Correlation of mutated gene and signalling pathways in ASD

Abstract

Autism is a complicated spectrum of neurodevelopmental illnesses characterized by repetitive and constrained behaviors and interests, as well as social interaction and communication difficulties that are first shown in infancy. More than 18 million Indians, according to the National Health Portal of India, and 1 in 160 children worldwide, according to the WHO, are diagnosed with autism spectrum disorders. This review aims to discuss the complex genetic architecture that underlies autism and summarizes the role of proteins likely to play in the development of autism. We also consider how genetic mutations can affect convergent signaling pathways and hinder the development of brain circuitry and the role of cognition development and theory of mind with Cognition-behavior therapy benefits in autism.

1. Introduction

Autism is characterized by difficulties in communication and repetitive actions (Frye et al., 2022), it is a complicated neurodevelopmental disease and the ASD stands for autism spectrum disorder which includes a group of diseases like Autism, Asperger’s syndrome, and pervasive developmental disorder (Adams et al., 2021, Md Ashraf and Alexiou, 2021). DSM-IV criteria recognize Motor abnormalities, epilepsy, sleep disorders, gastrointestinal problems, and intellectual disability as common comorbid diseases, Language disorders are commonly co-occurring (Lai et al., 2014).

The prevalence of ASD has surpassed 1 % globally, and this increases the awareness among the public, government, and healthcare industry to manage this illness (Mohameddess and Waliddqoronn, n.d.). The commencement of ASD occurs in the starting 3 years of childhood. If parents start accepting that their child is suffering from ASD and start the treatment at an early stage then it has a greater chance to be cured.

Idiopathic autism, also known as primary autism, affects around 85 % of autistic people. The specific source of the disorder is unknown. Symptomatic or secondary autism, on the other hand, occurs in only 15 % of instances where the underlying factor can be identified (Alanazi, 2013).

2. Genetics of ASD

In the developing brain, ASD risk factors concentrate on neurogenesis, transcriptional/epigenetic control, and synaptogenesis. Psychiatric disease risk is influenced by a wide range of hereditary factors (Eyring and Geschwind, 2021 Oct 1, Anttila et al., 1979), and ASD genetic risk is heavily anchored throughout the early cortical development period of neurogenesis and migration (Parikshak et al., 2013, Grove et al., 2019), Some risk genes have been implicated in developing interneurons and non-neuronal cells as well as glutamatergic neurons (Eyring and Geschwind, 2021 Oct 1, Polioudakis et al., 2019).

Cohort datasets, which integrate deep phenotypic information with biological datasets, are one way to unravel this heterogeneity and determine how genetics influences autism-related clinical characteristics (Yap et al., 2021). Numerous studies show that regardless of the huge heterogeneity that comes from a gene-centric perspective on the genetic root of ASD (Iakoucheva et al., 2019), a larger degree of convergence arises when focusing on impacted molecular processes and pathways (Cheroni et al., 2020) such as neurotransmitter release regulation, synaptic function and plasticity, immune system function, and signaling pathways, these pathways play critical roles in brain development and function, and changes in these processes and pathways are thought to contribute to autistic symptoms.

Epigenetic gene control, alternative splicing, and translation regulation (Iakoucheva et al., 2019, Ruzzo et al., 2019a, Pinto et al., 2014) are the primary emerging mechanisms (Cheroni et al., 2020). Single-gene disorders such as Fragile X syndrome (FMRI mutations), Dup15q syndrome, tuberous sclerosis complex (TSC1 and TSC2 mutation), Rett syndrome (MeCP2 mutation), deletions in the 16p11.2 region, and neurofibromatosis (NF1) are present in 3–5 % of patients with ASD (Malik et al., 2019).

They are well-known for having both an ASD phenotype and concomitant conditions (Yap et al., 2021). In an investigation of 18,381 cases and 27,969 controls, the biggest reported ASD genome-wide association study (GWAS) (Yap et al., 2021, Grove et al., 2019) discovered five genome-wide substantial loci (Yap et al., 2021), and a multi-trait study of GWAS identified another seven loci (Turley et al., 2018).

A greater understanding of the genetic basis of ASD can enhance diagnosis, provide insights into the underlying biological mechanisms, and identify new targets for treatments. and make it easier to create personalized treatment plans. There are many unanswered genetic questions in ASD, including the exact amount and types of genetic mutations that contribute to the condition's development, as well as how genetic mutations interact with one another and with environmental factors to generate ASD symptoms, the genetic diversity among persons with ASD, including how genetic mutations may differ across different racial and ethnic communities, as well as the identification of all genetic risk factors, may remain unknown.

2.1. Proteins involved in ASD

The proteins provide a variety of activities, and many reproducible hits are found in two groups (Fig. 1): the first one involved in synapse development and the second one involved in transcriptional regulation and chromatin remodeling pathways (Rylaarsdam and Guemez-Gamboa, 2019, de Rubeis et al., 2014).

Fig. 1.

