Genetic Variants Synthesize to Produce Paneth Cell Phenotypes That Define Subtypes of Crohn's Disease

Abstract

Background & Aims Genetic susceptibility loci for Crohn’s disease (CD) are numerous, complex, and likely interact with undefined components of the environment. It has been a challenge to link the effects of particular loci to phenotypes of cells associated with pathogenesis of CD, such as Paneth cells. We investigated whether specific phenotypes of Paneth cells associated with particular genetic susceptibility loci can be used to define specific subtypes of CD. Methods We performed a retrospective analysis of 119 resection specimens collected from patients with CD at 2 separate medical centers. Paneth cell phenotypes were classified as normal or abnormal (with disordered, diminished, diffuse, or excluded granule phenotypes) based on lysozyme-positive secretory granule morphology. To uncover the molecular basis of the Paneth cell phenotypes, we developed methods to determine transcriptional profiles from whole-thickness and laser-capture microdissected, formalin-fixed, paraffin-embedded tissue sections. Results The proportion of abnormal Paneth cells was associated with the number of CD-associated NOD2 risk alleles. The cumulative number of NOD2 and ATG16L1 risk alleles had an additive effect on the proportion of abnormal Paneth cells. Unsupervised clustering analysis of demographic and Paneth cell data divided patients into 2 principal subgroups, defined by high and low proportions of abnormal Paneth cells. The disordered and diffuse abnormal Paneth cell phenotypes were associated with an altered transcriptional signature of immune system activation. We observed an inverse correlation between abnormal Paneth cells and the presence of granuloma. Moreover, high proportions of abnormal Paneth cells were associated with shorter time to disease recurrence after surgery. Conclusions Histologic analysis of Paneth cell phenotypes can be used to divide patients with CD into subgroups with distinct pathognomonic and clinical features.

Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense

“…1 C and D and Fig. S1C), similar to findings from patients with CD with T300A mutations (7,17). Furthermore, analysis of Periodic acid-Schiff (PAS)-stained sections of murine colons revealed goblet cell abnormalities without alterations in goblet cell differentiation, similar to what was observed in mice with complete absence of autophagy proteins in the epithelium (Fig.…”

ATG16L1: A multifunctional susceptibility factor in Crohn disease

“…77 Similar observations in both Paneth cells and myeloid cells have been noted in humans 76,79 where disease-linked NOD2 and ATG16L1 gene variants have been shown to affect Paneth cell morphology and transcriptome, and to correlate with a more fulminant clinical course of Crohn disease. 76,80,81 The elevated production of IL1B in autophagy-deficient mice is associated with an increased inflammasome-mediated processing of pro-IL1B, whereas inflammasome-independent mechanisms, such as IL1B gene transcription, have been described in human cells. 77,82,83 Moreover, Lee et al 84 found that in loss-offunctionality of ATG16L1, elevated receptor protein SQSTM1/ p62 levels cause increased activation of IL1B.…”

Using Markers in IBD to Predict Disease and Treatment Outcomes: Rationale and a Review of Current Status

“…In time, the development of inception cohorts may help properly determine the usefulness of these markers. In one such study looking at genetic variation associated with postoperative recurrence in CD, neither NOD2 nor ATG16L1 was associated with disease recurrence ( 25 ). Nevertheless, genetic variants from both genes were associated with Paneth cell morphological changes that were associated with more severe disease, suggesting that these genes likely highlight pathways or processes involved in disease severity ( 25 ).…”

“…In one such study looking at genetic variation associated with postoperative recurrence in CD, neither NOD2 nor ATG16L1 was associated with disease recurrence ( 25 ). Nevertheless, genetic variants from both genes were associated with Paneth cell morphological changes that were associated with more severe disease, suggesting that these genes likely highlight pathways or processes involved in disease severity ( 25 ). Th e fact that IBD-associated genetic variants may not be the only variants associated with disease behavior, a group from Cambridge investigated the role of a variant in the transcription factor FOXO3P previously associated with malaria ( 26 ).…”