Clinical and microarray analysis of breast cancers of all subtypes from two prospective preoperative chemotherapy studies

Okuma, Hidemi; Koizumi, Fumiaki; Hirakawa, Akihiro; Nakatochi, Masahiro; Komori, Osamu; Hashimoto, Jun; Kodaira, Makoto; Yunokawa, Mayu; Yamamoto, Hitoshi; Yonemori, Kan; Shimizu, Chikako; Fujiwara, Yasuhiro; Tamura, Kenji

doi:10.1038/bjc.2016.184

Cited by 13 publications

(9 citation statements)

References 62 publications

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“…cDNA expression profiling was performed using total RNA with the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, USA) according to the manufacturer’s instructions and a previous report [27].…”

Section: Methodsmentioning

confidence: 99%

Sphere-forming culture enriches liver cancer stem cells and reveals Stearoyl-CoA desaturase 1 as a potential therapeutic target

Sun

Wang

et al. 2019

BMC Cancer

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Backgrounds The role of sphere-forming culture in enriching subpopulations with stem-cell properties in hepatocellular carcinoma (HCC) is unclear. The present study investigates its value in enriching cancer stem cells (CSCs) subpopulations and the mechanism by which HCC CSCs are maintained. Methods HCC cell lines and fresh primary tumor cells were cultured in serum-free and ultra-low attachment conditions to allow formation of HCC spheres. In vitro and in vivo experiments were performed to evaluate CSC characteristics. Expression levels of CSC-related genes were assessed by qRT-PCR and the correlation between sphere formation and clinical characteristics was investigated. Finally, gene expression profiling was performed to explore the molecular mechanism underlying HCC CSC maintenance. Results We found that both cell lines and primary tumor cells formed spheres. HCC spheres possessed the capacity for self-renewal, proliferation, drug resistance, and contained different subpopulations of CSCs. Of interest, 500 sphere-forming Huh7 cells or 200 primary tumor cells could generate tumors in immunodeficient animals. Sphere formation correlated with size, multiple tumors, satellite lesions, and advanced stage. Further investigation identified that the PPARα-SCD1 axis plays an important role in maintenance of the CSC properties of HCC sphere cells by promoting nuclear accumulation of β-Catenin. Inhibition of SCD1 interfered with sphere formation, down-regulated expression of CSC-related markers, and reduced β-Catenin nuclear accumulation. Conclusions Sphere-forming culture can effectively enrich subpopulations with stem-cell properties, which are maintained through activation of the PPARα-SCD1 axis. Therefore, we suggest that targeting the SCD1-related CSC machinery might provide a novel insight into HCC treatment. Electronic supplementary material The online version of this article (10.1186/s12885-019-5963-z) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Sphere-forming culture enriches liver cancer stem cells and reveals Stearoyl-CoA desaturase 1 as a potential therapeutic target

Sun

Wang

et al. 2019

BMC Cancer

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“…The expression levels of GBP1 and its pseudogene were signi cantly upregulated in tumor samples (3.4 and 5.7 fold, respectively). The GBP1 has anti-proliferative activity in endothelial cells that have been associated with a variety of cancers [31][32][33][34][35][36][37][38][39][40][41]. Its pseudogene counterpart, GBP1P1, has been proposed to have a role in GBP1 regulation.…”

Section: Discussionmentioning

confidence: 99%

“…However, overexpression of GBP1P1 has been observed in cervical carcinoma, breast cancer, and nasopharyngeal carcinoma [44][45][46]. In addition, it has been proposed that the GBP1P1 expression pro le could predict complete response to chemotherapy in early breast cancers [35].…”

Section: Discussionmentioning

confidence: 99%

Analysis of lncRNA-associated ceRNA network in breast cancer: A new insight into the role of GBP1P1 pseudogene in breast cancer

