Autoimmune Enteropathy

Other names
Types
Causes
Symptoms
Diagnostic tests
Non-pharmacological treatments (therapies & others)
Drug treatments
Dietary molecular supplements
Immunity-booster / regenerative / stem-cell–oriented” drugs
Surgeries (when and why)
Preventions
When to see a doctor (red flags)
What to eat and what to avoid
Frequently asked questions

Autoimmune enteropathy is a rare disease where the immune system attacks the lining of the small intestine. The attack makes the villi (tiny finger-like absorptive projections) flatten. This causes long-lasting watery diarrhea, weight loss, and poor absorption of nutrients. It can happen in infants, children, and adults. Some people have autoantibodies that target intestinal cells (anti-enterocyte or anti-goblet cell antibodies). But some patients are “seronegative” and still have the disease. Biopsy usually shows villous atrophy, crypt inflammation and apoptosis, and malabsorption that does not improve with diet changes alone. Doctors must rule out celiac disease, infections, medications, and other causes. Treatment is usually immune suppression. Lippincott Journals+3PMC+3PMC+3

Autoimmune enteropathy (AIE) is a rare disease where a person’s immune system attacks the lining of the small intestine. The attack causes damage to the villi (tiny finger-like projections that absorb nutrients). The villi become short and flat (villous atrophy). Because of this damage, people develop persistent watery diarrhea, dehydration, weight loss, and poor absorption of vitamins, minerals, fat, and protein. Symptoms often last more than six weeks and do not improve with routine diet changes. Endoscopy with biopsy shows villous blunting, crypt inflammation and apoptosis, and sometimes loss of goblet and Paneth cells. Blood tests may show antibodies against intestinal cells (anti-enterocyte or anti-goblet cell), but these antibodies can be absent and are not perfectly specific. Diagnosis requires excluding other causes of villous atrophy (for example, celiac disease, drug-induced enteropathy, infections, common variable immunodeficiency). Lippincott Journals+3PMC+3CGH Journal+3

AIE can occur in infants, children, and adults. In babies, it may be part of a genetic immune problem such as IPEX syndrome (a FOXP3 gene defect causing loss of regulatory T-cell function). In children and adults, it can occur by itself or together with other autoimmune or immune-regulatory conditions (for example, CTLA-4 haploinsufficiency or LRBA deficiency). The disease course can be severe and lead to malnutrition and intestinal failure if not treated promptly with immune-modulating therapy and nutrition support. NCBI+2JACI Online+2

In some families, AIE is part of a genetic immune-regulation disorder. The best known is IPEX (immune dysregulation, polyendocrinopathy, enteropathy, X-linked) from FOXP3 mutations. Other “IPEX-like” disorders include CTLA-4 haploinsufficiency and LRBA deficiency. These conditions can present with severe diarrhea, multiple autoimmune problems, and may respond to targeted therapies like abatacept (CTLA-4-Ig) or, in some cases, stem-cell transplant. PMC+4NCBI+4Frontiers+4

Other names

People may use several names for the same clinical picture. These include: “autoimmune enteropathy,” “immune-mediated enteropathy,” “autoimmune small-intestinal enteropathy,” “anti-enterocyte antibody–associated enteropathy,” “seronegative autoimmune enteropathy,” and “IPEX-associated enteropathy” (when due to FOXP3 mutation). The adult-onset form is often called “adult autoimmune enteropathy.” PMC+2ScienceDirect+2

Types

1) Classic (antibody-positive) AIE. Patients have chronic diarrhea, villous atrophy, and anti-enterocyte and/or anti-goblet cell antibodies. Antibodies support the diagnosis but are not perfectly sensitive or specific. PMC+2Lippincott Journals+2

2) Seronegative AIE. Same clinical picture and biopsy changes, but no detectable gut autoantibodies; other causes are excluded. Diagnosis relies on histology, clinical course, and response to immune therapy. Lippincott Journals

3) Pediatric syndromic AIE (e.g., IPEX). Early onset, severe diarrhea plus other autoimmune features (e.g., type 1 diabetes, thyroiditis, dermatitis). FOXP3 mutations are typical. NCBI+1

4) IPEX-like AIE (CTLA-4, LRBA). Enteropathy with broader immune dysregulation due to CTLA-4 haploinsufficiency or LRBA deficiency; abatacept can help some patients. PMC+2PMC+2

5) Adult-onset AIE. Presents with intractable diarrhea and malnutrition in adults; often requires careful exclusion of celiac disease and drug-induced enteropathies. PMC+1

Causes

Below are causes or contributors that clinicians consider when they say “autoimmune enteropathy” or “autoimmune-like enteropathy.” Some are direct (genetic immune dysregulation). Some are triggers or associations.

