{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T18:08:13Z","timestamp":1783361293232,"version":"3.54.6"},"reference-count":32,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2025,9,13]],"date-time":"2025-09-13T00:00:00Z","timestamp":1757721600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Consejer\u00eda de Salud y Consumo-Junta de Andaluc\u00eda","award":["PI-0070-2024"],"award-info":[{"award-number":["PI-0070-2024"]}]},{"name":"Consejer\u00eda de Salud y Consumo-Junta de Andaluc\u00eda","award":["C-CTS-301-UGR23"],"award-info":[{"award-number":["C-CTS-301-UGR23"]}]},{"name":"Consejer\u00eda de Universidad, Investigaci\u00f3n e Innovaci\u00f3n","award":["PI-0070-2024"],"award-info":[{"award-number":["PI-0070-2024"]}]},{"name":"Consejer\u00eda de Universidad, Investigaci\u00f3n e Innovaci\u00f3n","award":["C-CTS-301-UGR23"],"award-info":[{"award-number":["C-CTS-301-UGR23"]}]},{"name":"SPAO 2023","award":["PI-0070-2024"],"award-info":[{"award-number":["PI-0070-2024"]}]},{"name":"SPAO 2023","award":["C-CTS-301-UGR23"],"award-info":[{"award-number":["C-CTS-301-UGR23"]}]},{"name":"Sociedad Espa\u00f1ola de Gastroenterolog\u00eda, Hepatolog\u00eda y Nutrici\u00f3n Pedi\u00e1trica (SEGHNP) 2023 edition","award":["PI-0070-2024"],"award-info":[{"award-number":["PI-0070-2024"]}]},{"name":"Sociedad Espa\u00f1ola de Gastroenterolog\u00eda, Hepatolog\u00eda y Nutrici\u00f3n Pedi\u00e1trica (SEGHNP) 2023 edition","award":["C-CTS-301-UGR23"],"award-info":[{"award-number":["C-CTS-301-UGR23"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Celiac disease (CD) is a chronic autoimmune disorder triggered by gluten in genetically susceptible individuals. While gluten-free diet (GFD) remains the primary treatment, the molecular mechanisms underlying immune reconstitution remain poorly understood in pediatric populations. This study aimed to characterize T cell receptor (TCR) repertoire remodeling in pediatric CD patients following short-term GFD. We conducted a longitudinal observational study analyzing peripheral blood circulating T cells from five pediatric CD patients at two time points: pre-GFD (at diagnosis) and post-GFD (after 9\u201310 months of strict dietary adherence). Single-cell TCR sequencing was performed to analyze clonotype diversity, gene usage patterns and TRAV-TRBV pairing combinations. Analysis of 9661 T cells revealed significant TCR repertoire remodeling post-GFD. Expanded clones, predominantly cytotoxic CD8+ T cells, contracted post-GFD (p = 0.02), while increasing clonotype diversity. Notably, specific \u03b1\u03b2 chain pairings underwent clear reorganization in the complete T cell compartment. Pathogenic combinations were depleted post-GFD, especially in CD4+ T cells, while beneficial pairings became enriched. GFD induced comprehensive TCR repertoire remodeling, revealing that changes occur at the level of specific TCR pairings rather than individual gene usage. Our findings highlight the precision of single-cell approaches in capturing functionally relevant immune changes for monitoring treatment response in pediatric CD.<\/jats:p>","DOI":"10.3390\/ijms26188927","type":"journal-article","created":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T07:33:02Z","timestamp":1758007982000},"page":"8927","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Single-Cell TCR Sequencing Uncovers Remodeling of the Immune Repertoire After a Short-Term Gluten-Free Diet in Pediatric Celiac Disease"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0113-9904","authenticated-orcid":false,"given":"Rafael","family":"Mart\u00edn-Masot","sequence":"first","affiliation":[{"name":"Secci\u00f3n de Gastroenterolog\u00eda y Nutrici\u00f3n Infantil, Hospital Regional Universitario de M\u00e1laga, 29010 M\u00e1laga, Spain"},{"name":"Instituto de Nutrici\u00f3n y Tecnolog\u00eda de los Alimentos \u201cJos\u00e9 Mataix Verd\u00fa\u201d (INYTA), Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), Universidad de Granada, 18071 Granada, Spain"},{"name":"Departamento de Farmacolog\u00eda y Pediatr\u00eda, Facultad