the following default sequential criteria, which apply to both chain contigs, were applied: ( 1 ) identical v and j genes usage; ( 2 ) identical junctional cdr3 amino acid length; and ( 3 ) cdr3 sequence similarity: 100 % nucleot ide sequence identity at the cdr3 junction for tcrs and 85 % amino acid sequence similarity ( based on hamming distance ) for bcrs. tcr or bcr data were then transferred into the corresponding anndata object. cells without receptor data or that presented more than one receptor were discarded from further immunoreceptor analysis. for t cell analysis, cells annotate d as mait cells or ɣδ t cells were also discarded. clonality of the different populations was calculated as 1 − pielou ’ s evenness index, varying from zero ( more diverse ) to one ( less diverse ), with the pielou ’ s evenness corresponding h s / h max, where h s is the shannon entropy of sample s and h max = log 2 c, where c is the number of unique clonotypes in s. all clonality scores were calculated on a subsample of 100 cells for each donor, cell type, tissue or cell type and tissue. to detect shifts in the bcr isotype composition of specific b cell lineages across the age groups ( supplementary table 20 ), we performed generalized linear modeling by fitting a statsmodels. glm model for each tissue subset, considering sex, sequencing chemistry, cmv serostatus and processing site as additional covariates. donors with fewer than 50 cells for a particular tissue - group – lineage combination or tissue - group – lineage combinations with fewer than for suitable donors were excluded from analysis. the estimated coefficients were used to calculate a covariate - aware log 2 ( fc ) for visualization. we used the statsmodels. multipletests function to adjust p values for multiple comparisons ( benjamini – hochberg method ), and subset – tissue combinations with adjusted p < 0. 05 were considered significantly changing across age. further information on research design is available in the nature portfol io reporting summary linked to this article. any methods, additional references, nature portfol io reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at 10. 1038 / s41590 - 025 - 02241 - 4. immune – epithelial – stromal networks define the cellular ecosystem of the small intestine in celiac disease source paper: pmc12133578 the immune – epithelial – stromal interactions underpinning intestinal damage in celiac disease ( cd ) are incompletely understood. to address this, we performed single - cell transcriptomics ( rna sequencing; 86, 442 immune, parenchymal and epithelial cells; 35 participants ) and spatial transcriptomics ( 20 participants ) on cd intestinal biopsy samples. here we show that in cd, epithelial populations shifted toward a progenitor state, with interferon - driven transcriptional responses, and perturbation of secretory and enteroendocrine populations. mucosal t cells showed numeric and functional changes in regulatory and follicular helper - like cd4 t cells, intraepithelial lymphocytes, cd8 and γδ t cell subsets, with skewed t cell antigen receptor repertoires. mucosal changes remained detectable despite treatment, representing a persistent immune – epithelial ‘ scar ’. spatial transcriptomics defined transcriptional niches beyond those captured in conventional histological scores, including cd - specific lymphoid aggregates containing t cell – b cell interactions. receptor – ligand spatial analyses integrated with disease susceptibility gene expression defined networks of altered chemok ine and morphogen signaling, and provide potential therapeutic targets for cd prevention and treatment. celiac disease ( cd ) is a common gastrointestinal disor der affecting 1 – 2 % of european and north american populations, in which small intestinal inflammation and damage are driven by aberrant adaptive immune responses to gluten. the only treatment is a lifelong gluten - free diet ( gfd ). there is an unmet therapeutic need for those living with cd, including refractory cd, where ongoing tissue damage occurs despite a gfd. a strong genetic component drives cd, dominated by hla - dq2 and hla - dq8 ( ref. ), with association studies identifying over 40 non - hla genomic loci, implicating over 100 candidate genes and a role for immunoregulatory mechanisms. murine models implicate viral infection as a trigger of loss of tolerance driving cd pathogenesis, a hypothesis supported by epidemiological studies. cd pathophysiology is multifactorial with several cell types implicated. dietary gluten is deamidated by tissue transglutaminase 2, and deamidated gluten peptides presented via hla - dq2 / hla - dq8 to cd4 t cells. gluten - specific cd4 t cells possess a distinc t type 1 helper t ( t h 1 ) / follicular helper t ( t fh ) cell phenotype, emphasizing the importance of t cell – b cell interactions. tissue plasma and b cells may present gluten peptides via hla - dq. subsequent stimulation of disease-specific plasma cells drives anti - tissue transglutaminase and anti - deamidated gliadin peptide antibod y production. gluten - specific t cells are necessary but not sufficient to generate mucosal damage. the mechanisms by which this response leads to tissue architectural change are incompletely understood. intraepithelial lymphocytes ( iels ), mainly cd8 t iels, are highly enriched in cd, likely driven by epithelial and myeloid - derived interleukin ( il ) - 15, in combination with cd4 t cell - derived il - 2, il - 21 and interferon gamma ( ifnγ ). iels may be directly involved in ec killing in a t cell antigen receptor ( tcr ) - independent manner, via nkg2c and nkg2d and their epithelial ligands mica and hla - e. however, the transcriptional state and involvement of tcr signaling in these cd8 t cell populations remains unclear. while novel treatments are under development, recent therapeutic trials targeting gluten degradation, gluten - specific cd4 t cell tolerance and il - 15 have been unsuccessful. however, therapies including tissue transglutaminase inhibitors and inducers of immune tolerance have shown promise. single - cell transcriptomics have redefined cellular landscapes in the gastrointestinal tract, offering insights into cd immunopathology. recent studies have sought to understand the cellular basis of cd using mass cytometry, including studies of refractory cd, gluten - specific t cells, and mucosal and circulating t cells. single - cell rna sequencing ( scrna - seq ) has been used to study mucosal immune cells, t cells, circulating immune cells and mucosal plasma cells. here, we combined single - cell and spatial transcriptomics to define the network of intestinal immune, epithelial and parenchymal cell populations in adults and children with cd. our description of spatially localized immune – parenchymal interactions driving inflammation and remodeling of the mucosa, and with specific disease-associated t cell subsets occupying distinc t mucosal niches, will facilitate identification of therapeutic targets. we generated scrna - seq profiles of duodenal epithelial, immune and parenchymal populations from 35 participants: 21 with cd ( 16 children, 5 adults ) and 14 controls ( 5 children, 9 adults; fig. 1 and supplementary table 1 ). we used complementary single - cell techniques for adult and pediatric datasets, with 86, 442 cells sequenced. in adults ( datasets 1 and 3 ), we performed scrna - seq ( 10x genomics ) on epithelial, immune ( supplementary fig. 1a, b ), stromal and endothelial cells. in children ( dataset 2 ), we performed targeted scrna - seq ( bd rhapsody; 504 targeted gene primer pairs ) and surface protein expression ( 79 oligo nucleot ide - conjugated antibod ies ) on intestinal immune cells ( supplementary fig. 1c, d and supplementary tables 2 and 3 ).