Systems Biology of Alzheimer's Disease, 1st ed. 2016
Methods in Molecular Biology Series, Vol. 1303

Alzheimer?s disease (AD) and many other neurodegenerative disorders are multifactorial in nature, involving a combination of genomic, epigenomic, network dynamic and environmental factors. A proper investigation requires new integrative Systems Biology approaches, at both the experimental and computational level. The interplay of disease mechanisms and homeostatic networks will underlie the time of onset and rate of progression of the disease.

This book addresses such an integrated approach to AD. It aims to present Systems Biology, including both experimental and computational approaches, as a new strategy for the study of AD and other multifactorial diseases, with the hope that the results will translate into more effective diagnosis and treatment, as well as improved public health policies.

Written for the highly successful Methods in Molecular Biology series, practical and cutting-edge, Systems Biology of Alzheimer?s Disease is intended for post-graduate students, post-doctoral researchers and experts in different fields with an interest in comprehensive Systems Biology strategies applicable to AD and other complex multifactorial diseases (including other neurodegenerative diseases and cancers). This book aims to complement other excellent volumes and monographs on AD that cover fundamental, physiological or medical aspects of the disease.

Part I: Systems Biology of Multifactorial Diseases: Alzheimer’s Disease

1. Alzheimer’s as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks

            Juan I. Castrillo and Stephen G. Oliver

2. Application of Systems Theory in Longitudinal Studies on the Origin and Progression of Alzheimer’s Disease

            Simone Lista, Zaven S. Khachaturian, Dan Rujescu, Francesco Garaci, Bruno Dubois, and Harald Hampel

Part II: Alzheimer’s Disease: Main Underlying Pathways and Networks

3. The APP Proteolytic System and Its Interactions with Dynamic Networks in Alzheimer’s Disease

            Sally Hunter, Steven Martin, and Carol Brayne

4. Effects of Mild and Severe Oxidative Stress on BACE1 Expression and APP Amyloidogenic Processing

            Jiangli Tan, Qiao-Xin Li,  and Genevieve Evin

5. Advanced Assay Monitoring APP-Carboxyl-Terminal Fragments as Markers of APP Processing in Alzheimer Disease Mouse Models

            Ana García-Osta and Mar Cuadrado-Tejedor

6. Advanced Optical Super-Resolution Method and Techniques for the Study of β-Amyloid Aggregation In Vitro and In Vivo

            Dorothea Pinotsi, Gabriele S. Kaminski Schierle, and Clemens F. Kaminski

7. Protocols for Monitoring the Development of Tau Pathology in Alzheimer’s Disease

            Alberto Rábano, Raquel Cuadros, Paula Merino

8. LC3-II Tagging and Western Blotting for Monitoring Autophagic Activity in Mammalian Cells

            Anne Streeter, Fiona M. Menzies, and David C. Rubinsztein

9. Advanced Mitochondrial Respiration Assay for Evaluation of Mitochondrial Dysfunction in Alzheimer’s Disease

            Amandine Grimm, Karen Schmitt, and Anne Eckert

10. Analysis of Microglial Proliferation in Alzheimer’s Disease

            Diego Gomez-Nicola and V. Hugh Perry

Part III: Comprehensive Disease Models Recapitulating Alzheimer’s Disease Features: From Cellular Models to Human

11. Yeast as a Model for Alzheimer’s Disease: Latest Studies and Advanced Strategies

            Mathias Verduyckt, Hélène Vignaud, Tine Bynens, Jeff Van den Brande, Vanessa Franssens, Christophe Cullin, and Joris Winderickx

12. Yeast as a Model for Studies on Aβ Aggregation Toxicity in Alzheimer’s Disease, Autophagic Responses, and Drug Screening

            Afsaneh Porzoor and Ian Macreadie

13. Drosophila melanogaster as a Model for Studies on the Early Stages of Alzheimer’s Disease

            Jung Yeon Lim, Stanislav Ott, and Damian C. Crowther

14. Chronic Mild Stress Assay Leading to Early Onset and Propagation of Alzheimer’s Disease Phenotype in Mouse Models

            Mar Cuadrado-Tejedor and Ana García-Osta

15. Gene Expression Studies on Human Trisomy 21 iPSCs and Neurons: Towards Mechanisms Underlying Down’s Syndrome and Early Alzheimer’s Disease-Like Pathologies

