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MicroRNA target-predicting algorithms, ISIS-SGLT2Rx Phase I trials, and Sandra Porter on DIYbio


In March 2005, Genome Technology examined the buzz surrounding the study of microRNAs, which at the time had only just been dubbed the 'next big thing' in basic biomedical research. At the beginning of that year, two independent research groups had demonstrated that miRNA regulation affects nearly one-third of the human genome. Ben Lewis, a graduate student in the lab of David Bartel and Christopher Burge at MIT's Whitehead Institute, had developed a computer algorithm that could scan the human, mouse, and rat genomes in order to apply a comparative analysis to decipher potential analogous miRNA targets among them. The algorithm, TargetScan, has been maintained by Bartel and the Bioinformatics and Research Computing division at MIT since 2006, and the newest version, 5.1, was released in April 2009 at

In that same article, GT prospectively named Isis Pharmaceuticals a "player to watch out for" in the realm of miRNA clinical research and development. In last year's March issue, we reported that the Carlsbad, Calif.-based antisense technologies firm had begun a Phase I study for a drug, ISIS-SGLT2Rx, designed to inhibit the production of a sodium-dependent glucose transporter to treat type II diabetes. At present, Amy Blackley, assistant director of corporate communications at Isis, says that the team is "well over halfway" through the Phase I trials, and has begun to plan multiple Phase II trials for later this year.

Last year, Sandra Porter gave us her take on the grassroots group DIYbio after joining the Seattle chapter. At the time, Porter was skeptical of the philosophy behind the initiative. Today, Porter says that she is still on the DIYbio Seattle listserv, but hasn't witnessed much progress. "What I predict is that the group will consist of smaller groups in biotech-heavy places like Boston, Seattle, and San Francisco," Porter says. "I suspect the most useful thing is that a larger number of people will get interested in the science and go study synthetic biology and bioengineering in grad school, so they can get the background they need to actually accomplish something."

Also in the March 2009 issue, we spoke with Molly Hammell, a University of Massachusetts Medical School postdoc, who was spearheading an effort to elucidate the function of miR-34, a small, non-coding RNA, in C. elegans, while at the same time co-developing mirWIP, a computational model to predict miRNA targets. In January, she published a review article in the journal Seminars in Cell & Developmental Biology that compares the computational miRNA analysis models currently available.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.