Showing papers in "Advances in Genetics in 2010"

DNA methylation and cancer.

Abstract: DNA methylation is one of the most intensely studied epigenetic modifications in mammals. In normal cells, it assures the proper regulation of gene expression and stable gene silencing. DNA methylation is associated with histone modifications and the interplay of these epigenetic modifications is crucial to regulate the functioning of the genome by changing chromatin architecture. The covalent addition of a methyl group occurs generally in cytosine within CpG dinucleotides which are concentrated in large clusters called CpG islands. DNA methyltransferases are responsible for establishing and maintenance of methylation pattern. It is commonly known that inactivation of certain tumor-suppressor genes occurs as a consequence of hypermethylation within the promoter regions and a numerous studies have demonstrated a broad range of genes silenced by DNA methylation in different cancer types. On the other hand, global hypomethylation, inducing genomic instability, also contributes to cell transformation. Apart from DNA methylation alterations in promoter regions and repetitive DNA sequences, this phenomenon is associated also with regulation of expression of noncoding RNAs such as microRNAs that may play role in tumor suppression. DNA methylation seems to be promising in putative translational use in patients and hypermethylated promoters may serve as biomarkers. Moreover, unlike genetic alterations, DNA methylation is reversible what makes it extremely interesting for therapy approaches. The importance of DNA methylation alterations in tumorigenesis encourages us to decode the human epigenome. Different DNA methylome mapping techniques are indispensable to realize this project in the future.

Induction of epigenetic alterations by dietary and other environmental factors.

Abstract: Dietary and other environmental factors induce epigenetic alterations which may have important consequences for cancer development. This chapter summarizes current knowledge of the impact of dietary, lifestyle, and environmental determinants of cancer risk and proposes that effects of these exposures might be mediated, at least in part, via epigenetic mechanisms. Evidence is presented to support the hypothesis that all recognized epigenetic marks (including DNA methylation, histone modification, and microRNA (miRNA) expression) are influenced by environmental exposures, including diet, tobacco, alcohol, physical activity, stress, environmental carcinogens, genetic factors, and infectious agents which play important roles in the etiology of cancer. Some of these epigenetic modifications change the expression of tumor suppressor genes and oncogenes and, therefore, may be causal for tumorigenesis. Further work is required to understand the mechanisms through which specific environmental factors produce epigenetic changes and to identify those changes which are likely to be causal in the pathogenesis of cancer and those which are secondary, or bystander, effects. Given the plasticity of epigenetic marks in response to cancer-related exposures, such epigenetic marks are attractive candidates for the development of surrogate endpoints which could be used in dietary or lifestyle intervention studies for cancer prevention. Future research should focus on identifying epigenetic marks which are (i) validated as biomarkers for the cancer under study; (ii) readily measured in easily accessible tissues, for example, blood, buccal cells, or stool; and (iii) altered in response to dietary or lifestyle interventions for which there is convincing evidence for a relationship with cancer risk.

Histone modifications and cancer.

Abstract: It is now widely recognized that epigenetic events are important mechanisms underlying cancer development and progression. Epigenetic information in chromatin includes covalent modifications (such as acetylation, methylation, phosphorylation, and ubiquitination) of core nucleosomal proteins (histones). A recent progress in the field of histone modifications and chromatin research has tremendously enhanced our understanding of the mechanisms underlying the control of key physiological and pathological processes. Histone modifications and other epigenetic mechanisms appear to work together in establishing and maintaining gene activity states, thus regulating a wide range of cellular processes. Different histone modifications themselves act in a coordinated and orderly fashion to regulate cellular processes such as gene transcription, DNA replication, and DNA repair. Interest in histone modifications has further grown over the last decade with the discovery and characterization of a large number of histone-modifying molecules and protein complexes. Alterations in the function of histone-modifying complexes are believed to disrupt the pattern and levels of histone marks and consequently deregulate the control of chromatin-based processes, ultimately leading to oncogenic transformation and the development of cancer. Consistent with this notion, aberrant patterns of histone modifications have been associated with a large number of human malignancies. In this chapter, we discuss recent advances in our understanding of the mechanisms controlling the establishment and maintenance of histone marks and how disruptions of these chromatin-based mechanisms contribute to tumorigenesis. We also suggest how these advances may facilitate the development of novel strategies to prevent, diagnose, and treat human malignancies.

