Exploring the shared genetic basis between autism spectrum disorder and gastrointestinal disorders: a bioinformatic study

Abstract

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with early-appearing social communication deficits and repetitive behaviors. ASD is associated with various comorbidities, including gastrointestinal (GI) conditions. This study aims to identify shared genetic mutations between ASD, inflammatory bowel disease (IBD), and celiac disease through bioinformatics, to uncover mechanisms contributing to GI issues in ASD patients. In this study, databases including DisGeNET, Genome Wide Association Study (GWAS) Catalog, and Ensembl were utilized to identify variation disease associations (VDAs) for ASD, celiac disease and IBD. Shared VDAs were identified using the Molbiotools website and validated by reviewing original articles and resources provided by the databases. In our screening 2367 VDAs found for ASD, 458 for Celiac disease and 1912 for IBD. However, search across these databases revealed only 3 shared VDAs among ASD, celiac disease and IBD. These shared VDAs were found in the Methylenetetrahydrofolate reductase (MTHFR), Myosin IXB (MYO9B), and Transcobalamin 2 (TCN2) genes. However, the association between the TCN2 gene and celiac disease was not confirmed during the validation process. In this study, we investigated the shared genetic basis between ASD and genetically defined GI disorders based on previously published papers. The findings of this study provide valuable insights into the shared genetic basis of these diseases; however, further investigations are needed to understand these genetic implications.

Supplementary Information

The online version contains supplementary material available at 10.1038/s41598-025-15476-w.

Introduction

Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders characterized by social communication deficits and repetitive behaviors¹. ASD presents a significant burden on individuals, families, and society, with a prevalence of 100 per 10,000 persons annually^2,3. Medical comorbidities are common in ASD including genetic, neurologic, gastrointestinal (GI), metabolic, and allergic disorders^4–8. Early identification and treatment of comorbidities in ASD are essential because they significantly influence a child’s behavior and development. Addressing these conditions can enhance the child’s learning abilities and overall quality of life, preventing the worsening of ASD-related behaviors and ensuring effective learning and skill retention⁴.

GI conditions are prevalent in 48.67% of patients with ASD, causing pain, discomfort, sleeping difficulty, and behavior changes^9,10. Common GI disorders in ASD include chronic diarrhea, gastroesophageal reflux, chronic constipation, GI ulcers, inflammatory bowel disease (IBD), and celiac disease^10,11. Common mechanisms that play a role in developing GI disorders in patients with ASD include immune dysfunction, dietary metabolites, microbiota dysregulation, gut inflammation, dysautonomia and medication adverse reactions¹². Furthermore, genetic mutations have been shown to be important in the co-occurrence of GI disorders and ASD¹³.

IBD and celiac are two comorbid GI conditions of ASD that their underlying genetic alterations had been previously studied in various studies. IBD, comprising Crohn’s disease (CD) and Ulcerative colitis (UC), has a higher incidence in autistic children compared to the general population^14,15. Incidence of IBD, UC, and CD in autistic children are 1.66, 1.91, and 1.37 times higher than the general population, respectively¹⁶. Genetic factors and prenatal conditions contribute to the co-occurrence of IBD and ASD^17,18. Also celiac is another GI disease that is prevalent among ASD patients but its prevalence is less than in IBD. Children with ASD have significantly higher levels of IgG antibodies to gliadin compared to children without ASD, suggesting increased intestinal permeability^19–21. HLA-DRB1 *11-DQB1*07 haplotypes are also more prevalent in patients with ASD and these haplotypes are possibly associated with pediatric celiac disease²².

Bioinformatic methods are essential for understanding disease mechanisms and predicting gene-disease associations. These tools leverage diverse biomedical data, from phenotype to genotype, to evaluate disease relationships at different levels. Bioinformatic approaches can enhance our knowledge of disease associations, leading to improved diagnosis, prognosis, and treatment strategies^23–25. Several bioinformatics approaches can be used to identify biological associations between different diseases, including the analysis of shared differentially expressed genes, pathway enrichment analysis, genome-wide association study (GWAS)-based genetic correlations, and identification of overlapping genetic variants. For example, by analyzing transcriptomic data in a study, it was found that autism and epilepsy share similar biological pathways, pointing to common underlying mechanisms²⁶. In the same way, analyses of GWAS data have revealed that autism is genetically linked to allergic conditions²⁷. On top of that, our own research showed that temporal lobe epilepsy shares genetic risk factors with systemic autoimmune diseases²⁵.

