Download or read book Systems Biology and Single cell Analysis of Cancer Metabolism and its Role in Cancer Emergent Properties written by Dongya Jia and published by Frontiers Media SA. This book was released on 2023-06-21 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Systems Biology and the Challenge of Deciphering the Metabolic Mechanisms Underlying Cancer written by Osbaldo Resendis-Antonio and published by Frontiers Media SA. This book was released on 2017-11-23 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the discovery of the Warburg effect in the 1920s cancer has been tightly associated with the genetic and metabolic state of the cell. One of the hallmarks of cancer is the alteration of the cellular metabolism in order to promote proliferation and undermine cellular defense mechanisms such as apoptosis or detection by the immune system. However, the strategies by which this is achieved in different cancers and sometimes even in different patients of the same cancer is very heterogeneous, which hinders the design of general treatment options. Recently, there has been an ongoing effort to study this phenomenon on a genomic scale in order to understand the causality underlying the disease. Hence, current “omics” technologies have contributed to identify and monitor different biological pieces at different biological levels, such as genes, proteins or metabolites. These technological capacities have provided us with vast amounts of clinical data where a single patient may often give rise to various tissue samples, each of them being characterized in detail by genomescale data on the sequence, expression, proteome and metabolome level. Data with such detail poses the imminent problem of extracting meaningful interpretations and translating them into specific treatment options. To this purpose, Systems Biology provides a set of promising computational tools in order to decipher the mechanisms driving a healthy cell’s metabolism into a cancerous one. However, this enterprise requires bridging the gap between large data resources, mathematical analysis and modeling specifically designed to work with the available data. This is by no means trivial and requires high levels of communication and adaptation between the experimental and theoretical side of research.

Download or read book Tumor Cell Metabolism written by Sybille Mazurek and published by Springer. This book was released on 2015-01-19 with total page 373 pages. Available in PDF, EPUB and Kindle. Book excerpt: The four sections of this book cover cell and molecular biology of tumor metabolism, metabolites, tumor microenvironment, diagnostics and epigenetics. Written by international experts, it provides a thorough insight into and understanding of tumor cell metabolism and its role in tumor biology. The book is intended for scientists in cancer cell and molecular biology, scientists in drug and diagnostic development, as well as for clinicians and oncologists.

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 Systems Biology and the Challenge of Deciphering the Metabolic Mechanisms Underlying Cancer written by and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the discovery of the Warburg effect in the 1920s cancer has been tightly associated with the genetic and metabolic state of the cell. One of the hallmarks of cancer is the alteration of the cellular metabolism in order to promote proliferation and undermine cellular defense mechanisms such as apoptosis or detection by the immune system. However, the strategies by which this is achieved in different cancers and sometimes even in different patients of the same cancer is very heterogeneous, which hinders the design of general treatment options.Recently, there has been an ongoing effort to study this phenomenon on a genomic scale in order to understand the causality underlying the disease. Hence, current "omics" technologies have contributed to identify and monitor different biological pieces at different biological levels, such as genes, proteins or metabolites. These technological capacities have provided us with vast amounts of clinical data where a single patient may often give rise to various tissue samples, each of them being characterized in detail by genomescale data on the sequence, expression, proteome and metabolome level. Data with such detail poses the imminent problem of extracting meaningful interpretations and translating them into specific treatment options. To this purpose, Systems Biology provides a set of promising computational tools in order to decipher the mechanisms driving a healthy cell's metabolism into a cancerous one. However, this enterprise requires bridging the gap between large data resources, mathematical analysis and modeling specifically designed to work with the available data. This is by no means trivial and requires high levels of communication and adaptation between the experimental and theoretical side of research.