Epigenetics and miRNAs in human cancer.

Abstract: Epigenetic factors and microRNAs (miRNAs) are regulators of gene expression. Their regulatory function is frequently aberrant in cancer. In this chapter, we show that a tight connection occurs between miRNAs and epigenetics. Epigenetic factors can be responsible for the aberrancies of the miRNome (defined as the full spectrum of miRNAs for a specific genome) observed in cancer. Indeed, miRNAs undergo the same epigenetic regulatory laws like any other protein-coding gene. Moreover, a specific group of miRNAs (defined as epi-miRNAs) can directly target effectors of the epigenetic machinery (such as DNA methyltransferases, histone deacetylases, and polycomb repressive complex genes) and indirectly affect the expression of tumor suppressor genes, whose expression is controlled by epigenetic factors. The result of this epigenetic-miRNA interaction is a new layer of complexity in gene regulation, whose comprehension opens new avenues to understand human cancerogenesis and to achieve new cancer treatments.

Interplay between different epigenetic modifications and mechanisms.

Abstract: Cellular functions including transcription regulation, DNA repair, and DNA replication need to be tightly regulated. DNA sequence can contribute to the regulation of these mechanisms. This is exemplified by the consensus sequences that allow the binding of specific transcription factors, thus regulating transcription rates. Another layer of regulation resides in modifications that do not affect the DNA sequence itself but still results in the modification of chromatin structure and properties, thus affecting the readout of the underlying DNA sequence. These modifications are dubbed as "epigenetic modifications" and include, among others, histone modifications, DNA methylation, and small RNAs. While these events can independently regulate cellular mechanisms, recent studies indicate that joint activities of different epigenetic modifications could result in a common outcome. In this chapter, I will attempt to recapitulate the best known examples of collaborative activities between epigenetic modifications. I will emphasize mostly on the effect of crosstalks between epigenetic modifications on transcription regulation, simply because it is the most exposed and studied aspect of epigenetic interactions. I will also summarize the effect of epigenetic interactions on DNA damage response and DNA repair. The involvement of epigenetic crosstalks in cancer formation, progression, and treatment will be emphasized throughout the manuscript. Due to space restrictions, additional aspects involving histone replacements [Park, Y. J., and Luger, K. (2008). Histone chaperones in nucleosome eviction and histone exchange. Curr. Opin. Struct. Biol.18, 282-289.], histone variants [Boulard, M., Bouvet, P., Kundu, T. K., and Dimitrov, S. (2007). Histone variant nucleosomes: Structure, function and implication in disease. Subcell. Biochem. 41, 71-89; Talbert, P. B., and Henikoff, S. (2010). Histone variants-Ancient wrap artists of the epigenome. Nat. Rev. Mol. Cell Biol.11, 264-275.], and histone modification readers [de la Cruz, X., Lois, S., Sanchez-Molina, S., and Martinez-Balbas, M. A. (2005). Do protein motifs read the histone code? Bioessays27, 164-175; Grewal, S. I., and Jia, S. (2007). Heterochromatin revisited. Nat. Rev. Genet.8, 35-46.] will not be addressed in depth in this chapter, and the reader is referred to the reviews cited here.

Identification of driver and passenger DNA methylation in cancer by epigenomic analysis

Abstract: Human cancer genomes are characterized by widespread aberrations in DNA methylation patterns including DNA hypomethylation of mostly repetitive sequences and hypermethylation of numerous CpG islands. The analysis of DNA methylation patterns in cancer has progressed from single gene studies examining potentially important candidate genes to a more global analysis where all or almost all promoter and CpG island sequences can be analyzed. We provide a brief overview of these genome-scale methylation-profiling techniques, summarize some of the information that has been obtained with these approaches, and discuss what we have learned about the specificity of methylation aberrations in cancer at a genome-wide level. The challenge is now to identify those methylation changes that are thought to be crucial for the processes of tumor initiation, tumor progression, or metastasis and distinguish these from methylation changes that are merely passenger events that accompany the transformation process but have no effect per se on the process of carcinogenesis.