de Medicina, Universidad de M\u00e1laga, 29071 M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4093-4900","authenticated-orcid":false,"given":"Marta","family":"Herrador-L\u00f3pez","sequence":"additional","affiliation":[{"name":"Secci\u00f3n de Gastroenterolog\u00eda y Nutrici\u00f3n Infantil, Hospital Regional Universitario de M\u00e1laga, 29010 M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3004-252X","authenticated-orcid":false,"given":"V\u00edctor Manuel","family":"Navas-L\u00f3pez","sequence":"additional","affiliation":[{"name":"Secci\u00f3n de Gastroenterolog\u00eda y Nutrici\u00f3n Infantil, Hospital Regional Universitario de M\u00e1laga, 29010 M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1427-7639","authenticated-orcid":false,"given":"Francisco David","family":"Carmona","sequence":"additional","affiliation":[{"name":"Departamento de Gen\u00e9tica e Instituto de Biotecnolog\u00eda, Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), Universidad de Granada, 18071 Granada, Spain"},{"name":"Reproducci\u00f3n Humana y Enfermedades Hereditarias y Complejas (IBS-TEC14), Terapias Avanzadas y Tecnolog\u00edas Biom\u00e9dicas, Instituto de Investigaci\u00f3n Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Gonz\u00e1lez-Mu\u00f1oz","sequence":"additional","affiliation":[{"name":"Departamento de Gen\u00e9tica e Instituto de Biotecnolog\u00eda, Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), Universidad de Granada, 18071 Granada, Spain"},{"name":"Reproducci\u00f3n Humana y Enfermedades Hereditarias y Complejas (IBS-TEC14), Terapias Avanzadas y Tecnolog\u00edas Biom\u00e9dicas, Instituto de Investigaci\u00f3n Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8806-5148","authenticated-orcid":false,"given":"Elena","family":"L\u00f3pez-Isac","sequence":"additional","affiliation":[{"name":"Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular II, Facultad de Farmacia, Instituto de Biotecnologia, Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), Universidad de Granada, 18071 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9573-3244","authenticated-orcid":false,"given":"Teresa","family":"Nestares","sequence":"additional","affiliation":[{"name":"Instituto de Nutrici\u00f3n y Tecnolog\u00eda de los Alimentos \u201cJos\u00e9 Mataix Verd\u00fa\u201d (INYTA), Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), Universidad de Granada, 18071 Granada, Spain"},{"name":"Departamento de Fisiolog\u00eda, Facultad de Farmacia, Universidad de Granada, 18071 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5471-5824","authenticated-orcid":false,"given":"Lara","family":"Bossini-Castillo","sequence":"additional","affiliation":[{"name":"Departamento de Gen\u00e9tica e Instituto de Biotecnolog\u00eda, Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), Universidad de Granada, 18071 Granada, Spain"},{"name":"Reproducci\u00f3n Humana y Enfermedades Hereditarias y Complejas (IBS-TEC14), Terapias Avanzadas y Tecnolog\u00edas Biom\u00e9dicas, Instituto de Investigaci\u00f3n Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Caio, G., Volta, U., Sapone, A., Leffler, D.A., De Giorgio, R., Catassi, C., and Fasano, A. (2019). Celiac Disease: A Comprehensive Current Review. BMC Med., 17.","DOI":"10.1186\/s12916-019-1380-z"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1097\/MPG.0000000000002497","article-title":"European Society Paediatric Gastroenterology, Hepatology and Nutrition Guidelines for Diagnosing Coeliac Disease 2020","volume":"70","author":"Husby","year":"2020","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1001\/jama.2017.9730","article-title":"Celiac Disease and Nonceliac Gluten Sensitivity: A Review","volume":"318","author":"Leonard","year":"2017","journal-title":"JAMA"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1038\/s41586-020-2003-8","article-title":"IL-15, Gluten and HLA-DQ8 Drive Tissue Destruction in Coeliac Disease","volume":"578","author":"Abadie","year":"2020","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"3005","DOI":"10.4049\/jimmunol.1601693","article-title":"T