Neurobiology of Autism Spectrum Disorders

This comprehensive scientific text examines the neurobiology of autism spectrum disorder across multiple biological systems, integrating research on genetic mechanisms, environmental exposures, neurobiological dysfunction, and developmental processes. The book synthesizes evidence from molecular, cellular, systems, and population-level studies to elucidate how converging genetic, epigenetic, and environmental factors produce the diverse neurobiological features observed in autism spectrum disorder (ASD), while also exploring competing frameworks for understanding autism as disease versus neurological difference.

Core Concepts & Guidance

Excitation-Inhibition Imbalance As Central Mechanism

Excitation-inhibition imbalance (E/I) dysfunction represents a core neurobiological feature of ASD, particularly arising from impaired inhibitory neurotransmission. Disruption of inhibitory circuits—mediated by parvalbumin interneurons, somatostatin neurons, and VIP neurons—leads to reduced stimulus selectivity, hyperarousal, and cascading cognitive and social deficits. In Fragile X Syndrome and related conditions, hypoactivity of parvalbumin interneurons in sensory cortices impairs perceptual learning and stimulus discrimination.

Elevated baseline cholinergic tone disrupts VIP neuron dynamics, reducing cortical dynamic range and producing enhanced sensory responses. Chemogenetic rescue of PV function in animal models restores orientation selectivity and perceptual learning, demonstrating direct causality between inhibitory function and behavior.

Multiple converging mechanisms produce E/I imbalance including altered glutamatergic and GABAergic synapse formation, dysregulation of interneuron differentiation, and disrupted development of inhibitory circuits. Markers of E/I imbalance include reduced gamma oscillations, impaired gamma synchrony, altered event-related potentials (reduced N1 amplitudes, enhanced P1 latencies), and increased baseline neural excitability. The heterogeneity of findings suggests multiple developmental pathways converge to E/I dysregulation.

Sensory Processing Dysfunction Across Multiple Domains

sensory-processing hypersensitivity and atypical processing represent core features of ASD across visual, auditory, and somatosensory domains. Visual processing shows disrupted ocular dominance plasticity, immature dendritic spines, center-bias in image fixation, deficits in motion coherence detection, and reduced low-frequency oscillations.

Auditory processing displays enhanced pre-pulse inhibition (reduced startle suppression), broader frequency tuning, enhanced gamma-band power, reduced habituation, and in severe cases, audiogenic seizures. Critical to sensory dysfunction is the finding that individuals with ASD process simple perceptual stimuli relatively normally but show impairment at higher levels of semantic integration and complexity.

Somatosensory processing reveals reduced PV cell density and fast-spiking inhibitory neuron activity, prolonged neuronal depolarization (“UP states”), reduced gamma synchrony, tactile defensiveness, and impaired network adaptation correlating with reduced stimulus-selective neurons.

Beyond laboratory measurements, individuals with autism exhibit both sensory avoidance (hypersensitivity) and sensory seeking (hyposensitivity), often in the same individual across different sensory domains. This variability reflects circuit-level disruptions where inhibitory tone—normally filtering irrelevant stimuli—is compromised. Sensory seeking behaviors (spinning, intense visual fixation, repetitive tactile exploration) may represent attempts to generate predictable, controllable sensory input in an otherwise chaotic perceptual landscape.

Theory of Mind and Semantic Integration Deficits

Theory of Mind (ToM)—the ability to attribute mental states to oneself and others—shows reliable deficits in autism. The classic Sally-and-Anne false-belief task demonstrates that autistic children fail to represent others’ false beliefs despite maintaining intact memory, naming, and reality orientation capabilities.

However, significant evidence suggests ToM deficits reflect impaired integration of multidimensional contextual information rather than unique “mind-reading” failure. Alternative frameworks including Weak Central Coherence Hypothesis and stimulus overselectivity hypothesis propose that ToM deficits arise from difficulties integrating contextual and multidimensional information. This aligns with broader evidence showing that semantic processing complexity, not sensory modality, determines processing difficulty in ASD—both linguistic and visual processing show relative preservation at simple levels but impairment at complex semantic levels.

