Genetics of Autism Spectrum Disorders

Autism spectrum disorders (ASDs) are characterized by impaired socialization, reduced communication, and restricted, repetitive, or stereotyped activities and interests. ^[1] Autism spectrum disorder consists of the following: (1) deficits in social communication and social interaction and (2) restricted repetitive behaviors, interests, and activities (RRBs). These symptoms are present from early childhood and limit or impair everyday functioning. Both components are required for diagnosis of ASD. Individuals who have marked deficits in social communication but whose symptoms do not otherwise meet the criteria for ASD should be evaluated for social (pragmatic) communication disorder. ^{[2, 3]}

As defined by the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5), ASD encompasses the previous manual's autistic disorder (autism), Asperger's disorder, childhood disintegrative disorder, and pervasive developmental disorder not otherwise specified. ^{[2, 4]}  (Note that Asperger’s syndrome was previously considered a high-functioning form of autism, although this is no longer believed to be the case. Symptoms of Asperger’s tend to be less severe than typical autism, and Asperger’s syndrome may manifest later, with average age of diagnosis reported as 7 years. Individuals with Asperger’s usually do not experience delay in speech development and have average to above average intelligence. However, symptoms such as significant impairment in social interaction and restricted behaviors and interests are shared with other ASDs. ^[5] )

Symptoms of ASD typically present before 3 years of age and often are accompanied by abnormalities in cognitive functioning, learning, attention, and sensory processing. ^[6] According to data from the Centers for Disease Control and Prevention, ASD affected 1 in 54 children in the United States in 2021. ^[5]  Increased prevalence in males is known; the affected male–to–affected female ratio is approximately 4:1. ^{[7, 8]}

The prevalence of ASD, which has been dramatically increasing, ^[9]  is still not well defined, with multiple studies across the globe identifying significantly higher figures in different countries and continents. Additionally, case figures in low-income countries are not definitive because of lack of assessment and diagnostic tools. Statistics from 2020 suggest that Hong Kong, South Korea, the United States, Japan, and Ireland have the highest prevalence of cases, whereby 372 of 10,000 children in Hong Kong have an ASD. ^[5]

In a study that used a twin design to explore the etiology of ASDs and autistic traits over time, Taylor and colleagues found that genetic factors played a consistently larger role than environmental factors and concluded that environmental factors are unlikely to explain the increase in prevalence of ASD. ^[10]

Epidemiologic studies have provided no evidence for vaccination posing an autism risk. ^[11]

High heritability has been reported in ASD; identical twins have a concordance rate of 70-90%. It has been reported that up to 40% of cases of ASD in children have a genetic cause (eg, genetic syndromes such as fragile X syndrome, Rett syndrome, tuberous sclerosis, mutations in the phosphatase and tensin homolog [PTEN] gene, and structural chromosomal deletions or duplications that can be detected using chromosomal microarrays). In addition, metabolic disorders caused by mitochondrial DNA abnormalities are relatively common in individuals with ASD. ^[5]

Genome-wide association studies (GWASs) have attracted attention as a method that can identify disease-associated genetic loci, especially for multifactorial diseases. Many GWASs on ASD have been conducted, and more than 100 loci have been reported as associated with ASD. Future GWAS analyses using these new methods may lead to the discovery of novel ASD risk genes. ^[5]

Although ASDs are known to be extremely heritable, their common genetic causes remain largely elusive because of the complex behavioral phenotypes and multigenic etiology of these disorders. ^[12]

Autism spectrum disorders are highly heterogeneous because of complex underlying pathomechanisms triggered by various factors. Some children and adults with ASD are fully able to perform all activities of daily living; others require substantial support to perform basic activities. To date, the etiology and pathogenic mechanisms involved in ASD remain incompletely understood. However, the presence of common behavioral features that form the basis of ASD diagnosis hints at a core pathology shared by most individuals with this condition. ^[5]

