Download or read book Defining Sites of Replication Fork Collapse Caused by ATR Inhibition written by Nishita K. Shastri and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Replication stress, characterized by stalling of DNA replication and the accumulation of abnormal replication intermediates, has been linked to the genomic instability observed in cancer. Previous studies have defined specific genomic sequences that are difficult to replicate to be more vulnerable to replication-associated breaks and rearrangements. However, many of these sequences have been identified through indirect and potentially biased approaches. To identify DNA sequences that contribute to replication-associated genomic instability, I will describe genome-wide screens I have performed to determine the location, sequence, and frequency of replication perturbations within the mammalian genome upon replication stress. Ataxia telangiectasia and Rad3-related protein (ATR) is a checkpoint kinase that is a key upstream regulator of the response pathway to replication fork stalling during replication stress that prevents fork collapse. Through inhibition of this response pathway in mouse embryonic fibroblasts, my aims are to 1) characterize regions that lead to frequent replication fork stalling and collapse, and 2) further define genomic regions that become processed into double-strand breaks. Since replication protein A (RPA) binds to single-stranded DNA that becomes exposed when replication forks stall, RPA ChIP-Seq has been performed to map sites of frequently collapsed replication forks; however, not all stalled replication forks result in breaks. To differentiate a replication fork that has simply stalled from a fork that has become sensitized to double-strand break formation, I developed and applied a novel and specific break-detection assay, BrITL. With these complementary approaches to map replication-problematic loci, subsequent bioinformatics methods have been utilized to characterize features of the identified genomic regions that make it prone to fork collapse and detrimental DNA break formation when cells experience replication stress. While well-established difficult-to-replicate sequences (e.g. triplet and telomere repeats) exhibited enhanced fork collapse in RPA ChP'd cells exposed to replication stress, these sequences were overshadowed by sites composed of previously uncharacterized simple tandem repeats. Circular dichroism and thermal difference absorption spectra indicate that the most commonly observed simple repeat at RPA-enriched sites (CAGAGG) folds into a stable intramolecular secondary structure and is sufficient to stall DNA replication in vitro and in vivo. BrITL analysis confirmed that these repetitive regions of RPA accumulation are also sites of DNA breakage. Interestingly, a majority of break sites identified by BrITL do not associate with RPA accumulation, but rather tend to locate around inverted retroelements that are predicted to form highly stable intrastrand stem-loop structures. Due to the lack of available ssDNA at these potential hairpin-forming sites, RPA accumulation would be limited. Overall, my studies represent the first unbiased identification of mammalian genomic sites that are vulnerable to replication stress and rely on ATR for stability.

Download or read book Dissecting the Functions of Atr in Replication Fork Stability written by Theonie Anastassiadis and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome maintenance is required for cellular viability, and failure to preserve genomic integrity is associated with an increased risk of diseases, such as cancer. To ensure genomic stability, cells have checkpoints that control cell cycle progression in the event of DNA damage or incomplete DNA replication. The DNA replication checkpoint is regulated by the ATR-CHK1 pathway that stabilizes stalled replication forks and prevents their collapse into DNA double-strand breaks (DSBs). Two distinct models have been proposed to explain how ATR stabilizes stalled forks: 1) through local modulation of fork remodelers, such as SMARCAL1 inhibition, and 2) through inhibition of CDK-dependent pathways, such as inhibition of the AURKA-PLK1 pathway, which prevent cell cycle progression. However, it remains unclear which stabilization function is essential for fork stability and whether specific sites in the genome depend on one function over the other.In an effort to test if an essential part of fork stabilization is mediated through inhibiting CDK-dependent pathways, such as inhibiting premature activation of the AURKA-PLK1 pathway, we established a system to hyper-activate the AURKA-PLK1 pathway to determine if it is sufficient to cause fork collapse. We found that fork collapse was not achievable solely through Aurora A overexpression nor with overexpression of its co-activators, TPX2 and BORA, but rather that CDK1 activation was also required. To test if CDK1-activation is sufficient to promote fork collapse, we inhibited WEE1, which short-circuits the cell cycle checkpoint function of ATR without inhibiting its fork-proximal activity. Using flow cytometry based fork collapse assays and genome-wide detection of RPA accumulation using RPA ChIP-Seq, we show that WEE1 and ATR inhibition cause similar levels of fork collapse at overlapping genomic locations in a CDK1-depdendent manner under conditions of partial replication inhibition (low dose aphidicolin). Notably, treatment with WEE1 inhibitor (WEE1i) alone was also sufficient to cause replication fork collapse, and did so more rapidly and to a higher degree than treatment with ATR inhibitor (ATRi) alone. Interestingly, clear differences in site specificity were observed when WEE1i was combined with ATRi, suggesting that particular sites in the genome may be slightly more dependent on the local functions of ATR than others. Thus, cell cycle checkpoint abrogation by WEE1i is sufficient to cause replication fork collapse in a manner similar to ATRi; however, site-specific roles for ATR remain. Together our findings indicate that the cell cycle checkpoint of ATR is key in stabilizing replication forks at a majority of sites in the genome. These findings could be leveraged to develop cancer treatments that exploit combinations of oncogenic genomic breakage signatures with that of WEE1 or ATR inhibitors.

