Gastroenterology 2017;152:322–326
Paneth Cell Alterations in the Development and Phenotype
of Crohn’s Disease
Thaddeus S. Stappenbeck1 Dermot P. B. McGovern2
1
Department of Pathology and Immunology, Washington University, Saint Louis, Missouri; 2The F. Widjaja Foundation
Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
Pathogenesis of Crohn’s disease (CD) involves immune and relevant cell types. These studies often identify a cell type
microbial dysregulation, induced by environmental factors that is susceptible to altered function for a specific gene.
in genetically susceptible individuals. There are believed to For example, Paneth cell function is altered in mice with
be multiple subtypes of CD, which contributes to its loss of function for ATG16L1, as well as other autophagy
observed clinical heterogeneity. This concept has been proteins.4,5 An important next step is to engineer mice
reinforced by recognition of the complexity of the genetic, with mutations in disease-associated genes and test
microbial, immune, and environmental factors that affect for altered function of the gene products. As an example,
risk for CD. Paneth cells mediate immunity and maintain mice with the Atg16L1 mutation encoding T300A6
the small intestinal epithelium; defects in activities of confirmed which cell activities were disrupted by specific
these cells have been observed in high proportions of mutations.
patients with CD, and are associated with a more aggres- A further challenge is to identify the environmental
sive CD phenotype. Paneth cells integrate complex genetic,
factors that affect disease susceptibility in people or animal
immune, and environmental signals, therefore alterations
models with risk-associated variants. In patients, this is
in their function could lead to different subtypes of CD, as
performed through studies of specific activities or lifestyle
observed in studies in cohorts of primarily European
descent. Subtypes of CD associated with Paneth cell func- factors, such as diet. A more unbiased approach is to
tion have been observed even among patients from monitor the environment in the home and workplace for
different genetic backgrounds. We discuss genetic suscep- exposures. However, it is a challenge to develop hypotheses
tibility loci for CD and how these affect Paneth cell activity. for specific factors and these types of studies are difficult to
perform, expensive, and prone to error and bias.7 A less-
biased approach would be to track markers of environ-
Keywords: Crohn’s Disease; Paneth Cell; Autophagy; Subtype. mental exposures by screening urine, blood, or stool
samples. However, there are not many validated biomarkers
of exposures associated with CD. We propose that a cellular-
A combination of genetic and environmental factors
contributes to the pathogenesis of complex diseases
such as Crohn’s disease (CD).1,2 Although genetic factors
based pathophysiologic target may leave a detectable
imprint that is quantifiable in body fluid.
determine susceptibility, most susceptibility loci increase Inherited epigenetic changes could affect susceptibility
risk by only a small amount—hereditary factors are only to disease,8 although this idea has not been well studied in
one piece of the puzzle. Most susceptibility loci likely have patients with CD. We propose that Paneth cells, located
conferred, over the ages, some selective benefit.3 As society primarily in the small intestine (also in the proximal colon
has evolved, such selection advantages may no longer be as a metaplastic response to inflammation), integrate ge-
beneficial—subsequent changes in environmental pres- netic and environmental factors. Differences in Paneth cell
sures, instead, now might promote disease in genetically activities and features might be used to classify different
susceptible individuals. This paradigm can explain the types of CD.
increasing incidence of CD—new environmental factors
induce inappropriate immune responses that cause inflam-
Abbreviations used in this paper: CD, Crohn’s disease; IBD, inflammatory
matory disorders in genetically susceptible individuals. bowel disease.
