A Network-Based Perspective in Alzheimer's Disease: Current State and an Integrative Framework

A major rise in the prevalence and impact of Alzheimer's disease (AD) is projected in the coming decades, resulting from increasing life expectancy, thus leading to substantially increased healthcare costs. While brain disfunctions at the time of diagnosis are irreversible, it is widely accepted that AD pathology develops decades before clinical symptoms onset. If incipient processes can be detected early in the disease progression, prospective intervention for preventing or slowing the disease can be designed. Currently, there is no noninvasive biomarker available to detect and monitor early stages of disease progression. The complex etiology of AD warrants a systems-based approach supporting the integration of multimodal and multilevel data, while network-based modeling provides the scaffolding for methods revealing complex systems-level disruptions initiated by the disease. In this work, we review current state-of-the-art, focusing on network-based biomarkers at molecular and brain functional connectivity levels. Particular emphasis is placed on outlining recent trends, which highlight the functional importance of modular substructures in molecular and connectivity networks and their potential biomarker value. Our perspective is rooted in network medicine and summarizes the pipelines for identifying network-based biomarkers, as well as the benefits of integrating genotype and brain phenotype information for a comprehensively noninvasive approach in the early diagnosis of AD. Finally, we propose a framework for integrating knowledge from molecular and brain connectivity levels, which has the potential to enable noninvasive diagnosis, provide support for monitoring therapies, and help understand heretofore unexamined deep level relations between genotype and brain phenotype.

[1]  Weixiong Zhang,et al.  Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases , 2008, Genome Biology.

[2]  Katherine E. Prater,et al.  Functional connectivity tracks clinical deterioration in Alzheimer's disease , 2012, Neurobiology of Aging.

[3]  Alzheimer’s Association 2017 Alzheimer's disease facts and figures , 2017, Alzheimer's & Dementia.

[4]  Yong He,et al.  Identifying and Mapping Connectivity Patterns of Brain Network Hubs in Alzheimer's Disease. , 2015, Cerebral cortex.

[5]  Jan Baumbach,et al.  Syddansk Universitet De novo pathway-based biomarker identification , 2017 .

[6]  Masayuki Satoh,et al.  Plasma protein profiling for potential biomarkers in the early diagnosis of Alzheimer’s disease , 2017, Neurological research.

[7]  Jes Olesen,et al.  The Cost of Brain Diseases: A Burden or a Challenge? , 2014, Neuron.

[8]  K. Blennow,et al.  Amyloid biomarkers in Alzheimer's disease. , 2015, Trends in pharmacological sciences.

[9]  Timothy O. Laumann,et al.  Functional Network Organization of the Human Brain , 2011, Neuron.

[10]  Danielle S. Bassett,et al.  Choosing Wavelet Methods, Filters, and Lengths for Functional Brain Network Construction , 2015, PloS one.

[11]  Jinglong Wu,et al.  Network-Based Biomarkers in Alzheimer’s Disease: Review and Future Directions , 2014, Front. Aging Neurosci..

[12]  Majnu John,et al.  Graph analysis of structural brain networks in Alzheimer’s disease: beyond small world properties , 2016, Brain Structure and Function.

[13]  W. M. van der Flier,et al.  CSF biomarkers and incipient Alzheimer disease in patients with mild cognitive impairment. , 2009, JAMA.

[14]  Limsoon Wong,et al.  Why Batch Effects Matter in Omics Data, and How to Avoid Them. , 2017, Trends in biotechnology.

[15]  M. Breakspear,et al.  The connectomics of brain disorders , 2015, Nature Reviews Neuroscience.

[16]  Dinggang Shen,et al.  Deep Learning-Based Feature Representation for AD/MCI Classification , 2013, MICCAI.

[17]  Athanasios K. Tsakalidis,et al.  CHRONOS: a time-varying method for microRNA-mediated subpathway enrichment analysis , 2016, Bioinform..

[18]  Gabriele Sales,et al.  graphite - a Bioconductor package to convert pathway topology to gene network , 2012, BMC Bioinformatics.

[19]  O. Sporns,et al.  Network neuroscience , 2017, Nature Neuroscience.

[20]  K. Robasky,et al.  The role of replicates for error mitigation in next-generation sequencing , 2013, Nature Reviews Genetics.

[21]  Atul J. Butte,et al.  Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges , 2012, PLoS Comput. Biol..

[22]  R. Nagele,et al.  Diagnosis of Alzheimer's Disease Based on Disease-Specific Autoantibody Profiles in Human Sera , 2011, PloS one.

[23]  Juhan Nam,et al.  Multimodal Deep Learning , 2011, ICML.

