The Roles of Blood Lipid-Metabolism Genes in Immune Infiltration Could Promote the Development of IDD.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35223859", "kind": "science-record", "revision": 5, "content_hash": "sha256:032621d8261e3ef3fe924de50278cda5656a4e2fda1ec891658a510527bd2acd", "created_at": "2026-11-01T17:36:59Z", "updated_at": "2026-11-01T22:06:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Roles of Blood Lipid-Metabolism Genes in Immune Infiltration Could Promote the Development of IDD.", "doi": "10.3389/fcell.2022.844395", "pmid": "35223859", "authors": ["Weihang Li", "Ziyi Ding", "Huan Zhang", "Quan Shi", "Dong Wang", "Shilei Zhang", "Songjie Xu", "Bo Gao", "Ming Yan"], "journal": "Frontiers in cell and developmental biology", "year": 2022, "abstract": "Objectives: Intervertebral disc degeneration is a progressive and chronic disease, usually manifesting as low back pain. This study aimed to screen effective biomarkers for medical practice as well as figuring out immune infiltration situations between circulation and intervertebral discs. Methods: Gene expression profiles of GSE124272 was included for differentially analysis, WGCNA and immune infiltration analysis from GEO database, and other GSE series were used as validation datasets. A series of validation methods were conducted to verify the robustness of hub genes, such as principal component analysis, machine learning models, and expression verification. Lastly, nomogram was established for medical practice. Results: 10 genes were commonly screened via combination of DEGs, WGCNA analysis and lipid metabolism related genes. Furthermore, 3 hub gens CYP27A1, FAR2, CYP1B1 were chosen for subsequent analysis based on validation of different methods. GSEA analysis discovered that neutrophil extracellular traps formation and NOD-like receptor signaling pathway was activated during IDD. Immune infiltration analysis demonstrated that the imbalance of neutrophils and γδT cells were significantly correlated with IDD progression. Nomogram was established based on CYP27A1, FAR2, CYP1B1 and age, the calibration plot confirmed the stability of our model. Conclusion: CYP27A1, FAR2, CYP1B1 were considered as hub lipid metabolism related genes (LMRGs) in the development of IDD, which were regarded as candidate diagnostic biomarkers especially in circulation. The effects are worth expected in the early diagnosis of IDD through detecting these genes in blood.", "claims": [{"id": "claim-method", "statement": "All genes of whole blood from GSE124272 were included for WGCNA (“WGCNA” and related packages in R) analysis, to avoid the inaccurate results that may generate from the top of 5,000 genes (according to variance).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35223859", "locator": "sections[8] \"Weight Gene Co-Expression Network Analysis\" paragraph 2", "quote": "All genes of whole blood from GSE124272 were included for WGCNA (“WGCNA” and related packages in R) analysis, to avoid the inaccurate results that may generate from the top of 5,000 genes (according to variance)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35223859", "locator": "sections[26] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Furthermore, 3 hub gens CYP27A1, FAR2, CYP1B1 were chosen for subsequent analysis based on validation of different methods.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35223859", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Furthermore, 3 hub gens CYP27A1, FAR2, CYP1B1 were chosen for subsequent analysis based on validation of different methods."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Furthermore, 3 hub gens CYP27A1, FAR2, CYP1B1 were chosen for subsequent analysis based on validation of different methods.", "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:35223859"], "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:GSE124272"], "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:GSE124272"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35223859", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcell.2022.844395", "sha256": "sha256:002e3bfb729ec71e478ad9c5e5bb95157471e1bf18c90ab2eb89e5a8b06dd54e", "bytes": 59528, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcell.2022.844395", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8864150", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE124272", "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=GSE124272", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE124272", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3526782", "GSM3526783", "GSM3526784", "GSM3526785", "GSM3526786", "GSM3526787", "GSM3526788", "GSM3526789", "GSM3526790", "GSM3526791", "GSM3526792", "GSM3526793", "GSM3526794", "GSM3526795", "GSM3526796", "GSM3526797"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "21185", "taxon": "Homo sapiens", "title": "Transcriptome signatures reveal candidate key genes in the whole blood of patients with lumbar disc prolapse", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE147383", "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=GSE147383", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE147383", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4429807", "GSM4429808", "GSM4429809", "GSM4429810", "GSM4429811", "GSM4429812", "GSM4429813", "GSM4429814"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data for human intervertebral