Download or read book The Mechanisms of DNA Replication written by David Stuart and published by BoD – Books on Demand. This book was released on 2013-02-20 with total page 502 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA replication is a fundamental part of the life cycle of all organisms. Not surprisingly many aspects of this process display profound conservation across organisms in all domains of life. The chapters in this volume outline and review the current state of knowledge on several key aspects of the DNA replication process. This is a critical process in both normal growth and development and in relation to a broad variety of pathological conditions including cancer. The reader will be provided with new insights into the initiation, regulation, and progression of DNA replication as well as a collection of thought provoking questions and summaries to direct future investigations.

Download or read book Systems Biology of Cancer written by Sam Thiagalingam and published by Cambridge University Press. This book was released on 2015-04-09 with total page 597 pages. Available in PDF, EPUB and Kindle. Book excerpt: An overview of the current systems biology-based knowledge and the experimental approaches for deciphering the biological basis of cancer.

Download or read book DNA Replication and Human Disease written by Melvin L. DePamphilis and published by CSHL Press. This book was released on 2006 with total page 814 pages. Available in PDF, EPUB and Kindle. Book excerpt: At least 5 trillion cell divisions are required for a fertilized egg to develop into an adult human, resulting in the production of more than 20 trillion meters of DNA! And yet, with only two exceptions, the genome is replicated once and only once each time a cell divides. How is this feat accomplished? What happens when errors occur? This book addresses these questions by presenting a thorough analysis of the molecular events that govern DNA replication in eukaryotic cells. The association between genome replication and cell proliferation, disease pathogenesis, and the development of targeted therapeutics is also addressed. At least 160 proteins are involved in replicating the human genome, and at least 40 diseases are caused by aberrant DNA replication, 35 by mutations in genes required for DNA replication or repair, 7 by mutations generated during mitochondrial DNA replication, and more than 40 by DNA viruses. Consequently, a growing number of therapeutic drugs are targeted to DNA replication proteins. This authoritative volume provides a rich source of information for researchers, physicians, and teachers, and will stimulate thinking about the relevance of DNA replication to human disease.

Download or read book Molecular Themes in DNA Replication written by Lynne Suzanne Cox and published by Royal Society of Chemistry. This book was released on 2009 with total page 467 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by leading experts, this learned but accessible book highlights the latest work on eukaryotic DNA replication.

Download or read book The DNA Damage Response Implications on Cancer Formation and Treatment written by Kum Kum Khanna and published by Springer Science & Business Media. This book was released on 2009-09-18 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ?eld of cellular responses to DNA damage has attained widespread recognition and interest in recent years commensurate with its fundamental role in the ma- tenance of genomic stability. These responses, which are essential to preventing cellular death or malignant transformation, are organized into a sophisticated s- tem designated the “DNA damage response”. This system operates in all living organisms to maintain genomic stability in the face of constant attacks on the DNA from a variety of endogenous by-products of normal metabolism, as well as exogenous agents such as radiation and toxic chemicals in the environment. The response repairs DNA damage via an intricate cellular signal transduction network that coordinates with various processes such as regulation of DNA replication, tr- scriptional responses, and temporary cell cycle arrest to allow the repair to take place. Defects in this system result in severe genetic disorders involving tissue degeneration, sensitivity to speci?c damaging agents, immunode?ciency, genomic instability, cancer predisposition and premature aging. The ?nding that many of the crucial players involved in DNA damage response are structurally and functionally conserved in different species spurred discoveries of new players through similar analyses in yeast and mammals. We now understand the chain of events that leads to instantaneous activation of the massive cellular responses to DNA lesions. This book summarizes several new concepts in this rapidly evolving ?eld, and the advances in our understanding of the complex network of processes that respond to DNA damage.

