we analyzed epcam epithelial populations from dataset 1. nine transcriptionally distinc t epithelial cell ( ec ) clusters were identified, representing progenitor, secretory and absorptive lineages along the developmental progression of the crypt – villus axis ( fig. 2a, b, extended data fig. 1a and supplementary table 4 ). best4 enterocytes ( best4 ca7 cpa2 ), first identified in the colon, were seen, expressing cftr and showing chloride channel activity ( fig. 2b and extended data fig. 1a ). goblet cells ( itln1 muc2 spink4 ) and tuft cells ( plcg2 trpm5 irag2 ) were also identified. a lyz paneth cell - like population ( mmp7 reg1a sod3 pla2g2a ) was also identified ( fig. 2a, b ), although defensin gene expression was not detected. this population expressed pgc, mucins including muc5ac, muc1 and muc6 and aqp5, suggesting it also contained brunner ’ s gland cells or ectopic gastric pyloric gland cells. this cell type was enriched in active celiac disease ( acd; fig. 2c, d ), perhaps in response to ifnγ. thus, this population could represent inflammation - driven gastric cell metaplasia. transit - amplifying ( ta ) cells were increased in cd, along with enrichment of uniform manifold approximation and projection ( umap ) areas corresponding to ec progenitors ( stem cells, ta cells and early enterocytes; fig. 2c, d ). this persisted in treated celiac disease ( tcd; extended data fig. 1b, c ). in parallel, more actively cycling ecs were observed in acd and tcd ( extended data fig. 1d, e ). pseudotime analyses identified epithelial developmental trajectories, from undifferentiated progenitor states toward absorptive and secretory lineages ( fig. 2e ). in cd, ecs were shifted to earlier pseudotime states, with loss of mature ecs ( fig. 2f ). ccl25, encoding the ligand for ccr9 ( implicated in cd pathogenesis ), was expressed predominantly by progenitor cells ( fig. 2b and extended data fig. 1f ). we examined putative ec functions through functional gene - set analysis ( extended data fig. 1a ), identifying functions of secretory paneth - like / brunner ’ s gland cells ( secreted protein and vesicle pathways ), best4 enterocytes ( chloride / anion channel activity ), tuft cells ( taste perception ) and enteroendocrine cells ( eecs; peptide hormone processing / secretion ). mature enterocytes expressed key metabolic and macronutrient catabol ic pathways, and active transport and absorption mechanisms. early ecs and ta cells did not express these pathways. absorptive function genes were limited to cell states at the end of absorptive epithelium pseudotime trajectories, consistent with ec development along the crypt – villus axis ( fig. 2g ). notably, gene sets related to lipid, carbohydrate, cholesterol, vitamin and iron processing and absorption were all downregulated in mature enterocytes in acd ( extended data fig. 1g – i ). these transcriptional changes normalized in tcd, although some pathways, including fructose metabolism and lipid catabol ism, remained reduced ( extended data fig. 1h ). overall, absorptive capacity is reduced in acd not simply by reduction in villus surface area, but through a relative increase of ec progenitors lacking absorptive machinery, and pathway downregulation in mature enterocytes. ecs in acd upregulated multiple antigen - presentation molecules, including classical hla class i and class ii genes ( except hla - dq ) and nonclassical genes including hla - e and hla - f ( fig. 2h ). interferon - stimulated genes ( types i and ii ) dominated the epithelial response, including stat1 ( fig. 2h and supplementary table 5 ). the major disease-associated responses were observed in all ec lineages ( extended data fig. 1j – l ), including antigen - presentation pathways, type i / ii interferon responses, lymphocyte - mediated immunity and cytotoxicity and cell adhesion regulation ( extended data fig. 1m, n ). some transcriptional changes were cell - type specific. il32 was highly expressed in acd by mature