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Paneth cell

Paneth cells are specialized, post-mitotic epithelial cells located at the base of the crypts of Lieberkühn in the small intestine of mammals, including humans and mice.^[1] These pyramidal-shaped cells are distinguished by their abundant rough endoplasmic reticulum, well-developed Golgi apparatus, and prominent apical secretory granules filled with antimicrobial peptides, enzymes such as lysozyme, and growth factors.^[1] First identified in the late 19th century by Gustav Schwalbe based on their eosinophilic granules and later detailed by Josef Paneth in 1888—for whom they are named—Paneth cells have a lifespan of approximately two months and are integral to intestinal epithelial architecture.^[2] The primary functions of Paneth cells revolve around supporting intestinal homeostasis and defense. They secrete antimicrobial peptides (AMPs), including α-defensins and cathelicidins, to shape and regulate the gut microbiota by limiting bacterial overgrowth and invasion.^[1] Additionally, these cells provide essential niche signals, such as Wnt3a and epidermal growth factor (EGF), to neighboring intestinal stem cells, promoting their proliferation and differentiation within the crypt niche.^[1] Paneth cells also exhibit phagocytic and efferocytotic capabilities to clear debris and apoptotic cells, uptake heavy metals like zinc for storage and release, and contribute to barrier integrity by modulating inflammation and epithelial repair.^[1] Dysfunction of Paneth cells has profound implications for health, linking them to various gastrointestinal disorders. Genetic mutations, environmental factors, or stressors like endoplasmic reticulum stress can impair their secretory functions, leading to dysbiosis and increased susceptibility to inflammatory bowel diseases such as Crohn's disease.^[1] In preterm infants, immature Paneth cell development—emerging around 13.5 weeks gestation but reaching full competence near term—heightens vulnerability to necrotizing enterocolitis due to reduced antimicrobial activity.^[2] Ongoing research utilizes organoid models and cell sorting techniques (e.g., CD24+ markers) to study Paneth cell biology, underscoring their role as cornerstones of intestinal and organismal health.^[1]

Anatomy and Morphology

Location and Distribution

Paneth cells are specialized epithelial cells primarily located at the base of the crypts of Lieberkühn in the small intestine, where they occupy the lowest positions within these glandular invaginations.^[1] They are interspersed with Lgr5+ crypt base columnar intestinal stem cells (ISCs), forming a critical component of the stem cell niche at the crypt base, while also supporting quiescent stem cells in the +4 position approximately four to six cells above the base.^[2] This positioning allows Paneth cells to directly interact with ISCs, contributing to epithelial renewal.^[3] The density of Paneth cells varies along the small intestine, with numbers generally increasing from the proximal to the distal regions; for instance, human ileal crypts contain a higher average density (approximately 5–15 Paneth cells per crypt) compared to jejunal or duodenal segments.^[4] In mice, this ranges from 5 to 16 cells per crypt, influenced by genetic strain and showing a similar proximal-to-distal gradient that correlates with escalating microbial load toward the ileum.^[1] Paneth cells are typically absent or exceedingly rare in the large intestine, though they are normally present in the human cecum and ascending colon, becoming scarce in the descending colon and rectum.^[5] Under pathological conditions, such as inflammatory bowel disease or chronic gastritis, ectopic Paneth cells can appear in atypical sites like the stomach or distal colon through a process known as metaplasia, potentially reflecting adaptive responses to inflammation.^[6] This aberrant distribution is not observed in healthy tissue and may indicate underlying mucosal injury.^[3] Paneth cells exhibit evolutionary conservation across mammals, including humans, rodents, and other species like horses and sheep, underscoring their fundamental role in intestinal defense.^[3] However, species-specific differences exist, such as variations in α-defensin expression and crypt cell counts, with rodents displaying particularly prominent populations that make them valuable models for study.^[1]

