The mucosal immune system protects the internal surfaces of the body, including those of the intestinal, respiratory, and urogenital tracts. The mucosal surfaces are permeable barriers to the inner part of the body, which makes them especially vulnerable to the entry of pathogenic microorganisms and other antigens that can cause infections and inflammatory diseases. To prevent the entry of unwanted antigens, mucosal surfaces are lined by a mucus-secreting epithelium, which represents our first line of defense. The mucus layer, primarily produced by goblet cells, forms a critical mucosal barrier that traps pathogens and shapes the local microbiota, providing both a physical and immunological defense at the mucosal surface.

Epithelial cells not only form a physical barrier but also play active roles in immune defense. Specialized epithelial cells, such as M cells in the small intestine and ciliated epithelial cells in the respiratory tract, are essential for antigen uptake and immune surveillance at mucosal surfaces, facilitating communication between the external environment and underlying immune cells.

To protect us while creating tolerance to symbiotic microbiota, the mucosal immune system has evolved very sophisticated mechanisms where specialized CD4+ T cells, CD8+ T cells (including intraepithelial lymphocytes-IELs), Innate Lymphoid cells (ILC), Ig-secreting plasma cells, macrophages, and dendritic cells compromise between suppression and activation of an immune response. Mucosal immune responses involve both innate and adaptive immunity, with effector functions such as antibody secretion, cytokine production, and cytotoxic activity carried out by effector cells at mucosal effector sites. Cell receptors on immune cells, including T-cell receptors and other cell receptors, are crucial for recognizing antigens and initiating cell responses. If this fine balance is disrupted, inflammatory conditions can arise. A clear example of this balance disruption is seen in inflammatory disorders in the gut in patients with inflammatory bowel disease or in the lung in allergic diseases.

Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract that includes Crohn’s disease and ulcerative colitis and is characterized by severe epithelium damage and intestinal inflammation. Although the pathogenesis of IBD is still unknown, several disease-associated genes, including NOD2, ATG16L1, and IL23R, have been identified. The mucosal epithelium of IBD patients has decreased secretion of antimicrobial molecules, impaired bacterial recognition, and defective IgA production, leading to changes in microbiota composition and bacterial translocation. In response to microbial products, CD4+ T cells (Th1, Th2, Th17) are infiltrated into the lamina propria and secrete pro-inflammatory cytokines including TNF, IFN, IL-5, IL-6, IL-13, IL-17, or IL-22 5,16,17 through activation of certain STATs. Tumor necrosis factor (TNF) is a key inflammatory cytokine that influences epithelial cell apoptosis and tissue responses during mucosal inflammation. In addition to T cells, innate lymphoid cells (ILC), NK cells, and macrophages also secrete pro-inflammatory cytokines promoting epithelial damage, ulcers, and, in some cases, the development of colitis-associated cancer. Several of these cytokines are being investigated as potential targets for IBD treatment. In healthy individuals, regulatory T cells (Tregs) maintain immune tolerance and suppress effector T cell responses through anti-inflammatory cytokines such as IL‑10 and TGFβ. In contrast, Tregs are decreased in the gut of IBD patients. The gastrointestinal mucosal immune system, particularly in the small intestine, relies on structures such as Peyer's patches, isolated lymphoid follicles, and the intestinal lamina propria, where M cells sample antigens and initiate immune activation with the help of intestinal dendritic cells.

The mucosal immune system is organized into distinct mucosal tissues and mucosal lymphoid tissues, including mucosa-associated lymphoid tissue (MALT), gut-associated lymphoid tissues (GALT), and inductive and effector sites such as mucosal inductive sites and mucosal effector sites. Key anatomical structures include the mesenteric lymph node, which serves as a hub for immune induction, lymphocyte activation, and effector functions. Isolated lymphoid follicles and the intestinal lamina propria are important for local immune responses, while blood vessels facilitate immune cell migration and trafficking. Resident immune cells, such as macrophages and lymphocytes, are permanently located in mucosal tissues to provide rapid responses and maintain tissue homeostasis.

Antigen-presenting cells, including dendritic cells and intestinal dendritic cells, play a central role in orchestrating mucosal immune responses by presenting antigens to T cells and B cells. Activated B cells undergo cell differentiation and T cell differentiation processes, leading to the generation of plasma cells and memory cells that contribute to long-term immunity at mucosal surfaces.

