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.

   Keywords: Autism, Autism spectrum disorder, Genetics, Inflammatory
   bowel disease, Celiac disease

   Subject terms: Genetics, Medical genetics

Introduction

   Autism spectrum disorder (ASD) is a group of neurodevelopmental
   disorders characterized by social communication deficits and repetitive
   behaviors^[36]1. ASD presents a significant burden on individuals,
   families, and society, with a prevalence of 100 per 10,000 persons
   annually^[37]2,[38]3. Medical comorbidities are common in ASD including
   genetic, neurologic, gastrointestinal (GI), metabolic, and allergic
   disorders^[39]4–[40]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 retention^[41]4.

   GI conditions are prevalent in 48.67% of patients with ASD, causing
   pain, discomfort, sleeping difficulty, and behavior
   changes^[42]9,[43]10. Common GI disorders in ASD include chronic
   diarrhea, gastroesophageal reflux, chronic constipation, GI ulcers,
   inflammatory bowel disease (IBD), and celiac disease^[44]10,[45]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 reactions^[46]12. Furthermore, genetic mutations have been
   shown to be important in the co-occurrence of GI disorders and
   ASD^[47]13.

   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^[48]14,[49]15. Incidence of IBD, UC, and CD in
   autistic children are 1.66, 1.91, and 1.37 times higher than the
   general population, respectively^[50]16. Genetic factors and prenatal
   conditions contribute to the co-occurrence of IBD and
   ASD^[51]17,[52]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^[53]19–[54]21. HLA-DRB1 *11-DQB1*07 haplotypes are also
   more prevalent in patients with ASD and these haplotypes are possibly
   associated with pediatric celiac disease^[55]22.

   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^[56]23–[57]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 mechanisms^[58]26. In the same way,
   analyses of GWAS data have revealed that autism is genetically linked
   to allergic conditions^[59]27. On top of that, our own research showed
   that temporal lobe epilepsy shares genetic risk factors with systemic
   autoimmune diseases^[60]25.

   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 DisGeNET^[61]28 (disgenet.com), GWAS Catalog^[62]29
   (ebi.ac.uk/gwas) and Ensembl^[63]30 (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 databases^[64]28. 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
   data^[65]29. 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 regulation^[66]30. 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^[67]31,[68]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. [69]1). A complete
   list of VDAs for each disease and shared VDAs between diseases can be
   found in Additional File 1.

Fig. 1.

   [70]Fig. 1
   [71]Open in a new tab

   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 [72]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
   [73]Open in a new tab

   As shown in Fig. [74]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.

   [75]Fig. 2
   [76]Open in a new tab

   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)^[77]33. The 5-MTHF molecule
   acts as a methyl group donor, crucial for the enzymatic conversion of
   homocysteine (Hcy) back into methionine^[78]33,[79]34. The reduction in
   MTHFR enzyme activity results in decreased plasma folate levels and
   elevated Hcy concentrations among individuals carrying the C677T
   polymorphism^[80]34,[81]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^[82]35–[83]39 and associated
   with overactivity^[84]39. Additionally, a direct correlation between
   urinary Hcy concentration and the severity of communication deficits in
   children with autism was noted in other studies^[85]40,[86]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 variants^[87]42. 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^[88]43–[89]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^[90]46–[91]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 Hcy^[92]49. 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 folate^[93]50. 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 synthesis^[94]33.

   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^[95]51–[96]59. These effects have consistently
   been proposed as integral components of the pathophysiology shared
   between ASD, IBD, and celiac disease^[97]54,[98]60–[99]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. [100]3.

Fig. 3.

   [101]Fig. 3
   [102]Open in a new tab

   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 properties^[103]63.

   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 autism^[104]64. 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 disease^[105]65. 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 revealed^[106]66.
   Research indicates that different MYO9B gene polymorphisms may enhance
   susceptibility to IBD in various populations^[107]67.

   Several proposed mechanisms of action offer insights into how MYO9B
   polymorphisms may influence the development of both ASD and GI diseases
   (Fig. [108]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^[109]68–[110]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 cells^[111]71.

Fig. 4.

   [112]Fig. 4
   [113]Open in a new tab

   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^[114]72–[115]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 encephalomyelitis^[116]75. 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^[117]76,[118]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 symptoms^[119]78. Dysbiosis may also contribute to
   systemic inflammation and alter the permeability of the blood-brain
   barrier, further influencing neurodevelopment in individuals with
   ASD^[120]12,[121]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 proposed^[122]16. 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.
   [123]Supplementary Material 1^ (2.3MB, xlsx)

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.

Footnotes

   Publisher’s note

   Springer Nature remains neutral with regard to jurisdictional claims in
   published maps and institutional affiliations.

References