Genetic Causes and Modifiers of Autism Spectrum Disorder

Genetic Causes and Modifiers in Autism Spectrum
Disorder
Lauren E. Rylaarsdam1, Alicia Guemez Gamboa1*
1
Northwestern University, United States
Submitted to Journal:
Frontiers in Cellular Neuroscience
Specialty Section:
Cellular Neuropathology
ISSN:
1662-5102
Article type:
Review Article
Received on:
l
07 May 2019
a
Accepted on:
n
06 Aug 2019
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Provisional PDF published on:
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P r o Citation:
Rylaarsdam LE and Guemez_gamboa A(2019) Genetic Causes and Modifiers in Autism Spectrum
Disorder. Front. Cell. Neurosci. 13:385. doi:10.3389/fncel.2019.00385
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1 Genetic Causes and Modifiers of Autism Spectrum Disorder
2 Lauren Rylaarsdam1, Alicia Guemez-Gamboa1*
1
3 Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL,
4 United States.
5 * Correspondence:
6 Alicia Guemez-Gamboa
7 [email protected]
8 Keywords: Autism (ASD)1, genetic modifiers2, CNV3, epigenetics4, gene-environment

9 interaction5.
10 Abstract
11 Autism Spectrum Disorder (ASD) is one of the most prevalent neurodevelopmental disorders,
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12 affecting an estimated 1 in 59 children. ASD is highly genetically heterogeneous and may be caused
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13 by both inheritable and de novo gene variations. In the past decade, hundreds of genes have been
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14 identified that contribute to the serious deficits in communication, social cognition, and behavior that
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patients often experience. However, these only account for 10-20% of ASD cases, and patients with
similar pathogenic variants may be diagnosed on very different levels of the spectrum. In this review,
we will describe the genetic landscape of ASD and discuss how genetic modifiers such as copy number
variation, single nucleotide polymorphisms, and epigenetic alterations likely play a key role in
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modulating the phenotypic spectrum of ASD patients. We also consider how genetic modifiers can
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alter convergent signaling pathways and lead to impaired neural circuitry formation. Lastly, we review
sex-linked modifiers and clinical implications. Further understanding of these mechanisms is crucial
for both comprehending ASD and for developing novel therapies.
1 Introduction
24 Autism was first described by Leo Kanner in a study published in 1943, in which he provides a
25 detailed report of 11 children with similar unusual tendencies.(Kanner, 1943) Intriguing common
26 symptoms such as improper facilitation of language, indifference to other people, and obsessive
27 interests can clearly be discerned while reading Kanner’s thorough patient history. Twenty-three years
28 later, the first epidemiological study of autism estimated prevalence to be 4.5 per 10,000 individuals.
29 Estimates have since increased drastically to 1 in 59 individuals affected, with at least three times as
30 many males diagnosed as females.(Loomes et al., 2017) This significant increase in prevalence is
31 partially attributable to both increase in awareness and evolvement of Diagnostic and Statistical
32 Manual of Mental Disorders (DSM) criteria, from a childhood form of schizophrenia in 1952, to a core
33 diagnosis covering a spectrum of disorders in the present.(Zeldovich, 2018) The changing landscape
34 of factors required for diagnosis makes it difficult to quantify the actual increase in prevalence.
35 According to the current DSM-5 criteria, only two core features make up an ASD diagnosis: 1)
36 persistent deficits in social communication and social interaction across multiple contexts; and 2)
37 restricted, repetitive patterns of behavior, interests, or activities. (Lai et al., 2014) Because of the broad
38 nature of these definitions, an ASD diagnosis often co-occurs with other conditions. Motor
39 abnormalities (79%), gastrointestinal problems (up to 70%), epilepsy (up to 30%), intellectual
Genetic Modifiers in ASD
40 disability (45%), and sleep disorders (50-80%) are common examples.(Lai et al., 2014) Language
41 disorders are frequently co-occurring and were even included in the DSM-IV criteria.
42 Since autism’s identification as a diagnosis, the medical and scientific community have put
43 immense effort into determining the risk factors and etiology. In Kanner’s original assessment, he
44 makes the unfortunate observation that in addition to patients having highly intelligent parents, “One
45 other fact stands out prominently. In the whole group, there are very few really warm-hearted fathers
46 and mothers.”(Kanner, 1943) Thankfully, this “Refrigerator Mother” theory of autism was quickly
47 disproved. ASD is now understood to be a disease of complex interaction between genetics and the
48 environment, with heritability estimates ranging from 40-80%.(Chaste and Leboyer, 2012) Extensive
49 genetic studies have revealed hundreds of genes linked to autism. Epidemiological investigations have
50 begun to elucidate which environmental factors might be contributing to risk, but there is a lot left to
51 understand about how they interact with genetic predisposition to contribute to ASD etiology.
52 As is often the case with complex diseases, individuals with similar pathogenic variants may
53 have drastically varying phenotypes. For example, people with duplications of proximal 15q range
54 from unaffected to severely disabled.(Bolton et al., 2001; Cook et al., 1997) Genetic modifiers - factors
55 that modulate the expression of other genes - likely exist when individuals with the same pathogenic
56 variant present on opposite ends of the spectrum. In this review, we will discuss what is presently
57 known about the genetic landscape of ASD, then look at potential modifiers including copy number
58 variation (CNV), double-hit mutations, epigenetic influences, and sex-linked effects.
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60 2 Genetics of ASD
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61 2.1 Identification of candidate ASD risk genes
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Following the classification of autism by Kanner, research efforts were undertaken to determine
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the disease etiology. Though it was initially assumed to be of environmental origin, an improved
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understanding of the role of genetics in human health soon suggested otherwise. In 1977, Folstein and
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Rutter conducted twin studies upon the observation that incidence among siblings was 50x higher than
average.(Folstein and Rutter, 1977) They found that monozygotic twins were more likely to share a
diagnosis than dizygotic twins, suggesting a genetic influence. Bailey and coworkers supported this
finding, documenting 60% concordance for monozygotic twins versus no concordant dizygotic pairs.
(Bailey et al., 1995) In addition, risk of a child having ASD was found to be proportional to the
percentage of the genome they shared with an affected sibling or parent.(Constantino et al., 2010; Risch
et al., 2014; Sandin et al., 2014) By the turn of the century, ASD was established to have some genetic
72 component, though which genes were involved remained a mystery.
73 Early karyotype studies documenting chromosomal abnormalities began to shed light on which
74 regions of the genome were involved.(Gillberg and Wahlström, 1985) Additional susceptibility loci
75 screens implicated regions on chromosome 7q, 1p, 3q, 16p, and 15q.(Auranen et al., 2002; Barrett et
76 al., 1999; Buxbaum et al., 2001; IMGSAC, 1998; International Molecular Genetic Study of Autism
77 Consortium (IMGSAC), 2001; Lamb et al., 2002; Liu et al., 2001; Risch et al., 2014; Shao et al., 2003)
78 However, to investigate at gene-level resolution, early studies had to use the candidate approach.
79 Hypothesized targets included genes from suspected chromosomal regions that played a critical role in
80 neurodevelopment, such as homeobox (Hox) family or Wnt genes. Unsurprisingly, many early studies
81 using this method were largely inconclusive.(Krebs et al., 2002; Lamb et al., 2002; Talebizadeh et al.,
82 2002; Zhang et al., 2002) Starting in 2001, the candidate approach experienced moderate success with
83 findings supporting reelin (RELN), aristaless related homeobox (Arx), methyl-CpG binding protein 2
84 (MeCP2), neuroligin 3 (NLGN3), neuroligin 4 (NLGN4), tuberous sclerosis complex 2 (TSC2), and
85 ubiquitin protein ligase E3A (UBE3A)’s involvement in ASD etiology (Carney et al., 2003; Jamain et
86 al., 2003; Jiang et al., 2004; Persico et al., 2001; Serajee et al., 2003; Strømme et al., 2002)
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87 In the early 2000s, the advent of high throughput sequencing revolutionized genetic research and
88 enabled investigators to study ASD on a genome-wide level. Sequencing technology quickly confirmed
89 that the etiology of ASD was multigenic and highly heterogeneous, with very few of the same
90 pathogenic variants present in a significant percentage of afflicted individuals. It is now known that
91 the average case is a product of many susceptibility-increasing variations. Only a handful of ASD-
92 related diseases have monogenic causes, such as Rett syndrome, fragile X syndrome, tuberous
93 sclerosis, and Schuurs-Hoeijmakers syndrome. (Artuso et al., 2011; Stern et al., 2017; Woodbury-
94 Smith and Scherer, 2018) Dozens of large-scale genetic studies have since been conducted on ASD
95 patients and their families, leading to hundreds of risk genes being identified. While these proteins
96 have diverse functions, a majority of reproducible hits come from two broad classes of proteins: those
97 involved in synapse formation, and those involved in transcriptional regulation and chromatin-
98 remodeling pathways.(De Rubeis et al., 2014)
99 Synapse-related risk genes include those encoding cell-adhesion proteins such as neuroligins,
100 neurexins, and cadherins; synaptic vesicle cycling proteins synapsin-1 (SYN1) and synapsin-2
101 (SYN2); ion transport proteins such as sodium voltage-gated channel alpha subunit 2 (SCN2A),
102 calcium voltage-gated channel subunit alpha1 E (CACNA1E), calcium voltage-gated channel auxiliary
103 subunit beta 2 (CACNB2), potassium voltage-gated channel subfamily Q members 3 and 5 (KCNQ3
104 and KCNQ5), potassium voltage-gated channel subfamily D member 2 (KCND2), glutamate receptor
105 signaling protein SH3 and multiple ankyrin repeat domains 3 (SHANK3), synaptic Ras GTPase
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activating protein 1 (SYNGAP1), and gamma-aminobutyric acid type A receptor gamma3 subunit
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(GABRG3).(Durand et al., 2012; Giovedí et al., 2014; Jamain et al., 2003; Schmunk and Gargus, 2013;
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Stessman et al., 2017) In vivo data supports the implication of synapse pathology and abnormal neural
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109 network formation in ASD.
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110 Additional susceptibility loci impact transcription of other proteins through various mechanisms.
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For example, multiple studies have found an increased de novo mutation load in regulatory elements
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of ASD risk genes in patients.(Short et al., 2018; Turner et al., 2016, 2017) The broad class of
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susceptibility genes that impacts transcription and chromatin-remodeling pathways includes MeCP2,
UBE3A, chromodomain helicase DNA binding protein 8 (CHD8), activity dependent neuroprotector
homeobox (ADNP), pogo transposable element derived with ZNF domain (POGZ), fragile X mental
retardation protein (FMRP), and RNA binding forkhead box (RBFOX) genes. (Carney et al., 2003, 2;
De Rubeis et al., 2014; Samaco et al., 2005; Stessman et al., 2017; Tran et al., 2019) These pathogenic
118 variants have the potential to induce extremely widespread effects. For example, Tran and coworkers
119 recently showed that FMRP and fragile X related protein 1 (FXRP1) mutations can result in abnormal
120 RNA-editing enzyme activity, resulting in a global bias for adenosine-to-inosine hypoediting in ASD
121 brains.(Tran et al., 2019) Diverse phenotypes that may result are further discussed in the epigenetics
122 section.
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124 2.1.1 Somatic mosaicism and ASD risk
125 Disease-causing variations were conventionally thought to be familial/inherited and present in
126 every cell in the body. However, the role of somatic mosaicism, which is the result of a post-zygotic
127 DNA mutation, is increasingly being recognized as crucial to various neurodevelopmental diseases
128 including autism.(D’Gama and Walsh, 2018; Poduri et al., 2013; Ronemus et al., 2014) During
129 neurogenesis, each progenitor gives rise to roughly five single nucleotide variants (SNV) per day as
130 the brain rapidly develops.(Bae et al., 2018; D’Gama and Walsh, 2018) Studies estimate that of de
131 novo pathogenic variations, roughly 5-7% are postzygotic, though estimates of up to 22% have been
132 reported.(Acuna-Hidalgo et al., 2015; Freed and Pevsner, 2016; Krupp et al., 2017; Lim et al., 2017)
133 Most mutations are harmless, but variations in exons can be extremely detrimental. Pathogenic somatic
134 variations have been connected to ASD, Rett syndrome, tuberous sclerosis, intellectual disability,
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135 schizophrenia, and many other disorders.(Acuna-Hidalgo et al., 2015; Bourdon et al., 2001; Clayton-
136 Smith et al., 2000; D’Gama and Walsh, 2018; Dou et al., 2017; Doyle et al., 2017; Freed and Pevsner,
137 2016; Gilissen et al., 2014; Krupp et al., 2017; Qin et al., 2010; Tyburczy et al., 2015)
138 Until recently, our understanding of somatic mosaicism in ASD was restricted primarily to case
139 reports.(Castermans et al., 2008; Havlovicova et al., 2007; Kakinuma et al., 2008; Oliveira et al., 2003;
140 Papanikolaou et al., 2006; Sauter et al., 2003; Vorstman et al., 2011; Yurov et al., 2007) Several recent
141 investigations of whole exome-sequencing (WES) data from large cohorts have been instrumental in
142 shaping our understanding of the role of somatic mosaicism, which is currently estimated to account
143 for roughly 3-5% of simplex ASD cases.(Freed and Pevsner, 2016; Krupp et al., 2017) Lim and
144 coworkers used WES analysis of 5,947 ASD-affected families and determined that somatic variations
145 in autistic individuals were more likely to be in critical exons than variations in control siblings.(Lim
146 et al., 2017) Interestingly, they found that the pathogenic variants had enhanced expression in the
147 amygdala, an area critical for emotional response and social awareness.(Rasia-Filho et al., 2000) In
148 another large WES study, new risk genes identified were enriched in the cerebellum, which suggests
149 potential coordination difficulty that could be related to gait disorders common in autistic
150 children.(Dou et al., 2017) Freed and colleagues analyzed 2,388 families and identified an
151 ascertainment bias for pathogenic mosaic variations in ASD individuals relative to unaffected
152 siblings.(Freed and Pevsner, 2016) These large-scale sequencing studies of post-zygotic mutations
153 have both confirmed previously implicated candidate genes, such as SCN2A, in addition to revealing
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etiology.(Lim et al., 2017)
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dozens of new risk genes and establishing somatic mosaicism as a significant factor in ASD
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157 2.1.2 CNVs contribute to ASD susceptibility
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Copy number variations (CNVs) are submicroscopic structural variants in chromosomes that
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include duplications, deletions, translocations, and inversions, sometimes stretching several
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kilobases.(Marshall et al., 2008) CNV can either be inherited or arise de novo.(Thapar and Cooper,
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2013) Many genes may be affected with these changes, but not all are necessarily drivers of disease.
Studies have found a higher load of rare, genic CNVs in autistic individuals, implicating these variants
in ASD pathology.(Pinto et al., 2010; Pizzo et al., 2019; Sebat et al., 2007) CNV is now understood as
an extremely important contributing factor in ASD susceptibility, and current estimates postulate that
these variations directly cause roughly 10% of ASD cases.(Geschwind, 2011)
Studies of how individual CNVs contribute to ASD have been done for more frequent structural
variants, such as 16p11.2 duplications. The majority of the 25 genes in this region are highly active
168 during nervous system development and are critical for proper formation.(Blaker-Lee et al., 2012)
169 While the alteration of many genes involved in development suggests a mechanism for the diverse
170 symptoms observed in ASD, Golzio and coworkers reported that only one gene in the 16p11.2 region,
171 potassium channel tetramerization domain containing 13 (KCTD13), seems to be the major driver for
172 neuropsychiatric disease.(Golzio et al., 2012) Duplications or deletions of this gene are thought to
173 affect synaptic transmission through altered regulation of Ras homolog family member A
174 (RHOA).(Escamilla et al., 2017) However, Escamilla and colleagues also hypothesized that KCTD13
175 deletions alone are not likely to be sufficient for disease. Mouse models suggest another gene in the
176 16p11.2 region as a driver of disease - mitogen-activated protein kinase 3 (MAP3) - with deletions
177 resulting in altered cortical cytoarchitecture and reduced brain size.(Pucilowska et al., 2015). Likely,
178 the real driver of disease in 16p11.2 duplications or deletions is not from just one gene, but an
179 interaction of all 25 contributing to susceptibility. Iyer and coworkers systematically investigated
180 interaction between genes in the 16p11.2 region, using RNAi in Drosophila to test 565 pairwise
181 knockdowns. In addition to 24 modifying interactions discovered between pairs of genes within the
182 16p11.2 region, they also found 46 interactions between 16p11.2 genes and others involved in
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183 neurodevelopment.(Iyer et al., 2018) This strongly suggests that modifying interactions within CNVs
184 result in the complex phenotypes observed and may not be elucidated from studies with single genes,
185 a phenomenon that is likely true for other CNV regions in addition to 16p11.2.
186 The disease mechanisms of other CNVs are less frequently studied due to the paucity of
187 commonly affected regions. Even the most prevalent ASD-associated CNVs, such as 15q11-13 as well
188 as 16p11.2, are only present in roughly 1% of autism cases.(Kumar et al., 2008; Marshall et al., 2008;
189 Marshall and Scherer, 2012; Weiss et al., 2008) In addition, there are no known CNVs with complete
190 penetrance; studies that find CNVs with significant correlation to ASD often detect non-ASD carriers,
191 or ASD siblings without the variant.(Marshall et al., 2008) One useful approach in the midst of this
192 heterogeneity is to assess common functional networks affected. Repeatedly, studies have shown that
193 autistic individuals have deletions in synaptic genes, such as SHANK3, dipeptidyl peptidase-like 10
194 (DPP10), neuroligins, and neurexins.(Glessner et al., 2009; Marshall et al., 2008; Marshall and
195 Scherer, 2012; Pinto et al., 2010, 2014; The Autism Genome Project Consortium et al., 2007) Other
196 common functional gene sets with rare CNVs include those involved in cell proliferation and
197 development, chromatin regulation, and ubiquitin pathways.(Glessner et al., 2009; Pinto et al., 2010,
198 2014)
199 With certain CNVs, copy number dosage appears to affect disease phenotype. For example,
200 Horev and colleagues observed a dose-dependent effect and change in brain structure in mice with
201 16p11.2 deletions and duplications, but this effect is not as established in humans.(Horev et al., 2011;
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Kumar et al., 2008) Another study investigating CNV in the locus containing the UBE3A gene also
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report a positive correlation between duplication and autistic traits in mice, as well as decreased
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glutamatergic synaptic transmission.(Smith et al., 2011) In humans, Stefansson and colleagues
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205 analyzed a 15q11.2 CNV region of autistic individuals and found two brain areas with dose-dependent
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206 structural and functional effects. Interestingly, some non-ASD/schizophrenic controls who were
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diagnosed with dyslexia and dystaxia also exhibited the same structural changes.(Stefansson et al.,
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2014) In another study with humans, Girirajan and coworkers reported a dose-dependent effect from
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their microarray analysis with identified CNVs in ASD-associated genes, finding a positive correlation
between duplication size increase and autism severity increase, but no correlation between duplication
size and nonverbal IQ.(Girirajan et al., 2013) CNV are often critical and complex contributors to ASD
risk, but patients with similar structural variants may have highly variable phenotypes. Following
sections will discuss how non-causative modifiers play an important role in modulating CNV
214 pathogenicity.
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216 2.1.3 Epigenetic regulation and ASD
217 Genes with epigenetic-modulating functions are highly involved in ASD susceptibility. A recent
218 review of 215 candidate genes estimated that 19.5% are epigenetic regulators, suggesting the potential
219 for diverse disease phenotypes from few pathogenic variants.(Duffney et al., 2018) Another study
220 suggested that risk genes with high penetrance were typically located in the nucleus and involved in
221 modulation of expression, or tied to the protein-protein interaction network essential in guiding CNS
222 developmental patterning.(Casanova et al., 2016) Twin studies particularly demonstrate the profound
223 ways epigenetics can modulate disease phenotype; for example, a study of 50 pairs of monozygotic
224 twins discordant for ASD reported numerous autism-associated differentially methylated regions, with
225 methylation patterns at some CpG sites common to symptom groups.(Wong et al., 2014)
226 Though the scientific and medical community still has a great deal to learn about epigenetic
227 modulation of ASD, patterns have emerged from large-scale epigenomic studies. Susceptibility loci
228 often include genes involved in methylation such as KMT2C, lysine methyltransferase 5B (KMT5B),
229 and lysine demethylase 6B (KDM6B); chromatin remodeling proteins including MeCP2, CHD8, and
230 POGZ; RNA-binding/splicing proteins such as FMRP and the RBFOX family, post-translational
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231 modification proteins like UBE3A, mindbomb E3 ubiquitin protein ligase 1 (MIB1); or transcription
232 factors like ADNP and additional sex combs like 3 (ASXL3).(De Rubeis et al., 2014) Targets of these
233 proteins can range from few to hundreds, and often include pathways previously implicated in autism,
234 such as synaptic formation. To demonstrate how mutations in a single epigenetic regulator can modify
235 many other risk genes, we will look more in depth at two key susceptibility genes: MeCP2 and UBE3A.
236 MeCP2 is a chromatin modifier that is consistently implicated in ASD. In a healthy individual,
237 the binding action of MeCP2 has been shown to regulate many genes with synaptic function, such as
238 GABRB3, brain derived neurotrophic factor (BDNF), distal-less homeobox 5 (DLX5), insulin like
239 growth factor binding protein 3 (IGFBP3), cyclin dependent kinase like 1 (CDKL1), protocadherin
240 beta 1 (PCDHB1), protocadherin 7 (PCDH7), and lin-7 homolog A (LIN7A).(Kubota and Mochizuki,
241 2016; Samaco et al., 2005) It also serves post-translational functions.(Cheng and Qiu, 2014) In
242 addition, MeCP2 is the rate-limiting factor in regulating glutamatergic synapse formation during
243 development, which implicates its involvement in yet another important aspect of ASD
244 pathology.(Chao et al., 2007) MeCP2 is shown to be reduced in the frontal cortex of ASD individuals
245 due to increased methylation of its promoter.(Nagarajan et al., 2006, 2008; Samaco et al., 2005)
246 UBE3A, an E3 ubiquitin protein ligase, is a second important epigenetic regulator strongly
247 implicated in ASD pathology. It is modulated by MeCP2, but can be causative on its own.(Samaco et
248 al., 2005, 2) UBE3A lies in the chromosomal region 15q11-13, which is commonly duplicated in
249 autism. Dose-dependent effects have been positively correlated with reduced excitatory synaptic
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transmission, delay of first word, and psychomotor regression.(Guffanti et al., 2011; Smith et al., 2011;
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Xu et al., 2018) The mechanism of UBE3A’s pathological activity can be hypothesized based on its
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function as a ubiquitin ligase, which targets proteins for degradation, but research is still revealing
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253 exactly how these dose-dependent impairments occur. Lee and coworkers identified four proteosome-
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254 related proteins that were direct substrates of UBE3A.(Lee et al., 2014) Overexpression of UBE3A and
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one of its substrates, proteasome 26S subunit, non-ATPase 4 (Rpn10), led to increased accumulation
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of ubiquitinated proteins, suggesting a proteostatic imbalance. Proteosome health has been strongly
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implicated in dendritic spine outgrowth, linking UBE3A with one of the key pathologies observed in
autism.(Hamilton et al., 2012; Puram et al., 2013) Its involvement in Wnt signaling could also cause
significant perturbation during development.(Yi et al., 2017) MeCP2 and UBE3A are just two examples
of how one altered gene can have extremely far-reaching effects.
Large-scale epigenetic studies have also helped achieve a broader picture of epigenetic mis-
262 regulation in ASD. Sun and coworkers conducted a histone acetylome-wide association study on 257
263 post-mortem prefrontal and temporal cortex samples. Surprisingly, they found that >68% of both
264 syndromic and idiopathic cases shared a common acetylome signature at roughly 5,000 enhancer
265 regions.(Sun et al., 2016) Intriguingly, a SHANK3 mouse model of autism displayed rescued
266 behavioral phenotypes when treated with a potent histone deacetylase inhibitor, reinforcing the role of
267 epigenetics in ASD.(Qin et al., 2018) Ladd-Acosta and coworkers measured over 485,000 CpG loci in
268 post-mortem brain tissue from 40 individuals and identified four differentially methylated regions.
269 Three sites were found in cortical tissue: the proline rich transmembrane protein 1 (PRRT1) 3′ UTR,
270 promoter regions of tetraspanin 32 (TSPAN32), and C11orf21. The last site, an alternative promoter
271 for succinate dehydrogenase complex flavoprotein subunit A pseudogene 3 (SDHAP3), was found in
272 cerebellar tissue.(Ladd-Acosta et al., 2014) Affected pathways implied in these studies and others
273 include synaptic transmission, immune function, ion transport, and GABAergic genes.(Andrews et al.,
274 2017; Nardone and Elliott, 2016; Sun et al., 2016; Zhubi et al., 2017)
275 Mor and colleagues took a different approach, using small RNA sequencing data and correlating
276 results to genome-wide DNA methylation data to find dysregulated miRNAs. miRNAs that were found
277 to be significantly expressed in the ASD brain were linked to synaptic function, consistent with data
278 from numerous other studies.(Mor et al., 2015) They also discovered a link to the oxytocin receptor
279 (OXTR) gene, suggesting attenuated OXTR expression in the autistic brain. This finding was supported
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280 by a study that found fetal membranes from preterm birth had hypermethylated OXTR, potentially
281 linking an environmental risk factor to a pathological mechanism.(Behnia et al., 2015) Another risk
282 gene with epigenetic functions is engrailed homeobox 2 (EN2), a homeobox gene with an unusual
283 methylation pattern in ASD that has been hypothesized to cause abnormal cerebellar Purkinje
284 growth.(James et al., 2013) The list of ASD risk genes with epigenetic functions is vast, suggesting a
285 mechanism by which few mutations can result in widespread misregulation of gene expression.
286 Because of this, genes with epigenetic functions and their substrates may be promising targets of
287 therapies. For example, mutations in FMRP, a chromatin remodeler, result in widespread gene
288 expression abnormalities, but a recent study found that inhibition of FMRP target bromodomain
289 containing 4 (BRD4) alleviated many of the disease characteristics.(Korb et al., 2017) Proteins with
290 epigenetic-regulating function may also be key targets of disease modifiers, a concept that will be
291 discussed later in this review.
292 2.2 ASD risk genes overlap with other diseases

