Computational Biology 13
Although the murine models have limited utility for predicting the
efficacy of human therapeutics in clinical trials, they have been quite
useful for identifying genetic susceptibility elements for human disease.
As in the human population, inbred mouse strains are differentially
susceptible to developing organ-specific inflammation in response to
experimental antigen exposure protocols. Therefore, these experimental
mouse models of human inflammatory disease have been genetically
analyzed to identify genetic elements contributing to susceptibility or
resistance to the diseaserelated process. It is striking that different
investigators have identified similar genetic loci regulating susceptibility
in different experimental rodent models of human disease-related traits
(38,41). Most importantly, the genetic regions identified in some rodent
experimental models are syntenic to the regions identified by analysis of
human cohorts with immunemediated diseases. Analysis of 21
previously published genome-wide scans indicated that several clinically
distinct human autoimmune diseases—including asthma, rheumatoid
arthritis, and multiple sclerosis— may be controlled by a common set of
susceptibility loci, and the loci were syntenic to those found through
analysis of experimental mouse models (42). The similarities in genetic
loci identified in human and rodent models extend beyond
inflammatory disease. Six chromosomal regions regulating
hypertension were identified in a murine genetic model. There was a
high degree of concordance between the chromosomal regions identified
in the mouse model and those found in human populations (four of six)
and rat experimental models (five of six) (43). It is not known how often
the genetic loci regulating complex traits in murine models will directly
translate into human susceptibility elements. However, it is very likely
that the genes and pathways identified in the experimental rodent
models will provide key insight into how complex disease-associated
traits are genetically controlled in human populations. Most human
disease genes isolated by positional cloning have highly similar
homologs in rodents (44).
6. Understanding the biological impact of the genetic changes nderlying
complex traits will require the development of new methods for
iological analysis. Most biological experimentation examines pathways
that have a major effect on cell and tissue function. This is similar to the
rather profound phenotypic changes associated with genetic changes
underlying Mendelian traits. In contrast, the biological impact of
genetic changes underlying complex traits will be much more subtle,
more difficult to dissect in isolation, and will be sensitive to the overall
genetic
background and the environment. It will not be possible to confirm the
identity of many complex trait loci by functional complementation or
with gene knockouts (2). This makes it much more difficult to identify
and understand the biological impact of genetic variation at complex
trait loci. It is likely that the criteria and methods currently used for
biological analysis will have to be altered for complex traits. Phenotypic
effects in gene knockout mice or changes caused by exogenous gene
complementation are unlikely to be seen in these complex systems. The
supporting evidence for the biological effect of an individual genetic
alteration underlying a complex trait is likely to be indirect. A
preponderance of supporting evidence and the absence of negative
evidence will often be the determining criteria. Gene or protein
expression differences, response to environmental factors, effects of
other components in the pathway, and the involvement of orthologs in
other species will be analyzed for subtle biological effects produced by
genetic alterations underlying complex traits. The plethora of
information generated by genetic analysis of complex traits will spur
advances in cell biology and organ physiology. It is likely that QTL
affect cellular differentiation and organ development. Therefore, more
sensitive and efficient methods for studying cellular differentiation
process and tissue development will have to be developed. Small
molecules will be more extensively used to analyze the biological
pathways impacted by genetic variation. Small molecules have provided
key information about protein function in several areas of biology.
Tetrodotoxin was used to analyze the action potential (45), whereas
prostaglandin J2 and peroxisome proliferatoractivated receptor(PPAR-) agonists enabled a pathway regulating adipogenesis to be
analyzed (46,47). However, a large amount of time and cost is required
to produce a highly specific chemical inhibitor for adesired gene
product. Therefore, small interfering RNAs (siRNAs),which decrease
the expression of a selected mRNA by gene silencing,provide a powerful
new tool for biological analysis (reviewed in ref. 48).
Although there are limitations that are because of the limited extent and
time of siRNA-mediated RNA knockdown, siRNAs can be used to assess
the biological importance of many different types of candidate genes in
vitro. Furthermore, the availability of siRNA libraries targeting a large
number of specific mouse and human genes (49) further increases the
utility of this tool. Once the current limitations resulting from off-target
and temporally limited effects are overcome, siRNAs will be the first of
a number of new tools that enable a more efficient process of biological
characterization of genetically identified gene candidates.