themiRNASeed

Rewiring miRNAs

RLR — Mon, 03 May 2010 20:45:25 +0000

Is there anybody out there? It could be the questions some scientists have when looking at the huge amount of informations residing in the gene expression microarray experiments deposited in databases and available for download. Is the power of meta analyses ever be exploited for microRNAs?

A recent paper in Genome Research from a team headed by Carlo Croce (Reprogramming of miRNA networks in cancer and leukemia) dived deep among data of 4419 cancer or normal tissue samples allowing them to perform a detailed analysis of miRNA activities and inferring genetic networks from miRNA expression in normal tissues and cancer.

It appeared from the study that miRNA expression networks tend to be more fragmented in cancerous tissues than in healthy tissues. It’s more and more evident that miRNAs cooperate together in groups, or cluster, and that activities due to the action of single miRNAs could be just a part of the story. Considering miRNAs one by one could be a heavy underestimation of their role and this study tries to exactly address this more-than-additive cooperation among miRNAs.

As always in biology patterns emerging from complexity help understanding the rationale of an apparent chaos. Rewiring existing knowledge, a step at a time…

miRNA protocols literature links

RLR — Tue, 09 Feb 2010 19:32:27 +0000

Under the section “bioprotocols”, SciClips gathered a number of link to papers with different microRNA protocols. Read them here.

New Pri-miRNA TaqMan Assays available

RLR — Mon, 01 Feb 2010 20:13:05 +0000

Applied Biosystems (Life Technology) recently launched new sets of pre-designed TaqMan real-time PCR assays for the detection of pri-miRNA and long non coding RNAs.

Tuschl IP timeline

RLR — Mon, 01 Feb 2010 20:02:48 +0000

For those of you following the Tuschl IP litigation Genome Web’s RNAi News has a nice timeline here.

A Nature Collection on microRNAs

RLR — Fri, 18 Dec 2009 10:12:37 +0000

MicroRNAs are under the spotlight once again and this time Nature focuses on them with a Collection issue dedicated to the subject. Notably nine among letters and articles are free access, available to the ones without a Nature subscription. Other articles are gathered from the Nature’s archive and put together giving a nice preview of the top notch publications about this topic.

The microRNA Nature Collection webpage.

You can also request a printed copy for yourself here.

microRNA in human disease and development

RLR — Fri, 11 Dec 2009 00:15:51 +0000

The Cambridge Healthtech Institute’s sixth annual conference will be held in Cambridge, Massachusetts from march 22nd to 24th.
A number of tecnology focused pre conference short courses will be also presented.

More info on the CHI website.

miR-122 silencing in HCV phase 1 trial

RLR — Thu, 10 Dec 2009 23:50:39 +0000

miR-122 is a well known liver expressed miRNA. A number of reports already reported it as essential for HCV (hepatitis C virus) RNA accumulation and everyboby working on liver and microRNAs knows miR-122.

In collaborating with Santaris Pharma, we proved that the drug worked exceptionally well in treating HCV infections in chimpanzees

Early last week Science Magazine published online (december 3rd) a report in which scientists from the Southwest Foundation for Biomedical Research in San Antonio, Texas and from Santaris Pharma – a Copenhagen based company founded in 2003 – show that chronically infected chimpanzees treated with SPC3649, a LNA-modified oligonucleotide complementary to miR-122, leads to long-lasting suppression of HCV viremia without evidence for viral resistance or side effects in the animals.

PC3649 is the first microRNA-targeted drug to enter human clinical trials and is currently undergoing Phase 1 clinical studies in healthy volunteers and holds promise as a novel treatment for patients infected with the Hepatitis C virus (HCV).

The previous year Santaris put the bases for their LNA mediated microRNA silencing in non-human primates publishing results in Nature.