293 Large-scale sequencing studies of major psychiatric diseases have revealed extensive overlap in
294 risk loci, challenging the classification of these conditions as distinctive disorders. In 2013, the Cross-
295 Disorder Group of the Psychiatric Genomics Consortium (PGC) conducted a massive study with
296 33,332 cases and 27,888 controls in order to identify pathogenic variants shared between ASD,
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297 schizophrenia, bipolar disorder, ADHD, and major depressive disorder.(Cross-Disorder Group of the
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Psychiatric Genomics Consortium, 2013; Cross-Disorder Group of the Psychiatric Genomics
Consortium et al., 2013) In addition to establishing varying degrees of pair-wise crossover, they found
loci that reached genome-wide significance for all five disorders near the following genes: inter-alpha-
trypsin inhibitor heavy chain 3 (ITIH3), arsenite methyltransferase (AS3MT), calcium voltage-gated
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channel subunit alpha1 C (CACNA1C), and CACNB2. Glessner and coworkers have also conducted a
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large-scale meta-analysis of structural variants across the same diseases and correlated structural
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variants in the loci of dedicator of cytokinesis 8 (DOCK8) and KN motif and ankyrin repeat domains
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1 (KANK1) with all five conditions.(Glessner et al., 2017) Schork and colleagues recently
hypothesized that abnormal gene regulation in radial glia and interneurons during mid-gestation is a
mechanism of shared risk, after using GWAS to identify susceptibility loci in genes including
phosphodiesterase 1A (PDE1A), protein phosphatase 1 regulatory inhibitor subunit 1C (PPP1R1C),
RHOA, immunoglobulin superfamily member 11 (IGSF11), and sortilin related VPS10 domain
containing receptor 3 (SORC3).(Schork et al., 2019)
Studies also report shared susceptibility genes across a more restricted set of psychiatric diseases.
312 For example, ASD, intellectual disability (ID), and schizophrenia have been found to share risk loci in
313 FMRP targets, CHD5, CHD8, SCN2A, and neurexin 1 (NRXN1).(Iossifov et al., 2014; Wang et al.,
314 2019) Wang and coworkers also found commonalities across ASD, ID, and bipolar disorder with
315 increased incidence of de novo pathogenic variants in periodic circadian regulator 1 (PER1) and lysine
316 methyltransferase 2C (KMT2C). Khanzada and colleagues found 23 susceptibility genes common to
317 ASD, bipolar disorder, and schizophrenia including dopamine receptor D2 (DRD2), cholinergic
318 receptor nicotinic alpha 7 subunit (CHRNA7), 5-hydroxytryptamine receptor 2A (HTR2A), solute
319 carrier family 6 member 3 (SLC6A3), and tryptophan hydroxylase 2 (TPH2). Hit genes were primarily
320 involved in dopamine and serotonin homeostasis, suggesting a potential mechanism for abnormal
321 emotional regulation observed across all three disorders.(Khanzada et al., 2017) The immense
322 crossover revealed in these studies intriguingly suggests some level of shared etiology across
323 psychiatric conditions, despite having clinically distinct presentations.
324 Of the four other diseases assessed in the PGC study, the most highly correlated disease to ASD
325 was schizophrenia.(Cross-Disorder Group of the Psychiatric Genomics Consortium et al., 2013)
326 Previous epidemiological studies had suggested their linkage, reporting increased risk of ASD in
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327 children with schizophrenic parents and significant co-morbidity of child-onset schizophrenia and
328 autism.(Rapoport et al., 2009; Sullivan et al., 2012) A follow-up report to the 2013 PGC study
329 estimated genetic correlation between the two diseases to be 23%, with shared risk loci including
330 several genes involved in neurodevelopment, such as forkhead box P1 (FOXP1), exostosin
331 glycosyltransferase 1 (EXT1), astrotactin 2 (ASTN2), mono-ADP ribosylase 2 (MACROD2), and
332 histone deacetylase 4 (HDAC4).(The Autism Spectrum Disorders Working Group of The Psychiatric
333 Genomics Consortium, 2017) In addition to susceptibility genes involved in neurodevelopment, other
334 studies also reported shared susceptibility in genes affecting chromatin remodeling, oxidative stress
335 response, and lipid metabolism.(Lim et al., 2017; McCarthy et al., 2014).
336 Many studies have also found a significant correlation between autistic and ADHD scored traits.
337 This includes a study of autistic symptoms in ADHD probands and siblings, autistic trait correlation in
338 an ADHD twin sample, and an association between autistic and ADHD traits in the general population.
339 (Mulligan et al., 2009; Reiersen et al., 2007; Ronald et al., 2008; Stergiakouli et al., 2017) Nijmeijer
340 and coworkers identified five specific genetic loci that were associated with ASD traits in children with
341 ADHD: 7q36, 16p13, 18p11, 15q24, and 12q24.(Nijmeijer et al., 2010) A study investigating the
342 overlap of pathological structural variants in ADHD and ASD found significant overlap in genes
343 related to a wide variety of processes, including the nicotinic receptor signaling pathway and cell
344 division.(Martin et al., 2014) The shared heritability of ASD and ADHD is still being explored, and is
345 further discussed in a review by Rommelse and coworkers.(Rommelse et al., 2010)
346
347
348
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Since ASD is a multigenic and highly heterogeneous disease that often co-occurs with other
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conditions, it can be difficult to distinguish which genes truly have overlapping risk for multiple
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psychiatric conditions, and which variations are responsible for the common disease phenotypes. For
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349 example, the ubiquitin ligase gene UBE3A is implicated in both autism and Angelman Syndrome, a
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350 condition distinct from ASD but with similar symptoms, such as movement and speech defects.
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352
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354
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Interestingly, Angelman Syndrome is generally associated with UBE3A deletions, while ASD can be
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caused by duplications - yet the same individual can be diagnosed with both syndromes.(Kalsner and
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Chamberlain, 2015; Peters et al., 2004; Smith et al., 2011; Williams et al., 2010; Yi et al., 2015)
Another example is intellectual disability, which co-occurs with autism in roughly 45% of cases.(Lai
et al., 2014) Multiple studies have found that ASD and intellectual disability share risk loci,(McCarthy
et al., 2014; Pinto et al., 2010) but overlapping phenotypes are a potentially confounding factor.
Similarly, other risk genes for ASD are epigenetic regulators whose effectors are associated with
358 different diseases.(Michaelson et al., 2017; Pinto et al., 2010; Samaco et al., 2005, 2) The interaction
359 and overlap between psychiatric disorders is complex, and much is left to discern regarding shared
360 disease mechanisms.
361 3 Modifiers in ASD
362 3.1 Genetic modifiers

