February 05, 2004
Massively Parallel Gene Activity Screening Technique Developed

Researchers at Howard Hughes Medical Institute (HHMI), Harvard Medical School, the University of Heidelberg and the Max Planck Institute for Molecular Genetics in Germany have demonstrated in the fruit fly Drosophila a general technique usable in any organism to simultaneously assay thousands of genes to determine whether each gene is involved in a particular aspect of cell function.

“A major challenge now that many genome sequences have been determined, is to extract meaningful functional information from those projects,” said HHMI researcher Norbert Perrimon, who directed the study. “While there are a number of analytical approaches that can measure the level of gene expression or the interaction between proteins, ours is really the first high-throughput, full-genome screening method that allows a systematic interrogation of the function of every gene.”

The technique uses double-stranded RNA made to match every known gene in the target organism that is of interest. The double-stranded RNA causes a phenomenon called RNA interference (RNAi) which blocks the action of the corresponding RNA strand which gets made from each gene. Nornally cellular machinery reads a gene in the DNA and creates what is called messenger RNA (mRNA) which has a matching sequence to that gene. Then that mRNA is read to make proteins. But dsRNA prevents that step and therefore blocks the creation of proteins. This effectively blocks the gene from having any effect and then the automated assay system of these researchers watches what the effect is on cell growth or on whatever other aspect of cellular activity the system could be set up to measure.

The screening technique developed by Perrimon and his colleagues builds on methods developed in one of the hottest areas of biology, RNA interference (RNAi) research. In RNAi, double-stranded RNA (dsRNA) that matches the messenger RNA produced by a given gene degrades that messenger RNA — in effect wiping out the function of that gene in a cell. RNAi is widely used as a research tool to selectively erase the cellular contributions of individual genes to study their function.

In their mass screening technique, Perrimon and his colleagues first created a library of 21,000 dsRNA that corresponded to each of the more than 16,000 genes in the Drosophila genome. They then applied each of these dsRNA molecules to cultures of Drosophila cells and assayed how knocking down the function of a targeted gene affected cell numbers in the cultures. This basic measure, said Perrimon, revealed genes that are not only involved in general cell growth, but also in the cell cycle, cell survival and other such functions.

The researchers then selected 438 genes for further characterization. The degradation of these genes produced profound affects on cell number. “Out of this subset, we found many that produced proteins involved in general metabolic processes such as the ribosomes that are components of the protein synthesis machinery,” said Perrimon. “But we also found genes that are more specific to cell survival.”

According to Perrimon, only 20 percent of the genes that were identified had corresponding mutations — an important characteristic for studying gene function. “The classic approach to studying gene function is to identify mutations in genes and select those that produce interesting phenotypes that yield insight into function,” said Perrimon. “But this approach has never really given us access to the full repertoire of genes. With this high-throughput technology, however, we can study the function of a complete set of genes. We can systematically identify all the genes involving one process.”

The technique can be used to screen for genes involved in intercellular communication, cancer cell proliferation, and other cellular activity. Combined with drug screening the technique can accelerate the search for drugs that operate on particular cellular pathways and processes.

The RNAi assay will contribute to the screening of new drugs, he said. “One exciting aspect of this approach is that we can combine our assay with screening of potential therapeutic compounds,” he said. “One of the big problems in the pharmaceutical industry is that researchers may discover pharmacologically active compounds but have no idea what their targets are in the cell. However, it would be possible to perform coordinated screens — one for compounds that interfere with a target pathway and an RNA interference screen for genes that act in that pathway. This correlation would allow you to match the compounds with the proteins they affect in a much more useful way.”

One can see by reading between the lines here how this technique has to be built on top of a lot of other existing tools that automate the creation of needed components. There has to be a fairly automated existing technique to generate all the different kinds of dsRNA strands used in this techinque. Also, the technique must rely on an automated tool for, feeding cells, measuring cell growth, and doing other steps in this process.

Results of studies for new ways to treat diseases or discoveries of ways that genes and cells work get a lot of press attention. But the ability to automate and therefore accelerate massive parallel screening and manipulation of genes, proteins, and other parts of cells is what makes possible the faster rate of discoveries of disease causes and disease treatments. Cells are so complex with so many pieces, subsystems, and types of interactions that only with the development of massively parallel techniques can we hope to fully figure out how cells work and how to cure most diseases in the next few decades.

Share |      Randall Parker, 2004 February 05 12:13 PM  Biotech Advance Rates

Stephen Gordon said at February 5, 2004 8:47 PM:

It's not just the scientific techniques that are massively parallel. The relationships between the scientists has become massively parallel.

To the extent it was ever true, the idea of the lone scientist toiling away in his lab to come up with a world changing discovery is long gone.

Each step forward requires an army of scientists sometimes working together, sometimes in competition, but always subject to peer review. Review used to take place months after a project was completed in print journals. While the journals are still important, the contemporaneous review that scientists can provide each other through the Internet is more powerful. Contemporaneous review can suggest new paths to take as the research continues. What used to take years now takes months.

Patrick said at February 5, 2004 10:29 PM:

These sorts of results are like hearing about the development of the lathe or the drop hammer in the 1500s. You don't know what someone will build using these new tools, but it's clear that it will be a whole new world.

Zach said at February 29, 2004 9:17 PM:

> While the journals are still important, the contemporaneous review that scientists can provide each other through the Internet is more powerful.

I'm responding way late, but thought I'd see whether anyone reads old threads and is likely to have any further thoughts on this. I don't actually think that the above assertion is at all true, at least in the biological fields that encompass the research described in this article.

I'm actually pretty interested in the question of how to get biologists to communicate more effectively over the internet, but I'm pretty sure that right now the vast majority of between-lab communication still occurs through journals and face-to-face interaction at meetings. Any ideas about why preprint servers and internet-mediated discussions haven't caught on in biology and how we might go about increasing communication?

Randall Parker said at February 29, 2004 9:47 PM:


Aside: Over half the traffic on this site comes from Google searches. So old posts do get read well after they are made and new comments get added to them. I get email notifications each time this happens and so I know pretty quickly when someone makes a comment.

As for scientists communicating over the internet: At the very least the speed with which articles can be submitted for publication, sent around for peer review, and then published and dstributed has been sped up by the internet. The new journals popping up that do not even have paper versions demonstrate the direction of this trend. Also, email allows scientists to query other scientists around the globe much faster than snail mail.

As for internet-mediated discussions: The "mediated" part is probably part of the problem. To make a specialist discussion group work what is needed is for someone to serve as mediator or at least as gatekeeper for who gets to post on some discussion group. Usenet tends to suffer low signal/noise as anyone can come in and post in some Usenet group. How to create a mechanism to regulate who gets to post in some discussion groups either in something like Yahoo email list groups or some private nntp server or in something running phpBB or something similar? Someone has to be administrator and some group has to be able to vote on whether a given applicant will be allowed to post.

There are, btw, some rather specialized discussion lists for some niches in biology. I came across one once that was dedicated to gene arrays.

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