scholarly journals Identification of dysregulated microRNAs associated with diagnosis and prognosis in triple‑negative breast cancer: An in silico study

2019 ◽  
Author(s):  
Chunni Fan ◽  
Ning Liu
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
In Silico ◽  
Triple Negative ◽  
Diagnosis And Prognosis ◽  
In Silico Study

scholarly journals In Silico Analysis Guides Selection of BET Inhibitors for Triple-Negative Breast Cancer Treatment

2016 ◽  
Vol 15 (8) ◽  
pp. 1823-1833 ◽  
Author(s):  
Javier Pérez-Peña ◽  
Gemma Serrano-Heras ◽  
Juan Carlos Montero ◽  
Verónica Corrales-Sánchez ◽  
Atanasio Pandiella ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Treatment ◽  
Triple Negative Breast Cancer ◽  
In Silico ◽  
Triple Negative ◽  
In Silico Analysis ◽  
Breast Cancer Treatment ◽  
Bet Inhibitors ◽  
Silico Analysis ◽  
Selection Of

scholarly journals An In Silico Analysis Identified FZD9 as a Potential Prognostic Biomarker in Triple-Negative Breast Cancer Patients

2021 ◽  
Vol 17 (1) ◽  
pp. 42-52
Author(s):  
Daniel Rodrigues de Bastos ◽  
Mércia Patrícia Ferreira Conceição ◽  
Ana Paula Picaro Michelli ◽  
Jean Michel Rocha Sampaio Leite ◽  
Rafael André da Silva ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Patients ◽  
Triple Negative Breast Cancer ◽  
In Silico ◽  
Triple Negative ◽  
Prognostic Biomarker ◽  
Breast Cancer Patients

scholarly journals Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9975
Author(s):  
Xiuming Zhai ◽  
Zhaowei Yang ◽  
Xiji Liu ◽  
Zihe Dong ◽  
Dandan Zhou
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Survival Curve ◽  
Treatment Options ◽  
Hub Genes ◽  
Expression Levels ◽  
Link Type ◽  
Diagnosis And Prognosis ◽  
Potential Biomarkers

Background Breast cancer is a heterogeneous disease. Compared with other subtypes of breast cancer, triple-negative breast cancer (TNBC) is easy to metastasize and has a short survival time, less choice of treatment options. Here, we aimed to identify the potential biomarkers to TNBC diagnosis and prognosis. Material/Methods Three independent data sets (GSE45827, GSE38959, GSE65194) were downloaded from the Gene Expression Omnibus (GEO). The R software packages were used to integrate the gene profiles and identify differentially expressed genes (DEGs). A variety of bioinformatics tools were used to explore the hub genes, including the DAVID database, STRING database and Cytoscape software. Reverse transcription quantitative PCR (RT-qPCR) was used to verify the hub genes in 14 pairs of TNBC paired tissues. Results In this study, we screened out 161 DEGs between 222 non-TNBC and 126 TNBC samples, of which 105 genes were up-regulated and 56 were down-regulated. These DEGs were enriched for 27 GO terms and two pathways. GO analysis enriched mainly in “cell division”, “chromosome, centromeric region” and “microtubule motor activity”. KEGG pathway analysis enriched mostly in “Cell cycle” and “Oocyte meiosis”. PPI network was constructed and then 10 top hub genes were screened. According to the analysis results of the Kaplan-Meier survival curve, the expression levels of only NUF2, FAM83D and CENPH were associated with the recurrence-free survival in TNBC samples (P < 0.05). RT-qPCR confirmed that the expression levels of NUF2 and FAM83D in TNBC tissues were indeed up-regulated significantly. Conclusions The comprehensive analysis showed that NUF2 and FAM83D could be used as potential biomarkers for diagnosis and prognosis of TNBC.

scholarly journals Identification of Metastasis-Associated Genes in Triple-Negative Breast Cancer Using Weighted Gene Co-expression Network Analysis

2020 ◽  
Vol 16 ◽  
pp. 117693432095486
Author(s):  
Wenting Xie ◽  
Zhongshi Du ◽  
Yijie Chen ◽  
Naxiang Liu ◽  
Zhaoming Zhong ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Network Analysis ◽  
Candidate Genes ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Characteristic Curve ◽  
Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Functional Enrichment ◽  
Diagnosis And Prognosis

