Gastroenterology

Gastroenterology

Volume 146, Issue 1, January 2014, Pages 200-209
Gastroenterology

Original Research
Full Report: Basic and Translational—Alimentary Tract
Genetic Variants Synthesize to Produce Paneth Cell Phenotypes That Define Subtypes of Crohn's Disease

https://doi.org/10.1053/j.gastro.2013.09.048Get rights and content

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 presence of granuloma. In addition, 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.

Section snippets

Description and Genotyping of Patient Cohort

Full methods are provided in the Supplementary Detailed Methods. Patients were recruited at Barnes-Jewish Hospital, St Louis between 2005 and 2013 or at Cedars-Sinai Medical Center, Los Angeles between 1999 and 2013. Patient DNA samples were genotyped for ATG16L1 T300A and the CD-associated NOD2 variants.10, 20, 21 Patients from the Barnes-Jewish Hospital cohort were genotyped by the Digestive Disease Research Core Center using matrix-assisted laser desorption ionization-time of flight mass

Association of NOD2 CD Susceptibility Variants With Abnormal Paneth Cell Phenotype

We performed a retrospective analysis of Paneth cell phenotypes in genotyped CD patients (N = 119) using resection specimens. In order to study tissue that might exhibit early pathologic and molecular changes associated with disease pathogenesis, we examined ileal tissue samples that demonstrated no evidence of active/chronic disease. Paneth cell analysis was performed using our previously developed system for robust, quantitative scoring of Paneth cell phenotypes based on high-resolution

Discussion

Here we have provided the first evidence that a defined cellular phenotype (in Paneth cells) is linked to multiple CD genetic susceptibility loci and subdivides patients into 2 groups. In addition, we defined the molecular consequences of this phenotype in human Paneth cells and found an association with immune activation. We demonstrated that Paneth cell phenotypes are associated with the presence of granuloma, a classic histological finding associated with CD. We also showed that the Paneth

Acknowledgments

Transcript Profiling: Microarray data are deposited at ArrayExpress http://www.ebi.ac.uk/arrayexpress/ (accession number E-MTAB-1281).

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    Conflicts of interest The authors disclose no conflicts.

    Funding K.L.V. was supported by a National Institutes of Health training grant (T32 AI007163). The research was funded by a Washington University Institute of Clinical and Translational Sciences Pilot Award (CTSA308). The Washington University Digestive Disease Research Core Center is supported by a grant from the National Institute of Diabetes and Digestive and Kidney Disease (P30DK052574). IBD Research at Cedars-Sinai is supported by US Public Health Service grant PO1DK046763 and the Cedars-Sinai F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute Research Funds. Genotyping at Cedars-Sinai Medical Center is supported in part by the National Center for Research Resources grant M01-RR00425, UCLA/Cedars-Sinai/Harbor/Drew Clinical and Translational Science Institute grant (UL1 TR000124-01), the Southern California Diabetes and Endocrinology Research grant (DK063491). Project investigators are supported by The Helmsley Charitable Trust (D.P.B.M.), The European Union (D.P.B.M.), The Crohn's and Colitis Foundation of America (CCFA) (D.P.B.M.), The Feintech Family Chair in IBD (S.R.T.), The Joshua L. and Lisa Z. Greer Chair in IBD Genetics (D.P.B.M.), and grants DK043351, DK097485, DK092405 (R.J.X.), DK062413, DK046763-19, AI067068, HS021747 (D.P.B.M.), and AI084887 (T.S.S.). T.S.S. and R.J.X. are supported by the CCFA Genetics initiative.

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