[24]  Solve Sæbø,et al.  A gene expression pattern in blood for the early detection of Alzheimer's disease. , 2011, Journal of Alzheimer's disease : JAD.

[25]  M E J Newman,et al.  Finding and evaluating community structure in networks. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[26]  John Bond,et al.  The worldwide economic impact of dementia 2010 , 2013, Alzheimer's & Dementia.

[27]  Gang Li,et al.  Topographical Information-Based High-Order Functional Connectivity and Its Application in Abnormality Detection for Mild Cognitive Impairment. , 2016, Journal of Alzheimer's disease : JAD.

[28]  Zhi-jun Zhang,et al.  Modular reorganization of brain resting state networks and its independent validation in Alzheimer's disease patients , 2013, Front. Hum. Neurosci..

[29]  Wei Niu,et al.  Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data , 2011, PLoS Comput. Biol..

[30]  Antonio Greco,et al.  Potential neuroimaging biomarkers of pathologic brain changes in Mild Cognitive Impairment and Alzheimer’s disease: a systematic review , 2016, BMC Geriatrics.

[31]  H. Matsuda MRI morphometry in Alzheimer’s disease , 2016, Ageing Research Reviews.

[32]  Joaquín Dopazo,et al.  Understanding disease mechanisms with models of signaling pathway activities , 2014, BMC Systems Biology.

[33]  Daniel H. Geschwind,et al.  Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders , 2015, Nature Reviews Genetics.

[34]  L. Tran,et al.  Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease , 2013, Cell.

[35]  Athanasios Alexiou,et al.  Biomarkers for Alzheimer’s Disease Diagnosis , 2017, Current Alzheimer research.

[36]  Liang Chen,et al.  Multi-modal classification of Alzheimer's disease using nonlinear graph fusion , 2017, Pattern Recognit..

[37]  Sidong Liu,et al.  Multimodal Neuroimaging Feature Learning for Multiclass Diagnosis of Alzheimer's Disease , 2015, IEEE Transactions on Biomedical Engineering.

[38]  Fuhai Song,et al.  AlzBase: an Integrative Database for Gene Dysregulation in Alzheimer’s Disease , 2014, Molecular Neurobiology.

[39]  Anastasios Bezerianos,et al.  Disrupted Functional Brain Connectivity and Its Association to Structural Connectivity in Amnestic Mild Cognitive Impairment and Alzheimer’s Disease , 2014, PloS one.

[40]  Athanasios K. Tsakalidis,et al.  Identifying miRNA-mediated signaling subpathways by integrating paired miRNA/mRNA expression data with pathway topology , 2015, 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).

[41]  Zheng Guo,et al.  Identification of molecular alterations in leukocytes from gene expression profiles of peripheral whole blood of Alzheimer’s disease , 2017, Scientific Reports.

[42]  Francesca Baglio,et al.  High-Dimensional ICA Analysis Detects Within-Network Functional Connectivity Damage of Default-Mode and Sensory-Motor Networks in Alzheimer’s Disease , 2015, Front. Hum. Neurosci..

[43]  Xi Chen,et al.  Simulating the Evolution of Functional Brain Networks in Alzheimer’s Disease: Exploring Disease Dynamics from the Perspective of Global Activity , 2016, Scientific Reports.

[44]  Vince D. Calhoun,et al.  Replicability of time-varying connectivity patterns in large resting state fMRI samples , 2017, NeuroImage.

[45]  Kwangsik Nho,et al.  Adult neurogenesis and neurodegenerative diseases: A systems biology perspective , 2017, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

[46]  Michael A. Thomas,et al.  Integrating the Alzheimer's disease proteome and transcriptome: a comprehensive network model of a complex disease. , 2012, Omics : a journal of integrative biology.

[47]  Hongxing Lei,et al.  Characteristic transformation of blood transcriptome in Alzheimer's disease. , 2013, Journal of Alzheimer's disease : JAD.

[48]  Joaquín Dopazo,et al.  A comparison of mechanistic signaling pathway activity analysis methods , 2018, Briefings Bioinform..

[49]  Magda Tsolaki,et al.  A blood gene expression marker of early Alzheimer's disease. , 2013, Journal of Alzheimer's disease : JAD.

[50]  L. Tsai,et al.  The road to restoring neural circuits for the treatment of Alzheimer's disease , 2016, Nature.

[51]  Abbas Babajani-Feremi,et al.  Identifying patients with Alzheimer’s disease using resting-state fMRI and graph theory , 2015, Clinical Neurophysiology.