Download or read book Mechanistic Studies of Genome Integrity Environmental Health and Cancer Etiology written by Shan Yan and published by Frontiers Media SA. This book was released on 2022-11-10 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Eukaryotic DNA Damage Surveillance and Repair written by Keith William Caldecott and published by Springer Science & Business Media. This book was released on 2004-05-31 with total page 180 pages. Available in PDF, EPUB and Kindle. Book excerpt: Eukaryotic DNA Damage Surveillance and Repair contains chapters from experts in the field of DNA damage detection, repair, and cell cycle control. The work reviews current understanding of how different types of DNA damage are detected and focuses on how these surveillance mechanisms are coupled to processes of DNA repair, cell cycle control, and apoptosis. The title will be of interest to undergraduate/postgraduate students and academics alike.

Download or read book Comprehensive Toxicology written by and published by Elsevier. This book was released on 2017-12-01 with total page 8639 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comprehensive Toxicology, Third Edition, Fifteen Volume Set discusses chemical effects on biological systems, with a focus on understanding the mechanisms by which chemicals induce adverse health effects. Organized by organ system, this comprehensive reference work addresses the toxicological effects of chemicals on the immune system, the hematopoietic system, cardiovascular system, respiratory system, hepatic toxicology, renal toxicology, gastrointestinal toxicology, reproductive and endocrine toxicology, neuro and behavioral toxicology, developmental toxicology and carcinogenesis, also including critical sections that cover the general principles of toxicology, cellular and molecular toxicology, biotransformation and toxicology testing and evaluation. Each section is examined in state-of-the-art chapters written by domain experts, providing key information to support the investigations of researchers across the medical, veterinary, food, environment and chemical research industries, and national and international regulatory agencies. Thoroughly revised and expanded to 15 volumes that include the latest advances in research, and uniquely organized by organ system for ease of reference and diagnosis, this new edition is an essential reference for researchers of toxicology. Organized to cover both the fundamental principles of toxicology and unique aspects of major organ systems Thoroughly revised to include the latest advances in the toxicological effects of chemicals on the immune system Features additional coverage throughout and a new volume on toxicology of the hematopoietic system Presents in-depth, comprehensive coverage from an international author base of domain experts

Download or read book Targeting the DNA Damage Response for Anti Cancer Therapy written by John Pollard and published by Springer. This book was released on 2018-05-26 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the past decade a complex role for DNA damage response (DDR) in tumorigenesis has emerged. A proficient DDR has been shown to be a primary cause for cellular resistance to the very many DNA damaging drugs, and IR, that are widely used as standard-of-care across multiple cancer types. It has also been shown that defects in this network, predominantly within the ATM mediated signaling pathway, are commonly observed in cancers and may be a primary event during tumorigenesis. Such defects may promote a genomically unstable environment, facilitating the persistence of mutations, any of which may provide a growth or survival advantage to the developing tumor. In addition, these somatic defects provide opportunities to exploit a reliance on remaining repair pathways for survival, a process which has been termed synthetic lethality. As a result of all these observations there has been a great interest in targeting the DDR to provide anti-cancer agents that may have benefit as monotherapy in cancers with high background DNA damage levels or as a means to increase the efficacy of DNA damaging drugs and IR. In this book we will review a series of important topics that are of great interest to a broad range of academic, industrial and clinical researchers, including the basic science of the DDR, its role in tumorigenesis and in dictating response to DNA damaging drugs and IR. Additionally, we will focus on the several proteins that have been targeted in attempts to provide drug candidates, each of which appear to have quite distinct profiles and could represent very different opportunities to provide patient benefit.

