Current Genomics - Volume 6, Issue 3, 2005

Conrad H. Waddington (1905-1975) is the developmental biologist generally known as the inventor of the term “epigenetics,” which literally means “outside of genetics” [1]. In modern usage, “epigenetics” refers to “all meiotically and mitotically heritable changes in gene expression that are not coded in the DNA sequence itself” [2]. Methylation of the C5 position of cytosine in DNA, 5meC, has been recognized as a principle epigenetic silencing mechanism since the 1970s [3]. The methylation of CpG sites within the genome in mammals is maintained by three classes of DNA methyltransferases (DNMTs) and has numerous roles from the silencing of transposable elements to the transcriptional repression of certain developmental genes [2]. In the early 1980s, Feinberg and Vogelstein pioneered the field of cancer epigenetics by showing that tumor cells have generally hypomethylated DNA [4, 5]. Feinberg's laboratory subsequently showed that loss of DNA methylation is a general characteristic of tumor cells, but, paradoxically, hypermethylation at specific genes also occurs (reviewed in [6]). In the 20 years since these early studies, epigenetic regulation of gene expression in cancer and development has continued to increase in importance. This special issue features three papers that review emerging issues in epigenetic regulation. The first review, “The epigenetics of breast cancer carcinogenesis and metastasis,” by Phipps et al. discusses recent pharmacological interventions to inhibit the DNA methylation status in breast cancer cells. The role of DNA methylation in the maintenance of breast cancer stem cells and the implications for treating breast cancer is also discussed. The second review, “The epigenomic viewpoint on cellular differentiation of myeloid progenitor cells as it pertains to leukemogenesis,” by Sollars explores how epigenetic regulation controls the differentiation of myeloid lineages. Issues such as cellular memory and how it is influenced by the environment and the implications for treating leukemia will be discussed. Finally, in the third review, “Epigenetic regulation of trinucleotide repeat expansions and contractions and the ”biased embryos“ hypothesis for rapid morphological evolution,” members of my laboratory and I discuss recent evidence by Fondon and Garner that morphological evolution in dogs involves trinucleotide repeat expansions and contractions [7]. We noticed that vertebrate trinucleotide repeats often contain CpG dinucleotides, so we proposed a hypothesis that CpGs are hypomethylated during stress, and that this facilitates expansions and contractions of key developmental genes in germ cells. Obviously, the field of epigenetics is expanding so rapidly that it is impossible to cover all of the exciting new developments in this area. “Epigenomics,” which refers to global epigenetic regulatory mechanisms in cancer, development, evolution, and other areas, will continue being important topics for this journal. References [1] Van Speybroeck, L. From epigenesis to epigenetics: the case of C. H. Waddington. Annals of the New York Academy of Sciences 2002, 981: 61-81. [2] Egger, G., Liang, G., Aparicio, A., Jones, P.A. Epigenetics in human disease and prospects for epigenetic therapy. Nature 2004, 429(6990): 457-63. [3] Holliday, R., Pugh, J.E. DNA modification mechanisms and gene activity during development. Science 1975, 187(4173): 226-32. [4] Feinberg, A.P., Vogelstein, B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 1983, 301(5895): 89-92. [5] Feinberg, A.P., Vogelstein, B. Hypomethylation of ras oncogenes in primary human cancers. Biochemical & Biophysical Research Communications 1983, 111(1): 47-54. [6] Feinberg, A.P., Tycko, B. The history of cancer epigenetics. Nature Reviews Cancer 2004, 4(2): 143-53. [7] Fondon, J.W., Garner, H.R. Molecular origins of rapid and continuous morphological evolution. Proc. Natl. Acad. Sci. USA 2004, 101(52): 18058-63.

The study of epigenetic regulation of genes involved in breast cancer provides a level of complexity that lends understanding to the factors contributing to this prevalent disease. Recent evidence from studies that employ pharmacological agents such as trichostatin A and/or 5-aza-cytidine to alter epigenetic changes have been shown to reactivate key regulators such as p21 in breast cancer cells or explain silencing mechanisms of p16 that could lead to carcinogenesis. The roles of telomerase and Bmi-1 expression in the cellular processes of senescence, aging, and the maintenance of stem cells are discussed in relation to breast carcinogenesis, the implications of breast cancer stem cells, and the feasibility of these genes as epigenetic targets in cancer therapy.

The new millennium has brought with it a surge of research in the field of epigenetics. This has included advances in our understanding of stem cell characteristics and mechanisms of commitment to cell lineages prior to differentiation. The nature of stem cells is similar to that of malignant cells in that they have unlimited self-renewal and protection from apoptosis, leading researchers to suspect that stem cells are the target of oncogenesis. This review will explore the idea of how epigenetic control of gene expression may contribute to mechanisms controlling differentiation of myeloid progenitor cells and its importance to our understanding of myelogenous leukemias. Recent developments in epigenetic research pertaining to differentiation of myeloid progenitor cells and hematopoietic stem cells are presented including aspects of cellular memory, general myelopoiesis, change in gene expression patterns, signal transduction, and the influence of the microenvironment.

