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Frontiers In Autism Research: New Horizons For Diagnosis And Treatment

Frontiers In Autism Research: New Horizons For Diagnosis And Treatment

Hu Valerie W

(2014)

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Book Details

Abstract

This book focuses on the emerging and expanding areas of research on ASD and their potential to lead to better diagnosis and more effective therapies. These areas include innovative and integrative approaches to genetic/genomic analyses and investigations of epigenetic contributions, including the role of noncoding RNAs, DNA methylation, alternative splicing, RNA editing, and faulty translation in gene regulation and expression, metabolic and immune dysfunction, co-morbidities, as well as hormonal and gene-environment interactions that may increase risk for ASD.Within each chapter, experts review cutting-edge research as well as provide their perspective on the future of research in their respective areas, including the challenges involved and the types of studies or advances that are necessary to move the field forward to achieve predicted translational goals.Contributors: Argel Aguilar-Valles, Evdokia Anagnostou, Emma Ashwin, Bonnie Auyeung, Kelly M Bakulski, Simon Baron-Cohen, Margaret L Bauman, Donna Betts, Chad A Bousman, Daniel B Campbell, Manuel F Casanova, Bhismadev Chakrabarti, Gursharan Chana, Abha Chauhan, Ved Chauhan, Jessica DeWitt, Keith W Dunaway, Alal Eran, Ian P Everall, M Daniele Fallin, Richard E Frye, Piers Gillett, Matthew Ginsberg, Christos G Gkogkas, Rhonda J Greenhaw, Simon G Gregory, Elena L Grigorenko, Feng Gu, Rebecca Harmer, Martha Herbert, Valerie W Hu, Karen L Jones, Petra Kern, Arkady Khoutorsky, Rebecca Knickmeyer, Isaac S Kohane, Louis M Kunkel, Janine M LaSalle, Michael V Lombardo, Deepali Mankad, Marvin Natowicz, Laura Nicholls, Christos Pantelis, Natalia Rakhlin, Radhika Ramadas, Daniel A Rossignol, Tewarit Sarachana, Stephen W Scherer, Gabriela Schmulevich, Ayten Shah, Frank R Sharp, Alison B Singer, Efstratios Skafidas, Estate M Sokhadze, Nahum Sonenberg, Boryana Stamova, Zohreh Talebizadeh, Renee Testa, Judy Van de Water, Irina Voineagu, Daniel Williams, Ryan K C Yuen, Daniela Zantomio.

Table of Contents

Section Title Page Action Price
Contents vii
Dedication v
Preface xi
About the Editor xv
List of Contributors xvii
Dissecting the Genetic Architecture of ASD 1
Chapter 1 Phenotype Definition: A Cornerstone of Autism Research, Diagnosis and Therapy 3
Introduction 4
Heterogeneity: Categorical and Dimensional Approaches to Stratification of ASD 5
Incorporation of ASD Phenotypes into Transcriptome Analyses 7
Subtype-dependent Class Prediction Analyses for Biomarker Identification 9
Value of ADI-R-derived Phenotypic Subgroups in Genetic Analyses 12
Value of Phenotype-Definition for Targeted Therapies and Pharmacogenomics 13
Future Directions 15
Executive Summary 16
Acknowledgements 17
References 17
Chapter 2 From Molecular Pathways to ASD Therapy: Insights from Syndromic Forms of Autism 23
Introduction 24
Genetics of Idiopathic ASD 26
Common genetic variation 26
Rare genetic variation 27
Syndromic ASD 28
Rett syndrome 29
Fragile X syndrome 30
Tuberous sclerosis 32
Emerging Pharmacological Therapies for Syndromic ASD 34
Evidence for Convergent Pathways between Syndromic and Idiopathic ASD 34
Future Directions 37
Executive Summary 38
References 38
Chapter 3 Language Impairment in Autism Spectrum Disorders 47
Introduction 47
Language Impairments in ASD 50
Sources of phenotypic heterogeneity 50
Types of language deficits in ASD 52
Language skills and the diagnosis of ASD 56
Family Studies of ASD and LD Overlap 56
Molecular Genetic Studies of ASD/LD Overlap 57
Conclusions 58
Future Directions 60