It is a challenge to determine the functional conse- Most current article
quences of disease-associated variants. Typically, initial
© 2017 by the AGA Institute
attempts to characterize functional changes use knockout 0016-5085/$36.00
This study source was downloaded by 100000901307859 from CourseHero.com
and overexpression techniques in animal models and in on 10-21-2025 04:10:35 GMT -05:00
http://dx.doi.org/10.1053/j.gastro.2016.10.003
https://www.coursehero.com/file/252053445/Paneth-Cell-Alterations-in-the-Development-and-Phepdf/
, January 2017 Paneth Cells and CD 323
Paneth Cell Function and Abnormalities Paneth cell phenotypes can be analyzed using archived
biopsy material obtained during endoscopy. Analysis of
in CD Patients uninvolved ileal tissue from surgical resection specimens18
Paneth cells are long lived (w60 days),9 which makes allowed evaluation of Paneth cell morphology in areas
them a good target to integrate information from other with little or no inflammation. Systemic analyses of matched
immune cells and components of the microbiome, compared specimens and mathematic models showed that level of
with enterocytes, which live for only several days. Paneth disease activity in specimens was not associated with Pan-
cells are also a source of inflammatory signals.10–16 Paneth eth cell phenotype, and that Paneth cell phenotypes
cells produce, package, and export cytoplasmic granules that remained stable over time (up to >20 y). Biopsy specimens
contain many different broad-spectrum antimicrobial pro- with 40–50 intestinal crypts were sufficient to generate
teins—some of these are produced constitutively whereas results equivalent to those from resection specimens.19 It
others are produced in response to microbial challenges therefore is feasible to analyze Paneth cell phenotypes using
(Figure 1A). materials obtained from routine endoscopic biopsy speci-
Mice with engineered defects in autophagy proteins such mens (our success rate was w70%), therefore this method
as ATG16L1, and patients with CD who carry the mutation of analysis might be used in studies with large patient
in ATG16L1 that encodes T300A, have abnormal granule populations.
morphology and packaging of antimicrobial proteins.
Localization of lysozyme and a-defensins (ie, HD5 in human
beings) can be used to evaluate and quantify Paneth cell Association of Paneth Cell Phenotypes
granule morphology. This method is superior to routine With Patient Outcomes
H&E and periodic acid–Schiff staining techniques because Genome-wide association studies of North American and
the shape, size, amount, and distribution of these cyto- European cohorts identified more than 200 loci that in-
plasmic granules can be determined. Each Paneth cell can be crease susceptibility to IBD, including more than 150 that
classified as normal or assigned to 1 of 5 different categories increase risk for CD.3,20 Thus far, CD risk alleles associated
of abnormal: disordered (abnormal distribution and size of with ATG16L1 and NOD2 lead to defects in packaging and
the granules); diminished (10 granules); diffuse (smear of secretion of antimicrobial peptides in Paneth cells.4,17
cytoplasmic lysozyme or defensing, no recognizable gran- In an analysis of the small intestinal Paneth cell pheno-
ules); excluded (most granules do not contain stainable types from large cohorts of genotyped adults with CD with
material); and enlarged (megagranules).4,17–19 well-annotated clinical information, the type I Paneth cell
Paneth cell phenotypes of individual patients with CD or phenotype was associated with disease-associated geno-
mouse models of inflammatory bowel disease (IBD) can be types (ATG16L1 T300A and single-nucleotide poly-
defined by the percentage of total abnormal Paneth cells in morphisms in NOD2).18,19 These variants appear to have
the sample. A 20% cut-off value has been used to differen- additive effects because carriage of increasing numbers of
tiate type I Paneth cell phenotype (20% of abnormal ATG16L1 T300A and CD-associated NOD2 risk alleles in any
Paneth cells) from a type II Paneth cell phenotype (<20% of individual correlate with increased proportions of abnormal
abnormal Paneth cells).4,17–19 By using these criteria, Paneth Paneth cells in patients. Larger sample sizes are needed to
cell abnormalities are found in 20%–50% of patients with study how these variants interact and what pathways they
CD.18,19 alter that lead to Paneth cell defects.
Figure 1. (A) Paneth cells produce antimicrobial proteins (AMPs) that help shape the microbiome composition. (B) Abnormal
Paneth cells when found in patients without disease are not associated with an alteration of the microbiome. (C) Crohn’s
patients with inflammation and abnormal Paneth cells show alterations in microbiome composition.
