TOP2A Promotes Tumorigenesis of High-grade Serous Ovarian Cancer by Regulating the TGF-β/Smad Pathway

Association of TOP2A and ADH1B with lipid levels and prognosis in patients with lung adenocarcinoma and squamous cell carcinoma

BACKGROUND

Although lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) have different pathological and clinical features, they may share common driver genes. It was found that lipid levels can be used for early diagnosis of NSCLC; however, the relationship between driver genes and genes regulating lipid metabolism and their relationship with patient prognosis needs further investigation.

METHODS

Genes whose expression was up- or down-regulated in both LUAD and LUSC were identified using the GEO database. Online tools like GEPIA 2, PrognoScan, UALCAN, and TIMER2.0 were used to investigate the association of these gene expressions with the patient's prognosis and lipid regulatory genes. The association between clinical lipid levels and the risk of LUAD and LUSC was analyzed by using a multiple logistic regression model.

RESULTS

Topoisomerase II alpha (TOP2A) and alcohol dehydrogenase 1B (ADH1B) were identified as the only genes up- and down-regulated in both LUAD and LUSC. TOP2A and ADH1B expression levels significantly correlated with the patient's gender, age, individual cancer stage, histological subtype, nodal metastasis status, and TP53 mutation status. Additionally, only LUAD patients with higher TOP2A or lower ADH1B expressions displayed poor overall and relapse-free survival rates. Moreover, TOP2A levels exhibited a negative correlation with adipose triglyceride lipase (ATGL) and ATP-binding cassette transporter A1 (ABCA1) in both LUAD and LUSC. However, ADH1B showed inverse associations with the above-mentioned genes when compared to TOP2A expressions in both LUAD and LUSC. Furthermore, elevated triglyceride (OR = 1.59; 95% CI = 1.01 to 2.49; P < 0.05) and total cholesterol (OR = 2.45; 95% CI = 1.08 to 5.57; P < 0.05) levels might increase the risk of LUAD.

CONCLUSIONS

TOP2A and ADH1B can be used as diagnostic markers for LUAD and LUSC, but only as independent prognostic factors for LUAD, and may be involved in lipid metabolism in LUAD patients but not in LUSC. Thus, combining genetic diagnostics with lipid panel tests might be an effective method for an early diagnosis and improved prognosis of LUAD.

SKIL/SnoN attenuates TGF-β1/SMAD signaling-dependent collagen synthesis in hepatic fibrosis

The ski-related novel gene (SnoN), encoded by the SKIL gene, has been shown to negatively regulated transforming growth factor-β1 (TGF-β1) signaling pathway. However, the roles of SnoN in hepatic stellate cell (HSC) activation and hepatic fibrosis (HF) are still unclear. To evaluate the role of SnoN in HF, we combined bulk RNA sequencing analysis and single-cell RNA sequencing analysis to analyse patients with HF. The role of SKIL/SnoN was verified using liver samples from rat model transfected HSC-T6 and LX-2 cell lines. Immunohistochemistry, immunofluorescence, PCR, and western blotting techniques were used to demonstrate the expression of SnoN and its regulatory effects on TGF-β1 signaling in fibrotic liver tissues and cells. Furthermore, we constructed competitive endogenous RNA regulatory network and potential drug network associated with the SnoN gene. We identified SKIL gene as a differentially expressed gene in hepatic fibrosis. SnoN protein was found to be widely expressed in the cytoplasm of normal hepatic tissues, whereas it was almost absent in HF tissues. In the rat group subjected to bile duct ligation (BDL), SnoN protein expression decreased, while TGF-β1, collagen III, tissue inhibitor of metalloproteinase 1 (TIMP-1), and fibronectin levels increased. We observed the interaction of SnoN with p-SMAD2 and p-SMAD3 in the cytoplasm. Following SnoN overexpression, apoptosis of HSCs was promoted, and the expression of HF-associated proteins, including collagen I, collagen III, and TIMP-1, was reduced. Conversely, downregulation of SnoN inhibited HSC apoptosis, increased collagen III and TIMP-1 levels, and decreased matrix metalloproteinase 13 (MMP-13) expression. In conclusion, SnoN expression is downregulated in fibrotic livers, and could attenuate TGF-β1/SMADs signaling-dependent de-repression of collagen synthesis.