Download or read book Premature Chromosome Condensation written by P.N. Rao and published by Elsevier. This book was released on 2012-12-02 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: Premature Chromosome Condensation: Application in Basic, Clinical, and Mutation Research emerged from a workshop supported by the International Union against Cancer that reviewed the status of research on premature chromosome condensation and explored future possibilities, not least in relation to cancer. The workshop was held at the Institut für Humangenetik, Freie Universität Berlin, on September 6, 1980. The book begins with a review of the process of premature chromosome condensation. This is followed by separate chapters on the functional and morphological aspects of premature chromosome condensation; the behavior of prematurely condensed chromosomes (PCC) during mitosis in binucleate and multinucleate cells; chromosomes from spermatogenic cells; and micronucleus-derived PCC. Subsequent chapters discuss the application of banding techniques to the study of PCC; the factors involved in the condensation of interphase chromatin into chromosomes; and the induction of premature chromosome condensation in somatic plant cells. This book will be helpful to readers working in basic and applied research or in teaching. These include cytogeneticists, cell biologists, biochemists, and investigators in the field of mutation research.

Download or read book Checkpoint Controls and Targets in Cancer Therapy written by Zahid H. Siddik and published by Springer Science & Business Media. This book was released on 2010-03-12 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: Much work over the last two decades has firmly established that loss of cell cycle checkpoint regulation, and resultant unabated cellular proliferation, is an inherent characteristic of cancer. This loss may occur through aberration in any single component involved in signal transduction pathways that orchestrate checkpoint regulation, which may manifest through either a failure to activate the checkpoint or a failure to respond to the activated checkpoint. In normal cells, checkpoint pathways are activated when genetic or cellular homeostasis is compromised, and signals are then transduced to re-stabilize homeostasis, and, failing this, to activate the apoptotic machinery to induce a cellular suicidal response. This implies that both survival and cell death pathways are induced following checkpoint activation, and that the final decision is dependant on the net result of integrating the two sets of signals. It is intriguing that checkpoint pathways are also critical in cancer therapy to provide an apoptotic stimulus when cellular damage induced by the therapeutic agent is detected by the sensor system. Therefore, it is not surprising that failure in pro-survival checkpoint response will render tumor cells hypersensitive to cytotoxics and, conversely, failure in pro-apoptotic checkpoint response will induce genetic instability and/or therapeutic resistance. Understanding the intricacies of checkpoint response is, therefore, central to the design of therapeutic regimen that will enhance antitumor effects. Although early versions of this design entail combination of cytotoxic agents with cell cycle or checkpoint inhibitors, a greater understanding of the concepts could make such combinations clinically more effective. The contributions in this book will consolidate the current state of knowledge on checkpoint responses that may lay the foundation for hypothesis-driven rational approaches in advancing the management of cancer. The immediate attraction of the book to the scientific community is that it represents a timely opportunity to build upon existing concepts of checkpoints to expand our understanding of the inner workings of the critical checkpoint machinery. The present understanding has provided ample appreciation that response to checkpoint activation is manifested through coordinated inhibition of cyclin-dependent kinase (CDK) complexes in G1, S and/or the G2 phase in order to arrest the cell cycle. Kinase inhibition can occur through several mechanisms, including inhibitory phosphorylation of CDK, destruction of the cognate cyclins, and recruitment of CDK inhibitors from the INK and WAF1/CIP1 families. However, the wealth of information from recent discoveries needs to be examined critically to consolidate our conceptual knowledge of checkpoints. At the same time, there is acute awareness in the diversity of checkpoint response between cytotoxic agents, and this serves as a reminder of the magnitude of complexity that is inherent in checkpoint regulation. This volume is intended to bring the cancer research community closer toward an improved understanding of this regulation, how checkpoint abnormalities can impact negatively on cancer therapy, and emerging strategies to target checkpoint response as a therapeutic end-point.