Proteins Involved in ASD: Includes synapse-related protein and protein for transcription regulation and chromatin remodeling path.

The most often identified genetic abnormalities in ASD are mutations in synaptic genes, including SH3, neuroligins (NLGN), multiple ankyrin repeat domains (SHANK) (Kundu and Islam, 2021), contactin-associated protein-like 2 (CNTNAP2), and neurexin (NRXN) families (Durand et al., 2007, Xu et al., 2014). These genes are responsible for the proper functioning of a specific behavior in humans (see table 1). A single ASD risk gene is likely to produce multiple protein isoforms, each of which is found in multiple cell types.

Table 1.

Most significant terms enriched using the GOBP database (Rodriguez-Gomez et al., 2021).

Term	Genes
Social behavioral patterns	SHANK2, AVPR1A, DRD3, OXTR, PTCHD1, NRXN1, NLGN4X, SHANK3, CNTNAP2, MECP2, NRXN2 NLGN4Y, SLC6A4
Vocalization patterns	SHANK2, CNTNAP2, NRXN1, NLGN4X, NLGN4Y, SHANK3, DLG4, NRXN2
Assembly of synapse	SHANK2, BDNF, DRD2, NRXN1, NLGN4Y, SHANK3, DRD1, MECP2, NRXN2, NRCA M
Memory	HTR2A, SHANK2, CHRNA7, GRIN2A, PTGS2, SLC6A4, CX3CR1, SHANK3, DRD1, OXTR
Synaptic transmission is regulated positively.	SHANK2, DRD1, NRXN1, SHANK3, PTGS2, RELN, OXTR
Learning	SHANK2, SHANK3, CNTNAP2, DRD1, DRD3, NRXN1, NLGN4X, NLGN4Y, PTGS2
Vocal learning	SHANK3, CNTNAP2, FOXP2, NRXN1, NRXN2

Depending on the model system being researched, these various protein isoforms may then contribute to various microcircuits that support a variety of expectations and perceptions. Additional aspects of this intricacy include developmental time (Manoli and State, 2021). An imbalance in E/I synaptic activity in the brain is a significant element in the development of ASD (Eyring and Geschwind, 2021). CHD8 and CHD2 (both ASD high-risk genes), CTNBB1, MECP2, and HDAC4 are examples of major regulators of chromatin remodeling with a well-established relation to ASD. When compared to healthy controls, extensive cohort studies show a greater rate of deletions in the NRXN1 region of chromosome 2p16.3 in probands with ASD (Chen et al., 2013, Dabell et al., 2013). These findings point to the idea that ASD is caused by synaptic plasticity disorders, as evidenced by proteins involved in synapse formation and modification (Powell and Boucard, 2013).

2.2. Identification of candidate ASD risk genes

The goal of finding autism risk genes is to gain insight into the disease's currently unknown molecular underpinnings, etiology, and therapeutic options. Rare variations, particularly de novo variants that appear causal, are viewed as interesting for potentially revealing hints about potential biology because of their high effect size (Thapar and Rutter, 2021).

The initial single-cell gene expression analysis of ASD tissue shows the presence of changed gene expression profiles in astrocytes and microglia, as well as differently translated synaptic genes in cortical neurons and interneurons, which was validated (Eyring and Geschwind, 2021 Oct 1, Velmeshev et al., 2019). Genetically, two types of gene networks are enriched for the risk of autism spectrum disorder (ASD): the first is related to transcriptional regulation, seen in mid-fetal development, and the second one is functionally related to synaptic activity and expressed later in development (around birth). These ASD-related gene modules were increased in excitatory neuron development in a laminar-specific manner (Eyring and Geschwind, 2021; Parikshak et al., 2013).

The precise genes responsible for specific human behaviors and their association to autism are still unknown. Several genes, including SHANK3, CNTNAP2, and CHD8, have been linked to an increased chance of developing autism, according to research. Variations in the SHANK3 gene have been linked to the development of autism and other behavioral problems. The SHANK3 gene is hypothesized to be involved in the appropriate functioning of human social and communication activities.

Phelan-McDermid syndrome (PMS) and 22q13 deletion syndrome are both connected to SHANK3 mutations, which are one of the recognized genetic causes of autism spectrum disorder (ASD) (Yoo, 2015, Phelan and McDermid, 2011). Synaptic genes like neuroligins, SHANK3, neurexins, and dipeptidyl peptidase-like 10 (DPP10) exhibit deletions in autistic patients., according to numerous research (Yoo, 2015, 2017).

The CNTNAP2 gene has also been linked to the development of autism and the regulation of behavior. This gene encodes a protein that is involved in the development of neural connections in the brain (Palmer, 2021) and is hypothesized to be involved in the regulation of language and social behavior in humans (Patel et al., 2014). However, it is important to emphasize that these genes are only likely to play a minor influence in the development of autism and that the condition is most likely caused by a complex interplay of several genes and environmental factors.