Prenatal and Early-Life Environmental Exposures

Critical developmental windows during prenatal and early postnatal periods create vulnerability to environmental chemical exposures that can produce lasting neurobiological disruptions. Valproic Acid prenatal exposure carries an 8.9% risk of autism/Asperger syndrome diagnosis. VPA acts as a histone deacetylase (HDAC) inhibitor, causing hyperacetylation during critical embryonic development windows.

Hyperserotonemia from prenatal/perinatal exposure to elevated serotonin or SSRIs produces distinct pathology. High peripheral serotonin reaching the fetal brain during peak serotonergic development (weeks 5-15 of gestation) triggers negative feedback-mediated loss of serotonin terminals. Maternal Immune Activation from prenatal infections triggers placental IL-6 elevation through JAK/STAT3 pathway activation. Prenatal lipopolysaccharide-exposed offspring exhibit elevated anxiety, reduced social interaction, and impaired learning/memory.

Endocrine disruptors including bisphenol-A (BPA), polychlorinated biphenyls (PCBs), and phthalates disrupt endocrine function during critical neurodevelopmental windows. Heavy metals (lead, mercury, cadmium, arsenic, aluminum) accumulate in autistic individuals at elevated levels. One study found autistic children had lead levels of 78% vs. 16% in controls, mercury 43% vs. 10%, and cadmium 38% vs. 8%.

Multiple pesticide classes associate with ASD risk, including organophosphate agents, pyrethroids, and organophosphorus pesticides.

Nutritional Deficiencies and Metabolic Disruptions

Multiple studies across nations and racial groups show children/adolescents with ASD have significantly lower vitamin D levels than controls. Low prenatal 25-(OH)D levels correlate with more ASD-related symptoms and lower social skills at age 5. Plasma amino acid differences between ASD and non-ASD individuals include high lysine, lysine deficiency, elevated tryptophan/phenylalanine, and low tyrosine.

B-vitamin complex abnormalities include vitamin B6 with elevated blood PLP levels suggesting impaired cellular utilization, vitamin B3 with abnormal metabolism and elevated urinary nicotinamide, and vitamin B12 significantly lower in autistic individuals’ serum and brain tissue. Folate-related genetic polymorphisms and folate receptor α autoantibodies occur in ASD.

Exclusive breastfeeding for 6 months significantly reduces autism prevalence compared to formula feeding. Human milk contains higher IGF-1 levels and more vitamin D than bovine milk.

Mitochondrial Dysfunction and Oxidative Stress

Mitochondrial dysfunction is identified as a significant contributor to ASD pathophysiology, with approximately 5% of children with ASD meeting diagnostic criteria for mitochondrial disease. Reduced phosphocreatine levels in prefrontal cortex indicate impaired ATP generation, and pyruvate dehydrogenase activity is reduced in 35% of ASD individuals.

Deficiencies in complexes I and III of the electron transport chain are most common, with multiple studies finding decreased activity of all five mitochondrial complexes in frontal cortex cells of ASD individuals. There is a twofold higher frequency of mtDNA deletions, 2.4-fold higher GC→AT transitions, and deletions confirmed in 16.6% of ASD patients.

Children with ASD exhibit higher mitochondrial hydrogen peroxide production, increased lipid hydroperoxides across multiple brain regions, and elevated 3-nitrotyrosine (protein damage marker). In cerebellum and temporal cortex, reduced glutathione (GSH) significantly decreases with concomitant increase in oxidized glutathione (GSSG). Infant hippocampus shows age-specific glutathione reductase requirements for long-term memory formation at postnatal day 17, which becomes dispensable in juveniles and adults.

Lipid Metabolism and Cholesterol Dysfunction

Cholesterol is the most cholesterol-rich organ, containing ~25% of the body’s total cholesterol. During embryogenesis, cholesterol functions as a transporter molecule for hedgehog (Hh) signaling proteins required for normal morphogenesis. Beyond cholesterol, lipoproteins transport neuroactive steroids, which are transported to the CNS and produce rapid, nongenomic effects. HDL transports proteins, hormones, carotenoids, vitamins, bioactive lipids, and microRNAs—approximately 90% of extracellular miRNAs are packaged with HDL.