[52]  R. Nagele,et al.  Diagnosis of Parkinson's Disease Based on Disease-Specific Autoantibody Profiles in Human Sera , 2011, PloS one.

[53]  Seong-Whan Lee,et al.  Hierarchical feature representation and multimodal fusion with deep learning for AD/MCI diagnosis , 2014, NeuroImage.

[54]  Byunghan Lee,et al.  Deep learning in bioinformatics , 2016, Briefings Bioinform..

[55]  A. Barabasi,et al.  Network medicine : a network-based approach to human disease , 2010 .

[56]  Jesse S. Jin,et al.  Identification of Conversion from Mild Cognitive Impairment to Alzheimer's Disease Using Multivariate Predictors , 2011, PloS one.

[57]  Matthias Dehmer Structural Analysis of Complex Networks , 2010 .

[58]  J. Morris,et al.  The Alzheimer's Disease Neuroimaging Initiative 3: Continued innovation for clinical trial improvement , 2017, Alzheimer's & Dementia.

[59]  Weixiong Zhang,et al.  Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks , 2010, BMC Systems Biology.

[60]  Margarita Zachariou,et al.  Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches , 2017, Briefings Bioinform..

[61]  P. Snyder,et al.  Blood-based biomarkers in Alzheimer disease: Current state of the science and a novel collaborative paradigm for advancing from discovery to clinic , 2017, Alzheimer's & Dementia.

[62]  David Meyre,et al.  From big data analysis to personalized medicine for all: challenges and opportunities , 2015, BMC Medical Genomics.

[63]  Xiaohong Cui,et al.  Classification of Alzheimer's Disease, Mild Cognitive Impairment, and Normal Controls With Subnetwork Selection and Graph Kernel Principal Component Analysis Based on Minimum Spanning Tree Brain Functional Network , 2018, Front. Comput. Neurosci..

[64]  Eric Salmon,et al.  Pitfalls and Limitations of PET/CT in Brain Imaging. , 2015, Seminars in nuclear medicine.

[65]  Giorgio Favrin,et al.  Network Approaches to the Understanding of Alzheimer's Disease: From Model Organisms to Humans. , 2016, Methods in molecular biology.

[66]  Winston Haynes,et al.  Differential Expression Analysis for Pathways , 2013, PLoS Comput. Biol..

[67]  J. Trojanowski,et al.  Diagnosis-independent Alzheimer disease biomarker signature in cognitively normal elderly people. , 2010, Archives of neurology.

[68]  Jakub Jończyk,et al.  Therapeutic strategies for Alzheimer’s disease in clinical trials , 2016, Pharmacological reports : PR.

[69]  R. Mayeux,et al.  Review - Part of the Special Issue: Alzheimer's Disease - Amyloid, Tau and Beyond Alzheimer disease: Epidemiology, diagnostic criteria, risk factors and biomarkers , 2014 .

[70]  Dinggang Shen,et al.  Feature Learning and Fusion of Multimodality Neuroimaging and Genetic Data for Multi-status Dementia Diagnosis , 2017, MLMI@MICCAI.

[71]  Richard F. Betzel,et al.  Modular Brain Networks. , 2016, Annual review of psychology.

[72]  Jörg Menche,et al.  Interactome-based approaches to human disease , 2017 .

[73]  George Vradenburg,et al.  A pivotal moment in Alzheimer’s disease and dementia: how global unity of purpose and action can beat the disease by 2025 , 2015, Expert review of neurotherapeutics.

[74]  S. Horvath,et al.  Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways , 2010, Proceedings of the National Academy of Sciences.

[75]  Gang Chen,et al.  Classification of Alzheimer disease, mild cognitive impairment, and normal cognitive status with large-scale network analysis based on resting-state functional MR imaging. , 2011, Radiology.

[76]  C. Stam,et al.  Alzheimer's disease: connecting findings from graph theoretical studies of brain networks , 2013, Neurobiology of Aging.

[77]  Andreas Zanzoni,et al.  A Computational Network Biology Approach to Uncover Novel Genes Related to Alzheimer's Disease. , 2016, Methods in molecular biology.

[78]  Daoqiang Zhang,et al.  Topological graph kernel on multiple thresholded functional connectivity networks for mild cognitive impairment classification , 2014, Human brain mapping.

[79]  Avi Ma'ayan,et al.  Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool , 2013, BMC Bioinformatics.

[80]  P. Mecocci,et al.  Clinical trials and late‐stage drug development for Alzheimer's disease: an appraisal from 1984 to 2014 , 2014, Journal of internal medicine.

[81]  I. Grundke‐Iqbal,et al.  Alzheimer's disease, a multifactorial disorder seeking multitherapies , 2010, Alzheimer's & Dementia.

