miRNA profiling

CINCINNATI CHILDRENS HOSPITAL MEDICAL CENTER LOGOCINCINNATI, March 9, 2012 /PRNewswire-USNewswire/ – Researchers have identified a genetic signature for a severe, often painful food allergy – eosinophilic esophagitis – that could lead to improved diagnosis and treatment for children unable to eat a wide variety of foods.

The scientists, from Cincinnati Children’s Hospital Medical Center, report in the Journal of Allergy and Clinical Immunology that they have pinpointed a dysregulated microRNA signature for eosinophilic esophagitis (EoE), a disease that also may cause weight loss, vomiting, heartburn and swallowing difficulties.

Interestingly, the dysregulated microRNA was reversible with steroid treatment, according to the study’s senior investigator, Marc E. Rothenberg, MD, PhD, director of Allergy and Immunology and the Center for Eosinophilic Disorders at Cincinnati Children’s. MicroRNAs are short segments of RNA that can regulate whether genetic messengers (mRNAs) are degraded or translated into protein.

“The identification of biomarkers specific to EoE is a significant advancement for both the diagnosis and treatment of the disease,” explains Rothenberg. “The microRNA signature provides an opportunity for more precise analysis of esophageal biopsies.”

Rothenberg said children with EoE now undergo anesthesia and invasive endoscopy to diagnose and monitor the allergy. The ability to determine the presence and status of EoE with a noninvasive method, such as blood test that measures microRNAs, would have a positive impact on individuals and families.

In the current study, investigators analyzed esophageal microRNA expression of patients with active EoE, steroid-induced EoE remission, patients with chronic (non-eosinophilic) esophagitis and of healthy individuals. Additionally, they assessed plasma microRNA expression of patients with active EoE, remission of EoE remission and of healthy individuals.

The researchers found that EoE was associated with 32 differentially regulated microRNAs and distinguishable from the non-eosinophilic forms of esophagitis (such as reflux disease). Esophageal eosinophil levels correlated significantly with [click to continue…]

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Low-Level Expression of miR-375 Correlates with Poor Outcome and Metastasis While Altering the Invasive Properties of Head and Neck Squamous Cell Carcinomas.

Researchers at Department of Pathology, Albert Einstein College of Medicine used global miRNA expression profiling of head and neck squamous cell carcinoma (HNSCC) samples and adjacent normal tissue to rank those miRNAs that were most significantly altered in a patient population of 123. Harris et al. evaluated 736 of the currently known 1898 unique mature human microRNAs. Rank Consistency Score analysis revealed miR-375 to have the most significantly lowered miRNA levels in tumors relative to matched adjacent nonmalignant tissue from the same patient.

While this result has been previously observed by other groups, this latest study reveals that low miR-375 expression levels correlate significantly with cancer survival and distant metastasis. In a study of 123 primary HNSCC patients using multivariable Cox proportional hazard ratios (HR) and 95% confidence intervals (CI), both death from disease (HR: 12.8, 95% CI: 3 to 49) and incidence of distant metastasis (HR: 8.7, 95% CI: 2 to 31) correlated with lower expression levels of miR-375 regardless of the site or stage of the tumor. In addition, oral cavity tumor cell lines (eg, UMSCC1 and UMSCC47) overexpressing miR-375 were significantly less invasive in vitro than their matched empty vector controls.

The authors conclude that miR-375 may be suitable as a potential prognostic marker of poor outcome and metastasis in HNSCC and that it may function by suppressing the tumor’s invasive properties.

Harris T, Jimenez L, Kawachi N, Fan JB, Chen J, Belbin T, Ramnauth A, Loudig O, Keller CE, Smith R, Prystowsky MB, Schlecht NF, Segall JE, Childs G.
Low-Level Expression of miR-375 Correlates with Poor Outcome and Metastasis While Altering the Invasive Properties of Head and Neck Squamous Cell Carcinomas.
Am J Pathol., in press.