Cellular Structure

Paneth cells exhibit a distinctive pyramidal morphology, with a broader base compared to neighboring columnar enterocytes, contributing to their identification in histological sections of the small intestinal crypts.^[7] This granulated appearance arises primarily from numerous large secretory granules that dominate the apical cytoplasm, measuring 0.5-1 μm in diameter and containing antimicrobial peptides essential for innate defense.^[8] These granules stain eosinophilically in hematoxylin and eosin preparations, appearing as prominent supranuclear structures that are positive for lysozyme via immunohistochemical detection, distinguishing Paneth cells from other epithelial cell types.^[9] Ultrastructural analysis by electron microscopy reveals the granules as electron-dense organelles with homogeneous cores, reflecting their packed proteinaceous content. The basal nucleus is oval and euchromatic, supporting active transcription, while the perinuclear and mid-cytoplasmic regions feature extensive rough endoplasmic reticulum and a prominent supranuclear Golgi apparatus, which together enable robust protein synthesis and granule maturation.^[10] In contrast to absorptive enterocytes, the apical surface of Paneth cells bears shorter, stubby microvilli, optimized for secretion rather than nutrient uptake.^[11] Key molecular markers further define Paneth cell identity, including lysozyme for lysosomal activity, human α-defensins such as HD5 and HD6 stored within the granules, and the zinc transporter ZIP4 involved in metal ion homeostasis for granule function.^[12]^[10] These features collectively underscore the specialized secretory architecture of Paneth cells, setting them apart from adjacent crypt cells.^[13]

Development and Maintenance

Differentiation from Stem Cells

Paneth cells primarily originate from Lgr5+ intestinal stem cells (ISCs) positioned at the crypt base through asymmetric cell division, which produces one renewing ISC and one transit-amplifying progenitor committed to the secretory lineage. Reserve stem cells at the +4 position, marked by markers such as Bmi1, also contribute to Paneth cell generation, particularly under homeostatic conditions or following injury when Lgr5+ ISCs are depleted. This process ensures a steady supply of Paneth cells intermingled with ISCs to maintain the niche.^[14]^[15] Differentiation along the secretory lineage into Paneth cells is governed by key transcription factors, including Gfi1, Sox9, and Foxo1. Gfi1 functions downstream of Atoh1 to specify Paneth cells, as evidenced by the complete absence of Paneth cells in Gfi1-deficient mice. Sox9 is essential for Paneth cell maturation, with its conditional deletion in the intestinal epithelium blocking differentiation and reducing progenitor proliferation. Foxo1 regulates the transition from stem to secretory fates, where its loss increases Paneth cell numbers by promoting secretory differentiation at the expense of ISC maintenance. Wnt and Notch signaling gradients further direct fate decisions, with elevated Wnt activity at the crypt base promoting Paneth specification over goblet cell differentiation through interactions with these factors.^[16]^[17]^[18] The timeline for Paneth cell differentiation spans 3-5 days post-ISC activation, involving 4-5 rounds of transit-amplifying divisions before terminal commitment at the crypt base. In neonatal development, microbiota colonization accelerates this process by inducing immune signaling that enhances Paneth maturation, as germ-free models show delayed differentiation until microbial exposure. Stochastic mathematical models of lineage commitment incorporate BMP/Wnt signaling ratios to predict Paneth fate probabilities.^[19]^[20]^[21] Environmental factors, such as diet, modulate differentiation efficiency; for example, high-fat diets impair Paneth cell formation via PPARδ activation and microbiome alterations, while caloric restriction boosts ISC-driven Paneth production and niche function.^[22]

