Mining gene expression profiles: expression signatures as cancer phenotypes

Many examples highlight the power of gene expression profiles, or signatures, to inform an understanding of biological phenotypes. This is perhaps best seen in the context of cancer, where expression signatures have tremendous power to identify new subtypes and to predict clinical outcomes. Although the ability to interpret the meaning of the individual genes in these signatures remains a challenge, this does not diminish the power of the signature to characterize biological states. The use of these signatures as surrogate phenotypes has been particularly important, linking diverse experimental systems that dissect the complexity of biological systems with the in vivo setting in a way that was not previously feasible.     

Deconvoluting lung evolution: from phenotypes to gene regulatory networks

Speakers in this symposium presented examples of respiratoryregulation that broadly illustrate principles of evolution fromwhole organ to genes. The swim bladder and lungs of aquaticand terrestrial organisms arose independently from a commonprimordial "respiratory pharynx" but not from each other. Pathwaysof lung evolution are similar between crocodiles and birds buta low compliance of mammalian lung may have driven the developmentof the diaphragm to permit lung inflation during inspiration.To meet the high oxygen demands of flight, bird lungs have evolvedseparate gas exchange and pump components to achieve unidirectionalventilation and minimize dead space. The process of "screening"(removal of oxygen from inspired air prior to entering the terminalunits) reduces effective alveolar oxygen tension and potentiallyexplains why nonathletic large mammals possess greater pulmonarydiffusing capacities than required by their oxygen consumption.The "primitive" central admixture of oxygenated and deoxygenatedblood in the incompletely divided reptilian heart is actuallyco-regulated with other autonomic cardiopulmonary responsesto provide flexible control of arterial oxygen tension independentof ventilation as well as a unique mechanism for adjusting metabolicrate. Some of the most ancient oxygen-sensing molecules, i.e.,hypoxia-inducible factor-1alpha and erythropoietin, are up-regulatedduring mammalian lung development and growth under apparentlynormoxic conditions, suggesting functional evolution. Normalalveolarization requires pleiotropic growth factors acting viahighly conserved cell–cell signal transduction, e.g.,parathyroid hormone-related protein transducing at least partlythrough the Wingless/int pathway. The latter regulates morphogenesisfrom nematode to mammal. If there is commonality among thesediverse respiratory processes, it is that all levels of organization,from molecular signaling to structure to function, co-evolveprogressively, and optimize an existing gas-exchange framework.     

Circadian rhythms: from gene expression to behavior

Circadian rhythms regulate the functions of living systems at virtually every level of organization, from molecule to organism. In the past year, our understanding of the cellular and molecular processes involved in the generation and regulation of circadian rhythms has advanced considerably. New in vitro model systems for studying circadian oscillators have been developed, a potential regulatory role for cellular immediate-early genes in circadian behavior has been discovered, critical periods for macromolecular synthesis for progression of the circadian clock through its cycle have been defined, and studies of the Drosophila period gene have offered new insight into the clock mechanism. These findings are of particular interest because independent approaches using vertebrates, mollusks and Drosophila all point to a common theme that involves the expression of 'clock proteins' as the basis of the timing mechanism.     

Genetic background influences murine prostate gene expression: implications for cancer phenotypes

Background  

Cancer of the prostate is influenced by both genetic predisposition and environmental factors. The identification of genes capable of modulating cancer development has the potential to unravel disease heterogeneity and aid diagnostic and prevention strategies. To this end, mouse models have been developed to isolate the influences of individual genetic lesions in the context of consistent genotypes and environmental exposures. However, the normal prostatic phenotypic variability dictated by a genetic background that is potentially capable of influencing the process of carcinogenesis has not been established.     

Speciation in Drosophila: from phenotypes to molecules

Study of the genetics of speciation--and especially of the genetics of intrinsic postzygotic isolation-has enjoyed remarkable progress over the last 2 decades. Indeed progress has been so rapid that one might be tempted to ask if the genetics of postzygotic isolation is now wrapped up. Here we argue that the genetics of speciation is far from complete. In particular, we review 2 topics where recent work has revealed major surprises: 1) the role of meiotic drive in hybrid sterility and 2) the role of gene transposition in speciation. These surprises, and others like them, suggest that evolutionary biologists may understand less about the genetic basis of speciation than seemed likely a few years ago.     