363 Though significant progress has been made in determining genetic causes of ASD, many aspects
364 of how pathogenic variants regulate genetic susceptibility remain unknown. Individuals with the same
365 variants can have widely heterogeneous disease presentations and levels of disability. Presence of
366 second modulating variants that may interact with other susceptibility loci are one possible explanation
367 of this heterogeneity. This “second hit” could be somatic – a phenomenon first proposed to cause
368 disease by Alfred Knudson in the context of retinoblastomas - or in the germline, a “two-locus model”
369 previously explored in conditions such as Hirschprung disease.(Knudson, 1971; Fisher and Scambler,
370 1994; McCallion et al., 2003) To date, genetic evidence supporting a multiplex theory of autism has
371 primarily been found for germline second-hits. Studies with CNVs will be discussed first, followed by
372 a brief overview of known modulating SNPs. These investigations of how non-causative variants may
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373 modify the ASD phenotype are challenging to undertake, as few autistic individuals have the same
374 pathogenic variants. In addition, there is not yet a complete understanding of which CNVs and SNPs
375 are pathogenic in ASD.
376 One way to circumvent these issues is to investigate an autism subtype with a monogenic cause,
377 such as Rett Syndrome. Artuso and coworkers used this strategy and identified 15 “likely” and 14
378 “unlikely” modulators of the RTT phenotype based on array comparative genome hybridization with
379 eight RTT subjects.(Artuso et al., 2011) Another valuable approach is to assess monozygotic twins
380 with a discordant phenotype. Several studies have assessed potential differences in CNVs or epigenetic
381 regulation in discordant monozygotic twins, revealing potential methylation pattern differences in one
382 case and anomalies in the 2p25.3 region in another.(Kunio et al., 2013; Rio et al., 2013) However, a
383 study involving 100 twin pairs failed to find differences in CNVs that could explain the discordant
384 phenotypes.(Stamouli et al., 2018) The authors still acknowledge postzygotic mosaicism as a potential
385 modifier and encourage more studies to help develop a clearer understanding of CNV modulating
386 activity.
387 A handful of reports also exist of putative modifying CNVs in polygenic ASD cases with
388 unrelated subjects. For example, Girirajan and coworkers found that children with two CNVs not
389 known to be pathological were eight times more likely to be diagnosed with developmental delay than
390 controls.(Girirajan et al., 2012) In the same year, a study of SHANK2 pathogenic variants found
391 abnormalities in both individuals with neuropsychiatric disease and controls, suggesting the presence
392
393
394
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of additional variants in order to cause disease. Three of the patients with de novo SHANK2 mutations
a
were also found to have deletions of CHRNA7 and cytoplasmic FMR1 interacting protein 1 (CYFIP1)
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- both previously implicated in ASD - supporting a “multiple-hit” model of autism.(Leblond et al.,
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395 2012) CHRNA7 was also suggested as a potential modifier in an earlier study by Szafranski and
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396 coworkers.(Szafranski et al., 2010) Barber and colleagues provided further support for a multiple-loci
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398
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model of ASD upon finding that patients with 16p12.1 duplications had a more severe phenotype when
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a second large CNV was present.(Barber et al., 2013) Included in these hypothesized modifier regions
r
were genes G protein regulated inducer of neurite outgrowth 2 (GPRIN2) - previously implicated as a
modifier in the study by Artuso and coworkers - and steroid sulfatase (STS), which was formerly
thought to be non-causative.(Artuso et al., 2011; Li et al., 2010) More recently, an analysis of 20,226
patient records revealed 19 patients with CNVs in contactin 6 (CNTN6), a gene hypothesized to be
involved in neurodevelopmental disorders including ASD.(Repnikova et al., 2019) The authors were
404 not able to find any significant genotype-phenotype relationships and concluded that CNV in CNTN6
405 were likely benign or modifying, but not causative of disease.
406 In addition to CNVs, there may be thousands of smaller pathogenic variants - such as SNPs and
407 indels - that also modulate severity. For example, in a study of developmental delay, individuals that
408 only carried a specific 16p12.1 microdeletion had a less severe phenotype than individuals with random
409 second variants.(Girirajan et al., 2010) One study of individuals with 22q11.2 deletion syndrome - all
410 haploinsufficient for an mGluR network gene - found that 20% who were co-diagnosed with autism
411 had second-hit pathogenic variants, while only 2% of 22q11DS individuals without autism had second
412 hits.(Wenger et al., 2016) Bonnet-Brilhault and coworkers assessed a family affected with ID and ASD
413 due to NLGN4X pathogenic variants and found that individuals with ASD - but not ID or controls - had
414 second-hit variants in glycine receptor beta (GRLB) and ankyrin 3 (ANK3). (Bonnet-Brilhault et al.,
415 2016) Additional evidence may exist, but GWAS and WES studies have tended to focus on causative
416 susceptibility loci. Therefore, other variants which are not causative by themselves are not often
417 emphasized or even reported. The emerging study of all types of genetic modifiers is a relatively recent
418 development, and continuing advancements in sequencing technology, analyzing software, and
419 expansion of databases should lay the framework for significant advancements in the near future.
420 3.2 Epigenetics and the environment
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421 Autism susceptibility is currently estimated to be 40%-80% genetic. Environmental factors -

422 likely acting through epigenetic regulation as the major mechanism - presumably compromise the
423 remainder of the risk. Hundreds of potential environmental factors have been suggested to contribute
424 to risk, such as increased parental age (especially paternal), maternal complications or infections during
425 pregnancy, or prenatal exposure to anticonvulsants.(Kong et al., 2012; Ohkawara et al., 2015; O’Roak
426 et al., 2012; Rasalam et al., 2005) In-depth reviews of these findings can be found elsewhere.(Bölte et
427 al., 2019; Chaste and Leboyer, 2012; Karimi et al., 2017; Liu et al., 2016; Modabbernia et al., 2017)
428 In this review, we will only discuss the epigenetic modifying effects of valproic acid - an anticonvulsant
429 - as one example of the widespread modifications that an environmental factor can induce. Valproic
430 acid has been hypothesized to modify gene expression through histone deacetylase inhibition activity
431 and is sometimes used to induce an autistic phenotype in animal models.(Kataoka et al., 2013)
432 Examples of its far-reaching effects include apoptotic cell death in the neocortex, decreased
433 proliferation in the ganglionic eminence, increased homeobox A1 (HOXA1) expression, abnormal
434 serotonergic differentiation via Achaete-Scute family BHLH transcription factor 1 (ASCL1) silencing,
435 disrupted serotonin homeostasis in the amygdala, dendritic spine loss, reduced prefrontal dopaminergic
436 activity, and disruption of the glutamatergic/GABAergic balance.(Dufour-Rainfray et al., 2010; Hara
437 et al., 2015; Iijima et al., 2016; Jacob et al., 2014; Kataoka et al., 2013; Mahmood et al., 2018; Stodgell
438 et al., 2006; Takuma et al., 2014; Wang et al., 2013)
439 In more thorough studies of the mechanism of action, Go and coworkers found that rats exposed
440
441
442
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to valproic acid in utero presented enhanced proliferation of neural progenitors and delayed
a
neurogenesis by upregulating Wnt1 expression and activating the GSK-3β/β-catenin pathway, leading
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to macrocephaly.(Go et al., 2012) Another study found that valproic acid increased BDNF by two
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443 transcriptional mechanisms involving MeCP2 and tissue plasminogen activator (tPA). This increase in
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444 BDNF is proposed to alter neurite outgrowth, impairing synapse formation.(Ko et al., 2018) Finally,
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Koloszi and coworkers observed a downregulation of NLGN3 - a highly implicated autism risk gene
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involved in synapse formation - in both hippocampal and somatosensory cortex of valproate-exposed
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mice.(Kolozsi et al., 2009) Examples of other proposed environmentally-modulated mechanisms of
ASD risk exist, but the literature supporting valproic acid is an excellent example of the heterogeneous
effects one environmental factor can induce. Further research is strongly needed to determine how the
environment modulates ASD risk.
Clearly, epigenetics can have a profound impact on the transcriptome of an organism. Pathogenic
452 variants in even one epigenetic-regulating gene or effects from the environment can cause widespread
453 gene dysregulation. Epigenetic modulators can themselves be causative of disease, but they may also
454 exacerbate or ameliorate the disease phenotype by influencing expression of risk genes. More genome-
455 wide studies are needed to understand the common ASD epigenome, and whether certain epigenetic
456 markings might be protective or detrimental to individuals who are genetically susceptible. In addition,
457 more studies are needed to decipher epigenetics as a link between environmental risk factors and
458 genetic susceptibility. There is a small possibility that certain environmental factors could have
459 protective epigenetic effects, providing potential avenues for therapy.
460 3.3 Sex-linked modifiers