http://www.sciencedirect.com/science/article/pii/S0002944011010947

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Firefly BioWorks looking for beta-testers of new kit

by Christoph on November 18, 2011

in New Kits

Firefly BioWorks is a startup company introducing an innovative technology platform for multiplexed quantification of biomolecules. Their products offer simultaneous detection of many targets per sample with minimal hands-on time. The assay is designed to work on standard flow cytometers and takes 4 hours from experiment to data.
The company is launching an Early Access program for owners of benchtop cytometers and are looking for scientists interested in microRNA profiling. Participants will receive a 100-assay kits free of charge, in exchange for feedback on robustness and usability.
Details are available at:
http://www.fireflybio.com/beta/2011-11-19_Firefly_miRNA_early_access.pdf

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New study connects the cancer gene Lin28 to glucose metabolism; may shed light on unifying principles in type 2 diabetes

BOSTON, Sept. 29, 2011 /PRNewswire-USNewswire/ — A pathway activated in cancer plays an unexpected key role in metabolic diseases like type 2 diabetes, according to a study by researchers at Children’s Hospital Boston. Evidence that the Lin28/let-7 pathway influences the cellular response to glucose provides a unifying theme to perplexing data that associates human genetic variation with diabetes risk.

The multi-institutional research team led by George Q. Daley, MD, PhD, director of Stem Cell Transplantation and a leader in the Stem Cell Research Program at Children’s Hospital Boston – reported their findings in the September 30 issue of the journal Cell.

Let-7 is a microRNA, a small RNA that dampens the expression of a large set of genes related to cell growth and development. Previously, the Daley lab reported that Lin28, an RNA-binding protein found at high levels in the embryo, blocks let-7 production and is aberrantly expressed in about 15% of all cancers.

“The relationship between Lin28 and let-7 is ancient, found in organisms as diverse as worms, mice, and humans,” said Daley, a professor of biological chemistry and molecular pharmacology at Harvard Medical School [click to continue…]

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Houston, TX (PRWEB)   -  A week after the latest miRBase update LC Sciences announced use of miRBase Version 17 probe content as new default for their miRNA microarrays. Arrays for all species included in the latest miRBase 17 release are available. Looking at the most common species: while the changes in probe content for rat are negligible, additions to the list of human miRNAs are substantial: 521 new unique human mature miRNA sequences were added (see our post miRBase Version 17 Update Released).

The full press release: http://www.prweb.com/releases/2011/5/prweb8404968.htm

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microRNA at Plant & Animal Genomes Conference

January 5, 2011

Plant & Animal Genomes Conference – Jan 15th-19th, San Diego The upcoming Plant & Animal Genomes Conference will feature multiple posters and workshops focusing on microRNA research. Here is a sampling of the abstracts: PAG-XIX(P672) Characterization Of MiRNA From Subcutaneous Adipose Tissue Of Grizzly Bears (Ursus arctos horriblis) PAG-XIX(P786) Porcine Endometrial MiRNA Expression During The […]

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Normalization strategies for microRNA profiling experiments

November 24, 2010

Normalization strategies for microRNA profiling experiments: a ‘normal’ way to a hidden layer of complexity? MicroRNA (miRNA) profiling is a first important step in elucidating miRNA functions. Real time quantitative PCR (RT-qPCR) and microarray hybridization approaches as well as ultra high throughput sequencing of miRNAs (small RNA-seq) are popular and widely used profiling methods. All […]

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MicroRNAs play a critical role in immune system by regulating/fine tuning inflammatory response

September 8, 2009

MicroRNAs (miRNAs) have proven to be an extremely important part of the gene expression regulation mechanism. Expression profiling and functional studies indicate that miRNAs participate in the regulation of almost every cellular process investigated and that changes in their expression have a profound effect on their gene targeting activities. While the role of miRNAs in […]

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MicroRNA Profiling Increases Understanding of Molecular Circuitry

June 9, 2009

Researchers at Stanford University compared the microRNA-omes of human iPSCs, hESCs, and fetal fibroblasts to unravel the regulatory networks of pluripotency and cell reprogramming.

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MicroRNA Discovery and Validation in Silkworm – Case Study

May 4, 2009

The study of microRNA (miRNA) is growing rapidly as researchers discover new miRNA sequences and uncover the importance of these small regulatory elements linked to a wide range of biological functions. The miRBase sequence database (1) is the primary public repository for newly discovered miRNAs and the number of miRBase entries has grown rapidly from […]

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