Interpretation of complex phenotypes: lessons from the Mitf gene

SUMMARY: Mutations provide important structure–function relationships by allowing the correlation of phenotypes to the underlying genotypes. Knockout mutations that lead to loss-of-function are important and informative in this respect. However, spontaneous and induced mutations sometimes provide surprising phenotypes, which lead to unexpected functional insights and novel biochemical pathways, especially when multiple mutations(alleles) exist at a locus. An excellent example is provided by the microphthalmia (Mitf) locus in the mouse.The multiple Mitf alleles have their own phenotypic properties, most of which have been explained by the underlying mutation. However, one allele, the Mitf (Mi-White) (Mitf (Mi-Wh)) mutation, exhibits phenotypes that have not yet been fully explained. Here, the molecular, genetic, and phenotypic properties of this mutation are reviewed and an attempt made to explain the underlying biochemical reason for its observed effects.     

A phylogenetic approach to gene expression data: evidence for the evolutionary origin of mammalian leukocyte phenotypes

SUMMARY The evolution of multicellular organisms involved the evolution of specialized cell types performing distinct functions; and specialized cell types presumably arose from more generalized ancestral cell types as a result of mutational event, such as gene duplication and changes in gene expression. We used characters based on gene expression data to reconstruct evolutionary relationships among 11 types of lymphocytes by the maximum parsimony method. The resulting phylogenetic tree showed expected patterns including separation of the lymphoid and myeloid lineages; clustering together of granulocyte types; and pairing of phenotypically similar cell types such as T-helper cells type 1 and T-helper cells type 2 (Th1 and Th2). We used phylogenetic analyses of sequence data to determine the time of origin of genes showing significant expression difference between Th1 and Th2 cells. Many such genes, particularly those involved in the regulation of gene expression or activation of proteins, were of ancient origin, having arisen by gene duplication before the most recent common ancestor (MRCA) of tetrapods and teleosts. However, certain other genes with significant expression difference between Th1 and Th2 arose after the tetrapod–teleost MRCA, and some of the latter were specific to eutherian (placental) mammals. This evolutionary pattern is consistent with previous evidence that, while bony fishes possess Th1 and Th2 cells, the latter differ phenotypically in important respects from the corresponding cells of mammals. Our results support a gradualistic model of the evolution of distinctive cellular phenotypes whereby the unique characteristics of a given cell type arise as a result of numerous independent mutational changes over hundreds of millions of years.     

Microarray gene expression data with linked survival phenotypes: diffuse large-B-cell lymphoma revisited

Diffuse large-B-cell lymphoma (DLBCL) is an aggressive malignancy of mature B lymphocytes and is the most common type of lymphoma in adults. While treatment advances have been substantial in what was formerly a fatal disease, less than 50% of patients achieve lasting remission. In an effort to predict treatment success and explain disease heterogeneity clinical features have been employed for prognostic purposes, but have yielded only modest predictive performance. This has spawned a series of high-profile microarray-based gene expression studies of DLBCL, in the hope that molecular-level information could be used to refine prognosis. The intent of this paper is to reevaluate these microarray-based prognostic assessments, and extend the statistical methodology that has been used in this context. Methodological challenges arise in using patients' gene expression profiles to predict survival endpoints on account of the large number of genes and their complex interdependence. We initially focus on the Lymphochip data and analysis of Rosenwald et al. (2002). After describing relationships between the analyses performed and gene harvesting (Hastie et al., 2001a), we argue for the utility of penalized approaches, in particular least angle regression-least absolute shrinkage and selection operator (Efron et al., 2004). While these techniques have been extended to the proportional hazards/partial likelihood framework, the resultant algorithms are computationally burdensome. We develop residual-based approximations that eliminate this burden yet perform similarly. Comparisons of predictive accuracy across both methods and studies are effected using time-dependent receiver operating characteristic curves. These indicate that gene expression data, in turn, only delivers modest predictions of posttherapy DLBCL survival. We conclude by outlining possibilities for further work.     