Beyond difficulties in processing information within single sensory domains, including both hypersensitivity and hyposensitivity, difficulties in multisensory processing are becoming a core issue of focus in ASD. These difficulties may be targeted by treatment approaches such as "sensory integration," which is frequently applied in autism treatment but is not yet based on clear evidence. Sensory and multisensory deficits are commonly found in ASD and may result in cascading effects that impact social communication. Studies in animal models may enhance our understanding of the brain mechanisms that underlie difficulties in multisensory integration, with the ultimate goal of developing new treatments. ^[13]

Neuroimaging approaches have been widely employed to parse the neurophysiologic mechanisms underlying ASD and to gain critical insights into anatomic, functional, and neurochemical changes. Longitudinal structural magnetic resonance imaging (MRI) has delineated an abnormal developmental trajectory of ASD that is associated with cascading neurobiologic processes, and functional MRI has pointed to disrupted functional neural networks. Meanwhile, positron emission tomography (PET) and single-photon emission computed tomography (SPECT) have revealed that metabolic and neurotransmitter abnormalities may contribute to shaping the aberrant neural circuits of ASD. Future large-scale, multicenter, multimodal investigations are essential to elucidate the neurophysiologic underpinnings of ASD, while facilitating the development of novel diagnostic biomarkers and better-targeted therapies. ^[14]

Autism spectrum disorder is considered a complex genetic disorder with high heritability. Epidemiologic twin studies support a strong genetic component of ASD. The concordance rate for identical twins is 70-90%, and for fraternal twins 0-10%. In families with existing cases of ASD, familial clustering can be observed. Younger siblings of family members with an ASD diagnosis face increased risk for ASD, which is even greater among younger male siblings. In 20-25% of children or adults with ASD, genetic causes can be identified in the form of de novo mutations, common and rare genetic variations, and ASD-associated common polymorphisms. ^[5]

Autism spectrum disorder is a polygenic disorder that is multifactorial in origin. Copy number variations (CNVs) of several genes that regulate the synaptogenesis and signaling pathways are among major factors responsible for the pathogenesis of autism. The complex integration of various CNVs causes mutations in genes that code for molecules involved in cell adhesion, voltage-gated ion channels, scaffolding proteins, and signaling pathways (phosphatase and tensin homolog [PTEN] and mammalian target of rapamycin [mTOR] pathways). These mutated genes affect synaptic transmission by causing plasticity dysfunction, which is responsible, in turn, for expression of ASD. ^[15]

Epigenetic modifications affecting DNA transcription and various prenatal and postnatal exposures to a variety of environmental factors are other precipitating factors for the occurrence of ASD. All of these together cause dysregulation of glutamatergic signaling, as well as imbalance in excitatory:inhibitory pathways, resulting in glial cell activation and release of inflammatory mediators responsible for the aberrant social behavior observed in autistic individuals. ^[15]

Copy number variations in other sets of genes have implicated the ubiquitin-proteasome system, which regulates synaptic attributes such as neurotransmitter release, synaptic vesicle recycling in presynaptic terminals, and dynamic changes in dendritic spines and postsynaptic density. ^[16]

Sophisticated analyses of these sporadic CNVs in the more biologically relevant context of gene networks reveal that CNV defects in patients with ASD tend to cluster in genes controlling various biologic pathways important for neurotransmission. For example, CNV defects in cadherins and protocadherins have implicated the neuronal cell adhesion pathway, which plays a critical role in development of the nervous system by contributing to axonal guidance, synaptic formation and plasticity, and neuronal-glial interactions.

Significant genetic factors and mechanisms underlie the causation of ASD. Indeed, many affected individuals are diagnosed with chromosomal abnormalities, submicroscopic deletions or duplications, single-gene disorders, or variants. ^[17]

Autism spectrum disorder is highly genetically heterogeneous and may be caused by both inheritable and de novo gene variations. Hundreds of genes have been identified that contribute to the serious deficits in communication, social cognition, and behavior that patients often experience. However, these account for only 10-20% of ASD cases, and individuals with similar pathogenic variants may be diagnosed on very different levels of the spectrum. ^[18]

Although the common genetic mechanisms underlying ASDs may be varied and unknown, mounting evidence suggests that defects at the neuronal synapse may underlie the pathophysiology. ^{[19, 20]} Early studies showed that genes involved in serotonin physiology are among the most significant reproducible susceptibility loci in both linkage analyses ^{[21, 22, 23, 24, 25]} and biochemical studies. ^[26]