Lipid abnormalities appear prominently in syndromic ASD. Smith-Lemli-Opitz Syndrome (SLOS) is caused by variants in DHCR7, resulting in low cholesterol and abnormally elevated 7DHC. ASD is one of the most pervasive behavioral traits, associating with ~50% of SLOS cases. Fragile X Syndrome (FXS) results from CGG triplet repeat expansion in the FMR1 gene, with 46% of males and 16% of females with FXS diagnosed with ASD. Multiple studies found significantly reduced total cholesterol, LDL, and HDL levels in males with FXS. Rett Syndrome (RTT) is caused by variants in MECP2, with plasma lipoprotein analysis showing significant increases in total cholesterol, LDL, and HDL compared to controls.

Circadian Rhythm Development and Sleep Dysfunction

Sleep-wake rhythm abnormalities precede and predict autism development. Ultradian rhythm formation begins at 28-33 weeks gestation, circadian rhythm formation starts during fetal period and is nearly complete by 12-18 months of age, with critical fixation in the suprachiasmatic nuclei (SCN) by age 2 years.

Sleep characteristics associated with future ASD include short nocturnal sleep (<8 hours), sleep onset after 22:00 weekdays or 23:00 holidays, frequent awakening (>3 times) or prolonged awakening (>60 minutes), and night-time Basic Sleep Duration not changing with age.

Optimal sleep habits for preventing ASD include sleeping between 7:00 p.m.-7:00 a.m. with sleep onset before 10:00 p.m., <2 awakening episodes per night on <3 nights/week for <20 min awakening duration, 9-12 hours nocturnal sleep (average 10 hours), and wake time variation ≤60 minutes between weekdays/weekends.

Neural Circuits Regulating Social Behavior

Discrete neural circuits mediate sequential social behaviors, with oxytocin (OXT) and arginine vasopressin (AVP) playing pivotal regulatory roles. OXT neurons in paraventricular nucleus (PVN) projecting to medial amygdala (MeA) are crucial for social approach expression. Parvocellular OXT neurons activated by social contact project to nucleus accumbens (NAc), and OXT activates GABAergic OTR-expressing neurons projecting to NAc for stress-related social avoidance.

AVP circuits mediate social investigation and rejection signaling, with synthesis in PVN, SON, and extended amygdala. The BnST-Lateral Septum Circuit facilitates defensive attack and aggression, while the BnST-Lateral Habenula (LHb) circuit mediates scent marking and territorial rejection, with sex differences in steroid hormone control of AVP neuron activity.

Intranasal OXT administration enhances positive social behaviors but may fail to alleviate overall ASD symptoms, though it specifically facilitates prosocial attention and decreases social vigilance. AVP levels (but not OXT) are significantly lower in cerebrospinal fluid of ASD children. AVP administration alleviates behavioral ASD symptoms in transgenic mouse models and human children.

Seizures, Epilepsy, and Comorbid ASD

The relationship between ASD and seizure disorders is bidirectional and complex, with 44% of children with ASD receiving subsequent epilepsy diagnosis and 54% of children with epilepsy receiving ASD diagnosis, positively correlated with presence/severity of intellectual disability. A prospective study found epileptic EEG discharges in 85.8% of ASD children despite lack of epilepsy diagnosis.

When ASD and epilepsy co-occur, male predominance significantly decreases. Meta-analysis found autistic females had higher relative risk of epilepsy than autistic males. Evidence suggests early abnormal electrical activity may precede ASD manifestation, with one study finding 6/20 children with infantile spasms had ASD (higher than general population prevalence).

Genetic Basis and Molecular Pathways

ASD involves both common polygenic risk (explaining ~20% liability) and rare de novo variants, with approximately 20% of cases having identifiable genetic causes. Twin studies show 77-95% concordance in monozygotic (MZ) twins versus 31% in dizygotic (DZ) twins, with genetic heritability estimates ranging from 56-95%.

Approximately 2,145 copy number variations (CNVs) are implicated in ASD, with key ASD-related CNVs located at multiple chromosomal regions including 1q21 (BCL9), 7q11.23 (AUTS2), 15q11-q13 (UBE3A, GABRB3, GABRG3, GABRA5), 16p11.2 (MVP, GDPD3), 22q11.2 (PI4KA, SNAP29, TBX1), and 22q13.33 (SHANK3).