Statistical methods for pathway analysis of genome-wide data for association with complex genetic traits

Abstract: A number of statistical methods have been developed to test for associations between pathways (collections of genes related biologically) and complex genetic traits. Pathway analysis methods were originally developed for analyzing gene expression data, but recently methods have been developed to perform pathway analysis on genome-wide association study (GWAS) data. The purpose of this review is to give an overview of these methods, enabling the reader to gain an understanding of what pathway analysis involves, and to select the method most suited to their purposes. This review describes the various types of statistical methods for pathway analysis, detailing the strengths and weaknesses of each. Factors influencing the power of pathway analyses, such as gene coverage and choice of pathways to analyze, are discussed, as well as various unresolved statistical issues. Finally, a list of computer programs for performing pathway analysis on genome-wide association data is provided.

Genomic imprinting syndromes and cancer.

Abstract: Genomic imprinting represents a form of epigenetic control of gene expression in which one allele of a gene is preferentially expressed according to the parent-of-origin of the allele Genomic imprinting plays an important role in normal growth and development Disruption of imprinting can result in a number of human imprinting syndromes and predispose to cancer In this chapter, we describe a number of human imprinting syndromes to illustrate the concepts of genomic imprinting and how loss of imprinting of imprinted genes their relationship to human neoplasia

GRP78 signaling hub a receptor for targeted tumor therapy.

Abstract: Glucose-regulated protein 78 (GRP78) is a potential receptor for targeting therapy in cancer and chronic vascular disease due to its overexpression at the cell surface in tumor cells and in atherosclerotic lesions. Presence of the GRP78 autoantibody in cancer patient sera is generally associated with poor prognosis since it signals a prosurvival mechanism in response to cellular stress. Association of GRP78 with various binding partners involves coordination of multiple signaling pathways that result in either cell survival or cell death. Binding of activated alpha2-macroglobulin to cell-surface GRP78 activates Akt to suppress apoptotic pathways through multiple downstream effectors, and concomitantly upregulates NF-kappaBeta and induces the unfolded protein response (UPR) so that cell proliferation prevails. Interaction of GRP78 with cell-surface T-cadherin promotes endothelial cell survival. Association of oncogenic Cripto with GRP78 nullifies TGF-beta superfamily-dependent signaling through Smad2/3 to promote cell proliferation. In contrast, association of GRP78 with the plasminogen kringle 5 domain or extracellular Par-4 promotes apoptosis. Interaction of GRP78 with microplasminogen induces the UPR while association with tissue factor inhibits procoagulant activity. The diverse and multiple binding proteins of GRP78 and their equally diverse functional outcomes reflect the regulatory cellular functions that GRP78 orchestrates. Several GRP78 targeting peptides have been isolated from different tumors and they show remarkable tumor specificity. Conjugation of GRP78-targeting peptides to an apoptosis-inducing peptide suppresses tumor growth in tumor xenografts, thereby demonstrating that GRP78 is a viable target by which clinical cancer therapies can be successfully developed as well as its potential utility in treating vascular disease.

Epigenetic alterations as cancer diagnostic, prognostic, and predictive biomarkers.

Abstract: Alterations of DNA methylation and transcription of microRNAs (miRNAs) are very stable phenomena in tissues and body fluids and suitable for sensitive detection. These advantages enable us to translate some important discoveries on epigenetic oncology into biomarkers for control of cancer. A few promising epigenetic biomarkers are emerging. Clinical trials using methylated CpG islands of p16, Septin9, and MGMT as biomarkers are carried out for predication of cancer development, diagnosis, and chemosensitivity. Circulating miRNAs are promising biomarkers, too. Breakthroughs in the past decade imply that epigenetic biomarkers may be useful in reducing the burden of cancer.

Folate and one-carbon metabolism and its impact on aberrant DNA methylation in cancer.

Abstract: Folate is a methyl donor that plays an essential role in DNA synthesis and biological methylation reactions, including DNA methylation. Folate deficiency may be implicated in the development of genomic DNA hypomethylation, which is an early epigenetic event found in many cancers, particularly colorectal cancer (CRC). Numerous studies employing in vitro systems, animal models, and human interventional studies have tested this hypothesis. Here, we describe the role of folate as a methyl donor in the one-carbon metabolism cycle, and the consequences of cellular folate deficiency. The existing evidence on folate and its relationship to DNA methylation is discussed using CRC as an example. While there remain numerous technical challenges in this important field of research, changes to folate intake appear to be capable of modulating DNA methylation levels in the human colonic mucosa and this may potentially alter CRC risk.

In utero life and epigenetic predisposition for disease.