Differential expression of mRNA 3'-end isoforms in cervical and ovarian cancers

Early diagnosis and therapeutic targeting are continuing challenges for gynecological cancers. Here, we focus on cancer transcriptomes and describe the differential expression of 3'UTR isoforms in patients using an algorithm to detect differential poly(A) site usage. We find primarily 3'UTR shortening cases in cervical cancers compared with the normal cervix. We show differential expression of alternate 3'-end isoforms of FOXP1, VPS4B, and OGT in HPV16-positive patients who develop high-grade cervical lesions compared with the infected but non-progressing group. In contrast, in ovarian cancers, 3'UTR lengthening is more evident compared with normal ovary tissue. Nevertheless, highly malignant ovarian tumors have unique 3'UTR shortening events (e.g., CHRAC1, SLC16A1, and TOP2A), some of which correlate with upregulated protein levels in tumors. Overall, our study shows isoform level deregulation in gynecological cancers and highlights the complexity of the transcriptome. This transcript diversity could help identify novel cancer genes and provide new possibilities for diagnosis and therapy.

Role of LRRN4 in promoting malignant behavior in a p53- and Rb-defective human fallopian tube epithelial cell line

This study explored the role of leucine-rich repeat neuronal 4 (LRRN4) in ovarian carcinogenesis using the p53- and Rb-defective human fallopian tube epithelial cell line FE25. We evaluated the expression of LRRN4 in FE25 cells with and without LRRN4 knockdown by short hairpin RNA (shRNA) and studied its effects on cell proliferation, cell cycle, migration, invasion, chemotherapeutic sensitivity, apoptosis, and xenograft formation. The results showed that FE25 shRNA-LRRN4 cells exhibited more aggressive malignant behaviors than FE25 cells, including faster proliferation and increased cell distribution in the G2/M phase, Akt pathway activation, cell migration, and cell invasion, as well as decreased sensitivity to chemotherapeutic drugs. FE25 shRNA-LRRN4 cells exhibited reduced levels of apoptosis and decreased expression of cleaved caspase 3, 7, 8, and 9, indicating reduced apoptotic activity. Additionally, FE25 shRNA-LRRN4 cells showed decreased LRRN4 and CK7 expression and increased WT1 expression, suggesting a potential role for LRRN4 in ovarian carcinogenesis. FE25 shRNA-LRRN4 generated a xenograft in mice with increased levels of WT1 and TP53 expression compared to their levels in cells. Overall, this study suggests that LRRN4 may play a role in ovarian carcinogenesis by promoting aggressive malignant behavior in FE25 cells through the activation of the Akt pathway. These findings provide insights into the potential molecular mechanisms underlying ovarian cancer and may have implications for the development of new therapeutic targets for this disease.

AURKA, TOP2A and MELK are the key genes identified by WGCNA for the pathogenesis of lung adenocarcinoma

The comprehensive analysis of single or multiple microarray datasets is currently available in Gene Expression Omnibus (GEO) databases, with several studies having identified genes strongly associated with the development of lung adenocarcinoma (LUAD). However, the mechanisms of LUAD development remain largely unknown and has not yet been systematically studied; thus, further studies are required in this field. In the present study, weighted gene co-expression network analysis (WGCNA) was used for the evaluation of key genes with potential high risk of LUAD, and to provide more reliable evidence concerning its pathogenesis. The GSE140797 dataset from the high-throughput GEO database was downloaded and was first analyzed using the Limma package in the R language in order to determine the differentially expressed genes. The dataset was then analyzed using the WGCNA package to analyze the co-expressed genes, and the modular genes with the highest correlation with the clinical phenotype were identified. Subsequently, the pathogenic genes shared in common between the result of the two analyses were imported into the STRING database for protein-protein interaction network analysis. The hub genes were screened out using Cytoscape, and then The Cancer Genome Atlas analysis, receiver operating characteristic analysis and survival analysis were subsequently performed. Finally, the key genes were evaluated using reverse transcription-quantitative PCR and western blot analysis. Bioinformatics analysis of the GSE140797 dataset revealed eight key genes: AURKA, BUB1, CCNB1, CDK1, MELK, NUSAP1, TOP2A and PBK. Finally, the AURKA, TOP2A and MELK genes were evaluated in samples from patients with lung cancer using WGCNA and RT-qPCR, western blot analysis experiments, providing basis for further research on the mechanisms of LUAD development and targeted therapy.