Arabidopsis gene knockout: phenotypes wanted

Gene knockout is considered to be a major component of the functional genomics toolbox, and is aimed at revealing the function of genes discovered through large-scale sequencing programs. In the past few years, several Arabidopsis populations mutagenized with insertion elements, such as the T-DNA of Agrobacterium or transposons, have been produced. These large populations are routinely screened for insertions into specific genes, allowing mass-isolation of knockout lines. Although many Arabidopsis knockouts have already been obtained, few of them have been reported to present informative phenotypes that provide a direct clue to gene function. Although functional redundancy explains the lack of phenotypical alterations in some cases, it also appears that many mutations are conditional and/or do not alter plant morphology even in the presence of severe physiological defects. Consequently, gene knockout per se is not sufficient to assess gene function and must be integrated into a more global approach for determining biological functions.     

Acclimation to high-light conditions in cyanobacteria: from gene expression to physiological responses

Photosynthetic organisms have evolved various acclimatory responses to high-light (HL) conditions to maintain a balance between energy supply (light harvesting and electron transport) and consumption (cellular metabolism) and to protect the photosynthetic apparatus from photodamage. The molecular mechanism of HL acclimation has been extensively studied in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Whole genome DNA microarray analyses have revealed that the change in gene expression profile under HL is closely correlated with subsequent acclimatory responses such as (1) acceleration in the rate of photosystem II turnover, (2) downregulation of light harvesting capacity, (3) development of a protection mechanism for the photosystems against excess light energy, (4) upregulation of general protection mechanism components, and (5) regulation of carbon and nitrogen assimilation. In this review article, we survey recent progress in the understanding of the molecular mechanisms of these acclimatory responses in Synechocystis sp. PCC 6803. We also briefly describe attempts to understand HL acclimation in various cyanobacterial species in their natural environments.     

Drosophila gustatory receptors: from gene identification to functional expression

Recent years have seen long-awaited progress in understanding of the molecular mechanisms of taste perception in insects. The breakthrough came in the early 2000 with the identification of a novel family of candidate gustatory receptor (Gr) genes in the first release of the Drosophila melanogaster genome sequence. The 60 Gr genes are expressed in the subsets of gustatory neurons in the fly's taste organs and, without exception, encode heptahelical G protein-coupled receptors (GPCRs). Here I review our current knowledge about Gr genes and their products focusing on the newly emerging information regarding the function of the Gr-encoded proteins.     

Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information

MOTIVATION: The analysis of genome-scale data from different high throughput techniques can be used to obtain lists of genes ordered according to their different behaviours under distinct experimental conditions corresponding to different phenotypes (e.g. differential gene expression between diseased samples and controls, different response to a drug, etc.). The order in which the genes appear in the list is a consequence of the biological roles that the genes play within the cell, which account, at molecular scale, for the macroscopic differences observed between the phenotypes studied. Typically, two steps are followed for understanding the biological processes that differentiate phenotypes at molecular level: first, genes with significant differential expression are selected on the basis of their experimental values and subsequently, the functional properties of these genes are analysed. Instead, we present a simple procedure which combines experimental measurements with available biological information in a way that genes are simultaneously tested in groups related by common functional properties. The method proposed constitutes a very sensitive tool for selecting genes with significant differential behaviour in the experimental conditions tested. RESULTS: We propose the use of a method to scan ordered lists of genes. The method allows the understanding of the biological processes operating at molecular level behind the macroscopic experiment from which the list was generated. This procedure can be useful in situations where it is not possible to obtain statistically significant differences based on the experimental measurements (e.g. low prevalence diseases, etc.). Two examples demonstrate its application in two microarray experiments and the type of information that can be extracted.