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E-GEOD-41972

ABSTRACT: In vivo NCL-targeting affects breast cancer aggressiveness through miRNA regulation [Affymetrix]

OTHER RELATED OMICS DATASETS IN: PRJNA178628PRJNA178627

PROVIDER: E-GEOD-41972 | ExpressionAtlas | 2015-08-19

REPOSITORIES: ExpressionAtlas

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Dataset's files

Source:

			Action	DRS
	E-GEOD-41972-analysis-methods.tsv	Tabular
	E-GEOD-41972-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-41972-configuration.xml	Xml
	E-GEOD-41972-percentile-ranks.tsv	Tabular
	E-GEOD-41972.condensed-sdrf.tsv	Tabular

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Project description:In vivo NCL-targeting affects breast cancer aggressiveness through miRNA regulation [Affymetrix]

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Project description:This SuperSeries is composed of the following subset Series: GSE41971: In vivo NCL-targeting affects breast cancer aggressiveness through miRNA regulation [NanoString] GSE41972: In vivo NCL-targeting affects breast cancer aggressiveness through miRNA regulation [Affymetrix] Refer to individual Series

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Project description:MicroRNA (miRNA/miR) miR526b and miR655 overexpressed tumor cell-free secretions promote breast cancer phenotypes in the tumor microenvironment (TME). However, the mechanisms of miRNA regulating TME have never been investigated. With mass spectrometry analysis of MCF7-miRNA-overexpressed versus miRNA-low MCF7-Mock tumor cell secretomes, we identified 34 novel secretory proteins coded by eight genes YWHAB, TXNDC12, MYL6B, SFN, FN1, PSMB6, PRDX4, and PEA15 those are differentially regulated. We used bioinformatic tools and systems biology approaches to identify these markers’ role in breast cancer. Gene ontology analysis showed that the top functions are related to apoptosis, oxidative stress, membrane transport, and motility, supporting miRNA-induced phenotypes. These secretory markers expression is high in breast tumors, and a strong positive correlation exists between upregulated markers’ mRNA expressions with miRNA cluster expression in luminal A breast tumors. Gene expression of secretome markers is higher in tumor tissues compared to normal samples, and immunohistochemistry data supported gene expression data. Moreover, both up and downregulated marker expressions are associated with breast cancer patient survival. miRNA regulates these marker protein expressions by targeting transcription factors of these genes. Premature miRNA (pri-miR526b and pri-miR655) are established breast cancer blood biomarkers. Here we report novel secretory markers upregulated by miR526b and miR655 (YWHAB, MYL6B, PSMB6, and PEA15) are significantly upregulated in breast cancer patients’ plasma, and are potential breast cancer biomarkers.

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López-Cortés2020 - Prediction of Breast Cancer (BC) proteins involved in cancer immunotherapy using molecular descriptors and Multi Layer Perceptron (MLP) neural network

Project description:This study introduces a predictive classifier for breast cancer-related proteins, utilising a combination of protein sequence descriptors and machine learning techniques. The best-performing classifier is a Multi Layer Perceptron (artificial neural network) with 300 features, achieving an average Area Under the Receiver Operating Characteristics (AUROC) score of 0.984 through 3-fold cross-validation. Notably, the model identified top-ranked cancer immunotherapy proteins associated with breast cancer that should be studied for further biomarker discovery and therapeutic targeting. Please note that in this model, the output '0' means BC non-related protein and '1' means BC related protein. The original GitHub repository can be accessed at https://github.com/muntisa/neural-networks-for-breast-cancer-proteins

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In vivo NCL-targeting affects breast cancer aggressiveness through miRNA regulation [Affymetrix]

Project description:Numerous studies have described the altered expression and the causal role of miRNAs in human cancer. However, to date efforts to modulate miRNA levels for therapeutic purposes have been challenging to implement. Here, we find that Nucleolin (NCL), a major nucleolar protein, post-transcriptionally regulates the expression of a specific subset of miRNAs, including miR-21, miR-221, miR-222, and miR-103, causally involved in breast cancer initiation, progression and drug-resistance. We also show that NCL is commonly overexpressed in human breast tumors, and its expression correlates with that of NCL-dependent miRNAs. Finally, this study indicates that NCL-binding guanosine-rich aptamers affect the levels of NCL-dependent miRNAs and their target genes, reducing breast cancer cell aggressiveness, both in vitro and in vivo. These findings illuminate a path to novel therapeutic approaches based on NCL-targeting aptamers for the modulation of miRNA expression in the treatment of breast cancer. MCF7 cells were treated with the control drug or AS1411 aptamer. After 72hours total RNA was collected and analyzed by Affymetrix U133 plus.

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