biology and offer potential diagnostic biomarkers and therapeutic targets for further investigation. Further experimental validation and clinical studies are warranted to translate these findings into clinical applications.

The bioinformatics analysis and experimental validation of the carcinogenic role of EXO1 in lung adenocarcinoma

Background

Exonuclease 1 (EXO1), a protein involved in mismatch repair and recombination processes, has been identified as a prognostic biomarker in lung adenocarcinoma (LUAD). Nevertheless, its role in LUAD progression remains elusive. This study seeks to elucidate the functional significance of EXO1 in LUAD and evaluate its potential as a therapeutic target.

Materials and methods

Patient RNA-seq and clinical data were acquired from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Subsequently, a protein-protein interaction (PPI) network was constructed using differentially expressed genes (DEGs) to identify pivotal genes. Validation of the expression of signature genes was carried out through quantitative real-time PCR (qRT-PCR). Additionally, the association between EXO1 expression and clinical data was investigated. Immunohistochemistry was utilized to assess EXO1 expression in 93 cases of invasive pulmonary adenocarcinoma. Finally, cellular functional assays were conducted to investigate the impact of EXO1 on LUAD cells.

Results

Ten key molecules (PBK, ASPM, NCAPG, EXO1, MKI67, RRM2, AURKA, DLGAP5, UBE2C, and CDC6) exhibited significantly elevated expression levels in LUAD tissues. Moreover, elevated levels of EXO1 gene expression correlated strongly with advanced T, N, and M stages and were significantly associated with immune cell infiltration in LUAD. Furthermore, marked increases in EXO1 protein expression were observed in patients diagnosed with invasive pulmonary adenocarcinoma. Notably, patients diagnosed with invasive pulmonary adenocarcinoma who exhibited elevated EXO1 expression levels exhibited increased lymph node metastasis, pleural invasion, poor tumor differentiation, and advanced clinical stage. Additionally, this study employed wound healing assay and CCK-8 cell proliferation assays to investigate the significant role of EXO1 in promoting the growth and migration of lung adenocarcinoma cells.

Conclusions

This study identified ten hub genes associated with the initiation and progression of LUAD. Additionally, EXO1 may serve as a prognostic marker for LUAD patients, offering new perspectives for clinical treatments.

Targeting NUF2 suppresses gastric cancer progression through G2/M phase arrest and apoptosis induction

BACKGROUND

Gastric cancer (GC), a malignant tumor with poor prognosis, is one of the leading causes of cancer-related deaths worldwide; consequently, identifying novel therapeutic targets is crucial for its corresponding treatment. NUF2 , a component of the NDC80 kinetochore complex, promotes cancer progression in multiple malignancies. Therefore, this study aimed to explore the potential of NUF2 as a therapeutic target to inhibit GC progression.

METHODS

Clinical samples were obtained from patients who underwent radical resection of GC at Lanzhou University Second Hospital from 2016 to 2021. Cell count assays, colony formation assays, and cell-derived xenotransplantation (CDX) models were used to determine the effects of NUF2 on GC progression. Flow cytometry was used to detect the effect of NUF2 or quercetin on cell cycle progression and apoptosis. A live-cell time-lapse imaging assay was performed to determine the effect of NUF2 on the regulation of mitotic progression. Transcriptomics was used to investigate the NUF2 -associated molecular mechanisms. Virtual docking and microscale thermophoresis were used to identify NUF2 inhibitors. Finally, CDX, organoid, and patient-derived xenograft (PDX) models were used to examine the efficacy of the NUF2 inhibitor in GC.

RESULTS

NUF2 expression was significantly increased in GC and was negatively correlated with prognosis. The deletion of NUF2 suppressed GC progression both in vivo and in vitro . NUF2 significantly regulated the mitogen-activated protein kinase (MAPK) pathway, promoted G2/M phase transition, and inhibited apoptosis in GC cells. Additionally, quercetin was identified as a selective NUF2 inhibitor with low toxicity that significantly suppressed tumor growth in GC cells, organoids, CDX, and PDX models.

CONCLUSIONS

Collectively, NUF2 -mediated G2/M phase transition and apoptosis inhibition promoted GC progression; additionally, NUF2 inhibitors exhibited potent anti-GC activity. This study provides a new strategy for targeting NUF2 to suppress GC progression in clinical settings.