Differentially expressed discriminative genes and significant meta-hub genes based key genes identification for hepatocellular carcinoma using statistical machine learning

Hepatocellular carcinoma (HCC) is the most common lethal malignancy of the liver worldwide. Thus, it is important to dig the key genes for uncovering the molecular mechanisms and to improve diagnostic and therapeutic options for HCC. This study aimed to encompass a set of statistical and machine learning computational approaches for identifying the key candidate genes for HCC. Three microarray datasets were used in this work, which were downloaded from the Gene Expression Omnibus Database. At first, normalization and differentially expressed genes (DEGs) identification were performed using limma for each dataset. Then, support vector machine (SVM) was implemented to determine the differentially expressed discriminative genes (DEDGs) from DEGs of each dataset and select overlapping DEDGs genes among identified three sets of DEDGs. Enrichment analysis was performed on common DEDGs using DAVID. A protein-protein interaction (PPI) network was constructed using STRING and the central hub genes were identified depending on the degree, maximum neighborhood component (MNC), maximal clique centrality (MCC), centralities of closeness, and betweenness criteria using CytoHubba. Simultaneously, significant modules were selected using MCODE scores and identified their associated genes from the PPI networks. Moreover, metadata were created by listing all hub genes from previous studies and identified significant meta-hub genes whose occurrence frequency was greater than 3 among previous studies. Finally, six key candidate genes (TOP2A, CDC20, ASPM, PRC1, NUSAP1, and UBE2C) were determined by intersecting shared genes among central hub genes, hub module genes, and significant meta-hub genes. Two independent test datasets (GSE76427 and TCGA-LIHC) were utilized to validate these key candidate genes using the area under the curve. Moreover, the prognostic potential of these six key candidate genes was also evaluated on the TCGA-LIHC cohort using survival analysis.

Target Selection for T-Cell Therapy in Epithelial Ovarian Cancer: Systematic Prioritization of Self-Antigens

Adoptive T cell-receptor therapy (ACT) could represent a promising approach in the targeted treatment of epithelial ovarian cancer (EOC). However, the identification of suitable tumor-associated antigens (TAAs) as targets is challenging. We identified and prioritized TAAs for ACT and other immunotherapeutic interventions in EOC. A comprehensive list of pre-described TAAs was created and candidates were prioritized, using predefined weighted criteria. Highly ranked TAAs were immunohistochemically stained in a tissue microarray of 58 EOC samples to identify associations of TAA expression with grade, stage, response to platinum, and prognosis. Preselection based on expression data resulted in 38 TAAs, which were prioritized. Along with already published Cyclin A1, the TAAs KIF20A, CT45, and LY6K emerged as most promising targets, with high expression in EOC samples and several identified peptides in ligandome analysis. Expression of these TAAs showed prognostic relevance independent of molecular subtypes. By using a systematic vetting algorithm, we identified KIF20A, CT45, and LY6K to be promising candidates for immunotherapy in EOC. Results are supported by IHC and HLA-ligandome data. The described method might be helpful for the prioritization of TAAs in other tumor entities.

An integrated multi-omics analysis of topoisomerase family in pan-cancer: Friend or foe?

BACKGROUND

Topoisomerases are nuclear enzymes that get to the bottom of topological troubles related with DNA all through a range of genetic procedures. More and more studies have shown that topoisomerase-mediated DNA cleavage plays crucial roles in tumor cell death and carcinogenesis. There is however still a lack of comprehensive multi-omics studies related to topoisomerase family genes from a pan-cancer perspective.

METHODS

In this study, a multiomics pan-cancer analysis of topoisomerase family genes was conducted by integrating over 10,000 multi-dimensional cancer genomic data across 33 cancer types from The Cancer Genome Atlas (TCGA), 481 small molecule drug response data from cancer therapeutics response portal (CTRP) as well as normal tissue data from Genotype-Tissue Expression (GTEx). Finally, overall activity-level analyses of topoisomerase in pan-cancers were performed by gene set variation analysis (GSVA), together with differential expression, clinical relevancy, immune cell infiltration and regulation of cancer-related pathways.