Abstract: Regulatory regions of the human genome can be modified through epigenetic processes during prenatal life to make an individual more likely to suffer chronic diseases when they reach adulthood. The modification of chromatin and DNA contributes to a larger well-documented process known as "programming" whereby stressors in the womb give rise to adult onset diseases, including cancer. It is now well known that death from ischemic heart disease is related to birth weight; the lower the birth weight, the higher the risk of death from cardiovascular disease as well as type 2 diabetes and osteoporosis. Recent epidemiological data link rapid growth in the womb to metabolic disease and obesity and also to breast and lung cancers. There is increasing evidence that "marked" regions of DNA can become "unmarked" under the influence of dietary nutrients. This gives hope for reversing propensities for cancers and other diseases that were acquired in the womb. For several cancers, the size and shape of the placenta are associated with a person's cardiovascular and cancer risks as are maternal body mass index and height. The features of placental growth and nutrient transport properties that lead to adult disease have been little studied. In conclusion, several cancers have their origins in the womb, including lung and breast cancer. More research is needed to determine the epigenetic processes that underlie the programming of these diseases.

Histone modification therapy of cancer.

Abstract: The state of modification of histone tails plays an important role in defining the accessibility of DNA for the transcription machinery and other regulatory factors. It has been extensively demonstrated that the posttranslational modifications of the histone tails, as well as modifications within the nucleosome domain, regulate the level of chromatin condensation and are therefore important in regulating gene expression and other nuclear events. Together with DNA methylation, they constitute the most relevant level of epigenetic regulation of cell functions. Histone modifications are carried out by a multipart network of macromolecular complexes endowed with enzymatic, regulatory, and recognition domains. Not surprisingly, epigenetic alterations caused by aberrant activity of these enzymes are linked to the establishment and maintenance of the cancer phenotype and, importantly, are potentially reversible, since they do not involve genetic mutations in the underlying DNA sequence. Histone modification therapy of cancer is based on the generation of drugs able to interfere with the activity of enzymes involved in histone modifications: new drugs have recently been approved for use in cancer patients, clinically validating this strategy. Unfortunately, however, clinical responses are not always consistent and do not parallel closely the results observed in preclinical models. Here, we present a brief overview of the deregulation of chromatin-associated enzymatic activities in cancer cells and of the main results achieved by histone modification therapeutic approaches.

Epigenetic drivers of genetic alterations.

Abstract: DNA methylation plays a key role in the silencing of cancer-related genes, thereby affecting numerous cellular processes, including the cell cycle checkpoint, apoptosis, signal transduction, cell adhesion, and angiogenesis. DNA methylation also affects the expression of genes involved in maintaining the integrity of the genome through DNA repair and detoxification of reactive oxygen species. Here, we discuss how epigenetic changes lead to genetic alterations, including microsatellite instability and nucleotide and chromosomal alterations. Epigenetic inactivation of hMLH1 is a major cause of microsatellite instability in sporadic colorectal cancers, and germline epimutation of hMLH1 and hMSH2 is a cause of hereditary nonpolyposis colorectal cancers, which do not show mutation of mismatch repair genes. Epigenetic inactivation of MGMT is often associated with G:C-to-A:T mutations in K-ras and p53, while epigenetic inactivation of BRCA1, WRN, FANCF, and CHFR impairs the machinery involved in maintaining genomic integrity. Epigenetic alteration of the genes involved in the induction of senescence is often associated with cancers showing mutations in the Ras signaling pathway. In addition to regional hypermethylation, global hypomethylation is also a common feature of tumors. Hypomethylation of short and long interspersed repetitive elements has been reported, and hypomethylation affecting the integrity of the genome has been observed in ICF syndrome and various cancers. Dissection of the epigenetic drivers of genetic instability may be important for the development of novel approaches to the treatment of cancer.

DNA demethylating agents and epigenetic therapy of cancer.

