Breaking Down Barriers: Epithelial Contributors to Monogenic IBD Pathogenesis

Abstract

Monogenic causes of inflammatory bowel diseases (IBD) are increasingly being discovered. To date, much attention has been placed in those resulting from inborn errors of immunity. Therapeutic efforts have been largely focused on offering personalized immune modulation or curative bone marrow transplant for patients with IBD and underlying immune disorders. To date, less emphasis has been placed on monogenic causes of IBD that pertain to impairment of the intestinal epithelial barrier. Here, we provide a comprehensive review of monogenic causes of IBD that result in impaired intestinal epithelial barrier that are categorized into 6 important functions: (1) epithelial cell organization, (2) epithelial cell intrinsic functions, (3) epithelial cell apoptosis and necroptosis, (4) complement activation, (5) epithelial cell signaling, and (6) control of RNA degradation products. We illustrate how impairment of any of these categories can result in IBD. This work reviews the current understanding of the genes involved in maintaining the intestinal barrier, the inheritance patterns that result in dysfunction, features of IBD resulting from these disorders, and pertinent translational work in this field.

Introduction

Inflammatory bowel diseases (IBD), including Crohn’s disease (CD), ulcerative colitis (UC), and inflammatory bowel disease-undefined (IBD-U), are a group of chronic inflammatory disorders that affect the intestine. Host genetics, gut microbiome, mucosal immune system, and environmental factors are all believed to contribute to pathogenesis. Monogenic causes of IBD are being increasingly discovered, with over 80 identified to date.^1-3 The majority of these represent underlying inborn errors of immunity.⁴ Much attention has been placed on these, with emphasis in offering personalized immune modulation or curative bone marrow transplantation. Comparatively, to date, less effort has been devoted to raising awareness on the latest advancements of nonimmune causes of IBD, specifically those that result in an impaired intestinal epithelial barrier. While barrier dysfunction is recognized as a meaningful contributor to the development and perpetuation of IBD, targeted manipulation of this aspect of IBD is currently lacking.

The intestinal barrier normally serves to protect the host from harmful molecules and microorganisms in the intestinal lumen, enables tolerance of commensal organisms, and optimizes absorption of nutrients and solutes. Several components contribute to its physical barrier defense. The mucus layer sits on top, forming a porous gel structure that prevents large particles and bacteria from contacting the underlying cells.⁵ The intestinal epithelium is lined with a single layer of polarized cells including enterocytes, goblet cells, Paneth cells, and microfold (M) cells. Each has a specific function, ranging from mucus production to secretion of antimicrobial peptides to transport of molecules, all with the goal of maintaining a physical barrier permitting controlled regulation of trafficking of solutes, and fluids.⁵ Intestinal epithelial cells (IECs) maintain a nearly impervious wall with intracellular space connected by tight junctions, adherens, and desmosomes.^5,6 Tight junctions are particularly important for regulating travel across the monolayer, and when disrupted, luminal contents including bacteria and other pathogens can translocate into the mucosa. The intestinal barrier is also a highly dynamic tissue, replenishing itself every 5-7 days,⁷ with tight regulation of cell restitution, apoptosis, and differentiation to assure maintenance of a healthy barrier.

To illustrate the myriad of epithelial cell functions associated with monogenic IBD, we categorize epithelial functions into the following categories: (1) epithelial cell organization, (2) epithelial cell intrinsic functions, (3) epithelial cell apoptosis and necroptosis, (4) complement activation, (5) epithelial cell signaling, and (6) control of RNA degradation products. These categorizations are somewhat arbitrary, and many of the monogenic causes of impaired barrier function can serve roles in overlapping categories. When these functions break down, pathologies result (Figure 1 and Table 1). This work reviews the current understanding of nonimmune monogenic causes of IBD that result in impaired intestinal epithelial barrier, inheritance patterns that result in dysfunction, features of IBD resulting from these disorders, and pertinent translational work in this field. Such knowledge is anticipated to foster innovative research efforts to better understand and manipulate the epithelial components driving IBD.

Figure 1.

Overview of important components of the epithelial barrier that serve to maintain intestinal homeostasis: The intestinal epithelium is a highly organized system, made of many tightly regulated components. Examples of breakdown within 5 of the 6 categories of intestinal epithelial function are depicted in the pink shaded area, resulting in pathology: (1) An example of disrupted epithelial cell organization is illustrated by dysregulation of tight junctions; (2) Disturbed epithelial intrinsic functions are depicted by aberrant nutrient and solute absorption; (3) Impaired regulation of epithelial cell apoptosis and necroptosis is depicted by increased apoptosis and disrupted cell polarity; (4) Unchecked complement activation is shown by increased membrane attack complex (MAC) formation, with excessive and uncontrolled complement attack; (5) Disruption of epithelial cell signaling is not illustrated, and (6) Impaired control of RNA degradation products, is portrayed by inappropriate accumulation of noncoding RNA in epithelial cells. Figure was created with BioRender.com.

Table 1.

Monogenetic causes of inflammatory bowel disease resulting from disruption of epithelial function.