Lifespan and Turnover

Paneth cells exhibit a notably long lifespan within the intestinal epithelium, typically ranging from 20 to 60 days, in stark contrast to the rapid turnover of neighboring enterocytes, which survive only 3 to 5 days.^[23]^[24] This extended duration allows Paneth cells to maintain stable antimicrobial defenses at the crypt base, where they number approximately 5 to 15 per crypt.^[23] Their slow turnover rate, estimated at about 0.2 to 0.5 cells replaced per crypt per day based on average crypt occupancy and lifespan, underscores their role in long-term epithelial homeostasis rather than rapid renewal.^[25] This rate can be modeled using exponential decay kinetics, where the decay constant \lambda is given by \lambda = \frac{\ln(2)}{t_{1/2}}, with a half-life t_{1/2} of approximately 30 days for Paneth cells.^[26] Replacement of Paneth cells occurs through continuous differentiation from intestinal stem cells (ISCs) located at the crypt base, ensuring steady-state maintenance without significant proliferation of mature Paneth cells themselves.^[27] Disruption of this differentiation process, such as through genetic ablation of key regulators like Math1, can lead to crypt loss and impaired epithelial regeneration, highlighting the interdependence between Paneth cell renewal and overall crypt integrity.^[28] Under homeostatic conditions, this replacement mechanism supports a balanced niche environment, with Paneth cells contributing factors that reciprocally sustain ISC function. Apoptosis in Paneth cells is primarily regulated to preserve their longevity, with survival promoted by the PI3K/Akt signaling pathway, which inhibits pro-apoptotic signals and enhances cellular resilience.^[29] Under stress conditions, such as radiation or inflammation, apoptosis becomes Bax/Bak-dependent, involving mitochondrial outer membrane permeabilization to execute programmed cell death and prevent accumulation of damaged cells. This controlled elimination ensures that only viable Paneth cells persist to support the stem cell niche. With aging, Paneth cell numbers and functionality decline in the elderly, often linked to ISC exhaustion and diminished Wnt signaling within the crypt niche, resulting in reduced antimicrobial peptide production and compromised epithelial barrier integrity. Studies in human and mouse models show lower levels of defensins like human defensin 5 in older individuals, correlating with age-related stem cell dysfunction and increased susceptibility to intestinal perturbations.^[30] Recent studies (as of 2025) indicate that while Paneth cells enhance stem cell niche function, they are dispensable for basic maintenance, and compounds like lipoic acid can prevent age-related declines in human organoids and mouse models.^[31]^[32] This progressive loss contributes to broader declines in regenerative capacity, though compensatory mechanisms like altered crypt architecture may partially mitigate effects in some contexts.^[33]

Physiological Functions

Antimicrobial Secretions

Paneth cells secrete a variety of antimicrobial agents stored within their characteristic granules, primarily as inactive proforms that are processed into mature, active molecules prior to or during release. The major antimicrobial peptides include α-defensins, such as human defensins 5 (HD5) and 6 (HD6) or their murine counterparts known as cryptdins, which exhibit broad-spectrum activity against bacteria, fungi, and viruses by disrupting microbial membranes. Additional key secretions encompass lysozyme, which hydrolyzes bacterial peptidoglycans; secretory phospholipase A2 (sPLA2), which targets phospholipid components of microbial membranes; and trefoil factor 3 (TFF3), a peptide that supports mucosal integrity while contributing to host defense through stabilization of the antimicrobial environment. These components are packaged in large, electron-dense granules located at the apical pole of the cell, ensuring targeted delivery into the intestinal crypt lumen.^[34] The release of these antimicrobial agents occurs through a regulated process of stimulus-secretion coupling, involving calcium ion (Ca²⁺) influx that triggers exocytosis at the apical surface. Stimuli such as bacterial lipopolysaccharide (LPS) or extracellular ATP bind to receptors on the Paneth cell, leading to an increase in intracellular Ca²⁺ levels, which promotes granule fusion with the plasma membrane and discharge of contents into the crypt lumen. This mechanism allows rapid response to microbial challenges, maintaining a sterile environment immediately adjacent to the stem cell niche.^[34]^[35] Paneth cell granules create a specialized microenvironment enriched with high concentrations of zinc ions (Zn²⁺), which significantly enhances the antimicrobial efficacy of α-defensins. The zinc transporter ZIP4 (also known as SLC39A4) facilitates Zn²⁺ uptake into the cell and subsequent sequestration into granules, where it stabilizes defensin structure and potentiates their membrane-disrupting activity. Additionally, the granules support the proteolytic maturation of pro-defensins into their active forms by enzymes like matrix metalloproteinase 7 (MMP7). The interaction between defensins and zinc can be represented as:

\text{Def} + \text{Zn}^{2+} \rightleftharpoons \text{Def-Zn} \quad (K_d \approx 10^{-10} \, \text{M})

This high-affinity binding (with dissociation constants in the picomolar range) underscores zinc's role in optimizing defensin function under physiological conditions.^[34] Upon stimulation, a single Paneth cell can release a large number of antimicrobial peptides, contributing to microbicidal concentrations in the crypt lumen and profoundly shaping the composition of the intestinal microbiota by selectively enriching beneficial bacteria while limiting pathogens. This secretory output not only provides direct innate immunity but also indirectly supports epithelial homeostasis by preventing microbial overgrowth.^[34]