461 It is well established that ASD affects males at much higher rates than females. The reasons for
462 this are not yet completely clear. Some studies argue that differential expression between genders may
463 result in an under-diagnosis of females, as males tend to present more external behavior (e.g.,
464 aggression or increased repetitive behavior) and females tend to present more internal behavior (e.g.,
465 depression and avoiding demands).(Werling and Geschwind, 2013) While this may contribute to the
466 rates of diagnosis, other possibilities include that the female sex is protective and/or males are
467 particularly vulnerable. This may be due to influence from hormones, genetics, or other unknown
10
468 factors. The genetically heterogeneous nature of ASD makes it likely that all these elements are
469 involved – sex bias varies drastically based on factors such as which CNVs are causative or which
470 comorbidities are present, suggesting diverse means by which a sex bias may occur.(Polyak et. al.,
471 2015; Amiet et al., 2008) Potential mechanisms of sex-specific modulation will be discussed briefly,
472 although more thorough reviews are available elsewhere.(Ferri et al., 2018)
473 Multiple studies argue that the female sex is protective towards ASD susceptibility.(Pinto et al.,
474 2014; Robinson et al., 2013) For example, the average mutational burden in diagnosed females is much
475 higher than in males, suggesting that males have a lower mutational burden threshold.(Desachy et al.,
476 2015; Jacquemont et al., 2014) Another study by Robinson and coworkers investigated nearly 10,000
477 dizygotic autistic twin pairs and found that siblings of female probands had significantly worse
478 symptoms than siblings of male probands.(Robinson et al., 2013) Many investigations have also found
479 that unaffected mothers may carry the same mutation as their affected male children. One particularly
480 well-documented example for this is the 15q11-13 duplication.(Boyar et al., 2001; Cook et al., 1997;
481 Gurrieri et al., 1999; Schroer et al., 1998) This region codes for GABAA receptors, which is supported
482 by the observation of perturbed GABA signaling in ASD.(Al-Otaish et al., 2018) The discovery that
483 estrogens rescue ASD phenotypes in both zebrafish and mouse models of autism is an especially
484 convincing piece of evidence for the female protective theory.(Hoffman et al., 2016; Macrì et al., 2010)
485 It is also possible that the female sex is not protective, but males are particularly vulnerable. Three
486 studies of gene expression patterns noted males generally had a higher expression of genes implicated
487
488
489
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in ASD, such as chromatin regulators and genes related to immune involvement.(Shi et al., 2016;
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Werling et al., 2016; Ziats and Rennert, 2013) A study with rat models of ASD reported male-specific
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downregulation of MeCP2 leading to abnormal glutamate activity, providing another potential
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490 mechanism for male-specific vulnerability.(Kim et al., 2016, 2) Interestingly, multiple studies have
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491 found decreased levels of aromatase - an enzyme that catalyzes the conversion of testosterone to
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495
496
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estradiol - in the brains of adolescent ASD individuals.(Crider et al., 2014; Sarachana et al., 2011)
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Decreased aromatase has also been associated with decreased RAR-related orphan receptor A (RORA),
r
an ASD-associated gene that is oppositely regulated by male and female hormones.(Nguyen et al.,
2010; Sarachana et al., 2011) Hu and colleagues found a much stronger correlation between RORA
expression and that of its targets in the cortex of male mice relative to female mice, suggesting that
RORA-deficient males may have greater dysregulation of genes than females.(Hu et al., 2015)
Of course, there may also be a combination of female-specific protective and male-specific
499 deleterious effects. For example, Jung and colleagues recently assessed sexually dimorphic traits in a
500 CHD8+/N2373K mouse model of autism.(Jung et al., 2018) While male mice demonstrated abnormal
501 social behaviors such as isolation-induced self-grooming, female behavior was similar to controls.
502 Neuronal excitability was also enhanced in males and suppressed in females. Transcriptomes were
503 distinct, with female mice revealing an enrichment for ECM molecules, likely providing a protective
504 effect.
505 A likely mechanism of divergent modulation is from differential effects of sex hormones, which
506 have been hypothesized to play an important role in ASD pathology for both males and females.(Baron-
507 Cohen et al., 2005, 2015; Ferri et al., 2018; Honk et al., 2011; Whitehouse et al., 2010) For example,
508 testosterone and estrogen have been shown to have contrasting effects on the immune system (Lenz et
509 al., 2013; Roved et al., 2017), which has been repeatedly shown to play a pathological role in
510 ASD.(Estes and McAllister, 2015; Kim et al., 2017; Koyama and Ikegaya, 2015; McCarthy and Wright,
511 2017; Nadeem et al., 2019) Schwarz and colleagues analyzed biomarkers from individuals with
512 Asperger’s syndrome and found 24 male-specific and 17 female-specific hits, including many immune-
513 related molecules.(Schwarz et al., 2011) Spine density, another phenotype strongly implicated in
514 autism (Comery et al., 1997; Durand et al., 2012; Hutsler and Zhang, 2010; Irwin et al., 2001; Liu et
515 al., 2017; Soltani et al., 2017; Takuma et al., 2014; Tang et al., 2014), is also affected by
516 testosterone.(Hatanaka et al., 2015) Key molecules involved in neurotransmission such as GABA,
11
517 glutamate, serotonin, and BDNF are all implicated in ASD and modulated by sex hormones.(Al-Otaish
518 et al., 2018; Edwards et al., 2018; Ferri et al., 2018; Garbarino et al., 2018; Kim et al., 2016, 2;
519 Saghazadeh and Rezaei, 2017; Zieminska et al., 2018) It is not yet clear whether the majority of
520 differences between male and female presentation of ASD arise from differential regulatory actions of
521 sex hormones or from other modifiers, but the presence of a sexually dimorphic phenotype is well
522 established. Future research will likely elucidate a clearer picture of the identity and mechanisms of
523 sex-specific modifiers.
524 4 Clinical Implications and Future Perspectives
525 When autism was first described, it was hypothesized to be an environmentally-caused disease.
526 Decades of research have since revealed that autism is a highly heterogeneous and extremely complex
527 genetic condition. Even though great progress had been made in identifying hundreds of implicated
528 genes conferring risk, very little is known about the different types of modifiers that may exacerbate
529 or ameliorate disease severity. Such modifiers could include epigenetics, sex-linked modifiers, CNVs,
530 double-hit mutations, or environmental factors (see Figure 1).
531 It may take many more decades of research before the scientific community has an accurate
532 picture of how these modulators contribute to the etiology of ASD. However, this understanding is
533 critical for the development of effective therapies. Due to the extremely diverse genetic phenotype of
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534 patients, personalized medicine may be a future avenue for maximally effective treatment. A
535
536
537
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condensed series of genetic tests - such as a microarray with identified risk loci - could be an expedient
n
and cost-effective solution to determining genetic etiology. Alternatively, therapies may be developed
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to address convergent disease phenotypes that encompass multiple genetic etiologies, such as neuronal
i
538 hyperexcitability and abnormal synaptic function. Autism research has come astonishingly far in just
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539 a half a century. There is much more work to be done, but continued investigation will eventually lead
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540 to a cohesive understanding of the interplay between causative genetic factors and disease modifiers in
541
542
543
544
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5.1 P r
the etiology of ASD.
Figure Legends
Figure 1
Genetic modifiers in autism spectrum disorder. Autism is estimated to be 40%-80% heritable.
545 However, both genetic and non-genetic factors modulate the penetrance of risk genes, resulting in a
546 highly heterogeneous disease phenotype for similar pathogenic variants. Examples of genetic
547 modulators include CNV, epigenetics, and double-hit mutations. Examples of non-genetic modifiers
548 include environmental exposures and sex-linked modifiers.
549 6 References
550 Acuna-Hidalgo, R., Bo, T., Kwint, M. P., van de Vorst, M., Pinelli, M., Veltman, J. A., et al. (2015).
551 Post-zygotic Point Mutations Are an Underrecognized Source of De Novo Genomic Variation.
552 Am. J. Hum. Genet. 97, 67–74. doi:10.1016/j.ajhg.2015.05.008.
553 Al-Otaish, H., Al-Ayadhi, L., Bjørklund, G., Chirumbolo, S., Urbina, M. A., and El-Ansary, A. (2018).
554 Relationship between absolute and relative ratios of glutamate, glutamine and GABA and
555 severity of autism spectrum disorder. Metab. Brain Dis. 33, 843–854. doi:10.1007/s11011-018-
556 0186-6.
557 Amiet, C., Gourfinkel-An, I., Bouzamondo, A., Tordjman, S., Baulac, M., Lechat, P., et al. (2008).
558 Epilepsy in autism is associated with intellectual disability and gender: evidence from a meta-
559 analysis. Biol. Psychiatry 64, 577–582. doi:10.1016/j.biopsych.2008.04.030.
12
560 Andrews, S. V., Ellis, S. E., Bakulski, K. M., Sheppard, B., Croen, L. A., Hertz-Picciotto, I., et al.
561 (2017). Cross-tissue integration of genetic and epigenetic data offers insight into autism
562 spectrum disorder. Nat. Commun. 8, 1011. doi:10.1038/s41467-017-00868-y.
563 Artuso, R., Papa, F. T., Grillo, E., Mucciolo, M., Yasui, D. H., Dunaway, K. W., et al. (2011).
564 Investigation of modifier genes within copy number variations in Rett syndrome. J. Hum. Genet.
565 56, 508–515. doi:10.1038/jhg.2011.50.
566 Auranen, M., Vanhala, R., Varilo, T., Ayers, K., Kempas, E., Ylisaukko-oja, T., et al. (2002). A
567 Genomewide Screen for Autism-Spectrum Disorders: Evidence for a Major Susceptibility Locus
568 on Chromosome 3q25-27. Am. J. Hum. Genet. 71, 777–790.
569 Bae, T., Tomasini, L., Mariani, J., Zhou, B., Roychowdhury, T., Franjic, D., et al. (2018). Different
570 mutational rates and mechanisms in human cells at pregastrulation and neurogenesis. Science
571 359, 550–555. doi:10.1126/science.aan8690.
572 Bailey, A., Le Couteur, A., Gottesman, I., Bolton, P., Simonoff, E., Yuzda, E., et al. (1995). Autism as
573 a strongly genetic disorder: evidence from a British twin study. Psychol. Med. 25, 63–77.
574 Barber, J. C. K., Hall, V., Maloney, V. K., Huang, S., Roberts, A. M., Brady, A. F., et al. (2013).
575 16p11.2–p12.2 duplication syndrome; a genomic condition differentiated from euchromatic
576 variation of 16p11.2. Eur J Hum Genet 21, 182–189. doi:10.1038/ejhg.2012.144.
577 Baron-Cohen, S., Auyeung, B., Nørgaard-Pedersen, B., Hougaard, D. M., Abdallah, M. W., Melgaard,
578 L., et al. (2015). Elevated fetal steroidogenic activity in autism. Mol. Psychiatry 20, 369–376.
579
580
581
doi:10.1038/mp.2014.48.
n al
Baron-Cohen, S., Knickmeyer, R. C., and Belmonte, M. K. (2005). Sex Differences in the Brain:
o
Implications for Explaining Autism. Science 310, 819–823. doi:10.1126/science.1115455.
si
582 Barrett, S., Beck, J. C., Bernier, R., Bisson, E., Braun, T. A., Casavant, T. L., et al. (1999). An
583
584
585
i
autosomal genomic screen for autism. Collaborative linkage study of autism. Am. J. Med. Genet.
v
88, 609–615.
r o
Behnia, F., Parets, S. E., Kechichian, T., Yin, H., Dutta, E. H., Saade, G. R., et al. (2015). Fetal DNA
P
586 methylation of autism spectrum disorders candidate genes: association with spontaneous preterm
587 birth. Am. J. Obstet. Gynecol. 212, 533.e1-533.e9. doi:10.1016/j.ajog.2015.02.011.
588 Blaker-Lee, A., Gupta, S., McCammon, J. M., De Rienzo, G., and Sive, H. (2012). Zebrafish homologs
589 of genes within 16p11.2, a genomic region associated with brain disorders, are active during
590 brain development, and include two deletion dosage sensor genes. Dis Model Mech 5, 834–851.
591 doi:10.1242/dmm.009944.
592 Bölte, S., Girdler, S., and Marschik, P. B. (2019). The contribution of environmental exposure to the
593 etiology of autism spectrum disorder. Cell. Mol. Life Sci. 76, 1275–1297. doi:10.1007/s00018-
