Diagnostic Utility of CD3 Immunohistochemistry for Detecting Intraepithelial Lymphocytes in Early or Missed Celiac Disease: A Systematic Review and Meta-analysis with Complementary In Silico Analysis

Celiac disease (CD) involves immune-mediated intestinal injury driven by gluten in genetically susceptible individuals. Because early and subtle lesions rely on accurate detection of intraepithelial lymphocytes (IELs), refined diagnostic tools are essential. The primary objective of this systematic review and meta-analysis was to evaluate and quantitatively synthesize the diagnostic utility of CD3 immunohistochemistry compared with conventional hematoxylin and eosin (H&E) staining for the detection of intraepithelial lymphocytes (IELs) in celiac disease, through systematic comparison of IEL counts per 100 enterocytes, particularly in early or missed cases. The secondary objective was to integrate in silico HLA-DQ molecular expression and CD3/T-cell receptor (TCR) network analyses to elucidate the genetic and immune mechanisms underlying celiac disease, provide mechanistic support for the observed diagnostic findings, and refine diagnostic thresholds for improved immune marker detection. It gathered studies from PubMed, Scopus, Web of Science, and Cochrane. They included directly compared CD3/IHC with H&E staining for IEL detection in CD patients and reported quantitative diagnostic outcomes (IEL counts, sensitivity, specificity, or AUC values). Study quality was evaluated using the Newcastle–Ottawa Scale. Sixteen studies were included in qualitative synthesis. Thirteen favored CD3/IHC for celiac disease diagnosis, while three found no difference with H&E. Comparative analysis of 13 studies showed CD3-IEL counts had higher mean IELs (40.20±4.51) and AUC 0.574, versus H&E (36.34±3.69) with AUC 0.426. Subgroup meta-analysis showed no significant difference (p=0.72). Computational analyses revealed strong interactions between CD-variant genes and CD3 expression in IELs, highlighting their impactful role in celiac disease pathology. Inconclusion, CD3 immunohistochemistry demonstrates superior sensitivity over conventional H&E staining for detecting intraepithelial lymphocytes, particularly in early or missed cases of celiac disease. Integrating computational in silico HLA-DQ molecular expression analyses further refines diagnostic thresholds, linking genetic susceptibility with immune activation and IEL expansion. This combined approach not only enhances diagnostic precision but also provides mechanistic insights into celiac disease pathology.