Loss of immune tolerance to intestinal epithelial cells. The immune system mistakenly targets enterocytes and goblet cells. PMC
Anti-enterocyte antibodies. These antibodies can mediate or mark the attack on the gut lining. Lippincott Journals
Anti-goblet-cell antibodies. Similar concept; presence supports autoimmunity against mucus-producing cells. ScienceDirect
FOXP3 mutation (IPEX). Defective T-regulatory cells lead to uncontrolled autoimmunity and enteropathy. NCBI
CTLA-4 haploinsufficiency. Faulty inhibitory signaling promotes autoimmunity, including enteropathy. PMC
LRBA deficiency. Impaired CTLA-4 recycling causes immune over-activation and gut inflammation. PMC
Other monogenic immune dysregulation syndromes (IPEX-like). Diverse genes affecting T-reg or checkpoint pathways can present with enteropathy. Frontiers
Checkpoint pathway imbalance (T-cell costimulation). Dysregulated CTLA-4 pathway activity contributes to persistent intestinal autoimmunity. PMC
Aberrant mucosal cytokine signaling. Pro-inflammatory signals drive villous atrophy and crypt damage. (Mechanistic review) PMC
Breaks in epithelial barrier integrity. Barrier failure increases antigen exposure and sustains autoimmunity. (Review) PMC
Autoimmunity clustering. AIE often coexists with other autoimmune diseases, suggesting shared susceptibility. PMC
Environmental triggers (nonspecific). Infections or exposures may precipitate disease in predisposed hosts. (Review) BioMed Central
Medication-related immune shifts (association, rule-out first). Some drugs can mimic AIE or unmask autoimmunity; careful medication review is essential in the work-up. Lippincott Journals
Post-infectious dysregulation. Rarely, immune activation after infection may persist and resemble AIE. (Review) BioMed Central
Genetic background beyond monogenic forms. Polygenic risk likely modulates susceptibility in adult AIE. (Review) Wiley Online Library
Autoantigen exposure and molecular mimicry. Shared epitopes may sustain autoantibody production. (Mechanistic overview) PMC
Dendritic/T-cell imbalance in the lamina propria. Skewed activation sustains epithelial damage. (Mechanistic overview) PMC
Regulatory T-cell (Treg) deficiency or dysfunction (non-FOXP3). Tregs fail to suppress intestinal autoimmunity. ScienceDirect
Immune checkpoint inhibitor biology (by analogy). CTLA-4 pathway lessons inform targeted treatment (abatacept) in CTLA-4/LRBA disorders with enteropathy. ScienceDirect
Unknown/idiopathic mechanisms. Many adult cases have no single identified trigger but behave as immune-mediated disease. PMC

Symptoms

Watery diarrhea that does not stop (often >6 weeks). PMC
Weight loss and muscle wasting. PMC
Signs of dehydration (thirst, dizziness, low urine). PMC
Abdominal cramps or discomfort. Lippincott Journals
Bloating or gas. Lippincott Journals
Greasy, hard-to-flush stools (fat malabsorption in some). PMC
Nutrient deficiencies (iron, B12, folate, fat-soluble vitamins). PMC
Fatigue or low energy. PMC
Poor growth in children or failure to thrive. Nature
Skin rashes (from associated autoimmunity, especially in IPEX). NCBI
Autoimmune signs elsewhere (thyroiditis, diabetes in IPEX). NCBI
Loss of appetite or early fullness. Lippincott Journals
Swelling of legs (protein loss, low albumin). PMC
Bone pain or fractures later from vitamin D/calcium loss. PMC
Mouth ulcers or sore mouth (micronutrient deficiency). PMC