Mohebifer

Sabaghian

Kalani

et al. 2022

Preprint

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Background: Pseudogenes are a type of long noncoding RNAs (lncRNA) demonstrated to have a remarkable ability in post-transcriptional regulation, including cancer. Pseudogenes regulate parental gene expression via the competing endogenous RNA (ceRNA) mechanism. In this study, we present an lncRNA ceRNA network in breast cancer.Methods: 378 samples from 10 GEO databases were used to search for significant differentially expressed genes and lncRNAs. Following, the results were confirmed in the TCGA breast cancer database. The experimentally validated miRNAs that target genes and lncRNAs were explored in the DIANA tool to construct a ceRNA network. Finally, the result of ceRNA network analysis was validated in 40 breast cancer patients in lab experiments.Results: We have found 962 genes and lncRNAs in breast cancer. A ceRNA network with the topmost correlated gene-lncRNA and 73 common miRNAs was constructed. Several cancer-related pathways were deregulated, including AKT/mTOR and mTORC1-mediated pathways. We have found three genes with pseudogene pairs with the highest correlations, including GBP1-GBP1P1, PDE4DIP- PDE4DIPP2, and CD24-CD24P4. The GBP1-GBP1P1 had the best correlation with age, menopause status, nodal metastasis, stage, and subclass of patients. Then we assessed the expression of GBP1 and GBP1P1 in 40 breast cancer patients. The expression levels of GBP1 and its pseudogene were significantly upregulated in tumor samples (3.4 and 5.7 fold, respectively). In conclusion, we report a gene-lncRNA ceRNA network in breast cancer that may provide new insights into the role of GBP1P1 in the development of breast cancer.

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“…These genes were then analyzed via gene ontology and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and their protein interactions were then modulated. The authors calculated the correlation between survival rate and gene expression levels to discover potent targets for diagnosis and prognosis, which later on could also be evaluated as potential therapeutic targets as well [110].…”

Section: Pathway Analysis Of Tumor Cells Leading To Genomic Instabilitymentioning

confidence: 99%

Theranostic Interpolation of Genomic Instability in Breast Cancer

Rasool

Ullah

Mubeen

et al. 2022

IJMS

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Breast cancer is a diverse disease caused by mutations in multiple genes accompanying epigenetic aberrations of hazardous genes and protein pathways, which distress tumor-suppressor genes and the expression of oncogenes. Alteration in any of the several physiological mechanisms such as cell cycle checkpoints, DNA repair machinery, mitotic checkpoints, and telomere maintenance results in genomic instability. Theranostic has the potential to foretell and estimate therapy response, contributing a valuable opportunity to modify the ongoing treatments and has developed new treatment strategies in a personalized manner. “Omics” technologies play a key role while studying genomic instability in breast cancer, and broadly include various aspects of proteomics, genomics, metabolomics, and tumor grading. Certain computational techniques have been designed to facilitate the early diagnosis of cancer and predict disease-specific therapies, which can produce many effective results. Several diverse tools are used to investigate genomic instability and underlying mechanisms. The current review aimed to explore the genomic landscape, tumor heterogeneity, and possible mechanisms of genomic instability involved in initiating breast cancer. We also discuss the implications of computational biology regarding mutational and pathway analyses, identification of prognostic markers, and the development of strategies for precision medicine. We also review different technologies required for the investigation of genomic instability in breast cancer cells, including recent therapeutic and preventive advances in breast cancer.

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Clinical and microarray analysis of breast cancers of all subtypes from two prospective preoperative chemotherapy studies

Cited by 13 publications

References 62 publications

Sphere-forming culture enriches liver cancer stem cells and reveals Stearoyl-CoA desaturase 1 as a potential therapeutic target

Sphere-forming culture enriches liver cancer stem cells and reveals Stearoyl-CoA desaturase 1 as a potential therapeutic target

Analysis of lncRNA-associated ceRNA network in breast cancer: A new insight into the role of GBP1P1 pseudogene in breast cancer

Theranostic Interpolation of Genomic Instability in Breast Cancer

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