Executive Summary 60
Acknowledgements 61
References 61
Chapter 4 Whole Genome Sequencing in Autism: Clinical Translation 69
Introduction 70
Understanding of ASD Genetics from Pre- and Post-high-throughput Sequencing Eras 71
Genetic architecture of ASD — Knowledge before the advent of high-throughput sequencing 71
Genetic discoveries from high-throughput sequencing 74
Strategies of Analyzing the Genetic Variants Identified by WGS 76
Genetic variant discovery 78
De Novo SNVs and indels 79
Manual assessment of potential de novo exonic variants 79
CNV detection by WGS 80
Rare variant characterization 81
Medical classification 82
Implications of ASD Whole Genome Sequencing on Diagnosis and Treatment 83
Revealing clinical and genetic heterogeneity of ASD 84
Facilitating decision-making on medical management 84
Providing potential pharmacological clues 85
Increasing diagnostic yield with improved genomic coverage 85
Future Directions of Autism Clinical Genetic Research using Whole Genome Sequencing 86
Resolving incomplete penetrance and variable expressivity of variants 87
Improving the quality of CNV calling from whole genome sequencing 87
Analyzing non-coding regions in the genome 88
Conclusion 89
Executive Summary 89
Acknowledgements 90
References 91
Chapter 5 The Impact of Integrative Unconventional Data Analysis Approaches on Advancing Autism Genetics Research 99
Introduction 100
Whole Genome Studies 100
Gender Bias in Autism 104
Phenotypic Stratification 107
Network Analysis 109
Interactome Networks 110
Future Directions 111
Executive Summary 112
References 113
Chapter 6 Construction of a Genetic Classifier for ASD Using Gene Pathway Analysis 119
Introduction 120
Clinical Diagnosis of ASD 121
Genetic Studies in ASD 125
Monogenic disorders with increased incidence of ASD 125
Copy number variants (CNVs) in ASD 126
Single nucleotide polymorphisms (SNPs) in ASD 127
Development of a Genetic Classifier for ASD using Gene Pathway Analysis 127
SNP quality control 132
Determining Ethnicity/Ancestry and Controlling for Population Stratification 133
Development of Genetic Classifiers for Other Psychiatric Disorders 134
Future Directions 135
Executive Summary 136
Acknowledgements 137
References 137
Gene Dysregulation in ASD: From Transcription to Translation 145
Chapter 7 Genome-Wide Expression Studies of Blood and Lymphoblastoid Cell Lines in Autism Spectrum Disorders 147
Introduction 148
mRNA Expression Studies of LCL in ASD 150
microRNA ( miRNA) Expression Studies of LCL in ASD 152
RNA Expression Studies in Relation to Genotype 153
RNA Expression Studies of Blood in ASD 154
Pathways Associated with ASD 160
Examining Dysregulated Pathways in Individual ASD Subjects 161
Importance of Pathway Studies for ASD 162
Future Directions 164
Executive Summary 165
References 166
Chapter 8 Searching in the “Dark”: Non-coding RNA as a New Avenue of Autism Research 175
Introduction 176
The Genomic “ Dark Matter” 178
Non-coding RNAs and ASD 179
miRNAs and ASD 179
snoRNAs and ASD 188
Biological functions associated with ncRNAs reported in ASD 190
Future Directions in ASD Biomarker Research 192
Executive Summary 195
Acknowledgements 196
References 196
Chapter 9 Targeting Noncoding RNA for Treatment of Autism Spectrum Disorders 203
Evidence that lncRNAs Contribute to ASD 203
What is a ncRNA? 207
Small ncRNA 208
Long ncRNA (lncRNA) 209
Therapeutic Targeting of ncRNA — A New Type of Pharmacology 210
Cancer 210
Neurodegenerative Disorders 212
Ataxias 212
Alzheimer’s disease 213
Neurodevelopmental Disorders 214
Fragile X syndrome 214
Down’s syndrome 214
NcRNA in Clinical Trials 215
Future Directions and Conclusions 217
Executive Summary 218
References 218
Chapter 10 A-to-I RNA Editing in Autism Spectrum Disorder 229
Introduction 230
