Identification of immune-related biomarkers in embryos with neural tube defects via a bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35928755", "kind": "science-record", "revision": 5, "content_hash": "sha256:3d4efae83d5dddd242afa9585505ff9b58b977fa3c53196b64b274ae8a4888ce", "created_at": "2026-11-01T18:15:01Z", "updated_at": "2026-11-01T22:49:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of immune-related biomarkers in embryos with neural tube defects via a bioinformatics analysis.", "doi": "10.21037/atm-22-1273", "pmid": "35928755", "authors": ["Qingli Huang", "Li Yang", "Binbin Nong", "Haisi Gan", "Huizhen Wu", "Meiyan Li", "Mingyang Jin", "Liling Xie"], "journal": "Annals of translational medicine", "year": 2022, "abstract": "Background: Neural tube defects (NTDs) are one of the most common types of birth defects. Oral folic acid (FA) prophylaxis is currently available, but the pathogenesis of NTDs is not fully understood. We conducted this study to examine the role of the immune landscape of NTDs and identify novel diagnostic and therapeutic biomarkers.\nMethods: We downloaded the GSE33111 data set of 12 NTD embryos and 12 healthy embryos in the same period of fetal development from the Gene Expression Omnibus (GEO) database. We compared the healthy embryos and NTD embryos to identify the differentially expressed genes (DEGs). We also performed a functional enrichment analysis of the DEGs using the clusterProfiler package. We extracted the top 10 ranked genes as hub immune-related biomarkers. We then used receiver operating characteristic (ROC) curves to determine the expression levels of the hub immune-related genes and the accuracy of the diagnosis of NTDs. Finally, we analyzed the immune landscape of the NTD embryos and healthy embryos via a single-sample gene set enrichment analysis (ssGSEA).\nResults: A total of 611 DEGs were identified by the differential analysis, including 95 immune genes. The functional enrichment analysis indicated that Epstein-Barr virus infection, antigen processing and presentation, inflammatory bowel disease, and type I diabetes mellitus were associated with NTDs. The results of the expression level analysis showed that the hub immune-related genes were more highly expressed in the NTD embryos than the healthy embryos. Additionally, the ROC curve analysis also indicated that the expression levels of the 10 hub immune-related genes were highly accurate in the diagnosis of NTDs [area under the curve (AUC) range, 0.708-0.812]. The immune infiltration analysis demonstrated that 20 of the 28 immune cell types were more highly infiltrated in the NTD embryos than the healthy embryos.\nConclusions: Immune-related genes are important regulators of the occurrence and development of NTDs.", "claims": [{"id": "claim-method", "statement": "Differential analysis of healthy and NTD embryos was performed using the limma package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35928755", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "Differential analysis of healthy and NTD embryos was performed using the limma package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We downloaded the GSE33111 data set from Gene Expression Omnibus (GEO) database, which contained the messenger ribonucleic acid profiles of 12 NTD-affected fetal samples and 12 healthy control samples in the same period of fetal development.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35928755", "locator": "sections[3] \"Raw data\" paragraph 2", "quote": "We downloaded the GSE33111 data set from Gene Expression Omnibus (GEO) database, which contained the messenger ribonucleic acid profiles of 12 NTD-affected fetal samples and 12 healthy control samples in the same period of fetal development."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 611 DEGs were identified by the differential analysis, including 95 immune genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35928755", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 611 DEGs were identified by the differential analysis, including 95 immune genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 611 DEGs were identified by the differential analysis, including 95 immune genes.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:35928755"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE33111"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE33111"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35928755", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm-22-1273", "sha256": "sha256:cec8aef1ec8844efce13c7cc865aefc4a0191a50affd2c7da4de7e58b9bc8fa9", "bytes": 22590, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/atm-22-1273", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9347061", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE33111", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33111", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33111", "version": null, "note": "We downloaded the GSE33111 data set from Gene Expression Omnibus (GEO) database, which contained the messenger ribonucleic acid profiles of 12 NTD-affected fetal samples and 12 healthy control samples in the same period of fetal development.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded the GSE33111 data set from Gene Expression Omnibus (GEO) database, which contained the messenger ribonucleic acid profiles of 12 NTD-affected fetal samples and 12 healthy control samples in the same period of fetal development.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM820012", "GSM820013", "GSM820014", "GSM820015", "GSM820016", "GSM820017", "GSM820018", "GSM820019", "GSM820020", "GSM820021", "GSM820022", "GSM820023", "GSM820024", "GSM820025", "GSM820026", "GSM820027", "GSM820028", "GSM820029", "GSM820030", "GSM820031", "GSM820032", "GSM820033", "GSM820034", "GSM820035"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "mRNA 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