γδ t cells were uncommon within ifng t rm ( 2 ) and cycling clusters. trdv1 and trdv3 expression was higher in the ccl4, ikzf2 t rm ( 2 ) and natural iel populations, with trdv3 in particular enriched in the natural iel cluster ( extended data fig. 8f ). we analyzed the tcr repertoire of cd8 t cells in this dataset. the t rm and il7r clusters showed greatest clonal expansion ( extended data fig. 8g ). in all participants with cd, trbv28 - containing clonotypes were more clonally expanded than their non - trbv28 counterparts. trbv28 clonotypes were enriched in the top quintile of expanded clones, which were almost exclusively found within the t rm ( 2 ) and cycling clusters ( extended data fig. 8h, i ). we validated these findings through bulk rna - seq of sorted intestinal αβ cd8 and γδ t cells from participants with and without cd ( dataset 6 ). gene - set enrichment analysis of cd8 t cell gene expression in acd showed upregulation of tcr activation gene sets, and enrichment of cluster marker gene sets from t rm ( 2 ) and cycling populations ( supplementary fig. 3a – c ), with upregulation of cxcr6, entpd1 and mki67 ( supplementary fig. 3d ). cd8 t cells showed upregulation of ifng and il26 ( supplementary fig. 3e ). there was a shift from klrc1 ( nkg2a ) to klrc2 ( nkg2c ) expression, but klrk1 ( nkg2d ) expression was not increased. inhibitory kirs were upregulated in this dataset, consistent with recent findings. gene expression between health and cd was different in γδ and αβ cd8 t cells ( supplementary fig. 3f, g ). ifng and mki67 expression were not increased to the same extent in γδ t cells, nor were t rm ( 2 ) ifng cluster markers like entpd1. there were also differences in nk cell receptor changes, kirs, pdcd1 and tyrobp, a natural iel marker ( supplementary fig. 3h ). bulk γδ tcr repertoire sequencing ( dataset 7 ) revealed a skewed trgv repertoire, with reduced trgv4 and increased trgv3 use in acd ( supplementary fig. 4a, b ), which persisted after treatment, as previously described. most trd cdr3 sequences were private; however, increased sequence sharing was noted between acd repertoires ( supplementary fig. 4c ), with longer shared cdr3 sequences in acd ( supplementary fig. 4d ). previously reported cd - associated trdv cdr3 motifs, were increased in acd; however, we were unable to replicate the previously described association between the trdv h - j1 motif and cd ( supplementary fig. 4e – i ). samples from adults with tcd ( gfd with good symptomatic, serological and histological response ) were included in scrna - seq, bulk rna - seq and tcr - seq experiments ( supplementary table 1 ). we hypothesized that cell - type and transcriptional changes would normalize with treatment. however, many biological changes persisted. specifically, ec changes including increased ta cell proportions and cycling cells ( extended data fig. 1b – e ) and the shift toward progenitor states ( fig. 2f ) persisted despite treatment. however, absorptive function gene expression within mature enterocytes had predominantly normalized, aside from the ongoing reduction in fructose metabolism and lipid catabol ism ( extended data fig. 1g ). while t fh - like cd4 t cells and t reg cells returned toward control levels on treatment, the cd8 compartment remained perturbed, with reduced natural iels and increases in t rm ( 2 ) cd8 t cells. however, the t rm ( 2 ) population showed reduced activation in tcd ( lower ifng, il32 and pro - inflammatory markers ). intestinal cd8 tcr repertoire changes remained ( specifically trbv28 enrichment ), as did increased circulating trbv28 gut - homing cd8 t cells. we next analyzed duodenal stromal and endothelial populations in cd ( dataset 3; supplementary fig. 5a – d ). annotation of stromal populations based on previous descriptions showed s1, s2 and s3 fibroblasts, as well as myof ibroblasts, with s1 fibroblasts most common in the duodenum. the pro - inflammatory s4 phenotype seen in colonic