Abstract: Epigenetic events have been associated with virtually every step of tumor development and progression, and epigenetic alterations are believed to occur early in tumor development and may precede the malignant process. In contrast to genetic changes, epigenetic alterations arise in a gradual manner, leading to a progressive silencing of specific genes. An important distinction between epigenetic and genetic alterations is intrinsic reversibility of the former, making cancer-associated changes in DNA methylation, histone modifications, and expression of noncoding RNAs attractive targets for therapeutic intervention. This realization has triggered an impressive quest for the development of "epigenetic drugs" and epigenetic therapies. A number of agents have been subjected to an intensive investigation, many of which have been found capable of altering epigenetic states, including DNA methylation patterns and histone modification states. Many of these agents are currently being tested in clinical trials, while several of them are already used in clinics. This review will focus on the recent advances in the development of epigenetic drugs based on the inhibition of DNA methylation. Combinatorial therapies that couple DNA demethylating agents with histone deacetylase inhibitors will also be discussed.

Diet, epigenetic, and cancer prevention.

Abstract: Disruption of the epigenome has been a hallmark of human cancers and has been linked with tumor pathogenesis and progression. Since epigenetic changes can be reversed in principle, studies have been carried out to identify modifiable (such as diet and lifestyle) factors, which possess epigenetic property, in hope for developing epigenetically based prevention/intervention strategies. The goal is to achieve some degree of epigenetic reprogramming, which would maintain normal gene expression status and reverse tumorigenesis through chemoprevention or lifestyle intervention such as diet modification. The ability of dietary compounds to act epigenetically in cancer cells has been studied and evidence continues to surface for constituents in food and dietary supplements to influence the epigenome and ultimately individual's risk of developing cancer. In this chapter, we summarized the existing data, both from animal and human studies, on the capacity of natural food products to influence three key epigenetic processes: DNA methylation, histone modification, and microRNA expression. As discussed in the perspective, while diet-based intervention that targets epigenetic pathways is promising, significant challenges remain in translating these scientific findings into clinical or public health practices in the context of cancer prevention.

Inheritance of epigenetic aberrations (constitutional epimutations) in cancer susceptibility.

Abstract: The pathogenic role for heritable mutations in the DNA sequence of tumor suppressor and DNA repair genes has been well established in familial cancer syndromes. These germ line mutations confer a high risk of developing particular types of cancer, according to the gene affected, at a young age of onset when compared to sporadically arising cancers of a similar type. The widespread role for epigenetic dysregulation in the development and progression of sporadic cancers is also well recognized. However, it has only become apparent in recent years that epigenetic aberrations can also occur constitutionally to confer a similar cancer phenotype as a genetic mutation within the same gene. These epigenetic errors are termed "constitutional epimutations" and are characterized by promoter methylation and transcriptional silencing of a single allele of the gene in normal somatic tissues in the absence of a sequence mutation within the affected locus. This is best exemplified in Lynch syndrome, which is an autosomal dominant cancer susceptibility syndrome characterized by the early development of colorectal, uterine, and additional cancers exhibiting microsatellite instability due to impaired mismatch repair. Lynch syndrome is usually caused by heterozygous loss-of-function germ line mutations of the mismatch repair genes, namely MLH1, MSH2, MSH6, and PMS2. Tumors develop following an acquired somatic loss of the remaining functional allele. However, a subset of Lynch syndrome cases without genetic mutations instead has a constitutional epimutation of MLH1 or MSH2. These epimutations are associated with distinct patterns of inheritance depending on the nature of the mechanisms underlying them.

Detecting, characterizing, and interpreting nonlinear gene-gene interactions using multifactor dimensionality reduction.

Abstract: Human health is a complex process that is dependent on many genes, many environmental factors and chance events that are perhaps not measurable with current technology or are simply unknowable Success in the design and execution of population-based association studies to identify those genetic and environmental factors that play an important role in human disease will depend on our ability to embrace, rather that ignore, complexity in the genotype to phenotype mapping relationship for any given human ecology We review here three general computational challenges that must be addressed First, data mining and machine learning methods are needed to model nonlinear interactions between multiple genetic and environmental factors Second, filter and wrapper methods are needed to identify attribute interactions in large and complex solution landscapes Third, visualization methods are needed to help interpret computational models and results We provide here an overview of the multifactor dimensionality reduction (MDR) method that was developed for addressing each of these challenges

Induction of Epigenetic Alterations by Chronic Inflammation and Its Significance on Carcinogenesis

