Search Results for: long noncoding rna expression

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.

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

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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.

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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.

lncrna

  • 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.

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

 

Long Noncoding RNAs in Cardiovascular Diseases

lncRNA

In recent years, increasing evidence suggests that noncoding RNAs play important roles in the regulation of tissue homeostasis and pathophysiological conditions. Besides small noncoding RNAs (eg, microRNAs), >200-nucleotide long transcripts, namely long noncoding RNAs (lncRNAs), can interfere with gene expressions and signaling pathways at various stages. In the cardiovascular system, studies have detected and characterized the expression of lncRNAs under normal physiological condition and in disease states. Several lncRNAs are regulated during acute myocardial infarction (eg, Novlnc6) and heart failure (eg, Mhrt), whereas others control hypertrophy, mitochondrial function and apoptosis of cardiomyocytes. In the vascular system, the endothelial-expressed lncRNAs (eg, MALAT1 and Tie-1-AS) can regulate vessel growth and function, whereas the smooth-muscle-expressed lncRNA smooth muscle and endothelial cell-enriched migration/differentiation-associated long noncoding RNA was recently shown to control the contractile phenotype of smooth muscle cells.

This review article summarizes the data on lncRNA expressions in mouse and human and highlights identified cardiovascular lncRNAs that might play a role in cardiovascular diseases. Although our understanding of lncRNAs is still in its infancy, these examples may provide helpful insights how lncRNAs interfere with cardiovascular diseases.

  • Uchida S, Dimmeler S. (2015) Long Noncoding RNAs in Cardiovascular Diseases. Circ Res 116(4):737-750. [article]