Synaptic and developmental genes play crucial roles. RELN (Reelin) maps to AUTS1 locus and plays crucial roles in neuronal cell positioning, with studies showing 44% decreased reelin levels in cerebellum of autistic subjects versus controls. SHANK genes encode postsynaptic scaffolding proteins organizing protein structures at postsynaptic densities of glutamatergic synapses, with SHANK3 mutations and duplications linked to ASD development. NLGN (Neuroligin) genes are transmembrane molecules mediating heterophilic adhesion with presynaptic neurexin proteins, with NLGN3 and NLGN4 loss-of-function mutations causing substantial dysregulation of reciprocal social interactions.

Multiple other genes have identified roles including OXTR (Oxytocin Receptor), GABR (Gamma-Aminobutyric Acid Receptor) genes, MET (Mesenchymal Epithelial Transition), SLC6A4 (Serotonin Transporter), SLC25A12 (Mitochondrial Aspartate/Glutamate Carrier), MAO (Monoamine Oxidase) genes, and ITGB3 (Integrin-β 3). iPSC-derived neural progenitor cells (NPCs) from ASD individuals show altered proliferation patterns due to dysregulation of the β-catenin/BRN2 transcriptional cascade.

Metabolic Approaches and Micronutrient Treatment

Many children with ASD have metabolic abnormalities not linked to specific inborn errors of metabolism, potentially related to dietary restrictions and toxin exposures. Comprehensive evaluation requires multidisciplinary assessment following the ABCDEFG Assessment Model: Anthropometry (weight, height, head circumference), Biochemical investigations, Clinical assessment, Dietary assessment, Exposure history, Functional imaging, and Genetic studies.

B Vitamin Complex supplementation evidence includes vitamin B1 (Thiamine) with 11-24% of individuals with ASD having below-average whole blood thiamine levels, vitamin B6 (Pyridoxine) studied in 18 studies (11 double-blind placebo-controlled), vitamin B9 (Folate) with meta-analysis supporting leucovorin (folinic acid) as effective for neurological symptoms in ASD, and vitamin B12 (Cobalamin) with 17 studies including four DBPC trials.

Fat-soluble vitamins and antioxidants include vitamin D with meta-analyses documenting lower levels in autistic children and prenatally in those developing ASD, vitamin C with DBPC trial in 18 autistic children showing reduced stereotyped behaviors, and vitamin E with single-group study of patients with verbal apraxia showing 97% reported dramatic improvements following vitamin E combined with polyunsaturated fatty acids.

Minerals, trace elements, and cofactors with evidence include zinc (critical roles in gastrointestinal, endocrine, immune, and nervous systems), magnesium (cofactor for vitamin B1 and B6-dependent enzymes), and molybdenum (essential cofactor for molybdoenzymes including sulfite oxidase).

Amino acids and mitochondrial nutrients include N-acetyl cysteine (NAC) as safe and effective at reducing irritability and improving glutathione production, Coenzyme Q10 (CoQ10) as essential inner mitochondrial membrane cofactor for electron transport chain function, alpha-lipoic acid as essential prosthetic group of mitochondrial enzymes with antioxidant and chelation properties, carnitine (lower in autistic individuals; controlled trials show significant improvements in core ASD symptoms), and tetrahydrobiopterin (BH4) as essential cofactor for monoamine neurotransmitter synthesis.

Phytonutrients and circadian biomarkers include omega-3 fatty acids (lower in autistic children; meta-analysis shows supplementation improves ASD symptoms), sulforaphane (systematic review shows improved core ASD symptoms and significant changes in biomarkers), and melatonin (accumulating evidence supports treating reduced sleep duration and sleep-onset latency).

Dietary interventions include ketogenic dietary therapies (KDTs) comprising classical ketogenic diet (KD), modified Atkins diet (MAD), medium-chain triglyceride ketogenic diet (MCTKD), and low glycemic index therapy (LGIT), as well as other approaches like FODMAP diet, low oxalate diet, Feingold diet, and gluten-free/casein-free (GFCF) diet.