Figure 1. High-throughput in vivo screening using microchamber technology. A live worm (the nematode C. elegans) is immobilized in a microfluidic chip by fluidic pressure in order to image its neurons at sub-cellular resolution. Fluorescence and white-light images are taken simultaneously, such that part of the microfluidic device, the animal’s body and its green fluorescent protein (GFP) expressing neurons and their axons are all visible in the same pseudo-colored image. (Source: Yanik, MIT)

The nematode C. elegans has been a geneticist’s friend since the early 1960’s. The simplicity, transparency and speed of its biological functions have made C. elegans an ideal model organism for studying genes and their function. However, working with C. elegans is not easy. It requires a lot of time and effort as many assays remain fairly archaic, involving manual handling, picking and sorting of the tiny organism. The large-scale genome-wide assays using C. elegans often take months or even years to complete.

Mehmet Fatih Yanik, Ph.D., an assistant professor in the department of Electrical Engineering at the Massachusetts Institute of Technology (MIT) in Cambridge, MA is using C. elegans as a model to study genes involved in neural regeneration and degeneration. “I started looking at how people did assays using C. elegans and one of the things that became clear is that people are still manipulating this organism using manual techniques, transferring worms from one plate to another by hand,” says Yanik. Some genetic screens using C. elegans have been performed in a high-throughput fashion by modifying technologies developed for screening and sorting cells. However, these techniques are fairly limited in their use. “[Using these techniques] you can tell that the fluorescence is coming from the head of the worm but the head contains hundreds of cells,” says Yanik. “It doesn’t show any cellular resolution.”

To overcome this limitation Yanik, who has a background in engineering and physics, has proceeded to develop a microfluidic chip that offers both speed and resolution. This technology promises to automate and accelerate most of the genetic screens currently performed using C. elegans. The chips are designed and fabricated in Yanik’s laboratory using polymers that are transparent to light and keep the worms healthy. The details of the chip design and its applications are published in the August 2007 issue of the Proceedings of the National Academy of Sciences of the USA. Yanik’s laboratory is now developing methods for high-throughput, large-scale screens using this microfluidic chip.

Figure 2: An image showing the microfluidic screening chambers where one of the chambers is filled with a different color dye than the other chambers to show selective addressing of each chamber for drug/compound/RNAi delivery. This technology can be used to perform large-scale RNAi and drug screens. (Source: Yanik, MIT)

By changing its configuration, the chip can be modified to perform various types of fluorescence-based genetic screens. For instance, the chip can be used as an automated sorter device for genome-wide mutagenesis screens. A mutagenesis screen involves randomly mutating genes in the worms and examining the phenotypes of the mutants. Using the sorter device, the worms are sucked into the microfluidic chamber one at a time and immobilized to obtain a high resolution image to examine its phenotype. “This way, if you have 40,000 mutagenized worms, the sorter can go through it really fast, in fractions of a second,” says Yanik. “You can potentially screen the entire genome in a few hours and you can do this at a very high resolution to see the cellular detail.”

The microfluidic device can also be used to perform large-scale RNA interference (RNAi) assays and compound screens. For RNAi screens the microfluidic chip is divided into several microchambers. One worm and one RNAi vector that is specific for silencing a single gene is delivered to each chamber and the phenotypes are observed under a microscope. “We know what gene is targeted and so we can map out what phenotype is observed when that gene is silenced,” says Yanik. The same methodology can also be used to perform drug and compound screens. He is also looking to extrapolate this technology to other model organisms, such as zebrafish and others that grow in liquid culture. “But we cannot extend it to Drosophila because it cannot be cultured in liquid,” says Yanik.

This technology is drawing a lot of interest in the C. elegans community, where researchers are always on the lookout for means to accelerate their research. Yanik is also talking to some companies that have expressed an interest in commercializing the technology. “The challenge of running a system like this right now is like driving a Ferrari,” he says. “A Ferrari is a fast car, nice car but it’s not practical. What we want to do is make it like a Toyota and make it extremely easy to run so that we can send it to someone and they can run it very rapidly without our help.”

Mehmet Fatih Yanik is an assistant professor in the department of Electrical Engineering and is a member of the Computational and Systems Biology program at Massachusetts Institute of Technology (MIT). His research expertise lies at the confluence of applied physics, bioengineering and neurobiology. He received his B.S. and M.S. degrees in Electrical Engineering and Physics from MIT. He went to Stanford University for his Ph.D. in Applied Physics and continued his post-doctoral work in Bioengineering and Neurosurgery there. Yanik is “one of the world’s top 35 innovators under the age of 35” according to MIT’s Technology Review magazine. His work related to the development of the microfluidic chip for high-throughput, whole-animal screening was recently awarded the NIH Director’s New Innovator Award. This award will provide Yanik’s lab with nearly $2.5 million dollars in funding over the next five years.