A-to-I RNA Editing Enables Fine-tuned Response to Environmental Cues 231
A-to-I RNA Editing Modulates Complex Behavior in Model Organisms 233
The Genomics Technology Revolution is Enabling Rapid Discoveries of A-to-I RNA Editing in Humans 234
A-to-I RNA Editing in Postmortem Brains of Children with ASD 235
Future Directions 238
Executive Summary 239
Acknowledgements 240
References 240
Chapter 11 Translational Control of Autism and Fragile-X Syndrome 249
Introduction 250
mRNA translation 250
Translational control 251
Autism Spectrum Disorders (ASD) 253
Fragile-X Syndrome (FXS) 255
Dysregulated translational control in ASD 257
Dysregulated translational control in FXS 260
Future Perspectives 263
Translation is a “druggable” pathway 263
Clinical trials in FXS and ASD 264
Executive Summary 267
References 268
Epigenetic, Environmental, and Physiological Contributions to ASD 277
Chapter 12 Epigenetics in Autism 279
Introduction 279
Fundamentals of Epigenetics 280
Epigenetics in Disease 283
Syndromic Autism 285
Fragile X syndrome 285
Rett syndrome 286
Angelman syndrome 287
Environmental Epigenetics 288
Epigenetic Dysregulation in Non-Syndromic Autism 289
Potential Sources of Epigenetic Dysregulation 291
Future Directions 292
Conclusions 294
Executive Summary 295
References 295
Chapter 13 The Epigenetics of Autism — Running Beyond the Bases 303
Introduction 303
DNA Methylation 304
Regulation by DNA Methylation 308
Epigenetics and Autism 309
MECP2 309
FRAX 310
Angelman/Prader-Willi syndromes 310
15q11-13 311
Chromosome 7 312
Methylation pathways 312
Candidate Genes 313
OXTR 313
SHANK3 314
RELN 314
PRRT1 and ZFP57 315
Influences of the Environment on the Epigenome 315
Assisted Reproduction 316
Technologies for Profiling of DNA Methylation 317
Histones and Chromatin Modifications 319
Histones and Autism 321
Future Directions 321
Executive Summary 322
Acknowledgements 323
References 323
Chapter 14 Genes and Environment in Autism Spectrum Disorders: An Integrated Perspective 335
Etiologic Models for ASD — Genes, Environment, or Both? 335
Heritability evidence 337
Historical perspective on genetic and environmental etiologic work in ASD 337
Genetic Risk Factors for ASD 338
Inherited genetics in ASD 339
De novo genetic change in ASD 340
Genetics summary 340
Environmental Risk Factors for ASD 341
Windows of susceptibility 341
Parental characteristics 342
Toxicants 343
Combined Genetic and Environmental Risk Paradigm 346
The potential applications of gene-environment interaction studies 346
GxE mechanisms 348
Current GxE autism epidemiology studies 352
Challenges and Suggestions for an Integrated Approach 353
Genetic measures 353
Exposure assessment 354
Phenotype assessment 356
Analysis tools 356
Study designs and available samples 357
Summary and Future Directions 358
Executive Summary 359
References 360
Chapter 15 The Potential Brain Drain from Environmental Exposures on the Methylome and Genome Across Generations 375
Why Consider a Potential Chemical “ Brain Drain” of Generationally Cumulative Environmental Exposures in Autism Risk? 376
The Complex Etiology of Autism Spectrum Disorders 376
DNA Methylation at the Interface of Genomic Interactions with the Environment 378
The Neuronal Methylome and Its Importance in Autism 379
How Do Environmental Toxins Affect Metabolic Pathways Regulating DNA Methylation? 382
Evidence for Environmental Exposures Affecting Brain Methylation 384
Evidence for Transgenerational Effects of Environmental Exposures 389
Evidence for Environmental Exposures and Transgenerational Effects in ASD 392
Future Directions 393
Executive Summary 395
References 396
Chapter 16 Oxidative Stress and Mitochondrial Dysfunction in ASDs 407
Introduction 408
Oxidative Stress in Autism 410
Increased markers of oxidative damage in autism 410