This study source was downloaded by 100000901307859 from CourseHero.com on 10-21-2025 04:10:35 GMT -05:00
https://www.coursehero.com/file/252053445/Paneth-Cell-Alterations-in-the-Development-and-Phepdf/
Paneth Cell Alterations in the Development and Phenotype
of Crohn’s Disease
Thaddeus S. Stappenbeck1 Dermot P. B. McGovern2
1
Department of Pathology and Immunology, Washington University, Saint Louis, Missouri; 2The F. Widjaja Foundation
Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
Pathogenesis of Crohn’s disease (CD) involves immune and relevant cell types. These studies often identify a cell type
microbial dysregulation, induced by environmental factors that is susceptible to altered function for a specific gene.
in genetically susceptible individuals. There are believed to For example, Paneth cell function is altered in mice with
be multiple subtypes of CD, which contributes to its loss of function for ATG16L1, as well as other autophagy
observed clinical heterogeneity. This concept has been proteins.4,5 An important next step is to engineer mice
reinforced by recognition of the complexity of the genetic, with mutations in disease-associated genes and test
microbial, immune, and environmental factors that affect for altered function of the gene products. As an example,
risk for CD. Paneth cells mediate immunity and maintain mice with the Atg16L1 mutation encoding T300A6
the small intestinal epithelium; defects in activities of confirmed which cell activities were disrupted by specific
these cells have been observed in high proportions of mutations.
patients with CD, and are associated with a more aggres- A further challenge is to identify the environmental
sive CD phenotype. Paneth cells integrate complex genetic,
factors that affect disease susceptibility in people or animal
immune, and environmental signals, therefore alterations
models with risk-associated variants. In patients, this is
in their function could lead to different subtypes of CD, as
performed through studies of specific activities or lifestyle
observed in studies in cohorts of primarily European
descent. Subtypes of CD associated with Paneth cell func- factors, such as diet. A more unbiased approach is to
tion have been observed even among patients from monitor the environment in the home and workplace for
different genetic backgrounds. We discuss genetic suscep- exposures. However, it is a challenge to develop hypotheses
tibility loci for CD and how these affect Paneth cell activity. for specific factors and these types of studies are difficult to
perform, expensive, and prone to error and bias.7 A less-
biased approach would be to track markers of environ-
Keywords: Crohn’s Disease; Paneth Cell; Autophagy; Subtype. mental exposures by screening urine, blood, or stool
samples. However, there are not many validated biomarkers
of exposures associated with CD. We propose that a cellular-
A combination of genetic and environmental factors
contributes to the pathogenesis of complex diseases
such as Crohn’s disease (CD).1,2 Although genetic factors
based pathophysiologic target may leave a detectable
imprint that is quantifiable in body fluid.
determine susceptibility, most susceptibility loci increase Inherited epigenetic changes could affect susceptibility
risk by only a small amount—hereditary factors are only to disease,8 although this idea has not been well studied in
one piece of the puzzle. Most susceptibility loci likely have patients with CD. We propose that Paneth cells, located
conferred, over the ages, some selective benefit.3 As society primarily in the small intestine (also in the proximal colon
has evolved, such selection advantages may no longer be as a metaplastic response to inflammation), integrate ge-
beneficial—subsequent changes in environmental pres- netic and environmental factors. Differences in Paneth cell
sures, instead, now might promote disease in genetically activities and features might be used to classify different
susceptible individuals. This paradigm can explain the types of CD.
increasing incidence of CD—new environmental factors
induce inappropriate immune responses that cause inflam-
Abbreviations used in this paper: CD, Crohn’s disease; IBD, inflammatory
matory disorders in genetically susceptible individuals. bowel disease.