Abstract: Chronic inflammation is deeply involved in development of human cancers, such as gastric and liver cancers. Induction of cell proliferation, production of reactive oxygen species, and direct stimulation of epithelial cells by inflammation-inducing factors have been considered as mechanisms involved. Inflammation-related cancers are known for their multiple occurrences, and aberrant DNA methylation is known to be present even in noncancerous tissues. Importantly, for some cancers, the degree of accumulation has been demonstrated to be correlated with risk of developing cancers. This indicates that inflammation induces aberrant epigenetic alterations in a tissue early in the process of carcinogenesis, and accumulation of such alterations forms "an epigenetic field for cancerization." This also suggests that inhibition of induction of epigenetic alterations and removal of the accumulated alterations are novel approaches to cancer prevention. Disturbances in cytokine and chemokine signals and induction of cell proliferations are important mechanisms of how inflammation induces aberrant DNA methylation. Aberrant DNA methylation is induced in specific genes, and gene expression levels, the presence of RNA polymerase II (active or stalled), and trimethylation of H3K4 are involved in the specificity. Expression of DNA methyltransferases (DNMTs) is not necessarily induced by inflammation, and local imbalance between DNMTs and factors that protect genes from DNA methylation seems to be important.

An Integrated Approach for the Rational Design of Nanovectors for Biomedical Imaging and Therapy

Abstract: The use of nanoparticles for the early detection, cure, and imaging of diseases has been proved already to have a colossal potential in different biomedical fields, such as oncology and cardiology. A broad spectrum of nanoparticles are currently under development, exhibiting differences in (i) size, ranging from few tens of nanometers to few microns; (ii) shape, from the classical spherical beads to discoidal, hemispherical, cylindrical, and conical; (iii) surface functionalization, with a wide range of electrostatic charges and biomolecule conjugations. Clearly, the library of nanoparticles generated by combining all possible sizes, shapes, and surface physicochemical properties is enormous. With such a complex scenario, an integrated approach is here proposed and described for the rational design of nanoparticle systems (nanovectors) for the intravascular delivery of therapeutic and imaging contrast agents. The proposed integrated approach combines multiscale/multiphysics mathematical models with in vitro assays and in vivo intravital microscopy (IVM) experiments and aims at identifying the optimal combination of size, shape, and surface properties that maximize the nanovectors localization within the diseased microvasculature.

9 - Cancer Epigenome

Abstract: Cancer is a heterogeneous disease caused largely by abnormalities of the genome and the epigenome. Typically, such abnormalities include genetic changes such as mutations and other genomic rearrangements or epigenetic changes such as aberrant DNA methylation and histone modifications that are frequently mediated by exposure to environmental or lifestyle factors. Therefore, comprehensive genetic and epigenetic analysis of cancer genomes is the most effective way to identify causative changes involved in tumorigenesis, irrespective of whether they are inherited or acquired. In this chapter, we review recent progress in the field and discuss some of the pilot studies that have already established epigenomic analysis as integral part of modern cancer research and present a major step toward personalized treatment of this disease in the future.

Logic Regression and Its Extensions

Abstract: Logic regression is an adaptive classification and regression procedure, initially developed to reveal interacting single nucleotide polymorphisms (SNPs) in genetic association studies. In general, this approach can be used in any setting with binary predictors, when the interaction of these covariates is of primary interest. Logic regression searches for Boolean (logic) combinations of binary variables that best explain the variability in the outcome variable, and thus, reveals variables and interactions that are associated with the response and/or have predictive capabilities. The logic expressions are embedded in a generalized linear regression framework, and thus, logic regression can handle a variety of outcome types, such as binary responses in case-control studies, numeric responses, and time-to-event data. In this chapter, we provide an introduction to the logic regression methodology, list some applications in public health and medicine, and summarize some of the direct extensions and modifications of logic regression that have been proposed in the literature.

Multigenic modeling of complex disease by random forests.

Abstract: The genetics and heredity of complex human traits have been studied for over a century. Many genes have been implicated in these complex traits. Genome-wide association studies (GWAS) were designed to investigate the association between common genetic variation and complex human traits using high-throughput platforms that measured hundreds of thousands of common single-nucleotide polymorphisms (SNPs). GWAS have successfully identified many novel genetic loci associated with complex traits using a univariate regression-based approach. Even for traits with a large number of identified variants, only a small fraction of the interindividual variation in risk phenotypes has been explained. In biological systems, protein, DNA, RNA, and metabolites frequently interact to each other to perform their biological functions, and to respond to environmental factors. The complex interactions among genes and between the genes and environment may partially explain the “missing heritability.” The traditional regression-based methods are limited to address the complex interactions among the hundreds of thousands of SNPs and their environmental context by both the modeling and computational challenge. Random Forests (RF), one of the powerful machine learning methods, is regarded as a useful alternative to capture the complex interaction effects among the GWAS data, and potentially address the genetic heterogeneity underlying these complex traits using a computationally efficient framework. In this chapter, the features of prediction and variable selection, and their applications in genetic association studies are reviewed and discussed. Additional improvements of the original RF method are warranted to make the applications in GWAS to be more successful.