Category of Epithelial Function	Gene	Gene Function	Mode of Inheritance of IBD Phenotype	Intestinal Phenotype	Histologic Features	Extra-Intestinal Phenotype
Epithelial Cell Organization	COL7A1	Anchors basement membrane to dermis	AR	Colitis, GERD, esophageal strictures, dysphagia, constipation, diarrhea, malnutrition	Variable severity of inflammation; increased lamina propria inflammatory cell density, prominent eosinophilia, superficial lamina propria karyorrhectic cellular debris and hemosiderin-laden macrophages within the lamina propria
	FERMT1	Cell adhesion and polarity	AR	UC Esophageal and intestinal strictures	Focal detachment of colonic epithelium from underlying tissue, extensive ulceration, altered cell polarity, increased mitotic activity, infiltration of plasma cells and eosinophils.	Skin blistering, skin atrophy, photosensitivity, pigmentation defects, increased risk of SCC
	ITGA6	Hemidesmosome anchoring important for adhesion to basal membrane	AR	IBD, pyloric atresia	Intraepithelial T cell infiltration with lifting of the surface epithelium, desquamated epithelial fragments, atrophic enterocytes	Defects in nails, teeth and urinary tract
	ITGB4	Hemidesmosome anchoring important for adhesion to basal membrane	AR	IBD, pyloric atresia, pyloric stenosis		Defects in nails, teeth and urinary tract. Airway involvement
Epithelial Cell Intrinsic Function	GUCY2C	Receptor for endogenous ligands and enterotoxins resulting in increased intracellular cGMP	AD GoF	Congenital sodium diarrhea; Subset develop Crohn’s disease with dysbiosis	Expansion of lamina propria with lymphoplasmacytic infiltrate, chronic inflammation of small and large intestine.	Meconium ileus (with AR LoF)
	SLC9A3	Na/H exchanger for Na reabsorption and controlling acid base balance	AR	Congenital sodium diarrhea; Crohn’s disease with dysbiosis	Partial villous atrophy, ileal ulcerations, inflammatory infiltrates with increased eosinophils	In utero polyhydramnios
	SLC26A3	Cl-/HCO3- exchange	AR	Congenital chloride diarrhea; concurrent IBD as early as infancy with dysbiosis	Mild colonic inflammation, apoptotic debris, granulomas may be present.	Polyhydramnios in utero, profound chloride losses and systemic metabolic alkalosis; male subfertility, inguinal hernias, chronic kidney disease, hyperuricemia
	STXBP2	Regulator of intracellular granule trafficking and docking at the plasma membrane	AR	Enteropathy and colitis	Shortened or loss of microvilli, subapical accumulation of vesicles and tubules, some exhibit intracellular microvillus inclusions	Impaired NK cell degranulation and cytotoxicity, FHL, MAS, hearing deficits, bleeding disorders, hypo-gammaglobulinemia, renal tubular disorders
	STXBP3	Regulator of intracellular vesicular trafficking	AR and AD	Infantile-onset diarrhea affecting small and large intestine	Expanded lamina propria with lymphoplasmacytic inflammation, neutrophilic crypt abscesses, villous atrophy, eosinophilia and apoptosis	Bilateral sensorineural hearing loss, immune dysregulation with recurrent infections, low NK and CD8 T cells, some with craniofacial defects, hypotonia, skin blisters and joint contractures
Epithelial Cell Apoptosis and Necroptosis	EPCAM	Cell adhesion, specific function unclear	AR	Congenital tufting enteropathy IBD-like inflammation of small and large intestine	Epithelial “tufts” of crowded enterocytes, chronic intestinal inflammation in small and large intestine
	TTC7A	Scaffolding protein important for PI4-phosphate synthesis important in preventing apoptosis and promoting proliferation	AR	Multiple intestinal atresias, VEOIBD	Prominent apoptosis, neutrophilic colitis with eosinophilia in the lamina propria, hypertrophy of the muscularis mucosa with spindle cell nodules	Combined immune deficiency
	IKBKG	Subunit of IKK complex essential for activation of NF-κΒ	X-linked	Inflammatory colitis	Increased apoptosis, neutrophilic infiltrates	Immunodeficiency, anhidrotic ectodermal dysplasia with skin, eye, nasal and hair features, osteopetrosis, vascular anomalies, autoinflammatory conditions, chronic arthritis, hemophagocytic syndrome, susceptibility to infection
Complement Activation	CD55	Complement regulatory protein; accelerates decay of convertases C3 and C5	AR	Protein losing enteropathy, malnutrition, vomiting, colitis Bowel wall thickening and edema, intestinal lymphangiectasia	Lymphangiectasia, IBD-like bowel inflammation with ulcers and lymphocytic infiltrates.	Recurrent respiratory infections, thrombocytosis, hypothyroidism, arthritis, finger clubbing
Epithelial Cell Signaling	ADAM17	Cleaves membrane bound TNF to soluble TNF. Formation of active EGFR ligands	AR	Chronic diarrhea with chronic inflammatory changes, esophageal atresia	Not well described: chronic inflammation or transient inflammation	Erythroderma, hair abnormalities, recurrent severe infections, sepsis, occasionally other features such as cardiac malformations, renal enlargement, and contractures
Control of RNA Degradation Products	SKIV2L	RNA surveillance and degradation of anomalous or redundant mRNA transcripts	Usually AR, rarely AD	Tricohepatoenteric syndrome: liver disease, early onset enteropathy, intestinal inflammation	Villous atrophy, variable inflammatory infiltrates	Brittle/wooly hair (trichorrhexis nodosa)
	TTC37	Mediates protein-protein interactions and assembly of multiprotein complexes. Important for surveillance and degradation of anomalous or redundant mRNA transcripts	Usually AR, rarely AD	Tricohepatoenteric syndrome: liver disease, early onset enteropathy, intestinal inflammation		Brittle/wooly hair (trichorrhexis nodosa)

Abbreviations: AR, autosomal recessive; AD, autosomal dominant; cGMP, cyclic guanosine monophosphate; EGFR, epidermal growth factor receptor; FHL, familial hemophagocytic lymphohistiocytosis; GERD, gastroesophageal reflux disease; GoF, gain of function; IBD, inflammatory bowel disease; IKK, inhibitor of nuclear factor-κΒ; LoF, loss of function; MAS, macrophage activating syndrome; NK, natural killer; PI4, phosphatidylinositol 4; SCC, squamous cell carcinoma; TNF, tumor necrosis factor; UC, ulcerative colitis; VEOIBD, very early onset inflammatory bowel disease.

Epithelial Cell Organization

The importance of appropriate anchorage of IECs to the underlying lamina propria are well-depicted in patients with epidermolysis bullosa (EB). Epidermolysis bullosa compromises a group of clinically heterogeneous disorders of skin fragility, which can also affect the gastrointestinal mucosa. There are 4 subtypes of EB, based on the level at which skin cleavage occurs: EB simplex, where damage occurs at the level of the epidermis; junctional EB, where damage occurs within the basal membrane between the epidermis and dermis; dystrophic EB, where damage occurs in the dermis; and Kindler syndrome, which can affect many levels.⁸ Inflammatory bowel disease has been described in association with all subtypes except for EB simplex. It is believed that disorganized epithelial organization drives the inception of barrier breakdown leading to development of IBD in patients with EB.

COL7A1

The gene COL7A1 encodes the alpha 1 chain of type 7 collagen. Disease-causing mutations in COL7A1 lead to dystrophic EB (DEB), which affects the dermis.⁹ Type 7 collagen is predominantly produced by keratinocytes and dermal fibroblasts and is the main component of the anchoring fibrils that link the epidermal basement membrane to the dermis. Type 7 collagen is expressed in basement membranes more broadly, including in the colonic epithelium^10-12 and in the stratified squamous epithelium in the upper third of the esophagus. In colonic tissue, type 7 collagen has been shown to link IECs to the lamina propria.¹¹ Over 700 distinct disease-causing mutations in COL7A1 have been reported, some with autosomal recessive inheritance and others with autosomal dominant inheritance.^8,13 Some genotypes result in reduced numbers of anchoring fibrils or disturbed assembly of anchoring fibrils and have mild or moderate phenotypes. Others result in total absence of anchoring fibrils and are associated with severe disease.¹⁴

Phenotypic features of DEB caused by COL7A1 mutations include epithelial fragility characterized by blistering followed by scarring, affecting both the skin and involved mucosal surfaces (eg, oral, esophageal, colonic, anal, urogenital, and ocular).^8,15 Gastrointestinal manifestations of DEB have been reported in 70% of patients and include painful oral lesions, gastroesophageal reflux, esophageal strictures, dysphagia, constipation, diarrhea, and malnutrition. Diarrhea can be the presenting symptom of IBD, with endoscopic findings ranging from colitis with mucosal friability to petechiae.¹⁶ Histologic features are variable, ranging from normal to severe inflammatory changes, including increased lamina propria inflammatory cell density, focal neutrophilic inflammation, and prominent eosinophilia. More rare histologic findings include prominent superficial lamina propria karyorrhectic cellular debris and hemosiderin-laden macrophages within the lamina propria.^16,17 Those exhibiting IBD tend to be associated with a recessive mode of inheritance.^18-20 As molecular genetic diagnoses are increasingly being made in EB and very early onset IBD (VEOIBD), whole exome sequencing is increasingly playing a diagnostic role.^3,9,21

Pathogenesis of IBD in patients with DEB secondary to COL7A1 mutations is attributed to lack of functional type 7 collagen resulting in aberrant anchorage of IECs to the lamina propria and thus disruption of the intestinal barrier. Factors contributing to the incomplete penetrance of IBD are not understood. Interestingly, a role for type 7 collagen in pathogenesis of nonmonogenic IBD has been described, with 1 study reporting higher prevalence of auto-antibodies to type 7 collagen in patients with CD and UC compared with healthy controls and those with other autoimmune diseases.¹¹

While precision medicine approaches are of burgeoning interest in both EB and IBD, given the current absence of targeted therapeutics, colitis associated with DEB is typically treated with conventional IBD therapies, with 1 study reporting response to aminosalicylic acids and prednisone¹⁶ and a case report describing response to antitumor necrosis factor (TNF) antibody therapy.²⁰ This may suggest that breach of the barrier function incites propagation of IBD that can be circumvented via immune modulation.