Cells in Celiac Disease","volume":"198","author":"Jabri","year":"2017","journal-title":"J. Immunol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1038\/s41584-025-01218-9","article-title":"Antigen-Driven T Cell Responses in Rheumatic Diseases: Insights from T Cell Receptor Repertoire Studies","volume":"21","author":"Brown","year":"2025","journal-title":"Nat. Rev. Rheumatol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2819","DOI":"10.4049\/jimmunol.1501152","article-title":"Healthy HLA-DQ2.5+ Subjects Lack Regulatory and Memory T Cells Specific for Immunodominant Gluten Epitopes of Celiac Disease","volume":"196","author":"Christophersen","year":"2016","journal-title":"J. Immunol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1038\/s41576-019-0093-7","article-title":"Integrative Single-Cell Analysis","volume":"20","author":"Stuart","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/nri.2017.76","article-title":"Single-Cell RNA Sequencing to Explore Immune Cell Heterogeneity","volume":"18","author":"Papalexi","year":"2018","journal-title":"Nat. Rev. Immunol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1038\/s41590-019-0378-1","article-title":"Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-Cell Transcriptomics and Mass Cytometry","volume":"20","author":"Zhang","year":"2019","journal-title":"Nat. Immunol."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Hanna, S.J., Tatovic, D., Thayer, T.C., and Dayan, C.M. (2021). Insights From Single Cell RNA Sequencing Into the Immunology of Type 1 Diabetes- Cell Phenotypes and Antigen Specificity. Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.751701"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1038\/mi.2015.57","article-title":"Responsive Population Dynamics and Wide Seeding into the Duodenal Lamina Propria of Transglutaminase-2-Specific Plasma Cells in Celiac Disease","volume":"9","author":"Snir","year":"2016","journal-title":"Mucosal Immunol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1038\/ajg.2014.77","article-title":"Potential Celiac Children: 9-Year Follow-up on a Gluten-Containing Diet","volume":"109","author":"Auricchio","year":"2014","journal-title":"Am. J. Gastroenterol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1136\/gutjnl-2017-314461","article-title":"HLA-DQ:gluten Tetramer Test in Blood Gives Better Detection of Coeliac Patients than Biopsy after 14-Day Gluten Challenge","volume":"67","author":"Sarna","year":"2018","journal-title":"Gut"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cgh.2017.06.037","article-title":"Global Prevalence of Celiac Disease: Systematic Review and Meta-Analysis","volume":"16","author":"Singh","year":"2018","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/s41385-019-0222-9","article-title":"Single-Cell TCR Sequencing of Gut Intraepithelial \u03b3\u03b4 T Cells Reveals a Vast and Diverse Repertoire in Celiac Disease","volume":"13","author":"Risnes","year":"2020","journal-title":"Mucosal Immunol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1002\/path.5592","article-title":"Classification of Intestinal T-Cell Receptor Repertoires Using Machine Learning Methods Can Identify Patients with Coeliac Disease regardless of Dietary Gluten Status","volume":"253","author":"Foers","year":"2021","journal-title":"J. Pathol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"13073","DOI":"10.1073\/pnas.1311861110","article-title":"Dietary Gluten Triggers Concomitant Activation of CD4+ and CD8+ \u03b1\u03b2 T Cells and \u03b3\u03b4 T Cells in Celiac Disease","volume":"110","author":"Han","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1038\/s41385-021-00385-8","article-title":"Circulating CD103 \u03b3\u03b4 and CD8 T Cells Are Clonally Shared with Tissue-Resident Intraepithelial Lymphocytes in Celiac Disease","volume":"14","author":"Risnes","year":"2021","journal-title":"Mucosal Immunol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1182\/blood-2015-06-649145","article-title":"Autologous Stem Cell