[82]  Margarita Zachariou,et al.  Integrating multi-source information on a single network to detect disease-related clusters of molecular mechanisms. , 2018, Journal of proteomics.

[83]  Derek K. Jones,et al.  Improving the Reliability of Network Metrics in Structural Brain Networks by Integrating Different Network Weighting Strategies into a Single Graph , 2017, Front. Neurosci..

[84]  J. Cummings,et al.  Alzheimer's disease drug development pipeline: 2017 , 2017, Alzheimer's & dementia.

[85]  Kun‐Hsing Yu,et al.  Omics Profiling in Precision Oncology* , 2016, Molecular & Cellular Proteomics.

[86]  Daoqiang Zhang,et al.  Multimodal classification of Alzheimer's disease and mild cognitive impairment , 2011, NeuroImage.

[87]  Yong He,et al.  Discriminative analysis of early Alzheimer's disease using multi-modal imaging and multi-level characterization with multi-classifier (M3) , 2012, NeuroImage.

[88]  K. Blennow,et al.  CSF and blood biomarkers for the diagnosis of Alzheimer's disease: a systematic review and meta-analysis , 2016, The Lancet Neurology.

[89]  Chunquan Li,et al.  SubpathwayMiner: a software package for flexible identification of pathways , 2009, Nucleic acids research.

[90]  Marwan N. Sabbagh,et al.  Increasing Precision of Clinical Diagnosis of Alzheimer's Disease Using a Combined Algorithm Incorporating Clinical and Novel Biomarker Data , 2017, Neurology and Therapy.

[91]  Dominique Drouin,et al.  Toward an Alzheimer's disease diagnosis via high-resolution blood gene expression , 2010, Alzheimer's & Dementia.

[92]  Sid O'Bryant,et al.  Developing novel blood-based biomarkers for Alzheimer's disease , 2014, Alzheimer's & Dementia.

[93]  Nagiza F. Samatova,et al.  Complex biomarker discovery in neuroimaging data: Finding a needle in a haystack☆ , 2013, NeuroImage: Clinical.

[94]  Shumpei Niida,et al.  MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer’s Disease from Public Data , 2015, Biomarker insights.

[95]  S. Jamal,et al.  Integrating network, sequence and functional features using machine learning approaches towards identification of novel Alzheimer genes , 2016, BMC Genomics.

[96]  Magda Tsolaki,et al.  A Pathway Based Classification Method for Analyzing Gene Expression for Alzheimer’s Disease Diagnosis , 2015, Journal of Alzheimer's disease : JAD.

[97]  Qianlan Yao,et al.  Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways , 2013, Nucleic acids research.

[98]  Christian Humpel,et al.  Identifying and validating biomarkers for Alzheimer's disease , 2011, Trends in biotechnology.

[99]  Fan Zhang,et al.  Machine Learning Classification Combining Multiple Features of A Hyper-Network of fMRI Data in Alzheimer's Disease , 2017, Front. Neurosci..

[100]  Daniel J. Gaffney,et al.  A survey of best practices for RNA-seq data analysis , 2016, Genome Biology.

[101]  M. Jorge Cardoso,et al.  Accurate multimodal probabilistic prediction of conversion to Alzheimer's disease in patients with mild cognitive impairment☆ , 2013, NeuroImage: Clinical.

[102]  Daniel L. Rubin,et al.  Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease , 2008, PLoS Comput. Biol..

[103]  Minoru Kanehisa,et al.  KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..

[104]  Marie Chupin,et al.  Automatic classi fi cation of patients with Alzheimer ' s disease from structural MRI : A comparison of ten methods using the ADNI database , 2010 .

[105]  Daoqiang Zhang,et al.  Sub-Network Kernels for Measuring Similarity of Brain Connectivity Networks in Disease Diagnosis , 2018, IEEE Transactions on Image Processing.

[106]  Jiawei Han,et al.  gSpan: graph-based substructure pattern mining , 2002, 2002 IEEE International Conference on Data Mining, 2002. Proceedings..

[107]  Michael W. Weiner,et al.  The future of blood-based biomarkers for Alzheimer's disease , 2014, Alzheimer's & Dementia.

[108]  Clifford R. Jack,et al.  A robust biomarker of large-scale network failure in Alzheimer's disease , 2017, Alzheimer's & dementia.

[109]  Nitish V. Thakor,et al.  Comparison method for community detection on brain networks from neuroimaging data , 2016, Applied Network Science.

[110]  Lincoln Stein,et al.  Reactome knowledgebase of human biological pathways and processes , 2008, Nucleic Acids Res..