FERMT1

Kindlin-1, encoded by FERMT1 is a protein component of focal adhesions, which are the intracellular attachment points to the extracellular matrix. Kindlin-1 is predominantly expressed in the skin, periodontal tissues, and colon.^22,23 In the colon, Kindlin-1 is localized to the plasma membrane of IECs and with talins, directly binds the beta-subunit of integrins, contributing to integrin activation and trafficking²⁴ (Figure 2). It is important in cell adhesion and polarity.²⁵ Recessive mutations in FERMT1 lead to Kindler EB,⁸ a syndromic form of EB that can affect different levels of the skin.

Figure 2.

Defects in FERMT1 (kindlin-1) lead to impaired integrin-mediated adhesion of intestinal epithelial cells to the basement membrane. Left panel reflects normal kindlin-1 function in health, where intracellular kindlin-1 and talin bind the subunits of α-integrin and β-integrin to anchor the basolateral membrane of intestinal epithelial cells (IECs) to the basement membrane. Right panel illustrates consequences of impaired kindlin-1 with detachment of IECs and altered cell polarity, increasing microbial penetrance, contributing to IBD pathogenesis. Figure was created with BioRender.com.

Kindler syndrome encompasses numerous skin abnormalities, such as skin blistering, skin atrophy, photosensitivity, pigmentation defects, and increased risk of squamous cell carcinoma, while gastrointestinal abnormalities resemble UC.^24-27 Ulcerative colitis developing in patients as young as neonates have been described.²⁸ Other gastrointestinal manifestations include stricturing disease of the anus, esophagus, and ileum.^16,29 Macroscopically, the colitis is notable for marked friability of mucosa, erosions, and ulcers with pseudomembranous changes.²⁷ Histologically, focal detachment of colonic epithelium from underlying tissue is appreciated, along with extensive ulceration, altered cell polarity,²⁵ increased mitotic activity, and infiltration of plasma cells and eosinophils.^25,27 Kindlin-1 knock out (KO) mice exhibit an even more severe phenotype than humans, characterized by severe colitis and extensive epithelial detachment, ensuing perinatal lethality.²⁸

Pathogenesis of IBD in patients with mutations in FERMT1 is assumed to result from epithelial detachment compromising the intestinal epithelial barrier, with altered cell polarity enabling penetration of antigens with associated inflammation.²⁵ Advances in management of Kindler syndrome are needed. The UC phenotype in patients with FERMT1 mutations mimics the colonic distribution of this protein. Like COL7A1, inflammation can sometimes be addressed with conventional IBD therapeutics such as aminosalicylic acids¹⁶ or immune modulators,¹⁹ while others remain medically refractory requiring colectomy.²⁵

ITGA6 and ITGB4

The integrin subunits α6 and β4, encoded by ITGA6 and ITGB4 respectively, form a transmembrane component of hemidesmosomes. The α6β4 integrin is important in dermal-epidermal adhesion in the skin^30,31 and anchors the IECs to the stroma in the intestine.^32,33 These integrins are normally expressed in small and large intestine³³ and in numerous epithelial tissues including skin, mucous membranes, urinary tract,³⁰ as well as nonepithelial cell types such as endothelial cells, astrocytes, neurons, and Schwann cells.³¹ Damaging recessive mutations in ITGA6 and ITGB4 result in junctional EB by impairing adhesion within the basal membrane.^30,34,35 Both can result in skin blistering and pyloric atresia.^30,32,34,35 Patients with mutations in ITGB4 can also have defects in nails and teeth, as well as disease of the urinary and respiratory tracts.^30,34,36 Enteropathy with inflammatory changes resembling IBD has been described in patients with junctional EB due to recessive mutations in ITGB4^34,36 and ITGA6.³² In some with ITGB4 mutations, protein-losing enteropathy (PLE) includes an inflammatory component and can respond to immunomodulators.^34,36 Histologically, patients exhibit intraepithelial T cell infiltration with lifting of the surface epithelium and desquamated epithelial fragments interspersed with atrophic enterocytes.³⁶ Small numbers are described, but some show response to immune modulation,^34,36 while another passed away during infancy secondary to generalized infection.³⁵ A single patient with junctional EB secondary to mutations in ITGA6 was described as having medically refractory VEOIBD, in addition to congenital pyloric atresia, severe pyloric stenosis, and imperforate anus and developed necrotizing enteritis during infancy.³² Despite relatively mild skin blistering, she developed chronic severe terminal ileitis and extensive ulcerating disease by 3 years of age. She presented with generalized edema and hypoalbuminemia and required admission and parenteral nutrition but passed away shortly after, presumably from the severity of her medically refractory CD.³²

The specific mechanism contributing to IBD in these patients is not fully elucidated. It may involve epithelial detachment from deficient α6β4 integrin, with potential exacerbation from antigenic exposure secondary to mucosal fragility.³⁴ The magnitude of skin involvement is variable.^30,34,36 This puzzling dichotomy between severe enteropathy and relatively mild skin disorder in some patients may be related to the differential expression of at least β4 in the skin compared with the gastrointestinal tract.³⁷ In line with this theory, low expression of α6β4 has been found to be sufficient to maintain hemidesmosomal integrity in the skin, resulting in a mild skin phenotype.³⁰ Regardless, at least some patients’ intestinal disease can be circumvented by immune modulation, pointing to the immune contribution following a breach of epithelial barrier integrity.

Epithelial Cell Intrinsic Functions

Impaired epithelial cell intrinsic functions such as solute and water transport, acid-base balance, and vesicular trafficking have also been implicated in IBD pathogenesis. Compromised intrinsic functions of IEC is also a shared feature driving various forms of congenital diarrheas, characterized by profound diarrhea resulting in life-threatening electrolyte and acid-base imbalances, in absence of inflammation. In some scenarios, a mixed picture of congenital diarrhea and IBD can occur. Factors that determine whether dysfunction of epithelial intrinsic functions results in IBD or congenital diarrheas remain incompletely understood. Herein, focus is directed to those genetic abnormalities associated with intrinsic epithelial defects that are also associated with IBD.

GUCY2C

The gene GUCY2C encodes guanylate cyclase C (GC-C), the receptor for endogenous ligands (uroguanylin and guanylin) produced by epithelial cells, as well as enterotoxins produced by enterotoxigenic E. Coli.^38-40 It is expressed as a homodimer in the plasma membrane of enterocytes. Ligand binding to GC-C increases intracellular cyclic guanosine monophosphate (cGMP), which holds numerous consequences. First, it activates cGMP-dependent protein kinase 2 (PKGII) thereby activating the cystic fibrosis transmembrane receptor (CFTR), resulting in increased chloride secretion.³⁸ Secondly, increased cGMP enhances bicarbonate secretion in the duodenum. Third, cGMP activates cyclic nucleotide-gated channels, leading to calcium influx which promotes cell differentiation and migration.³⁸ Taken together, activation of GC-C results in chloride and bicarbonate secretion and calcium influx. Guanylate cyclase C is most highly expressed in the intestine of newborns and declines in the first few months of life.^41,42

Recessive loss of function mutations in GUCY2C results in neonatal meconium ileus.⁴³ In contrast, dominant gain of function mutations cause fully penetrant congenital sodium diarrhea.^38,44 Intriguingly, a subset of these patients also develop CD, sometimes involving small bowel obstruction, alongside esophagitis and esophageal hernias.³⁸ Unlike many monogenic causes of IBD that generally present very early in life, patients with gain of function mutations in GUCY2C tend to develop Crohn’s as older children or in adulthood.^1,38,45