Decreased antioxidant defense in autism 411
Mitochondrial Dysfunction in Autism 412
Defects in energy metabolism in autism 413
Defects in activities and protein expression of mitochondrial ETC complexes in autism 414
Defects in mtDNA in autism 415
Defects in maintaining calcium homeostasis in autism 417
Future Perspectives 417
Executive Summary 418
References 419
Chapter 17 Maternal Autoantibodies in Autism Spectrum Disorder 429
Introduction 429
Immune Review 430
Immune system overview 430
Maternal immunity and the gestational environment 431
Maternal Autoantibodies in Autism 433
Observational studies 433
Animal models 436
Maternal antibodies and genetic susceptibility 438
Future Directions 439
Conclusions 440
Executive Summary 444
References 444
Chapter 18 Why is Autism More Common in Males? 451
The Male Bias in Autism 452
Are ASC an Extreme Expression of the Male Brain? 453
Sexual Dimorphism in the Human Brain 454
The Fetal Testosterone (fT) Theory 456
Fetal androgens affect the brain: Evidence from animal and human studies 456
Fetal androgens affect ASC traits: Evidence from amniotic fluid testosterone 457
Future Directions 459
Executive Summary 461
Acknowledgments 461
References 461
Moving Towards Personalized Treatment of ASD and Lifespan Issues 471
Chapter 19 Future Directions in Psychopharmacology of Autism Spectrum Disorder 473
Introduction 474
Stratification Based on Biomarkers 475
Medications Targeting Emerging Pathophysiology of ASD 476
Drugs altering the excitation to inhibition (E:I) balance 476
Immune Modulators 479
Medications that Target Neurocircuitry which May Modify Severity of Core Symptoms 483
Future Directions: Combining Pharmaco-therapeutics Targeting the Biology of ASD with Behavioral Interventions 485
Conclusion 485
Executive Summary 486
References 486
Chapter 20 Medical Co-Morbidities in Autism: Clues to Underlying Biological Mechanisms and/or Diagnostic Subtypes? 497
Introduction 498
Seizure 499
Gastrointestinal Disorders 501
Sleep Disorders 503
Metabolic Disorders 505
Mitochondrial disorders 505
Other potentially significant metabolic disorders 507
Discussion 509
Future Directions 511
Executive Summary 511
References 512
Chapter 21 Translational Implications of a Whole-Body Approach to Brain Health in Autism: How Transduction between Metabolism and Electrophysiology Points to Mechanisms for Neuroplasticity 515
Introduction 516
Beyond Hardwired: Autism Not Born but Made 517
What are These New Observations Telling Us About How Autism “Works”? 520
New Directions for Research and Treatment: Whole-Body Approach to Brain 521
How a Whole Body Approach Reframes the Role of the Brain in Autism 522
Multi-Scale Interacting Aspects of Brain Biology and Function 523
Problems in the body that have parallels in the brain 523
Brain: Transduction between Physical and Informational Levels 524
Brain as a Physical Organ: The Poorly Explored Relationships between Anatomy and Pathophysiology 525
Microscopic findings 525
Macroscopic findings 528
Brain as a System for Information Processing 530
“ Structural connectivity” through fiber tracts 531
Specific regions that “light up” during brain activity 532
Tissue-level contributors to brain activation measured by fMRI 532
Problems with blood perfusion of brain tissues 533
Electrical oscillations or “brain waves” 534
Temporal vs. spatial resolution of measurements and learning about autism as a PROCESS 534
Molecular and Cellular Underpinnings of Brain Information Processing 535
Underlying systems supporting brain function: Differences between cell types 535
Underlying systems supporting brain function: Gap junctions and voltage-gated calcium channels 536
Fast Tracking Progress in Autism Research: From Bottom-up to Middle-out and Multi-scale Approaches 538
