Functional genomics finds a new home in forensics and biodefense, so it’s not just for basic research and drug discovery anymore.
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Biological systems defined as networks: Examples of different graphical representations. (Source: Francisco Azuaje, PhD)
Like the Thanksgiving smörgåsbord on grandma’s dining room table this year, the mega-field of functional genomics seems to spread out as far as the eye can see. Encompassing the comparatively smaller disciplines of proteomics, transcriptomics, and metabolomics, just to name a few, functional genomics is applied to everything from genome sequencing to drug design. And the best part of it is that more and more life scientists are applying functional genomics to their work everyday. But don’t just take my word for it. There are many projects in the pipeline, one of which is pretty popular and is called …
… Project Bioshield
“[Functional genomics] was a very obvious tool to adopt, initially to find more genes, and then as time has gone on, to really try to build pathways and understand how all of these molecules interact in response to stress,” says Sally A. Amundson, PhD, associate professor of radiation oncology, Center for Radiological Research, Columbia University Medical Center, New York. Amundson’s background is in radiation biology and her current interest is in determining which stress response genes are expressed in response to radiation exposure. Specifically, she is interested in the expression patterns of these genes in response to radiation dose.
According to Amundson, the response of these genes can be measured by DNA microarray. And, she uses the Agilent (Santa Clara, Calif.) microarray platform to perform these studies. The response to radiation results in an increase in the expression of specific stress-response genes. For each gene, this increase is expressed as a ratio of “exposed” to “control” signal. And because Amundson is interested in ratios for most of these studies, she has used the two-color approach to label samples for microarray analysis. More recently, however, she has started to use the one-color approach (a more recent development for the Agilent platform) for some of her latest studies.
Results from some of these studies are now being used to develop signatures that will act as biomarkers for radiation dose; this will be a component of “Project Bioshield”—a federally-funded initiative to prepare people of the United States for the possibility of a nuclear or bioterror attack. “One of the things that [the federal government] is very interested in is that, in the event of a dirty bomb or an actual nuclear explosion, you would have a large number of people that you should want to determine dose for very quickly,” says Amundson. “In the more likely event of a dirt bomb, you’re going to have many people who are completely freaked out and panicked, but the vast majority will not have had any actual exposure … so having an actual test you can do instead just going on TV and saying ‘everything is fine’ will really help to reduce the panic.” Amundson is using the one-color method to assay for the person-to-person variability in radiation dose-response. “We want to be able to take a measurement and know where it sits on a dose continuum without having a pre-exposure sample.”
Genomics to forensics
Amundson’s involvement in Project Bioshield is not the only way functional genomics is being used for defense. It is also being used for defense in the legal system. “In my particular field, forensics, we are looking at functional genomics in terms of how we can apply it to identify body fluids,” says Phillip B. Danielson, PhD, professor of forensic genetics, University of Denver, Denver, Colo., and science advisor, National Law Enforcement and Corrections Technology Center, Denver, Colo.
Danielson has adapted comparative proteomics for the purpose of performing forensic analysis. Specifically, he is trying to compare the proteomes of different body fluids in an effort to find differential biomarkers that can pinpoint the body fluid origin of a source of DNA. The hope is that eventually these markers might be used to solve crimes. He gives the following story of a sexual assault as an example.
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This proteome map of saliva was generated by the ProteomeLab PF2D system from Beckman Coulter Inc. (Source; Phillip Danielson, PhD)
In this case, the alleged victim and alleged suspect know each other. The victim alleges that the suspect had digitally molested her in a hotel room. She goes to the police, who are able to apprehend the suspect a short time later. The police take a swab of the suspect’s fingers and perform a DNA analysis; the DNA matches the victim. Although the evidence corroborates her story, when the case goes to court, the suspect and his attorney counter that this was not what happened. What happened, he claims, is that the alleged victim and suspect were eating some ice cream. Then, after the suspect dipped his fingers in the ice cream, the victim licked it off of his fingers. That would also account for the presence of her DNA on his fingers.