discs", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE23130", "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=GSE23130", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE23130", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM569830", "GSM569831", "GSM569832", "GSM569833", "GSM569834", "GSM569835", "GSM569836", "GSM569837", "GSM569838", "GSM569839", "GSM569840", "GSM569841", "GSM569842", "GSM569843", "GSM569844", "GSM569845", "GSM569846", "GSM569847", "GSM569848", "GSM569849", "GSM569850", "GSM569851", "GSM569852"], "sample_count": 23, "group_sizes": null, "group_sizes_basis": null, "platform": "1352", "taxon": "Homo sapiens", "title": "Gene Array Data from Human Annulus Disc Tissue", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE34095", "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=GSE34095", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE34095", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM841717", "GSM841718", "GSM841719", "GSM841720", "GSM841721", "GSM841722"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data between human degenerative and non-degenerative intervertebral discs", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE70362", "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=GSE70362", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70362", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1725780", "GSM1725781", "GSM1725782", "GSM1725783", "GSM1725784", "GSM1725785", "GSM1725786", "GSM1725787", "GSM1725788", "GSM1725789", "GSM1725790", "GSM1725791", "GSM1725792", "GSM1725793", "GSM1725794", "GSM1725795", "GSM1725796", "GSM1725797", "GSM1725798", "GSM1725799", "GSM1725800", "GSM1725801", "GSM1725802", "GSM1725803", "GSM1725804", "GSM1725805", "GSM1725806", "GSM1725807", "GSM1725808", "GSM1725809", "GSM1725810", "GSM1725811", "GSM1725812", "GSM1725813", "GSM1725814", "GSM1725815", "GSM1725816", "GSM1725817", "GSM1725818", "GSM1725819", "GSM1725820", "GSM1725821", "GSM1725822", "GSM1725823", "GSM1725824", "GSM1725825", "GSM1725826", "GSM1725827"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "17810", "taxon": "Homo sapiens", "title": "Gene Expression Profiling Identifies Interferon Signalling Molecules and IGFBP3 in Human Degenerative Annulus Fibrosus", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE124272 not downloaded", "asset:data:geo:GSE124272 licence not read", "asset:data:geo:GSE147383 not downloaded", "asset:data:geo:GSE147383 licence not read", "asset:data:geo:GSE23130 not downloaded", "asset:data:geo:GSE23130 licence not read", "asset:data:geo:GSE34095 not downloaded", "asset:data:geo:GSE34095 licence not read", "asset:data:geo:GSE70362 not downloaded", "asset:data:geo:GSE70362 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "principal component analysis"}}, {"id": "method-3", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-5", "family": null, "specific": null, "label": "weighted gene co-expression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "All genes of whole blood from GSE124272 were included for WGCNA (“WGCNA” and related packages in R) analysis, to avoid the inaccurate results that may generate from the top of 5,000 genes (according to variance)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE124272", "GSE23130", "GSE70362", "GSE34095", "GSE147383"], "resolved_accessions": ["GSE124272", "GSE23130", "GSE70362", "GSE34095", "GSE147383"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material."], "basis": "The paper names GSE124272, GSE23130, GSE70362, GSE34095, GSE147383 in gene expression omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:35223859", "data:geo:GSE124272"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE124272"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:36:12Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16529, "completion_tokens": 2261, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35223859", "type": "paper", "label": "pmid:35223859"}, {"id": "source:pmid:35223859", "type": "manuscript", "label": "PMID 35223859 full text"}, {"id": "data:geo:GSE124272", "type": "dataset", "label": "GEO GSE124272"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35223859", "type": "paper", "label": "pmid:35223859"}, {"id": "source:pmid:35223859", "type": "manuscript", "label": "PMID 35223859 full text"}, {"id": "data:geo:GSE124272", "type": "dataset", "label": "GEO GSE124272"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35223859", "type": "extraction", "used": ["source:pmid:35223859"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE124272", "type": "accession_resolution", "used": ["data:geo:GSE124272"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:35223859", "parent_hash": "sha256:8a9402e7b58f2fbe61ef20a48579e598f4ca4fca9a1b92eccc73180a19790e86", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE124272 licence not read", "asset:data:geo:GSE124272 not downloaded", "asset:data:geo:GSE147383 licence not read", "asset:data:geo:GSE147383 not downloaded", "asset:data:geo:GSE23130 licence not read", "asset:data:geo:GSE23130 not downloaded", "asset:data:geo:GSE34095 licence not read", "asset:data:geo:GSE34095 not downloaded", "asset:data:geo:GSE70362 licence not read", "asset:data:geo:GSE70362 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["tween IDD and normal patients, blood tissues microarray data from GSE124272 series was conducted for"], "order_basis": "paper_text_order:6758", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["ANOVA"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}