2.3. Genetic architecture

Extremely diverse genetic backgrounds contribute to the heterogeneity of the ASD genetic architecture, which is characterized by a spectrum of genetic loads between two extremes: one is composed primarily of poorly characterized low-risk single nucleotide polymorphisms (SNPs), and the other is made up of numerous highly penetrant rare variants, often copy number variations (CNVs), whose expressivity is also influenced by the diversity of genetic backgrounds (Jeste and Geschwind, 2014)Fig. 2.

Fig. 2.

Genetic architecture used to study the etiology of ASD: Includes Frequency, Mode of Inheritance and Type of variation. Abbreviations: CNV - Copy number variation; SNP - single nucleotide polymorphism; INDEL - Initial Map of Insertion and Deletion.

2.3.1. Frequency

2.3.1.1. Common variation

GWAS (Genome-Wide Association Studies) has primarily been used to investigate the role of common polymorphisms in autism. In GWAS, high-throughput genotyping of common variants is used, which are genetic variations that are seen in at least 5 % of the population (Ramaswami and Geschwind, 2018). ASD risk is thought to be significantly influenced by common variants, which account for 40–60 % of the total risk (Gaugler et al., 2014). Intergenic polymorphisms between CDH9 and CDH10 on chromosome 5p14.1 and MACROD2 gene variants on chromosome 20p12.1 are the only two ASD loci of genome-wide relevance (Persico et al., 2020).

2.3.1.2. Rare inherited variation

Rare X-linked mutations in two Neuroligin (NLGN3 and NLGN4) (Ramaswami and Geschwind, 2018), were detected in male ASD patient diagnosis (Ramaswami and Geschwind, 2018). ASD has been linked to over 100 rare Mendelian syndromes, implying that ASD is a collection of rare illnesses. Rare possible deleterious inherited mutations have also been found in three members of the scaffolding protein family (SHANK1, SHANK2, and SHANK3) and two members of the neurexin family (NRXN1 and NRXN3) (Ramaswami and Geschwind, 2018), implying that these genes may play a role in ASD (Persico et al., 2020). hinting that these genes may play a role in autism spectrum disorder (Berkel et al., 2010).

2.3.2. Mode of inheritance and types of variation

• •De Novo Variation

De novo mutations in the paternal germline are responsible for any occurrences of ASD (Ramaswami and Geschwind, 2018). Using cytogenetic methods, large deletions or duplications were identified as genetic risk factors for ASD (Ramaswami and Geschwind, 2018), such as:

• •15q duplication,
• •22q11.2 deletion,
• •Xp22.3 deletion,
• •16p11.2 duplication or deletion.

Despite the functional diversity of the genes found thus far, many of them play a role in synapse development, transcriptional regulation, and chromatin remodeling (Ramaswami and Geschwind, 2018, Sebat et al., 1979). There are 400–1000 ASD susceptibility genes with known mutation frequencies. De novo and uncommon hereditary mutations account for about 10 % of autism diagnoses (Geschwind, 2011).

De novo mutations in the paternal germline have been implicated in a higher rate of autism spectrum disorder (ASD) than de novo mutations in the maternal germline, due to several factors, including the higher rate of DNA replication errors in sperm compared to eggs, the accumulation of mutations over the lifespan of a man compared to a woman, due to differences in the age of the father at the time of conception, differences in the number of germline cell divisions, or differences in exposure to environmental factors that can increase the risk of mutations. However, the precise cause for the greater rate of occurrence of paternal mutations is unknown, it is crucial to remember, however, that both paternal and maternal de novo mutations can increase the risk of having ASD, and other genetic and environmental factors also play a part in the disorder's development (Anon, 2013).

Based on the incidence of de novo mutations within a gene, Hundreds of genes and copy number variations (CNVs) have been linked to ASD in large-scale sequencing studies (Eyring and Geschwind, 2021) thanks to consortium efforts led by the Simons Simplex Collection (Abrahams and Geschwind, 2008, Sanders et al., 2015), Autism Sequencing Consortium (de Rubeis et al., 2014, Neale et al., 2012), and Autism Genetic Resource Exchange (Sebat et al., 1979)).

Using data from more than 35,000 people's whole-exome sequencing (WES), 102 ASD risk genes were revealed (11.9 thousand of whom have ASD) (Eyring and Geschwind, 2021), several of which overlap with previously published studies (de Rubeis et al., 2014, Iossifov et al., 2014).

Although most CNVs, especially those that extend more than 100 kb and contain many genes (Eyring and Geschwind, 2021 Oct 1), overlap with minor insertions and deletions previously linked to ASD (Sanders et al., 2015, Sebat et al., 1979), the association between individual genes and symptoms implicated in most CNVs remains unexplained. It is found that in multiplex families, there is a rare hereditary variation that is not visible in simplex families (Leppa et al., 2016). De novo variation appears to play a less role in ASD risk in multiplex families than in simplex households (Ruzzo et al., 2019b), even though it does occur.

• •CNV

CNVs are sub-microscopic structural alterations in chromosomes that include duplications, deletions, translocations, and inversions that can reach many kilobases (Marshall et al., 2008).