Subsequently, models involving more generalized deficits or disturbances in ASD at the level of central processing have emerged through studies addressing weak central coherence, ^[27] impaired complex processing, ^[28] network abnormalities, ^{[29, 30]} disordered information processing, ^[31] and defects at the neurochemical level. ^[32]

Brain connectivity has been reported to be different in individuals with ASD. Lower connectivity between distal brain regions and increased connectivity within proximal brain regions have been noted. However, data are conflicting, and studies have not definitively confirmed this finding. Abnormalities have also been reported in the cytoarchitecture of the brain of individuals with ASD. For example, a decreased number of cerebellar Purkinje cells was found in ASD brains. ^[5]

However, the clearest neuropathology of ASD is synaptic dysfunction. Widely recognized and well-published high-risk candidates for ASD susceptibility include members of the SHANK (SH3 and multiple ankyrin repeat domains) family of postsynaptic scaffolding proteins (ie, SHANK2/3), the cell adhesion family of neurexins (ie, NRXN1), and neuroligins (ie, NLGN2, NLGN4X). ^[5]

A portion of the sporadic nature of ASD may be attributed to spontaneous mutation; this may explain why the search for common shared mutations has yielded such inconclusive results.

A range of metabolic abnormalities have been highlighted in many patients through identification of biofluid metabolome and proteome profiles potentially usable as ASD biomarkers. Indeed, next-generation sequencing and other omics platforms, including proteomics and metabolomics, have uncovered early age disease biomarkers, which may lead to novel diagnostic tools and treatment targets that may vary from patient to patient, depending on specific genomic and other omics findings. ^[17]

Beyond the brain, researchers have started to investigate the role of organ systems other than the brain that are altered in ASD. One system that has been heavily implicated in ASD is the gastrointestinal (GI) system, with many individuals reporting GI dysfunction. Reports about the prevalence of GI disturbances within the autistic population vary between studies, with estimates ranging from 20 to 86%. Gastrointestinal dysfunction has been found to be more prevalent among individuals with ASD than in non-autistic individuals. The severity of GI abnormalities seems to be correlated with the severity of ASD, pointing toward a potential role of the GI system as a modifier of ASD behavior and a factor in ASD etiology. Abdominal pain, bloating, diarrhea, constipation, and gastroesophageal reflux are the most commonly reported GI problems. ^[5]

As the etiology and pathogenesis of ASD have not yet been elucidated, specific treatments and reliable diagnostic biomarkers are not available. Early behavioral interventions have been shown to substantially improve symptoms in children with ASD. Given the rapidly increasing prevalence of ASD, there is an urgent need to identify related diagnostic biomarkers. Although specific diagnostic markers for ASD have not been identified, related research has made progress in different aspects. ^[33]

The complex pathophysiology of ASD encompasses interactions between genetic and environmental factors. On the one hand, hundreds of genes, converging at the functional level on selective biological domains such as epigenetic regulation and synaptic function, have been identified to be causative or risk factors for autism. On the other hand, exposure to chemicals that are widespread in the environment, such as endocrine disruptors, has been associated with adverse effects on human health, including neurodevelopmental disorders. ^[34]

Pharmacogenomic studies exploring ASD have been scarce despite the promise of optimizing treatment outcomes. ^[35]  However, in view of mounting evidence that neurophysiologic processes are disrupted in ASD, it is not surprising that various psychotropic drugs—including stimulants, antidepressants, adrenergic agonists, antipsychotics, antiepileptics, and cholinesterase inhibitors approved for Alzheimer disease (eg, donepezil, galantamine, rivastigmine, tacrine) ^{[36, 37, 38, 39, 40]} —are typically prescribed to mitigate ASD symptoms.

The US Food and Drug Administration (FDA) has approved 2 atypical antipsychotics—risperidone ^[41] and aripiprazole ^{[42, 43, 44, 45]} —for treatment of severe irritability symptoms such as aggression and self-injurious behavior associated with ASD.