In immune regulation, oral tolerance is a critical mechanism that prevents immune responses to harmless antigens, such as food proteins, by inducing antigen-specific unresponsiveness and maintaining mucosal homeostasis.

Up to 30% of the population in industrialized countries suffers from allergy, and its prevalence is increasing over time. Allergic rhinitis and allergic asthma are the main allergic diseases affecting the upper and lower airways and are often seen coexisting in allergic patients. Allergy is characterized by the presence and production of immunoglobulin E (IgE), which binds to its main receptor (FcƐRI) in basophils and mast cells, and the subsequent release of histamine and leukotrienes. During the late phase, endothelial-cell adhesion and eosinophil recruitment increase, and T cells are activated. Activated Th1 and Th2 in the lungs secrete IL-5, IL-9, and IL-13, leading to allergic inflammation. The mucosal immune response in the respiratory tract and upper respiratory tract involves both innate and adaptive immune mechanisms, with effector functions such as cytokine secretion and antibody production by effector cells. Cell receptors on airway epithelial cells and immune cells are essential for recognizing inhaled antigens and orchestrating the immune response. Mucosal vaccine strategies targeting the respiratory tracts, including the upper respiratory tract, aim to induce protective immunity at these mucosal barriers, with airway ciliated epithelial cells playing important roles in vaccine-induced immune responses.

The structure and function of the mucosal immune system are closely linked to the balance between local and systemic immunity. The mucosal immune system interacts with the systemic immune system to coordinate responses to pathogens, and adaptive immunity is essential for long-term protection and immune memory at both mucosal and systemic levels.

NOD2

Nucleotide oligomerization domain (NOD2), also known as CARD-15 or IBD1, is an intracellular pattern-recognition receptor involved in gastrointestinal immunity and expressed in monocytes and macrophages. Gut-associated lymphoid tissues and the gastrointestinal mucosal immune system play a central role in maintaining gut immune homeostasis, and their dysfunction is highly relevant to the pathogenesis of Crohn’s disease. Mutations in the NOD2 gene are associated with Crohn’s disease. In Crohn’s disease, intestinal dendritic cells, isolated lymphoid follicles, the mesenteric lymph node, and the intestinal lamina propria are all involved in antigen sampling and immune regulation, contributing to disease development and progression.

Figure 1. Immunohistochemistry (Formalin/PFA-fixed paraffin-embedded sections) - Anti-CARD15/NOD2 antibody [2D9] (ab31488).

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ATG16L1

Autophagy related 16 like 1 (ATG16L1) is an intracellular protein that plays a critical role in the autophagy pathway. Several single-nucleotide polymorphisms (SNPs) in the ATG16L1 gene have been linked to an increased risk of Crohn’s disease.

Figure 2. Western blot - Anti-ATG16L1 antibody [EPR15638] - N-terminal (ab187671).

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IL23R

Interleukin-23 receptor (IL23R) is strongly expressed on the cell membrane of memory T cells and other immune cells, including monocytes, dendritic cells, and natural killer cells. IL23R interacts with the cytokine IL23, which regulates immune cell activity and is essential in the inflammatory response. Several IL23R variants are associated with Crohn’s disease.

Figure 3. Immunocytochemistry/ Immunofluorescence - Anti-IL-23R antibody [EPR22838-4] (ab222104).

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Defensins

Defensins are small antimicrobial peptides produced by epithelial cells and innate immune system cells. Altered defensin production has been implicated in IBD pathogenesis.

Defensins and IL-2 receptor signaling play crucial roles in modulating the cell response during immune activation, influencing T lymphocyte behavior, immune regulation, and memory formation in mucosal and respiratory tissues.

Figure 4. Immunohistochemistry (Formalin/PFA-fixed paraffin-embedded sections) - Anti-alpha Defensin 5 antibody [EPR14309(B)] - BSA and Azide free (ab245946).

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REG3

Regenerating islet-derived protein 3 (REG3) is a member of the REG family – a group of small secretory proteins involved in intestinal homeostasis. REG3 is abundantly expressed in the small intestine and modulates the host defense mechanism in the gut via bactericidal activity. However, the precise roles of REG proteins in IBD have not yet been defined.