Autistic people have a larger burden of rare, genic CNVs, according to studies, suggesting these variants in ASD. Since the increased likelihood of ASD was evident in relatively small cohort sizes, it was possible to conclude that affected individuals were the result of a higher concentration of certain risk regions in the ASD population by highlighting CNVs with a strong impact collectively (Manoli and State, 2021).

Neurodevelopmental abnormalities have been linked to increases and decrease in copy number at the same gene (Manoli and State, 2021). One of the earliest CNVs to be linked to the typical ASD was on chromosome 16p11.2 (the most common risk CNV gene in cases of idiopathic ASD) (Marshall et al., 2008, Manoli and State, 2021). CNVs cause more structural differences, such as 16p11.2 duplications, which contribute to ASD. Most of the 25 genes in this area, involved in the development of the nervous system, are necessary for ideal development (Yoo, 2015, Blaker-Lee et al., 2012).

One of the genes in the 16p11.2 area is the potassium channel tetramerization domain 13 (KCTD13), which appears to be the main contributor to ASD (Yoon et al., 2020, Rylaarsdam and Guemez-Gamboa, 2019). CNV in the UBE3A gene locus has also been linked to autistic symptoms in mice, as well as a decrease in glutamatergic synaptic transmission (Smith et al., 2011). Rare, significant CNVs have been linked to ASD, in addition to typical co-occurring disorders such as developmental delay (DD) and intellectual disability (ID) (Yap et al., 2021, Klei et al., 2012) Using software like PennCNV and iPattern, larger CNVs can be discovered from genome-wide SNP arrays (Wang et al., 2007).

• •SNP

Common genetic variation accounts for the majority of the genetic diversity in autism, heritability determined by single nucleotide polymorphisms (SNPs) is thought to account for 40–50 % of autism cases (Yap et al., 2021), acting either additively or synergistically as risk factors (Gaugler et al., 2014) Single nucleotide polymorphisms (SNPs) are variations in the DNA sequence that occur when a single nucleotide (A, C, G, or T) is altered. Each progenitor generates about five single nucleotide variants (SNV) every day during neurogenesis, and Postzygotic mutations account for about 5–7 % of de novo harmful mutations, however, estimates as high as 22 % have been reported (Acuna-Hidalgo et al., 2015). In simplex ASD probands, the De novo genic point mutations (single-nucleotide mutations) variations increased statistically significantly, similar to CNVs (Iossifov et al., 2012, Sanders et al., 2012) SNVs that are projected to harm the encoded protein are known as specific sorts of SNVs.

The most harmful variants, known as Mutations that cause a premature stop codon are known as presumptive loss-of-function or likely-gene-disrupting (LGD) mutations (Manoli and State, 2021)., frameshift mutation, or modification of a canonical splice site–was determined to have the strongest evidence.

Importantly, each of these heterozygous (present in only one of two copies of a gene) LGD mutations was anticipated to cause haploinsufficiency, a 50 % reduction in overall gene production (Sanders et al., 2012). Human research has discovered SNPs in xenobiotic metabolism-related enzymes, evaluating the influence of certain genetic polymorphisms on sensitivity to toxicants, such as:

• •d-aminolevulinic acid dehydratase (ALAD) (Cheroni et al., 2020),
• •paraoxonase 1 (PON1),
• •glutathione- S-transferases (GSTM1 and GSTP1),
• •solute carrier family 40 members 1 (SLC40A1) (Cheroni et al., 2020),
• •MTF1 (metal regulatory transcription factor 1) was linked to an increased incidence of ASD (Rossignol et al., 2014).

The genes that are expressed in the brain seem to be concentrated on the X chromosome, and the symptoms of intellectual disability associated with X-linked mutations are typically more common in boys than in girls (Manoli and State, 2021; Jacquemont et al., 2014). Extremely few NLGN3 and NLGN4 genes, all of which are located on the X chromosome, carry LGD mutations (Robinson et al., 2013).

SNPs in gene coding areas can cause autism by changing the amino acid sequence of a protein, which affects its function, or by altering gene expression through multiple processes. For example, SNPs in regulatory areas, such as the promoter region, can alter transcription factor binding, changing gene expression and contributing to autism development. According to research, both coding and non-coding SNPs can influence the risk of autism. For instance, a study by O’Roak et al. (2012b) identified de novo mutations in coding regions of autism-associated genes in affected individuals. Additionally, a genome-wide association study (Anney et al., 2010) identified common SNPs in non-coding regions associated with autism.

It is crucial to emphasize, however, that most SNPs in coding areas do not affect gene function (Manolio, 2010). In many cases, many SNPs are involved in the development of autism, and each SNP's impact can be minor (Anney et al., 2010).

Furthermore, the association between SNPs and autism is complex and not entirely understood; not all people with autism have SNPs in coding regions, and not all people with SNPs in coding regions acquire autism (Geschwind and State, 2015).