This study aims to utilize bioinformatics to detect shared genetic mutations between ASD, IBD, and celiac disease, potentially uncovering underlying mechanisms that contribute to GI issues in ASD patients. By identifying these common genetic links, we hope to provide insights that could lead to better diagnosis, prognosis, and treatment strategies for individuals affected by these conditions.

Method

Databases including DisGeNET²⁸ (disgenet.com), GWAS Catalog²⁹ (ebi.ac.uk/gwas) and Ensembl³⁰ (ensembl.org) were used to find variation disease associations (VDAs). VDAs are genetic mutations associated with certain diseases. DisGeNET is a publicly accessible collection of information on genes and variants linked to human diseases. DisGeNET includes data from expertly curated sources, catalogs of genome-wide association studies, animal models, scientific literature and various public databases²⁸. The GWAS Catalog is an online resource that collects and organizes data from genome-wide association studies. It transforms unstructured information from various literature sources into accessible, high-quality, and curated data²⁹. The Ensembl database, a project of the European Bioinformatics Institute, is a central resource for researchers examining genomes through comparative genomics, evolution, sequence variation, and transcriptional regulation³⁰. VDAs for ASD, Celiac and IBD, were obtained from each database. We included different VDAs from multiple databases for a comprehensive approach, incorporating a broad range of candidate genes to enhance candidate identification. These candidates were then validated by reviewing the original source articles. In this study, ASD was considered broadly, encompassing both genetic susceptibility and clinically defined subtypes, including early-onset and later-diagnosed cases. Since IBD encompasses two major subtypes, CD and ulcerative colitis UC, we retrieved VDAs for CD and UC to ensure comprehensive coverage of IBD. We collected data from GWASes with a p-value threshold of less than 10⁻⁶ to identify statistically significant and potentially relevant SNPs associated with diseases. VDAs were collected from multiple studies across diverse ethnic groups. Shared VDAs were identified using the multiple lists comparator tool on the Molbiotools website (molbiotools.com). To validate the shared VDAs and alleles, the original articles and resources provided by the databases were reviewed by two medical doctors, MM and FG, who are familiar with genetic studies and have previously published works on similar studies. The presence of the reported VDAs in the original study, the statistical significance of the association reported, and the consistency of the findings across different sources and studies were evaluated. During the review process, each shared VDA was independently reviewed by the two authors (MM and FG) to confirm its presence and relevance, with discrepancies in the initial reviews discussed in regular meetings where the evidence from the original sources was re-evaluated. If consensus could not be reached, a third independent reviewer (MP) was consulted to resolve the disagreements and discrepancies between databases. Since, to the best of our knowledge, no studies have directly investigated the genetic associations between ASD, IBD, and celiac disease, we reported all candidate genes.

In the next step, the Human Protein Atlas database (proteinatlas.org) searched to assess mRNA and protein expression of the VDAs-associated genes in the central nervous system (CNS) and GI tract^31,32. This analysis helped evaluate their potential functional relevance in the CNS and GI regions.

Results

In a search across three databases, 2367 unique VDAs were identified for Autism, 458 for Celiac disease, 1912 for IBD compromising 1297 for CD, and 925 for UC. However, only 3 VDAs were found to be shared among Autism, Celiac and IBD (or its subtypes) in different ethnic groups. These shared VDAs were rs1217691063 of the Methylenetetrahydrofolate reductase (MTHFR) gene, rs1545620 of the Myosin IXB (MYO9B) gene, and rs1801198 of the Transcobalamin 2 (TCN2) gene (Fig. 1). A complete list of VDAs for each disease and shared VDAs between diseases can be found in Additional File 1.

Fig. 1.

Venn diagram (A) and intersection table (B) of variation disease associations (VDAs) showing shared number of VDAs between different diseases.

During the article review, the association between rs1801198 and celiac disease was found to lack statistically significant correlations. Although it was hypothesized that TCN2 mutations might contribute to celiac disease, the minor allele frequency was low among celiac disease patients. However, T allele of rs181133 (C677T) of the MTHFR gene as well as the C and G alleles of rs1545620 of the MYO9B gene were shared genetic factors between these diseases (Table 1).

Table 1.