Diagnostic tests

A) Physical examination

Hydration and vital signs. Check pulse, blood pressure (including standing), and signs of dehydration. This guides urgent fluid care. PMC
Body weight and growth (children). Look for weight loss or poor growth; track BMI or growth curves. Nature
General nutrition exam. Hair, skin, nails, glossitis, and edema can point to deficiencies from malabsorption. PMC
Abdominal exam. Diffuse tenderness or distension supports active enteropathy and fluid loss. Lippincott Journals
Screen for associated autoimmunity. Skin rashes, thyroid enlargement, or signs of diabetes suggest syndromic disease (e.g., IPEX). NCBI

B) “Manual”/bedside tests and simple clinic procedures

Digital rectal exam and stool inspection. Look for occult blood or steatorrhea clues; can prompt targeted testing. PMC
Fecal occult blood (guaiac). A quick bedside screen when inflammation or bleeding is suspected. Lippincott Journals
Stool osmotic gap calculation. Helps separate osmotic from secretory diarrhea; AIE often behaves as secretory/inflammatory. Lippincott Journals
72-hour fecal fat (collection). Confirms malabsorption in severe cases. PMC
Targeted diet trials (only to exclude mimics). Lack of response to gluten-free diet or elemental diet supports non-celiac, immune-driven process. F6 Publishing

C) Laboratory and pathology tests

Complete blood count and iron studies. Anemia, leukocytosis, or eosinophilia may appear; iron deficiency is common with malabsorption. PMC
Comprehensive metabolic panel and albumin. Low albumin, electrolyte loss, and kidney function changes reflect severity. PMC
Micronutrient panel. B12, folate, vitamins A/D/E/K, calcium, magnesium, zinc levels show malabsorption burden. PMC
Celiac serology (tTG-IgA, total IgA). Negative celiac tests alongside villous atrophy raise suspicion for AIE. PMC
Autoantibodies to enterocytes/goblet cells. Helpful when positive; absence does not rule out AIE. Lippincott Journals
Inflammation markers (CRP) and fecal calprotectin. Support intestinal inflammation and help exclude functional diarrhea. Lippincott Journals
Stool infectious panel (culture/PCR, ova/parasites, C. difficile). Exclude infections before labeling AIE. PMC
Small-bowel biopsy (gold standard tissue). Duodenal/jejunal biopsies show partial/total villous blunting, crypt hyperplasia/lymphocytosis, increased crypt apoptosis, and often minimal intraepithelial lymphocytosis—features that help separate AIE from celiac disease. Lippincott Journals

D) “Electrodiagnostic/physiologic” gastrointestinal tests

Antroduodenal manometry. Measures pressure patterns; can reveal disordered motility that accompanies inflammation and malabsorption. (Supportive/adjunct). PMC
Electrogastrography (EGG). Records gastric myoelectrical rhythms; sometimes used in chronic unexplained diarrhea to document dysrhythmias (adjunct only). (Review context) PMC
Esophageal pH-impedance (if prominent reflux/upper symptoms). Helps separate coexisting disorders in complex immune enteropathies. (Adjunct). PMC
Breath tests (lactose/fructose intolerance, small-bowel bacterial overgrowth). Not diagnostic of AIE, but rule out added causes of diarrhea. PMC

E) Imaging and endoscopic visualization

Upper endoscopy with small-bowel biopsies. Direct view plus tissue is central to diagnosis. PMC
Capsule endoscopy. Shows diffuse small-bowel inflammation, scalloping, fissures, or mosaic patterns when disease is extensive. Lippincott Journals
MR or CT enterography. Noninvasive mapping of small-bowel wall inflammation and complications; also excludes other causes. PMC
Ultrasound (adjunct). May show bowel wall thickening and guides evaluation without radiation. PMC

Non-pharmacological treatments (therapies & others)

(each: brief description, purpose, mechanism—evidence is mostly from case series, nutrition guidelines, and expert consensus in rare disease)

1) Aggressive oral rehydration (ORS).
Purpose: Prevent dehydration and kidney injury.
Mechanism: Glucose–sodium cotransport in the small intestine improves water absorption even when villi are damaged. PMC