Sensing and Response to Microbiota

Paneth cells detect microbial signals primarily through pattern recognition receptors (PRRs), including Toll-like receptors (TLRs) and nucleotide-binding oligomerization domain-like receptors (NLRs). Specifically, TLR4 recognizes lipopolysaccharide (LPS) from Gram-negative bacteria, while NOD2, an NLR, senses peptidoglycan motifs from bacterial cell walls. These receptors initiate signaling cascades that are largely dependent on the adaptor protein MyD88, which is essential for Paneth cell responses to commensal bacteria.^[36]^[37]^[38]^[39] Upon microbial detection, these PRRs activate downstream response pathways in Paneth cells, culminating in NF-κB transcription factor activation, which upregulates the expression of antimicrobial defensins such as α-defensins. NOD2 signaling further enhances this process by cooperating with TLR pathways to amplify NF-κB activity and defensin production. Additionally, the IL-17/STAT3 axis contributes to chronic adaptations, where IL-17 signaling promotes antimicrobial functions and STAT3-dependent maturation in response to microbial cues, helping maintain long-term homeostasis.^[40]^[41]^[42]^[43] The presence of microbiota profoundly influences Paneth cell development and function; in germ-free mice, Paneth cells exhibit immature morphology, reduced granule numbers, and diminished antimicrobial peptide expression compared to conventionally raised counterparts. Specific commensal bacteria, such as Bacteroides thetaiotaomicron, promote Paneth cell granule maturation and secretion of bactericidal proteins like angiogenin-4, thereby enhancing host defense.^[44]^[45]^[46] Paneth cell secretions establish feedback loops that shape the microbiota composition and prevent dysbiosis by selectively enriching beneficial bacteria while inhibiting pathogens. This reciprocal interaction ensures microbial balance, as disruptions in Paneth cell function lead to shifts favoring pro-inflammatory species. Recent studies from 2023 highlight how microbiota-derived short-chain fatty acids (SCFAs), such as butyrate, modulate Paneth cell sensing via G-protein-coupled receptor 43 (GPR43), ameliorating defects and restoring antimicrobial responses in dysbiotic conditions.^[47]^[48]^[49]^[50] Dysregulation of these sensing mechanisms, particularly NOD2 mutations, impairs bacterial recognition and reduces α-defensin production in Paneth cells, leading to microbiota dysbiosis and increased susceptibility to ileal Crohn's disease. Patients with NOD2 variants show abnormal Paneth cell granules and defective responses to microbial stimuli, underscoring the link between genetic alterations in sensing pathways and inflammatory pathology.^[51]^[52]^[53]^[54]

Support for Stem Cell Niche

Paneth cells play a crucial role in providing the niche for intestinal stem cells (ISCs) by secreting key signaling molecules that promote ISC proliferation and maintenance. These cells produce Wnt ligands, such as Wnt3a, which activate canonical Wnt/β-catenin signaling essential for ISC self-renewal.^[55] Additionally, Paneth cells express and secrete Notch pathway activators, including the ligands Dll1 and Dll4, which sustain Notch signaling to prevent ISC differentiation and support their undifferentiated state.^[56] They also release members of the epidermal growth factor (EGF) family, further enhancing ISC proliferation through receptor tyrosine kinase pathways.^[55] The physical proximity of Paneth cells to ISCs at the crypt base facilitates juxtacrine and paracrine signaling, forming a supportive niche microenvironment. This close apposition is dispensable for ISC maintenance under steady-state conditions, where other cells like mesenchymal stromal cells can partially compensate, but it becomes essential during intestinal regeneration following injury or stress.^[57] In the small intestinal crypt, Paneth cells and ISCs are present in roughly equal numbers, reflecting their balanced distribution to optimize niche support without overcrowding the proliferative compartment.^[55]^[1] Dynamic regulation of the niche involves bidirectional interactions between Paneth cells and ISCs. Experimental depletion of Paneth cells, such as through diphtheria toxin administration in Defa6-Cre;iDTR mouse models, results in slowed ISC proliferation and reduced crypt regenerative capacity.^[57] Reciprocally, ISCs contribute to niche homeostasis by signaling back to modulate BMP signaling, helping to inhibit differentiation cues that could disrupt the balance.^[57] This interplay ensures robust stem cell function, particularly evident in neonatal development where early Paneth cell maturation around postnatal day 7-14 is critical for de novo crypt establishment and the transition from fetal to adult ISC niches.^[57] Recent research as of 2024 has further elucidated that enteric glia regulate Paneth cell secretion, influencing microbial homeostasis and indirectly supporting the stem cell niche through modulated antimicrobial activity.^[58]