Autism can potentially be caused by single nucleotide polymorphisms (SNPs) in non-coding areas of DNA (Levy et al., 2011). They could affect the function of regulatory elements, resulting in alterations in the expression of genes important in brain development and function (Geschwind, 2011). For example, SNPs in gene enhancers or promoter regions can impact gene expression, resulting in changes in brain development and function that are likely to contribute to autistic symptoms (Parikshak et al., 2013). It has the potential to interact with other genetic polymorphisms, such as those found in coding areas, to influence the chance of developing autism (Betancur, 2011).

• •INDEL

The human genome has a large number of Initial Maps of Insertion and Deletion (INDEL) variations, which are common in the genomes of model species and are predicted to be common in humans as well. In exome sequencing data, insertions and deletions (indels) have proven particularly challenging to find. Indels were discovered in the exome data of 787 families with ASD and showed a connection between ASD and de novo indels that change the reading frame (Dong et al., 2014). De novo frameshift indels have a 1.6 odds ratio of being related to ASD. KMT2E and RIMS1 have been linked to ASD through many de novo indels.

They are predicted to increase risk in about 3 % of people with ASD based on mutation rates in probands compared to unaffected siblings. De novo indels are created on the paternal chromosome in 88 % of cases. ASD is largely influenced by synaptic function, chromatin remodeling, and FMRP targets. Although chromatin regulation in fetal development has been identified as a key risk factor for ASD (Dong et al., 2014, Willsey et al., 2013) KMT2E has not previously been linked to neurological disorders. The gene is also highly coexpressed throughout the brain, particularly during fetal development (Dong et al., 2014, Kang et al., 2011).

CNV (Copy Number Variation) and INDEL (Insertion/Deletion) are two different forms of genetic variants that can arise in an organism's DNA. CNV denotes a change in the number of copies of a certain DNA sequence (Conrad et al., 2010), whereas INDEL denotes the insertion or deletion of a specific DNA segment (Inlow and Restifo, 2004). CNVs can encompass extensive DNA segments ranging from a few kilobases to entire chromosomes (Redon et al., 2006), but INDELs are typically smaller, ranging from a single base pair to several kilobases (Stenson et al., 2003).

CNV and INDEL can both have major consequences on an organism by altering gene expression, disrupting coding sequences, and causing disease. CNVs, on the other hand, can cause alterations in gene dosage (Redon et al., 2006), whilst INDELs can disrupt a gene's reading frame, resulting in premature termination of protein synthesis (Stankiewicz and Lupski, 2010).

3. Epigenetic regulation and ASD

ASD risk is heavily influenced by genes with epigenetic-modulating effects. Risk genes having significant penetrance were frequently found in the nucleus, where they were implicated in expression modulation or the protein-protein interaction network that controls CNS development patterns, according to a recent assessment of 215 potential genes (Casanova et al., 2016).

The study of changes in gene expression or cellular phenotype that do not entail changes to the underlying DNA sequence is referred to as epigenetics, Environmental factors such as stress or pollutants can trigger these changes, which can be handed down from generation to generation (Bird, 2007 May 23). Epigenetic changes have been linked to the control of genes involved in brain development and function in autism, prompting researchers to speculate that epigenetic processes and their substrates could be attractive therapeutic targets (Fraga et al., 2005).

It may be able to ameliorate the symptoms of autism and the quality of life for persons affected by the illness by modifying these epigenetic changes (Braidy et al., 2015). Recent research suggests that aberrant epigenetic regulation may play a role in the development of autism spectrum disease (ASD), it may be able to design new treatments for ASD that improve brain function and behavior by targeting these epigenetic modifications and their substrates (Ladd-Acosta et al., 2014a, Wong et al., 2014).

Large-scale epigenomic research reveals Genes involved in methylation are frequently found in susceptibility regions like: -

• •lysine methyltransferase 5B (KMT5B), lysine demethylase 6B (KDM6B) and KMT2C
• •MeCP2, CHD8, and POGZ are chromatin-remodeling proteins;
• •FMRP and the RBFOX family of RNA-binding/splicing proteins,
• •UBE3A, mind bomb E3 ubiquitin-protein ligase 1 (MIB1), and other post-translational modification proteins;
• •Additional sex combs like 3 (ASXL3) and transcription factors like ADNP (de Rubeis et al., 2014)

MeCP2 and UBE3A are two major susceptibility genes that highlight how a single epigenetic regulator's mutations can affect numerous additional risk genes. MeCP2 is a chromatin modification that has been linked to ASD on numerous occasions. In healthy persons, MeCP2's binding action has been identified to influence several genes involved in synaptic function., including (Kubota and Mochizuki, 2016).

• •brain-derived neurotrophic factor (BDNF),
• •GABRB3
• •cyclin-dependent kinase-like 1 (CDKL1),
• •distal-less homeobox 5 (DLX5),
• •protocadherin 7 (PCDH7),
• •lin-7 homolog A (LIN7A)
• •protocadherin beta 1 (PCDHB1)

During development, MeCP2 is the rate-limiting element in governing glutamatergic synapse formation, it is decreased in the frontal brain of ASD patients due to higher methylation of its promoter, implicating it in yet another crucial characteristic of ASD pathogenesis (Samaco et al., 2005).

