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Genetic and Phenotypic Subtypes of Autism Spectrum Disorder

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (20 February 2022) | Viewed by 42828

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Dr. M. E. Suzanne Lewis

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The Department of Medical Genetics and Genomics, University of British Columbia and BC Children’s Hospital Research Institute, Vancouver, BC V6H 3N1, Canada
Interests: autism genomics; multivariant genotypes and clinical subtypes of Autism; whole exome/genome sequencing; multi-omics; precision medicine; molecular medicine and therapeutics
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Dear Colleagues,

Autism Spectrum Disorder (ASD) is a heterogeneous spectrum, both clinically and etiologically, making it a prime candidate for ‘precision medicine’ based on understanding of cause, rather than behaviours alone. The diagnosis of ASD does not imply etiology, but rather a complex constellation of behavioural and developmental symptoms of a group of conditions comprising discrete genetic, metabolic, congenital, and environmental causes. For complex genetic disorders, such as ASDs, it is important to identify biological markers that distinguish subtypes. For some disorders, this could be a phenotypic trait that is specific to one subgroup of individuals with the condition; for others, it could be a genomic, biochemical or chromosomal difference. With current genomics technologies, it is possible to capture a molecular profile of individuals with ASD through their DNA, gut and organ microbes, metabolomic by-products, and the physical and developmental outcomes caused by the interaction of these factors with the environment.

In this special issue we welcome contributions that integrate standardized metrics for subgrouping the ASD phenome (the sum of all phenotypic traits) with its genomic underpinnings. It is the aim of this issue to provide a deeper understanding of genetic and phenotypic subtypes of ASD that can serve as etiologically valid biomarkers for incisive molecular analyses of genes, and gene pathways, which underlie susceptibility to autism and its pathogenesis, that may ultimately enable early diagnosis and more precise, effective treatments.

Dr. M. E. Suzanne Lewis
Guest Editor

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Keywords

Autism
Genomics
Next Generation Sequencing
Deep Phenotypes
Clusters/Subtypes
Precision Medicine
Gene Pathways
Pathogenesis
Neurodevelopment

Published Papers (12 papers)

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Research

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9 pages, 450 KiB

Open AccessArticle

Complex Autism Spectrum Disorder with Epilepsy, Strabismus and Self-Injurious Behaviors in a Patient with a De Novo Heterozygous POLR2A Variant

by Daniel R. Evans, Ying Qiao, Brett Trost, Kristina Calli, Sally Martell, Steven J. M. Jones, Stephen W. Scherer and M. E. Suzanne Lewis

Genes 2022, 13(3), 470; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030470 - 07 Mar 2022

Cited by 3 | Viewed by 3468

Abstract

Autism spectrum disorder (ASD) describes a complex and heterogenous group of neurodevelopmental disorders. Whole genome sequencing continues to shed light on the multifactorial etiology of ASD. Dysregulated transcriptional pathways have been implicated in neurodevelopmental disorders. Emerging evidence suggests that de novo POLR2A variants cause a newly described phenotype called ‘Neurodevelopmental Disorder with Hypotonia and Variable Intellectual and Behavioral Abnormalities’ (NEDHIB). The variable phenotype manifests with a spectrum of features; primarily early onset hypotonia and delay in developmental milestones. In this study, we investigate a patient with complex ASD involving epilepsy and strabismus. Whole genome sequencing of the proband–parent trio uncovered a novel de novo POLR2A variant (c.1367T>C, p. Val456Ala) in the proband. The variant appears deleterious according to in silico tools. We describe the phenotype in our patient, who is now 31 years old, draw connections between the previously reported phenotypes and further delineate this emerging neurodevelopmental phenotype. This study sheds new insights into this neurodevelopmental disorder, and more broadly, the genetic etiology of ASD. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

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11 pages, 249 KiB

Open AccessArticle

Evidence from Characteristics and Comorbidities Suggesting That Asperger Syndrome Is a Subtype of Autism Spectrum Disorder

by Stephen M. Edelson

Genes 2022, 13(2), 274; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13020274 - 30 Jan 2022