Phagocytic and Autophagic Roles

Paneth cells exhibit phagocytic activity, enabling them to engulf and clear apoptotic epithelial cells and luminal debris through apical endocytosis. This process involves the uptake of dying intestinal cells, as demonstrated in enteroid models where Paneth cells internalize membrane-labeled apoptotic material via their apical surface.^[59] Phagocytosis in Paneth cells is actin-dependent, relying on cytoskeletal rearrangements to facilitate membrane invagination and particle internalization, similar to mechanisms in other professional phagocytes.^[60] Under inflammatory conditions, such as those induced by irradiation or microbial challenge, phagocytic efficiency increases, aiding in the rapid clearance of cellular debris to maintain epithelial integrity.^[59] Additionally, Paneth cells can phagocytose luminal bacteria and trophozoites, contributing to direct pathogen elimination beyond secretory defenses.^[61] Autophagy plays a critical role in Paneth cell function, particularly through secretory autophagy that supports the biogenesis of antimicrobial granules. This process is dependent on core autophagy genes such as Atg5 and Atg7, which facilitate the formation and maturation of secretory granules containing defensins and lysozyme.^[62] In Atg7-deficient Paneth cells, granule size is reduced and numbers increased, leading to impaired packaging and secretion of antimicrobial peptides like lysozyme, highlighting autophagy's necessity for unconventional protein secretion pathways.^[63] Secretory autophagy ensures the proper delivery of granule contents to the apical lumen, linking intracellular degradation machinery to extracellular antimicrobial activity.^[64] Phagocytosis and autophagy in Paneth cells intersect via phagolysosomal fusion, where engulfed pathogens or debris are degraded within lysosome-fused compartments. This crosstalk enhances intracellular clearance, with autophagosomes delivering ubiquitinated cargo to lysosomes for hydrolysis.^[65] The mTOR pathway negatively regulates this autophagic flux; inhibition by rapamycin promotes autophagosome formation and lysosomal fusion in Paneth cells, boosting degradation capacity during stress.^[66] Recent studies have shown that α-lipoic acid (ALA) suppresses mTOR signaling specifically in Paneth cells, enhancing autophagic processes to restore granule secretion and reduce atypical Paneth cell accumulation in aging models, thereby exerting anti-inflammatory effects through improved barrier function.^[32] Autophagy in Paneth cells maintains basal turnover of cytoplasmic components to support overall cellular homeostasis.^[67]

Clinical and Pathological Relevance

Role in Inflammatory Bowel Diseases

Paneth cells play a central role in the pathogenesis of inflammatory bowel diseases (IBD), particularly Crohn's disease (CD), where their dysfunction contributes to intestinal barrier impairment and chronic inflammation. In CD, which frequently affects the ileum, Paneth cell abnormalities lead to reduced secretion of antimicrobial peptides such as human α-defensins HD5 and HD6, promoting bacterial translocation and dysbiosis.^[68] This dysfunction is less pronounced in ulcerative colitis (UC), which primarily involves the colon and lacks Paneth cells in the healthy state, though metaplastic Paneth cells may emerge in inflamed colonic mucosa.^[69] Pathophysiologically, Paneth cell defects in CD are characterized by erosions and dropout in the ileal crypts, exacerbating mucosal inflammation. Reduced defensin expression is strongly linked to NOD2 mutations, a key genetic risk factor for ileal CD, as NOD2 normally regulates Paneth cell antimicrobial responses; variants impair granule formation and peptide release, leading to increased susceptibility to luminal pathogens.^[68] Similarly, histological findings reveal dysmorphic Paneth cells with abnormal granules and metaplastic changes in active CD lesions, contrasting with normal architecture in controls.^[1] Mechanistically, genetic variants like ATG16L1 mutations disrupt autophagy in Paneth cells, causing accumulation of dysfunctional granules and impaired bacterial clearance, which further drives IBD progression.^[69] Microbiota dysbiosis amplifies this loss, as defective Paneth cells fail to maintain microbial diversity, allowing overgrowth of adherent-invasive Escherichia coli and other pathobionts that perpetuate inflammation.^[1] Endoplasmic reticulum stress in Paneth cells, triggered by these genetic and microbial factors, promotes barrier breakdown, as highlighted in recent studies linking unfolded protein response activation to ileal erosions.^[68] Clinically, Paneth cell depletion correlates with disease severity; dysmorphic or reduced Paneth cells in ileal biopsies predict postoperative relapse in up to 50% of pediatric CD patients and are observed in approximately 20-50% of adult cases, with higher rates in ileal-predominant disease affecting 70% of CD patients overall.^[70] Therapeutic interventions like anti-TNF agents, such as infliximab, can restore Paneth cell function by alleviating inflammation-induced stress, improving defensin expression and reducing dysbiosis in responsive patients.^[1] A 2023 review underscores that targeting Paneth cell stress pathways may enhance barrier integrity and prevent relapse in IBD.^[69]