Table of share genetic mutations between autism, Celiac disease and IBD from literature review. Abbreviations: single nucleotide polymorphism (SNP), pubmed identifier (PMID), methylenetetrahydrofolate reductase (MTHFR), ulcerative colitis (UC), crohn’s disease (CD), myosin IXB (MYO9B), transcobalamin 2 (TCN2), inflammatory bowel disease (IBD).

Gene	SNP	Disease	Allele	PMID	Ethnicity	P-value
MTHFR	rs1801133	Autism	T	31,033,224	Egyptian (Arab descent)	< 0.001
				27,755,291	South Asian (Indian descent)	< 0.0001
				23,653,228	Caucasian	< 0.01
					South Asian (Indian descent)
					East Asian (Chinese descent)
					European descent
					Caucasian descent
					Mixed
				22,648,721	Hispanic	< 0.01
					Asian
					Non-Hispanic black
					Non-Hispanic white
					Mixed
					Other
		Celiac	T	11,244,621	European (French descent)	NR
		UC	TT	10,446,107	European (Irish descent)	0.01
		CD	T	28,002,332	Ashkenazi Jewish	0.0027
					non-Ashkenazi Jewish
			TT	10,446,107	European (Irish descent)	0.02
		IBD	TT	21,967,576	Caucasian (Iranian descent)	0.09
			TT	10,446,107	European (Irish descent)	0.02
			T	14,560,147	European (Portuguese descent)	< 0.001
MYO9B	rs1545620	Autism	T	35,215,271	Arab descent	8.44*10−6
			T/G	32,996,047	Arab descent	< 1.24*10−5
		Celiac	A/C/G	26,628,973	European	0.001
				17,967,566	European (Dutch descent)	0.04
		UC	A/C/G	27,435,931	Caucasian	0.001
				17,087,940	European (Dutch descent)	0.028
					European (British descent)	0.0035
					Italian and European Canadian descent	0.015
			T	21,648,020	East Asian (Chinese descent)	0.017
			G	17,944,996	European (Italian descent)	0.005
		CD	A/C/G	27,435,931	Caucasian	0.001
				17,087,940	European (Dutch descent)	0.019
					European (British descent)	0.038
			C	24,966,617	East Asian (Chinese descent)	0.42
			G	17,944,996	European (Italian descent)	0.01
		IBD	C	27,556,856	East Asian (Chinese descent)	0.793
					Caucasian	0.301
			CC	27,556,856	East Asian (Chinese descent)	0.212
					Caucasian	< 0.001
			A/C/G	17,087,940	European (Dutch descent)	1.9*10−6
					European (British descent)
					Canadian/Italian
			G	17,944,996	European (Italian descent)	0.001
TCN2	rs1801198	Autism	C	30,676,283	South Asian (Indian descent)	0.009
			CG	30,676,283	South Asian (Indian descent)	0.005
		Celiac	-	-	-	-
		UC	G	28,526,947	East Asian (Chinese descent)	< 0.001
			CG + GG	28,526,947	East Asian (Chinese descent)	< 0.001
		CD	G	28,472,811	East Asian (Chinese descent)	< 0.05
			CG + GG	28,472,811	East Asian (Chinese descent)	< 0.05

As shown in Fig. 2, both mRNA and protein expression of MTHFR and MYO9B were detected in the GI tract and CNS Their widespread distribution in these organs highlights their potential functional importance in both neurological and gastrointestinal processes.

Fig. 2.

The gene and protein expression of MTHFR and MYO9B in central nervous system and gastrointestinal tract.

Discussion

In this study, we identified shared genetic mutations between ASD, IBD, and celiac disease to gain insights into the underlying mechanisms contributing to GI issues in ASD patients. Our findings reveal the rs1217691063 polymorphism of the MTHFR gene as a noteworthy genetic variant, demonstrating an association with an increased risk rate of these conditions. Additionally, our investigation highlights the MYO9B rs1545620 polymorphism as another potential genetic link that appears to play a role in susceptibility to ASD, IBD, and celiac disease.

In the present study, we found that the rs1217691063 (C677T) polymorphism of the MTHFR gene is frequently found in ASD, IBD, and celiac disease. MTHFR is a pivotal enzyme involved in the folate cycle, responsible for converting 5, 10-methylene-tetrahydrofolate (5,10-MTHF) to 5-methylene-tetrahydrofolate (5-MTHF)³³. The 5-MTHF molecule acts as a methyl group donor, crucial for the enzymatic conversion of homocysteine (Hcy) back into methionine^33,34. The reduction in MTHFR enzyme activity results in decreased plasma folate levels and elevated Hcy concentrations among individuals carrying the C677T polymorphism^34,35.