A Further Problem: Heterogeneity — How Can There be So Many Routes to “Autism”? 539
Okay, So What “is” the “Autism” Anyway? 540
Autism as an Emergent Property of a System with Many Shifted “Settings” 541
From “what causes autism” to “how is autism caused” 542
From “how is autism caused” to “how does autism work”: Dynamical process approach 542
Autism as What Emerges from the Moment-to-Moment Impact on Electrophysiology of Depleted Function of Cells Supporting Brain Electrical Activity 543
Practical Implications for Conducting Research and Clinical Care? 544
Lifestyle interventions for the brain: Public health implications 544
What it Will Take to Implement a Public Health, Everyday Epigenetics Approach to Autism 545
Future Directions: Toward True Translational Research 545
Conclusion: Multi-Scale Dynamical Biology Gives Hope and Empowerment 546
Executive Summary 547
References 548
Chapter 22 Achieving Optimal Outcomes in Autism: Treating Potentially Reversible Conditions Associated with Autism Spectrum Disorder 557
Introduction 558
Specific Metabolic Disorders Amenable to Novel Treatments 560
Mitochondrial metabolism 560
Folate metabolism 563
Redox metabolism 566
Tetrahydrobiopterin metabolism 567
Common Molecular Mechanisms are Associated with Novel Treatments 568
Future Prospective 570
Executive Summary 571
References 572
Chapter 23 Transcranial Magnetic Stimulation: Application in Autism Treatment 583
Introduction 584
Inhibition Defects in Autism and the Potential Role of TMS 587
Electrophysiological Studies on Autism 589
Our Studies in Autism using rTMS 592
Conclusions 597
Future Directions 598
Executive Summary 599
References 600
Chapter 24 Music Therapy: Personalized Interventions for Individuals with Autism Spectrum Disorder 607
Introduction 608
Why Music Matters 608
Music Therapy Services for ASD 609
Professional health discipline 609
Music therapy practice 610
Therapeutic process 610
Music Therapy Intervention Studies 611
Building on the past: Anecdotal reports and narrative literature reviews 611
Learning from the data: Three systematic reviews 612
Moving forward: Emerging research and initiatives 614
Outlook on Future Research and Developments 617
Sample size and scientific rigor 618
Goal areas and aspects of interventions 619
Context of intervention and collaborations 619
Research to practice 620
Conclusion 621
Executive Summary 622
Acknowledgements 623
References 623
Chapter 25 The Contributions of Art Therapy in Treatment, Assessment, and Research with People Who Have Autism Spectrum Disorders 627
Introduction 628
Art Therapy 628
Art Therapy and Autism 628
Art Therapy Treatment & Autism 630
Art Therapy School-Based Programs 633
Family Art Therapy and Autism 634
Art Therapy Assessment & Autism 636
The FSA: Case Examples 638
Future Directions: Art Therapy Research & Autism 643
Neuroscience, Art Therapy and Autism 647
Executive Summary 648
References 648
Appendix A: Martin’s (2009) characteristics of artwork by children with autism: Definitions of terms 653
Chapter 26 Shifting Paradigms: An Examination of Our Understanding of Adult Autism 655
Introduction 656
Conditions Impacting Adults on the Spectrum 657
Therapeutic and medicated childhoods 657
Bullying, abuse and isolation 658
Co-occurring conditions 659
Housing 660
Education 661
Transition-aged youth 661
New post-secondary academic options 662
Post-secondary training options 664
Employment 664
Supported employment 666
Work-based learning and job trials 666
Customized employment 667
Future Trends in Adult Autism 668
Translational research 668
Psychiatry 669
Embracing the social model of disability 670
Trauma-informed programming 675
Technology and social media and peer-to-peer support 675
Executive Summary 677
References 678
Index 683