The role of GC-C in intestinal homeostasis continues to be explored, and available literature is conflicting. Guanylate cyclase C normally restricts abnormal cell proliferation and can induce cell cycle arrest.^46,47 In a study, Gucy2c^-/- mice were protected from dextran sodium sulfate (DSS)-induced colitis, exhibiting increased proliferation and reduced apoptosis of IECs compared with wild types.⁴⁸ One can postulate that patients with GUCY2C gain of function mutations might manifest diminished proliferative capacity during intestinal injury, exacerbating the propagation of intestinal inflammation. In support of this concept, another study demonstrated that Gucy2c gain of function mice exhibit increased susceptibility to DSS-induced colitis along with dysbiosis, suggesting that disturbances in epithelial function, fluid, and electrolyte balance may perturb gut flora, predisposing to IBD.⁴⁹ This was characterized by enhanced STAT1 activation and downstream interferon-stimulating gene expression.⁴⁹ Humans with gain of function GUCY2C mutations similarly display prominent changes in intestinal microbiota, which may contribute to IBD susceptibility.⁵⁰ However, another murine study revealed discrepant findings whereby Gucy2c^-/- mice had increased intestinal permeability and bacterial translocation with reduced expression of claudin-2 and JAM-A at tight junctions.⁵¹ Other work supports that GC-C maintains a healthy intestinal barrier by reducing v-akt murine thymoma viral oncogene homolog (AKT1), increasing expression of junctional proteins thereby enhancing the intestinal barrier.⁵² While it is challenging to reconcile these differences, it appears clear that GC-C is tightly controlled to regulate epithelial cell homeostasis, which when dysregulated in specific contexts can contribute to IBD. Another possible contribution to IBD pathogenesis is that patients with gain of function GUCY2C mutations have downregulated metallothioneins in ileal mucosa.⁵³ These proteins are important in protecting against DNA damage and oxidative stress, reflecting another epithelial-driven pathway whereby patients may be predisposed to uncontrolled inflammation.

While manipulation of GUCY2C in patients with aberrant GUCY2C signaling and IBD has been considered, with either antagonists (BPIPP, SSP2518) or agonists (Linaclotide), further investigation is warranted.^45,52,54

SLC9A3

The sodium proton antiporter (NHE3), encoded by SLC9A3, is an apical Na/H exchanger key for sodium absorption and acid base homeostasis in the small and large intestine, as well as in renal proximal tubules.^55,56

Clostridioides difficile toxin B results in internalization of epithelial NHE3, followed by defective sodium and water reabsorption, with associated diarrhea.⁵⁷ Recessive mutations in SLC9A3 results in congenital sodium diarrhea. In utero, polyhydramnios is often seen, followed by watery secretory diarrhea and abdominal distension soon after birth, suggesting that secretory diarrhea starts prenatally.⁵⁸ Janecke et al describe 2 of 9 patients with congenital sodium diarrhea with recessive mutations in SLC9A3 who developed CD at ages 4 and 16 years.⁵⁸ The first patient required ileo-cecal resection for recurrent small intestinal obstructions, and the other was managed with budesonide. Histologically, they had partial villous atrophy, ileal ulcerations, and inflammatory infiltrates with increased eosinophils.⁵⁸ Management of IBD in this population is limited to the 2 patients described. Interestingly, genome wide association studies (GWAS) have also found an association between SLC9A3 and UC.⁵⁹

Similar to GC-C, Slc9a3^-/- mice exhibit altered gut microbiota.⁶⁰ These mice have increased luminal sodium, an alkaline pH of stools, and a significant increase in both total luminal and mucosa-associated bacteria, harboring expansion of Bacteroidetes and contraction of Firmicutes.⁶⁰ The Slc9a3^-/- mice develop colitis spontaneously and have enhanced bacterial adhesion and translocation in their distal colon.^61,62 Moreover, colitis was ameliorated with broad spectrum antibiotics, highlighting the importance of disturbed microbiome resulting from impaired epithelial sodium absorption.^61,62 Moreover, Slc9a3^-/-Il10^-/- double KO mice are more susceptible to DSS-induced colitis than Il10^-/- alone⁶³ and exhibit notably more apoptotic cells, further confirming the essential role of NHE3 in maintaining a healthy intestinal barrier. All in all, these data support the concept that altered ion transport can regulate the gut microbiome and contribute to IBD pathogenesis.⁶⁰

SLC26A3

A transmembrane apical epithelial Cl-HCO3^- exchanger, encoded by SLC26A3, is expressed in the colon at much higher magnitudes than it is in the ileum.^64,65 It is also expressed in the duodenum⁶⁶ and some extraintestinal tissues including the male reproductive tract.⁶⁷

Congenital chloride diarrhea (CLD) results from autosomal recessive mutations in SLC26A3, resulting in defective intestinal absorption of chloride and secretion of bicarbonate in the ileum and colon, which is coupled to NHE3, resulting also in defective Na/H exchange.^68-70 Watery diarrhea starts in utero, so pregnancies are characterized by polyhydramnios and dilated intestinal loops, and newborns present with large distended abdomens.⁶⁹ Once born, patients experience significant watery diarrhea with profound chloride losses.⁶⁸ If untreated, hypochloremia, hyponatremia, and dehydration activates the renin-angiotensin system resulting in metabolic alkalosis^68,71,72 that can be life-threatening in the first months of life.⁷³ Diarrhea is managed supportively.⁷² The gene SLC26A3 has also been identified via GWAS as a susceptibility gene for IBD.⁷⁴

Several groups described IBD occurring concurrently among patients with CLD,^75-78 some commencing as early as infancy.⁷⁹ A large European multicenter study including 72 patients with CLD by Norsa et al identified that 17% (12 patients) developed concurrent IBD: 9 with CD, 2 with UC, and 1 with IBD-U.⁷⁸ In this cohort, age of onset of IBD was variable, ranging between 8.5-23.5 years old.⁷⁸ A third of patients with concurrent IBD required surgical interventions, one of whom developed stage 2 colon cancer.⁷⁸ Medical management included anti-TNF or anti-integrins (5 of 12), immune modulators (5 of 12), and aminosalicylates (1 of 12), while the patient with IBD-U was off treatment after 2.5 years of full remission on azathioprine.⁷⁸ An intriguing clinical feature of patients exhibiting combined CLD-IBD is significantly lower height compared with those with CLD alone.⁷⁸ Histologically, some patients exhibit granulomas, and others had apoptotic debris with mild colonic inflammation.⁷⁹ In addition to risk of IBD, additional manifestations of CLD include male subfertility, inguinal hernias, chronic kidney disease, and hyperuricemia.⁷²

The mechanism of IBD in CLD patients is unclear. Tumor necrosis factor may act reciprocally with SLC26A3,⁸⁰ yet evidence points to a role of SLC26A3 in its ability to maintain intestinal epithelial homeostasis distinct from immunoregulatory functions. Mice with SLC26A3 deficiency do not have a firm mucus layer and exhibit impaired barrier function with increased susceptibility to DSS-induced colitis.⁸¹ The Slc26a3^-/- mice exhibit increased intestinal paracellular permeability, microbial dysbiosis, and decreased tight and adherens junction protein expression.⁸² In humans, patients with CLD have dysbiosis, but no unique microbial features have been identified among patients with concurrent IBD-CLD.⁸³ While further mechanistic understanding is needed, mutations in SLC26A3 further support a critical role for ion transport in regulating microbiome communities and intestinal barrier function.

