Celiac disease (CD) provides a unique human model in which the initiating environmental antigen is known and can be removed, enabling intestinal injury and repair to be followed prospectively. Yet after initiating a gluten-free diet (GFD), mucosal recovery varies markedly, ranging from rapid restoration of villous architecture to persistent injury despite strict adherence. To define the cellular programs governing this divergent response, we performed longitudinal single-cell RNA sequencing of intestinal biopsies from 35 non-celiac controls and 50 CD patients at three timepoints after GFD initiation (day 0, month 3, and year 1), generating >1.1 million single-cell transcriptomes, the largest atlas of human intestinal injury and repair.
Beyond the expected composition shifts accompanying active disease and their normalization after gluten withdrawal, we identified coordinated transcriptional programs across epithelial, immune, stromal, and myeloid compartments that tracked with villous height-to-crypt depth ratio independently of changes in cell abundance. These findings reveal mucosal healing to be a multicellular process of state reprogramming rather than simple reversal of inflammatory cell accumulation. A distinct IFNγ- and IL-17-producing CD8 T-cell population emerged as a prominent correlate of tissue injury: expanded in active CD, rapidly contracted following gluten withdrawal, and closely tracking villous injury severity. Critically, in patients undergoing gluten re-challenge, this population re-expanded within six weeks of exposure, directly linking its dynamics to the disease-driving antigen. Conversely, recovery was associated with the emergence of anti-inflammatory macrophages, a distinct γδ T-cell population, and transcriptionally remodeled goblet cells, revealing cellular states specific to regeneration rather than a simple return to baseline.
Together, these data establish a longitudinal cellular framework for human intestinal injury and repair, revealing that successful mucosal healing is not merely reversal of disease-associated inflammation. Rather, gluten withdrawal initiates coordinated remodeling across cellular compartments, generating a distinct regenerative tissue state whose emergence tracks with restored intestinal architecture.