Am J Physiol Lung Cell Mol Physiol 293: L290-L291, 2007.
First published June 15, 2007; doi:10.1152/ajplung.00220.2007
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EDITORIAL FOCUS
Progress toward a systems biology approach to acute lung injury
James A. Frank1,2,3 and
David J. Erle1,4,5
1Department of Medicine, 2Cardiovascular Research Institute, 3San Francisco Veterans Affairs Medical Center, 4San Francisco General Hospital, and the 5University of California at San Francisco Lung Biology Center, University of California, San Francisco, California
PRESENTING THE COMROE LECTURE at the Experimental Biology 2002 conference in New Orleans, Norman Staub, a pioneer of modern research into the mechanisms of pulmonary edema and acute lung injury, decried the disconnection between clinical medicine and molecular biology (12). He attributed this disconnection in part to a fashionable neglect of physiology, the "queen and mother of biological sciences." Mouse model systems offer tremendous opportunities for genetic and genomic approaches to dissecting disease, but the small size of mice often makes detailed measurements of multiple relevant physiological endpoints impractical. Larger animals are typically better suited for physiological analysis, but fewer genetic and genomic tools are available. In 2001, an exciting development with the promise of reuniting physiology and molecular biology was introduced: a collaborative effort between Medical College of Wisconsin and Charles River with funding from the National Heart, Lung, and Blood Institute yielded the first commercially available set of consomic rats (4). Rat models, of course, have a long and distinguished record in physiology. Consomic rats are produced using a breeding and genetic screening strategy that substitutes a single chromosome from one inbred strain with the same chromosome from a different strain. Consomic rats offer certain advantages over traditional segregating crossbreeding strategies used for complex trait mapping (3). Panels of consomic rats can be used to dissect the contribution of genes on specific chromosomes to various traits, as is now being done with hundreds of baseline physiological measurements relevant to cardiovascular and lung disease (http://pga.mcw.edu).
In the recent article by Nonas and colleagues (9), they give us an instructive progress report on their combined consomic and genomic approach to a clinically relevant complex disease phenotype: ventilator-induced lung injury (VILI). Two rat strains were screened for susceptibility to VILI resulting from high tidal volume ventilation without positive end-expiratory pressure. Bronchoalveolar lavage (BAL) fluid protein concentration and cell count were compared in Brown Norway (BN) rats and Dahl salt-sensitive (SS) rats before and after mechanical ventilation. BN rats were relatively susceptible to injury by these measures compared with SS rats. DNA microarrays were used to identify hundreds of genes that were differentially expressed in lungs of these two strains at baseline or following injury. Some of these genes have been previously identified using conventional, gene expression profiling (8, 11), or proteomic (7) approaches, whereas others are novel candidates. Although genome-wide expression profiling is an excellent method for generating long lists of candidates, it is proving to be more difficult to develop follow-on approaches to select critical genes. In this VILI study, the investigators attempt to use consomic rats for this purpose. They reasoned that chromosomes with a higher density of differentially expressed genes may be more likely to contain genes important in VILI. Using this approach, they found chromosomes 2, 13, 16, and 17 to be most enriched for differentially expressed genes. Using consomic strains, they tested the potential contribution of chromosomes 2, 13, and 16 from BN rats to VILI in the SS background. A consomic chromosome 17 rat was not available. Chromosome 20 consomic rats were used as a control, of sorts, in that relatively few differentially expressed probes from the array study reside on this chromosome. Examination of the consomic rats showed a range of phenotypes. For example, SS:BN16 (SS rats with BN chromosome 16) had a higher BAL cell count after VILI, but an intermediate change in BAL protein concentration. SS:BN2 rats showed no change in BAL cell count with VILI but a greater increase in BAL protein concentration during VILI. These results suggest that genes on these two chromosomes make important and distinct contributions to VILI, although the identity of the genes involved and their roles in VILI remain to be determined.
How can future studies with genomics and consomics help us to decipher the complex relationships between genetic variation, gene expression, and physiology? It is important to keep in mind that genetic variation can influence gene expression in many ways. Perhaps the most obvious example involves a change in the sequence of a gene that results directly in a change in level of expression of the transcript of that gene itself. These kinds of cis-regulatory effects could be seen as changes in the promoter sequence that affect transcription or as changes in transcribed regions that affect mRNA stability. "Genetical genomics" approaches that relate gene expression levels to loci of genetic variation suggest the existence of many such cis-acting polymorphisms (1, 10). However, in many other cases variations in gene expression are due to trans-acting polymorphisms. In these cases, the polymorphism will be in a different location (usually on a different chromosome) from the gene with the altered level of transcript expression. For example, a polymorphism that affects the function or expression level of a transcription factor that regulates many other genes could affect the level of large sets of transcripts on many chromosomes. Polymorphisms affecting sequences outside of protein-coding genes, including those affecting miRNAs, could also have extensive trans-regulatory effects. To the extent that cis-acting polymorphisms account for the differences in gene expression and phenotype between strains, the approach used in the present study to prioritize consomic rats in the VILI model may be helpful. However, known examples of trans-acting loci that affect expression of hundreds of genes across the genome (1) make it clear that many important loci will not be selected for by simply looking for changes in expression of nearby genes. By using genetical genomics to profile gene expression in consomic rats (and eventually in congenic strains with smaller, subchromosomal substitutions) it should be possible to obtain a much more detailed understanding of how cis- and trans-acting genetic polymorphisms affect gene expression in VILI and other model systems.
This still leaves us with the daunting task of relating genetics and genomics to physiology. As we approach this task, it will be critical to remember that physiological systems (like genetic ones) have complex and sometimes unpredictable interrelationships. Furthermore, it is likely that a large number of genes affect susceptibility to VILI by influencing different physiological variables. For example, some loci may be associated with differences in the inflammatory response to injury, while others may be important in determining baseline differences in lung size or structure. As an example, based on data available from the PhysGen web site (http://pga.mcw.edu), the lung weight-to-body weight ratio is different at baseline in the two parental strains used in the present study. The higher dry lung weight in BN rats might be associated with structural differences in the pulmonary parenchyma or vasculature that affect susceptibility to VILI. Several other respiratory and cardiovascular physiological variables differ at baseline between the strains. Therefore, although the approach used in this study may identify loci important to VILI in the two strains studied, additional physiological data will be required to understand how specific chromosome substitutions contribute to the VILI phenotype. A more detailed physiological characterization of parental and consomic rat strains will help us to separate out distinct physiological mechanisms that contribute to VILI susceptibility, and the rat is a suitable model for these measures (2, 5, 6, 13). As Dr. Staub reminds us, valuable insights can still be gained from basic physiological measurements. By combining detailed physiological measurements with genetic tools such as consomic rats and genomics tools like microarrays, we now seem poised to reach a new systems biology understanding of an old problem: acute lung injury.
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GRANTS
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This study was supported by National Heart, Lung, and Blood Institute Grant HL-69900 (to J. A. Frank).
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FOOTNOTES
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Address for reprint requests and other correspondence: J. A. Frank, Univ. of California, San Francisco, Cardiovascular Research Institute, San Francisco VA Medical Center, 4150 Clement St. Box 111D, San Francisco, CA 94121 (e-mail: James.frank{at}ucsf.edu)
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Copyright © 2007 by the American Physiological Society.
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