Autism genetic variants cause gut neuron migration defects and gut motility issues

Autism gene variants disrupt enteric neuron migration and cause gastrointestinal dysmotility

Kate E. McCluskey, Katherine M. Stovell, Karen Law, Elina Kostyanovskaya, James D. Schmidt, Cameron R. T. Exner, Jeanselle Dea, Elise Brimble, Matthew W. State, A. Jeremy Willsey & Helen Rankin Willsey 

Nature Communications volume 16, Article number: 2238 (2025)

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Summary

Autism and severe gastrointestinal distress often co-occur, but the underlying molecular mechanisms are unknown. The discovery of autism genes affords the opportunity to study these genes in the context of the developing gut to unravel these mechanisms. Here we show that patients with genetic variants in autism genes do indeed have gastrointestinal issues, primarily severe constipation. We describe how the expression of autism genes is enriched in embryonic gut neurons and their migratory progenitors and use Xenopus tropicalis to discover that mutations in any 5 of these autism genes cause gut neuron migration defects. Via in vivo drug screening, we identify two serotonin pathway activators that can rescue gut motility issues in a model of DYRK1A syndrome. Together, these findings indicate that autism genes are important for embryonic gut neuron development and that therapeutic efforts around the serotonin pathway may be productive.

Abstract

The co-occurrence of autism and gastrointestinal distress is well-established, yet the molecular underpinnings remain unknown. The identification of high-confidence, large-effect autism genes offers the opportunity to identify convergent, underlying biology by studying these genes in the context of the gastrointestinal system. Here we show that the expression of these genes is enriched in human prenatal gut neurons and their migratory progenitors, suggesting that the development and/or function of these neurons may be disrupted by autism-associated genetic variants, leading to gastrointestinal dysfunction. Here we document the prevalence of gastrointestinal issues in patients with large-effect variants in sixteen autism genes, highlighting dysmotility, consistent with potential enteric neuron dysfunction. Using Xenopus tropicalis, we individually target five of these genes (SYNGAP1, CHD8, SCN2A, CHD2, and DYRK1A) and observe disrupted enteric neuronal progenitor migration for each. Further analysis of DYRK1A reveals that perturbation causes gut dysmotility in vivo, which can be ameliorated by treatment with either of two serotonin signaling modulators, identified by in vivo drug screening. This work suggests that atypical development of enteric neurons contributes to the gastrointestinal distress commonly seen in individuals with autism and that serotonin signaling may be a productive therapeutic pathway.

Figure 1.
hcASD gene expression is enriched in ENS cells and individuals with pathogenic variants in these genes experience GI issues.

a Enrichment of 252 hcASD genes is higher in Enteric Neuron Progenitors (ENCCs) and Enteric Neurons compared to all other cell types in single-cell RNA-sequencing data from the human prenatal gut26. b 252 hcASD genes are enriched in ENCCs and Enteric Neurons compared to all other Non-ENS cells in the human prenatal gut. A one-way Kruskal-Wallis test was performed, followed by Wilcoxon rank-sum tests and Bonferroni adjustment for multiple comparisons. Non-ENS vs ENCCs padj = 5.20e91, Non-ENS vs Enteric neurons padj = 0, ENCCs vs Enteric Neurons padj = 5.90e81. ce The number of individuals affected and the total number of people surveyed is tallied at the end of each bar. c Simons Searchlight data documenting the percentage of affected individuals (teal bars) and their unaffected family members (gray bars) who reported GI issues in caregiver surveys. d Citizen Health medical record data showing the percentage of individuals with a SYNGAP1, SCN2A, CHD2, STXBP1 or SLC6A1 genetic variant with medical record diagnoses related to GI dysmotility. e Citizen Health medical record data by variant for dysmotility phenotypes including constipation, abdominal pain, and diarrhea.

Figure. 2. 
hcASD gene depletion in vivo causes ENCC migration defects.
a Schematic of phox2b staining in NF stage 40 animals to mark enteric neural crest-derived cells (ENCCs, enteric neuron progenitors) in the gut, circled by a blue dashed line. phox2b also labels the hindbrain region and other migrating vagal neural crest cells. b Unilateral mutants were made by injecting the Cas9 protein and an sgRNA targeting an hcASD gene into one cell at the two-cell embryonic stage. Three days later, injected embryos were stained and ENCC area and gut area was measured on each side of the animal and compared to quantify relative gut area (CRISPR side / Control side) of migration. c Individual CRISPR mutagenesis of hcASD genes syngap1, chd8, scn2a, chd2, or dyrk1a reduce the area of ENCC migration in the gut compared to control mutagenesis of pigmentation gene slc45a2. d Area of gut migration quantification by target gene. Control in gray, hcASD genes in blue. A two-way Kruskal-Wallis test was performed followed by Wilcoxon matched-pairs signed rank test to compare the CRISPR side to the control side within each animal and a Holm-dk test to adjust for multiple comparisons. Control (N=24, padj = 0.9248), syngap1 (N=38, padj = 0.0046), chd8 (N=25, padj = 0.001), scn2a (N=33, padj = 0.001), chd2 (N=31, padj = 0.0011), dyrk1a (N=38, padj = 0.0011). All samples are independent biological replicates from the same mating pair. In the box plot, whiskers show minimum and maximum values, box represents the 25th and 75th quartiles, and the center line describes the median. Source data are provided as a Source Data file.

Figure. 4. 
Dyrk1a-associated gut dysmotility is ameliorated by acute exposure to an SSRI or 5-HTR6 agonist.
a Schematic of a serotonergic synapse labeling the presumed location of action for the drugs tested. b Acute exposure of wildtype tadpoles to escitalopram oxalate (selective serotonin reuptake inhibitor, SSRI) alone increases the average number of fluorescent beads excreted by more than one standard deviation compared to the average DMSO treatment, blue. c Acute treatment of an SSRI (10M escitalopram oxalate) rescued, while a 5HTR6 agonist (10M WAY-181187) partially rescued the decreased fluorescent bead excretion from developmentally inhibited Dyrk1a (5M TG003 starting at stage NF 20) animals. d Fluorescent beads per well quantified for each treatment condition. A one-way ANOVA was performed followed by unpaired one-tailed t tests with welchs correction. Compared to TG003 treatment (N=6 wells, 20 tadpoles each), DMSO (N=6 wells, 20 tadpoles each p=0.002), TG003+SSRI (N=3 wells, 20 tadpoles each p=0.0423), TG003+WAY-181187 (N=3 wells, 20 tadpoles each p=0.0033). Compared to DMSO, TG003+SSRI p=0.4264 and TG003+WAY-181187 p=0.0462. All samples are independent biological replicates from the same mating pair. Data are presented as mean values +/ SEM. Source data are provided as a Source Data file. e Model of how hcASD gene large-effect variants could contribute to GI dysmotility. An hcASD genetic variant leads to perturbed ENCC migration and ultimately GI dysmotility. Created in BioRender. McCluskey, K. (2025) https://BioRender.com/n91b055.

Adapted with permission from AAAS on behalf of Springer Nature: McCluskey et al. (2025). Autism gene variants disrupt enteric neuron migration and cause gastrointestinal dysmotility. Nature Communications volume 16, Article number: 2238 (2025).

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