Download or read book Redox and Metabolic Circuits in Cancer written by Salvatore Rizza and published by Frontiers Media SA. This book was released on 2018-12-21 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Living cells require a constant supply of energy for the orchestration of a variety of biological processes in fluctuating environmental conditions. In heterotrophic organisms, energy mainly derives from the oxidation of carbohydrates and lipids, whose chemical bonds breakdown allows electrons to generate ATP and to provide reducing equivalents needed to restore the antioxidant systems and prevent from damage induced by reactive oxygen and nitric oxide (NO)-derived species (ROS and RNS). Studies of the last two decades have highlighted that cancer cells reprogram the metabolic circuitries in order to sustain their high growth rate, invade other tissues, and escape death. Therefore, this broad metabolic reorganization is mandatory for neoplastic growth, allowing the generation of adequate amounts of ATP and metabolites, as well as the optimization of redox homeostasis in the changeable environmental conditions of the tumor mass. Among these, ROS, as well as NO and RNS, which are produced at high extent in the tumor microenvironment or intracellularly, have been demonstrated acting as positive modulators of cell growth and frequently associated with malignant phenotype. Metabolic changes are also emerging as primary drivers of neoplastic onset and growth, and alterations of mitochondrial metabolism and homeostasis are emerging as pivotal in driving tumorigenesis. Targeting the metabolic rewiring, as well as affecting the balance between production and scavenging of ROS and NO-derived species, which underpin cancer growth, opens the possibility of finding selective and effective anti-neoplastic approaches, and new compounds affecting metabolic and/or redox adaptation of cancer cells are emerging as promising chemotherapeutic tools. In this Research Topic we have elaborated on all these aspects and provided our contribution to this increasingly growing field of research with new results, opinions and general overviews about the extraordinary plasticity of cancer cells to change metabolism and redox homeostasis in order to overcome the adverse conditions and sustain their “individualistic” behavior under a teleonomic viewpoint.

Download or read book Understanding Cancer from a Systems Biology Point of View written by Irina Kareva and published by Academic Press. This book was released on 2018-02-07 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding Cancer from a Systems Biology Point of View: From Observation to Theory and Back starts with a basic question, why do we sometimes observe accelerated metastatic growth after resection of primary tumors? Next, it helps readers understand the systemic nature of cancer and how it affects treatment approaches and decisions. The book puts together aspects of cancer that many readers have most likely never combined, using unfamiliar, novel methods. It is a valuable resource for cancer researchers, cancer biologists, mathematicians and members of the biomedical field who are interested in applying systems biology methodologies for understanding and treating cancer. Explains the systemic nature of cancer and how it affects decisions on treatment Brings a variety of methods together, showing, in detail, the logical approach to finding answers to complex questions Discusses the theoretical underpinnings of cancer as a systemic disease, providing the reader with valuable information on applicable cases

Download or read book Correlation Based Network Analysis of Cancer Metabolism written by Emily G. Armitage and published by . This book was released on 2014-05-31 with total page 68 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Cancer as a Metabolic Disease written by Thomas Seyfried and published by John Wiley & Sons. This book was released on 2012-05-18 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book addresses controversies related to the origins of cancer and provides solutions to cancer management and prevention. It expands upon Otto Warburg's well-known theory that all cancer is a disease of energy metabolism. However, Warburg did not link his theory to the "hallmarks of cancer" and thus his theory was discredited. This book aims to provide evidence, through case studies, that cancer is primarily a metabolic disease requring metabolic solutions for its management and prevention. Support for this position is derived from critical assessment of current cancer theories. Brain cancer case studies are presented as a proof of principle for metabolic solutions to disease management, but similarities are drawn to other types of cancer, including breast and colon, due to the same cellular mutations that they demonstrate.