A second key Epigenetic regulator implicated in ASD is UBE3A, an E3 ubiquitin-protein ligase (Qoronfleh et al., 2022). UBE3A is located on chromosome 15q11–13, which is frequently duplicated in autism. UBE3A functions as a ubiquitin ligase, which targets proteins for destruction, explaining the mechanism of UBE3A's pathogenic activity. Its role in Wnt signaling could cause considerable developmental disruption (Yi et al., 2017). Examples of how a single changed gene can have wide-ranging effects are MeCP2 and UBE3A. Surprisingly, when a powerful histone deacetylase inhibitor was used to treat a SHANK3 mice model of autism, the behavioral abnormalities were rescued, confirming the importance of epigenetics in ASD (Qin et al., 2018).

Various genome-scale investigations have found multiple changes in DNA methylation in the brains of people with ASD (Ladd-Acosta et al., 2014b). The greatest meta-analysis of over 800 autistic patients' blood samples collected found that 55 of the analyzed CpGsites were associated with ASD (Andrews et al., 2018). Epigenetic pathways can stimulate immunological responses during pregnancy, as well as enhance ASD vulnerability (Atladóttir et al., 2012) Furthermore, changes in maternal immunological responses during pregnancy raise the incidence of ASD in children, according to a mouse model of maternal allergy asthma (Wiśniowiecka-Kowalnik and Nowakowska, 2019).

Differentially methylated regions in fetal microglia were found as a result of MAA, which were enriched for genes involved in signaling pathways and synaptic function (Wiśniowiecka-Kowalnik and Nowakowska, 2019, Vogel Ciernia et al., 2018), these findings imply that maternal immunological responses can result in epigenetic alterations, which can lead to ASD development.

Changes in epigenetic regulation have been discovered in autism, which may contribute to the disorder's symptoms and characteristics hence epigenetic activities and their substrates may be considered therapeutic targets in autism because they regulate gene expression for example, epigenetic activities, such as DNA methylation and histone modifications, can influence the expression of genes involved in brain development and function (Loke et al., 2015), dysregulation of these epigenetic processes have been linked to the symptoms and characteristics of autism, including social and communication deficits, repetitive behaviors, and sensory sensitivities, which can affect brain and behavior development (Hsiao et al., 2012).

As a result, targeting these epigenetic processes and their substrates may offer potential therapeutic strategies for individuals with autism. For example, drugs that modify DNA methylation or histone acetylation have been shown to ameliorate behavioral symptoms in animal models of autism. One example is valproic acid, a medication used to treat seizures and bipolar disorder, which has been shown to increase histone acetylation and improve social behavior in mouse models of autism (Kim et al., 2011).

4. Relationship between the mutant gene and the signalling pathways

4.1. mTOR pathway and ASD relation

The mTOR (mammalian target of Rapamycin) pathway is important for synaptic protein synthesis (Hay and Sonenberg, 2004, Hoeffer and Klann, 2010 Feb), and a primary pathogenic mechanism for ASDs is synaptic dysfunction mediated by abnormal protein production (Kelleher and Bear, 2008). Upstream mTOR signaling has been associated with ASDs in previous research. Tuberous sclerosis complex (TSC1/TSC2), Phosphatase and tensin homolog (PTEN), and neurofibromatosis 1 (NF1) mutations cause Tuberous sclerosis neurofibromatosis or macrocephaly associated with syndromic ASD (Hoeffer and Klann, 2010 Feb, Kelleher and Bear, 2008).

TSC1/TSC2, PTEN, and NF1 are negative regulators of the mTOR complex 1 (mTORC1), which is activated by the PI3K pathway (Kelleher and Bear, 2008, Wang and Doering, 2013). Impaired synaptic plasticity has been linked to a hyperactivated mTORC1–eIF4E pathway in fragile X syndrome, The findings suggest that ASDs may be causally related to an autistic disorder characterized by a fragile X mental retardation protein (FMRP) deficit due to a mutation in the FMR1 gene (Wang and Doering, 2013).

Notably, autism families had an EIF4E promoter mutation, according to research (Neves-Pereira et al., 2009)., suggesting that ASDs may be caused by dysregulation of downstream mTOR signaling (eIF4E), Fig. 3 shows a schematic representation of the mTORC Signaling Pathway.

Fig. 3.

Autism and the mTOR Signaling Pathway: The mTOR pathway combines information from various sources, including NMDAR, mGluR. Increased NLGN translation results in a higher synaptic E/I ratio, which may lead to ASD symptoms. Abbreviations: •mGluR - Metabotropic glutamate receptor •NMDAR – N-Methyl- D-Aspartate receptor •Akt (PKB) - Protein kinase B •ERK- Extracellular signal Regulated Kinase •FMRP - Fragile X mental retardation protein •MEK - Mitogen-activated protein/ERK kinase •mTOR - Mammalian target of rapamycin •NLGN - Neuroligin •PDK - Phosphoinositide Dependent Kinase •PI3K - Phosphoinositide-3 kinase •PTEN - Phosphatase and Tensin Homolog •TSC - Tuberous Sclerosis Complex. • Ras - Reticular activating system.