2) Intravenous fluids and electrolytes (acute care).
Purpose: Correct severe dehydration and electrolyte losses.
Mechanism: Direct IV replacement bypasses the gut during flares. PMC

3) High-calorie, high-protein diet with small frequent meals.
Purpose: Counter malnutrition and support healing.
Mechanism: Increases intake despite limited absorption; reduces osmotic load per meal. ESPN

4) Lactose-reduced or lactose-free eating pattern.
Purpose: Lower osmotic diarrhea when secondary lactase deficiency coexists.
Mechanism: Reduces unabsorbed lactose fermentation and water draw into bowel. PubMed

5) Low-fat or modified-fat diet with medium-chain triglycerides (MCT).
Purpose: Improve fat absorption and lessen steatorrhea.
Mechanism: MCTs are absorbed more directly via portal vein and require less bile. ESPN

6) Micronutrient repletion (iron, folate, B12, fat-soluble vitamins A/D/E/K, zinc, magnesium, calcium).
Purpose: Correct deficiencies that worsen fatigue, anemia, bone loss, and immune function.
Mechanism: Supplements bypass limited dietary uptake and restore stores. Medscape

7) Elemental or semi-elemental enteral formulas.
Purpose: Provide easier-to-absorb nutrition.
Mechanism: Pre-digested amino acids and simple carbs reduce digestive work. BioMed Central

8) Total parenteral nutrition (TPN) during severe flares or intestinal failure.
Purpose: Maintain hydration and nutrition when gut absorption is inadequate.
Mechanism: Intravenous delivery of calories, protein, fat, and micronutrients; often temporary but sometimes prolonged. PubMed+1

9) Home parenteral nutrition (HPN) programs.
Purpose: Support long-term intestinal failure outside the hospital.
Mechanism: Structured home IV nutrition following ESPEN guidance; careful monitoring prevents complications. ESPN

10) Infection prevention and catheter care education (if on TPN/HPN).
Purpose: Reduce central-line infections and sepsis risk.
Mechanism: Aseptic technique and routine surveillance. PubMed

11) Dietitian-led nutrition counseling.
Purpose: Tailor meal plans to symptoms and labs.
Mechanism: Adjust macronutrients, fiber, and meal timing to improve tolerance and weight. ESPN

12) Symptom-guided fiber strategy (soluble fiber when tolerated).
Purpose: Improve stool form in some patients.
Mechanism: Soluble fiber can thicken stool; adjust to avoid worsening bloating. PubMed

13) Oral nutritional supplements (ONS).
Purpose: Bridge calorie and protein gaps.
Mechanism: Ready-to-drink formulas proven to reduce malnutrition risk and may shorten diarrhea in broader populations. PGHN

14) Skin care and barrier creams.
Purpose: Protect perianal skin from frequent stools.
Mechanism: Reduces irritation and secondary infection risk. PMC

15) Bone health measures (vitamin D, calcium, weight-bearing activity as feasible).
Purpose: Counter steroid-related and malabsorption-related bone loss.
Mechanism: Replenishes deficits and stimulates bone, per general malabsorption care. Medscape

16) Vaccination review (before immunosuppression).
Purpose: Update non-live vaccines; evaluate live vaccines case-by-case.
Mechanism: Lowers preventable infection risk in immunosuppressed patients. NCBI

17) Psychosocial support and caregiver training.
Purpose: Reduce stress, improve adherence, and manage feeding programs at home.
Mechanism: Education and support improve outcomes in chronic intestinal failure. PubMed

18) Multidisciplinary clinic follow-up (GI, immunology, nutrition).
Purpose: Coordinate immune therapy and nutrition safely.
Mechanism: Regular labs, growth/weight checks, and therapy adjustments. PMC

19) Careful medication review and avoidance of offending drugs.
Purpose: Exclude drug-induced enteropathy that mimics AIE; avoid agents worsening diarrhea.
Mechanism: Dechallenge/switch when history suggests. Lippincott Journals

20) Transitional planning for adolescents/young adults.
Purpose: Smooth transfer from pediatric to adult services without gaps in nutrition or immunosuppression.
Mechanism: Shared care reduces relapse and hospitalizations. PMC

Drug treatments

*Doses are common adult starting points unless noted; individualization is essential. Evidence is from case reports/series and expert reviews because AIE is rare.