“What would be very useful would be if you could also tell the court whether or not her DNA from his fingers was present along with saliva or with vaginal secretions because being able to distinguish between saliva and vaginal secretions would help to support or to refute the person’s story,” says Danielson. That’s where comparative proteomics comes into play. If Danielson can find a specific protein biomarker that can distinguish one body fluid from another, that could help in cases like this one.
To find such a biomarker, Danielson is using an instrument called the PF-2D (Beckman Coulter, Fullerton, Calif.), a 2D HPLC system that can separate a very complex mixture of proteins (e.g., a body fluid sample) into thousands of fractions containing zero to five proteins each. The system works by separating the sample first by isoelectric focusing and then by hydrophobicity. “We could not do that in the past. It simply would have been way too expensive and far too tedious. So this is having a major impact in the field of forensic biology.” Danielson cites other major tools that have made an impact on the field of functional genomics, in general, include microarrays that feature human single nucleotide polymorphisms (SNP) and human genes for drug metabolism.
Strengths, weaknesses, challenges
Like every tool and approach in the life science arena, functional genomics has its share of strengths and weaknesses, pros and cons. But every researcher has their own idea of what these are in the context of their own research. “The major strength and weakness is actually the same thing: the tremendous amount of data,” says David W. Galbraith, PhD, professor of plant sciences, and professor, Bio5 Institute, University of Arizona, Tucson, Ariz. “In functional genomics now, we can gather a tremendous amount of data very rapidly concerning the properties of individual cells, tissues, and organs. … And, this enormous amount of data comes from many sources—microarrays, proteomics, metabolomics, the complete gene sequences from an increasing number of organisms. And next-generation sequencing technologies threaten to or promise to increase the flux of data even more.”
Over the last 20 years, Galbraith has been developing technologies for functional genomics to study the biology of higher plants such as Arabidopsis thaliana, rice, maize, and grapes. Specifically, he is looking at gene expression in different specialized plant cell types. “If you want to understand the functional genomics of individual tissues or organs or the whole organism, you need to be able to understand the contributions of all of the individual cell types,” says Galbraith. The technologies he has been developing build on flow cytometry and cell sorting, instrumentation that allow researchers to isolate and then study different cell types. After separation by these technologies, Galbraith can use the power of DNA microarray technology to study the functional genomics of these different cell types.
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This proteome comparison output results for semen was generated by the ProteomeLab PF2D system from Beckman Coulter Inc. (Source: Phillip Danielson, PhD)
Here’s how he works. The individual cell types express green fluorescent protein using promoters that are cell-type specific to end up with a transgenic organism in which the individual cells are highlighted with green fluorescence. The cell sorter then separates these different cell types based on this fluorescence. RNA from these different cell types is then analyzed via customized plant microarrays to study gene expression. This example illustrates that the coupling of a separation technology to a high-throughput “omic” is also one of the strengths of functional genomics.
Another researcher chimes into this discussion: “One of the major strengths [of functional genomics] is the capacity to offer global, large-scale perspectives of complex biological systems, but one of its major limitations is the variety of potential sources of noise, artifacts, and errors found in the different data sources,” says Francisco Azuaje, PhD, reader and principal investigator, University of Ulster, UK. Azuaje, who has been in the field of functional genomics since 2000, says that “there is also a need to promote experimental and bioinformatics standards and good practices to facilitate a better reproducibility of results.”
There are also challenges to the advancement of functional genomics as a science. “I believe that our capacity to produce cheaper, more reliable tools to measure functional properties at different levels of complexity and organization (e.g. single cell measurements) will be essential for future advancements. Another challenge is the development of more open, shareable, and user-friendly tools and resources for performing integrative bioinformatics.”
At the end of the day, functional genomics, with its many branches, is undoubtedly one of the most powerful approaches to enter the life sciences arena since the dawn of molecular biology. And just like with molecular biology, it will likely take many years to develop the necessary tools to serve the many applications of functional genomics. Fortunately, there is an army of researchers prepared to meet the challenge.
This article was published in Drug Discovery & Development magazine: Vol. 10, No. 12, December, 2007, pp. 40-42.
Filed Under: Genomics/Proteomics