Download or read book Increasing the Therapeutic Ratio of Radiotherapy written by Philip J. Tofilon and published by Springer. This book was released on 2016-11-21 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current cancer therapies are focused on three general strategies: modifying intrinsic radiosensitivity via molecular targeting, manipulating microenvironmental factors to enhance tumor susceptibility to radiation, and improving delivery of radiation to critical tumor locations while sparing normal tissues. The goal of this volume is to describe a number of promising approaches corresponding to each strategy. In general, research in radiation oncology tends to be siloed into fundamental biology, physics or treatment delivery. The strategies for improving therapeutic ratio encompassed in this book will involve each of these components of radiation oncology. Thus, they will illustrate the variety of disparate approaches available for potentially improving the efficacy of radiotherapy, which may then stimulate discussion across disciplines and foster further translational investigations. Although a goal of each chapter will be to highlight advances within an approach, of equal importance will be the delineation of barriers to successful clinical application and how to overcome or minimize such impediments. Along these lines, because therapeutic ratio incorporates both tumor and normal tissue radio response, a point of emphasis will be the mechanistic rationale for selectively modifying tumor (sensitization) or normal cells (protection). Finally, whereas the literature is replete with studies describing potential targets/strategies for increasing the therapeutic ratio for radiotherapy, this book will focus on those supported by in vivo data consistent with impending translational application along with those that are already being evaluated in the clinic.

Download or read book Genome Stability written by Igor Kovalchuk and published by Academic Press. This book was released on 2021-07-17 with total page 762 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome Stability: From Virus to Human Application, Second Edition, a volume in the Translational Epigenetics series, explores how various species maintain genome stability and genome diversification in response to environmental factors. Here, across thirty-eight chapters, leading researchers provide a deep analysis of genome stability in DNA/RNA viruses, prokaryotes, single cell eukaryotes, lower multicellular eukaryotes, and mammals, examining how epigenetic factors contribute to genome stability and how these species pass memories of encounters to progeny. Topics also include major DNA repair mechanisms, the role of chromatin in genome stability, human diseases associated with genome instability, and genome stability in response to aging. This second edition has been fully revised to address evolving research trends, including CRISPRs/Cas9 genome editing; conventional versus transgenic genome instability; breeding and genetic diseases associated with abnormal DNA repair; RNA and extrachromosomal DNA; cloning, stem cells, and embryo development; programmed genome instability; and conserved and divergent features of repair. This volume is an essential resource for geneticists, epigeneticists, and molecular biologists who are looking to gain a deeper understanding of this rapidly expanding field, and can also be of great use to advanced students who are looking to gain additional expertise in genome stability. - A deep analysis of genome stability research from various kingdoms, including epigenetics and transgenerational effects - Provides comprehensive coverage of mechanisms utilized by different organisms to maintain genomic stability - Contains applications of genome instability research and outcomes for human disease - Features all-new chapters on evolving areas of genome stability research, including CRISPRs/Cas9 genome editing, RNA and extrachromosomal DNA, programmed genome instability, and conserved and divergent features of repair

Download or read book DNA Repair in Cancer Therapy written by Mark R. Kelley and published by Academic Press. This book was released on 2011-09-12 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mark R. Kelley

Download or read book DNA Replication written by Hisao Masai and published by Springer. This book was released on 2018-01-22 with total page 581 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews the latest trends and future directions of DNA replication research. The contents reflect upon the principles that have been established through the genetic and enzymatic studies of bacterial, viral, and cellular replication during the past decades. The book begins with a historical overview of the studies on eukaryotic DNA replication by Professor Thomas Kelly, a pioneer of the field. The following chapters include genome-wide studies of replication origins and initiation factor binding, as well as the timing of DNA replications, mechanisms of initiation, DNA chain elongation and termination of DNA replication, the structural basis of functions of protein complexes responsible for execution of DNA replication, cell cycle-dependent regulation of DNA replication, the nature of replication stress and cells’ strategy to deal with the stress, and finally how all these phenomena are interconnected to genome instability and development of various diseases. By reviewing the existing concepts ranging from the old principles to the newest ideas, the book gives readers an opportunity to learn how the classical replication principles are now being modified and new concepts are being generated to explain how genome DNA replication is achieved with such high adaptability and plasticity. With the development of new methods including cryoelectron microscopy analyses of huge protein complexes, single molecular analyses of initiation and elongation of DNA replication, and total reconstitution of eukaryotic DNA replication with purified factors, the field is enjoying one of its most exciting moments, and this highly timely book conveys that excitement to all interested readers.