Eg5 and Diseases: From the Well-Known Role in Cancer to the Less-Known Activity in Noncancerous Pathological Conditions

Eg5 is a protein encoded by KIF11 gene and is primarily involved in correct mitotic cell division. It is also involved in nonmitotic processes such as polypeptide synthesis, protein transport, and angiogenesis. The scientific literature sheds light on the ubiquitous functions of KIF11 and its involvement in the onset and progression of different pathologies. This review focuses attention on two main points: (1) the correlation between Eg5 and cancer and (2) the involvement of Eg5 in noncancerous conditions. Regarding the first point, several tumors revealed an overexpression of this kinesin, thus pushing to look for new Eg5 inhibitors for clinical practice. In addition, the evaluation of Eg5 expression represents a crucial step, as its overexpression could predict a poor prognosis for cancer patients. Referring to the second point, in specific pathological conditions, the reduced activity of Eg5 can be one of the causes of pathological onset. This is the case of Alzheimer's disease (AD), in which Aβ and Tau work as Eg5 inhibitors, or in acquired immune deficiency syndrome (AIDS), in which Tat-mediated Eg5 determines the loss of CD4+ T-lymphocytes. Reduced Eg5 activity, due to mutations of KIF11 gene, is also responsible for pathological conditions such as microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability (MCLRI) and familial exudative vitreous retinopathy (FEVR). In conclusion, this review highlights the double impact that overexpression or loss of function of Eg5 could have in the onset and progression of different pathological situations. This emphasizes, on one hand, a possible role of Eg5 as a potential biomarker and new target in cancer and, on the other hand, the promotion of Eg5 expression/activity as a new therapeutic strategy in different noncancerous diseases.

circRACGAP1 Promotes Proliferation of Non-Small Cell Lung Cancer Cells through the miR-1296/CDK2 Pathway

Circular RNAs (circRNAs) have played an essential role in cancer development. This study aimed to illustrate the impact and potential mechanism of circRACGAP1 action in NSCLC development. The expression patterns of circRACGAP1, miR-1296, and CDK2 in NSCLC tissues and cell lines were analysed by RT-qPCR. The function of circRACGAP1 in NSCLC cell proliferation and apoptosis was investigated using the CCK-8 assay, flow cytometry, TUNEL staining, and Western blot. The interaction among circRACGAP1, miR-1296, and CDK2 was clarified by dual-luciferase reporter assay while the correlation was confirmed by the Pearson correlation coefficient. The expression of circRACGAP1 and CDK2 was up-regulated in NSCLC tissues, while the expression of miR-1296 was down-regulated. Cell function studies further revealed that circRACGAP1 could promote NSCLC cell proliferation, accelerate the cell cycle process, up-regulate B-cell lymphoma 2 (Bcl2) expression, and down-regulate Bcl2-associated X (Bax) expression. miR-1296 was identified as a downstream target to reverse circRACGAP1-mediated cell proliferation. miR-1296 directly targeted the 3'-UTR of CDK2 to regulate proliferation and apoptosis of NSCLC cells. Additionally, the dual-luciferase reporter assay and Pearson correlation coefficient analysis proved that circRACGAP1 acted in NSCLC cells by negatively regulating miR-1296 expression and positively regulating CDK2 expression. In summary, our study revealed that circRACGAP1 promoted NSCLC cell proliferation by regulating the miR-1296/CDK2 pathway, providing potential diagnostic and therapeutic targets for NSCLC.

Bioengineered chimeric tRNA/pre-miRNAs as prodrugs in cancer therapy

Today, biologic prodrugs have led to targeting specific tumor markers and have increased specificity and selectivity in cancer therapy. Various studies have shown the role of ncRNAs in cancer pathology and tumorigenesis and have suggested that ncRNAs, especially miRNAs, are valuable molecules in understanding cancer biology and therapeutic processes. Most miRNAs-based research and treatment are limited to chemically synthesized miRNAs. Synthetic alterations in these miRNA mimics may affect their folding, safety profile, and even biological activity. However, despite synthetic miRNA mimics produced by automated systems, various carriers could be used to achieve efficient production of bioengineered miRNAs through economical microbial fermentation. These bioengineered miRNAs as biological prodrugs could provide a new approach for safe therapeutic methods and drug production. In this regard, bioengineered chimeric miRNAs could be selectively processed to mature miRNAs in different types of cancer cells by targeting the desired gene and regulating cancer progression. In this article, we aim to review bioengineered miRNAs and their use in cancer therapy, as well as offering advances in this area, including the use of chimeric tRNA/pre-miRNAs.