594 018-2988-4.
595 Bolton, P. F., Dennis, N. R., Browne, C. E., Thomas, N. S., Veltman, M. W. M., Thompson, R. J., et al.
596 (2001). The phenotypic manifestations of interstitial duplications of proximal 15q with special
597 reference to the autistic spectrum disorders. Am. J. Med. Genet. 105, 675–685.
598 doi:10.1002/ajmg.1551.
599 Bonnet-Brilhault, F., Alirol, S., Blanc, R., Bazaud, S., Marouillat, S., Thépault, R.-A., et al. (2016).
600 GABA/Glutamate synaptic pathways targeted by integrative genomic and electrophysiological
601 explorations distinguish autism from intellectual disability. Molecular Psychiatry 21, 411–418.
602 doi:10.1038/mp.2015.75.
603 Bourdon, V., Philippe, C., Bienvenu, T., Koenig, B., Tardieu, M., Chelly, J., et al. (2001). Evidence of
604 somatic mosaicism for a MECP2 mutation in females with Rett syndrome: diagnostic
605 implications. J. Med. Genet. 38, 867–871. doi:10.1136/jmg.38.12.867.
13
606 Boyar, F. Z., Whitney, M. M., Lossie, A. C., Gray, B. A., Keller, K. L., Stalker, H. J., et al. (2001). A
607 family with a grand-maternally derived interstitial duplication of proximal 15q. Clin. Genet. 60,
608 421–430.
609 Bruder, C. E. G., Piotrowski, A., Gijsbers, A. A. C. J., Andersson, R., Erickson, S., Diaz de Ståhl, T., et
610 al. (2008). Phenotypically Concordant and Discordant Monozygotic Twins Display Different
611 DNA Copy-Number-Variation Profiles. Am. J. Hum. Genet. 82, 763–771.
612 doi:10.1016/j.ajhg.2007.12.011.
613 Buxbaum, J. D., Silverman, J. M., Smith, C. J., Kilifarski, M., Reichert, J., Hollander, E., et al. (2001).
614 Evidence for a susceptibility gene for autism on chromosome 2 and for genetic heterogeneity.
615 Am. J. Hum. Genet. 68, 1514–1520. doi:10.1086/320588.
616 Carney, R. M., Wolpert, C. M., Ravan, S. A., Shahbazian, M., Ashley-Koch, A., Cuccaro, M. L., et al.
617 (2003). Identification of MeCP2 mutations in a series of females with autistic disorder. Pediatr.
618 Neurol. 28, 205–211.
619 Casanova, E. L., Sharp, J. L., Chakraborty, H., Sumi, N. S., and Casanova, M. F. (2016). Genes with
620 high penetrance for syndromic and non-syndromic autism typically function within the nucleus
621 and regulate gene expression. Mol. Autism 7. doi:10.1186/s13229-016-0082-z.
622 Castermans, D., Thienpont, B., Volders, K., Crepel, A., Vermeesch, J. R., Schrander-Stumpel, C. T., et
623 al. (2008). Position effect leading to haploinsufficiency in a mosaic ring chromosome 14 in a
624 boy with autism. Eur. J. Hum. Genet. 16, 1187–1192. doi:10.1038/ejhg.2008.71.
625
626
627
al
Chao, H.-T., Zoghbi, H. Y., and Rosenmund, C. (2007). MeCP2 Controls Excitatory Synaptic Strength
n
by Regulating Glutamatergic Synapse Number. Neuron 56, 58–65.
doi:10.1016/j.neuron.2007.08.018.
o
si
628 Chaste, P., and Leboyer, M. (2012). Autism risk factors: genes, environment, and gene-environment
629
630
631
i
interactions. Dialogues Clin. Neurosci. 14, 281–292.
v
Clayton-Smith, J., Watson, P., Ramsden, S., and Black, G. (2000). Somatic mutation in MECP2 as a
r o
non-fatal neurodevelopmental disorder in males. The Lancet 356, 830–832. doi:10.1016/S0140-
P
632 6736(00)02661-1.
633 Comery, T. A., Harris, J. B., Willems, P. J., Oostra, B. A., Irwin, S. A., Weiler, I. J., et al. (1997).
634 Abnormal dendritic spines in fragile X knockout mice: Maturation and pruning deficits. Proc.
635 Natl. Acad. Sci. 94, 5401–5404. doi:10.1073/pnas.94.10.5401.
636 Constantino, J. N., Zhang, Y., Frazier, T., Abbacchi, A. M., and Law, P. (2010). Sibling recurrence and
637 the genetic epidemiology of autism. Am. J. Psychiatry 167, 1349–1356.
638 doi:10.1176/appi.ajp.2010.09101470.
639 Cook, E. H., Lindgren, V., Leventhal, B. L., Courchesne, R., Lincoln, A., Shulman, C., et al. (1997).
640 Autism or atypical autism in maternally but not paternally derived proximal 15q duplication.
641 Am. J. Hum. Genet. 60, 928–934.
642 Crider, A., Thakkar, R., Ahmed, A. O., and Pillai, A. (2014). Dysregulation of estrogen receptor beta
643 (ERβ), aromatase (CYP19A1), and ER co-activators in the middle frontal gyrus of autism
644 spectrum disorder subjects. Mol. Autism 5, 46. doi:10.1186/2040-2392-5-46.
645 Cross-Disorder Group of the Psychiatric Genomics Consortium (2013). Identification of risk loci with
646 shared effects on five major psychiatric disorders: a genome-wide analysis. The Lancet 381,
647 1371–1379. doi:10.1016/S0140-6736(12)62129-1.
648 Cross-Disorder Group of the Psychiatric Genomics Consortium, Lee, S. H., Ripke, S., Neale, B. M.,
649 Faraone, S. V., Purcell, S. M., et al. (2013). Genetic relationship between five psychiatric
650 disorders estimated from genome-wide SNPs. Nat. Genet. 45, 984–994. doi:10.1038/ng.2711.
651 De Rubeis, S., He, X., Goldberg, A. P., Poultney, C. S., Samocha, K., Cicek, A. E., et al. (2014).
652 Synaptic, transcriptional and chromatin genes disrupted in autism. Nature 515, 209–215.
653 doi:10.1038/nature13772.
14
654 Desachy, G., Croen, L. A., Torres, A. R., Kharrazi, M., Delorenze, G. N., Windham, G. C., et al.
655 (2015). Increased female autosomal burden of rare copy number variants in human populations
656 and in autism families. Mol. Psychiatry 20, 170–175. doi:10.1038/mp.2014.179.
657 D’Gama, A. M., and Walsh, C. A. (2018). Somatic mosaicism and neurodevelopmental disease. Nat.
658 Neurosci. 21, 1504. doi:10.1038/s41593-018-0257-3.
659 Dou, Y., Yang, X., Li, Z., Wang, S., Zhang, Z., Ye, A. Y., et al. (2017). Postzygotic single-nucleotide
660 mosaicisms contribute to the etiology of autism spectrum disorder and autistic traits and the
661 origin of mutations. Hum. Mutat. 38, 1002–1013. doi:10.1002/humu.23255.
662 Doyle, G. A., Crist, R. C., Karatas, E. T., Hammond, M. J., Ewing, A. D., Ferraro, T. N., et al. (2017).
663 Analysis of LINE-1 Elements in DNA from Postmortem Brains of Individuals with
664 Schizophrenia. Neuropsychopharmacology 42, 2602–2611. doi:10.1038/npp.2017.115.
665 Duffney, L. J., Valdez, P., Tremblay, M. W., Cao, X., Montgomery, S., McConkie-Rosell, A., et al.
666 (2018). Epigenetics and autism spectrum disorder: A report of an autism case with mutation in
667 H1 linker histone HIST1H1E and literature review. Am. J. Med. Genet. B Neuropsychiatr.
668 Genet. 177, 426–433. doi:10.1002/ajmg.b.32631.
669 Dufour-Rainfray, D., Vourc’h, P., Le Guisquet, A.-M., Garreau, L., Ternant, D., Bodard, S., et al.
670 (2010). Behavior and serotonergic disorders in rats exposed prenatally to valproate: A model for
671 autism. Neurosci. Lett. 470, 55–59. doi:10.1016/j.neulet.2009.12.054.
672 Durand, C. M., Perroy, J., Loll, F., Perrais, D., Fagni, L., Bourgeron, T., et al. (2012). SHANK3
673
674
675
al
mutations identified in autism lead to modification of dendritic spine morphology via an actin-
n
dependent mechanism. Mol. Psychiatry 17, 71–84. doi:10.1038/mp.2011.57.
o
Edwards, K. A., Madden, A. M. K., and Zup, S. L. (2018). Serotonin receptor regulation as a potential
si
676 mechanism for sexually dimorphic oxytocin dysregulation in a model of Autism. Brain Res.
677
678
679
i
1701, 85–92. doi:10.1016/j.brainres.2018.07.020.
v
Escamilla, C. O., Filonova, I., Walker, A. K., Xuan, Z. X., Holehonnur, R., Espinosa, F., et al. (2017).
r o
Kctd13 deletion reduces synaptic transmission via increased RhoA. Nature 551, 227–231.
P
680 doi:10.1038/nature24470.
681 Estes, M. L., and McAllister, A. K. (2015). Immune mediators in the brain and peripheral tissues in
682 autism spectrum disorder. Nat. Rev. Neurosci. 16, 469–486. doi:10.1038/nrn3978.
683 Ferri, S. L., Abel, T., and Brodkin, E. S. (2018). Sex Differences in Autism Spectrum Disorder: a
684 Review. Curr. Psychiatry Rep. 20, 9. doi:10.1007/s11920-018-0874-2.
685 Fisher, E., and Scambler, P. (1994). Human haploinsufficiency — one for sorrow, two for joy. Nature
686 Genetics 7, 5. doi:10.1038/ng0594-5.
687 Folstein, S., and Rutter, M. (1977). Genetic influences and infantile autism. Nature 265, 726–728.
688 doi:10.1038/265726a0.
689 Freed, D., and Pevsner, J. (2016). The Contribution of Mosaic Variants to Autism Spectrum Disorder.
690 PLoS Genet. 12, e1006245. doi:10.1371/journal.pgen.1006245.
691 Garbarino, V. R., Gilman, T. L., Daws, L. C., and Gould, G. G. (2018). Extreme enhancement or
692 depletion of serotonin transporter function and serotonin availability in autism spectrum
693 disorder. Pharmacol. Res. doi:10.1016/j.phrs.2018.07.010.
694 Gardener, H., Spiegelman, D., and Buka, S. L. (2009). Prenatal Risk Factors for Autism: A
695 Comprehensive Meta-analysis. Br. J. Psychiatry J. Ment. Sci. 195, 7–14.
696 doi:10.1192/bjp.bp.108.051672.
697 Geschwind, D. H. (2011). Genetics of autism spectrum disorders. Trends Cogn. Sci. 15, 409–416.
698 doi:10.1016/j.tics.2011.07.003.
699 Gilissen, C., Hehir-Kwa, J. Y., Thung, D. T., van de Vorst, M., van Bon, B. W. M., Willemsen, M. H.,
700 et al. (2014). Genome sequencing identifies major causes of severe intellectual disability. Nature
701 511, 344–347. doi:10.1038/nature13394.
15
702 Gillberg, C., and Wahlström, J. (1985). Chromosome Abnormalities in Infantile Autism and Other
703 Childhood Psychoses: A Population Study of 66 Cases. Dev. Med. Child Neurol. 27, 293–304.
704 doi:10.1111/j.1469-8749.1985.tb04539.x.
705 Giovedí, S., Corradi, A., Fassio, A., and Benfenati, F. (2014). Involvement of Synaptic Genes in the
706 Pathogenesis of Autism Spectrum Disorders: The Case of Synapsins. Front. Pediatr. 2.
707 doi:10.3389/fped.2014.00094.
708 Girirajan, S., Dennis, M. Y., Baker, C., Malig, M., Coe, B. P., Campbell, C. D., et al. (2013).
709 Refinement and Discovery of New Hotspots of Copy-Number Variation Associated with Autism
710 Spectrum Disorder. Am. J. Hum. Genet. 92, 221–237. doi:10.1016/j.ajhg.2012.12.016.
711 Girirajan, S., Rosenfeld, J. A., Coe, B. P., Parikh, S., Friedman, N., Goldstein, A., et al. (2012).
712 Phenotypic heterogeneity of genomic disorders and rare copy-number variants. N. Engl. J. Med.
713 367, 1321–1331. doi:10.1056/NEJMoa1200395.
714 Girirajan, S., Rosenfeld, J. A., Cooper, G. M., Antonacci, F., Siswara, P., Itsara, A., et al. (2010). A
715 recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat.
716 Genet. 42, 203–209. doi:10.1038/ng.534.
717 Glessner, J. T., Wang, K., Cai, G., Korvatska, O., Kim, C. E., Wood, S., et al. (2009). Autism genome-
718 wide copy number variation reveals ubiquitin and neuronal genes. Nature 459, 569–573.
719 doi:10.1038/nature07953.
720 Go, H. S., Kim, K. C., Choi, C. S., Jeon, S. J., Kwon, K. J., Han, S.-H., et al. (2012). Prenatal exposure
721
722
723
al
to valproic acid increases the neural progenitor cell pool and induces macrocephaly in rat brain
n
via a mechanism involving the GSK-3β/β-catenin pathway. Neuropharmacology 63, 1028–1041.
doi:10.1016/j.neuropharm.2012.07.028.
o
si
724 Golzio, C., Willer, J., Talkowski, M. E., Oh, E. C., Taniguchi, Y., Jacquemont, S., et al. (2012).
725
726
727
i
KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number
v
variant. Nature 485, 363–367. doi:10.1038/nature11091.
r o
Guffanti, G., Lievers, L. S., Bonati, M. T., Marchi, M., Geronazzo, L., Nardocci, N., et al. (2011). Role
P
728 of UBE3A and ATP10A genes in autism susceptibility region 15q11-q13 in an Italian
729 population: A positive replication for UBE3A. Psychiatry Res. 185, 33–38.
730 doi:10.1016/j.psychres.2010.04.057.
731 Gurrieri, F., Battaglia, A., Torrisi, L., Tancredi, R., Cavallaro, C., Sangiorgi, E., et al. (1999). Pervasive
732 developmental disorder and epilepsy due to maternally derived duplication of 15q11-q13.
733 Neurology 52, 1694–1697.
734 Hamilton, A. M., Oh, W. C., Vega-Ramirez, H., Stein, I. S., Hell, J. W., Patrick, G. N., et al. (2012).
735 Activity-Dependent Growth of New Dendritic Spines Is Regulated by the Proteasome. Neuron
736 74, 1023–1030. doi:10.1016/j.neuron.2012.04.031.
737 Hara, Y., Takuma, K., Takano, E., Katashiba, K., Taruta, A., Higashino, K., et al. (2015). Reduced
738 prefrontal dopaminergic activity in valproic acid-treated mouse autism model. Behav. Brain Res.
739 289, 39–47. doi:10.1016/j.bbr.2015.04.022.
740 Hatanaka, Y., Wada, K., and Kabuta, T. (2015). Abnormal instability, excess density, and aberrant
741 morphology of dendritic spines in prenatally testosterone-exposed mice. Neurochem. Int. 85–86,
742 53–58. doi:10.1016/j.neuint.2015.04.008.
743 Havlovicova, M., Novotna, D., Kocarek, E., Novotna, K., Bendova, S., Petrak, B., et al. (2007). A girl
744 with neurofibromatosis type 1, atypical autism and mosaic ring chromosome 17. Am. J. Med.
745 Genet. A. 143A, 76–81. doi:10.1002/ajmg.a.31569.
746 Hoffman, E. J., Turner, K. J., Fernandez, J. M., Cifuentes, D., Ghosh, M., Ijaz, S., et al. (2016).
747 Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene,
748 CNTNAP2. Neuron 89, 725–733. doi:10.1016/j.neuron.2015.12.039.
16
749 Honk, J. van, Schutter, D. J., Bos, P. A., Kruijt, A.-W., Lentjes, E. G., and Baron-Cohen, S. (2011).
750 Testosterone administration impairs cognitive empathy in women depending on second-to-fourth