A systematic review and network analysis investigated pharmacologic and dietary supplement treatments for ASD in light of the fact that no medications have yet been approved for treatment of core symptoms of ASD. Researchers found that 41 drugs and 17 dietary supplements differed substantially in improving associated symptoms and in their side-effect profiles. Several medications such as carnosine, haloperidol, probiotics, and valproate led to some improvement, yet data were imprecise and were not robust, and this effect could be likely due to secondary improvement in associated symptoms. ^[46]

Venlafaxine has been found to be a useful adjuvant in children and adults with ASD for treatment of self-injurious behaviors, aggression, and symptoms of attention deficit hyperactivity disorder (ADHD) when given in doses lower than the antidepressant dosage. However, duloxetine was not found to show added benefit for treatment of any of the comorbid symptoms and behaviors associated with ASD when compared to other antidepressants. On the other hand, milnacipran was reported to produce improvements in impulsivity, hyperactivity symptoms, and social functioning through reduction of inattention of ADHD when comorbid with ASD. Overall, selective serotonin-norepinephrine reuptake inhibitors (SNRIs) have shown variable effectiveness in treatment of comorbid symptoms and behaviors in ASD. ^[47]  Evidence on the efficacy and safety of pharmacologic treatments is preliminary; therefore, routine prescription of medications for the core symptoms of ASD cannot be recommended. ^[46]

In a review by Baribeau and colleagues, it was reported that several large randomized, controlled trials have provided negative or ambiguous results regarding use of fluoxetine and oxytocin for treatment of individuals with ASD. They described that data support behavioral and psychological interventions for social communication and anxiety in ASD, but that findings are more limited regarding pharmacotherapy for core and associated symptoms. These review authors concluded that next steps should include replication of early findings, trials of new molecular targets, and identification of novel biomarkers, including genetic predictors, of treatment response. ^[48]

Another therapeutic strategy based on translational genomics targets the serotonergic system, which is altered in some patients with ASD. ^{[49, 50, 51]} Rare nonsynonymous mutations in the serotonin transporter (5-HTT) are associated with rigid-compulsive variants of autism, ^{[50, 51]} and circulating levels of serotonin are high in some individuals with ASD. ^[52]  Impairment in verbal communication abilities and dysfunction of the serotonergic system have been reported in ASD. However, it is still unknown how the brain serotonergic system relates to impairment in verbal communication abilities among individuals with ASD. ^[53]

In addition, the melatonin production pathway begins with serotonin, and individuals with ASD exhibit both abnormal melatonin levels and sleep disturbances ^[54] ; thus, it has been suggested that drugs targeting the serotonergic system may help children with ASD. ^[36] However, clinical trials with selective serotonin reuptake inhibitors (SSRIs) have yielded mixed results. ^[55]  

Neuropsychological functions, intestinal homeostasis, and functional GI disturbances are modulated by the gut microbiota through the so-called “microbiota-gut-brain axis.” Individuals with ASD with GI symptoms present microbial changes with plausible relation to deficiency of digestive enzymes, carbohydrate malabsorption, selective eating, bacterial toxins, serotonin metabolism, and inflammation. Strategies to mitigate GI distress through gut microbiota modulation comprise antimicrobials, probiotics, prebiotics, fecal microbiota transplantation, and dietary intervention. Modulation of the gut microbiota in individuals with ASD with GI disturbances seems a promising target for future medicine. ^[56]

The fact that ASD appears to be principally genetically driven and may be reversible postnatally has raised the exciting possibility of using gene therapy as disease-modifying treatment. Such therapies have already started to seriously impact human disease, particularly monogenic disorders (eg, metachromatic leukodystrophy, spinal muscular atrophy [SMA] type 1). With regard to ASD, technical advances in both our capacity to model the disorder in animals and our ability to deliver genes to the central nervous system (CNS) have led to the first preclinical studies in monogenic ASD involving both gene replacement and silencing. Furthermore, increasing awareness and understanding of common dysregulated pathways in ASD have broadened the potential scope of gene therapy to include various polygenic ASDs. Despite a number of outstanding challenges, gene therapy has excellent potential to address cognitive dysfunction in ASD. ^[57]