RESULTS

Dysregulated gene expression of topoisomerase family were related to genomic changes and abnormal epigenetic modifications. The expression levels of topoisomerase family genes could significantly impact cancer progression, intratumoral heterogeneity, alterations in the immunological condition and regulation of the cancer marker-related pathways, which in turn caused the differences in potential drugs sensitivity and the distinct prognosis of patients.

CONCLUSION

It was anticipated that topoisomerase family genes would become novel prognostic biomarkers for cancer patients and provide new insights for the diagnosis and treatment of tumors.

Identification of Novel Drugs Targeting Cell Cycle Regulators for the Treatment of High-Grade Serous Ovarian Cancer via Integrated Bioinformatics Analysis

High-grade serous ovarian carcinoma (HGSC), the most common and aggressive histological type of ovarian cancer, remains the leading cause of cancer-related deaths among females. It is important to develop novel drugs to improve the therapeutic outcomes of HGSC patients, thereby reducing their mortality. Symmetry is one of the most important properties of the biological network, which determines the stability of a biological system. As aberrant gene expression is a critical symmetry-breaking event that perturbs the stability of biological networks and triggers tumor progression, we aim in this study to discover new candidate drugs and predict their targets for HGSC therapy based on differentially expressed genes involved in HGSC pathogenesis. Firstly, 98 up-regulated genes and 108 down-regulated genes were identified from three independent transcriptome datasets. Then, the small-molecule compounds PHA-793887, pidorubicine and lestaurtinib, which target cell-cycle-related processes, were identified as novel candidate drugs for HGSC treatment by adopting the connectivity map (CMap)-based drug repositioning approach. Furthermore, through a topological analysis of the protein–protein interaction network, cell cycle regulators CDK1, TOP2A and AURKA were identified as bottleneck nodes, and their expression patterns were validated at the mRNA and protein expression levels. Moreover, the results of molecular docking analysis showed that PHA-793887, pidorubicine and lestaurtinib had a strong binding affinity for CDK1, TOP2A and AURKA, respectively. Therefore, our study repositioned PHA-793887, pidorubicine and lestaurtinib, which can inhibit cell cycle regulators, as novel agents for HGSC treatment, thereby helping to optimize the therapeutic strategy for HGSC.

Oncogenetic Function and Prognostic Value of DNA Topoisomerase II Alpha in Human Malignances: A Pan-Cancer Analysis

Increasing studies have revealed significant associations between TOP2A with oncogenesis and prognosis of human cancers; however, pan-cancer analysis has not been reported. Here, we explored the potential carcinogenic function and the association with clinical outcomes of TOP2A in 33 different human cancers. The results showed that TOP2A was amplified in 31 investigated cancers; TOP2A expression was significantly associated with metastasis of six different cancers and significantly associated with the survival of patients in ten different cancers; TOP2A-encoded protein was obviously upregulated in five available cancers; phosphorylated TOP2A protein at S1106 was significantly upregulated in all six available cancers. Moreover, TOP2A expression was found to be associated with the cancer-associated immune cell infiltration, including fibroblasts, Tregs, and macrophages. In addition, the Kyoto encyclopedia of genes and genomes (KEGG) pathway and Gene Ontology (GO) enrichment analyses revealed a most significant association between TOP2A with the Wnt signaling pathway and DNA conformation change. This work provides a comprehensive knowledge of TOP2A in different cancers, including carcinogenic function, prognostic values for metastasis, and clinical outcomes.

trans-Dichloro(triphenylarsino)(N,N-dialkylamino)platinum(II) Complexes: In Search of New Scaffolds to Circumvent Cisplatin Resistance

