Copy number variations of SHANK3 and related sensory profiles in Egyptian children with autism spectrum disorder

Highlights

• ASD children exhibit co-occurring sensory processing problems, and hyper- or hyporeactivity to sensory input.

• Chromosomal rearrangements, copy number variations and coding sequence variants, involving more than 100 genes, have been found in patients with ASD. Studying SHANK 3 gene CNVs and its associated phenotype in ASD patients might provide guidance for future treatment and intervention of ASD.

• The studied ASD children displayed sensory processing problems. SHANK3 copy number gains were found in three cases and it signifies the gene dosage effect of SHANK3 in ASD pathogenesis.

• To the best of our knowledge, this is the sixth report of 22q13 duplication including SHANK3.

Abstract

Background

Current estimates indicate that >80 % of children with autism spectrum disorder (ASD) exhibit concomitant sensory processing problems and hyper- or hypo-reactivity to sensory input. These are now included as diagnostic criteria for ASD in the Diagnostic and Statistical Manual of Mental Disorders—Fifth Edition. Chromosomal rearrangements, copy number variations (CNVs), and coding sequence variants involving >100 genes have been identified in patients with ASD. Studying the CNVs of one such gene, SHANK3, and the associated phenotype in patients with ASD could provide insights that will guide future ASD treatments and interventions.

Objective

To assess SHANK3 CNVs in children with ASD and investigate their sensory processing patterns using the Short Sensory Profile (SSP).

Subjects and methods

Forty children with ASD were assessed using the Autism Diagnostic Interview-Revised. SSP was used to evaluate atypical sensory behavior, e.g., hyper- or hypo-reactivity to sensory input or unusual sensory interests. SHANK3 CNVs were assessed in these children using Multiplex Ligation-dependent Probe Amplification.

Results

Of the 40 cases, 77.5 % showed sensory reactivity symptoms. The greatest difference from normality was observed in the under-responsive/seeks sensation domain, followed by the tactile sensitivity domain, whereas hypo-activity (low-energy/weak domain) was closest to normal. The sensory reactivity symptoms were significantly correlated with the severity of ASD. However, only three of the 40 cases had de novo duplications at 22q13.33. The duplications included SHANK3 in two of the cases and only the distal flanking region of SHANK3 in the third case. All three duplication cases also showed symptoms associated with the low-energy/weak domain.

Conclusion

We found that children with ASD exhibited sensory processing problems. The SHANK3 copy number gains found demonstrate the gene dosage effect of SHANK3 in ASD pathogenesis. This study adds to the growing understanding of 22q13 duplications that include SHANK3.

Introduction

Autism spectrum disorder (ASD) is a neuro-developmental disorder with great genetic/genomic components (Meguid et al., 2018). The Centers for Disease Control and Prevention (CDC) estimates that the prevalence of ASD among children aged 8 years has increased throughout the United States, from 1 in 150 children (2000–2002 survey) to 1 in 59 children (2014 survey) (CDC, 2018). According to the Diagnostic and Statistical Manual of Mental Disorders—Fifth Edition (DSM-5), ASD is characterized by social deficits and/or communication difficulties, stereotyped or repetitive behaviors and/or interests, sensory issues, and cognitive delays in some cases. All these symptoms are exhibited during the early neurodevelopmental stages (Mukherjee, 2017). Sensory reactivity abnormalities such as hyper- and hypo-reactivity and unusual sensory interests have recently been established as diagnostic criteria for ASD in the DSM-5 (American Psychiatric Association, 2013). Estimates suggest that the prevalence of sensory symptoms in children with ASD ranges from 60 % to 96 % (Schauder & Bennetto, 2016).

Alterations in sensory processing likely underlie many of the higher-order cognitive and social deficits associated with ASD. However, observational research that examines the existence of sensory processing dysfunctions within children with autism is limited (El-Ansary, Hassan, Qasem, & Das, 2016; Thye, Bednarz, Herringshaw, Sartin, & Kana, 2018). Because the prevalence of ASD is increasing, there is a need for further research into both the genetic and non-genetic risk factors associated with ASD, as well as improved behavioral, educational, residential, and occupational services to help treat the disorder (Centers for Disease Control, 2018).

In approximately 20 % of cases, susceptibility to ASD has been associated with a genetic component. For example, visible microscopic chromosomal abnormalities are observed in approximately 5% of ASD cases. In addition, de novo or inherited copy number variations (CNVs) have been detected in approximately 5–10 % of idiopathic ASD (iASD) cases, whereas a single gene disorder is typically present in approximately 5% of ASD cases. CNVs are defined as submicroscopic structural variations with an abnormal number of copies, deletions, or duplications of a DNA segment, in which the size is >1000 base pairs. Many of these abnormalities involve genes that are highly active in brain developmental processes (Eriksson et al., 2015; Kanduri et al., 2016; Meguid et al., 2018).

Some genes and proteins have been specifically associated with ASD risk. For example, Shank proteins have been strongly linked with ASD pathophysiology. SHANK family genes encode large synaptic scaffold proteins. They bind to a diversity of proteins at the postsynaptic density of excitatory synapses; therefore, they are important for synaptic development and function (Rosti, Sadek, Vaux, & Gleeson, 2014). Shank proteins are found in nearly all glutamatergic synapses in the central nervous system and are considered the “master” organizers of the postsynaptic density. They are crucial for ensuring appropriate responses of the intracellular machinery to glutamatergic stimulation (Braude et al., 2015; Chiocchetti, Bour, & Freitag, 2014; Sheng & Kim, 2000). Moreover, Mieses et al. (2016) suggest that there is an association between glutamatergic functioning and sensory processing.

The SHANK family comprises the SHANK1, SHANK2, and SHANK3 genes. SHANK3 is located on chromosome 22q13.3; it has 22 exons with multiple intragenic promoters and alternative splicing of coding exons. It is known to code for many mRNA and protein isoforms (Guilmatre, Huguet, Delorme, & Bourgeron, 2014; Sala, Vicidomini, Bigi, Mossa, & Verpelli, 2015). SHANK3 has been extensively investigated because of its role in Phelan–McDermid syndrome (PMS), which is a neurodevelopmental disorder that is caused by a 22q13.3 deletion and characterized by autistic-like behaviors, hypotonia, and delayed or absent speech (Phelan & McDermid, 2012). SHANK3 mutations have also been found in approximately 2% of ASD cases (Leblond et al., 2014; Moessner et al., 2007; Yi et al., 2016). Indeed, disruption of SHANK3 function is assumed to cause the core neurodevelopmental and behavioral deficits observed in ASD cases: in genetic screenings of patients with ASD who had not been diagnosed with PMS, many SHANK3 mutations were detected (Monteiro & Feng, 2017).

Multiplex Ligation-dependent Probe Amplification (MLPA) is a cost effective straightforward, rapid and efficient method to detect microdeletions and microduplications. Its application considerably increases the detection rate of various genetic disorders (Eid, 2017; Peixoto et al., 2017).

Studying SHANK3 CNVs and its associated phenotype in ASD children might provide guidance for future treatment and intervention of ASD. Thus, the present study aimed at detecting SHANK3 copy number variations (CNVs) in ASD children using MLPA and correlating SHANK3 CNVs with different clinical profiles of those children, focusing on their sensory manifestation.