751 digit ratio. Proc. Natl. Acad. Sci. 108, 3448–3452. doi:10.1073/pnas.1011891108.
752 Horev, G., Ellegood, J., Lerch, J. P., Son, Y.-E. E., Muthuswamy, L., Vogel, H., et al. (2011). Dosage-
753 dependent phenotypes in models of 16p11.2 lesions found in autism. Proc. Natl. Acad. Sci. 108,
754 17076–17081. doi:10.1073/pnas.1114042108.
755 Hu, V. W., Sarachana, T., Sherrard, R. M., and Kocher, K. M. (2015). Investigation of sex differences
756 in the expression of RORA and its transcriptional targets in the brain as a potential contributor to
757 the sex bias in autism. Mol. Autism 6, 7. doi:10.1186/2040-2392-6-7.
758 Huguet, G., Benabou, M., and Bourgeron, T. (2016). “The Genetics of Autism Spectrum Disorders,” in
759 A Time for Metabolism and Hormones Research and Perspectives in Endocrine Interactions.,
760 eds. P. Sassone-Corsi and Y. Christen (Cham: Springer International Publishing), 101–129.
761 doi:10.1007/978-3-319-27069-2_11.
762 Hutsler, J. J., and Zhang, H. (2010). Increased dendritic spine densities on cortical projection neurons
763 in autism spectrum disorders. Brain Res. 1309, 83–94. doi:10.1016/j.brainres.2009.09.120.
764 Iijima, Y., Behr, K., Iijima, T., Biemans, B., Bischofberger, J., and Scheiffele, P. (2016). Distinct
765 Defects in Synaptic Differentiation of Neocortical Neurons in Response to Prenatal Valproate
766 Exposure. Sci. Rep. 6, 27400. doi:10.1038/srep27400.
767 IMGSAC (1998). Full Genome Screen for Autism with Evidence for Linkage to a Region on
768
769
770
578.
o al
Chromosome 7q | Human Molecular Genetics | Oxford Academic. Hum. Mol. Genet. 7, 571–
n
International Molecular Genetic Study of Autism Consortium (IMGSAC) (2001). A genomewide
si
771 screen for autism: strong evidence for linkage to chromosomes 2q, 7q, and 16p. Am. J. Hum.
772
773
774
i
Genet. 69, 570–581. doi:10.1086/323264.
v
Iossifov, I., O’Roak, B. J., Sanders, S. J., Ronemus, M., Krumm, N., Levy, D., et al. (2014). The
r o
contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216–221.
P
775 doi:10.1038/nature13908.
776 Irwin, S. A., Patel, B., Idupulapati, M., Harris, J. B., Crisostomo, R. A., Larsen, B. P., et al. (2001).
777 Abnormal dendritic spine characteristics in the temporal and visual cortices of patients with
778 fragile-X syndrome: A quantitative examination. Am. J. Med. Genet. 98, 161–167.
779 doi:10.1002/1096-8628(20010115)98:2<161::AID-AJMG1025>3.0.CO;2-B.
780 Iyer, J., Singh, M. D., Jensen, M., Patel, P., Pizzo, L., Huber, E., et al. (2018). Pervasive genetic
781 interactions modulate neurodevelopmental defects of the autism-associated 16p11.2 deletion in
782 Drosophila melanogaster. Nature Communications 9, 2548. doi:10.1038/s41467-018-04882-6.
783 Jacob, J., Ribes, V., Moore, S., Constable, S. C., Sasai, N., Gerety, S. S., et al. (2014). Valproic acid
784 silencing of ascl1b/Ascl1 results in the failure of serotonergic differentiation in a zebrafish
785 model of fetal valproate syndrome. Dis. Model. Mech. 7, 107–117. doi:10.1242/dmm.013219.
786 Jacquemont, S., Coe, B. P., Hersch, M., Duyzend, M. H., Krumm, N., Bergmann, S., et al. (2014). A
787 higher mutational burden in females supports a “female protective model” in
788 neurodevelopmental disorders. Am. J. Hum. Genet. 94, 415–425.
789 doi:10.1016/j.ajhg.2014.02.001.
790 Jamain, S., Quach, H., Betancur, C., Råstam, M., Colineaux, C., Gillberg, I. C., et al. (2003). Mutations
791 of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism.
792 Nat. Genet. 34, 27–29. doi:10.1038/ng1136.
793 James, S. J., Shpyleva, S., Melnyk, S., Pavliv, O., and Pogribny, I. P. (2013). Complex epigenetic
794 regulation of Engrailed-2 (EN-2) homeobox gene in the autism cerebellum. Transl. Psychiatry 3,
795 e232. doi:10.1038/tp.2013.8.
17
796 Jiang, Y.-H., Sahoo, T., Michaelis, R. C., Bercovich, D., Bressler, J., Kashork, C. D., et al. (2004). A
797 mixed epigenetic/genetic model for oligogenic inheritance of autism with a limited role for
798 UBE3A. Am. J. Med. Genet. A. 131, 1–10. doi:10.1002/ajmg.a.30297.
799 Jung, H., Park, H., Choi, Y., Kang, H., Lee, E., Kweon, H., et al. (2018). Sexually dimorphic behavior,
800 neuronal activity, and gene expression in Chd8-mutant mice. Nat. Neurosci. 21, 1218–1228.
801 doi:10.1038/s41593-018-0208-z.
802 Kakinuma, H., Ozaki, M., Sato, H., and Takahashi, H. (2008). Variation in GABA-A subunit gene
803 copy number in an autistic patient with mosaic 4 p duplication (p12p16). Am. J. Med. Genet. B
804 Neuropsychiatr. Genet. 147B, 973–975. doi:10.1002/ajmg.b.30663.
805 Kalsner, L., and Chamberlain, S. J. (2015). Prader-Willi, Angelman, and 15q11-q13 duplication
806 syndromes. Pediatr. Clin. North Am. 62, 587–606. doi:10.1016/j.pcl.2015.03.004.
807 Kanner, L. (1943). Autistic disturbances of affective contact. Nerv. Child 2, 217–250.
808 Karimi, P., Kamali, E., Mousavi, S. M., and Karahmadi, M. (2017). Environmental factors influencing
809 the risk of autism. J. Res. Med. Sci. Off. J. Isfahan Univ. Med. Sci. 22. doi:10.4103/1735-
810 1995.200272.
811 Kataoka, S., Takuma, K., Hara, Y., Maeda, Y., Ago, Y., and Matsuda, T. (2013). Autism-like
812 behaviours with transient histone hyperacetylation in mice treated prenatally with valproic acid.
813 Int. J. Neuropsychopharmacol. 16, 91–103. doi:10.1017/S1461145711001714.
814 Khanzada, N. S., Butler, M. G., and Manzardo, A. M. (2017). GeneAnalytics Pathway Analysis and
815
816
817
Mol Sci 18. doi:10.3390/ijms18030527.
o al
Genetic Overlap among Autism Spectrum Disorder, Bipolar Disorder and Schizophrenia. Int J
n
Kim, H.-J., Cho, M.-H., Shim, W. H., Kim, J. K., Jeon, E.-Y., Kim, D.-H., et al. (2017). Deficient
si
818 autophagy in microglia impairs synaptic pruning and causes social behavioral defects. Mol.
819
820
821
i
Psychiatry 22, 1576–1584. doi:10.1038/mp.2016.103.
v
Kim, K. C., Choi, C. S., Kim, J.-W., Han, S.-H., Cheong, J. H., Ryu, J. H., et al. (2016). MeCP2
r o
Modulates Sex Differences in the Postsynaptic Development of the Valproate Animal Model of
P
822 Autism. Mol. Neurobiol. 53, 40–56. doi:10.1007/s12035-014-8987-z.
823 Knudson, A. G. (1971). Mutation and Cancer: Statistical Study of Retinoblastoma. PNAS 68, 820–823.
824 doi:10.1073/pnas.68.4.820.
825 Ko, H. M., Jin, Y., Park, H. H., Lee, J. H., Jung, S. H., Choi, S. Y., et al. (2018). Dual mechanisms for
826 the regulation of brain-derived neurotrophic factor by valproic acid in neural progenitor cells.
827 Korean J. Physiol. Pharmacol. Off. J. Korean Physiol. Soc. Korean Soc. Pharmacol. 22, 679–
828 688. doi:10.4196/kjpp.2018.22.6.679.
829 Kolozsi, E., Mackenzie, R. N., Roullet, F. I., deCatanzaro, D., and Foster, J. A. (2009). Prenatal
830 exposure to valproic acid leads to reduced expression of synaptic adhesion molecule neuroligin 3
831 in mice. Neuroscience 163, 1201–1210. doi:10.1016/j.neuroscience.2009.07.021.
832 Kong, A., Frigge, M. L., Masson, G., Besenbacher, S., Sulem, P., Magnusson, G., et al. (2012). Rate of
833 de novo mutations and the importance of father’s age to disease risk. Nature 488, 471–475.
834 doi:10.1038/nature11396.
835 Korb, E., Herre, M., Zucker-Scharff, I., Gresack, J., Allis, C. D., and Darnell, R. B. (2017). Excess
836 Translation of Epigenetic Regulators Contributes to Fragile X Syndrome and Is Alleviated by
837 Brd4 Inhibition. Cell 170, 1209-1223.e20. doi:10.1016/j.cell.2017.07.033.
838 Koyama, R., and Ikegaya, Y. (2015). Microglia in the pathogenesis of autism spectrum disorders.
839 Neurosci. Res. 100, 1–5. doi:10.1016/j.neures.2015.06.005.
840 Krebs, M. O., Betancur, C., Leroy, S., Bourdel, M. C., Gillberg, C., Leboyer, M., et al. (2002).
841 Absence of association between a polymorphic GGC repeat in the 5’ untranslated region of the
842 reelin gene and autism. Mol. Psychiatry 7, 801–804. doi:10.1038/sj.mp.4001071.
18
843 Krupp, D. R., Barnard, R. A., Duffourd, Y., Evans, S. A., Mulqueen, R. M., Bernier, R., et al. (2017).
844 Exonic Mosaic Mutations Contribute Risk for Autism Spectrum Disorder. Am. J. Hum. Genet.
845 101, 369–390. doi:10.1016/j.ajhg.2017.07.016.
846 Kubota, T., and Mochizuki, K. (2016). Epigenetic Effect of Environmental Factors on Autism
847 Spectrum Disorders. Int. J. Environ. Res. Public. Health 13. doi:10.3390/ijerph13050504.
848 Kumar, R. A., KaraMohamed, S., Sudi, J., Conrad, D. F., Brune, C., Badner, J. A., et al. (2008).
849 Recurrent 16p11.2 microdeletions in autism. Hum. Mol. Genet. 17, 628–638.
850 doi:10.1093/hmg/ddm376.
851 Kunio, M., Yang, C., Minakuchi, Y., Ohori, K., Soutome, M., Hirasawa, T., et al. (2013). Comparison
852 of Genomic and Epigenomic Expression in Monozygotic Twins Discordant for Rett Syndrome.
853 PLoS ONE 8. doi:10.1371/journal.pone.0066729.
854 Ladd-Acosta, C., Hansen, K. D., Briem, E., Fallin, M. D., Kaufmann, W. E., and Feinberg, A. P.
855 (2014). Common DNA methylation alterations in multiple brain regions in autism. Mol.
856 Psychiatry 19, 862–871. doi:10.1038/mp.2013.114.
857 Lai, M.-C., Lombardo, M. V., and Baron-Cohen, S. (2014). Autism. The Lancet 383, 896–910.
858 doi:10.1016/S0140-6736(13)61539-1.
859 Lamb, J. A., Parr, J. R., Bailey, A. J., and Monaco, A. P. (2002). Autism. NeuroMolecular Med. 2, 11–
860 28. doi:10.1385/NMM:2:1:11.
861 Leblond, C. S., Heinrich, J., Delorme, R., Proepper, C., Betancur, C., Huguet, G., et al. (2012). Genetic
862
863
864
al
and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism
n
Spectrum Disorders. PLoS Genet 8. doi:10.1371/journal.pgen.1002521.
o
Lee, S. Y., Ramirez, J., Franco, M., Lectez, B., Gonzalez, M., Barrio, R., et al. (2014). Ube3a, the E3
si
865 ubiquitin ligase causing Angelman syndrome and linked to autism, regulates protein homeostasis
866
867
868
i
through the proteasomal shuttle Rpn10. Cell. Mol. Life Sci. 71, 2747–2758. doi:10.1007/s00018-
v
013-1526-7.
r o
Lenz, K. M., Nugent, B. M., Haliyur, R., and McCarthy, M. M. (2013). Microglia are essential to
P
869 masculinization of brain and behavior. J. Neurosci. Off. J. Soc. Neurosci. 33, 2761–2772.
870 doi:10.1523/JNEUROSCI.1268-12.2013.
871 Li, F., Shen, Y., Köhler, U., Sharkey, F. H., Menon, D., Coulleaux, L., et al. (2010). Interstitial
872 microduplication of Xp22.31: Causative of intellectual disability or benign copy number
873 variant? European Journal of Medical Genetics 53, 93–99. doi:10.1016/j.ejmg.2010.01.004.
874 Li, Y., Wang, H., Muffat, J., Cheng, A. W., Orlando, D. A., Lovén, J., et al. (2013). Global
875 transcriptional and translational repression in human-embryonic-stem-cell-derived Rett
876 syndrome neurons. Cell Stem Cell 13, 446–458. doi:10.1016/j.stem.2013.09.001.
877 Lim, E. T., Uddin, M., De Rubeis, S., Chan, Y., Kamumbu, A. S., Zhang, X., et al. (2017). Rates,
878 distribution and implications of postzygotic mosaic mutations in autism spectrum disorder. Nat.
879 Neurosci. 20, 1217–1224. doi:10.1038/nn.4598.
880 Liu, J., Nyholt, D. R., Magnussen, P., Parano, E., Pavone, P., Geschwind, D., et al. (2001). A
881 genomewide screen for autism susceptibility loci. Am. J. Hum. Genet. 69, 327–340.
882 Liu, S., Zhou, L., Yuan, H., Vieira, M., Sanz-Clemente, A., Badger, J. D., et al. (2017a). A Rare
883 Variant Identified Within the GluN2B C-Terminus in a Patient with Autism Affects NMDA
884 Receptor Surface Expression and Spine Density. J. Neurosci. Off. J. Soc. Neurosci. 37, 4093–
885 4102. doi:10.1523/JNEUROSCI.0827-16.2017.
886 Liu, X., Campanac, E., Cheung, H.-H., Ziats, M. N., Canterel-Thouennon, L., Raygada, M., et al.
887 (2017b). Idiopathic Autism: Cellular and Molecular Phenotypes in Pluripotent Stem Cell-
888 Derived Neurons. Mol. Neurobiol. 54, 4507–4523. doi:10.1007/s12035-016-9961-8.
19
889 Liu, Z., Li, X., Zhang, J.-T., Cai, Y.-J., Cheng, T.-L., Cheng, C., et al. (2016). Autism-like behaviours
890 and germline transmission in transgenic monkeys overexpressing MeCP2. Nature 530, 98–102.
891 doi:10.1038/nature16533.
892 Loomes, R., Hull, L., and Mandy, W. P. L. (2017). What Is the Male-to-Female Ratio in Autism
893 Spectrum Disorder? A Systematic Review and Meta-Analysis. J. Am. Acad. Child Adolesc.
894 Psychiatry 56, 466–474. doi:10.1016/j.jaac.2017.03.013.
895 Macrì, S., Biamonte, F., Romano, E., Marino, R., Keller, F., and Laviola, G. (2010). Perseverative
896 responding and neuroanatomical alterations in adult heterozygous reeler mice are mitigated by
897 neonatal estrogen administration. Psychoneuroendocrinology 35, 1374–1387.
898 doi:10.1016/j.psyneuen.2010.03.012.
899 Mahmood, U., Ahn, S., Yang, E.-J., Choi, M., Kim, H., Regan, P., et al. (2018). Dendritic spine
900 anomalies and PTEN alterations in a mouse model of VPA-induced autism spectrum disorder.
901 Pharmacol. Res. 128, 110–121. doi:10.1016/j.phrs.2017.08.006.
902 Marshall, C. R., Noor, A., Vincent, J. B., Lionel, A. C., Feuk, L., Skaug, J., et al. (2008). Structural
903 Variation of Chromosomes in Autism Spectrum Disorder. Am. J. Hum. Genet. 82, 477–488.
904 doi:10.1016/j.ajhg.2007.12.009.
905 Marshall, C. R., and Scherer, S. W. (2012). Detection and characterization of copy number variation in
