Before the first bite: A missing gut protein may set the stage for peanut allergy

by Thomas Hughes, University of North Carolina at Chapel Hill School of Medicine

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For most people, a peanut butter sandwich poses no threat. But for the roughly 1.6 million children in the United States with peanut allergy, exposure can trigger a life-threatening reaction. Why some individuals are susceptible while others are not has remained one of the most pressing unsolved questions in allergy research. A new study from the UNC School of Medicine points to an unexpected answer: The gut lining itself may be primed for allergy before a child ever encounters a peanut.

Published Sept. 30 in Cellular and Molecular Gastroenterology and Hepatology, the study was led by graduate student Katelyn (Katie) Clough in a collaboration between the labs of Shehzad Z. Sheikh, M.D., Ph.D., and Erin C. Steinbach, M.D., Ph.D., in the Center for Gastrointestinal Biology and Disease (CGIBD) and Division of Rheumatology, Allergy & Immunology at UNC, respectively.

Using single-cell RNA sequencing, the team constructed a high-resolution map of every cell type in the small intestinal lining of a peanut allergy–susceptible mouse model and found a striking defect in a specialized cell population called Paneth cells. The finding was then confirmed in pediatric patients with peanut allergy.

A missing protein at the front line of gut defense

Paneth cells are the gut's antimicrobial sentinels, residing deep in the intestinal crypts and secreting protective proteins that regulate the local microbiome and help maintain the integrity of the gut barrier. The study found that in allergy-susceptible mice, Paneth cells completely lack expression of lysozyme 1 (Lyz1), a key antimicrobial enzyme. The reason is genetic: The allergy-susceptible CC027 mouse strain inherits its chromosome 10 from a wild-derived mouse strain, CAST/EiJ, which simply does not carry the Lyz1 gene.

This is not merely a mouse curiosity. When the team examined small intestinal biopsies from pediatric patients with peanut allergy, they observed a significant decrease in LYZ-positive crypts compared with patients without peanut allergy, suggesting that Paneth cell lysozyme deficiency is a biologically relevant feature of human peanut allergy susceptibility.

"What struck me most was that these Paneth cell changes were present in allergen-naive mice—the animals had never been exposed to peanut," said Clough. "This tells us the gut is already in an altered state before any allergic challenge. The barrier defect may come first, and allergy follows."

Charting the gut epithelium, cell by cell

To build the cell atlas, the team isolated and sequenced the RNA of thousands of individual intestinal epithelial cells from allergy-susceptible CC027 mice and allergy-resistant C3H/HeJ mice, identifying 13 distinct cell populations, including absorptive enterocytes, stem cells, goblet cells, enteroendocrine cells, tuft cells and Paneth cells. Beyond the lysozyme finding, the atlas revealed a coordinated pattern of epithelial remodeling in allergy-susceptible animals that was present before any allergen exposure:

A novel population of interferon-responsive absorptive enterocytes (AE-IFN) was significantly depleted in allergy-susceptible mice, suggesting impaired epithelial antiviral and immune surveillance programs.

Goblet cells, which form a protective mucus barrier, were expanded, while enteroendocrine cells, which regulate gut permeability signaling, were reduced.

Tuft cells, key initiators of type 2 allergic immune responses, were increased and showed elevated expression of allergic immune receptors, including IL-4Rα.

Paneth cells exhibited signs of cellular stress under electron microscopy, including dilated endoplasmic reticulum and dysmorphic secretory granules, consistent with secretory dysfunction, in addition to decreased production of the antimicrobial protein lysozyme-1.

From a missing gene to a skewed microbiome

The consequences of lysozyme deficiency extend beyond the Paneth cell. Lysozyme is a critical regulator of the gut microbiome, selectively eliminating bacteria that can promote allergic immune responses. Comparing the microbial profiles of Lyz1-deficient mice with allergy-susceptible CC027 mice, the team found that both share enrichment of the same bacterial genera, including Ruminococcus and Akkermansia, suggesting that the loss of lysozyme drives a microbiome composition that promotes type 2 (allergic) immune skewing, goblet and tuft cell expansion, and ultimately increased intestinal permeability.

"This study repositions the intestinal epithelium as a possible primary driver of allergic susceptibility, not a passive bystander," said Steinbach, an assistant professor in the Division of Rheumatology, Allergy & Immunology. "A genetic loss of a single antimicrobial protein in Paneth cells cascades into microbiome changes, immune skewing, and a gut barrier primed for allergy. That is a mechanistic chain in which we can potentially intervene."

Why it matters for patients and families

Peanut allergy affects approximately 2% of children in the United States and is responsible for the majority of fatal food-induced anaphylaxis cases. Current management relies on strict avoidance and emergency epinephrine use. Oral immunotherapy offers desensitization for some patients, but achieving sustained tolerance remains elusive. Understanding the epithelial and microbial underpinnings of susceptibility opens new avenues for prevention: Identifying high-risk individuals early or correcting the gut barrier before allergen exposure could prevent allergy from developing in the first place.

"My son has a life-threatening peanut allergy, and for our family, like most other families living with peanut allergy, every meal is a calculation," said Sheikh, professor of medicine and genetics. "This research gives us a new framework for asking why the gut becomes susceptible in the first place and ultimately for designing interventions that could protect children before their first allergic reaction."

The team plans to expand these findings in a larger pediatric patient cohort and to use human intestinal organoid models to explore whether correcting lysozyme deficiency or microbiome composition can restore barrier function in peanut allergy–susceptible backgrounds.

More information

Katelyn M. Clough et al, Single-Cell Mapping of the Gut Epithelium Reveals Paneth Cell Dysfunction and Lysozyme Deficiency in Peanut Allergy, Cellular and Molecular Gastroenterology and Hepatology (2026). DOI: 10.1016/j.jcmgh.2026.101914

Key medical concepts

Peanut HypersensitivityPaneth CellsEpithelium, IntestinalFlora, Intestinal

Clinical categories

Allergy and immunologyGastroenterologyCommon illnesses & PreventionChildren's health Provided by University of North Carolina at Chapel Hill School of Medicine Who's behind this story?

Gaby Clark

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