STXBP3

Syntaxin-binding protein 3 (STXBP3) regulates intracellular vesicular trafficking.^84-87 Syntaxin-binding protein 3 is ubiquitously expressed, including epithelial, stromal, and immune cells of adult colons.⁸⁷ Knock down of STXBP3 in Caco2 cells results in altered cell polarization and growth.⁸⁷

Patients with damaging mutations inherited in either a recessive or autosomal dominant fashion exhibit medically refractory infantile-onset IBD, and most have bilateral sensorineural hearing loss. Some also exhibit immune dysregulation with recurrent infections and low natural killer (NK) and CD8 T cell numbers.⁸⁷ Patients with recessively inherited disease exhibit additional features, including craniofacial defects, hypotonia, blistering skin abnormalities, and joint contractures.⁸⁷ Intestinal inflammation affects the small and large intestine characterized by an expanded lamina propria with lymphoplasmacytic inflammation, neutrophilic crypt abscesses, villous atrophy, eosinophilia, and apoptosis. Of the 10 described patients, 4 underwent colectomy, most with resolution of symptoms, and 1 underwent bone marrow transplant with resolution of symptoms, illustrating features of both immune and epithelial pathology. While an immune component may be at play, STXBP3 also holds important distinct roles in maintaining cell polarity, growth and vesicular trafficking, which may all serve important roles in maintaining intestinal homeostasis.

STXBP2

Additionally, syntaxin-binding protein 2 (STXBP2) is important in regulating intracellular vesicular trafficking and docking at the plasma membrane. This protein is normally expressed in epithelial tissues, such as the kidney and intestine, and localizes to the apical surface of the plasma membranes.^88,89 Damaging mutations in STXBP2 result in familial hemophagocytic lymphohistiocytosis (fHLH), with both recessive and dominant inheritance patterns described.^90-92 Other notable clinical features include hearing deficits, bleeding disorders, hypogammaglobulinemia, and renal tubular disorders; about 38% of patients develop IBD, characterized by severe chronic enteropathy and colitis, often within months of life.^92,93 Patients also exhibit impaired NK cell degranulation and cytotoxicity,⁹⁰ as well as defective granule mobilization in neutrophils resulting in inadequate bacterial killing.⁹⁴ Those who develop IBD inherit disease in a recessive fashion with incomplete penetrance.^18,91-93

Microscopically, IBD is characterized by short or loss of microvilli of enterocytes, subapical accumulation of vesicles, and tubules, and some exhibit intracellular microvillus inclusions.¹⁸ Many patients continue to exhibit enteropathy and renal tubular disorders despite successful bone marrow transplant, underscoring the nonimmune contribution of STXBP2 in membrane trafficking and IBD pathogenesis.^91,93 While this remains incompletely understood, STXBP2 is important in trafficking brush border components, including NHE3 (described previously), such that dysfunctional STXBP2 results in granule mislocalization.¹⁸ Definitive therapy for the persistent IBD among these patients is lacking.

Epithelial Cell Apoptosis and Necroptosis

The intestinal epithelium is an exceedingly dynamic tissue, replenishing itself every 5 to 7 days, in the midst of a constantly threatening environment.⁷ Interruption in the delicate balance of cell turnover and control of cell polarity can significantly disrupt the intestinal epithelial barrier and contribute to IBD pathogenesis. Examples of monogenic disorders that result in aberrant epithelial cell apoptosis and necroptosis and thereby disruption of the intestinal barrier resulting in IBD are described.

EPCAM

Epithelial cell adhesion molecule (EPCAM) is a transmembrane protein expressed in the basolateral cell membrane of epithelial tissues.^95-97 In the gastrointestinal tract, it is highly expressed in the small intestine and even more in the colon.⁹⁵ This cell-cell adhesion molecule is important in epithelial tissue development and in carcinogenesis, but its specific molecular function remains incompletely understood.^95,98 Increased EPCAM expression correlates with cell proliferation and is inversely related to cell differentiation.⁹⁵ It regulates the composition and function of tight junctions by regulating intracellular localization and degradation of claudins.⁹⁹ It also holds critical functions in postnatal development of the intestine and some extra-intestinal tissues.⁹⁸

Monoallelic deletions of EPCAM can result in Lynch syndrome, a hereditary nonpolyposis colon cancer syndrome.⁹⁷ Damaging recessive mutations in EPCAM, however, result in congenital tufting enteropathy (CTE).^100,101 Patients exhibit profound watery diarrhea and failure to thrive with dependence on parenteral nutrition.^100,102 Congenital tufting enteropathy is histologically characterized in the small intestine by villous atrophy, branching crypts, and pathognomonic epithelial “tufts” of crowded enterocytes at the villus tips, with apical rounding of the plasma membrane resulting in a tear drop shape,¹⁰² but tufts can also develop in the colon.¹⁰⁰ Congenital tufting enteropathy was first described in absence of intestinal inflammation.^101,102 More recently, CTE resulting from EPCAM mutations has revealed chronic intestinal inflammation mutations in some patients.^100,103,104 This inflammation is found in both small and large intestine and tends to be refractory to immune suppression but interestingly can self-resolve.¹⁰³ The cause of intestinal inflammation has not been elucidated. Its role in epithelial cell development and polarity, cell proliferation, and maintaining epithelial barrier raise several mechanisms by which dysfunction may contribute to IBD pathogenesis. Additionally, recent work proposes that intestinal inflammation may be related to downregulation of the polymeric immunoglobulin receptor in intestinal epithelial cells that normally transport IgA and IgG from the lamina propria to the intestinal lumen to help clear pathogens.¹⁰⁵ Further work is needed to better understand this phenomenon and the specific role of EPCAM in maintaining intestinal homeostasis.

TTC7A

Tetratricopeptide repeat domain 7A (TTC7A) is a scaffolding protein with 9 tetratricopeptide repeat domains, representing a structural motif that mediates multiprotein-protein interactions.¹⁰⁶ The TTC7A protein is normally expressed in intestinal cells, serving to localize phosphatidylinositol 4-Kinase 3 alpha (PI4KIII-α) to the plasma membrane in order to facilitate synthesis of PI4-phosphate.¹⁰⁷ The PI4-phosphate is an upstream precursor of the AKT signaling pathway, which plays a critical role in preventing apoptosis and promoting proliferation and has been implicated in other monogenic forms of IBD (eg, PIK3R1, PI4KA).^108-110 Additionally, TTC7A deficiency results in increased susceptibility to apoptosis¹⁰⁷ and aberrant intestinal epithelial cell polarity.¹¹¹

Deficiency of TTC7A is inherited in an autosomal recessive fashion^107,112 and can result in an array of phenotypes, including multiple intestinal atresias (MIA),¹¹² VEOIBD, and a combined immune deficiency (CID).^{107,111,113,114} All patients reported to date manifest some degree of intestinal disease (either MIA, VEOIBD or both, with or without CID). Very early onset IBD in this population is characterized by copious secretory bloody diarrhea shortly after birth, usually requiring parenteral nutrition.^107,113,114 Histologically, in keeping with the understanding of the role of TTC7A, patients have prominent apoptosis, along with a neutrophilic colitis with eosinophilia in the lamina propria, architectural distortion, crypt degeneration, and hypertrophy of the muscularis mucosa with spindle cell nodules.¹¹⁵

Deficiency of TTC7A is often fatal in infancy,¹¹⁶ with the intestinal disease being a major life-threatening feature^{107,111,114,117}: VEOIBD is resistant to immune suppression^114,116 and the MIA recur following surgical resection.¹¹⁸ Bone marow transplantation (BMT) corrects the CID, but it does not resolve the intestinal disease,^113,114,116 underlining the importance of the nonimmune component of TTC7A deficiency in IBD.