Within the field of autism research, numerous studies have suggested that hyperhomocysteinemia caused by the MTHFR C677T polymorphism may serve as potential risk factors for ASD^35–39 and associated with overactivity³⁹. Additionally, a direct correlation between urinary Hcy concentration and the severity of communication deficits in children with autism was noted in other studies^40,41. The connection between MTHFR C677T polymorphism and celiac disease is uncertain. A review by Wilcox et al. reported a possible link between resistant celiac disease and elevated Hcy, which may be due to the effects of the MTHFR gene variants⁴². In contrast to these findings, larger-scale studies did not identify significant differences in the frequency of the MTHFR C677T polymorphism between individuals with celiac disease and healthy controls^43–45. These discrepancies could stem from differences in population genetics, sample sizes, dietary folate intake, and diagnostic criteria across studies. There is evidence indicating a potential association between hyperhomocysteinemia, the MTHFR C677T polymorphism, and IBD^46–48.

We hypothesize, based on the current evidence, that the reduced activity of MTHFR could exert its effect on the development of these diseases by both reduced metabolism of folate and increased buildup of circulating Hcy⁴⁹. Animal studies have shown unmetabolized folate might be linked to synaptic defects, dysregulation of gene expression, and effects on brain DNA methylation when mothers are supplemented with large doses of folate⁵⁰. The reduction in levels of 5-MTHF is also significant since 5-MTHF is the sole form of folate in the CNS. This folate deficiency has been shown to be associated with mitochondrial DNA deletions resulting in reduced mitochondrial function, disruption of neurotransmitter synthesis caused by reduced methyl groups, and decreased proliferative function of regenerative cells in the brain due to impaired nucleotide synthesis³³.

Hcy has been linked with oxidative stress, reduction in antioxidant capacity, endothelial damage. This subsequently can lead to inflammation and apoptosis through an increase in the production of cytokines and chemokines that results in blood-brain barrier and GI endothelial disruption^51–59. These effects have consistently been proposed as integral components of the pathophysiology shared between ASD, IBD, and celiac disease^54,60–62. ASD seems to be linked with these GI diseases by elevated Hcy levels; however, the relationship between the specific molecular underpinning associated with MTHFR polymorphisms and elevated Hcy in the context of these diseases remains unclear, warranting further laboratory investigations. The role of Hcy in the molecular pathogenesis of ASD, celiac disease, and IBD is summarized in Fig. 3.

Fig. 3.

The effect of methylenetetrahydrofolate reductase (MTHFR) mutation in autism spectrum disorder, celiac, and inflammatory bowel disease.

Another finding of our study was the shared genetic mutation of rs1545620 polymorphism of the MYO9B gene. The MYO9B gene encodes Myo9b, which belongs to class IX of myosin. This class of myosin exhibits both motor and signaling properties⁶³.

The role of MYO9B mutations in the development of ASD is not fully understood. Several reports have indicated a higher prevalence of the rs1545620 SNP in children with autism⁶⁴. In a susceptibility study of Saudi males with autism, the T allele of the rs1545620 SNP significantly correlated with ASD. Furthermore, this study also highlighted a link between the MYO9B gene, dermatitis herpetiformis, and enteropathy-associated T-cell lymphoma, conditions typically associated with celiac disease⁶⁵. Substantial evidence supports the association of MYO9B with IBD and celiac disease, though the findings can be contradictory. A meta-analytic systematic review focused an association between rs1545620 and an increased risk of celiac disease in European populations had been revealed⁶⁶. Research indicates that different MYO9B gene polymorphisms may enhance susceptibility to IBD in various populations⁶⁷.

Several proposed mechanisms of action offer insights into how MYO9B polymorphisms may influence the development of both ASD and GI diseases (Fig. 4). Firstly, the rs1545620 SNP has been associated with reduced activity of the Myo9b protein in intestinal enterocytes, potentially resulting in an intestinal mucosal damage, causing the discontinuity of the epithelial lining and impaired mucosal barrier function that could contribute to the pathogenesis of celiac disease and IBD^68–70. Diminished function of the Myo9b has also been shown to result in impaired localization of tight junction proteins as well as disruption of wound closure and actin cytoskeletal organization in intestinal epithelial cells⁷¹.

