The Role of TOP2A Protein Expression and Aneuploidy in NSCLC

Purpose DNA topoisomerase II alpha (TOP2A) is a cell-cycle dependent protein associated with cell proliferation and division. Abnormal regulation of TOP2A and aneuploidy induces tumorigenesis and poor prognosis. Data related to TOP2A protein in non-small cell lung cancer (NSCLC) is limited to few studies on gene status. The present study aimed to investigate the consistency between aneuploidy and expression of TOP2A gene and protein, respectively, and the role of aneuploidy in the prognosis of NSCLC patients. Methods Clinical data and lung cancer tissues were collected from 244 patients with NSCLC. TOP2A protein and gene expression were detected using immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), respectively. Nonparametric Spearman’s rank sum test was used to analyze clinicopathological data. Kaplan–Meier and multivariate Cox regression methods were used for survival analysis. Results Enhanced expression and amplification rate of TOP2A protein and gene were 29.9% (73/244) and 0.4% (1/244), respectively. The aneuploidy rate was 31.6% (77/244). In NSCLC, patients with enhanced expression of TOP2A protein and aneuploidy correlated with clinical stages (p < 0.001) Enhanced expression of TOP2A protein was consistent with aneuploidy as detected by Kappa test (K = 0.307) and this correlation was confirmed by chi-square test (p < 0.001). The overall survival of patients with aneuploidy was shorter than diploidy (p < 0.001). Clinically advanced patients with aneuploidy together with TOP2A overexpression had poor prognosis (p < 0.001). Conclusion Aneuploidy and overexpression of TOP2A is a predictor of poor prognosis in patients with advanced NSCLC.

Tumor antigens and immune subtypes guided mRNA vaccine development for kidney renal clear cell carcinoma

Current treatment strategy for kidney renal clear cell carcinoma (KIRC) is limited. Tumor-associated antigens, especially neoantigen-based personalized mRNA vaccines represent new strategies and manifest clinical benefits in solid tumors, but only a small proportion of patients could benefit from them, which prompts us to identify effective antigens and suitable populations to facilitate mRNA vaccines application in cancer therapy. Through performing expression, mutation, survival and correlation analyses in TCGA-KIRC dataset, we identified four genes including DNA topoisomerase II alpha (TOP2A), neutrophil cytosol factor 4 (NCF4), formin-like protein 1 (FMNL1) and docking protein 3 (DOK3) as potential KIRC-specific neoantigen candidates. These four genes were upregulated, mutated and positively associated with survival and antigen-presenting cells in TCGA-KIRC. Furthermore, we identified two immune subtypes, named renal cell carcinoma immune subtype 1 (RIS1) and RIS2, of KIRC. Distinct clinical, molecular and immune-related signatures were observed between RIS1 and RIS2. Patients of RIS2 had better survival outcomes than those of RIS1. Further comprehensive immune-related analyses indicated that RIS1 is immunologically “hot” and represent an immunosuppressive phenotype, whereas RIS2 represents an immunologically “cold” phenotype. RIS1 and RIS2 also showed differential features with regard to tumor infiltrating immune cells and immune checkpoint-related genes. Moreover, the immune landscape construction identified the immune cell components of each KIRC patient, predicted their survival outcomes, and assisted the development of personalized mRNA vaccines. In summary, our study identified TOP2A, NCF4, FMNL1 and DOK3 as potential effective neoantigens for KIRC mRNA vaccine development, and patients with RIS2 tumor might benefit more from mRNA vaccination.

Identification of The Prognostic Genes For Early Basal-Like Breast Cancer With Weighted Gene Co-Expression Network Analysis