1) Prednisone (corticosteroid).
Dose/time: 0.5–1 mg/kg/day, short induction; taper over weeks.
Purpose: Rapidly suppress gut inflammation and stop diarrhea.
Mechanism: Broad anti-inflammatory and immunosuppressive effects on lymphocytes and cytokines.
Side effects: Hyperglycemia, edema, mood changes, infection risk, bone loss. PMC

2) Budesonide (locally acting steroid).
Dose/time: 9 mg/day (3 mg TID) for small-bowel-predominant disease; taper.
Purpose: Induce control with fewer systemic effects.
Mechanism: High first-pass hepatic metabolism concentrates action in gut.
Side effects: Less systemic, but can include adrenal suppression and dyspepsia. Lippincott Journals

3) Azathioprine (thiopurine).
Dose/time: 1.5–2.5 mg/kg/day; onset 6–12 weeks; monitor TPMT/NUDT15 and CBC/LFTs.
Purpose: Steroid-sparing maintenance.
Mechanism: Purine antimetabolite suppressing lymphocyte proliferation.
Side effects: Leukopenia, hepatotoxicity, pancreatitis, infection risk. PMC

4) 6-Mercaptopurine (thiopurine).
Dose/time: 1–1.5 mg/kg/day; similar monitoring as azathioprine.
Purpose/mechanism/risks: As above; used when azathioprine not tolerated. PMC

5) Mycophenolate mofetil.
Dose/time: 1–1.5 g twice daily; onset several weeks.
Purpose: Alternative steroid-sparing agent.
Mechanism: Inhibits inosine monophosphate dehydrogenase in lymphocytes.
Side effects: GI upset, leukopenia, infections. PMC

6) Tacrolimus (calcineurin inhibitor).
Dose/time: Trough-guided; often 0.05–0.1 mg/kg/day in divided doses.
Purpose: Rescue or maintenance in refractory AIE.
Mechanism: Inhibits T-cell activation (IL-2).
Side effects: Nephrotoxicity, tremor, hypertension, diabetes, infections. Karger

7) Cyclosporine (calcineurin inhibitor).
Dose/time: 2–4 mg/kg/day in divided doses with trough monitoring.
Purpose: Induction in severe pediatric AIE (older reports).
Mechanism: Blocks calcineurin–NFAT signaling in T cells.
Side effects: Nephrotoxicity, hypertension, gingival hyperplasia, infections. Gastrojournal

8) Sirolimus (mTOR inhibitor).
Dose/time: Trough-guided; often 1–2 mg/day adults (higher pediatric weight-based).
Purpose: Particularly useful in LRBA/CTLA-4 pathway disorders.
Mechanism: mTOR inhibition reduces T-cell proliferation.
Side effects: Hyperlipidemia, mouth ulcers, delayed wound healing, infections. eurannallergyimm.com

9) Infliximab (anti-TNF).
Dose/time: 5 mg/kg at weeks 0, 2, 6 then q8w (IBD regimen).
Purpose: Rescue in refractory AIE.
Mechanism: Neutralizes TNF-α–driven inflammation.
Side effects: Infusion reactions, TB/hepatitis B reactivation, infections. Karger

10) Adalimumab (anti-TNF).
Dose/time: 160 mg day 0, 80 mg day 14, then 40 mg q2w (adult IBD regimen).
Purpose: Alternative to infliximab when monoclonal anti-TNF is considered.
Mechanism/risks: As above. PMC

11) Vedolizumab (anti-integrin α4β7).
Dose/time: 300 mg IV at 0, 2, 6 weeks, then q8w.
Purpose: Gut-selective biologic; case reports/series show benefit in steroid-refractory AIE; mixed outcomes.
Mechanism: Blocks lymphocyte homing to gut.
Side effects: Upper respiratory infections, headache; overall favorable safety profile. PMC+1