Cited by 2 | Viewed by 6562

Abstract

The current version of the American Psychiatric Association’s Diagnostic and Statistical Manual of Mental Disorders (DSM-V) does not consider Asperger syndrome a diagnostic category. This study was undertaken to see if there is evidence that this diagnosis should be reinstated. An online survey was conducted to examine symptoms and behaviors associated with the current diagnostic criteria of autism spectrum disorders (ASD) (DSM-V), and those associated with Asperger syndrome based on the previous version (DSM-IV-TR). The study also examined other characteristics historically associated with autism, as well as impairments often reported in infancy/young childhood and medical comorbidities frequently associated with autism. The sample included 251 individuals who had received a diagnosis of Asperger syndrome and 1888 who were diagnosed with autism or ASD. Numerous similarities and differences were found between the two groups. The findings are discussed in relation to reestablishing Asperger syndrome as a valid diagnostic category as well as a subtype of ASD. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

10 pages, 1517 KiB

Open AccessArticle

Heterozygous De Novo Truncating Mutation of Nucleolin in an ASD Individual Disrupts Its Nucleolar Localization

by Taimoor I. Sheikh, Ricardo Harripaul, Nasim Vasli, Majid Ghadami, Susan L. Santangelo, Muhammad Ayub, Roksana Sasanfar and John B. Vincent

Genes 2022, 13(1), 51; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13010051 - 24 Dec 2021

Cited by 1 | Viewed by 2630

Abstract

Nucleolin (NCL/C23; OMIM: 164035) is a major nucleolar protein that plays a critical role in multiple processes, including ribosome assembly and maturation, chromatin decondensation, and pre-rRNA transcription. Due to its diverse functions, nucleolin has frequently been implicated in pathological processes, including cancer and viral infection. We recently identified a de novo frameshifting indel mutation of NCL, p.Gly664Glufs*70, through whole-exome sequencing of autism spectrum disorder trios. Through the transfection of constructs encoding either a wild-type human nucleolin or a mutant nucleolin with the same C-terminal sequence predicted for the autism proband, and by using co-localization with the nucleophosmin (NPM; B23) protein, we have shown that the nucleolin mutation leads to mislocalization of the NCL protein from the nucleolus to the nucleoplasm. Moreover, a construct with a nonsense mutation at the same residue, p.Gly664*, shows a very similar effect on the location of the NCL protein, thus confirming the presence of a predicted nucleolar location signal in this region of the NCL protein. Real-time fluorescence recovery experiments show significant changes in the kinetics and mobility of mutant NCL protein in the nucleoplasm of HEK293Tcells. Several other studies also report de novoNCL mutations in ASD or neurodevelopmental disorders. The altered mislocalization and dynamics of mutant NCL (p.G664Glufs*70/p.G664*) may have relevance to the etiopathlogy of NCL-related ASD and other neurodevelopmental phenotypes. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

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10 pages, 725 KiB

Open AccessArticle

Diagnostic Yield and Economic Implications of Whole-Exome Sequencing for ASD Diagnosis in Israel

by Rotem Tal-Ben Ishay, Apurba Shil, Shirley Solomon, Noa Sadigurschi, Hadeel Abu-Kaf, Gal Meiri, Hagit Flusser, Analya Michaelovski, Ilan Dinstein, Hava Golan, Nadav Davidovitch and Idan Menashe

Genes 2022, 13(1), 36; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13010036 - 23 Dec 2021

Cited by 4 | Viewed by 3249

Abstract

Whole-exome sequencing (WES) is an effective approach to identify the susceptibility of genetic variants of autism spectrum disorder (ASD). The Israel Ministry of Health supports WES as an adjunct tool for ASD diagnosis, despite its unclear diagnostic yield and cost effectiveness. To address this knowledge gap, we applied WES to a population-based sample of 182 Bedouin and Jewish children with ASD from southern Israel, and assessed its yield in a gene panel of 205 genes robustly associated with ASD. We then compared the incremental cost-effectiveness ratios (ICERs) for an ASD diagnosis by WES, chromosomal microarray analysis (CMA), and CMA + WES. Overall, 32 ASD candidate variants were detected in 28 children, corresponding to an overall WES diagnostic yield of 15.4%. Interestingly, the diagnostic yield was significantly higher for the Bedouin children than for the Jewish children, i.e., 27.6% vs. 11.1% (p = 0.036). The most cost-effective means for genetic testing was the CMA alone, followed closely by the CMA + WES strategy (ICER = USD 117 and USD 124.8 per child). Yet, WES alone could become more cost effective than the other two approaches if there was to be a 25% increase in its yield or a 50% decrease in its cost. These findings suggest that WES should be recommended to facilitate ASD diagnosis in Israel, especially for highly consanguineous populations, such as the Bedouin. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

