What is the differential diagnosis for a patient with villous atrophy on D2 (duodenal) biopsy and a negative Immunoglobulin A Tissue Transglutaminase (IgA TTG) test?

Differential Diagnosis of Villous Atrophy with Negative IgA TTG

When duodenal biopsy shows villous atrophy but IgA tissue transglutaminase (IgA TTG) is negative, you are dealing with seronegative enteropathy, and seronegative celiac disease remains the most common cause, representing up to one-third of cases in White patients. 1

Immediate Diagnostic Steps

Before considering the differential diagnosis, you must first exclude technical and testing errors:

• Confirm total IgA level - IgA deficiency occurs in 1-3% of celiac patients and causes false-negative IgA-based tests. If IgA is low or absent, order IgG-based tests (IgG TTG, IgG DGP, IgG EMA). 1
• Verify biopsy orientation - Have an experienced GI pathologist review the specimens to confirm true villous atrophy versus tangential sectioning artifact. 1
• Confirm adequate gluten intake - Patient must have consumed at least 10g gluten daily for 6-8 weeks before testing for accurate results. 2
• Check complete celiac serology panel - Ensure IgA DGP and IgA EMA were also tested, not just IgA TTG alone. 1

Primary Differential Diagnosis

1. Seronegative Celiac Disease (Most Common)

• Represents up to 33% of seronegative enteropathy cases in White populations. 1
• Order HLA-DQ2/DQ8 testing - Approximately 95% of celiac patients have HLA-DQ2 and 5% have HLA-DQ8; absence of both alleles has >99% negative predictive value and essentially rules out celiac disease. 1, 3
• If HLA-DQ2/DQ8 positive, consider empiric trial of strict gluten-free diet for 6 months with clinical and histologic monitoring. 1
• Clinical and histologic response to gluten-free diet confirms the diagnosis. 1

2. Medication-Induced Enteropathy

Review medication history specifically for:

• Olmesartan (most common drug cause) 1, 3
• NSAIDs 1
• Mycophenolate mofetil 1, 3
• Chemotherapy agents 1

3. Infectious Causes

Order targeted testing based on clinical context:

• Giardiasis - stool antigen or PCR 1, 3
• Cryptosporidium - especially in immunocompromised/AIDS patients 1, 3
• Tropical sprue - if travel history to endemic areas 1
• Whipple's disease - PAS staining of biopsy, PCR for Tropheryma whipplei 1, 3
• Small intestinal bacterial overgrowth - glucose or lactulose breath testing 1

4. Immune-Mediated Disorders

Look for specific histologic clues and order confirmatory tests:

• Common variable immunodeficiency - absent/reduced plasma cells in lamina propria on biopsy; check immunoglobulin levels 1
• Autoimmune enteropathy - decreased goblet cells on biopsy; test for anti-enterocyte and anti-goblet cell antibodies (93% positive) 1, 4
• IgA deficiency with celiac disease - check IgG-based celiac serology 1

5. Inflammatory Bowel Disease

• Crohn's disease - look for granulomas on biopsy, perform colonoscopy with ileoscopy and imaging 1

6. Other Causes to Consider

Based on clinical context:

• Food protein intolerance (cow's milk, soy, eggs) - particularly in children 1
• Eosinophilic gastroenteritis - check peripheral eosinophilia, tissue eosinophils 1
• Hypogammaglobulinemia 1
• Collagenous sprue - subepithelial collagen band on trichrome stain 1

Diagnostic Algorithm

Step 1: Verify IgA level and complete celiac serology panel (IgA/IgG TTG, DGP, EMA) 1

Step 2: Order HLA-DQ2/DQ8 testing 1, 3

• If negative → celiac disease excluded, pursue other causes
• If positive → seronegative celiac disease likely, consider gluten-free diet trial

Step 3: Review medications and discontinue potential offenders 1, 3

Step 4: Order infectious workup: stool studies for Giardia, Cryptosporidium; consider small bowel aspirate if bacterial overgrowth suspected 1, 3

Step 5: Have pathologist re-review biopsy for specific features:

• Absent plasma cells → common variable immunodeficiency 1
• Decreased goblet cells → autoimmune enteropathy 1
• Granulomas → Crohn's disease 1

Step 6: Check immunoglobulin levels and autoantibody panel if immune disorder suspected 1, 4

Step 7: If diagnosis remains unclear after above workup, consider empiric gluten-free diet trial for 6 months with repeat biopsy to assess histologic response 1

Critical Pitfalls to Avoid

• Do not assume negative serology excludes celiac disease - seronegative celiac disease is common and represents up to one-third of cases. 1
• Do not miss IgA deficiency - always check total IgA level with IgA-based tests. 1
• Do not rely on subjective response to gluten-free diet alone - this has poor predictive value; histologic response is required for confirmation. 5
• Do not overlook medication history - olmesartan and NSAIDs are frequently missed causes. 1, 3
• Do not accept poorly oriented biopsies - tangential sections can mimic villous atrophy; always have an experienced GI pathologist review. 1

When Seronegative Celiac Disease is Confirmed

If HLA-DQ2/DQ8 positive and other causes excluded:

• Initiate strict gluten-free diet with registered dietitian referral 3
• Repeat duodenal biopsy in 12-24 months to document histologic improvement 1
• Monitor for clinical response (symptom improvement, nutritional status) 1
• Screen for nutritional deficiencies and associated autoimmune conditions 3

The key distinction is that seronegative celiac disease shows clinical and histologic improvement on gluten-free diet, while other causes of seronegative enteropathy do not. 1, 5