906 autism spectrum disorder. Methods Mol. Biol. Clifton NJ 838, 115–135. doi:10.1007/978-1-
907 61779-507-7_5.
908
909
910
al
Martin, J., Cooper, M., Hamshere, M. L., Pocklington, A., Scherer, S. W., Kent, L., et al. (2014).
n
Biological overlap of attention-deficit/hyperactivity disorder and autism spectrum disorder:
o
evidence from copy number variants. J. Am. Acad. Child Adolesc. Psychiatry 53, 761-770.e26.
si
911 doi:10.1016/j.jaac.2014.03.004.
912
913
914
i
McCallion, A. S., Stames, E., Conlon, R. A., and Chakravarti, A. (2003). Phenotype variation in two-
v
locus mouse models of Hirschsprung disease: Tissue-specific interaction between Ret and
r o
Ednrb. PNAS 100, 1826–1831. doi:10.1073/pnas.0337540100.
P
915 McCarthy, M. M., and Wright, C. L. (2017). Convergence of Sex Differences and the Neuroimmune
916 System in Autism Spectrum Disorder. Biol. Psychiatry 81, 402–410.
917 doi:10.1016/j.biopsych.2016.10.004.
918 McCarthy, S. E., Gillis, J., Kramer, M., Lihm, J., Yoon, S., Berstein, Y., et al. (2014). De novo
919 mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with
920 autism and intellectual disability. Mol. Psychiatry 19, 652–658. doi:10.1038/mp.2014.29.
921 Michaelson, J. J., Shin, M.-K., Koh, J.-Y., Brueggeman, L., Zhang, A., Katzman, A., et al. (2017).
922 Neuronal PAS Domain Proteins 1 and 3 Are Master Regulators of Neuropsychiatric Risk Genes.
923 Biol. Psychiatry 82, 213–223. doi:10.1016/j.biopsych.2017.03.021.
924 Modabbernia, A., Velthorst, E., and Reichenberg, A. (2017). Environmental risk factors for autism: an
925 evidence-based review of systematic reviews and meta-analyses. Mol Autism 8, 13.
926 doi:10.1186/s13229-017-0121-4.
927 Mor, M., Nardone, S., Sams, D. S., and Elliott, E. (2015). Hypomethylation of miR-142 promoter and
928 upregulation of microRNAs that target the oxytocin receptor gene in the autism prefrontal
929 cortex. Mol. Autism 6. doi:10.1186/s13229-015-0040-1.
930 Mulligan, A., Anney, R. J. L., O’Regan, M., Chen, W., Butler, L., Fitzgerald, M., et al. (2009). Autism
931 symptoms in Attention-Deficit/Hyperactivity Disorder: a familial trait which correlates with
932 conduct, oppositional defiant, language and motor disorders. J Autism Dev Disord 39, 197–209.
933 doi:10.1007/s10803-008-0621-3.
934 Nadeem, A., Ahmad, S. F., Attia, S. M., Al-Ayadhi, L. Y., Al-Harbi, N. O., and Bakheet, S. A. (2019).
935 Dysregulated enzymatic antioxidant network in peripheral neutrophils and monocytes in
20
936 children with autism. Prog. Neuropsychopharmacol. Biol. Psychiatry 88, 352–359.
937 doi:10.1016/j.pnpbp.2018.08.020.
938 Nagarajan, R. P., Hogart, A. R., Gwye, Y., Martin, M. R., and LaSalle, J. M. (2006). Reduced MeCP2
939 expression is frequent in autism frontal cortex and correlates with aberrant MECP2 promoter
940 methylation. Epigenetics 1, e1-11.
941 Nagarajan, R. P., Patzel, K. A., Martin, M., Yasui, D. H., Swanberg, S. E., Hertz-Picciotto, I., et al.
942 (2008). MECP2 promoter methylation and X chromosome inactivation in autism. Autism Res. 1,
943 169–178. doi:10.1002/aur.24.
944 Nardone, S., and Elliott, E. (2016). The Interaction between the Immune System and Epigenetics in the
945 Etiology of Autism Spectrum Disorders. Front. Neurosci. 10. doi:10.3389/fnins.2016.00329.
946 Nguyen, A., Rauch, T. A., Pfeifer, G. P., and Hu, V. W. (2010). Global methylation profiling of
947 lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a
948 novel autism candidate gene, RORA, whose protein product is reduced in autistic brain. FASEB
949 J. 24, 3036–3051. doi:10.1096/fj.10-154484.
950 Nijmeijer, J. S., Arias-Vásquez, A., Rommelse, N. N. J., Altink, M. E., Anney, R. J. L., Asherson, P.,
951 et al. (2010). Identifying loci for the overlap between attention-deficit/hyperactivity disorder and
952 autism spectrum disorder using a genome-wide QTL linkage approach. J Am Acad Child
953 Adolesc Psychiatry 49, 675–685. doi:10.1016/j.jaac.2010.03.015.
954 Ohkawara, T., Katsuyama, T., Ida-Eto, M., Narita, N., and Narita, M. (2015). Maternal viral infection
955
956
957
doi:10.1016/j.braindev.2014.03.007.
o al
during pregnancy impairs development of fetal serotonergic neurons. Brain Dev. 37, 88–93.
n
Oliveira, G., Matoso, E., Vicente, A., Ribeiro, P., Marques, C., Ataíde, A., et al. (2003). Partial
si
958 tetrasomy of chromosome 3q and mosaicism in a child with autism. J. Autism Dev. Disord. 33,
959
960
961
177–185.
vi
O’Roak, B. J., Vives, L., Girirajan, S., Karakoc, E., Krumm, N., Coe, B. P., et al. (2012). Sporadic
r o
autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485,
P
962 246–250. doi:10.1038/nature10989.
963 Papanikolaou, K., Paliokosta, E., Gyftodimou, J., Kolaitis, G., Vgenopoulou, S., Sarri, C., et al. (2006).
964 A Case of Partial Trisomy of Chromosome 8p Associated with Autism. J. Autism Dev. Disord.
965 36, 705–709. doi:10.1007/s10803-006-0104-3.
966 Persico, A. M., D’Agruma, L., Maiorano, N., Totaro, A., Militerni, R., Bravaccio, C., et al. (2001).
967 Reelin gene alleles and haplotypes as a factor predisposing to autistic disorder. Mol. Psychiatry
968 6, 150–159. doi:10.1038/sj.mp.4000850.
969 Peters, S. U., Beaudet, A. L., Madduri, N., and Bacino, C. A. (2004). Autism in Angelman syndrome:
970 implications for autism research. Clin. Genet. 66, 530–536. doi:10.1111/j.1399-
971 0004.2004.00362.x.
972 Pinto, D., Delaby, E., Merico, D., Barbosa, M., Merikangas, A., Klei, L., et al. (2014). Convergence of
973 Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders. Am. J. Hum. Genet.
974 94, 677–694. doi:10.1016/j.ajhg.2014.03.018.
975 Pinto, D., Pagnamenta, A. T., Klei, L., Anney, R., Merico, D., Regan, R., et al. (2010). Functional
976 impact of global rare copy number variation in autism spectrum disorders. Nature 466, 368–372.
977 doi:10.1038/nature09146.
978 Pizzo, L., Jensen, M., Polyak, A., Rosenfeld, J. A., Mannik, K., Krishnan, A., et al. (2019). Rare
979 variants in the genetic background modulate cognitive and developmental phenotypes in
980 individuals carrying disease-associated variants. Genet. Med. 21, 816–825. doi:10.1038/s41436-
981 018-0266-3.
982 Poduri, A., Evrony, G. D., Cai, X., and Walsh, C. A. (2013). Somatic Mutation, Genomic Variation,
983 and Neurological Disease. Science 341, 1237758. doi:10.1126/science.1237758.
21
984 Polyak, A., Rosenfeld, J. A., and Girirajan, S. (2015). An assessment of sex bias in
985 neurodevelopmental disorders. Genome Med 7, 94. doi:10.1186/s13073-015-0216-5.
986 Pucilowska, J., Vithayathil, J., Tavares, E. J., Kelly, C., Karlo, J. C., and Landreth, G. E. (2015). The
987 16p11.2 Deletion Mouse Model of Autism Exhibits Altered Cortical Progenitor Proliferation and
988 Brain Cytoarchitecture Linked to the ERK MAPK Pathway. J. Neurosci. 35, 3190–3200.
989 doi:10.1523/JNEUROSCI.4864-13.2015.
990 Puram, S. V., Kim, A. H., Park, H.-Y., Anckar, J., and Bonni, A. (2013). The ubiquitin receptor
991 S5a/Rpn10 links centrosomal proteasomes with dendrite development in the mammalian brain.
992 Cell Rep. 4, 19–30. doi:10.1016/j.celrep.2013.06.006.
993 Qin, W., Chan, J. A., Vinters, H. V., Mathern, G. W., Franz, D. N., Taillon, B. E., et al. (2010).
994 Analysis of TSC cortical tubers by deep sequencing of TSC1, TSC2, and KRAS demonstrates
995 that small second hit mutations in these genes are rare events. Brain Pathol. Zurich Switz. 20,
996 1096–1105. doi:10.1111/j.1750-3639.2010.00416.x.
997 Qin, L., Ma, K., Wang, Z.-J., Hu, Z., Matas, E., Wei, J., et al. (2018). Social deficits in Shank3-
998 deficient mouse models of autism are rescued by histone deacetylase (HDAC) inhibition. Nat.
999 Neurosci. 21, 564–575. doi:10.1038/s41593-018-0110-8.
1000 Rapoport, J., Chavez, A., Greenstein, D., Addington, A., and Gogtay, N. (2009). Autism spectrum
1001 disorders and childhood-onset schizophrenia: clinical and biological contributions to a relation
1002 revisited. J Am Acad Child Adolesc Psychiatry 48, 10–18. doi:10.1097/CHI.0b013e31818b1c63.
1003
1004
1005
al
Rasalam, A. D., Hailey, H., Williams, J. H. G., Moore, S. J., Turnpenny, P. D., Lloyd, D. J., et al.
n
(2005). Characteristics of fetal anticonvulsant syndrome associated autistic disorder. Dev. Med.
Child Neurol. 47, 551–555.
o
si
1006 Rasia-Filho, A. A., Londero, R. G., and Achaval, M. (2000). Functional activities of the amygdala: an
1007
1008
1009
i
overview. J. Psychiatry Neurosci. 25, 14–23.
v
Reiersen, A. M., Constantino, J. N., Volk, H. E., and Todd, R. D. (2007). Autistic traits in a
r o
population-based ADHD twin sample. Journal of Child Psychology and Psychiatry 48, 464–
P
1010 472. doi:10.1111/j.1469-7610.2006.01720.x.
1011 Repnikova, E. A., Lyalin, D. A., McDonald, K., Astbury, C., Hansen-Kiss, E., Cooley, L. D., et al.
1012 (2019). CNTN6 copy number variations: Uncertain clinical significance in individuals with
1013 neurodevelopmental disorders. European Journal of Medical Genetics.
1014 doi:10.1016/j.ejmg.2019.02.008.
1015 Rio, M., Royer, G., Gobin, S., Blois, M. de, Ozilou, C., Bernheim, A., et al. (2013). Monozygotic twins
1016 discordant for submicroscopic chromosomal anomalies in 2p25.3 region detected by array CGH.
1017 Clin. Genet. 84, 31–36. doi:10.1111/cge.12036.
1018 Risch, N., Hoffmann, T. J., Anderson, M., Croen, L. A., Grether, J. K., and Windham, G. C. (2014).
1019 Familial recurrence of autism spectrum disorder: evaluating genetic and environmental
1020 contributions. Am. J. Psychiatry 171, 1206–1213. doi:10.1176/appi.ajp.2014.13101359.
1021 Robinson, E. B., Lichtenstein, P., Anckarsäter, H., Happé, F., and Ronald, A. (2013). Examining and
1022 interpreting the female protective effect against autistic behavior. Proc. Natl. Acad. Sci. 110,
1023 5258–5262. doi:10.1073/pnas.1211070110.
1024 Rommelse, N. N. J., Franke, B., Geurts, H. M., Hartman, C. A., and Buitelaar, J. K. (2010). Shared
1025 heritability of attention-deficit/hyperactivity disorder and autism spectrum disorder. Eur Child
1026 Adolesc Psychiatry 19, 281–295. doi:10.1007/s00787-010-0092-x.
1027 Ronald, A., Simonoff, E., Kuntsi, J., Asherson, P., and Plomin, R. (2008). Evidence for overlapping
1028 genetic influences on autistic and ADHD behaviours in a community twin sample. Journal of
1029 Child Psychology and Psychiatry 49, 535–542. doi:10.1111/j.1469-7610.2007.01857.x.
1030 Ronemus, M., Iossifov, I., Levy, D., and Wigler, M. (2014). The role of de novo mutations in the
1031 genetics of autism spectrum disorders. Nat. Rev. Genet. 15, 133–141. doi:10.1038/nrg3585.
22
1032 Roved, J., Westerdahl, H., and Hasselquist, D. (2017). Sex differences in immune responses: Hormonal
1033 effects, antagonistic selection, and evolutionary consequences. Horm. Behav. 88, 95–105.
1034 doi:10.1016/j.yhbeh.2016.11.017.
1035 Saghazadeh, A., and Rezaei, N. (2017). Brain-Derived Neurotrophic Factor Levels in Autism: A
1036 Systematic Review and Meta-Analysis. J. Autism Dev. Disord. 47, 1018–1029.
1037 doi:10.1007/s10803-016-3024-x.
1038 Samaco, R. C., Hogart, A., and LaSalle, J. M. (2005). Epigenetic overlap in autism-spectrum
1039 neurodevelopmental disorders: MECP2 deficiency causes reduced expression of UBE3A and
1040 GABRB3. Hum. Mol. Genet. 14, 483–492. doi:10.1093/hmg/ddi045.
1041 Sandin, S., Lichtenstein, P., Kuja-Halkola, R., Larsson, H., Hultman, C. M., and Reichenberg, A.
1042 (2014). The familial risk of autism. JAMA 311, 1770–1777. doi:10.1001/jama.2014.4144.
1043 Sarachana, T., Xu, M., Wu, R.-C., and Hu, V. W. (2011). Sex Hormones in Autism: Androgens and
1044 Estrogens Differentially and Reciprocally Regulate RORA, a Novel Candidate Gene for Autism.
1045 PLOS ONE 6, e17116. doi:10.1371/journal.pone.0017116.
1046 Sauter, S., von Beust, G., Burfeind, P., Weise, A., Starke, H., Liehr, T., et al. (2003). Autistic disorder
1047 and chromosomal mosaicism 46,XY[123]/46,XY,del(20)(pter --> p12.2)[10]. Am. J. Med.
1048 Genet. A. 120A, 533–536. doi:10.1002/ajmg.a.20089.
1049 Schmunk, G., and Gargus, J. J. (2013). Channelopathy pathogenesis in autism spectrum disorders.
1050 Front. Genet. 4. doi:10.3389/fgene.2013.00222.
1051
1052
1053
al
Schork, A. J., Won, H., Appadurai, V., Nudel, R., Gandal, M., Delaneau, O., et al. (2019). A genome-
n
wide association study of shared risk across psychiatric disorders implicates gene regulation
o
during fetal neurodevelopment. Nat. Neurosci. 22, 353–361. doi:10.1038/s41593-018-0320-0.
si
1054 Schroer, R. J., Phelan, M. C., Michaelis, R. C., Crawford, E. C., Skinner, S. A., Cuccaro, M., et al.
1055
1056
1057
327–336.
r o i
(1998). Autism and maternally derived aberrations of chromosome 15q. Am. J. Med. Genet. 76,
v
Schwarz, E., Guest, P. C., Rahmoune, H., Wang, L., Levin, Y., Ingudomnukul, E., et al. (2011). Sex-
P
1058 specific serum biomarker patterns in adults with Asperger’s syndrome. Mol. Psychiatry 16,
1059 1213–1220. doi:10.1038/mp.2010.102.
1060 Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., et al. (2007). Strong
1061 Association of De Novo Copy Number Mutations with Autism. Science 316, 445–449.
1062 doi:10.1126/science.1138659.