Involvement in Metabolic Disorders

Paneth cells contribute to the pathogenesis of non-alcoholic fatty liver disease (NAFLD), now termed metabolic dysfunction-associated steatotic liver disease (MASLD), by maintaining intestinal barrier integrity; their dysfunction promotes a leaky gut, allowing bacterial translocation and portal endotoxemia that exacerbates hepatic inflammation and steatosis.^[71] In a 2023 review, Paneth cells are described as the "missing link" in the progression from obesity-related NAFLD to metabolic dysfunction-associated steatohepatitis (MASH), as impaired antimicrobial secretions lead to dysbiosis and systemic endotoxemia via lipopolysaccharide (LPS) leakage into the portal vein.^[71] In obesity, high-fat diets reduce Paneth cell numbers and function, altering the gut microbiota composition—such as increasing Firmicutes and decreasing Bacteroidetes—which disrupts insulin signaling and promotes metabolic dysregulation.^[72] Animal models demonstrate that consumption of a Western diet (40% fat) for 8 weeks induces Paneth cell defects in mice, correlating with microbiome shifts involving elevated Clostridium species and secondary bile acids like deoxycholic acid, which activate farnesoid X receptor (FXR) and type I interferon pathways to impair Paneth cell integrity.^[73] Zinc deficiency, often linked to high-fat diets, further exacerbates these defects by limiting antimicrobial peptide production, though Paneth cells' zinc secretion supports barrier maintenance under normal conditions.^[73] Key pathways involve gut-derived LPS activating Toll-like receptor 4 (TLR4) and nuclear factor kappa B (NF-κB) in the liver, driving inflammation and fibrosis in NAFLD/MASH; this gut-liver axis is amplified by Paneth cell-mediated dysbiosis.^[71] Therapeutic strategies targeting Paneth cell restoration, such as probiotics to modulate microbiota and reduce endotoxemia, show promise in preclinical models for mitigating hepatic steatosis and portal hypertension.^[71] Epidemiological observations indicate Paneth cell alterations in a significant proportion of NAFLD cases, with overweight and obese individuals (BMI ≥ 25) exhibiting reduced normal Paneth cells and increased defects compared to lean controls.^[73] Animal studies corroborate this, showing Paneth cell depletion accelerates steatosis in high-fat diet models, with defects observed in up to 70% of affected mice after prolonged exposure.^[72] A 2022 study showed that Paneth cell depletion reduces portal hypertension and lymphangiogenesis in experimental models by downregulating vascular endothelial growth factor C/D and related proteins, attenuating hypertension in obesity-associated liver disease.^[74]

