Identification of Up-Regulated ANXA3 Resulting in Fracture Non-Union in Patients With T2DM.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35813617", "kind": "science-record", "revision": 4, "content_hash": "sha256:b0d4cf9d3513cd844c5b9553d3601f5988999ac2fde45fe3ed8039a3898b02f5", "created_at": "2026-11-01T18:14:52Z", "updated_at": "2026-11-01T22:06:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Up-Regulated ANXA3 Resulting in Fracture Non-Union in Patients With T2DM.", "doi": "10.3389/fendo.2022.890941", "pmid": "35813617", "authors": ["Changjiang Liu", "Yuhang Liu", "Yifeng Yu", "Yong Zhao", "Dong Zhang", "Aixi Yu"], "journal": "Frontiers in endocrinology", "year": 2022, "abstract": "Diabetes mellitus is a metabolic disorder that increases fracture risk and interferes with bone formation and impairs fracture healing. Genomic studies on diabetes and fracture healing are lacking. We used a weighted co-expression network analysis (WGCNA) method to identify susceptibility modules and hub genes associated with T2DM and fracture healing. First, we downloaded the GSE95849, GSE93213, GSE93215, and GSE142786 data from the Gene Expression Omnibus (GEO) website, analyzed differential expression genes and constructed a WGCNA network. Second, we screened out 30 hub genes, which were found to be enriched in neutrophil activation, translational initiation, RAGE receptor binding, propanoate metabolism, and other pathways through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) analyses. Third, we searched for genes related to bone metabolism and fracture healing in the published genome-wide single nucleotide polymorphism (SNP) data, built a protein-protein interaction (PPI) network with hub genes, and found that they were associated with metabolic process, blood vessel development, and extracellular matrix organization. ANXA3 was identified as the biomarker based on gene expression and correlation analysis. And the AUC value of it was 0.947. Fourth, we explored that ANXA3 was associated with neutrophils in fracture healing process by single-cell RNA sequencing analysis. Finally, we collected clinical patient samples and verified the expression of ANXA3 by qRT-PCR in patents with T2DM and fracture non-union. In conclusion, this is the first genomics study on the effect of T2DM on fracture healing. Our study identified some characteristic modules and hub genes in the etiology of T2DM-associated fracture non-union, which may help to further investigate the molecular mechanisms. Up-regulated ANXA3 potentially contributed to fracture non-union in T2DM by mediating neutrophils. It can be a prognostic biomarker and potential therapeutic target.", "claims": [{"id": "claim-method", "statement": "We used a weighted co-expression network analysis (WGCNA) method to identify susceptibility modules and hub genes associated with T2DM and fracture healing.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35813617", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We used a weighted co-expression network analysis (WGCNA) method to identify susceptibility modules and hub genes associated with T2DM and fracture healing."}], "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:35813617", "locator": "sections[23] \"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": "ANXA3 was identified as a biomarker with an AUC of 0.947, and its upregulation was linked to neutrophil-mediated fracture non-union in T2DM.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35813617", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "ANXA3 was identified as the biomarker based on gene expression and correlation analysis."}, {"asset": "source:pmid:35813617", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "And the AUC value of it was 0.947."}, {"asset": "source:pmid:35813617", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Up-regulated ANXA3 potentially contributed to fracture non-union in T2DM by mediating neutrophils."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ANXA3 was identified as a biomarker with an AUC of 0.947, and its upregulation was linked to neutrophil-mediated fracture non-union in T2DM.", "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:35813617"], "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:GSE142786"], "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:GSE142786"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35813617", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fendo.2022.890941", "sha256": "sha256:7390ceee45a6212b7c0d49c6f96baf10a8532a088c783ba62eaa8164109d837b", "bytes": 41059, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fendo.2022.890941", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9263855", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE142786", "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=GSE142786", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE142786", "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": ["GSM4240163", "GSM4240164"], "sample_count": 2, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Single-cell RNA-seq analysis reveals reduction of B