Current Genomics - Volume 4, Issue 1, 2003

The epidermal growth factor receptor (EGFR) is a membrane-anchored, 170 kDa, protein tyrosine kinase that has been implicated in tumorigenesis. Recent sequence data from the publicly funded Human Genome Project has led to a revision in the structure of the EGFR gene, as well as an improved understanding of its mutations in tumor cells. The exons and introns of the EGFR gene are contained within 168 kilobases of DNA, including a completely sequenced 123-kilobase first intron. The EGFR gene is frequently amplified and rearranged in malignant gliomas with expression of oncogenic deletion (DM) and tandem duplication (TDM) mutants. The most common mutant is EGFRvIII, which arises from recombination between introns 1 and 7 with deletion of intervening sequences. Some human gliomas express 185 kDa and 190 kDa EGFR tandem duplication mutants with constitutive functional activity. These tumors contain EGFR genes with an in-frame tandem duplication of exons 18 through 25 or exons 18 through 26 respectively. The TDM also arise from recombination between flanking introns 17 and either 25 or 26. DM and TDM have been found in the same tumors, suggesting that the mechanisms responsible for both types of mutants may be closely related. Each of the introns involved in tumor-specific recombination contain sequences with homology to the recombination signal sequence (RSS) heptamers present in the V(D)J region of the immunoglobulin and T lymphocyte antigen receptor genes. These observations suggest a possible mechanism for oncogenic EGFR gene recombination in malignant gliomas.

The p53 gene is a tumour suppressor gene frequently mutated in human cancers. Its product is a transcription factor that regulates the expression of various genes involved in cell cycle arrest and in apoptosis in response to different cellular stresses. The recent discovery of two p53 gene homologs, p73 and p63, has uncovered a family of transcription factors and widened the scenario of cell cycle control and apoptosis. p73 and p63 genes encode proteins showing significant structural and functional similarity to p53, although important differences are emerging. p73 and p63 have an additional domain in their carboxyl-terminal region with marked similarity to the structure of SAM (sterile alpha motif) domains, typical of proteins involved in development. Indeed, differently from p53, p63 and p73 seem to be involved in development and differentiation. Both p73 and p63, at least when overproduced, can activate some of the p53-responsive promoters and trigger growth arrest and apoptosis, although their answers in response to DNA damage differ from those of p53. The challenge is now to understand similarities and differences between family members especially in terms of their functions, regulation and interactions. This review summarizes the present knowledge on the structural, functional and evolutionary features of the p53 gene family and focuses on the differences among the three members of the family.

The representation of gene regulation on a large-scale needs new tools and models, since interconnected networks of signal transduction rather than linear cascades of events are involved in cellular perception. The Boolean language represents a convenient way to describe such a complexity. It allows a simple representation of experimental data generated through classical genetic approaches as well as microarray analyses. In addition, it provides the possibility of computer simulation, and unlimited qualitative and quantitative data processing, that may in turn ease the identification of new signaling elements and novel modes of gene regulation. This articlepresents the properties of a Boolean representation, with digital simulations exemplified in the case of light and pathogen signal perception in plants. The general structure of cellular perception is discussed, and the results of the logical interpretation of signaling are presented in relation with space- and time-related stimuli.

Recent progress in mammalian genomics raises enormous expectations for rapid advances in global understanding of the genetic program. The Human Genome Sequencing Project and parallel sequencing efforts addressing other genomes are in their final stages and will bring to the public domain an influx of tens of thousands of previously unknown genes whose cellular function will remain to be evaluated. Although DNA sequence information may assist and facilitate functional and comparative analyses of model organisms, a combination of systematic genotype- and phenotype-driven functional approaches will play a critical role in the upcoming research defining the gene function. For its physiological similarity to humans and for its genetic manipulability, the mouse emerges as a key model mammalian organism in these efforts. One powerful strategy for phenotype-driven mutagenesis studies in mice combines chromosome engineering techniques with mutagenesis. There are three key elements of this strategy. First, using the LoxP / Cre recombination system in embryonic stem (ES) cells, coat color-tagged segmental deletions and inversions are generated on selected chromosomes, and mouse strains are derived from these cells using conventional ES cell technology. These mice can serve as very potent and extremely convenient genetic tools that narrow the search area for gene(s) of interest to a limited chromosomal segment. Second, N-ethyl-N-nitrosourea, ENU, is used to mutagenize male mice in order to generate a source of genome-wide germ-line transmissible mutations. Third, mutagenized animals are crossed with inversion or deletion carriers to produce pedigrees uncovering ENU-induced recessive phenotypes. The genomic position of induced mutations underlying recessive phenotypes is instantly mapped to the chromosomal inversion or deletion intervals. Several large-scale projects have been launched using ENU alone or in combination with engineered chromosomes. A rapidly growing set of new phenotypes has begun to emerge from these studies which will ultimately provide insights into gene function.