MR Molecular Imaging of Tumor Vasculature and Vascular Targets

Abstract: Tumor angiogenesis and the ability of cancer cells to induce neovasculature continue to be a fascinating area of research. As the delivery network that provides substrates and nutrients, as well as chemotherapeutic agents to cancer cells, but allows cancer cells to disseminate, the tumor vasculature is richly primed with targets and mechanisms that can be exploited for cancer cure or control. The spatial and temporal heterogeneity of tumor vasculature, and the heterogeneity of response to targeting, make noninvasive imaging essential for understanding the mechanisms of tumor angiogenesis, tracking vascular targeting, and detecting the efficacy of antiangiogenic therapies. With its noninvasive characteristics, exquisite spatial resolution and range of applications, magnetic resonance imaging (MRI) techniques have provided a wealth of functional and molecular information on tumor vasculature in applications spanning from “bench to bedside”. The integration of molecular biology and chemistry to design novel imaging probes ensures the continued evolution of the molecular capabilities of MRI. In this review, we have focused on developments in the characterization of tumor vasculature with functional and molecular MRI.

Introduction: epigenetics and cancer.

Abstract: The field of epigenetics has witnessed a recent explosion in our knowledge on the importance of epigenetic events in the control of both normal cellular processes and abnormal events associated with diseases, moving this field to the forefront of biomedical research. Advances in the field of cancer epigenetics and epigenomics have turned academic, medical, and public attention to the potential application of epigenetics in cancer control. A tremendous pace of discovery in this field requires that these recent conceptual breakthroughs and technological state-of-the-art in epigenetics and epigenomics are updated and summarized in one book with cancer focus. This book is primarily intended to academic and professional audience; however, an attempt has been made to make it understandable by and appealing to a wider audience among healthcare workers. The main aim of this book is to produce an authoritative and comprehensive reference source in print and online, covering all critical aspects of epigenetics and epigenomics and their implications in cancer research. This book discusses the state of science and determines the future research needs, covering most recent advances, both conceptual and technological, and their implication for better understanding of molecular mechanisms of cancer development and progression, early detection, risk assessment, and prevention of cancer. In this chapter, we describe the main aim and scope of this book and provide a brief emphasis of each of 22 chapters regrouped into eight major parts.

Targeted systemic gene therapy and molecular imaging of cancer contribution of the vascular-targeted AAVP vector.

Abstract: Gene therapy and molecular-genetic imaging have faced a major problem: the lack of an efficient systemic gene delivery vector. Unquestionably, eukaryotic viruses have been the vectors of choice for gene delivery to mammalian cells; however, they have had limited success in systemic gene therapy. This is mainly due to undesired uptake by the liver and reticuloendothelial system, broad tropism for mammalian cells causing toxicity, and their immunogenicity. On the other hand, prokaryotic viruses such as bacteriophage (phage) have no tropism for mammalian cells, but can be engineered to deliver genes to these cells. However, phage-based vectors have inherently been considered poor vectors for mammalian cells. We have reported a new generation of vascular-targeted systemic hybrid prokaryotic-eukaryotic vectors as chimeras between an adeno-associated virus (AAV) and targeted bacteriophage (termed AAV/phage; AAVP). In this hybrid vector, the targeted bacteriophage serves as a shuttle to deliver the AAV transgene cassette inserted in an intergenomic region of the phage DNA genome. As a proof of concept, we assessed the in vivo efficacy of vector in animal models of cancer by displaying on the phage capsid the cyclic Arg-Gly-Asp (RGD-4C) ligand that binds to alphav integrin receptors specifically expressed on the angiogenic blood vessels of tumors. The ligand-directed vector was able to specifically deliver imaging and therapeutic transgenes to tumors in mice, rats, and dogs while sparing the normal organs. This chapter reviews some gene transfer strategies and the potential of the vascular-targeted AAVP vector for enhancing the effectiveness of existing systemic gene delivery and genetic-imaging technologies.