Fig. 4.

The effect of Myosin IXB (MYO9B) mutation in autism spectrum disorder, celiac, and inflammatory bowel diseases occurrence.

There is also evidence that Myo9b plays a role in phagocytosis by murine macrophages as well as dendritic morphogenesis, leading to altered synaptic pruning of neural cells^72–74. The absence of leukocyte Myo9b in mice has been linked with reduced leukocyte infiltration into the CNS, slower onset, and lack of recovery from experimental autoimmune encephalomyelitis⁷⁵. Furthermore, altered phagocytic function in microglia and the subsequent dysfunctional synaptic pruning have been linked to disruptions in social behavior and functional connectivity, both of which are manifestations of ASD^76,77. Therefore, the MYO9B rs1545620 polymorphism may contribute to ASD by impairing intestinal mucosal barrier function, disrupting immune responses, and altering synaptic pruning and dysregulating neural connectivity. Based on MYO9B rs1545620 polymorphism effects it may play a significant role in the pathophysiology of ASD and GI diseases.

These findings are significant in light of the emerging evidence that suggests gut dysbiosis in ASD may have a profound effect on neurological development through the gut-brain axis. Disruptions in the microbiome can lead to the production of microbial metabolites, such as short-chain fatty acids, which are known to modulate brain function and behavior. Butyrate and propionate, for example, are implicated in altering synaptic plasticity and immune responses, potentially exacerbating ASD symptoms⁷⁸. Dysbiosis may also contribute to systemic inflammation and alter the permeability of the blood-brain barrier, further influencing neurodevelopment in individuals with ASD^12,78.

Beyond mechanistic insights, the discovery of these variants could eventually enhance clinical approaches. For instance, recognition of these mutations might inform earlier diagnosis, targeted therapies, or preventive strategies for ASD individuals with GI symptoms. In particular, screening for MTHFR polymorphisms could help identify patients who may benefit from methylated folate supplementation, while MYO9B-related pathways may present therapeutic targets for modulating gut and immune function.

In light of the observed increased risk of IBD among ASD patients, screening of IBD in ASD patients has been proposed¹⁶. Our results offer explanation for these observations and may provide further justification for screening. However, the development of effective screening protocols requires robust, evidence-based frameworks and careful consideration of population-specific factors. Therefore, any implementation should proceed cautiously and be guided by further research.

Limitations

Our study aimed to identify shared genetic mutations among IBD, celiac disease, and ASD, despite these conditions rarely co-occurring, to uncover the genetic basis for GI issues in ASD patients. We focused on IBD and celiac due to their well-established genetic research, which helped us find common mutations linked to GI problems. However, our reliance on existing databases and bioinformatics tools, along with the need for further experimental validation, highlight our findings’ limitations. Additionally, other methods, including in-depth studies and analysis of various mutation types like tag SNPs, could reveal more comprehensive results. While we identified potential genetic links, understanding the multifaceted nature of ASD comorbidities requires more comprehensive research and validations.

Conclusion

In conclusion, in this article various data sources screened for finding the underlying genetic association between ASD, IBD and celiac disease, to identify possible mechanisms contributing to GI problems in ASD patients. Despite the large number of VDAs identified, only two VDAs were confirmed to be shared among these three conditions. While these VDAs hold promise for understanding disease mechanisms, their clinical significance and effect sizes remain to be fully established. Screening for MTHFR polymorphisms could help pinpoint patients who may benefit from methylated folate supplements, while MYO9B-related pathways might serve as potential targets for therapies aimed at regulating gut and immune function. Our findings also underscore the importance of the gut-brain axis in linking genetic, gastrointestinal, and neurological elements. Further studies should focus on validating these findings through knockout animal models, experimental approaches, longitudinal studies and large-scale genetic association studies. Comprehensive prevalence data collection is needed to assess the true impact of these genetic overlaps.

Supplementary Information

Below is the link to the electronic supplementary material.

Author contributions

MM contributed to data gathering, analyzing, writing, and reviewing. MP and FG contributed to data gathering, writing and reviewing. RT and MA contributed to writing and reviewing. SS and EC contributed to the study conceptualization and reviewing.

Data availability

All data generated in this study are available in the article and its additional files.

Declarations

Competing interests

The authors declare no competing interests.