Associations with Other Conditions

Paneth cells play a critical role in the pathogenesis of necrotizing enterocolitis (NEC), a severe inflammatory condition primarily affecting preterm infants, where immaturity of these cells leads to impaired antimicrobial defense and increased susceptibility to bacterial overgrowth in the immature gut. In preterm neonates, Paneth cells are underdeveloped, resulting in reduced secretion of antimicrobial peptides such as defensins, which compromises the intestinal barrier and contributes to dysbiosis and inflammation characteristic of NEC. Studies in murine models demonstrate that disruption or ablation of Paneth cells, particularly in the presence of pathogens like Klebsiella pneumoniae, induces NEC-like injury, highlighting their essential function in maintaining epithelial integrity during early postnatal development. Infants with NEC exhibit significantly fewer Paneth cells compared to age-matched controls, underscoring the link between Paneth cell deficiency and disease onset. Prematurity remains the primary risk factor for NEC, with incidence rates of 5-12% in infants born before 33 weeks gestation, where Paneth cell immaturity exacerbates vulnerability to enteral feeding and hypoxia. In colorectal cancer, Paneth cells promote tumorigenesis by supporting the stem cell niche through secretion of growth factors like Wnt ligands, fostering an environment conducive to adenoma initiation and progression. Accumulation of Paneth cells in early colorectal adenomas correlates with reduced disease-free survival in patients, as these cells provide essential niche signals that sustain cancer stem cells. IDO1-expressing Paneth cells within tumor crypts enhance immune evasion by colorectal cancer cells, leading to increased tumor burden in mouse models; their depletion in Stat1-deficient intestinal tumors reduces tumor load and improves anti-tumor immune infiltration. In some chemotherapy contexts, transient Paneth cell depletion facilitates intestinal regeneration by allowing stem cell repopulation without excessive niche support for residual malignant cells, potentially enhancing post-treatment recovery in preclinical models. With aging, Paneth cell function declines, contributing to intestinal barrier dysfunction and overall frailty in the elderly through altered homeostasis and reduced support for stem cell maintenance. Aged intestines show increased Paneth cell numbers per crypt but with impaired secretory capacity, leading to dysregulated microbiota and heightened inflammation that exacerbates age-related frailty. In celiac disease, gluten exposure induces stress in Paneth cells, resulting in reduced numbers and diminished lysozyme secretion, which impairs innate immunity and perpetuates mucosal damage in untreated patients. Paneth cell deficiency is observed in a subset of celiac cases, correlating with poor response to gluten-free diets and persistent malabsorption. Recent studies highlight emerging protective roles for Paneth cells in various pathologies. A 2025 investigation demonstrated that α-lipoic acid (ALA) supplementation targets Paneth cells to prevent intestinal stem cell aging, reducing atypical Paneth cell accumulation in human organoids and aged mouse intestines, thereby mitigating inflammation-associated decline. In radiation injury models, Paneth cell dysfunction disrupts α-defensin expression and microbiota balance, worsening enteritis; however, IL-17 receptor signaling to Paneth cells preserves epithelial integrity post-gamma irradiation, suggesting therapeutic potential for enhancing their resilience.