Triple-negative breast cancer (TNBC) is the most aggressive and fatal sub-type of breast cancer. This study aimed to identify metastasis-associated genes that could serve as biomarkers for TNBC diagnosis and prognosis. RNA-seq data and clinical information on TNBC from the Cancer Genome Atlas were used to conduct analyses. Expression data were used to establish co-expression modules using average linkage hierarchical clustering. We used weighted gene co-expression network analysis to explore the associations between gene sets and clinical features and to identify metastasis-associated candidate biomarkers. The K-M plotter website was used to explore the association between the expression of candidate biomarkers and patient survival. In addition, receiver operating characteristic curve analysis was used to illustrate the diagnostic performance of candidate genes. The pale turquoise module was significantly associated with the occurrence of metastasis. In this module, 64 genes were identified, and its functional enrichment analysis revealed that they were mainly associated with transcriptional misregulation in cancer, microRNAs in cancer, and negative regulation of angiogenesis. Further, 4 genes, IGSF10, RUNX1T1, XIST, and TSHZ2, which were negatively associated with relapse-free survival and have seldom been reported before in TNBC, were selected. In addition, the mRNA expression levels of the 4 candidate genes were significantly lower in TNBC tumor tissues compared with healthy tissues. Based on the K-M plotter, these 4 genes were correlated with poor prognosis of TNBC. The area under the curve of IGSF10, RUNX1T1, TSHZ2, and XIST was 0.918, 0.957, 0.977, and 0.749. These findings provide new insight into TNBC metastasis. IGSF10, RUNX1T1, TSHZ2, and XIST could be used as candidate biomarkers for the diagnosis and prognosis of TNBC metastasis.

scholarly journals Investigating the Anticancer Activity and Characterization of Bioactive Constituents of Moricandia sinaica (Boiss.) Boiss through In Vitro and In Silico Approaches in Triple-Negative Breast Cancer Cell Line

2021 ◽  
Vol 11 (3) ◽  
pp. 1244
Author(s):  
Muhammad Farooq Khan ◽  
Fahd A. Nasr ◽  
Almohannad A. Baabbad ◽  
Ali S. Alqahtani ◽  
Mohammad A. M. Wadaan
Keyword(s):  
Breast Cancer ◽  
Anticancer Activity ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Triple Negative Breast Cancer ◽  
In Silico ◽  
Triple Negative ◽  
Protein Target ◽  
Crude Extracts ◽  
M Phase

Resistance to chemotherapy and recurrence are major hurdles to treating hormone receptor-negative breast cancer. The crude extract and natural products obtained from medicinal plants are believed to be multitargeted and possess less toxicity as compared to synthetic compounds. The aerial parts and roots of Moricandia sinaica (Boiss.) Boiss were used to prepare the crude extracts in solvents of different polarities. Human breast cancer cell lines (MCF7 and MDA-MB-231), liver carcinoma (HepG2), and nontumorigenic cells of human origin (human umbilical vein endothelial cells (HUVEC)) were treated with a serial dilution of crude extracts obtained from the aerial and roots of Moricandia sinaica (Boiss.) Boiss. The methanol extract of the shoots exhibited a higher level of cytotoxicity against MDA-MB-231 cells than against any other cancer and nontumorigenic cells lines. Six new compounds were identified by gas chromatography–mass spectrophotometry analysis in the shoots extract of Moricandia sinaica (Boiss.) Boiss, and 2-Tridecen-1-ol was one of the major compounds that represent more than 35% of the extract. M-phase inducer phosphases 1 and 2 (CDC 25A and B) were identified as the specific protein target for 2-Tridecen-1-ol by the Swiss protein target prediction tool. In silico molecular docking showed the binding of 2-Tridecen-1-ol with CDC 25 B with a higher binding energy as compared to CDC 25A. The possible molecular mechanism of anticancer activity of Moricandia sinaica (Boiss.) Boiss in MDA-MB-231 breast cancer is through inhibition of M-phase inducer phosphatases 1 and 2 via 2-Tridecen-1-ol. Further investigations in breast cancer models are needed to explore the therapeutic potential of Moricandia sinaica (Boiss.) Boiss and 2-Tridecen-1-ol as an efficient remedy with a possibly less toxic approach to treat triple-negative breast cancer.

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