The high incidence of the resistance phenomenon represents one of the most important limitations to the clinical usefulness of cisplatin as an anticancer drug. Notwithstanding the considerable efforts to solve this problem, the circumvention of cisplatin resistance remains a challenge in the treatment of cancer. In this work, the synthesis and characterization of two trans-dichloro(triphenylarsino)(N,N-dialkylamino)platinum(II) complexes (1 and 2) were described. The trypan blue exclusion assay demonstrated an interesting antiproliferative effect for complex 1 in ovarian carcinoma-resistant cells, A2780cis. Quantitative analysis performed by ICP-AES demonstrated a scarce ability to platinate DNA, and a significant intracellular accumulation. The investigation of the mechanism of action highlighted the ability of 1 to inhibit the relaxation of supercoiled plasmid DNA mediated by topoisomerase II and to stabilize the cleavable complex. Cytofluorimetric analyses indicated the activation of the apoptotic pathway and the mitochondrial membrane depolarization. Therefore, topoisomerase II and mitochondria could represent possible intracellular targets. The biological properties of 1 and 2 were compared to those of the related trans-dichloro(triphenylphosphino)(N,N-dialkylamino)platinum(II) complexes in order to draw structure–activity relationships useful to face the resistance phenotype.

DNA topoisomerase II alpha promotes the metastatic characteristics of glioma cells by transcriptionally activating β-catenin

DNA topoisomerase II alpha (TOP2A) reportedly plays a crucial role in several cancers, however, the precise regulatory role of TOP2A in metastatic characteristics of glioma is still poorly understood. Herein, we sought to elucidate the mechanisms by which TOP2A affects the metastatic phenotypes of glioma. We observed that a high level of TOP2A expression was dramatically linked with inferior survival in glioma patients while silencing of TOP2A impaired glioma cell proliferation and aggressiveness. TOP2A was found to directly interact with β-catenin and facilitated its translocation into the nucleus. Mechanistically, TOP2A effectively induced glioma cell growth and invasion in a β-catenin-dependent manner. Overall, we pinpoint TOP2A as a critical activator of the Wnt/β-catenin pathway in glioma, promoting cell growth, migration, and invasion.

Integrated Bioinformatics Analysis for Identification of the Hub Genes Linked with Prognosis of Ovarian Cancer Patients

BACKGROUND

One of the most usual gynecological state of tumor is ovarian cancer and is a major reason of gynecological tumor-related global mortality rate. There have been multiple risk elements related to ovarian cancer like the background of past cases associated with breast cancer or ovarian cancer, or excessive body weight issues, case history of smoking, and untimely menstruation or menopause. Because of unclear expressions, more than 70% of the ovarian cancer patient cases are determined during the early stage. Material and Methods. GSE38666, GSE40595, and GSE66957 were the three microarray datasets which were analyzed using GEO2R for screening the differentially expressed genes. GO, Kyoto Encyclopedia of Genes, and protein expression studies were performed for analysis of hub genes. Then, survival analysis was performed for all the hub genes.

RESULTS

From the dataset, a total of 199 differentially expressed genes (DEGs) were identified. Through the KEGG pathway study, it was noted that the DEGs are mainly linked with the AGE-RAGE signaling pathway, central carbon metabolism, and human papillomavirus infection. The survival analysis showed 4 highly expressed hub genes COL4A1, SDC1, CDKN2A, and TOP2A which correlated with overall survival in ovarian cancer patients. Moreover, the expression of the 4 hub genes was validated by the GEPIA database and the Human Protein Atlas.

CONCLUSION

The results have shown that all 4 hub genes were found to be upregulated in ovarian cancer tissues which predict poor prognosis in patients with ovarian cancer.

Rhophilin rho GTPase binding protein 1-antisense RNA 1 (RHPN1-AS1) promotes ovarian carcinogenesis by sponging microRNA-485-5p and releasing DNA topoisomerase II alpha (TOP2A)

Ovarian cancer (OC) is the most common and lethal gynecological cancer worldwide. Long non-coding RNAs (lncRNAs) and sponging microRNAs (miRNAs) serve as key regulators in the biological processes of OC. We sought to evaluate the effect of the RHPN1-AS1-miR-485-5p-DNA topoisomerase II alpha (TOP2A) axis in regulating OC progression. RHPN1-AS1, miR-485-5p, and TOP2A levels in OC tissues and cells were determined by RT-qPCR. The interaction of RHPN1-AS1/miR-485-5p/TOP2A was assessed using luciferase, RNA immunoprecipitation, and RNA pull-down assays. RHPN1-AS1 silencing allowed us to explore its biological function by measuring cell viability, proliferation, migration, invasion, and apoptosis in OC cells. In vivo experiments were performed to verify the in vitro findings. We found that the RHPN1-AS1 and TOP2A levels were significantly enhanced, whereas the miR-485-5p levels were reduced in OC tissues and cells. RHPN1-AS1 silencing attenuated cell growth, facilitated apoptosis in OC cells, and inhibited tumor growth in vivo. Notably, RHPN1-AS1 negatively regulating miR-485-5p promoted the TOP2A expression in OC cells. In conclusion, RHPN1-AS1 sponging miR-485-5p accelerated the progression of OC by elevating TOP2A expression, which makes it a promising target for the treatment of OC patients.