The genomics revolution has provided an overwhelming choice of potential drug targets for cancer therapy. Central to this revolution are approaches that identify target genes by changes in gene expression or through bioinformatic searching of DNA / protein databases for homologous sequences. An alternative to these approaches is functional cloning which selects gene products based on the ability of a given sequence to directly alter a cellular phenotype of interest. In an effort to discover new cancer therapeutic targets, bioinformatic searching and functional cloning were utilized to identify novel gene products implicated in various aspects of tumorigenesis. Using homology searches of DNA databases for novel death domain-encoding expressed sequence tags (ESTs), a new member of the TNF receptor family, DR6, was identified that regulated apoptosis in a variety of cell types and exhibited deregulated expression in tumor cells. Functional cloning of cDNAs from tumor cells with the capacity to induce morphological transformation, uncovered a unique oncogene, FGFR2-FRAG1, that resulted from a chromosomal rearrangement between a receptor tyrosine kinase, FGFR2, and a novel gene, FRAG1. This review focuses on these approaches as a means to identify potential targets for therapeutic intervention in cancer and the unique challenges each of these techniques face to link the identified gene products to a given biological effect or disease state.

Increased longevity has been achieved by genetic and environmental manipulations in model organisms, from nematodes to mammals. Genes that can extend life span when altered are referred to as “gerontogenes.” The last several years have seen a dramatic increase in the number of identified gerontogenes (approximately seventy-four). The vast majority of these genes have been identified in the nematode, Caenorhabditis elegans. These genes include age-1 (a phosphatidylinositol 3-OH kinase gene) and daf-2 (an insulin-like receptor gene), as well as genes mediating behavior, metabolism, reproduction and sensory perception. age-1 and daf-2 play a role in a hormonal signaling cascade similar to the mammalian insulin / IGF-1 pathways. The age-1 / daf-2 signal functions to shorten life span and repress the positive regulators of life span, daf-16 and old-1. Similarly, studies of Dwarf mice indicate that the growth hormone-IGF-1 axis may play a role in regulating longevity. Signals from certain tissues, such as sensory neurons and gonads, also regulate life span in C. elegans. The gonadal signal is dependent on the daf-9 cytochrome P450 gene and the daf-12 steroid receptor gene, implicating roles of steroid hormones in longevity. Moreover, increased resistance to intrinsic and environmental stresses [heat, UV, and reactive oxygen species (ROS)] has been shown to be intimately related to increased longevity in a variety of species. ROS scavengers, including superoxide dismutase (SOD) and SOD mimetics, can extend life span in the fruit fly Drosophila melanogaster and in C. elegans, respectively. We suggest that environmental and intrinsic stresses, depending on the evolutionary niche occupied by the species, are key factors that control life span and aging. In summary, cellular signals regulate systemic mechanisms that play a role in stress resistance and also affect longevity.

Inadequate bone density is the strongest determinant of subsequent osteoporotic fracture. More than 70%of the variability in human bone density has been attributed to genetic factors. Therefore, the identification of genes regulating peak bone density represents a major advance in both the understanding of pathways that regulate bone density and the pathogenesis of diseases such as osteoporosis. Although association studies have revealed many candidate genes, the exact roles of these genes in the regulation of bone density are not clearly defined. Recently, a large number of bone density quantitative trait loci (QTLs) have been identified using mouse models and human populations. However, none of the genes responsible for these QTLs have been identified. Thus, the regulation of bone density is likely far more complicated than previously anticipated. Over the next decade, DNA microarrays, combined with sophisticated informatics and genomic databases, will provide a new generation of molecular tools for the identification and functional studies of genes responsible for bone density. This review intends to provide an update on the application of genomic resources and gene expression profiles to identify genes that regulate bone density. First, the progress and problems with association studies for QTL identification of bone density will be summarized. Then current resources of genomic sequences and ESTs that can be used for the identification of QTL genes will be discussed. Finally information on the 207 ESTs that are expressed in the bone and 39 ESTs that we have identified within the QTL regions will be presented. It is anticipated that this review will stimulate further studies on candidate genes that regulate bone density by taking advantage of the rapidly emerging genomic data.