It is discovered that both strains of transgenic mice have increased translation of neuroligin (NLGN) mRNAs. NLGN protein levels in the hippocampus are increased when 4E-BP2 is removed or eIF4E is overexpressed, but mRNA levels are unaffected, excluding transcriptional effects (Gkogkas et al., 2013).

These findings suggest that relieving translational repression by removing 4E-BP2 or overexpressing eIF4E preferentially increases NLGN synthesis. Various proteins (synaptic or non-synaptic) may be changed, contributing to autistic features in animals, which cannot be ruled out (Wang and Doering, 2013) In mouse models, genetic modification of NLGNs causes ASD-like symptoms with altered E/I balance. At excitatory synapses, NLGN1 is mostly postsynaptic and enhances excitatory synaptic transmission (Chubykin et al., 2007), and NLGN mRNA translation increases in tandem with higher E/I ratios.

NLGN1 increases excitatory synaptic transmission by being primarily postsynaptic at excitatory synapses (Varoqueaux et al., 2006). These findings reveal a relationship between IF4E-dependent NLGN translational control, E/I balance, and the emergence of ASD-like animal behaviors ((Wang and Doering, 2013). Spectrum traits such as ASD with microcephaly are caused by PTEN gene mutations that indirectly suppress the mTOR pathway (Herman et al., 2007).

4.2. Wnt/catenin signaling disturbances in ASD

The Wnt/- catenin signaling pathway is crucial for the growth and control of the central nervous system, and a number of its genes have been genetically linked to ASDs (Caracci et al., 2016). The identification of high-risk genes in Wnt signaling components, as well as their suspected relationship with ASD, has been made possible by recent breakthroughs in sequencing technology (Baranova et al., 2021).

Furthermore, transgenic animal research has shed light on the roles of Wnt in normal brain development as well as the consequences of any potential dysfunction (Hormozdiari et al., 2015), People with ASD frequently have mutations in the CHD8 gene. This gene produces ATP-dependent chromatin-remodeled protein that plays a key role in Wnt signaling. CHD8 operates as a negative regulator of Wnt in neural cells, and increased Wnt-dependent gene expression is associated with loss of function (LOF) mutations (O’Roak et al., 2012a) (Baranova et al., 2021).

Enhanced canonical Wnt signals, which are assumed to be the source of macrocephaly (as observed in the early-developing autistic brain) and ASD-like behavior in mice (Baranova et al., 2021), have been demonstrated to be caused by CHD8 LOF/knockout in vivo investigations (Baranova et al., 2021). For the canonical ligand Wnt2, FZD9 is the preferred receptor. Multiple ASD patients have been found to have mutations in the FZD9 gene. Indeed, LOF and FZD9 duplications have been associated with autism, suggesting that FZD9-mediated signaling must maintain a careful balance during neurodevelopment (Baranova et al., 2021). Wnt2 is also hypothesized as a potential contributor to ASD etiology, but human investigations have yielded mixed results.

WNT2 is found on chromosome 7q31, which is a high-mutational-frequency hotspot. In genetic ASD research, BCL9 was also found to be missing or duplicated causing ASD (Kalkman, 2012). Exome sequencing of ASD patients revealed de novo mutations in the gene that codes for ß-catenin (CTNNB1) (Klei et al., 2012).

5. ASD connection with neurobeachin and CADMI gene

Neurobeachin, a multi-domain scaffolding protein found in the brain, has been identified as a possible autism gene. Autism spectrum disorder has also been linked to mutations in the synaptic adhesion protein cell adhesion molecule 1 (CADM1) (Kitagishi et al., 2015), Protein kinase A (PKA), Protein kinase B (AKT) (Yang et al., 2015), and cAMP-dependent appear to play important roles in autism development.

Autism has also been linked to a single nucleotide polymorphism (SNP) in the Neurobeachin gene (Olszewski et al., 2012). Neurobeachin protein is linked with the synaptic plasma membrane and implicated in endosomal trafficking, which could be a negative regulator of notch function (Kitagishi et al., 2015), this scaffolding protein may play a role in neuronal trans-Golgi membrane trafficking (Volders et al., 2011). Another synaptic cell adhesion molecule is Cell-adhesion molecule 1 (CADM1, TSLC1/SynCAM1) mutations have been linked to autism.

As a result, the CADM1 synaptic receptor complex, which is found on the dendrites of neuron cells (Fujita et al., 2012), may be linked to autism pathogenesis CADM1 mutations linked to autism may cause improper membrane trafficking at the surface of mice neural cells (Kitagishi et al., 2015, Fujita et al., 2010) implying a link between autism's biological etiology and abnormal synaptogenesis.