12) Ustekinumab (anti-IL-12/23).
Dose/time: Weight-based IV induction then 90 mg SC q8w (IBD regimen).
Purpose: Case reports describing success when anti-TNF avoided or failed.
Mechanism: Down-regulates Th1/Th17 pathways.
Side effects: Infections; generally well tolerated. Lippincott Journals

13) Abatacept (CTLA-4–Ig).
Dose/time: 10 mg/kg IV q2–4w or 125 mg SC weekly (rheum regimens; individualized).
Purpose: Particularly effective in CTLA-4 haploinsufficiency or LRBA deficiency with enteropathy.
Mechanism: Restores inhibitory costimulatory signaling (CD80/86 binding).
Side effects: URTIs, infusion reactions; screen for infections. PMC+1

14) Rituximab (anti-CD20).
Dose/time: 375 mg/m² weekly ×4 or 1,000 mg ×2 two weeks apart.
Purpose: Selected refractory antibody-mediated cases or overlap immunopathology.
Mechanism: B-cell depletion lowers autoantibody production.
Side effects: Infusion reactions, hypogammaglobulinemia, infections. PMC

15) IVIG (immunoglobulin replacement).
Dose/time: 400–600 mg/kg every 3–4 weeks in hypogammaglobulinemia or select autoimmunity.
Purpose: Support immunity and modulate autoimmunity.
Mechanism: Immune modulation and antibody replacement.
Side effects: Headache, thrombosis risk, aseptic meningitis (rare). BioMed Central

16) Methotrexate (antimetabolite).
Dose/time: 15–25 mg weekly with folate.
Purpose: Alternative steroid-sparing agent.
Mechanism: Inhibits dihydrofolate reductase; immunomodulatory at low dose.
Side effects: Hepatotoxicity, cytopenias, teratogenicity. PMC

17) JAK inhibitors (e.g., tofacitinib).
Dose/time: 5 mg BID (IBD dosing, off-label in AIE); limited evidence.
Purpose: Considered in highly refractory immune-mediated gut inflammation.
Mechanism: Blocks JAK-STAT cytokine signaling.
Side effects: Herpes zoster, lipid changes, VTE risk. WJGnet

18) Corticosteroid enemas (for colonic-predominant disease).
Dose/time: Budesonide or hydrocortisone enemas nightly × 2–4 weeks.
Purpose: Target distal inflammation with fewer systemic effects.
Mechanism: Topical steroid anti-inflammatory action.
Side effects: Local irritation; minimal systemic effects. PMC

19) Cholestyramine (bile-acid binder) when bile-acid malabsorption suspected.
Dose/time: 4 g 1–3×/day.
Purpose: Reduce watery diarrhea due to bile acids reaching colon.
Mechanism: Binds bile acids to lower their laxative effect.
Side effects: Bloating, binds other meds/vitamins. NCBI

20) Pancreatic enzyme supplementation (selected cases of steatorrhea).
Dose/time: Standard pancrelipase dosing with meals.
Purpose: If coexisting pancreatic insufficiency suspected on testing.
Mechanism: Improves fat and protein digestion to ease symptoms.
Side effects: Constipation, perianal irritation. NCBI

Always individualize dosing and combine with nutrition support and close monitoring by gastroenterology and clinical immunology teams.

Dietary molecular supplements

1) Vitamin D (cholecalciferol).
Dose: Individualized to level; often 1,000–2,000 IU/day or repletion regimens.
Function/mechanism: Bone health, immune modulation; deficiency common in malabsorption. Medscape

2) Calcium.
Dose: Typically 1,000–1,200 mg/day elemental (diet + supplement).
Function: Bone mineral balance; counter steroid-related bone loss. Medscape

3) Iron (oral or IV).
Dose: 40–65 mg elemental iron daily (oral) or IV repletion if malabsorbed.
Function: Corrects iron-deficiency anemia; improves fatigue. NCBI

4) Vitamin B12.
Dose: 1,000 mcg IM monthly or high-dose oral if absorptive capacity allows.
Function: Prevents megaloblastic anemia and neuropathy in distal ileal involvement. NCBI

5) Folate.
Dose: 1 mg/day (adjust to labs).
Function: Supports red cell production; deficiency common in proximal small-bowel disease. NCBI