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Our study identifies IL–17R-dependent signaling in PCs as an important mechanism that maintains ileal homeostasis through the prevention of dysbiosis.
[41]
IL-22 receptor signaling in Paneth cells is critical for their maturation ...
Oct 15, 2020 · Furthermore, IL-22 signaling in Paneth cells regulates the intestinal commensal bacteria and microbiota-dependent IL-17A immune responses.
[42]
The enteric microbiota regulates jejunal Paneth cell number ... - NIH
Germ-free mice have fewer jejunal Paneth cells than conventionally raised mice ... immature mice. Dis Model Mech. 2012;5:522–32. doi: 10.1242/dmm.009001 ...
[43]
Paneth cells, defensins, and the commensal microbiota
Studies of germ-free rodents have demonstrated that an absence of intestinal commensal bacteria causes immature mucosal architecture in these animals and ...
[44]
Bacteroides: the Good, the Bad, and the Nitty-Gritty - PMC
In animal models, B. thetaiotaomicron can stimulate production of an antibiotic Paneth cell protein (Ang4) that can kill certain pathogenic organisms (e.g., ...
[45]
Cross talk between Paneth and tuft cells drives dysbiosis ... - PNAS
Intestinal Paneth cells are considered to be guardians of the gut microbiota, but the events linking Paneth cell dysfunction with dysbiosis remain unclear. We ...
[46]
Paneth Cell Defects Induce Microbiota Dysbiosis in Mice and ...
Mice with maternal separation developed visceral hypersensitivity and defects in Paneth cells, as reported from rats, compared with mice without maternal ...
[47]
BUTYRATE AMELIORATES PANETH CELL DEFECTS, TOTAL ...
Jan 26, 2023 · ... short chain fatty acids (SCFAs; acetate, propionate, and butyrate)-producing bacteria. SCFAs play a significant role in reducing intestinal ...
[48]
Article GPR43 mediates microbiota metabolite SCFA regulation of ...
Feb 7, 2018 · ... Paneth cells serve as the first line of defense against microbiota and occasionally pathogens. ... The blockade of STAT3 signaling ...
[49]
NOD2 mutations and Crohn's disease: are Paneth cells and ... - NIH
Paneth cells detect and respond to bacteria, and the CARD15/NOD2 protein may mediate their interaction with bacterial products. Inherited mutations in CARD15/ ...
[50]
Reduced Paneth cell α-defensins in ileal Crohn's disease - PNAS
NOD2/CARD15 mutations are especially associated with localization of CD in the small intestine (for reviews, see refs. 3 and 4). NOD2 is an intracellular ...Reduced Paneth Cell... · Sign Up For Pnas Alerts · Results
[51]
Paneth cell defects in Crohn's disease patients promote dysbiosis
Jun 2, 2016 · Paneth cell phenotype did not correlate with ATG16L1 T300A or NOD2 risk alleles in pediatric CD. We previously correlated the degree of Paneth ...Abstract · Introduction · Results · Discussion
[52]
An Update Review on the Paneth Cell as Key to Ileal Crohn's Disease
Apr 14, 2020 · Looking at Paneth cell morphology, Crohn's patients carrying at least two NOD2 mutations exhibited an increased number of abnormal granules in ...
[53]
Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts
Nov 28, 2010 · Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts. Toshiro Sato,; Johan H. van Es,; Hugo J. Snippert,; Daniel E ...
[54]
Dispensable yet Irreplaceable for the Intestinal Stem Cell Niche
In humans, immature Paneth cells arise around 19 weeks gestational age, with mature Paneth cells detected around 29 weeks and increasing in number until birth; ...Reviews · The Isc Niche And Paneth... · Paneth Cells Enhance Isc...Missing: timeline | Show results with:timeline
[55]
Efferocytosis by Paneth cells within the intestine - PubMed - NIH
Jun 7, 2021 · These data advance a new concept that Paneth cells can act as phagocytes and identify another way in which Paneth cells contribute to the ...Missing: apical bacteria
[56]
Paneth Cells: Development, Morphology, Function and Clinical ...
Jun 13, 2024 · Paneth cells (PCs) first described in the late 19th century are columnar epithelial cells of the intestinal glands.
[57]
Lack of Intestinal Epithelial Atg7 Affects Paneth Cell Granule ...
Genetic polymorphisms of autophagy-related genes have been associated with an increased risk to develop inflammatory bowel disease (IBD).
[58]
Impact of Paneth Cell Autophagy on Inflammatory Bowel Disease
It was reported that the dysfunction of Paneth cell autophagy disturbed the intestinal microbiota, leading to the higher level of AIEC and Salmonella ...
[59]
mTORC1 in the Paneth cell niche couples intestinal stem cell ... - NIH
Alternatively, ISCs and Paneth cells were mixed after sorting in a 1:1 ratio, centrifuged, and then seeded into matrigel. The matrigel drops with ISCs and ...
[60]
Lipoic acid functions in Paneth cells to prevent human intestinal ...
Jul 1, 2025 · Consistent with these findings, transmission electron microscopy revealed an increased prevalence of abnormal secretory granules ... Paneth cell ...
[61]
Measuring autophagosome flux - PMC - NIH
This approach provides a sensitive quantitative method to measure autophagosome flux, pool sizes and transition time in cells and tissues of clinical relevance.Missing: Paneth | Show results with:Paneth
[62]
An Update Review on the Paneth Cell as Key to Ileal Crohn's Disease
Apr 15, 2020 · Paneth cell dysfunction mediates alcoholic steatohepatitis through promoting bacterial translocation in mice: role of zinc deficiency ...
[63]
Implications of Paneth Cell Dysfunction on Gastrointestinal Health ...
Nov 1, 2023 · Paneth cell dysfunction has been linked to several gastrointestinal disorders, including Crohn's disease, enteric infections, graft-versus ...
[64]
Paneth cell defects in Crohn's disease patients promote dysbiosis
Jun 2, 2016 · Paneth cell defects in Crohn's disease patients promote dysbiosis. Ta ... prevalence of the Type I (abnormal) Paneth cell phenotype. We ...
[65]
https://www.sciencedirect.com/science/article/pii/S1934590923001502
[66]
https://pmc.ncbi.nlm.nih.gov/articles/PMC3387287/
[67]
https://pmc.ncbi.nlm.nih.gov/articles/PMC6103398/
[68]
Regulation of Lymphangiogenesis by Paneth Cells in Normal ... - EMJ
In the absence of Paneth cells, portal hypertension was attenuated ... 2024. EMJ Gastroenterology 13.1 2024 · Gastroenterology. November 2023. EMJ ...