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20 pages, 2396 KiB

Open AccessArticle

Prenatal Adversity Alters the Epigenetic Profile of the Prefrontal Cortex: Sexually Dimorphic Effects of Prenatal Alcohol Exposure and Food-Related Stress

by Alexandre A. Lussier, Tamara S. Bodnar, Michelle Moksa, Martin Hirst, Michael S. Kobor and Joanne Weinberg

Genes 2021, 12(11), 1773; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12111773 - 09 Nov 2021

Cited by 8 | Viewed by 3327

Abstract

Prenatal adversity or stress can have long-term consequences on developmental trajectories and health outcomes. Although the biological mechanisms underlying these effects are poorly understood, epigenetic modifications, such as DNA methylation, have the potential to link early-life environments to alterations in physiological systems, with long-term functional implications. We investigated the consequences of two prenatal insults, prenatal alcohol exposure (PAE) and food-related stress, on DNA methylation profiles of the rat brain during early development. As these insults can have sex-specific effects on biological outcomes, we analyzed epigenome-wide DNA methylation patterns in prefrontal cortex, a key brain region involved in cognition, executive function, and behavior, of both males and females. We found sex-dependent and sex-concordant influences of these insults on epigenetic patterns. These alterations occurred in genes and pathways related to brain development and immune function, suggesting that PAE and food-related stress may reprogram neurobiological/physiological systems partly through central epigenetic changes, and may do so in a sex-dependent manner. Such epigenetic changes may reflect the sex-specific effects of prenatal insults on long-term functional and health outcomes and have important implications for understanding possible mechanisms underlying fetal alcohol spectrum disorder and other neurodevelopmental disorders. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

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13 pages, 6232 KiB

Open AccessArticle

Autism Spectrum Disorders: Analysis of Mobile Elements at 7q11.23 Williams–Beuren Region by Comparative Genomics

by Francesca Anna Cupaioli, Chiara Fallerini, Maria Antonietta Mencarelli, Valentina Perticaroli, Virginia Filippini, Francesca Mari, Alessandra Renieri and Alessandra Mezzelani

Genes 2021, 12(10), 1605; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12101605 - 12 Oct 2021

Cited by 1 | Viewed by 1910

Abstract

Autism spectrum disorders (ASD) are a group of complex neurodevelopmental disorders, characterized by a deficit in social interaction and communication. Many genetic variants are associated with ASD, including duplication of 7q11.23 encompassing 26–28 genes. Symmetrically, the hemizygous deletion of 7q11.23 causes Williams–Beuren syndrome (WBS), a multisystem disorder characterized by “hyper-sociability” and communication skills. Interestingly, deletion of four non-exonic mobile elements (MEs) in the “canine WBS locus” were associated with the behavioral divergence between the wolf and the dog and dog sociability and domestication. We hypothesized that indel of these MEs could be involved in ASD, associated with its different phenotypes and useful as biomarkers for patient stratification and therapeutic design. Since these MEs are non-exonic they have never been discovered before. We searched the corresponding MEs and loci in humans by comparative genomics. Interestingly, they mapped on different but ASD related genes. The loci in individuals with phenotypically different autism and neurotypical controls were amplified by PCR. A sub-set of each amplicon was sequenced by Sanger. No variant resulted associated with ASD and neither specific phenotypes were found but novel small-scale insertions and SNPs were discovered. Since MEs are hyper-methylated and epigenetically modulate gene expression, further investigation in ASD is necessary. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

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21 pages, 1774 KiB

Open AccessArticle

Environmental Influences Measured by Epigenetic Clock and Vulnerability Components at Birth Impact Clinical ASD Heterogeneity

by Viviane Neri de Souza Reis, Ana Carolina Tahira, Vinícius Daguano Gastaldi, Paula Mari, Joana Portolese, Ana Cecilia Feio dos Santos, Bianca Lisboa, Jair Mari, Sheila C. Caetano, Décio Brunoni, Daniela Bordini, Cristiane Silvestre de Paula, Ricardo Z. N. Vêncio, John Quackenbush and Helena Brentani

Genes 2021, 12(9), 1433; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12091433 - 17 Sep 2021

