Molecular histomorphometry and the emerging role of transcriptomics in celiac disease diagnosis and therapeutic trials.

backgroundCeliac disease (CeD) is an autoimmune enteropathy in which diagnosis and disease monitoring rely on serology and small-intestinal histology. However, conventional histological assessment is semi-quantitative, subject to interobserver variability, and relatively insensitive to subtle mucosal changes, particularly in treated patients or during early disease. Recent advances in transcriptomic technologies have enabled detailed characterization of intestinal mucosal gene expression, revealing disease-specific molecular signatures. This review aims to synthesize current evidence on molecular histomorphometry and to evaluate the emerging role of transcriptomic profiling in improving diagnosis, disease monitoring, and therapeutic trial endpoints in CeD. In addition, we propose practical guidelines and a methodological pipeline for implementing transcriptomic analyses in this context. DISCUSSION: Transcriptomic analyses consistently identify characteristic epithelial and immune activation signatures in active CeD, including interferon-driven pathways, epithelial stress responses, and loss of mature enterocyte differentiation. Importantly, persistent molecular abnormalities are often detectable in patients adhering to a gluten-free diet despite histological normalization, highlighting limitations of conventional endpoints. Molecular histomorphometry integrates gene expression data with morphologic features to provide continuous, quantitative measures of mucosal injury. Regression-based molecular indices demonstrate improved sensitivity, reproducibility, and dynamic range compared with traditional histology. In clinical trials, these approaches have potential to enable detection of treatment effects with smaller sample sizes and shorter study durations, and they have shown particular promise as endpoints in gluten challenge models and studies of therapies such as transglutaminase 2 inhibitors. We further outline a practical analytical pipeline, including study design considerations, data processing, model construction, and reporting standards.

conclusionsMolecular histomorphometry and transcriptomic profiling represent a significant advancement in the assessment of CeD, offering quantitative, qualitative and highly sensitive measures of mucosal pathology. Coupled with clear methodological guidance, these approaches have the potential to complement or, in selected contexts, surpass traditional histological evaluation in both clinical practice and drug development. Continued validation, harmonization, and standardization will be essential for broader implementation and regulatory acceptance.