1063 Serajee, F., Nabi, R., Zhong, H., and Mahbubul, H. (2003). Association of INPP1, PIK3CG, and TSC2
1064 gene variants with autistic disorder: implications for phosphatidylinositol signalling in autism. J.
1065 Med. Genet. 40, e119. doi:10.1136/jmg.40.11.e119.
1066 Shao, Y., Cuccaro, M. L., Hauser, E. R., Raiford, K. L., Menold, M. M., Wolpert, C. M., et al. (2003).
1067 Fine Mapping of Autistic Disorder to Chromosome 15q11-q13 by Use of Phenotypic Subtypes.
1068 Am. J. Hum. Genet. 72, 539–548.
1069 Shi, L., Zhang, Z., and Su, B. (2016). Sex Biased Gene Expression Profiling of Human Brains at Major
1070 Developmental Stages. Sci. Rep. 6, 21181. doi:10.1038/srep21181.
1071 Short, P. J., McRae, J. F., Gallone, G., Sifrim, A., Won, H., Geschwind, D. H., et al. (2018). De novo
1072 mutations in regulatory elements in neurodevelopmental disorders. Nature 555, 611–616.
1073 doi:10.1038/nature25983.
1074 Smith, S. E. P., Zhou, Y.-D., Zhang, G., Jin, Z., Stoppel, D. C., and Anderson, M. P. (2011). Increased
1075 Gene Dosage of Ube3a Results in Autism Traits and Decreased Glutamate Synaptic
1076 Transmission in Mice. Sci. Transl. Med. 3, 103ra97. doi:10.1126/scitranslmed.3002627.
1077 Soltani, A., Lebrun, S., Carpentier, G., Zunino, G., Chantepie, S., Maïza, A., et al. (2017). Increased
1078 signaling by the autism-related Engrailed-2 protein enhances dendritic branching and spine
23
1079 density, alters synaptic structural matching, and exaggerates protein synthesis. PloS One 12,
1080 e0181350. doi:10.1371/journal.pone.0181350.
1081 Stamouli, S., Anderlid, B.-M., Willfors, C., Thiruvahindrapuram, B., Wei, J., Berggren, S., et al.
1082 (2018). Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental
1083 Disorders. Twin Res. Hum. Genet. Off. J. Int. Soc. Twin Stud. 21, 1–11. doi:10.1017/thg.2017.69.
1084 Stefansson, H., Meyer-Lindenberg, A., Steinberg, S., Magnusdottir, B., Morgen, K., Arnarsdottir, S., et
1085 al. (2014). CNVs conferring risk of autism or schizophrenia affect cognition in controls. Nature
1086 505, 361–366. doi:10.1038/nature12818.
1087 Stergiakouli, E., Davey Smith, G., Martin, J., Skuse, D. H., Viechtbauer, W., Ring, S. M., et al. (2017).
1088 Shared genetic influences between dimensional ASD and ADHD symptoms during child and
1089 adolescent development. Mol Autism 8, 18. doi:10.1186/s13229-017-0131-2.
1090 Stern, D., Cho, M. T., Chikarmane, R., Willaert, R., Retterer, K., Kendall, F., et al. (2017). Association
1091 of the missense variant p.Arg203Trp in PACS1 as a cause of intellectual disability and seizures.
1092 Clin. Genet. 92, 221–223. doi:10.1111/cge.12956.
1093 Stessman, H. A. F., Xiong, B., Coe, B. P., Wang, T., Hoekzema, K., Fenckova, M., et al. (2017).
1094 Targeted sequencing identifies 91 neurodevelopmental disorder risk genes with autism and
1095 developmental disability biases. Nat. Genet. 49, 515–526. doi:10.1038/ng.3792.
1096 Stodgell, C. J., Ingram, J. L., O’Bara, M., Tisdale, B. K., Nau, H., and Rodier, P. M. (2006). Induction
1097 of the homeotic gene Hoxa1 through valproic acid’s teratogenic mechanism of action.
1098
1099
1100
al
Neurotoxicol. Teratol. 28, 617–624. doi:10.1016/j.ntt.2006.08.004.
n
Strømme, P., Mangelsdorf, M. E., Scheffer, I. E., and Gécz, J. (2002). Infantile spasms, dystonia, and
o
other X-linked phenotypes caused by mutations in Aristaless related homeobox gene, ARX.
si
1101 Brain Dev. 24, 266–268.
1102
1103
1104
i
Sullivan, P. F., Magnusson, C., Reichenberg, A., Boman, M., Dalman, C., Davidson, M., et al. (2012).
v
FAMILY HISTORY OF SCHIZOPHRENIA AND BIPOLAR DISORDER AS RISK
r o
FACTORS FOR AUTISM. Arch Gen Psychiatry 69, 1099–1103.
P
1105 doi:10.1001/archgenpsychiatry.2012.730.
1106 Sun, W., Poschmann, J., Cruz-Herrera del Rosario, R., Parikshak, N. N., Hajan, H. S., Kumar, V., et al.
1107 (2016). Histone Acetylome-wide Association Study of Autism Spectrum Disorder. Cell 167,
1108 1385-1397.e11. doi:10.1016/j.cell.2016.10.031.
1109 Szafranski, P., Schaaf, C. P., Person, R. E., Gibson, I. B., Xia, Z., Mahadevan, S., et al. (2010).
1110 Structures and Molecular Mechanisms for Common 15q13.3 Microduplications Involving
1111 CHRNA7: Benign or Pathological? Hum Mutat 31, 840–850. doi:10.1002/humu.21284.
1112 Takuma, K., Hara, Y., Kataoka, S., Kawanai, T., Maeda, Y., Watanabe, R., et al. (2014). Chronic
1113 treatment with valproic acid or sodium butyrate attenuates novel object recognition deficits and
1114 hippocampal dendritic spine loss in a mouse model of autism. Pharmacol. Biochem. Behav. 126,
1115 43–49. doi:10.1016/j.pbb.2014.08.013.
1116 Talebizadeh, Z., Bittel, D., Miles, J., Takahashi, N., Wang, C., Kibiryeva, N., et al. (2002). No
1117 association between HOXA1 and HOXB1 genes and autism spectrum disorders (ASD). J. Med.
1118 Genet. 39, e70. doi:10.1136/jmg.39.11.e70.
1119 Tang, G., Gudsnuk, K., Kuo, S.-H., Cotrina, M. L., Rosoklija, G., Sosunov, A., et al. (2014). Loss of
1120 mTOR-Dependent Macroautophagy Causes Autistic-like Synaptic Pruning Deficits. Neuron 83,
1121 1131–1143. doi:10.1016/j.neuron.2014.07.040.
1122 Thapar, A., and Cooper, M. (2013). Copy Number Variation: What Is It and What Has It Told Us
1123 About Child Psychiatric Disorders? J. Am. Acad. Child Adolesc. Psychiatry 52, 772–774.
1124 doi:10.1016/j.jaac.2013.05.013.
24
1125 The Autism Genome Project Consortium, Szatmari, P., Paterson, A. D., Zwaigenbaum, L., Roberts,
1126 W., Brian, J., et al. (2007). Mapping autism risk loci using genetic linkage and chromosomal
1127 rearrangements. Nat. Genet. 39, 319–328. doi:10.1038/ng1985.
1128 The Autism Spectrum Disorders Working Group of The Psychiatric Genomics Consortium (2017).
1129 Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a
1130 novel locus at 10q24.32 and a significant overlap with schizophrenia. Mol Autism 8.
1131 doi:10.1186/s13229-017-0137-9.
1132 Tran, S. S., Jun, H.-I., Bahn, J. H., Azghadi, A., Ramaswami, G., Van Nostrand, E. L., et al. (2019).
1133 Widespread RNA editing dysregulation in brains from autistic individuals. Nat. Neurosci. 22,
1134 25–36. doi:10.1038/s41593-018-0287-x.
1135 Turner, T. N., Coe, B. P., Dickel, D. E., Hoekzema, K., Nelson, B. J., Zody, M. C., et al. (2017).
1136 Genomic patterns of de novo mutation in simplex autism. Cell 171, 710-722.e12.
1137 doi:10.1016/j.cell.2017.08.047.
1138 Turner, T. N., Hormozdiari, F., Duyzend, M. H., McClymont, S. A., Hook, P. W., Iossifov, I., et al.
1139 (2016). Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative
1140 Noncoding Regulatory DNA. Am. J. Hum. Genet. 98, 58–74. doi:10.1016/j.ajhg.2015.11.023.
1141 Tyburczy, M. E., Jozwiak, S., Malinowska, I. A., Chekaluk, Y., Pugh, T. J., Wu, C.-L., et al. (2015). A
1142 shower of second hit events as the cause of multifocal renal cell carcinoma in tuberous sclerosis
1143 complex. Hum. Mol. Genet. 24, 1836–1842. doi:10.1093/hmg/ddu597.
1144
1145
1146
al
Vorstman, J., van Daalen, E., Jalali, G., Schmidt, E., Pasterkamp, R., de Jonge, M., et al. (2011). A
n
double hit implicates DIAPH3 as an autism risk gene. Mol. Psychiatry 16, 442–451.
doi:10.1038/mp.2010.26.
o
si
1147 Wang, C.-C., Lin, H.-C., Chan, Y.-H., Gean, P.-W., Yang, Y. K., and Chen, P. S. (2013). 5-HT1A-
1148
1149
1150
i
receptor agonist modified amygdala activity and amygdala-associated social behavior in a
v
valproate-induced rat autism model. Int. J. Neuropsychopharmacol. 16, 2027–2039.
r o
doi:10.1017/S1461145713000473.
P
1151 Wang, W., Corominas, R., and Lin, G. N. (2019). De novo Mutations From Whole Exome Sequencing
1152 in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application. Front Genet
1153 10. doi:10.3389/fgene.2019.00258.
1154 Weiss, L. A., Shen, Y., Korn, J. M., Arking, D. E., Miller, D. T., Fossdal, R., et al. (2008). Association
1155 between Microdeletion and Microduplication at 16p11.2 and Autism. N. Engl. J. Med. 358, 667–
1156 675. doi:10.1056/NEJMoa075974.
1157 Wenger, T. L., Kao, C., McDonald-McGinn, D. M., Zackai, E. H., Bailey, A., Schultz, R. T., et al.
1158 (2016). The Role of mGluR Copy Number Variation in Genetic and Environmental Forms of
1159 Syndromic Autism Spectrum Disorder. Sci. Rep. 6, 19372. doi:10.1038/srep19372.
1160 Werling, D. M., and Geschwind, D. H. (2013). Sex differences in autism spectrum disorders. Curr.
1161 Opin. Neurol. 26, 146–153. doi:10.1097/WCO.0b013e32835ee548.
1162 Whitehouse, A. J. O., Maybery, M. T., Hart, R., Mattes, E., Newnham, J. P., Sloboda, D. M., et al.
1163 (2010). Fetal androgen exposure and pragmatic language ability of girls in middle childhood:
1164 Implications for the extreme male-brain theory of autism. Psychoneuroendocrinology 35, 1259–
1165 1264. doi:10.1016/j.psyneuen.2010.02.007.
1166 Williams, C. A., Driscoll, D. J., and Dagli, A. I. (2010). Clinical and genetic aspects of Angelman
1167 syndrome. Genet. Med. Off. J. Am. Coll. Med. Genet. 12, 385–395.
1168 doi:10.1097/GIM.0b013e3181def138.
1169 Wong, C. C. Y., Meaburn, E. L., Ronald, A., Price, T. S., Jeffries, A. R., Schalkwyk, L. C., et al.
1170 (2014). Methylomic analysis of monozygotic twins discordant for autism spectrum disorder and
1171 related behavioural traits. Mol. Psychiatry 19, 495–503. doi:10.1038/mp.2013.41.
25
1172 Woodbury-Smith, M., and Scherer, S. W. (2018). Progress in the genetics of autism spectrum disorder.
1173 Dev. Med. Child Neurol. 60, 445–451. doi:10.1111/dmcn.13717.
1174 Xu, X., Li, C., Gao, X., Xia, K., Guo, H., Li, Y., et al. (2018). Excessive UBE3A dosage impairs
1175 retinoic acid signaling and synaptic plasticity in autism spectrum disorders. Cell Res. 28, 48–68.
1176 doi:10.1038/cr.2017.132.
1177 Yi, J. J., Berrios, J., Newbern, J. M., Snider, W. D., Philpot, B. D., Hahn, K. M., et al. (2015). An
1178 Autism-Linked Mutation Disables Phosphorylation Control of UBE3A. Cell 162, 795–807.
1179 doi:10.1016/j.cell.2015.06.045.
1180 Yi, J. J., Paranjape, S. R., Walker, M. P., Choudhury, R., Wolter, J. M., Fragola, G., et al. (2017). The
1181 autism-linked UBE3A T485A mutant E3 ubiquitin ligase activates the Wnt/β-catenin pathway
1182 by inhibiting the proteasome. J. Biol. Chem. 292, 12503–12515. doi:10.1074/jbc.M117.788448.
1183 Yurov, Y. B., Vorsanova, S. G., Iourov, I. Y., Demidova, I. A., Beresheva, A. K., Kravetz, V. S., et al.
1184 (2007). Unexplained autism is frequently associated with low-level mosaic aneuploidy. J. Med.
1185 Genet. 44, 521–525. doi:10.1136/jmg.2007.049312.
1186 Zeldovich, L. (2018). The evolution of ‘autism’ as a diagnosis, explained. Spectr. Autism Res. News.
1187 Available at: https://www.spectrumnews.org/news/evolution-autism-diagnosis-explained/
1188 [Accessed December 4, 2018].
1189 Zhang, H., Liu, X., Zhang, C., Mundo, E., Macciardi, F., Grayson, D. R., et al. (2002). Reelin gene
1190 alleles and susceptibility to autism spectrum disorders. Mol. Psychiatry 7, 1012–1017.
1191
1192
1193
doi:10.1038/sj.mp.4001124.
n al
Zhubi, A., Chen, Y., Guidotti, A., and Grayson, D. (2017). Epigenetic regulation of RELN and GAD1
o
in the frontal cortex (FC) of autism spectrum disorder (ASD) subjects. Int. J. Dev. Neurosci. Off.
si
1194 J. Int. Soc. Dev. Neurosci. 62, 63–72. doi:10.1016/j.ijdevneu.2017.02.003.
1195
1196
1197
i
Ziats, M. N., and Rennert, O. M. (2013). Sex-biased gene expression in the developing brain:
v
implications for autism spectrum disorders. Mol. Autism 4, 10. doi:10.1186/2040-2392-4-10.
r o
Zieminska, E., Toczylowska, B., Diamandakis, D., Hilgier, W., Filipkowski, R. K., Polowy, R., et al.
P
1198 (2018). Glutamate, Glutamine and GABA Levels in Rat Brain Measured Using MRS, HPLC and
1199 NMR Methods in Study of Two Models of Autism. Front. Mol. Neurosci. 11, 418.
1200 doi:10.3389/fnmol.2018.00418.
1201 7 Conflict of Interest
1202 The authors declare that the research was conducted in the absence of any commercial or financial
1203 relationships that could be construed as a potential conflict of interest.
1204 8 Author Contributions
1205 L.R. contributed by writing the main text and gathering all references. A.G.-G. contributed by editing
1206 manuscript drafts and providing insight into structure and material that should be included.
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Genetic Causes and Modifiers of Autism Spectrum Disorder

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Genetic Causes and Modifiers of Autism Spectrum Disorder

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Genetic Causes and Modifiers in Autism Spectrum

vi Frontiers website link:

Frontiers in Cellular Neuroscience | www.frontiersin.org

8 Keywords: Autism (ASD)1, genetic modifiers2, CNV3, epigenetics4, gene-environment

292 2.2 ASD risk genes overlap with other diseases

361 3 Modifiers in ASD

362 3.1 Genetic modifiers

420 3.2 Epigenetics and the environment

421 Autism susceptibility is currently estimated to be 40%-80% genetic. Environmental factors -

460 3.3 Sex-linked modifiers

524 4 Clinical Implications and Future Perspectives

1201 7 Conflict of Interest

1204 8 Author Contributions

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