cells in the bone marrow promote fracture healing", "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:GSE93213", "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=GSE93213", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE93213", "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": ["GSM2448666", "GSM2448667", "GSM2448668", "GSM2448669", "GSM2448670", "GSM2448671"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "809094 Biomarker Identification in Fracture Healing (experiment #3873a mRNA performed Apr 2011)", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE93215", "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=GSE93215", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE93215", "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": ["GSM2448684", "GSM2448685", "GSM2448686", "GSM2448687", "GSM2448688", "GSM2448689", "GSM2448690", "GSM2448691", "GSM2448692", "GSM2448693", "GSM2448694", "GSM2448695", "GSM2448696", "GSM2448697", "GSM2448698", "GSM2448699", "GSM2448700", "GSM2448701", "GSM2448702", "GSM2448703", "GSM2448704", "GSM2448705", "GSM2448706", "GSM2448707", "GSM2448708", "GSM2448709", "GSM2448710", "GSM2448711"], "sample_count": 28, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "809094 Biomarker Identification in Fracture Healing (experiment #3341 performed 2010 Jun) [mRNA]", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE95849", "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=GSE95849", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE95849", "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": ["GSM2527022", "GSM2527023", "GSM2527024", "GSM2527025", "GSM2527026", "GSM2527027", "GSM2527028", "GSM2527029", "GSM2527030", "GSM2527031", "GSM2527032", "GSM2527033", "GSM2527034", "GSM2527035", "GSM2527036", "GSM2527037", "GSM2527038", "GSM2527039"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "22448", "taxon": "Homo sapiens", "title": "Transcriptional profiling of diabetic peripheral neuropathy patients, diabetic patients, and healthy participants", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE142786 not downloaded", "asset:data:geo:GSE142786 licence not read", "asset:data:geo:GSE93213 not downloaded", "asset:data:geo:GSE93213 licence not read", "asset:data:geo:GSE93215 not downloaded", "asset:data:geo:GSE93215 licence not read", "asset:data:geo:GSE95849 not downloaded", "asset:data:geo:GSE95849 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "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": "GO enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "weighted co-expression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used a weighted co-expression network analysis (WGCNA) method to identify susceptibility modules and hub genes associated with T2DM and fracture healing."}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE95849", "GSE93213", "GSE93215", "GSE142786"], "resolved_accessions": ["GSE95849", "GSE93213", "GSE93215", "GSE142786"], "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 GSE95849, GSE93213, GSE93215, GSE142786 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:35813617", "data:geo:GSE142786"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE142786"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:54:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10773, "completion_tokens": 2400, "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:35813617", "type": "paper", "label": "pmid:35813617"}, {"id": "source:pmid:35813617", "type": "manuscript", "label": "PMID 35813617 full text"}, {"id": "data:geo:GSE142786", "type": "dataset", "label": "GEO GSE142786"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35813617", "type": "paper", "label": "pmid:35813617"}, {"id": "source:pmid:35813617", "type": "manuscript", "label": "PMID 35813617 full text"}, {"id": "data:geo:GSE142786", "type": "dataset", "label": "GEO GSE142786"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35813617", "type": "extraction", "used": ["source:pmid:35813617"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE142786", "type": "accession_resolution", "used": ["data:geo:GSE142786"], "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:35813617", "parent_hash": "sha256:7ecc69c5f6b59a2771418b9174c7fc0e928115e9cc8a4bade5b4068a02711b4c", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE142786 licence not read", "asset:data:geo:GSE142786 not downloaded", "asset:data:geo:GSE93213 licence not read", "asset:data:geo:GSE93213 not downloaded", "asset:data:geo:GSE93215 licence not read", "asset:data:geo:GSE93215 not downloaded", "asset:data:geo:GSE95849 licence not read", "asset:data:geo:GSE95849 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["h neutrophils in fracture healing process by single-cell RNA sequencing analysis. Finally, we collected clinical pat"], "order_basis": "paper_text_order:1467", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["s in fracture healing process by single-cell RNA sequencing analysis. Finally, we collected clinical pat"], "order_basis": "paper_text_order:1479", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}