Comparing Genomes on a Chip

Last week at our lab meeting I had a chance to hear a presentation by Doug Berg, a microbiologist here at Washington University. Berg's work is a great combination of new technology, genomics and evolution, and it happens to also have potential medical relevance. He's studying the evolution of drug resistance in Helicobacter pylori, a ususally benign bacterium that is responsible for stomach ulcers. (Recall that the Nobel Prize in medicine was awarded last year to Barry Marshall and Robin Warren for their discovery of the link between H. pylori and ulcers.)

Berg is basically evolving highly drug resistant bacteria in the lab and using a new genome comparison technology to identify the genes that are changed as the bacterial strains become more resistant. The drug used in these experiments is metronidazole - a substance that itself is not harmful, but inside a bacterial cell it is metabolized into a toxin that causes significant DNA damage.

To create these drug-resistant strains, bacteria are spread on an agar plate - a peteri dish filled with a Jello-like substance that contains nutrients and metronidazole. Most bacteria are killed by the drug, but some individual bacteria survive, if they harbor random mutations that just happen to confer drug resistance. These surviving bacteria continue to divide, and after a few days a colony - a blob of bacteria all descended from the original surviving bacterium - has formed on the plate. You can pick off this colony with a toothpick and save it; you now have a drug resistant strain of bacteria. This process can be repeated - grow up the drug resistant strain, smear it on an agar plate with a higher concentration of the drug, and watch for the next round of colonies to grow from the survivors.

After doing many experiments like this, the Berg lab gets a series of H. pylori strains, each with varying drug resistance. The obvious question then is, how do the genomes of these strains differ? What specific (but randomly occuring) mutations had to take place in order for this level of drug resistance to evolve? Sequencing the genomes of each of these various drug-resistant strains would be the obvious way to find these differences, but doing that kind of sequencing is still prohibitively expensive and computationally intentive. But the Berg lab is using a new technique that rapidly compares genomes on a chip. (The link leads to an abstract of their paper; the full text is subscription only but you can check out more about the technique in a "webinar" found here, at the bottom of the page.). They use microarrays (DNA chips) that cover the entire genome (called a 'tiling array'). By hybridizing DNA from both the nomral and drug resistant strains to the microarray (check out my earlier summary of how a microarray works), they can identify those spots on the array (and thus in the genome) where the two strains differ.

Using this technique, the Berg lab has identified key genes involved in H. pylori resistance to metronidozole. There seem to be some genes that are always changed in these drug resistant strains, and some that can be different. In other words, there seem to be multiple evolutionary paths to drug resistance, but those paths often cross.

This techique of comparing genomes on a chip has a lot of potential, and within a few years, something like this may start showing up in common medical care and hospital labs, replacing the more primitive techniques that are currently used for classifying tumors or drug-resistant pathogens.