6) Zinc.
Dose: 20–40 mg elemental/day short term.
Function: Supports mucosal repair and immune function; diarrhea increases losses. Medscape

7) Magnesium.
Dose: 200–400 mg/day (as tolerated).
Function: Replaces GI losses; low Mg worsens cramps and arrhythmia risk. Medscape

8) Fat-soluble vitamins A/E/K.
Dose: Targeted per lab results.
Function: Vision, antioxidant function, and coagulation require adequate levels. Medscape

9) Glutamine (selected settings).
Dose: Variable; commonly 5–10 g TID in nutritional protocols.
Function/mechanism: Preferred fuel for enterocytes; parenteral/enteral support studies in diarrhea/TPN populations suggest potential benefit. Gut n Liver

10) Oral nutritional supplements (energy-dense shakes).
Dose: 1–2 servings/day as advised.
Function/mechanism: Increase energy and protein intake; pediatric data suggest improved nutrition and shorter diarrhea duration broadly. PGHN

Immunity-booster / regenerative / stem-cell–oriented” drugs

1) Hematopoietic stem cell transplantation (HSCT).
Dose/Timing: Transplant protocol individualized.
Function/mechanism: Curative in IPEX and some monogenic immune-dysregulation enteropathies by replacing defective immune system. NCBI

2) Abatacept (CTLA-4–Ig).
Dose: See above.
Function: Restores inhibitory costimulation; highly relevant in CTLA-4/LRBA disorders with enteropathy. PMC

3) Sirolimus (mTOR inhibitor).
Dose: See above.
Function: Helpful in LRBA/CTLA-4 pathway defects to rebalance T-cell responses. eurannallergyimm.com

4) Mesenchymal stromal cell infusions (experimental rescue).
Dose: Investigational.
Function: Immunomodulatory and mucosal healing potential reported in a refractory adult AIE case. acr.amegroups.org

5) Ustekinumab / Vedolizumab (biologic tissue-sparing).
Dose: See above.
Function: Targeted biologics with growing case-level evidence in steroid-refractory disease. PMC+1

6) Gene- and Treg-oriented approaches (research).
Dose: Not standard care.
Function: For IPEX and related disorders, gene-editing/Treg therapies are being explored to correct root immune defects. PMC

Surgeries (when and why)

1) Central venous catheter placement for TPN/HPN.
Why: Secure long-term IV access when intestinal failure prevents adequate oral/enteral nutrition; part of multidisciplinary intestinal failure care. PubMed

2) Feeding tube (PEG/PEJ) for enteral nutrition.
Why: Deliver elemental/semi-elemental feeds when oral intake is not enough and gut absorption is partially preserved. BioMed Central

3) Resection or diversion/stoma (selected complications).
Why: Manage strictures, perforation, or severe localized disease in monogenic enteropathies (e.g., TTC7A). Lippincott Journals

4) Intestinal transplantation (rare, last resort).
Why: For medically refractory intestinal failure due to AIE; case reports show lifesaving benefit in selected adults; outcomes vary. PubMed+2ScienceDirect+2

5) Thymectomy (thymoma-associated AIE).
Why: Treat the underlying tumor in paraneoplastic AIE; immune phenomena may improve. BioMed Central

Preventions

Early recognition of chronic diarrhea with weight loss; seek specialist care. PMC
Vaccination update before starting immunosuppression when possible. NCBI
Nutrition screening at every visit with prompt repletion of deficits. ESPN
Central-line care bundles to prevent bloodstream infection on HPN. PubMed
Bone protection plan when using steroids (vitamin D/calcium, exercise, minimize dose). Medscape
Regular medication review to avoid diarrhea-provoking drugs. Lippincott Journals
TB/hepatitis screening before anti-TNF or JAK inhibitors. Karger
Multidisciplinary clinic follow-up (GI, immunology, dietetics). PMC
Family genetic counseling in monogenic forms (IPEX, CTLA-4/LRBA, TTC7A). NCBI+1
Early escalation to immunology for biologic or HSCT consideration in severe pediatric cases. NCBI

When to see a doctor (red flags)

