Up-regulation of FOXN3-AS1 in invasive ductal carcinoma of breast cancer patients

Ramshe, Samira Molaei; Ghaedi, Hamid; Omrani, Mir Davood; Geranpayeh, Lobat; Alipour, Behnam; Ghafouri‐Fard, Soudeh

doi:10.1016/j.heliyon.2021.e08179

Cited by 4 publications

(2 citation statements)

References 31 publications

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“…Furthermore, we found that CYP1B1-AS1 had significantly higher expression levels in breast cancer tissues than in normal tissue adjacent to the cancer. In recent years, the long-stranded non-coding RNA CYP1B1-AS1 is gaining attention as an important factor in the development of tumors, such as breast cancer and glioblastoma ( Molaei Ramshe et al ., 2021 ; Ye et al ., 2021 ). A study noted that CYP1B1 was identified as a regulatory target of CYP1B1-AS1 ( Ye et al ., 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Functional variant rs10175368 which affects the expression of CYP1B1 plays a protective role against breast cancer in a Chinese Han population

Liu

Zhang

Tang

et al. 2023

European Journal of Cancer Prevention

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Objective Cytochrome P450 1B1 (CYP1B1) genetic variants are relevant in the pathogenesis of breast cancer. Exploring the relationships between CYP1B1 functional variants and breast cancer could improve our understanding of breast cancer molecular pathophysiology. Methods This is a two-stage hospital-based case–control study of a Chinese Han population. Genotyping was performed to identify candidate gene variants. 3DSNP, ANNOVAR, and RegulomeDB were used to determine functional single nucleotide polymorphisms (SNPs). The relationship between candidate variants and breast cancer risk was evaluated through unconditional logistic regression analysis. The PancanQTL platform was used to perform cis and trans expression quantitative trait loci (eQTL) analysis of positive SNPs. The GSCA platform was then used to compare the gene expression levels of potential target genes between breast cancer tissue and normal tissue adjacent to the cancer. Results rs10175368-T acted as a protective factor against breast cancer based on an additive model [odds ratio (OR) = 0.722, 95% confidence interval (CI) = 0.613–0.850; P < 0.001], and was identified as a protective factor in the postmenopausal population (OR = 0.601; 95% CI, 0.474–0.764; P < 0.001). eQTL analysis and analysis of differential expression in carcinoma and paracancerous tissues revealed that the expression level of CYP1B1-AS1 was associated with rs10175368 and that CYP1B1-AS1 had significantly higher expression levels in breast cancer tissues than in paracancerous tissues. Conclusion We show, for the first time in a Chinese Han population, that the functional variant rs10175368 plays a protective role against breast cancer, especially in the postmenopausal population.

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Section: Discussionmentioning

confidence: 99%

Functional variant rs10175368 which affects the expression of CYP1B1 plays a protective role against breast cancer in a Chinese Han population

Liu

Zhang

Tang

et al. 2023

European Journal of Cancer Prevention

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“…Among these CRlncRNAs, depletion of DIRC3-AS1 could increase the anchorage-independent growth, which means to malignant transformation, and reduce the survival time of melanoma 29 . Besides, the expression of FOXN3-AS1 was signi cantly elevated in breast cancer samples and associated with the tumor size 30 . Furthermore, LINC00682 correlated with the recurrence of hepatocellular carcinoma 31 .…”

Section: Discussionmentioning

confidence: 99%

A novel cuproptosis-related prognostic long non-coding RNAs signature model in neuroblastoma