Background: Breast cancer (BC) has become the leading cause of death for women's malignancies and increasingly threatens the health of women worldwide. However, the basal-like BC is lack of effective targeted drugs. Therefore, biomarkers that related to the prognosis of early breast cancer need to be found.Methods: The RNA-seq data of 87 cases of early basal-like BC and 111 cases of normal breast tissue from The Cancer Genome Atlas (TCGA) were explored by Weighted Gene Co-Expression Network Analysis (WGCNA)method and Limma package. Then intersected genes (IGs) were identified and hub genes were selected by Maximal Clique Centrality method. The prognostic effect of the hub genes was also evaluated in early basal-like BC. Results: A total of 601 IGs were identified in this study. APPI network was constructed and top 10 hub genes were selected, namely cyclin B1 (CCNB1), cyclin A2 (CCNA2), cyclin dependent kinase 1 (CDK1), cell division cycle 20 (CDC20), DNA topoisomerase II alpha (TOP2A), BUB1 mitotic checkpoint serine/threonine kinase (BUB1), aurora kinase B (AURKB), cyclin B2 (CCNB2), kinesin family member 11 (KIF11), and assembly factor for spindle microtubules (ASPM). Only AURKB was found to be significant with the overall prognosis of early basal-like BC. The immune cells infiltration analysis displayed that the infiltration numbers of CD4+ T cell and naïve CD8+ T cell were positively correlated with AURKB expression level, while that of naïve B cell and macrophage M2 cell were negatively correlated with AURKB expression level in basal-like BC.Conclusion: AURKB might be a potential prognostic indicator in early basal-like BC.

Topoisomerase II alpha inhibition can overcome taxane-resistant prostate cancer through DNA repair pathways

Cabazitaxel (CBZ) is approved for the treatment of docetaxel-resistant castration-resistant prostate cancer (CRPC). However, its efficacy against CRPC is limited, and there are no effective treatments for CBZ-resistant CRPC. This study explored the optimal treatment for CRPC in the post-cabazitaxel setting. PC3 (CBZ-sensitive) and PC3CR cells (CBZ-resistant) were used in this study. We performed in silico drug screening for candidate drugs that could reprogram the gene expression signature of PC3CR cells. The in vivo effect of the drug combination was tested in xenograft mice models. We identified etoposide (VP16) as a promising treatment candidate for CBZ-resistant CRPC. The WST assay revealed that VP16 had a significant antitumor effect on PC3CR cells. PC3CR cells exhibited significantly higher topoisomerase II alpha (TOP2A) expression than PC3 cells. Higher TOP2A expression was a poor prognostic factor in The Cancer Genome Atlas prostate cancer cohort. In the Fred Hutchinson Cancer Research Center dataset, docetaxel-exposed tissues and metastatic tumors had higher TOP2A expression. In addition, VP16 significantly inhibited the growth of tumors generated from both cell lines. Based on these findings, VP16-based chemotherapy may be an optimal treatment for CPRC in the post-CBZ setting.

Oncogenetic Function and Prognostic Value of DNA Topoisomerase II Alpha (TOP2A) 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, the association with clinical outcomes of TOP2A in 33 different human cancers. The results showed that TOP2A was amplified in 32 investigated cancers; TOP2A expression was significantly associated with metastasis of six different cancers, and significantly associated with the survivals 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, Kyoto encyclopedia of genes and genomes (KEGG) pathway and Gene Ontology (GO) enrichment analyses revealed a most significant association between TOP2A with 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.

Identification of Five Hub Genes as Key Prognostic Biomarkers in Liver Cancer via Integrated Bioinformatics Analysis

Liver cancer is one of the most common cancers and the top leading cause of cancer death globally. However, the molecular mechanisms of liver tumorigenesis and progression remain unclear. In the current study, we investigated the hub genes and the potential molecular pathways through which these genes contribute to liver cancer onset and development. The weighted gene co-expression network analysis (WCGNA) was performed on the main data attained from the GEO (Gene Expression Omnibus) database. The Cancer Genome Atlas (TCGA) dataset was used to evaluate the association between prognosis and these hub genes. The expression of genes from the black module was found to be significantly related to liver cancer. Based on the results of protein–protein interaction, gene co-expression network, and survival analyses, DNA topoisomerase II alpha (TOP2A), ribonucleotide reductase regulatory subunit M2 (RRM2), never in mitosis-related kinase 2 (NEK2), cyclin-dependent kinase 1 (CDK1), and cyclin B1 (CCNB1) were identified as the hub genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses showed that the differentially expressed genes (DEGs) were enriched in the immune-associated pathways. These hub genes were further screened and validated using statistical and functional analyses. Additionally, the TOP2A, RRM2, NEK2, CDK1, and CCNB1 proteins were overexpressed in tumor liver tissues as compared to normal liver tissues according to the Human Protein Atlas database and previous studies. Our results suggest the potential use of TOP2A, RRM2, NEK2, CDK1, and CCNB1 as prognostic biomarkers in liver cancer.