Transplantation Aids Autoimmune Patients by Functional Renewal and TCR Diversification of Regulatory T Cells","volume":"127","author":"Delemarre","year":"2016","journal-title":"Blood"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Lutter, L., Spierings, J., van Rhijn-Brouwer, F.C.C., van Laar, J.M., and van Wijk, F. (2018). Resetting the T Cell Compartment in Autoimmune Diseases With Autologous Hematopoietic Stem Cell Transplantation: An Update. Front. Immunol., 9.","DOI":"10.3389\/fimmu.2018.00767"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2642","DOI":"10.1172\/JCI98819","article-title":"Disease-Driving CD4+ T Cell Clonotypes Persist for Decades in Celiac Disease","volume":"128","author":"Risnes","year":"2018","journal-title":"J. Clin. Investig."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Yohannes, D.A., Freitag, T.L., de Kauwe, A., Kaukinen, K., Kurppa, K., Wacklin, P., M\u00e4ki, M., Arstila, T.P., Anderson, R.P., and Greco, D. (2017). Deep Sequencing of Blood and Gut T-Cell Receptor \u03b2-Chains Reveals Gluten-Induced Immune Signatures in Celiac Disease. Sci. Rep., 7.","DOI":"10.1038\/s41598-017-18137-9"},{"key":"ref_24","first-page":"38","article-title":"T Cell Receptor Sequencing in Autoimmunity","volume":"2","author":"Mitchell","year":"2020","journal-title":"J. Life Sci."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1111\/j.2047-6310.2012.00064.x","article-title":"Extended International (IOTF) Body Mass Index Cut-Offs for Thinness, Overweight and Obesity","volume":"7","author":"Cole","year":"2012","journal-title":"Pediatr. Obes."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1097\/MPG.0000000000002062","article-title":"Comparison of Clinical Methods With the Faecal Gluten Immunogenic Peptide to Assess Gluten Intake in Coeliac Disease","volume":"67","author":"Gerasimidis","year":"2018","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"ref_27","first-page":"106","article-title":"Detection and Quantification of Gluten Immunogenic Peptides in Feces of Infants and Their Relationship with Diet","volume":"111","author":"Roca","year":"2019","journal-title":"Rev. Esp. Enferm. Dig."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"670","DOI":"10.3945\/ajcn.111.026708","article-title":"Monitoring of Gluten-Free Diet Compliance in Celiac Patients by Assessment of Gliadin 33-Mer Equivalent Epitopes in Feces","volume":"95","author":"Comino","year":"2012","journal-title":"Am. J. Clin. Nutr."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Mart\u00edn-Masot, R., Correa-L\u00f3pez, N., Herrador-L\u00f3pez, M., Navas-L\u00f3pez, V.M., Carmona, F.D., Nestares, T., and Bossini-Castillo, L. (2025). Immunomodulatory effects of a short-term gluten-free diet on pediatric celiac disease: Findings from a single-cell transcriptomics study. J. Nutr. Biochem., 110063. in press.","DOI":"10.1016\/j.jnutbio.2025.110063"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Huang, Y., McCarthy, D.J., and Stegle, O. (2019). Vireo: Bayesian Demultiplexing of Pooled Single-Cell RNA-Seq Data without Genotype Reference. Genome Biol., 20.","DOI":"10.1186\/s13059-019-1865-2"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Yang, Q., Safina, K.R., Nguyen, K.D.Q., Tuong, Z.K., and Borcherding, N. (2025). scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling. PLoS Comput. Biol., 21.","DOI":"10.1371\/journal.pcbi.1012760"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary Learning for Integrative, Multimodal and Scalable Single-Cell Analysis","volume":"42","author":"Hao","year":"2024","journal-title":"Nat. Biotechnol."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/18\/8927\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:45:05Z","timestamp":1760035505000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/18\/8927"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,13]]},"references-count":32,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["ijms26188927"],"URL":"https:\/\/doi.org\/10.3390\/ijms26188927","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,13]]}}}