Fondon and Garner have recently offered a hypothesis that gene-associated tandem repeat expansions and contractions in the protein coding regions of developmental genes are a major source for rapid morphological variation in dog breeds [1]. Repeat expansions and contractions can occur at rates up to 100, 000 times higher than point mutations [2, 3], so this class of mutation potentially has a much greater effect on morphological evolution than point mutations. Wallace Arthur has recently proposed that developmental bias, the tendency for developmental systems to produce variant trajectories in some directions more readily than others, is as important as natural selection in driving morphological evolution [4]. In this review, we present arguments that repeat expansions and contractions, because they affect morphological features in a specific and graded manner, are examples of developmental bias, and therefore support Arthur's “biased embryos” hypothesis of morphological evolution. We also extend the “biased embryos” model by exploring the possibility that expansions, contractions, and retrotransposon mobilizations are epigenetically upregulated during times of stress, possibly through a genome scanning process that utilizes Hsp90 in germ cells. In support of this idea, we found that the incidence of CpG dinucleotides is much higher in vertebrate trinucleotide repeats than in other protein coding regions, thus suggesting that CpG methylation is under stabilizing selection. Based on these and other observations, we propose a model whereby the regulation of the CpG methylation status of repetitive sequences in germ cells could be a powerful means to increase the rate of morphological variation, and thereby the rate of morphological evolution, during times of stress.

The potential of a genome sequence for the rapid identification of genes encoding specific enzymes was evaluated using the Aspergillus nidulans genome and plant cell wall polysaccharide degrading enzymes as an example. These enzymes are used in many industrial applications and many genes encoding these enzymes have already been identified in Aspergillus. Detailed in silica analysis of the ORFs assigned to the relevant families of the Carbohydrate Active enzyme database (CAZY, http: / / afmb.cnrs-mrs.fr / CAZY / index.html), using the Blast and Clustal programs, resulted in a reliable assignment of enzymatic function for most ORFs. This analysis demonstrated that approximately two-third of the A. nidulans ORFs do not yet have a characterised Aspergillus orthologue and also identified some ORFs encoding enzyme functions that have not yet been cloned in Aspergillus. A comparison of the biochemical characteristics of previously purified enzymes from A. nidulans to the A. nidulans ORFs did not result in the identification of the ORF corresponding to the enzyme activity. However, using an elimination strategy the number of candidate ORFs could be reduced to between 2 and 5. The analysis also revealed that the A. nidulans genome contains at least 33 ORFs that encode putative intracellular oligosaccharides degrading enzymes as well as ORFs with homology to oligosaccharides transporters of other organisms. This suggests that oligosaccharides are not exclusively degraded extracellularly, but can also be imported and degraded inside the cell.

Polyglutamine (polyQ) expansion causes nine inherited neurodegenerative disorders, including Huntington's Disease, Spinobulbar Muscular Atrophy, Dentatorubral-Pallidoluysian Atrophy, and Spinocerebellar Ataxias 1, 2, 3, 6, 7, and 17. The common pathological feature of these diseases is the formation of intracellular polyglutamine inclusions or aggregates. Previous studies have focused on the intranuclear inclusions and found that polyQ proteins can affect gene transcription. Recent studies have revealed that polyQ proteins and their inclusions in neuronal processes can impair intracellular transport. Impaired intracellular trafficking, particularly in axons, may lead to neuronal dysfunction and early neuropathology. In this review, we will discuss the ways that polyQ proteins affect intracellular trafficking with an emphasis on the events that lead to neurodegeneration in Huntington's disease.

Tropheryma whipplei is a Gram positive human pathogen that is the causative agent of Whipple's disease. Nearly one century elapsed between the first description of the disease in 1907 and the cultivation of this bacterium within eukaryotic cell cultures in 2000. This achievement has made possible genome sequencing of this poorly studied microorganism. This review summarizes post-genomic knowledge resulting from these genomic data. To compare the theoretical genetic capabilities of T. whipplei with those of other sequenced bacteria, a virtual microarray representation was generated. This in silico analysis supports the concept of independent evolution pathways for microbial pathogens. Concrete post-genomic consequences related to clinical microbiology such as the analysis of antibiotic susceptibility or the design of molecular tools convenient for PCR detection and epidemiology studies are described. Analysis of wholecell metabolic networks of T. whipplei also provide clues for designing axenic media for this pathogen that is particularly recalcitrant to cultivation. This opens the way to investigate transcriptome analysis of T. whipplei by microarrays. Future prospects are also discussed.

Sequencing of the human genome has opened the door to the most exciting new era for studying complex genetic traits. Positional cloning is a powerful approach, and is aimed at the identification and cloning genes, based on their chromosomal location identified through linkage analysis. The past decade has seen substantial success in identifying genes responsible for monogenic disorders while progress in gene identification for more common, multifactorial diseases has been slower. With completion of human genome sequencing the relevance of this approach is growing, with the rapidly increasing information and characterization of the human genome providing the opportunity to resolve complex diseases, as demonstrated in several recent studies. Recently, we identified a susceptibility locus for human Uric Acid Nephrolithiasis (UAN) on 10q21-q22 and showed that a variant of a novel gene encoding a specific protein is associated with Uric Acid Nephrolithiasis (OMIM 605990). Inspired by this successful identification, this paper briefly summarizes the genetical basis of Uric Acid Nephrolithiasis, and the evolutionary adaptation of the predisposing gene in a complex puzzle of inherited factors that we have disclosed through a comparative genomic approach.