Robert Lanford, Ph.D., a scientist at the Southwest Foundation for Biomedical Research and one of the lead authors on the study said: “In collaborating with Santaris Pharma, we proved that the drug worked exceptionally well in treating HCV infections in chimpanzees. [...] The current standard anti-HCV treatment, which combines pegylated interferon-alpha with ribavirin, is effective in only about 50% of patients and is often associated with severe side effects. Because of the unique mechanism of action of SPC3649 and its tolerability profile, this new therapy could have the potential to replace interferon to treat disease progression or be combined with current treatments. (from the Santaris Pharma website)

The two publications: Lanford et al, 2009 in Science and Elmen et al, 2008 in Nature

A detailed story is also reported in the MIT Technology Review

HCV virus picture is taken from the Wikimedia Commons under the CC-BY-SA-3.0,2.5,2.0,1.0; Released under the GNU Free Documentation License.

Science Webinars abour miRNAs

RLR — Tue, 17 Nov 2009 22:34:24 +0000

MicroRNAs have been recently featured on the Science Magazine webinar page with a dedicated webinar by the title “microRNA Research Design: Strategies from the Experts” with Peter T. Nelson, Kai Wang and Neil Kubica. The webinar will be archived with all the past webinars and if you missed it you can watch it whenever you want here.

I want to point you to other two past Science webinars about microRNAs; they too can be watched online.

“miRNAs and Cancer” originally held on februrary 20th, 2008. Hosts: George A. Calin, Franck Slack and Scott M. Hammond.

“Noncoding RNAs: A New Paradigm for Gene Regulation” held on october 22nd, 2008. Hosts: George A. Calin and Joshua Mendell.

A pdf version of the slides can also be downloaded for each webinar.

Targets: the two faces of miRecords

RLR — Mon, 16 Nov 2009 23:57:46 +0000

miRecords, from University of Minnesota, is a double faced tool for miRNA target research. On one hand it integrates different target prediction algorithms and it’s useful to compare different tools’ performances in predicting miRNA targets. Given a specific miRNA, the user can filter for targets that are predicted by at least a number of algorithms/databases (11 of them are listed so far in the miRecords engine: DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid, and TargetScan). The use of the multi algorithms filter (“give me targets predicted by at least x algorithms”) is very powerful and the user can chop down the predicted target numbers from thousands to a few; if this is biologically relevant remains to be demonstrated but as an integration of results from the ever growing list of target prediction methods is more than welcome.

The other face of miRecords is a curated database of validated microRNA targets, which is probably even more useful. A very small number of targets are actually experimentally validated compared to the number of predicted putative targets. Here, given a specific miRNA, an annotated list of validated targets of that miRNA is displayed and compared with prediction results.

As of September 4, 2009, the Validated Targets component of miRecords hosts the 1597 records of interactions between 429 miRNAs and 1143 target genes in 9 animal species. Among these records, 916 were curated from “low throughput” experiments.

The reference paper for miRecords is published in NAR and the miRecors website is http://mirecords.umn.edu/miRecords/

Asuragen’s miRLink arrays

RLR — Thu, 29 Oct 2009 23:54:16 +0000

As taken from the Asuragen website, this is the summary description of the microRNA Expression Profiling Service using Asuragen’s miRLink^TM Arrays,

MicroRNA (miRNA) expression profiling, using robust and sensitive microarrays, can provide broad and novel insight into gene regulation. Asuragen has developed a microarray-based application for studying miRNAs that combines a unique miRNA labeling method with an innovative probe design and the established Codelink® technology. This custom miRLinkTM v11.0 Array is manufactured by Applied Microarrays Inc. (AMI) exclusively for Asuragen. miRLink v11.0 Array captures the entire human, mouse and rat content of the Sanger 11.0 database on a single array. The competitive cost of the miRLink array and service allows profiling of a significantly larger number of samples for a greater statistical power in your experiments. As a result, miRLink provides a cost effective yet robust and high performance miRNA array with validated Sanger content.

More info can be found here.

Anyone who already experienced this company’s profiling service is invited to comment and/or advise