Download or read book Novel Strategies to Investigate and Therapeutically Modulate Cancer Metabolism written by Woosuk Kim and published by . This book was released on 2018 with total page 134 pages. Available in PDF, EPUB and Kindle. Book excerpt: In response to increased anabolic demands to support their survival and growth, cancer cells rewire cellular signaling and metabolic networks. While analysis of this rewiring can reveal vulnerabilities within cancers, it is becoming clear that more profound understandings of fundamental cancer biology are required for the successful therapeutic exploitation of cancer signaling and metabolism, two very complex and highly-regulated systems with multiple pathways contributing to their plasticity and robustness. This thesis is the product of translational research efforts focused upon gaining a better understanding of fundamental aspects of cancer biology. The goals of the thesis are to 1) acquire novel insights of cancer biology to more precisely design therapeutic interventions to target cancers, more specifically pancreatic ductal adenocarcinoma (PDAC), one of most deadly cancers, and to 2) develop diagnostic tools that enable better characterization of metabolic characteristics of cancers. Chapter 1 concerns the development of a clinically-applicable positron emission tomography (PET) probe for monitoring nucleotide metabolism at the whole-body level in a non-invasive way. This study makes us think about biology across different scales, from molecular to whole-body levels. In Chapter 2, the synthetic lethality screening tethered to chloroquine, an inhibitor of lysosome-dependent recycling pathways, which PDAC cells rely on to generate metabolic substrates is performed. The findings reveal that the inhibition of lysosomal recycling makes PDAC cells rely on replication stress response pathway for the survival due to impaired de novo nucleotide biosynthesis. In chapter 3, I use multiple models of KRAS G12C mutant PDAC to profile the adaptive resistance mechanisms within cellular signaling and metabolic networks which arise from direct inhibition of mutant KRAS, the oncogenic driver of PDAC. This was followed by mapping the impacts of co-inhibition of oncogenic KRAS and the identified adaptive resistance mechanisms. Metabolomic analyses reveal metabolic vulnerabilities induced by co-inhibition of oncogenic KRAS and the adaptive resistance. In the final chapter, I summarize ongoing projects and future directions that concern fundamental biology of PDAC metabolism.

Download or read book A Systems Biology Approach to Cancer Metabolism written by Marina Wright Muelas and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Computational Approaches for Understanding One carbon Metabolism in Cancer written by Mahya Mehrmohamadi and published by . This book was released on 2017 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cancer metabolism is an emerging research area in cancer biology and therapeutics. One of the major metabolic pathways known to play important roles in the pathogenesis of cancer is one-carbon (1-C) metabolism. 1-C metabolism integrates the status of many dietary nutrients as inputs, and in turn regulates a variety of cellular processes including de novo nucleotide synthesis, lipid metabolism, protein biosynthesis, redox metabolism, transsulfuration, and epigenetics. As the regulation of these cellular processes is critical to cells, the tuning of the activity of 1-C metabolism plays important roles in cancer. Previous studies have established implications of genetic and dietary perturbations of multiple components of 1-C metabolism in human cancers. However, the heterogeneity among cancer types and subtypes with respect to the usage and flux distribution of 1-C metabolism has not been systematically quantified. There remain great potentials in deciphering how 1-C metabolism plays different roles in different human cancers, especially since this metabolic pathway is targeted by a number of the existing antimetabolite chemotherapeutic agents. In this dissertation, I quantitatively characterize various aspects of 1-C metabolism across human cancers. I first investigate the between-cancer-type variation in the usage of serine by 1-C metabolism using flux distribution analyses and find substantial heterogeneity. I also show that a common feature across cancers is correlated activation of nucleotide and redox metabolism. Next I assess the link between 1-C metabolism and DNA methylation using computational modeling and machine-learning. I find significant contribution from particular enzymes within 1-C metabolism - such as methionine adenosyltransferases - in explaining the within- cancer-type (inter-individual) variation in DNA methylation. My results provide evidence that misregulation of 1-C metabolism is at least in part responsible for disrupted DNA methylation profiles in tumors leading to epigenetic instability and higher malignancy. Given evidence for the role of 1-C metabolism and the methionine cycle in methylation dynamics, I next evaluate the potential for dietary intervention using the amino acid methionine. To this end, I model human serum methionine levels and quantify the contribution of various factors in determining the concentration of methionine. I discover that dietary factors could together explain nearly 30% of overall variation in methionine concentrations, and also provide evidence that the relationship between 1-C metabolism and methylation exists at physiological concentrations of methionine. Finally, I use a novel approach to identify gene expression markers of tumor response to 5-FU and Gemcitabine - two of the commonly used antimetabolite chemotherapies that target enzymes in 1-C metabolism. I discover that response to these agents is to a large degree determined by the metabolic state of tumors and the expression levels of specific target pathways of each of these agents. Together, my findings provide quantitative information about the heterogeneity among tumors with respect to the usage of 1-C metabolism, and delineate some of the ways this information can be translated into clinical decision- making. ...