FAST1 Predicts Poor Survival of Renal Carcinoma and Promotes Its Progression Through the TGF-β/Smad Pathway

Purpose

Renal carcinoma (RC) originates in the renal tubular epithelial system, among which renal cell carcinoma (RCC) is the most frequent one. The forkhead activin signal transducer 1 (FAST1) has been shown to interfere with tumor progression as an oncogene, while its role in RC is limited. Therefore, this paper explored the prognostic significance, specific effects, and related mechanisms of FAST1 on RC.

Patients and Methods

Cell colony formation assay, cell counting kit-8 (CCK8) assay, flow cytometry and Transwell assay were used to test cell proliferation, viability, apoptosis, migration and invasion, respectively. Western blot (WB) was employed to determine the protein level of FAST1.

Results

Our study confirmed that FAST1 was up-regulated in RC tissues and cell lines, and its overexpression often represented a poor prognosis of RC patients. Meanwhile, the in vitro experiments showed that overexpressing FAST1 facilitated RC cell viability, proliferation, migration, invasion and epithelial-mesenchymal transition (EMT), and repressed cell apoptosis. In addition, the in vivo experiments illustrated that the up-regulation of FAST1 strengthened tumor growth. On the contrary, knocking down FAST1 had the opposite effects. Mechanistically, The TGF-β/Smad pathway contributed to RC evolvement and was activated by FAST1 both in vitro and in vivo.

Conclusion

This article suggests that FAST1 exerts a carcinogenic role in RC by regulating the TGF-β/Smad signaling.

Identification of the Hub Genes Associated with the Prognosis of Ovarian Cancer Patients via Integrated Bioinformatics Analysis and Experimental Validation

Background

This study aimed to identify the hub genes associated with prognosis of patients with ovarian cancer by using integrated bioinformatics analysis and experimental validation.

Methods

Four microarray datasets (GSE12470, GSE14407, GSE18521 and GSE46169) were analyzed by the GEO2R tool to screen common differentially expressed genes (DEGs). Gene Ontology, the Kyoto Encyclopedia of Genes and Genomes, the (KEGG) pathway and Reactome pathway enrichment analysis, protein–protein interaction (PPI) construction, and the identification of hub genes were performed. Furthermore, we performed the survival and expression analysis of the hub genes. In vitro functional assays were performed to assess the effects of hub genes on ovarian cancer cell proliferation, caspase-3/7 activity and invasion.

Results

A total of 89 common DEGs were identified among these four datasets. The KEGG and Reactome pathway results showed that the DEGs were mainly associated with cell cycle, mitotic and p53 signaling pathway. A total of 20 hub genes were identified from the PPI network by using sub-module analysis. The survival analysis revealed that high expression of six hub genes (AURKA, BUB1B, CENPF, KIF11, KIF23 and TOP2A) were significantly correlated with shorter overall survival and progression-free survival of patients with ovarian cancer. Furthermore, the expression of the six hub genes were validated by the GEPIA database and Human Protein Atlas, and functional studies revealed that knockdown of KIF11 and KIF23 suppressed the SKOV3 cell proliferation, increased caspase-3/7 activity and attenuated invasive potentials of SKOV3 cells. In addition, knockdown of KIF11 and KIF23 up-regulated E-cadherin mRNA expression but down-regulated N-cadherin and vimentin mRNA expression in SKOV3 cells.

Conclusion

Our results showed that six hub genes were up-regulated in ovarian cancer tissues and may predict poor prognosis of patients with ovarian cancer. KIF11 and KIF23 may play oncogenic roles in ovarian cancer cell progression via promoting ovarian cancer cell proliferation and invasion.