Figure 5. Immunohistochemistry (Formalin/PFA-fixed paraffin-embedded sections) - Anti-REG3A + REG3G antibody [EPRR18188] - BSA and Azide free (ab251357).

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Cathelicidins

​Cathelicidins are small antimicrobial peptides that play a crucial role in the innate and adaptive immune systems by acting as “natural antibiotics”­. Human cathelicidin, LL-37, has been suggested to play an essential role in the development and progression of IBD. Thus, cathelicidin expression is increased in the intestinal mucosa of patients with ulcerative colitis.

Figure 6. Flow Cytometry (Intracellular) - Anti-Cathelicidin/CLP antibody [EPR28791-612] (ab318195).

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Toll-like receptors

Toll-like receptors (TLRs) are a family of pattern recognition receptors that constitute the first line of the antimicrobial defense system and are critical for maintaining intestinal homeostasis. TLRs act as key immune sensors of gut microbiota, recognizing abnormal microbes and inducing an immune response. Overactivation of TLRs can ultimately disrupt immune homeostasis, increasing the risk for inflammatory diseases and autoimmune disorders. Both TLRs and TLR-activated signaling pathways have been implicated in the pathogenesis of IBD.

Figure 7. Immunohistochemistry (Formalin/PFA-fixed paraffin-embedded sections) - Anti-TLR7 antibody [EPR2088(2)] (ab124928).

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TNF

Tumor necrosis factor (TNF) is a potent pro-inflammatory cytokine produced by a wide range of immune and stromal cells, including macrophages, T cells, and fibroblasts, particularly within mucosal tissues. It plays a critical role in the early stages of inflammatory bowel disease (IBD) by promoting immune cell activation, cytokine release, and disruption of epithelial barrier integrity. TNF is widely recognized as a key driver of mucosal inflammation and tissue damage in IBD. Due to its central role in pathogenesis, TNF is a major clinical target for biologic therapies such as anti-TNF antibodies.

Figure 8. Immunocytochemistry/ Immunofluorescence - Anti-TNF alpha antibody [EPR19147] (ab183218).

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IL-10

Interleukin 10 (IL-10) is an anti-inflammatory cytokine that plays an essential role in maintaining mucosal homeostasis and preventing pro-inflammatory responses. Loss-of-function mutations in genes encoding IL-10 cytokine and IL-10 receptor have been linked to very early-onset IBD.

Figure 9. Flow Cytometry (Intracellular) - Anti-IL-10 antibody [EPR1114] (ab133575).

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TGF-beta

Transforming growth factor-β (TGF-β) is an immune-suppressive cytokine produced by many cell types, including immune cells. TGF-β signaling regulates mucosal immune system reactions and is shown to be impaired in the intestines of patients with IBD.

Figure 10. Immunocytochemistry/ Immunofluorescence - Anti-TGF beta 3 antibody [EPR27093-72] (ab308300).

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Chemokines

Chemokines play a key role in the pathogenesis of Crohn’s disease and ulcerative colitis, triggering multiple inflammatory response actions, including leukocyte activation and chemoattraction. Several chemokines have been investigated in the IBD setting, with the receptors CCR9 and CXCR3 and their respective ligands CCL25 and CXCL10 being the principal targets for anti-chemokine therapy in IBD.

Figure 11. Flow Cytometry (Intracellular) - Anti-CXCR4 antibody [UMB2] (ab124824).

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Inflammasomes

Inflammasomes are cytosolic protein complexes of the innate immune system that induce inflammatory responses. Inflammasome activation results in the release of pro-inflammatory cytokines IL-1β and IL-18 and cleavage of Gasdermin D (GSDMD), subsequently inducing pyroptotic cell death.

The NLRP3 inflammasome has been linked to the pathogenesis of several inflammatory disorders, including Alzheimer’s disease and diabetes, but its detailed role in IBD is still being investigated.

Figure 11. Immunoprecipitation - Anti-GSDMD antibody [EPR19828] (ab209845).

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TSLP

Thymic stromal lymphopoietin (TSLP) is a cytokine strongly expressed in lung and skin-derived epithelial cells. TSLP is involved in the initiation of allergic inflammatory responses. Furthermore, recent human and mouse studies have linked TSLP to the development and progression of allergic diseases, including asthma and allergic rhinitis.

