{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Xiaoti Lin"],"organism":["Homo sapiens"],"software":["GeneSpring software V12 (Agilent)","GeneSpring GX (Agilent Technologies, Capital Biochip Corporation)"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-5584"],"description":["RNA extraction and microarray analysis total RNA from immortalized normal mammary epithelial cells (184A1, MCF-12A), breast cancer cells (MDA-MB-231, MCF-7, MDA-MB-468, SK-BR-3), BCSC (MDA-MB-231SC, MCF-7SC, XM322, XM607). MDA-MB-231SC and MCF-7SC originating from breast cancer cell lines; XM322 and XM607 derived from clinical specimens which had been described in previous submission (E-MTAB-5057). The miRNA profiling was performed using Agilent miRNA array. Microarray experiments were conducted according to the manufacturer's instructions. To select the differentially expressed genes, we used threshold values of ≥ 2 and ≤ −2-fold change and a Benjamini-Hochberg corrected p value of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of Cluster 3.0 software then further analyzed with hierarchical clustering with average linkage (genes which value more than 100 were evaluated)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA containing small RNA was extracted from cell lines (immortalized healthy mammary epithelial cells: 184A1 and MCF-12A, breast cancer cells: MDA-MB-231, MCF-7, MDA-MB-468 and SK-BR-3, as well as BCSC: MDA-MB-231.SC, MCF-7.SC, XM322 and XM607) by using the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA was tested by capillary electrophoresis on an Agilent 2100 bioanalyzer and high quality of samples was confirmed.","Scaning - Acquired images and the signal intensities of miRNA spots were evaluated by GeneSpring GX (Agilent Technologies, Capital Biochip Corporation) and normalized based on global signal intensity according to the manufacturer’s protocol.","Hybridization - Human miRNA Microarray, Release 19.0, 8x60K"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - Differential miRNA expression was determined using a two-sided Student’s t-test, significance was accepted for changes >2-fold."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Agilent 2100 bioanalyzer","NanoDrop ND-1000"],"pubmed_abstract":["<b>Rationale:</b> Cancer stem cells (CSCs) have been implicated as the seeds of therapeutic resistance and metastasis, due to their unique abilities of self-renew, wide differentiation potentials and resistance to most conventional therapies. It is a proactive strategy for cancer therapy to eradicate CSCs. <b>Methods:</b> Tumor tissue-derived breast CSCs (BCSC), including XM322 and XM607, were isolated by fluorescence-activated cell sorting (FACS); while cell line-derived BCSC, including MDA-MB-231.SC and MCF-7.SC, were purified by magnetic-activated cell sorting (MACS). Analyses of microRNA and mRNA expression array profiles were performed in multiple breast cell lines. The mentioned nanoparticles were constructed following the standard molecular cloning protocol. Tissue microarray analysis has been used to study 217 cases of clinical breast cancer specimens. <b>Results:</b> Here, we have successfully established four long-term maintenance BCSC that retain their tumor-initiating biological properties. Our analyses of microarray and qRT-PCR explored that miR-34a is the most pronounced microRNA for investigation of BCSC. We establish hTERT promoter-driven VISA delivery of miR-34a (TV-miR-34a) plasmid that can induce high throughput of miR-34a expression in BCSC. TV-miR-34a significantly inhibited the tumor-initiating properties of long-term-cultured BCSC <i>in vitro</i> and reduced the proliferation of BCSC <i>in vivo</i> by an efficient and safe way. TV-miR-34a synergizes with docetaxel, a standard therapy for invasive breast cancer, to act as a BCSC inhibitor. Further mechanistic investigation indicates that TV-miR-34a directly prevents C22ORF28 accumulation, which abrogates clonogenicity and tumor growth and correlates with low miR-34 and high C22ORF28 levels in breast cancer patients. <b>Conclusion:</b> Taken together, we generated four long-term maintenance BCSC derived from either clinical specimens or cell lines, which would be greatly beneficial to the research progress in breast cancer patients. We further developed the non-viral TV-miR-34a plasmid, which has a great potential to be applied as a clinical application for breast cancer therapy.","The identification and understanding of the molecular network of cancer stem cells (CSCs) have had a profound impact on our view of carcinogenesis and treatment strategy. Unfortunately, a major problem is that serial passages of CSCs from clinical solid tumor specimens currently are not available in any lab, and thus, reported data are difficult to confirm and intensively interrogated. Here, we have generated two tumor tissue-derived breast CSC (BCSC) lines that showed prolonged maintenance over 20 serial passages in vitro, while retaining their tumor-initiating biological properties. We then deciphered the intrinsic mechanism using analyses of mRNA expression array profiles. It has been determined that pro-opiomelanocortin (POMC) is closely related with protein phosphorylation mediated by G-protein-coupled estrogen receptor (GPER) in BCSC. Following, knockdown of POMC inhibits properties of mammosphere formation, CD44<sup>+</sup> CD24<sup>-</sup> population, CD44 expression, and clonogenicity ability in BCSC. We found that inhibition of POMC attenuates phosphorylation of AKT2 and GSK3β in BCSC. Further in vivo investigations demonstrated that POMC interference regulates proliferation of BCSC-bearing tumors. Combination of the clinical results that POMC positive expression is frequently upregulated in human breast cancer and POMC positivity correlated with a poor prognosis, POMC is a potential therapeutic target for BCSC. In conclusion, we have successfully established two long-term-cultured BCSC from clinical specimens. We further indicated that POMC acts as a potential therapeutic target and prognostic marker for future treatment of BCSC."],"study_type":["microRNA profiling by array"],"species":["Homo sapiens"],"pubmed_title":["Nanoparticle Delivery of miR-34a Eradicates Long-term-cultured Breast Cancer Stem Cells via Targeting C22ORF28 Directly.","POMC maintains tumor-initiating properties of tumor tissue-derived long-term-cultured breast cancer stem cells."],"pubmed_authors":["Lin X, Chen W, Wei F, Zhou BP, Hung MC, Xie X.","Xiaoti Lin"],"additional_accession":[]},"is_claimable":false,"name":"Microarray analyses of microRNA expressions in comparison with immortal healthy mammary epithelial cells, breast cancer cells, and long-term-cultured breast cancer stem cells","description":"RNA extraction and microarray analysis total RNA from immortalized normal mammary epithelial cells (184A1, MCF-12A), breast cancer cells (MDA-MB-231, MCF-7, MDA-MB-468, SK-BR-3), BCSC (MDA-MB-231SC, MCF-7SC, XM322, XM607). MDA-MB-231SC and MCF-7SC originating from breast cancer cell lines; XM322 and XM607 derived from clinical specimens which had been described in previous submission (E-MTAB-5057). The miRNA profiling was performed using Agilent miRNA array. Microarray experiments were conducted according to the manufacturer's instructions. To select the differentially expressed genes, we used threshold values of ≥ 2 and ≤ −2-fold change and a Benjamini-Hochberg corrected p value of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of Cluster 3.0 software then further analyzed with hierarchical clustering with average linkage (genes which value more than 100 were evaluated).","dates":{"release":"2017-12-01T00:00:00Z","modification":"2022-03-09T07:08:56.235Z","creation":"2022-03-09T07:08:56.235Z"},"accession":"E-MTAB-5584","cross_references":{"pubmed":["28214331","29187905"],"EFO":["EFO_0000753","EFO_0005518"],"doi":["10.7150/thno.20771","10.1002/ijc.30658"]}}