LEF1 gene mutation impairs the intestinal barrier and causes diarrhea

Researchers used whole-exome sequencing to identify a new spontaneous (de novo) mutation in the LEF1 gene in a young boy who had suffered from severe, treatment-resistant watery diarrhea since 18 months of age, with the illness persisting for four years and stunting his growth. LEF1 is a transcription factor best known for its role in the Wnt signalling pathway, which controls cell fate and tissue development — its involvement in intestinal barrier disease had not previously been established. To confirm that this specific variant (swapping the amino acid proline for serine at position 294) actually causes disease rather than merely correlating with it, the team engineered mice carrying the equivalent mutation and showed they were far more susceptible to chemically induced intestinal injury and exhibited intrinsic structural defects in their gut lining. Both the mice and the patient's own gut tissue showed reduced levels of tight junction proteins (the molecular 'zippers' that seal the gut wall) and aquaporin-4 (a water channel), along with disrupted ion transport and heightened inflammation. Mechanistically, the mutant LEF1 protein amplifies its own production and preferentially moves into cell nuclei, where it drives a process called epithelial-to-mesenchymal transition (EMT) — normally associated with wound healing and cancer — that dismantles the organised barrier architecture of the intestinal lining. This is the first report linking a LEF1 loss-of-function-style variant to chronic paediatric diarrhoeal disease, expanding the catalogue of monogenic causes of intractable diarrhoea in children. The findings suggest LEF1 variant status could serve as both a diagnostic marker for unexplained paediatric diarrhoea and a potential therapeutic target.

• A novel de novo heterozygous LEF1 variant (c.880 C>T; p.Pro294Ser) was identified by whole-exome sequencing in a paediatric patient with intractable chronic diarrhoea lasting 4 years from onset at 18 months; the variant was absent from all public population genomic databases, supporting its rarity and likely pathogenicity.
• Lef1 knock-in mice carrying the murine ortholog (p.Pro292Ser) showed increased susceptibility to DSS-induced colitis/diarrhoea and displayed intrinsic intestinal structural abnormalities and impaired barrier integrity even at baseline, confirming causality beyond case-level association.
• Molecular and proteomic analyses in both mutant mice and patient-derived intestinal tissue demonstrated downregulated tight junction proteins and aquaporin-4, dysregulated ion transport, and aberrant inflammatory pathway activation.
• Mechanistically, the mutant LEF1 protein enhances its own transcription and promotes nuclear accumulation, driving Epithelial-Mesenchymal Transition (EMT), which dismantles the epithelial barrier architecture and underlies the observed permeability defect.
• Gastrointestinal endoscopy in the patient revealed mucosal oedema and mild chronic inflammation, consistent with the barrier dysfunction model, while the clinical course included protein-energy malnutrition and growth failure refractory to standard therapy.

This study combined clinical genomics with functional animal modelling. Whole-exome sequencing was performed on a single paediatric male patient presenting with chronic intractable diarrhoea; identified variants were cross-referenced against public genomic databases to assess novelty. Functional validation used a CRISPR/knock-in mouse model carrying the murine ortholog of the human LEF1 p.Pro294Ser variant, subjected to DSS-induced colitis as well as baseline intestinal phenotyping. Mechanistic analyses included histology, immunofluorescence, quantitative proteomics, molecular pathway assays (Wnt/LEF1 signalling, EMT markers, tight junction proteins, aquaporin-4, ion transport), and comparisons between mutant mouse intestinal tissue and patient-derived intestinal biopsy material.

The clinical evidence rests on a single paediatric case, making it impossible to establish variant penetrance, expressivity range, or population-level frequency; a case series or cohort screen of unexplained paediatric diarrhoea patients would be needed to determine how often LEF1 variants contribute to this phenotype. The DSS model in mice, while useful for revealing susceptibility, reflects chemically induced rather than spontaneous disease, so the degree to which the knock-in mice faithfully recapitulate the patient's chronic, non-inflammatory diarrhoeal course remains uncertain. The study identifies EMT and tight junction downregulation as key intermediaries but does not yet establish the full transcriptional programme through which mutant LEF1 drives these changes; ChIP-seq or CUT&RUN experiments targeting mutant versus wild-type LEF1 chromatin binding would help define direct transcriptional targets. Finally, therapeutic proof-of-concept — for example, whether Wnt/LEF1 pathway inhibitors or tight junction restoration strategies can reverse the barrier defect in the mouse model — has not yet been tested.

This study extends the corpus on genetic and molecular determinants of intestinal barrier dysfunction. It parallels [§155], which examines how Saccharomyces boulardii CNCM I-745 supports intestinal barrier function through protein-level mechanisms, by demonstrating that the same barrier components (tight junction proteins, permeability regulation) are critically governed by LEF1 transcriptional control — together these articles bracket the barrier from genetic cause to probiotic remedy. It also extends [§56], which investigates PI3K/Akt-claudin-2 signalling as a driver of barrier loss and diarrhoea, by identifying a parallel upstream transcription-factor pathway (LEF1/Wnt/EMT axis) converging on tight junction dysregulation, suggesting that multiple distinct molecular routes can produce clinically similar paediatric diarrhoeal phenotypes. The DSS mouse model used here for functional validation is methodologically shared with several corpus articles including [§118], providing a direct experimental parallel for comparing severity and barrier-related outcomes across interventions. Taken together, the LEF1 article fills a notable gap in the corpus: while most peer articles address acquired or microbiota-mediated causes of barrier disruption, this is the only study establishing a monogenic, de novo germline variant as a primary driver, underscoring the diagnostic importance of genomic sequencing in refractory paediatric diarrhoea.

• Saccharomyces Boulardii CNCM I-745 on Intestinal Barrier Function
  Directly complementary: where this study identifies a genetic cause of intestinal barrier collapse via tight junction downregulation, [id=155] examines how a probiotic agent restores the same barrier components — reading both together frames the LEF1 pathway within a broader therapeutic landscape for barrier dysfunction.
• Polysaccharide from Atractylodes macrocephala Koidz. protects against avian pathogenic Escherichia coli-induced intestinal barrier Dysfunction via Suppressing PI3K/Akt-Mediated Claudin-2 upregulation
  Mechanistic parallel: [id=56] investigates PI3K/Akt-claudin-2 signalling as a route to barrier permeability and diarrhoea, while this article identifies LEF1/Wnt/EMT as a separate upstream pathway reaching the same tight junction targets — comparing the two clarifies how molecularly distinct perturbations converge on a shared intestinal barrier phenotype.
• Anti-inflammatory and gut microbiota-modulating effects of a novel mannan from Scilla scilloides on DSS-induced colitis in mice
  Methodological anchor: [id=118] uses the same DSS-induced colitis mouse model as the functional validation platform in this study, making side-by-side comparison of barrier disruption severity, inflammatory profiles, and recovery metrics directly interpretable across the two experiments.
• Mechanism of FODMAP Restriction on FGID Patients
  Clinical phenotype overlap: [id=154] addresses chronic functional diarrhoea and gut permeability through dietary mechanisms (FODMAP restriction), providing a useful contrast to this genetic aetiology — clinicians encountering refractory paediatric diarrhoea benefit from seeing how a monogenic LEF1 cause differs from functionally driven presentations in both workup and management implications.
• Combined heat and exercise stress disrupt gut microbiota and promote microbial translocation
  Opposite causal direction, same physiological outcome: [id=149] shows that environmental stressors (heat plus exercise) disrupt gut barrier integrity and promote microbial translocation, whereas this article demonstrates an intrinsic genetic route to the same outcome — comparing the two highlights how barrier fragility can be constitutive (genetic) versus acquired (environmental).