enterocytes ( extended data fig. 1k ), perhaps regulated by interferons. the reduction of fatty acid catabol ism / transport ( apoa1, fabp2 ), metal ion transport ( iron: fth1, ftl; zinc: slc39a4 ) and carbohydrate metabolism ( aldob, pck1 ) was restricted to absorptive lineages, mainly mature enterocytes ( extended data fig. 1k, n ). progenitor cells upregulated genes associated with cell division and differentiation, and downregulated those associated with tissue repair and homeostasis ( extended data fig. 1m, n ). secretory lineages showed increased expression of gut hormone genes, lyz, and chemok ines ( cxcl17, cxcl2; extended data fig. 1l ). the duodenum, where cd inflammation predominates, has sensory and neurohormonal functions. we extended eec clustering, revealing multiple transcriptional states, including neurog3 progenitors and eec subtypes, which showed similar cd - related transcriptional changes to other ecs ( extended data fig. 2 ). eec proportions altered in cd, with increases in neurog3 progenitor cells and somatostatin - producing d cells ( extended data fig. 2i – k ). in adults ( dataset 1 ), cd4 t cells formed subsets dominated by t h 1 - polarized and il - 17 - producing helper t ( t h 17 ) - polarized effectors, as well as small naive and foxp3 regulatory populations ( fig. 3a – c and supplementary table 6 ). there was a cluster of t fh - like cd4 t cells expressing pdcd1, btla, cd28, icos and intermediate cxcr5. dataset 2 ( pediatric ) contained analogous subsets ( extended data fig. 3a ), including cd31 cr2 recent thymic emigrants, a ccr7 t fh - like subset and the t fh - like subset expressing pd1, icos, ctla4, btla and cd161 at the protein level ( fig. 3d, e ). this t fh - like population in adults and children showed similar phenotypic profiles to those of gut - resident gluten - specific cd4 t cells in cd ( extended data fig. 3b ), and expressed tox2, cd200, il21 and cxcl13. the cluster showed enrichment of trbv7 - 2, a v - gene enriched in gluten - specific cd4 t cell hla - dq2. 5 tcr repertoires. t reg and t fh - like cd4 t cells were increased in acd in adults and children ( fig. 3f – i ). t cell populations showed distinc t cytokine and chemok ine expression patterns ( extended data fig. 3c ). the cd - associated t fh - like population, showed high cxcl13 and il21 expression, with ifng and il21 coexpression ( fig. 3j, k ), similarly to gluten - specific t cells. t fh - like cells expressed tnfsf8, ccl1, ccl22 and cxcl10, as well as il17f ( extended data fig. 3c ). il17f expression was not seen in the il17a rorc il23r ccr6 t h 17 population, nor did the t h 17 cluster show trbv7 - 2 enrichment ( extended data fig. 3b, d ). oral gluten challenge in cd drives rapid circulating cytokine responses, including il - 2, cxcl8, cxcl10 and il - 6 ( ref. ). cxcl8 expression was highest in ccr7 t fh cd4 t cells, cxcl10 was detected in t fh - like cd4 t cells, while il6 was detected in t reg cells ( extended data fig. 3c ). il2 expression was low within the cd4 compartment, as expected without gluten challenge. we examined transcription factor ( tf ), and regulon expression within cd4 subsets, with canonical tfs and regulons of t h 17 and t reg cell function expressed as expected ( extended data fig. 3e – g ). ikzf1 and its regulon were upregulated in t fh - like cells, with intermediate expression of runx1, batf and irf3. we examined b cell lineages in dataset 2 ( pediatric; extended data fig. 4a, b ). both iga and igm plasma cells were increased in cd ( extended data fig. 4c – f ). a population of cxcr5 b cells ( ms4a1 cd19 cd20 ) were present, with a shift toward the cd27 memory b cell phenotype in cd. gene signatures of age - related b cells ( an inflammation - associated population in autoimmune disease ), including itgam, itgax, cd86 and batf, were expressed most highly in cd27 b cell populations, while a key age - related b cell tf, tbx21, was highly expressed in cycling b cells ( extended data fig. 4b ).