Seek urgent care for severe dehydration, dizziness/fainting, very low urine output, blood in stools, high fever, or signs of sepsis (especially if you have a central line). Arrange specialist review if diarrhea lasts more than two weeks with weight loss, if you have night-time diarrhea, if you fail to gain weight as a child, or if you have other autoimmune diseases together with diarrhea. Anyone receiving steroids or biologics who develops fever, cough, chest pain, or jaundice should contact their clinician immediately. PMC

What to eat and what to avoid

Eat small, frequent meals to reduce gut load. ESPN
Prioritize protein (eggs, soft fish, tofu, lean meats) to support healing. Clinical Nutrition Journal
Use lactose-free milk/yogurt if milk worsens diarrhea. PubMed
Choose lower-fat cooking and try MCT oil to reduce steatorrhea. ESPN
Sip fluids between meals rather than large volumes with meals to limit rapid transit. Memorial Sloan Kettering Cancer Center
Replace electrolytes (oral rehydration) during flares. PMC
Limit very high-fiber, gas-producing foods if they worsen bloating; re-introduce gently as tolerated. PubMed
Avoid alcohol excess and sugar alcohols (sorbitol, mannitol) that can worsen diarrhea. PubMed
Work with a dietitian to tailor calories, vitamins, and minerals. ESPN
Use oral nutrition supplements if you cannot meet calorie/protein goals with food. PGHN

Frequently asked questions

1) Is AIE the same as celiac disease?
No. Both can show villous atrophy, but AIE does not improve with a gluten-free diet and often needs immunosuppression. PMC

2) Do I need positive anti-enterocyte antibodies to have AIE?
No. They help when present but are neither required nor perfectly specific. Diagnosis relies on the full picture. Lippincott Journals

3) What is the first treatment?
Most people need steroids to control inflammation plus nutrition support. Long-term control often uses steroid-sparing drugs. PMC

4) Which medicines work best?
Evidence is from case series. Thiopurines, calcineurin inhibitors (tacrolimus), anti-TNF, vedolizumab, ustekinumab, sirolimus, and abatacept (for CTLA-4/LRBA) are used based on the patient’s profile. eurannallergyimm.com+3Karger+3PMC+3

5) Will I need IV nutrition?
Sometimes—during severe flares or intestinal failure. The goal is to resume enteral/oral nutrition when safe. Home PN programs can support long-term needs. ESPN

6) Can surgery cure AIE?
Surgery is not routine. Rarely, intestinal transplant is considered for refractory intestinal failure; a few adult cases report success. PubMed

7) Is AIE inherited?
Classic “idiopathic” AIE is not clearly inherited. Some AIE-like disorders are genetic (FOXP3/IPEX, CTLA-4, LRBA, TTC7A). Genetic testing is considered when suspicion is high. NCBI+1

8) What is IPEX and how is it treated?
IPEX is an X-linked FOXP3 defect with severe autoimmunity including enteropathy. HSCT is the only curative treatment; supportive immunosuppression is used before transplant. NCBI

9) Can cancer immunotherapy cause AIE?
Checkpoint inhibitors can cause enteritis/enterocolitis that mimics AIE; it is treated with steroids and sometimes biologics. PMC

10) How is AIE different from CVID enteropathy?
CVID shows low immunoglobulins and often infections; both can have villous atrophy, so immune evaluation is essential. PMC

11) Are probiotics helpful?
Evidence is limited and mixed in this rare disease; use only under specialist advice. Priority is immunosuppression and nutrition. PMC

12) How fast do medicines work?
Steroids act within days. Thiopurines may take 6–12 weeks. Biologics vary—often weeks to a few months. PMC

13) What monitoring do I need?
Regular blood counts, liver tests, drug levels (for calcineurin/mTOR), vitamins/minerals, bone density if on steroids, and infection screening. ESPN

14) Can AIE relapse?
Yes. Many patients need maintenance immunosuppression and careful tapering. Nutrition support reduces complications. PMC

15) What is the outlook?
With early diagnosis, modern immunosuppression, and nutrition programs, outcomes have improved. Prognosis depends on severity, genetics, and response to therapy. PMC

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