CADM1 mutations may make it more vulnerable to processing mistakes and the build-up of some CADM1 degradation products in the endoplasmic reticulum (Kitagishi et al., 2015), reducing CADM1 function in cell adhesion and leading to synaptic abnormalities in neurons. The pathophysiology of autism is therefore based on impaired synaptogenesis. The activity-dependent brain networks that control synapse development and plasticity contain several autism-related genes (Castermans, 2003). As a result, disruption of activity-dependent signaling pathways in neurons likely contributes to autism's etiology.

6. Summary and discussion

Autism is a complex neurodevelopmental disorder that is believed to have a genetic component. While there is no single gene responsible for autism, multiple genes have been identified as contributing to the disorder. Studies have shown that autism has a strong heritable component, with estimates suggesting that as much as 90 % of the risk for autism may be attributed to genetics. However, the exact genes involved in the development of autism and the specific mechanisms by which they contribute to the disorder are not yet fully understood.

It's also important to note that autism is a heterogeneous disorder, meaning that there are likely many different genetic and environmental factors that can contribute to its development. As a result, there is no one-size-fits-all answer to the question of what genes are responsible for autism, and the answer is likely to vary from individual to individual.

It is challenging to determine the genetic risk for many ASD-related genetic variations because they are linked to other neurodevelopmental disorders or have inadequate penetrance. More research is required to better understand the causes of ASD and the various phenotypes present in those who are affected.

Although hundreds of risk genes have been identified, there is still much to learn about the different modifiers that could raise or lessen the disease's severity. Some examples of these modifiers are epigenetics, double-hit mutations, sex-linked modifiers, CNVs, and environmental influences. There is a lot of interest in exploiting gene discoveries to learn more about the biology behind autism. Both common and unusual genetic variants contribute to risk. However, autism exhibits significant clinical and genetic variation.

The observation of convergence in the biological processes and pathways impacted in autism suggests that there may be common underlying mechanisms involved in the development of the disorder and provides targets for the development of treatments. This convergence may provide targets for the development of treatments for autism and may help to explain why different genetic and environmental factors can lead to similar symptoms in individuals with autism. Further research is needed to fully understand the biological processes and pathways involved in the development of autism and to determine how these processes can be targeted for treatment.

It's important to note that the relationship between specific genes and behavior is complex and multi-factorial. Many genes, as well as environmental factors, can influence the proper functioning of behavior in humans. Additionally, not all individuals with autism will have variations in the genes mentioned above, and not all individuals with variations in these genes will develop autism.

Epigenetic activities and their substrates may represent interesting therapeutic targets. Epigenetic processes control the expression of many genes by modulating chromatin structure without changing the DNA sequence, targeting epigenetic activities and their substrates hold promise for improving the lives of individuals with autism by modulating gene expression and affecting brain development and function. However, more research is needed to fully understand the mechanisms involved and to develop effective and safe therapeutic approaches.

Through a better understanding of the relationship between mutated genes and signaling pathways leading to the etiology of ASD, and by finding specific genes associated with it in the individual patient, we can provide personalized treatment to the patient according to its need without altering other pathways functioning.

The role of mTOR in human learning and cognition, as well as downstream mTOR signaling in ASDs, has to be better understood. It may be difficult to find therapeutic targets for autism because inhibiting downstream mTOR signaling heals autism. In the future, patients with ASDs may benefit therapeutically from pharmacological modification of mTOR downstream effectors (eIF4E, 4E-BP2, and NLGNs).

Currently, most ASD-related factors involve synaptic plasticity signaling pathways, with Wnt/-catenin signaling being particularly important. According to this study numerous lines of evidence point to the major impact of Wnt signaling on the serine/threonine kinase GSK3 on activity-dependent synaptic plasticity and, in turn, on the control of the E/I balance. Wnt/-catenin signaling is probably involved in ASDs, according to research on Wnt/GSK3 activity and pharmacology in cellular and animal models of the disorder. Activity has several effects both during the early stages of brain structure formation and afterward, once these structures have been established.

Personalized medicine could be a future route to therapy that is as successful as possible due to the individuals' incredibly different genetic profiles. Overall, further basic and clinical research is needed due to the therapeutic potential of GSK3 modulation, which appears to restore synaptic plasticity events that may be altered in ASD brains.

Ethical statement

The manuscript is the authors original review work which has not been previously published elsewhere. Also, the paper is not currently being considered for publication elsewhere. All resources used are properly disclosed (correct citation). Literally copying of text must be indicated as such by using quotation marks and giving proper reference. Both the authors have been personally and actively involved in substantial work leading to the paper, and will take public responsibility for its content.

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

CRediT authorship contribution statement

Aayush Kumar: Data curation, Writing – original draft, Writing – review & editing. Madhavi Apte: Writing – review & editing, Supervision.

Conflicts of interest

The authors affirm that they have no financial or other conflicts of interest.