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MIT’s MicroRNA ’sponges’ could aid cancer studies


MIT researchers have developed a new way to study the function of microRNA, tiny strands of genetic material that help regulate at least 25 percent of a cell’s genes.

The new technique could shed light on microRNA’s hypothesized role in tumor development. Malfunctions in microRNA have been linked with cancer, but very few direct relationships have been established between specific microRNAs and the genes they regulate.

That could change, however, now that MIT Institute Professor Phillip Sharp and his colleagues have found a way to inhibit the activity of microRNA by genetically altering cells.

The technique, described in the August 12 online issue of Nature Methods, could “provide a tool to identify specific genes that are being regulated by microRNAs,” said Sharp.

MicroRNA consists of short strings of about 22 nucleotides, the building blocks that make up RNA and DNA. MicroRNA binds to messenger RNA (mRNA), preventing it from delivering protein assembly instructions, thereby inhibiting gene expression.

Sharp, who is affiliated with MIT’s Biology Department and Center for Cancer Research, said microRNA exists in every cell and controls a wide range of cell regulatory activities.

The MIT team has found a way to block microRNA activity by tricking cells into producing a microRNA “sponge,” which soaks up microRNA and renders it ineffective. By de-activating microRNA, researchers can observe the resulting effects and determine which genes the microRNA is targeting.

The new technique could shed more light on microRNA’s role in tumor development: Earlier studies have shown that a type of microRNA known as let-7 inhibits a cancer-inducing gene called RAS. Abnormally low levels of let-7 have been found in some types of tumor, said Sharp.

Sharp and MIT biology graduate student Margaret Ebert, lead author of the paper, decided to block microRNA activity by creating a gene that produces microRNA sponges and inserting it into their target cells. Each sponge can bind up to six microRNA molecules, but they could be engineered to bind more.

The sponge gene also includes a “reporter” gene that causes the cell to become fluorescent if it has taken up the gene, so the researchers can know for sure whether the microRNA sponge is being produced in a particular cell.

Ebert said the new sponge technique is an improvement over an older method that involves blocking microRNA activity with artificially synthesized strands of RNA, known as oligos. One advantage is the inclusion of the reporter gene; another is that the sponge genes can be expressed continuously, while oligos do not remain in the cell forever.

More importantly, the sponge technique could be used to create transgenic animals that express the sponge in all of their cells, allowing researchers to study microRNA function at the organismal level. With such animals, sponge genes could be designed so that the researchers can control when and where they are expressed.

Joel Neilson, a postdoctoral associate in the Center for Cancer Research, is also an author on the paper. The research was funded by the National Cancer Institute, the National Institutes of Health, a Howard Hughes Medical Institute Predoctoral Fellowship, a Paul and Cleo Schimmel Scholarship, and the Cancer Research Institute.

The MIT Center for Cancer Research was founded in 1974, and is one of eight National Cancer Institute-designated basic research centers. Its mission is to apply the tools of basic science and technology to determine how cancer is caused, progresses and responds to treatment.


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