Figure 12. Western blot - Anti-TSLP antibody [EPR25904-38] (ab309479).

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IL-25

IL-25 belongs to the IL-17 cytokine family, which are mostly produced by epithelial cells and innate immune cells and are critical in host defense responses and inflammatory diseases. Multiplex human and animal studies implicate IL-25 in the pathogenesis of some endotypes of asthma.

Figure 13. Western blot - Anti-IL-25 antibody [EPR5743(2)] (ab180594).

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IL-33

Interleukin-33 (IL-33) is a key cytokine that serves as an important marker of mucosal immune system activation. It plays a central role in initiating type-2 innate immune responses by stimulating immune cells involved in allergic inflammation, such as eosinophils, basophils, mast cells, and macrophages. IL-33 is released by epithelial and endothelial cells at mucosal surfaces in response to cellular damage or stress, acting as an alarmin. Its presence signals immune activation in tissues like the lungs, gut, and skin, contributing to the pathogenesis of asthma, allergic rhinitis, and other mucosal inflammatory disorders.

Figure 14. Flow Cytometry (Intracellular) - Anti-IL-33 antibody [EPR17831] (ab187060).

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Il-4 and Il-13

Interleukin-4 (IL-4) and Interleukin-13 (IL-13) are closely related cytokines that play central roles in regulating type-2 immune responses, particularly within mucosal tissues such as the respiratory and gastrointestinal tracts. These cytokines are produced predominantly by T helper 2 (Th2) cells and group 2 innate lymphoid cells (ILC2s) during the early stages of allergic sensitization. Their signaling influences a wide range of immune and non-immune cells, including lymphocytes, myeloid cells, and epithelial cells. IL-4 is essential for the class switching of B cells to produce immunoglobulin E (IgE), while both IL-4 and IL-13 promote the generation of allergen-specific memory B cells. In mucosal environments, these cytokines contribute to barrier dysfunction, mucus hypersecretion, and recruitment of effector cells, amplifying allergic inflammation. Their activity is strongly associated with diseases such as asthma, allergic rhinitis, and food allergies, making them key biomarkers and therapeutic targets in mucosal immunology.

Figure 15. Flow Cytometry (Intracellular) - Alexa Fluor® 647 Anti-IL-4 antibody [EPR22879-236] (ab303475).

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IL-5

Interleukin-5 (IL-5) is a key pro-inflammatory cytokine that plays a central role in regulating eosinophil biology, particularly within mucosal tissues such as the respiratory tract. It is primarily produced by Th2 cells and group 2 innate lymphoid cells (ILC2s) in response to allergen exposure. IL-5 drives the maturation, proliferation, activation, and prolonged survival of eosinophils in the bone marrow and peripheral tissues. It also facilitates their recruitment to mucosal sites, especially the airways, where they contribute to inflammation, tissue damage, and remodeling. This cytokine is critically involved in the pathogenesis of eosinophilic asthma, a subtype characterized by elevated eosinophil levels and persistent airway inflammation. Due to its pivotal role in disease progression, IL-5 has become a valuable therapeutic target, with monoclonal antibodies such as mepolizumab and reslizumab developed to neutralize its activity. IL-5’s presence and function make it a significant biomarker for mucosal immune activation and allergic airway diseases.

Figure 16. Immunohistochemistry (Formalin/PFA-fixed paraffin-embedded sections) - Anti-IL-5RA antibody [CAL40] (ab237716).

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IL-9

Interleukin-9 (IL-9) is a multifunctional cytokine produced by a variety of immune and epithelial cells, including Th9 cells, mast cells, and airway epithelial cells. It plays a significant role in mucosal immunity by contributing to allergic inflammation and promoting the activation and recruitment of inflammatory cells such as regulatory T cells (Tregs), Th17 cells, natural killer (NK) cells, and mast cells. IL-9 enhances mucus production, increases epithelial permeability, and supports mast cell proliferation and survival. Its expression is elevated in several mucosal inflammatory conditions, including asthma and allergic rhinitis, making it a relevant biomarker and potential therapeutic target.

Figure 17. Flow Cytometry (Intracellular) - Anti-IL-9 antibody [EPR23484-151] (ab227037).

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