Long noncoding RNA landscape in breast cancer [Mexico]
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PROVIDER: PRJNA554862 | ENA |
REPOSITORIES: ENA
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Project description:Long noncoding RNA landscape in breast cancer [Mexico]
| PRJNA554862 | ENA
Project description:Breast cancer (BC) is the most commonly diagnosed neoplasm in women worldwide and a well-recognized heterogeneous pathology classified into four molecular subtypes: Luminal A, Luminal B, HER2-enriched and Basal-like, each one with different biological and clinical characteristics. It is well recognize that clinical and molecular heterogeneity of BC is driven in part by mRNA and lncRNAs. We profiled mRNAs and lncRNA in 75 adjuvant tumors using an Affymetrix microarray platform.
2020-08-12 | GSE134359 | GEO
Project description:1. Evaluate the diagnostic value of long noncoding RNA (CCAT1) expression by RT-PCR in peripheral blood in colorectal cancer patients versus normal healthy control personal.
2. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in diagnosis of colorectal cancer patients & its relation to tumor staging.
3. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in precancerous colorectal diseases.
4. Compare long noncoding RNA (CCAT1) expression with traditional marker; carcinoembryonic antigen (CEA) and Carbohydrate antigen 19-9 (CA19-9) in diagnosis of colorectal cancer.
| 2330122 | ecrin-mdr-crc
Project description:To understand the role of long non-coding RNAs and interaction with coding RNAs in bladder urothelial cell carcinoma (BUCC), we performed genome-wide screening long non-coding RNAs and coding RNAs expression on primary BUCC tissues and normal tissues using long non-coding RNA array (Agilent plateform (GPL13825). By comparing these two groups, significantly differentially expressed lncRNAs and coding RNAs were identified. We further identifed a subset of long noncoding RNAs and their correlation with neighboring coding genes using bioinformatic tools. This analysis provides foundamental understaning of transcriptomic landscape changing during bladder carcinogenesis. 12 BUCC primary tumors and 3 normal tissues were used for long noncoding RNA array experiments which including long non-coding RNAs and coding RNAs. The differential expression of subset of long noncoding RNAs and their interaction with coding RNAs in BUCC compared with normal tissue will be identified with comtational analysis.
2013-12-31 | E-GEOD-51493 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE37705: Effects of the long noncoding RNA Malat1 on gene expression [Mouse430_2] GSE37706: Effects of the long noncoding RNA Malat1 on gene expression [MoEx-1_0-st] Refer to individual Series
2012-06-24 | E-GEOD-37707 | biostudies-arrayexpress
Project description:Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer
| PRJNA605352 | ENA
Project description:Long noncoding RNA expression profile of chemotherapy-sensitive and resistant breast cancer tissues
| PRJNA912687 | ENA
Project description:GM0637 cell were treated with or without DNA damaging agent neocarzinostatin (NCS), and cells were harvested after 4 hours and 8 hours for the microarray analyses of whole-genome long noncoding RNAs. To examine how long noncoding RNAs are regulated in the DNA damage response, we assessed the genome-wide long noncoding RNA expression in GM0637 cells treated with or without DNA damage
2013-01-17 | E-GEOD-43509 | biostudies-arrayexpress
Project description:Few long noncoding RNAs (lncRNAs) that act as oncogenic genes in breast cancer have been identified.Oncogenic lncRNAs associated with tumourigenesis and worse survival outcomes were examined and validated in Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), respectively. Then, the potential biological functions and expression regulation of these lncRNAs were studied via bioinformatics and genome data analysis. Moreover, progressive breast cancer subtype-specific lncRNAs were investigated via high-throughput sequencing in our cohort and TCGA validation. To elucidate the mechanisms of the regulation of these lncRNAs, genomic alterations from the TCGA, Broad, Sanger and BCCRC data, as well as epigenetic modifications from GEO data, were then applied and examined to meet this objective. Finally, cell proliferation assays, flow cytometry analyses and TUNEL assays were applied to validate the oncogenic roles of these lncRNAs in vitro.A cluster of oncogenic lncRNAs that was upregulated in breast cancer tissue and was associated with worse survival outcomes was identified. These oncogenic lncRNAs are involved in regulating immune system activation and the TGF-beta and Jak-STAT signalling pathways. Moreover, TINCR, LINC00511, and PPP1R26-AS1 were identified as subtype-specific lncRNAs associated with HER-2, triple-negative and luminal B subtypes of breast cancer, respectively. The up-regulation of these oncogenic lncRNAs is mainly caused by gene amplification in the genome in breast cancer and other solid tumours. Finally, the knockdown of TINCR, DSCAM-AS1 or HOTAIR inhibited breast cancer cell proliferation, increased apoptosis and inhibited cell cycle progression in vitro.These findings enhance the landscape of known oncogenic lncRNAs in breast cancer and provide insights into their roles. This understanding may potentially aid in the comprehensive management of breast cancer.
| S-EPMC5525255 | biostudies-literature
Project description:In this study, we have integrated RNA-seq data from subcellular fractionated RNA (i.e., cytoplasm, nucleoplasm, and chromatin-associated) with GRO-seq data using a novel bioinformatics pipeline. This has yielded a comprehensive catalog of polyadenylated lncRNAs in MCF-7 cells, about half of which have not been annotated previously and about a quarter of which are estrogen-regulated. Knockdown of selected lncRNAs, such as lncRNA152 and lncRNA67 followed by RNA-seq suggest that these lncRNAs regulate the expression of cell cycle genes. characterization of long noncoding RNAs
2015-07-30 | E-GEOD-63189 | biostudies-arrayexpress