Download or read book An Integrated Systems Biology Approach to Better Understand Cancer written by David (Wei) Dai and published by . This book was released on 2019 with total page 233 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cancer is an umbrella term that encompasses a collection of related diseases. In all types of cancer, as cells become unregulated, they begin to divide uncontrollably and spread into surrounding tissues. From early to late stages of disease progression, there are many alterations that occur and many criteria that must be met for cancer to proliferate uncontrollable, resist cell death, avoid the immune system, and metastasize. Targeted therapy have been developed for a wide range of dysregulated cancer pathways using different modalities and mechanism of actions. However, due to the diversity of cancer, the same treatment that may be effective for one type of cancer may not be responsive on another. Furthermore, patients may carry resistance forms of the disease. To alleviate this, new strategies have been developed to target specific mutations of known dysregulated proteins and to use combination therapies that target multiple pathways. However, both methods require vast amount of knowledge on the biological interactions and mechanism of actions that takes place within the cell. To address this knowledge gap, we believe that the metabolism can be used as a tool to better understand the dysregulations of signaling and gene expression. There is a great opportunity to study the system as a whole to gain key insights for combination therapies that target different regulatory pathways, such as the metabolism and signaling. In this work, we leveraged our current understanding of signaling transduction, transcription factor, and metabolic networks to develop an integrated systems biology approach to quantitatively unravel the mechanisms that regulate cancer. Ultimately, we were able to establish a computational model that incorporated mechanistic understanding of multiple layers of cellular decision making. We believe this work will be useful in the development and evaluation of new combination therapy across all form of cancers.

Download or read book The Heterogeneity of Cancer Metabolism written by Anne Le and published by Springer. This book was released on 2018-06-26 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic alterations in cancer, in addition to being the fundamental drivers of tumorigenesis, can give rise to a variety of metabolic adaptations that allow cancer cells to survive and proliferate in diverse tumor microenvironments. This metabolic flexibility is different from normal cellular metabolic processes and leads to heterogeneity in cancer metabolism within the same cancer type or even within the same tumor. In this book, we delve into the complexity and diversity of cancer metabolism, and highlight how understanding the heterogeneity of cancer metabolism is fundamental to the development of effective metabolism-based therapeutic strategies. Deciphering how cancer cells utilize various nutrient resources will enable clinicians and researchers to pair specific chemotherapeutic agents with patients who are most likely to respond with positive outcomes, allowing for more cost-effective and personalized cancer therapeutic strategies.

Download or read book The Science and Applications of Synthetic and Systems Biology written by Institute of Medicine and published by National Academies Press. This book was released on 2011-12-30 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

Download or read book Metabolism in Cancer written by Thorsten Cramer and published by Springer. This book was released on 2016-08-24 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook presents concise chapters written by internationally respected experts on various important aspects of cancer-associated metabolism, offering a comprehensive overview of the central features of this exciting research field. The discovery that tumor cells display characteristic alterations of metabolic pathways has significantly changed our understanding of cancer: while the first description of tumor-specific changes in cellular energetics was published more than 90 years ago, the causal significance of this observation for the pathogenesis of cancer was only discovered in the post-genome era. The first 10 years of the twenty-first century were characterized by rapid advances in our grasp of the functional role of cancer-specific metabolism as well as the underlying molecular pathways. Various unanticipated interrelations between metabolic alterations and cancer-driving pathways were identified and currently await translation into diagnostic and therapeutic applications. Yet the speed, quantity, and complexity of these new discoveries make it difficult for researchers to keep up to date with the latest developments, an issue this book helps to remedy.

Download or read book Analysis Of Biological Systems written by Corrado Priami and published by World Scientific. This book was released on 2015-01-29 with total page 431 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modeling is fast becoming fundamental to understanding the processes that define biological systems. High-throughput technologies are producing increasing quantities of data that require an ever-expanding toolset for their effective analysis and interpretation. Analysis of high-throughput data in the context of a molecular interaction network is particularly informative as it has the potential to reveal the most relevant network modules with respect to a phenotype or biological process of interest.Analysis of Biological Systems collects classical material on analysis, modeling and simulation, thereby acting as a unique point of reference. The joint application of statistical techniques to extract knowledge from big data and map it into mechanistic models is a current challenge of the field, and the reader will learn how to build and use models even if they have no computing or math background. An in-depth analysis of the currently available technologies, and a comparison between them, is also included. Unlike other reference books, this in-depth analysis is extended even to the field of language-based modeling. The overall result is an indispensable, self-contained and systematic approach to a rapidly expanding field of science.