Studies using intestinal organoids from TTC7A-deficient patients have advanced our understanding of this disease and shed light on potential therapeutic avenues. Patient intestinal organoids exhibit markedly disrupted apico-basal polarity, poor epithelial cell integrity, reduced proliferation, and absence of luminal space,¹¹¹ illustrating possible mechanisms whereby TTC7A normally maintains intestinal homeostasis. Many of these features were reversible following administration of a RhoA kinase inhibitor via mechanisms that remain to be deciphered.¹¹¹ Moreover, Jardine et al recently identified a variety of FDA-approved drugs that partially rescue the abnormal phenotype in TTC7A deficient cells.¹¹⁹ The most promising agent, leflunomide, an immune suppressant that inhibits de novo pyrimidine nucleotide biosynthesis, partially reverses the phenotype in patient-derived colonoids and in a zebrafish model.¹¹⁹ The exact mechanism of action remains to be clarified, but leflunomide rescues the defective AKT signaling.¹¹⁹ This work opens an encouraging avenue for refurbishing this agent to manage the life-threatening intestinal disease of patients with TTC7A deficiency.

IKBKG

Nuclear factor kappa-light chain-enhancer of activated B cells (NF-κΒ) is important for variety of functions including immune responses as well as cellular apoptosis, proliferation, differentiation and development.¹²⁰ While it is expressed in all cell types,¹²¹ it is usually retained in the cytoplasm bound to inhibitors maintaining it in an inactive form.^122,123 The IKBKG gene, known also as NEMO, encodes the regulatory gamma subunit of the IκΒ Kinase (IKK) complex, essential for the activation of NF-κΒ.¹²⁴ Once active, NF-κΒ can induce a variety of anti-apoptotic genes and pro-inflammatory genes.¹²⁵ Here, discussion of NF-κΒ is restricted to its role in epithelial cell apoptosis rather than its immunoregulatory functions, which are beyond the scope of this review.

Mice with specific inhibition of NF-κΒ in IECs develop severe spontaneous colitis, characterized by increased apoptosis and compromised epithelial barrier with translocation of bacteria.¹²⁶ In this model, NEMO deficiency sensitizes epithelial cells to TNF-induced apoptosis, such that colitis does not develop when these mice lack TNFR1, identifying TNF as a critical regulator of this pathway.¹²⁶ NEMO deficiency also results in significant disease in humans. When this X-linked gene is inherited in females in a heterozygous fashion, incontinentia pigmenti results, manifesting as specific skin lesions and other features involving the eyes and nervous system.^127,128 Complete loss of function mutations of IKBKG are lethal in males.¹²⁹ Males with hemizygous hypomorphic mutations exhibit immunodeficiency and anhidrotic ectodermal dysplasia with additional features including decreased skin pigmentation, sparse or absent hair, abnormal dentition, hypoplastic nasal alae,^127,130 inflammatory conditions, failure to thrive, arthritis, hemophagocytic syndrome, and susceptibility to infections.¹²⁹ Colitis is the most common inflammatory condition, affecting roughly 21% of patients.¹²⁹ Histologically, colitis is characterized by neutrophilic infiltrates.¹³¹ In line with the murine model, patients with colitis from IKBK deficiency respond to anti-TNF agents.^127,132,133 Notably, correction of immune defects with hematopoietic transplantation does not always rectify the underlying colitis,^130,131,134 pointing to NEMO’s critical role in maintaining the intestinal barrier, distinct from its immunoregulatory functions.

NEMO exerts both NF-κΒ-dependent and independent functions to maintain intestinal homeostasis by inhibiting receptor interacting protein kinase 1 (RIPK1)-dependent death of IECs.¹²⁵ Specifically, in the small intestine, NEMO-mediated NF-κΒ activation inhibits IEC death and loss of Paneth cells.¹²⁵ By contrast, in the large intestine, NEMO prevents IEC death and colonic inflammation in a NF-κΒ-independent fashion.¹²⁵ This work has led to enthusiasm in evaluating RIPK-1 inhibitors as a therapeutic alternative for managing colitis. Murine studies looking at RIPK-1 inhibitors in colitis were promising.^135,136 Efficacy of RIPK-1 inhibitors in patients with NEMO deficiency have not yet been explored.

Complement Activation

The complement system is a large group of plasma and cell surface proteins important for tissue homeostasis and bacterial clearance. Lacking complement proteins can lead to defective bacterial clearance. Complement function in the intestine is not fully understood, but there is a role in maintenance of the epithelial barrier.¹³⁷ Complement activation can occur via one of 3 pathways: classical pathway (CP), lectin pathway (LP), and/or alternative pathway (AP),¹³⁷ each converging at the C3 convertase step. The C3 convertases cleave C3 to C3a and C3b, allowing C3b to interact with other components to form C5 convertases. Further cascading occurs, whereby C5 convertases cleave C5 into C5a and C5b; C5b can interact with C6, C7, C8, and C9 to form the membrane attack complex (MAC). This culminates in MAC-driven opsonization of pathogens, cell lysis, and augmented inflammatory responses^6,137 (Figure 3). Regardless of the pathway, once activated, the complement system is unbiased against host and pathogenic cells, so host cells require anticomplement defenses to prevent self-damage.^137-139

Figure 3.

The complement system, regulated by CD55, is critical for maintaining tissue homeostasis. Complement activation can occur via three pathways; classical (CP), lectin (LP) and/or alternative (AP) pathway, each converging at the C3 convertase step. C3 convertases cleave C3 to C3a and C3b, allowing C3b to interact with other components to form C5 convertases. C5 convertases then cleave C5 into C5a and C5b (left). C5b can interact with C6, C7, C8, and C9 to form the membrane attack complex (MAC) (right). This results in opsonization of pathogens and cell lysis. CD55 is a complement checkpoint that inhibits formation of C3 and C5 convertases, thereby preventing formation of the MAC. Absence of functional CD55, as seen in patients with CD55 deficiency, exhibit unbiased complement attack. Eculizumab is a monoclonal antibody against C5, working downstream of CD55 which can ameliorate the effects of CD55 deficiency. Figure was created with BioRender.com.

Presence of complement components in the intestinal lumen is supported by identification of their byproducts in the mucosa.¹³⁷ Membrane attack complex, C3, C3b, and C4 have been found in the intestinal epithelium of patients with IBD (both CD and UC), although reports of which complement proteins are present vary based on study.^140-142 Epithelial cells have been suggested by many as a source of complement proteins, with C4 mRNA having been identified in mucosa of CD and healthy controls.¹³⁷

CD55

Decay-accelerating factor (DAF), also known as CD55, is a cell surface complement regulatory glycoprotein that prevents the activation of complement by inhibiting formation of convertases C3 and C5, preventing formation of the MAC.^143,144 Lacking CD55 function leads to accelerated and unchecked complement activation, causing cell membrane disruption^139,144,145 (Figure 3). CD55 is highly expressed on most epithelial cells, including small intestine and colonic tissue.¹⁴⁶ Epithelial CD55 expression is upregulated in chronic gastritis, celiac disease, and IBD, reflecting differential expression in inflamed states.¹⁴⁶

CD55 deficiency can lead to hyperactivation of complement, angiopathic thrombosis, and PLE (CHAPLE) syndrome.¹³⁹ CHAPLE syndrome, caused by recessive loss of function mutations in CD55, leads to profound PLE thought to result from increased intestinal permeability from lymphangiectasia in the lining of the small intestine, intestinal inflammation, and possibly thromboses.¹³⁹ However, patients have variable presentation, and not all exhibit lymphangiectasia. Clinical features include early onset diarrhea, vomiting, abdominal pain, malnutrition, hypoalbuminemia, edema, hypogammaglobulinemia, and infections. Of 23 patients reported in studies by Ozen et al, 7 had intestinal lymphangiectasia, and 5 had intestinal ulcers.^139,147 Patients with VEOIBD and CD55 deficiency can manifest PLE, dilated small intestine, jejunal ulcers, and luminal narrowing in absence of thromboembolic events and lymphangiectasia.^139,145

CHAPLE syndrome illustrates the importance of CD55 in maintaining the integrity of the epithelial barrier. In addition to loss of CD55 expression, patients have increased C3 fragments on CD4⁺ T cells and increased C5b on duodenal biopsies compared with healthy controls.¹³⁹ Eculizumab is a monoclonal antibody that binds to the terminal complement component C5, thereby inhibiting cleavage to C5a and C5b, thus preventing MAC-mediated damage^143,148 (Figure 3). CHAPLE patients with CD55 deficiency treated with eculizumab had improvement of GI symptoms, sustained increase in serum albumin, restoration of innate complement system defects, and resolution of intestinal pathology in 4 weeks.^147-149 While the exact mechanism is unclear, this improvement supports the hypothesis that PLE is driven by MAC-mediated intestinal damage, highlighting the importance of complement regulation in maintaining a healthy intestinal barrier and preventing intestinal inflammation.