Given that ASDs are associated with a substantial socioeconomic burden, more research investigating the etiology and pathology of ASD is needed to identify possible biomarkers, treatments, and prevention strategies and to improve existing therapies. Due to the large heterogeneity of this disorder, individuals with ASD will highly benefit from a personalized medicine approach. ^[5]  Authors of a review on clinical assessment, genetics, and treatment approaches in ASD concluded that treatment for patients with ASD should be prioritized based on targeted symptoms, as treatment will vary from patient to patient based on diagnosis, comorbidities, causation, and symptom severity. ^[58]

Progress in identification of genes and genomic regions contributing to ASD has had a broad impact on our understanding of the nature of genetic risk for a range of psychiatric disorders, on our understanding of ASD biology, and on our ability to define key challenges now facing professionals in the field who are working to translate gene discovery into an actionable understanding of pathology. Although these advances have not yet had a transformative impact on clinical practice, there is nonetheless cause for real optimism: reliable lists of risk genes are large and growing rapidly; identified encoded proteins have already begun to point to a relatively small number of areas of biology, where parallel advances in neuroscience and functional genomics are yielding profound insights; strong evidence points to mid-fetal prefrontal cortical development as one nexus of vulnerability for some of the largest-effect ASD risk genes; and multiple plausible paths are moving us forward toward development of rational therapeutics that, although admittedly challenging, represent a fundamental departure from what was possible prior to the era of successful gene discovery. ^[59]

Reduced melatonin secretion has been reported in ASD and has led to many clinical trials using immediate-release and prolonged-release oral formulations of melatonin. Melatonin represents a well-validated and tolerated treatment for sleep disorders in children and adolescents with ASD. More thorough consideration of factors influencing melatonin pharmacokinetics could illuminate the best use of melatonin in this population. Future studies are needed to explore additional dose-effect relationships of melatonin for sleep problems and autistic behavioral impairments. ^[60]

Autism spectrum disorder is associated with numerous genetic syndromes. ^[1]  Practice guidelines from various medical specialty societies, such as the American Academy of Child and Adolescent Psychiatry (AACAP), the American College of Medical Genetics, the American Neurological Association, and the American Academy of Pediatrics, indicate that genetic testing should be part of the evaluation for ASD. ^{[1, 2, 3, 4]} Studies have shown, however, that many patients do not receive indicated genetic testing; reported rates of testing vary widely, ranging from 1.5 to 60% of patients receiving genetic testing as part of the evaluation for ASD. ^{[3, 6, 7, 8, 61]}  Child and adolescent psychiatrists practicing in the United States (approximately 8300) ^[9]  far outnumber developmental behavioral pediatricians (approximately 900) and child neurologists (approximately 900), but in one study, child and adolescent psychiatrists were least likely to order genetic testing during evaluation of patients with diagnosed ASD. Thus, it is critical to understand attitudes of child and adolescent psychiatrists toward genetic testing as well as other barriers to genetic testing to attain optimal adherence to practice guidelines for appropriate genetic testing in people with ASD. ^[62]

Genetic testing of children with ASD is now standard in the clinical setting, with the American College of Medical Genetics and Genomics (ACMGG) guidelines recommending microarray for all children, fragile X testing for boys, and additional gene sequencing, including PTEN and MECP2, for appropriate patients. Testing utilizing high-throughput sequencing, including gene panels and whole exome sequencing, is offered as well. ^[63]

Copy number variants (CNVs) play a key role in the etiology of ASD. Therefore, guidelines recommend chromosomal microarrays (CMAs) as first-tier genetic tests. The TRAP12 and PARD3 genes in CNVs classified as variants of uncertain significance may be worth investigating for autism. Identification of both clinical and biological markers can facilitate monitoring, early intervention, or prevention and can advance our understanding of the neurobiology underlying ASD. ^[64]

Chromosomal microarray offers superior sensitivity for identification of submicroscopic CNVs and is recommended for initial genetic testing of patients with ASD. ^[65]