Cited by 3 | Viewed by 3023

Abstract

Although Autism Spectrum Disorders (ASD) is recognized as being heavily influenced by genetic factors, the role of epigenetic and environmental factors is still being established. This study aimed to identify ASD vulnerability components based on familial history and intrauterine environmental stress exposure, explore possible vulnerability subgroups, access DNA methylation age acceleration (AA) as a proxy of stress exposure during life, and evaluate the association of ASD vulnerability components and AA to phenotypic severity measures. Principal Component Analysis (PCA) was used to search the vulnerability components from 67 mothers of autistic children. We found that PC1 had a higher correlation with psychosocial stress (maternal stress, maternal education, and social class), and PC2 had a higher correlation with biological factors (psychiatric family history and gestational complications). Comparing the methylome between above and below PC1 average subgroups we found 11,879 statistically significant differentially methylated probes (DMPs, p < 0.05). DMPs CpG sites were enriched in variably methylated regions (VMRs), most showing environmental and genetic influences. Hypermethylated probes presented higher rates in different regulatory regions associated with functional SNPs, indicating that the subgroups may have different affected regulatory regions and their liability to disease explained by common variations. Vulnerability components score moderated by epigenetic clock AA was associated with Vineland Total score (p = 0.0036, adjR² = 0.31), suggesting risk factors with stress burden can influence ASD phenotype. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

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15 pages, 2681 KiB

Open AccessArticle

Environmental Enrichment Rescues Social Behavioral Deficits and Synaptic Abnormalities in Pten Haploinsufficient Mice

by Amy E. Clipperton-Allen, Angela Zhang, Ori S. Cohen and Damon Theron Page

Genes 2021, 12(9), 1366; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12091366 - 30 Aug 2021

Cited by 3 | Viewed by 2410

Abstract

Pten germline haploinsufficient (Pten^+/−) mice, which model macrocephaly/autism syndrome, show social and repetitive behavior deficits, early brain overgrowth, and cortical–subcortical hyperconnectivity. Previous work indicated that altered neuronal connectivity may be a substrate for behavioral deficits. We hypothesized that exposing Pten^+/− mice to environmental enrichment after brain overgrowth has occurred may facilitate adaptation to abnormal “hard-wired” connectivity through enhancing synaptic plasticity. Thus, we reared Pten^+/− mice and their wild-type littermates from weaning under either standard (4–5 mice per standard-sized cage, containing only bedding and nestlet) or enriched (9–10 mice per large-sized cage, containing objects for exploration and a running wheel, plus bedding and nestlet) conditions. Adult mice were tested on social and non-social assays in which Pten^+/− mice display deficits. Environmental enrichment rescued sex-specific deficits in social behavior in Pten^+/− mice and partially rescued increased repetitive behavior in Pten^+/− males. We found that Pten^+/− mice show increased excitatory and decreased inhibitory pre-synaptic proteins; this phenotype was also rescued by environmental enrichment. Together, our results indicate that environmental enrichment can rescue social behavioral deficits in Pten^+/− mice, possibly through normalizing the excitatory synaptic protein abundance. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

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8 pages, 553 KiB

Open AccessArticle

Contribution of Multiple Inherited Variants to Autism Spectrum Disorder (ASD) in a Family with 3 Affected Siblings

by Jasleen Dhaliwal, Ying Qiao, Kristina Calli, Sally Martell, Simone Race, Chieko Chijiwa, Armansa Glodjo, Steven Jones, Evica Rajcan-Separovic, Stephen W. Scherer and Suzanne Lewis

Genes 2021, 12(7), 1053; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12071053 - 08 Jul 2021

Cited by 10 | Viewed by 3568

Abstract

Autism Spectrum Disorder (ASD) is the most common neurodevelopmental disorder in children and shows high heritability. However, how inherited variants contribute to ASD in multiplex families remains unclear. Using whole-genome sequencing (WGS) in a family with three affected children, we identified multiple inherited DNA variants in ASD-associated genes and pathways (RELN, SHANK2, DLG1, SCN10A, KMT2C and ASH1L). All are shared among the three children, except ASH1L, which is only present in the most severely affected child. The compound heterozygous variants in RELN, and the maternally inherited variant in SHANK2, are considered to be major risk factors for ASD in this family. Both genes are involved in neuron activities, including synaptic functions and the GABAergic neurotransmission system, which are highly associated with ASD pathogenesis. DLG1 is also involved in synapse functions, and KMT2C and ASH1L are involved in chromatin organization. Our data suggest that multiple inherited rare variants, each with a subthreshold and/or variable effect, may converge to certain pathways and contribute quantitatively and additively, or alternatively act via a 2nd-hit or multiple-hits to render pathogenicity of ASD in this family. Additionally, this multiple-hits model further supports the quantitative trait hypothesis of a complex genetic, multifactorial etiology for the development of ASDs. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

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Review

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5 pages, 187 KiB

Open AccessReview

Impact of Genetic and Genomic Testing on the Clinical Management of Patients with Autism Spectrum Disorder

by Christine F. Stafford and Pedro A. Sanchez-Lara

Genes 2022, 13(4), 585; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13040585 - 25 Mar 2022