Epithelial Cell Signaling

To respond appropriately to both commensal and enteric pathogens in the intestine, IECs can communicate with mucosal immune cells and influence immune responses to promote intestinal homeostasis. The importance of cell signaling in maintaining epithelial barrier function and mucosal homeostasis has been illustrated in patients with ADAM17 deficiency.

ADAM17

A disintegrin and metalloprotease 17 (ADAM17), also known as TNF converting enzyme (TACE), is a shedding-protease that cleaves many membrane-bound proteins, including TNF, transforming growth factor-α (TGF-α), and epidermal growth factor receptor (EGFR). It is ubiquitously expressed, including in skin and intestine.^150-152 Patients with recessive mutations in ADAM17 present with neonatal inflammatory skin and bowel disease type 1 (NISBD1) which encompasses a range of phenotypes of varying severity, many being incompatible with life.^150,153 These features are mirrored in mice.^154-156 Patients usually exhibit erythroderma, hair abnormalities (alopecia, short, wiry or disorganized hair), chronic diarrhea with chronic inflammatory changes, recurrent severe infections and sepsis, and occasionally other features such as cardiac malformations, renal enlargement, contractures, and esophageal atresia.^150,153,157 Details pertaining to the intestinal inflammation in NISBD1 are poorly described: some report chronic inflammation in keeping with Crohn’s,¹⁵⁷ while others identified transient inflammation that normalizes over time.¹⁵⁰ In NISBD1, ADAM17 is nonfunctional such that it can no longer cleave membrane-bound proteins. Patient samples from small intestine and peripheral blood mononuclear cells (PBMCs) showed lacking or absent ADAM17 expression.¹⁵⁰ A patient with NISBID1 was described as having nonresponse to either blockade of TNF or interleukin (IL)-12/23 but demonstrated marked improvement in cutaneous manifestations when these agents were combined.¹⁵⁷ Their intestinal disease was resistant to combined blockade of TNF or IL-12/23 and improved with budesonide.¹⁵⁷

The phenotype associated with loss of ADAM17 function is thought to be related to the inability to cleave membrane-bound proteins, including TNF and EGFR. ADAM17 or TACE cleaves membrane-bound TNF (mTNF) to its soluble form. Both mTNF and soluble TNF act through 2 different surface receptors, TNFR1 and TNFR2. Both pathways lead to NF-κΒ activation with differing results: TNFR1 promotes either cell survival or cell death, inflammation, and tissue degradation, whereas TNFR2 results exclusively in cell survival.^150,158,159 It is not well understood what regulates differential TNFR1 vs TNFR2 mediated signaling.

In addition to modulating TNF signaling, ADAM17 is necessary for the formation of active EGFR ligands, whose function is critical for the development of epithelial tissue. The EGFR signaling is reduced in ADAM17 deficiency. This is demonstrated in Adam17^-/- mice, where a striking phenotype is observed affecting the gut, lung, eyes, and hair.¹⁵⁵ Mice hypomorphic for ADAM17, exhibit more severe DSS-induced colitis, thought to result from impaired EGFR activation in epithelial cells. Moreover, in humans, Shimura et al identified that epithelial cell–derived ADAM17 (but not myeloid-derived ADAM17) protects against colitis via EGFR activation whose signaling results in epithelial cell proliferation and goblet cell differentiation, key for resolving inflammatory damage and maintaining the intestinal epithelial barrier.¹⁵⁴ Interestingly, a single patient has been described with recessive mutation in EGFR with similar phenotypic features including intestinal and skin manifestations, further supporting the central role of EGFR signaling in maintaining intestinal homeostasis.¹⁶⁰ Collectively, patients with ADAM17 deficiency and EGFR mutations illustrate the important role of the ADAM17-EGFR axis in controlling cell restitution and differentiation, fundamentally required to maintain the integrity of the intestinal epithelial barrier.

Control of RNA Degradation Products

Adequate cellular housekeeping needs to be preserved to maintain cellular integrity. Processes controlling the metabolism of intracellular nucleic acids, such as the degradation of noncoding RNA molecules, are regulated by the RNA exosome and the human superkiller (SKI) complex.^161,162 Monogenic diseases affecting cofactors of the SKI complex result in IBD.

SKIV2L and TTC37

Trichohepatoenteric syndrome (THES) is a rare disorder caused by mutations in either SKIV2L, which encodes the protein SKI2W (40% of cases) or TTC37, which encodes the protein thespin (60% of cases).¹⁶³ It is usually inherited in an autosomal recessive fashion, though a minority have autosomal dominant disease.¹⁶⁴ Trichohepatoenteric syndrome affects multiple organs and, as the name implies, causes brittle/wooly hair (trichorrhexis nodosa), liver disease, and early onset enteropathy, characterized by severe diarrhea with IBD-like features including perianal disease and oral ulcers.^163,165-167 Patients often exhibit additional features including failure to thrive, facial dysmorphism, immunodeficiency, skin hyperpigmentation, abnormal platelets, and congenital heart disease and tend to have early mortality.^163,166,167 Intestinal histopathologic features are characterized by villous atrophy and variable inflammatory infiltrates.^168,169 Atypical THES secondary to TTC37 mutations have also been described with enteropathy in absence of facial and hair abnormalities.¹⁷⁰

Proteins SKI2W and thespin are expressed in many cell types including immune cells and the epithelium and are components of the RNA exosome complex involved in degradation of noncoding RNA molecules.^166,171 SKI2W is an RNA helicase critical for all aspects of RNA metabolism, and thespin is a tetratricopeptide repeat structural motif, forming scaffolds to mediate protein-protein interaction and assembly of multiprotein complexes.¹⁶³ While the exact function of these proteins are yet to be concretely identified, studies suggest they encode subunits of the human SKI complex.¹⁶³ The SKI complex is important for processing nuclear RNA precursors and degradation of aberrant cytoplasmic and nuclear RNA and mRNA. SKI2W is also responsible for turning off the RIG-I-like receptor (RLR)-mediated antiviral response. Cells with depleted SKI2W have RNA metabolism defects, in addition to increased type 1 interferon production.¹⁷¹ This diverges from thespin function, where interferon signaling was not found to be implicated.¹⁷¹ Trichohepatoenteric syndrome pathogenesis is therefore believed to be driven by the shared functions of TTC37 and SKIV2L pertaining to loss of RNA function, given nearly identical clinical phenotypes.^138,171 Lacking these functions results in accumulation of noncoding RNA molecules and dysregulation of gene expression in the intestinal epithelium.¹⁶³

Management for THES is largely supportive, and patients frequently require parenteral nutrition to support growth and compensate for intestinal losses. Patients with hypogammaglobulinemia can benefit from immunoglobulin treatment. Liver disease independent of parenteral nutrition is a feature of THES.^163,172 Small studies reflect poor sustained response of intestinal inflammation with conventional treatments for IBD, including mesalamine, immunomodulators, biologics, and steroids.¹⁶⁵ Hematopoietic transplant has been performed on a small number of patients with THES. While this may improve the immune dysregulation, it does not correct the intestinal disease, and there is a high rate of death from infection.¹⁷² Intestinal transplantation was pursued in a patient with THES, given the epithelial-based mechanism, but they succumbed to severe graft vs host disease and multi-organ failure.¹⁷³

Practical Considerations

At present, our ability to understand the drivers of an individual patient’s IBD and select the best therapy accordingly is quite limited. An underlying monogenic cause of IBD is more prevalent among patients diagnosed at young ages compared with older-onset IBD.^21,174 Identification of a monogenic cause can help guide clinical decision-making, enabling precision medicine approaches. However, it remains that the vast majority of IBD patients, regardless of age of diagnosis, will not have a clear monogenic cause identified. Herein we provide an approach to when one should suspect disease that is primarily driven by a monogenic epithelial disorder and considerations for their evaluation as well as histologic features that may be identified in this group.