inflammatory bowel disease was not seen. differential gene expression and gene - set enrichment analysis showed upregulation of interferon - induced genes including stat1, the major histocompatibility complex class ii invariant chain ( cd74 ), and slit2, encoding a secreted protein involved in intestinal homeostasis ( supplementary fig. 5e, f ). analysis of endothelial cells revealed arterial, capillary, venous and lymphatic populations, with upregulation of interferon - stimulated genes in cd ( supplementary fig. 5g – i ). we next performed spatial transcriptomics on duodenal biopsy samples ( dataset 4; fig. 6 ). spatial transcriptomics showed 13 transcriptionally distinc t regions within the mucosa, representing compartments of the crypt – villus axis ( stem cell niche, lower - crypt and mid - crypt regions and villus zones ), stromal cell - rich regions, several lamina propria regions with immune cell infiltrates dominated by plasma cell signatures and lymphoid aggregates ( las; fig. 6a, b ). in health, the epithelial villus compartments dominated; these were reduced in acd ( fig. 6c – e ). these villus regions expressed absorptive function genes, predominantly in the most mature villus compartment ( fig. 6b and supplementary fig. 6b ). in contrast, immune - rich regions and las were greatly expanded in acd ( fig. 6d, e ). these regions were themselves spatially organized, with las closely associated with lower - crypt and immune - rich regions, and telocyte - rich regions with villus structures ( fig. 6g ). these immune - rich regions and las showed gene expression patterns associated with b cells ( cd19, ms4a1 ( cd20 ) ), plasma cells ( ighm, igha1, txndc5 ) and t cells ( cd3d, ccr7, cxcl13 ). signals of cellular proliferation ( mki67, reg1a ) were highly localized in specific clusters. in health, cellular proliferation was limited to stem - cell and lower - crypt regions, while in acd, proliferative markers were more dispersed, including in immune - rich and la regions ( supplementary fig. 6c, d ). in acd, villus top regions showed increases in interferon - stimulated genes, markers of proliferation, and il32 ( fig. 6f ), analogous to epithelial scrna - seq results. tcr genes, tissue - residency markers ( itgae, cxcr6, klrb1 ), and cytotoxic cd8 markers ( gzma, klrd1, klrk1 ) were increased in acd, suggesting tissue - resident cytotoxic cd8 t cell enrichment in villi. we integrated spatial transcriptomics with scrna - seq data to predict cell - type locations in mucosa ( supplementary figs. 6e – j and 7 ). in acd, ta cell signatures expanded from crypt bases to most villus regions, while mature ec signatures were restricted to superficial epithelial layers. in acd, las showed highly localized enrichment of t fh - like cd4 t cell ( cxcr5, cxcl13 ) and b cell ( cd19, ms4a1; fig. 6b and supplementary fig. 7a ) signatures. plasma cell signatures were expanded in neighboring immune - rich regions. in acd, cd8 t rm ( 2 ) cell signatures were highly enriched in villus tip regions, colocalized with mature enterocytes ( fig. 6h and supplementary figs. 6h – j and 7b ). to further study las in cd, we performed further spatial transcriptomics experiments on duodenal biopsy samples in participants with and without cd ( dataset 5; fig. 7 and extended data fig. 9a – c ). analysis of spatial regions recapitulated our description of key transcriptional regions in the duodenal mucosa ( fig. 7a, b and extended data fig. 9c ), with enrichment of proliferating areas at crypt bases, muc5ac and pgc epithelium, immune - rich areas containing plasma cells, and las ( fig. 7c – f ). these las were enriched in both acd and tcd. these lamina propria las were located adjacent to stem cell niches and muscularis mucosa ( fig. 7g – i ), with enrichment of t fh - like cd4 t cell, t reg cell and b cell gene signatures. plasma cell signatures were more widely dispersed in immune - rich regions ( fig. 7i – k and extended data fig. 9d, e ).