Epigenetic codes in stem cells and cancer stem cells.

Abstract: Definition of stemness states that a stem cell population should be maintained over long periods of time, while generating all differentiated cell types of the corresponding tissues. Epigenetic regulation plays an important role in such process because the context of genome sequences is generally unchanged by differentiation process. Recent evidence indicates that an abnormal control of cellular differentiation is involved in the process of carcinogenesis [Hochedlinger, K., Yamada, Y., Beard, C., and Jaenisch, R. (2005). Ectopic expression of Oct-4 blocks progenitor-cell differentiation and causes dysplasia in epithelial tissues. Cell 121, 465-477]. Therefore, understanding how cellular differentiation is controlled would be useful for obtaining a better understanding of the mechanisms underlying carcinogenesis. In this chapter, we will describe recent advances in understanding the epigenetic codes that govern differentiation of stem cells, especially focusing on embryonic stem cells. We will also discuss the concept of cancer stem cells, in which the epigenetic regulations control differentiation of tumor cells and such regulations play a central role in the determination of whether a tumor cell is capable of tumor initiation or not.

Epigenetics in molecular epidemiology of cancer a new scope.

Abstract: Classical epidemiologic studies have made important contributions to identifying the etiology of most common cancers and have had substantive public health impact. Molecular epidemiology is an extension of classical epidemiologic research to incorporate biochemical and molecular biomarkers with questionnaire data to advance our understanding of mechanisms of carcinogenesis and of events between exposure and cancer development. Risk prediction, prognostication, and therapy prediction are the clinical uses of molecular epidemiology in cancer management. Lifestyle and environmental factors associated with carcinogenesis also strongly affect epigenetic statuses, and thus epigenetic mechanisms may mediate environmental influences on gene expression and even diseases, resulting in a focus of epidemiologic investigation. DNA methylation can be studied on candidate genes or on a genome-wide scale, although the genotype is fixed at conception but the epigenome is dynamic. Unlike simple genotyping, the levels and patterns of epigenetic changes differ in different tissues and cell types, and may not reflect events in target tissues. Still as a possible risk factor and surrogate marker for liability to cancer, the methylation statuses of blood leukocyte DNA seem to be ideal for the analysis and are emerging as a new scope. Epigenetic changes in comparison with genetic ones are reversible and are acquired in a gradual manner. These epigenetic features offer a huge potential for prevention strategies.

Genome simulation approaches for synthesizing in silico datasets for human genomics.

Abstract: Simulated data is a necessary first step in the evaluation of new analytic methods because in simulated data the true effects are known To successfully develop novel statistical and computational methods for genetic analysis, it is vital to simulate datasets consisting of single nucleotide polymorphisms (SNPs) spread throughout the genome at a density similar to that observed by new high-throughput molecular genomics studies In addition, the simulation of environmental data and effects will be essential to properly formulate risk models for complex disorders Data simulations are often criticized because they are much less noisy than natural biological data, as it is nearly impossible to simulate the multitude of possible sources of natural and experimental variability However, simulating data in silico is the most straightforward way to test the true potential of new methods during development Thus, advances that increase the complexity of data simulations will permit investigators to better assess new analytical methods In this work, we will briefly describe some of the current approaches for the simulation of human genomics data describing the advantages and disadvantages of the various approaches We will also include details on software packages available for data simulation Finally, we will expand upon one particular approach for the creation of complex, human genomic datasets that uses a forward-time population simulation algorithm: genomeSIMLA Many of the hallmark features of biological datasets can be synthesized in silico; still much research is needed to enhance our capabilities to create datasets that capture the natural complexity of biological datasets

Strategies for Targeting Tumors and Tumor Vasculature for Cancer Therapy

Abstract: Effective cancer therapy remains a challenge despite recent advances in the identification of novel targets. A major limitation of most chemotherapeutic drugs is their systemic toxicity and the efficacy of cancer treatments is, by and large, determined by the ability to balance their benefits against their toxicity. Targeted treatments for cancer, especially those that target the tumor vasculature, have provided promising antitumor results with minimal systemic toxicity. To date significant progress has been made in developing a variety of delivery systems to target cancer and its vasculature ranging from isolated limb and organ perfusion to tumor targeted biological and nonbiological vectors.