Underlying epithelial defects should be considered in patients with neonatal- or infantile-onset of diarrhea, especially when diarrhea is secretory and/or associated with hypovolemia and severe electrolyte disturbances. In these cases, diarrhea is often watery (as opposed to bloody), which can be a helpful distinguishing feature from more classic colitis. It is common that these patients exhibit dependence on total parenteral nutrition (TPN), as intestinal utilization often exacerbates the diarrhea. Of note, these clinical features can also be seen in immune-mediated small bowel enteropathies, such as those due to CTLA4 and FOXP3 mutations, and are not specific to epithelial defects. Other clues to an underlying monogenic epithelial defect tend to be comorbidities associated with the primary genetic defect. These include intestinal atresias, antenatal polyhydramnios, and abnormalities of the skin (as seen in EB, anhidrotic ectodermal dysplasia, and others). Such features should prompt consideration of evaluation for malabsorption (stool electrolytes, reducing substances, elastase, alpha-1 antitrypsin, fecal fat) and endoscopy and colonoscopy with standard histology in addition to consideration of electron microscopy. Next-generation sequencing should be performed, if available, as it will enable examination of known monogenic IBD genes and novel gene candidates. There is no clear guidance on when to consider complement studies in patients with suspected primary epithelial defects; at this time, disorders of the complement system likely reflect a minority of primary epithelial disorders seen clinically, and routine testing of the complement system is lower yield than next-generation sequencing, which has broad scope. Thereby, complement testing may be deferred unless there are specific features concerning for a complement disorder (eg, CD55 deficiency).

Histologically, when compared with older-onset IBD, patients with VEOIBD more commonly exhibit increased crypt apoptosis, small intestinal villous blunting, and prominent eosinophilic infiltration, yet none of these characteristics are unique to monogenic disease.¹⁷⁵ Histologic features specific to epithelial disorders have not been systematically evaluated to date, but there are emerging patterns described among some patients with epithelial defects including marked architectural distortions in patients with TTC7A deficiency,^107,115 karyorrhectic cellular debris within the lamina propria seen in some patients with DEB,¹⁷ and others (Table 1). Such patterns should also prompt suspicion for an epithelial-driven disease.

Concluding Remarks

The intestinal epithelial lining is an active structure that tightly regulates a variety of critical functions to preserve barrier integrity. These functions include (1) epithelial cell organization, (2) epithelial cell intrinsic functions, (3) epithelial cell apoptosis and necroptosis, (4) complement activation, (5) epithelial cell signaling, and (6) control of RNA degradation products. When any of these functions go awry, IBD can result.

This review focused on monogenic forms of IBD that relate primarily to impaired epithelial barrier. It is challenging to conceptualize epithelial barrier defects in isolation, since the ensuing increased intestinal permeability fosters bacterial translocation and is thereby closely intertwined with immune functions. Indeed, some forms of monogenic IBD resulting in impaired intestinal barrier respond to immune modulation, yet many remain refractory to conventional IBD approaches. The repertoire of therapeutic options for such patients is lacking, and novel approaches dedicated to optimizing the intestinal barrier are required.

There is a large unmet need to improve outcomes and successful therapeutics among patients with IBD, including those with monogenic epithelial-driven disorders, and the large proportion of patients without an identifiable single-gene defect. Several tools are currently available to rigorously evaluate barrier defects, with the goal that positive findings may eventually guide therapeutic approaches to modulate barrier breakdown. Harnessing intestinal organoids to recapitulate disease and single cell transcriptomic analyses are some examples that hold promise in advancing this field. Manipulation of intestinal organoids enables interrogation of the epithelial compartment of the intestine, in absence of immune and microbial contributions. This is nicely illustrated in the case of TTC7A deficiency, where studies with TTC7A-deficient patient-derived organoids led to meaningful advancements in understanding this disease and paved the way for a novel therapeutic that is under investigation.¹¹⁹ The use of intestinal organoids holds promise as a platform for interrogating functions that may be associated with monogenic causes including barrier function,¹⁷⁶ tissue repair,¹⁷⁷ and evaluating the effects of various stimuli that may be contributory in the pathology of intestinal disease.¹⁷⁸ Advancements in gene editing facilitates focused evaluation of specific genes and pathways of interest with the possibility of expanding organoids to perform large drug screens. Intestinal organoid-based platforms, including a gut-on-a-chip technologies¹⁷⁹ can be further augmented by utilization of an array of co-culture systems to better study interactions of epithelial cells with various components of the luminal compartment including microbiota, immune and stromal cells, vasculature, and neuronal compartments. These investigations can be further bolstered by use of single cell and spatial transcriptomics of intestinal tissue to identify cell-type specific signatures of disease and unveil pathways that may serve as personalized therapeutic targets.

Efforts in characterizing and optimizing the intestinal barrier holds strong potential in being valuable in guiding therapeutic approaches in a generalized fashion, including patients with and without monogenic disease. Leveraging samples from IBD patients with known monogenic causes as “guideposts” for those with IBD and unknown mechanism in multi-omic and organoid studies has overwhelming potential to expand understanding of mechanisms of disease on an individual patient basis. Innovative and interdisciplinary approaches in studying and therapeutically targeting barrier defects are feasible with available tools. Such advancements are expected to offer pioneering precision medicine that extends to many patients.

Author Contributions

J.D.O.: Substantial contribution to the concept and design of this review, significantly contributed to the preparation of the manuscript and revised it critically for important intellectual content.

A.G.: Contributed to the concept and design of the review and manuscript and figure preparation.

L.V.C.: Contribution to the concept and design of this review and manuscript preparation.

S.B.S.: Revised manuscript critically for important intellectual content.

Funding

J.D.O. is supported by National Institute of Diabetes and Digestive Kidney Diseases of the National Institutes of Health under (Award Number K08DK122133). L.V.C. is supported by Crohn’s and Colitis Foundation Research Fellows Award (Award Number 830997). S.B.S. is supported by National Institute of Diabetes and Digestive Kidney Diseases of the National Institutes of Health under (Award Number RC2DK122532) and the Leona M. and Harry B. Helmsley Charitable Trust. S.B.S. is supported by National Institute of Diabetes and Digestive Kidney Diseases of the National Institutes of Health under (Award Number P30DK03485), the Wolpow Family Chair in IBD Treatment and Research, the Translational Investigator Service at Boston Children’s Hospital, and the Children’s Rare Disease Cohort (CRDC) Study.

Conflicts of Interest

J.D.O. declares the following interest: independent contractor as “speaker” for Janssen and consultant for Skygenics. S.B.S. declares the following interests: scientific advisory board participation for Pfizer, BMS, Lilly, IFM therapeutics, Merck, and Pandion Inc; grant support from Pfizer, Novartis, Takeda; consulting for Hoffman La Roche, Takeda, and Amgen.