            Jason P. Weick, Huining Kang, George F. Bonadurer III, and Anita Bhattacharyya

16. Cortical Differentiation of Human Pluripotent Cells for In Vitro Modeling of Alzheimer’s Disease

            Nathalie G. Saurat, Frederick J. Livesey, and Steven Moore

Part IV: Experimental Systems Biology: Next Generation Molecular and High-Throughput Methods for the Study of Disease Susceptibility and Networks Dynamics Interplay in Complex Diseases

17. Next Generation Sequencing in Alzheimer’s Disease

            Lars Bertram

18. Pooled-DNA Sequencing for Elucidating New Genomic Risk Factors, Rare Variants Underlying Alzheimer’s Disease

            Sheng Chih Jin, Bruno A. Benitez, Yuetiva Deming, and Carlos Cruchaga

19. New Genome-Wide Methods for Elucidation of Candidate Copy Number Variations (CNVs) Contributing to Alzheimer’s Disease Heritability

            Kinga Szigeti

20. RNA-Sequencing to Elucidate Early Patterns of Dysregulation Underlying the Onset of Alzheimer’s Disease

            Bei Jun Chen, James D. Mills, Caroline Janitz, and Michael Janitz

21. Systems Biology Approaches to the Study of Biological Networ

            Wera Roth, David Hecker, and Eugenio Fava

22. The Emerging Role of Metalloproteomics in Alzheimer’s Disease Research

            Dominic J. Hare, Alan Rembach, and Blaine R. Roberts

23. Redox Proteomics in Human Biofluids: Sample Preparation, Separation and Immunochemical Tagging for Analysis of Protein Oxidation

            Fabio Di Domenico, Marzia Perluigi, and D. Allan Butterfield

24. Advanced Shotgun Lipidomics for Characterization of Altered Lipid Patterns in Neurodegenerative Diseases and Brain Injury

            Miao Wang and Xianlin Han

25. AlzPathway, an Updated Map of Curated Signaling Pathways: Towards Deciphering Alzheimer’s Disease Pathogenesis

            Soichi Ogishima, Satoru Mizuno, Masataka Kikuchi, Akinori Miyashita, Ryozo Kuwano, Hiroshi Tanaka, and Jun Nakaya

Part V: Computational Systems Biology, Network biology: Next Generation Computational and Integrative Network Biology Approaches for the Study of Modules, Network Dynamics, and Their Interplay in Complex Diseases

26. A Computational Network Biology Approach to Uncover Novel Genes Related to Alzheimer’s Disease

            Andreas Zanzoni

27. Network Approaches to the Understanding of Alzheimer’s Disease: From Model Organisms to Humans

            Justin Yerbury, Dan Bean, and Giorgio Favrin

28. Characterization of Genetic Networks Associated with Alzheimer's Disease

            Bin Zhang, Linh Tran, Valur Emilsson, and Jun Zhu

29. Network-Based Analysis for Uncovering Mechanisms Underlying Alzheimer’s Disease

            Masataka Kikuchi, Soichi Ogishima, Akinori Miyashita, Ryozo Kuwano, Jun Nakaya, and Hiroshi Tanaka

30. The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease Progression

            Anthony Gitter and Ziv Bar-Joseph

Part VI: Systems Biology of Alzheimer’s Disease in Practice: From Systems Biology to Early Diagnostics and Systems Medicine

31. Advanced Neuroimaging Methods Towards Characterization of Early Stages of Alzheimer’s Disease

            Jorge Sepulcre and Joseph C. Masdeu

32. Plasma Proteomics Biomarkers in Alzheimer's Disease: Latest Advances and Challenges

            Robert Perneczky and Liang-Hao Guo

33. A Practical Guide For Exploring Opportunities of Repurposing Drugs for CNS Diseases in Systems Biology

            Hongkang Mei, Gang Feng, Jason Zhu, Simon Lin, Yang Qiu, Yue Wang, and Tian Xia

Stephen G. Oliver

Department of Biochemistry & Cambridge Systems Biology Centre

University of Cambridge

Cambridge UK

steve.oliver@bioc.cam.ac.uk

Juan I. Castrillo

Department of Biochemistry & Cambridge Systems Biology Centre

University of Cambridge

Cambridge UK

Genetadi Biotech S.L. Praque

Tecnologico de Bizkaia

Derio, Bizkaia, Spain

jic28@genetadi.com

Includes cutting-edge systems biology methods and protocols for neuroscientific study

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts