Search Results for: long noncoding rna expression

Transcriptome profiling of esophageal squamous cell carcinoma reveals a long noncoding RNA acting as a tumor suppressor

Esophageal Squamous Cell Carcinoma (ESCC) is among the most common malignant cancers worldwide. In the past, extensive efforts have been made to characterize the involvement of protein-coding genes in ESCC tumorigenesis but few for long noncoding RNAs (lncRNAs).

To investigate the transcriptome profile and functional relevance of lncRNAs, researchers at the Chinese Academy of Sciences performed an integrative analysis of a customized combined lncRNA-mRNA microarray and RNA-seq data on ESCCs and matched normal tissues. They identified numerous lncRNAs that were differentially expressed between the normal and tumor tissues, termed “ESCC-associated lncRNAs (ESCALs)”, of which, the majority displayed restricted expression pattern. Also, a subset of ESCALs appeared to be associated with ESCC patient survival. Gene set enrichment analysis (GSEA) further suggested that over half of the ESCALs were positively- or negatively- associated with metastasis. Among these, the researchers identified a novel nuclear-retained lncRNA, named Epist, which is generally highly expressed in esophagus, and which is down-regulated during ESCC progression. Epist over-expression and knockdown studies further suggest that Epist inhibits the metastasis, acting as a tumor suppressor in ESCC. Collectively, this analysis of the ESCC transcriptome identified the potential tumor suppressing lncRNA Epist, and provided a foundation for future efforts to identify functional lncRNAs for cancerous therapeutic targeting.


Long noncoding RNAs associated with survival time of ESCC patients. A. The workflow of screening the mRNA and lncRNA probes whose expression level associates the survival time of ESCC patients, as described in Methods. (B, C, D) These panels show the Kaplan–Meier survival curves for three lincRNA examples of them. HOTAIR, linc-TMEM106A and LOC645638.

  • Wei G, Luo H, Sun Y, Li J, Tian L, Liu W, Liu L, Luo J, He J, Chen R. (2015) Transcriptome profiling of esophageal squamous cell carcinoma reveals a long noncoding RNA acting as a tumor suppressor. Oncotarget [Epub ahead of print]. [article]

Agilent Collaborates with Ghent University to Incorporate LNCipedia Content to Human v3 Gene Expression Microarray

lncRNASANTA CLARA, Calif.–(BUSINESS WIRE)–Agilent Technologies Inc. (NYSE:A) today announced updates to its SurePrint gene expression microarrays for messenger RNA profiling applications for human, mouse and rat models. The updates improve coding and noncoding content, which will provide up-to-date tools for researchers to investigate expression patterns on a highly accessible platform.

“Through the high performance and quantitative concordance of our gene expression microarrays, along with our RNA-Seq and target-enrichment products, we enable researchers to smoothly transition between microarray screening applications and deeper next-generation sequencing discovery.”

Agilent developed the updates to its flagship SurePrint G3 Human v3 gene expression microarray in collaboration with Ghent University for complete coverage of the LNCipedia 2.1 database to assay high-confidence, long noncoding RNA (lncRNA) transcripts.

Researchers use RNA-Seq to show that lincRNAs can also contribute to HER2+ breast cancers


Ahmad M. Khalil, PhD, knew the odds were against him — as in thousands upon thousands to one.

Yet he and his team never wavered from their quest to identify the parts of the body responsible for revving up one of the most aggressive forms of breast cancer, HER2+. This month in Breast Cancer Research and Treatment, Khalil and his colleagues at Case Western Reserve University proved the power of persistence; from a pool of more than 30,000 possibilities, they found 38 genes and molecules that most likely trigger HER2+ cancer cells to spread.

By narrowing what was once an overwhelming range of potential culprits to a relatively manageable number, Khalil and his team dramatically increased the chances of identifying successful treatment approaches to this particularly pernicious form of breast cancer. The HER2+ subtype accounts for approximately 20 to 30 percent of early-stage breast cancer diagnoses, which are estimated to be more than 200,000 new breast cancer diagnoses each year in this country, leading to approximately 40,000 deaths annually. Several cancer chemotherapy drugs do work well at early stages of the disease — destroying 95 to 98 percent of the cancer cells in HER2+ tumors.

Profiling of human long non-coding RNAs with CaptureSeq

Researchers from the Garvan Institute of Medical Research compared quantitative RT-PCR (qRT-PCR), RNA-seq and capture sequencing (CaptureSeq) in terms of their ability to assemble and quantify long noncoding RNAs and novel coding exons across 20 human tissues. CaptureSeq was superior for the detection and quantification of genes with low expression, showed little technical variation and accurately measured differential expression. This approach expands and refines previous annotations and simultaneously generates an expression atlas.


  • Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME. (2015) Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Nat Methods [Epub ahead of print]. [abstract]

ALDB – a domestic-animal long noncoding RNA database

The domestic-animal lncRNA database (ALDB) is the first comprehensive database with a focus on the domestic-animal lncRNAs. ALDB currently comprises 12,103 pig lincRNAs, 8,923 chicken lincRNAs, and 8,250 cow lincRNAs, which have been identified using computational pipeline in this study. Moreover, ALDB provides related useful data, such as genome-wide expression profile and animal quantitative trait loci (QTLs), that is not available in the existing lncRNA database (lncRNAdb and NONCODE), along with convenient tools, such as BLAST, GBrowse and flexible search functionalities.


  • Li, Aimin (2015): ALDB: a domestic-animal long noncoding RNA database. figshare.