{"doi":"10.3389/fimmu.2025.1725282","title":"Mapping the landscape of autoimmunity and autoinflammation in inborn errors of immunity: broad distribution with distinct clustering patterns","abstract":"Objective: In this study, we analyzed a large cohort of Algerian patients with inborn errors of immunity (IEI) to delineate the burden, spectrum, and distribution of autoimmune and autoinflammatory manifestations. Methods: This retrospective cohort study was based on recorded data from 825 Algerian patients with IEI. For each patient, autoimmune and autoinflammatory complications occurring before and/or after IEI diagnosis were systematically assessed and documented. Results: Autoimmune and/or autoinflammatory manifestations were observed in 217 patients (26.3%) and, notably, represented the initial clinical presentation in nearly half. Autoimmune features were documented in 163 patients (19.8%), including 26 (3.2%) with concurrent autoinflammatory findings, whereas isolated autoinflammatory conditions were observed in 54 patients (6.5%). A broad spectrum was observed, with autoimmune cytopenias predominating (11.4%), followed by gastrointestinal (7.8%), rheumatologic (5.3%), and endocrine (3.4%) disorders. Immune dysregulation was a recurrent theme across all IEI categories, with a distinct, disease-specific, clustering of autoimmunity and autoinflammation. Autoimmune cytopenias predominated in T-cell defects, including hypomorphic RAG and CD3γ deficiencies; Inflammatory bowel disease (IBD) was enriched in ARPC1B, DOCK8, and CD55 deficiencies, as well as in chronic granulomatous disease (CGD); endocrine autoimmunity, while a cardinal feature of APECED and IPEX, also characterized STAT1 gain-of-function; inflammatory granulomatous lung disease was a consistent feature in LRBA deficiency; and granulomatous inflammation, whether confined to the lungs or extending to other organs, was prominent in common variable immunodeficiency. Conclusion: Recognition of clustering patterns, particularly autoimmune cytopenias, IBD, and endocrine autoimmunity, has direct clinical implications. These manifestations should be regarded as red flags, guiding targeted evaluation and genetic testing. Mapping such associations not only refines our understanding of pathogenesis but also provides a practical framework for earlier diagnosis and tailored management.","journal":"Frontiers in Immunology","year":2025,"id":537348,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":22.178386323199504,"corpus_rank":9377,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7225,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":27.0833,"fair_percentile":42.25007642922654,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1423605,"name":"Souad Touri","orcid":null,"position":1,"is_corresponding":false},{"id":1423606,"name":"A. Saad-Djaballah","orcid":null,"position":2,"is_corresponding":false},{"id":1423607,"name":"Saliha Hakem","orcid":null,"position":3,"is_corresponding":false},{"id":1423608,"name":"Faiza Fernini","orcid":null,"position":4,"is_corresponding":false},{"id":1423136,"name":"Samira Aggoune","orcid":"0000-0002-6013-8066","position":5,"is_corresponding":false},{"id":1423609,"name":"Hayet Belhadj","orcid":null,"position":6,"is_corresponding":false},{"id":1423610,"name":"Chafa Bendahmane","orcid":null,"position":7,"is_corresponding":false},{"id":1423611,"name":"Linda Mokrane","orcid":null,"position":8,"is_corresponding":false},{"id":1423612,"name":"Tahar Bencharif Madani","orcid":null,"position":9,"is_corresponding":false},{"id":1423613,"name":"Zouleikha Benhacine","orcid":null,"position":10,"is_corresponding":false},{"id":1423614,"name":"Souhila Melzi","orcid":null,"position":11,"is_corresponding":false},{"id":1423615,"name":"R. Aboura","orcid":null,"position":12,"is_corresponding":false},{"id":1423616,"name":"Hassen Messaoudi","orcid":null,"position":13,"is_corresponding":false},{"id":631500,"name":"Houda Boudiaf","orcid":null,"position":14,"is_corresponding":false},{"id":1033796,"name":"Mohamed Samir Ladj","orcid":null,"position":15,"is_corresponding":false},{"id":1423617,"name":"Tahar Khelifi Touhami","orcid":null,"position":16,"is_corresponding":false},{"id":1423618,"name":"L. Taibi","orcid":null,"position":17,"is_corresponding":false},{"id":1423619,"name":"Samira Zobiri","orcid":null,"position":18,"is_corresponding":false},{"id":1423620,"name":"Rachid Bouhdjila","orcid":null,"position":19,"is_corresponding":false},{"id":1423621,"name":"Zahir Bouzerar","orcid":null,"position":20,"is_corresponding":false},{"id":1423137,"name":"Ouardia Ibsaine","orcid":"0000-0002-8796-662X","position":21,"is_corresponding":false},{"id":1423622,"name":"Leila Kedji","orcid":null,"position":22,"is_corresponding":false},{"id":1423138,"name":"Abdelghani Yagoubi","orcid":"0000-0002-5570-8810","position":23,"is_corresponding":false},{"id":1423623,"name":"Reda Belbouab","orcid":null,"position":24,"is_corresponding":false},{"id":1423139,"name":"Rachida Boukari","orcid":"0000-0003-1833-8002","position":25,"is_corresponding":false},{"id":1423624,"name":"Leila Smati","orcid":null,"position":26,"is_corresponding":false},{"id":246526,"name":"Sergio D. Rosenzweig","orcid":"0000-0002-5550-9678","position":27,"is_corresponding":false},{"id":105284,"name":"Dusan Bogunovic","orcid":"0000-0002-9277-3232","position":28,"is_corresponding":false},{"id":231247,"name":"Luigi D. Notarangelo","orcid":"0000-0002-8335-0262","position":29,"is_corresponding":false},{"id":1423625,"name":"Kamel Djenouhat","orcid":null,"position":30,"is_corresponding":false},{"id":1423135,"name":"Azzeddine Tahiat","orcid":"0000-0003-3272-8904","position":0,"is_corresponding":true}],"reference_count":34,"raw_metadata":null,"created_at":"2026-07-19T02:52:12.997494Z","pmid":"41394846","pmcid":"PMC12698554","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":11.1111,"fair_a":31.25,"fair_i":0.0,"fair_r":45.8333,"fair_zscore":-0.2916,"fair_rationale":{"fair_score":27.08,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":11.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No persistent identifier (DOI, Handle, ARK, or repository accession) is given for the dataset; only the article DOI is present.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"The original contributions presented in the study are included in the article/Supplementary Material.","grounded":false,"rationale":"No repository is named; the data are said to be held in the article and supplementary material.","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"The original contributions presented in the study are included in the article/Supplementary Material. 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'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Statistical analyses were performed with SPSS software, version 25.0 (IBM, Chicago, IL, USA).","why":"The text names software used for analysis but not the instruments or assays that produced the data. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No data dictionary, codebook, README, or variable-definition table is mentioned or provided.","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human clinical / human-subjects data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Further inquiries can be directed to the corresponding author.","why":"The only gatekeeper named is a natural person (the corresponding author), not an institutional committee. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier for an external resource (e.g., reference genome, database build) is provided; only bibliographic citations exist.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The original contributions presented in the study are included in the article/Supplementary Material.","why":"The statement indicates the data are available now but makes no commitment to how long they will persist. [downgraded to 'no' — no verifiable quote from the paper]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T13:33:30.128895Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}