Autism spectrum disorders comprise a highly heritable and heterogeneous group of neurodevelopmental phenotypes. Common genetic variants contribute substantially to ASD susceptibility, but to date no individual variants have been robustly associated with ASD. ^[66]

Over the past decade, genomic technologies have enabled rapid progress in identification of risk genes for ASD. ^[67]  Although the causes of ASDs remain largely unknown, studies have shown that both genetic and environmental factors play an important role in the etiology of these disorders. Array comparative genomic hybridization and whole exome/genome sequencing studies have identified common and rare copy number or single nucleotide variants in genes encoding proteins involved in brain development, which play an important role in neuron and synapse formation and function. Genetic etiology is recognized in approximately 25-35% of individuals with ASD. ^[68]

Up to 40% of those with ASD have been diagnosed with genetic syndromes or have chromosomal abnormalities. including small DNA deletions or duplications, single-gene conditions, or gene variants and metabolic disturbances with mitochondrial dysfunction. Although the heritability estimate for ASD is between 70 and 90%, the molecular diagnostic yield is lower than anticipated. A likely explanation may relate to multifactorial causation with etiologic heterogeneity and hundreds of genes involved in a complex interplay between inheritance and environmental factors influenced by epigenetics and capabilities to identify causative genes and their variants for ASD. ^[58]

For example, approximately 30% of patients with breast cancer overexpress HER2. When the monoclonal antibody trastuzumab binds to excess HER2 receptors, this prevents the HER2 receptor from signaling cells in the breast to reproduce uncontrollably; use of trastuzumab in combination with chemotherapy for patients with HER2-positive metastatic breast cancer has been shown to increase survival significantly. ^[69]

With better molecular diagnostics that dissect the sporadic genetic mutations underlying ASDs, a similar personalized approach to treating patients’ specific molecular defects becomes feasible.

For example, selective serotonin reuptake inhibitors (SSRIs) have proved efficacious for rare cases of ASD in which the serotonin system is defective, and work is under way to define analogous treatments for ASDs that are due to malfunctioning NLGN/NRXN pathways, neuronal cell adhesion pathways, glutamatergic receptor pathways, and various other neurophysiologic pathways and networks that have been shown to be defective in sporadic cases.

This type of approach to management of ASDs will facilitate development of a test-and-treat model for drugs that target genetically defined responder populations, as trastuzumab does for patients with HER2-positive breast cancer (see the image below). Such a rational approach to personalized drug design would restore normal neurophysiology in patients with ASDs by rescuing specific disrupted genetic pathways while preventing exposure of these patients to drugs that precipitate adverse effects.

Test-and-treat model for targeting therapeutics to specific pathways defective in disease. Generic test-and-treat model is shown in black, where molecular diagnostic is used for genetic definition of population with defective pathways likely to benefit from targeted intervention. Example of trastuzumab as targeted intervention for HER2-positive breast cancer is shown in blue. Extrapolation to behavioral programs and novel therapeutics that are being developed to target autism spectrum disorders due to NLGN/NRXN defective pathways is in red.

Given the clinical and genetic heterogeneity of ASDs, it is likely that the combination of early tailored behavioral and psychopharmacogenomic interventions will have a positive impact on prognosis for patients with these disorders.

Despite current guidelines, few children with ASD undergo genetic evaluation. More than half of pediatricians surveyed lacked knowledge of current guidelines, and many held beliefs about genetic evaluation that did not align with guidelines. Barriers were lack of insurance coverage for genetic evaluation/testing and long wait times to see geneticists. Pediatricians whose beliefs were aligned with guidelines and those aware of the role of genetic counselors were more likely to adhere to guidelines. Efforts to educate pediatricians are needed along with system-level solutions regarding availability of geneticists and reimbursement for genetic testing. ^[70]

Research on monogenic forms of ASD can inform our understanding of genetic contributions to the autism phenotype, yet there is much to be learned about the pathways from gene to brain structure to behavior. Brain abnormalities are common in this population of individuals—in particular, among children; however, a range of different brain abnormalities have been reported within and between genes. Future neuroimaging research should prove helpful. ^[71]