Cited by 2 | Viewed by 2478

Abstract

Research has shown that genetics play a key role in the development of autism spectrum disorder (ASD). ASD has been linked to many genes and is a prominent feature in numerous genetic disorders. A genetic evaluation should be offered to any patient who receives a diagnosis of ASD, including deep phenotyping and genetic testing when clinically indicated. When insurance does not cover genetic testing for ASD patients, the lack of medical utility is often cited as a reason for prior authorization request denial. However, ample evidence exists that genetic testing has the power to change clinical management in many of these patients. Genetic testing that results in a diagnosis guides clinicians to screen for associated medical conditions and can direct targeted medical interventions. Given the potential for clinically actionable results, it is important that genetic testing be available and accessible to all patients with ASD. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

23 pages, 1904 KiB

Open AccessReview

PTCHD1: Identification and Neurodevelopmental Contributions of an Autism Spectrum Disorder and Intellectual Disability Susceptibility Gene

by Stephen F. Pastore, Sangyoon Y. Ko, Paul W. Frankland, Paul A. Hamel and John B. Vincent

Genes 2022, 13(3), 527; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030527 - 17 Mar 2022

Cited by 6 | Viewed by 3981

Abstract

Over the last one and a half decades, copy number variation and whole-genome sequencing studies have illuminated the considerable genetic heterogeneity that underlies the etiologies of autism spectrum disorder (ASD) and intellectual disability (ID). These investigations support the idea that ASD may result from complex interactions between susceptibility-related genetic variants (single nucleotide variants or copy number variants) and the environment. This review outlines the identification and neurobiological characterization of two such genes located in Xp22.11, Patched domain-containing 1 (PTCHD1), and its antisense lncRNA PTCHD1-AS. Animal models of Ptchd1 disruption have recapitulated a subset of clinical symptoms related to ASD as well as to ID. Furthermore, these Ptchd1 mouse knockout studies implicate the expression of Ptchd1 in both the thalamic and the hippocampal brain regions as being crucial for proper neurodevelopment and cognitive function. Altered kynurenine metabolic signalling has been postulated as a disease mechanism in one of these animal studies. Additionally, ASD patient-derived induced pluripotent stem cells (iPSCs) carrying a copy number loss impacting the antisense non-coding RNA PTCHD1-AS have been used to generate 2D neuronal cultures. While copy number loss of PTCHD1-AS does not affect the transcription of PTCHD1, the neurons exhibit diminished miniature excitatory postsynaptic current frequency, supporting its role in ASD etiology. A more thorough understanding of risk factor genes, such as PTCHD1 and PTCHD1-AS, will help to clarify the intricate genetic and biological mechanisms that underlie ASD and ID, providing a foundation for meaningful therapeutic interventions to enhance the quality of life of individuals who experience these conditions. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

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18 pages, 344 KiB

Open AccessReview

In Prototypical Autism, the Genetic Ability to Learn Language Is Triggered by Structured Information, Not Only by Exposure to Oral Language

by Laurent Mottron, Alexia Ostrolenk and David Gagnon

Genes 2021, 12(8), 1112; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12081112 - 22 Jul 2021

Cited by 12 | Viewed by 4578

Abstract

What does the way that autistic individuals bypass, learn, and eventually master language tell us about humans’ genetically encoded linguistic ability? In this theoretical review, we argue that autistic non-social acquisition of language and autistic savant abilities provide a strong argument for an innate, human-specific orientation towards (and mastery of) complex embedded structures. Autistic non-social language learning may represent a widening of the material processed during development beyond oral language. The structure detection and manipulation and generative production of non-linguistic embedded and chained material (savant abilities in calendar calculation, musical composition, musical interpretation, and three-dimensional drawing) may thus represent an application of such innate mechanisms to non-standard materials. Typical language learning through exposure to the child’s mother tongue may represent but one of many possible achievements of the same capacity. The deviation from typical language development in autism may ultimately allow access to oral language, sometimes in its most elaborate forms, and also explain the possibility of the absence of its development when applied exclusively to non-linguistic structured material. Such an extension of human capacities beyond or in parallel to their usual limits call into question what we consider to be specific or expected in humans and therefore does not necessarily represent a genetic “error”. Regardless of the adaptive success or failure of non-social language learning, it is the duty of science and ethical principles to strive to maintain autism as a human potentiality to further foster our vision of a plural society. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

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