It is a challenge to determine the functional conse- Most current article
quences of disease-associated variants. Typically, initial
© 2017 by the AGA Institute
attempts to characterize functional changes use knockout 0016-5085/$36.00
This study source was downloaded by 100000901307859 from CourseHero.com
and overexpression techniques in animal models and in on 10-21-2025 04:10:35 GMT -05:00
http://dx.doi.org/10.1053/j.gastro.2016.10.003
https://www.coursehero.com/file/252053445/Paneth-Cell-Alterations-in-the-Development-and-Phepdf/
, January 2017 Paneth Cells and CD 323
Paneth Cell Function and Abnormalities Paneth cell phenotypes can be analyzed using archived
biopsy material obtained during endoscopy. Analysis of
in CD Patients uninvolved ileal tissue from surgical resection specimens18
Paneth cells are long lived (w60 days),9 which makes allowed evaluation of Paneth cell morphology in areas
them a good target to integrate information from other with little or no inflammation. Systemic analyses of matched
immune cells and components of the microbiome, compared specimens and mathematic models showed that level of
with enterocytes, which live for only several days. Paneth disease activity in specimens was not associated with Pan-
cells are also a source of inflammatory signals.10–16 Paneth eth cell phenotype, and that Paneth cell phenotypes
cells produce, package, and export cytoplasmic granules that remained stable over time (up to >20 y). Biopsy specimens
contain many different broad-spectrum antimicrobial pro- with 40–50 intestinal crypts were sufficient to generate
teins—some of these are produced constitutively whereas results equivalent to those from resection specimens.19 It
others are produced in response to microbial challenges therefore is feasible to analyze Paneth cell phenotypes using
(Figure 1A). materials obtained from routine endoscopic biopsy speci-
Mice with engineered defects in autophagy proteins such mens (our success rate was w70%), therefore this method
as ATG16L1, and patients with CD who carry the mutation of analysis might be used in studies with large patient
in ATG16L1 that encodes T300A, have abnormal granule populations.
morphology and packaging of antimicrobial proteins.
Localization of lysozyme and a-defensins (ie, HD5 in human
beings) can be used to evaluate and quantify Paneth cell Association of Paneth Cell Phenotypes
granule morphology. This method is superior to routine With Patient Outcomes
H&E and periodic acid–Schiff staining techniques because Genome-wide association studies of North American and
the shape, size, amount, and distribution of these cyto- European cohorts identified more than 200 loci that in-
plasmic granules can be determined. Each Paneth cell can be crease susceptibility to IBD, including more than 150 that
classified as normal or assigned to 1 of 5 different categories increase risk for CD.3,20 Thus far, CD risk alleles associated
of abnormal: disordered (abnormal distribution and size of with ATG16L1 and NOD2 lead to defects in packaging and
the granules); diminished (10 granules); diffuse (smear of secretion of antimicrobial peptides in Paneth cells.4,17
cytoplasmic lysozyme or defensing, no recognizable gran- In an analysis of the small intestinal Paneth cell pheno-
ules); excluded (most granules do not contain stainable types from large cohorts of genotyped adults with CD with
material); and enlarged (megagranules).4,17–19 well-annotated clinical information, the type I Paneth cell
Paneth cell phenotypes of individual patients with CD or phenotype was associated with disease-associated geno-
mouse models of inflammatory bowel disease (IBD) can be types (ATG16L1 T300A and single-nucleotide poly-
defined by the percentage of total abnormal Paneth cells in morphisms in NOD2).18,19 These variants appear to have
the sample. A 20% cut-off value has been used to differen- additive effects because carriage of increasing numbers of
tiate type I Paneth cell phenotype (20% of abnormal ATG16L1 T300A and CD-associated NOD2 risk alleles in any
Paneth cells) from a type II Paneth cell phenotype (<20% of individual correlate with increased proportions of abnormal
abnormal Paneth cells).4,17–19 By using these criteria, Paneth Paneth cells in patients. Larger sample sizes are needed to
cell abnormalities are found in 20%–50% of patients with study how these variants interact and what pathways they
CD.18,19 alter that lead to Paneth cell defects.
Figure 1. (A) Paneth cells produce antimicrobial proteins (AMPs) that help shape the microbiome composition. (B) Abnormal
Paneth cells when found in patients without disease are not associated with an alteration of the microbiome. (C) Crohn’s
patients with inflammation and abnormal Paneth cells show alterations in microbiome composition.
This study source was downloaded by 100000901307859 from CourseHero.com on 10-21-2025 04:10:35 GMT -05:00
https://www.coursehero.com/file/252053445/Paneth-Cell-Alterations-in-the-Development-and-Phepdf/