Chen

Wang

Xiao

et al. 2022

Preprint

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Background Neuroblastoma (NB) is the most common malignant solid tumor of the autonomic nervous system in children, which exhibits diverse with dramatic clinical behaviors. Cuproptosis, as a novel form of cell death, has already caused the extensive attention. However, the prognostic value of cuproptosis-related genes (CRGs) in NB remains unelucidated. In this research, we aimed to identify the association and construct a prognostic multigene signature of CRGs and cuproptosis-related long-chain non-coding RNAs (CRlncRNAs). Methods Obtaining RNA-sequence profiles and corresponding clinical data of NB patients from The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/, accessed on 22 June 2022) database. Next, constructing the co-expression of CRGs and CRlncRNAs, and utilizing lasso, univariate Cox and multivariate Cox regression analysis to develop a prognostic signature. Then, Kaplan-Meier analysis was used to compare the overall survival (OS) among the groups classified by median CRlncRNAs signature score. Moreover, GO/KEGG enrichment analysis, tumor mutation burden (TMB), immune infiltration and CIBERSORT were conducted in high-risk and low-risk groups. Results CRlncRNA DIRC3-AS1, FOXN3-AS1, LINC00682, RASSF8-AS1 formed the prognostic signature model and patients with high-risk score were demonstrated to have a poor OS (Hazard ratio: 1.177, 95% CI: 1.066-1.300, p < 0.001). Besides, the accuracy of this model was verified by receiver operating characteristic (ROC) and principal component analysis (PCA). Furthermore, prognostic nomogram showed that the risk group of CRlncRNAs signature model appeared to have the ability of prognostic prediction. After that, TMB revealed that there was no statistical difference of genetic alterations in low-risk and high-risk group patients. Immune infiltration was also evaluated and revealed that immune functions were enriched in low-risk group. Conclusion The CRlncRNAs signature model presented to have efficacious prognostic value in profiles of NB patients.

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The Identification of Key Genes and Biological Pathways in Polycystic Ovary Syndrome and its Complications by Next Generation Squancing (NGS) and Bioinformatics Analysis

Vastrad¹,

Vastrad²

2023

Preprint

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Polycystic ovary syndrome (PCOS) is is associated with infertility, obesity, insulin resistance, hyperinsulinemia, type 2 diabetes mellitus, hypertension, cardiovascular problems, neurological and psychological problems and cancer. The specific mechanism of PCOS and its complications remains unclear. The aim of this study was to apply a bioinformatics approach to reveal related pathways or genes involved in the development of PCOS and its complications. The next generation squancing (NGS) datset GSE199225 was downloaded from the gene expression omnibus (GEO) database. Differentially expressed gene (DEG) analysis was performed using DESeq2. The g:Profiler was utilized to analyze the functional enrichment, gene ontology (GO) and REACTOME pathway of the differentially expressed genes. A protein-protein interaction (PPI) network was constructed and module analysis was performed using HiPPIE and cytoscape. The miRNA-hub gene regulatory network and TF-hub gene regulatory network were also constructed for research. The expression of the hub genes was validated using receiver operating characteristic (ROC) curve analysis. We have identified 957 DEGs in total, including 478 up regulated genes and 479 down regulated gene. GO and REACTOME illustrated that DEGs in PCOS were significantly enriched in regulation of molecular function, developmental process, interferon signaling and platelet activation, signaling and aggregation. Finally, through analyzing the PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network, we screened hub genes HSPA5, PLK1, RIN3, DBN1, CCDC85B, DISC1, AR, MTUS2, LYN and TCF4 by the Cytoscape software. This study uses a series of bioinformatics technologies to obtain hug genes and key pathways related to PCOS and its complications. These analysis results provide us with novel ideas for finding biomarkers and treatment methods for PCOS and its complications.

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Up-regulation of FOXN3-AS1 in invasive ductal carcinoma of breast cancer patients

Cited by 4 publications

References 31 publications

Functional variant rs10175368 which affects the expression of CYP1B1 plays a protective role against breast cancer in a Chinese Han population

Functional variant rs10175368 which affects the expression of CYP1B1 plays a protective role against breast cancer in a Chinese Han population

A novel cuproptosis-related prognostic long non-coding RNAs signature model in neuroblastoma

The Identification of Key Genes and Biological Pathways in Polycystic Ovary Syndrome and its Complications by Next Generation Squancing (NGS) and Bioinformatics Analysis

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