Unraveling Key m6A Modification Regulators Signatures in Postmenopausal Osteoporosis through Bioinformatics and Experimental Verification.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38658320", "kind": "science-record", "revision": 4, "content_hash": "sha256:94de160709b51b8fb522f1f8b604b58c0c44d397b42f40c60f891092427b81da", "created_at": "2026-11-01T19:20:38Z", "updated_at": "2026-11-01T22:54:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Unraveling Key m6A Modification Regulators Signatures in Postmenopausal Osteoporosis through Bioinformatics and Experimental Verification.", "doi": "10.1111/os.14064", "pmid": "38658320", "authors": ["Zhi-Wei Feng", "He-Fang Xiao", "Xing-Wen Wang", "Yong-Kang Niu", "Da-Cheng Zhao", "Cong Tian", "Sheng-Hong Wang", "Bo Peng", "Fei Yang", "Bin Geng", "Ming-Gang Guo", "Xiao-Yun Sheng", "Ya-Yi Xia"], "journal": "Orthopaedic surgery", "year": 2024, "abstract": "OBJECTIVE: Bone marrow mesenchymal stem cells (BMSCs) show significant potential for osteogenic differentiation. However, the underlying mechanisms of osteogenic capability in osteoporosis-derived BMSCs (OP-BMSCs) remain unclear. This study aims to explore the impact of YTHDF3 (YTH N6-methyladenosine RNA binding protein 3) on the osteogenic traits of OP-BMSCs and identify potential therapeutic targets to boost their bone formation ability.\nMETHODS: We examined microarray datasets (GSE35956 and GSE35958) from the Gene Expression Omnibus (GEO) to identify potential m6A regulators in osteoporosis (OP). Employing differential, protein interaction, and machine learning analyses, we pinpointed critical hub genes linked to OP. We further probed the relationship between these genes and OP using single-cell analysis, immune infiltration assessment, and Mendelian randomization. Our in vivo and in vitro experiments validated the expression and functionality of the key hub gene.\nRESULTS: Differential analysis revealed seven key hub genes related to OP, with YTHDF3 as a central player, supported by protein interaction analysis and machine learning methodologies. Subsequent single-cell, immune infiltration, and Mendelian randomization studies consistently validated YTHDF3's significant link to osteoporosis. YTHDF3 levels are significantly reduced in femoral head tissue from postmenopausal osteoporosis (PMOP) patients and femoral bone tissue from PMOP mice. Additionally, silencing YTHDF3 in OP-BMSCs substantially impedes their proliferation and differentiation.\nCONCLUSION: YTHDF3 may be implicated in the pathogenesis of OP by regulating the proliferation and osteogenic differentiation of OP-BMSCs.", "claims": [{"id": "claim-method", "statement": "The limma package was employed to assess variations in m6A regulators between high‐ and low‐Bone Mineral Density (BMD) samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38658320", "locator": "sections[4] \"Investigation and Evaluation of m6A Regulators\" paragraph 2", "quote": "The limma package was employed to assess variations in m6A regulators between high‐ and low‐Bone Mineral Density (BMD) samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Supplementary Material, GitHub.com, GWAS summary data, and the publication include the original contributions that were presented in the research. Kindly contact the corresponding author with any further questions.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38658320", "locator": "sections[36] \"Data Availability Statement\" paragraph 2", "quote": "Supplementary Material, GitHub.com, GWAS summary data, and the publication include the original contributions that were presented in the research. Kindly contact the corresponding author with any further questions."}], "state": "complete"}, {"id": "claim-target-result", "statement": "YTHDF3 may be implicated in the pathogenesis of OP by regulating the proliferation and osteogenic differentiation of OP‐BMSCs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38658320", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "YTHDF3 may be implicated in the pathogenesis of OP by regulating the proliferation and osteogenic differentiation of OP‐BMSCs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "YTHDF3 may be implicated in the pathogenesis of OP by regulating the proliferation and osteogenic differentiation of OP‐BMSCs.", "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:38658320"], "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:GSE35956"], "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:GSE35956"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38658320", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/os.14064", "sha256": "sha256:e672baca89bcd098aaa98a3e06a4ebfd157a6549a5b6ee751ad3854aff74e6e2", "bytes": 54442, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/os.14064", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11144519", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE35956", "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=GSE35956", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE35956", "version": null, "note": "Supplementary Material, GitHub.com, GWAS summary data, and the publication include the original contributions that were presented in the research. Kindly contact the corresponding author with any further questions.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Supplementary Material, GitHub.com, GWAS summary data, and the publication include the original contributions that were presented in the research. Kindly contact the corresponding author with any further questions.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM878095", "GSM878096", "GSM878097", "GSM878098", "GSM878099", "GSM878104", "GSM878105", "GSM878106", "GSM878107", "GSM878108"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Effects of Primary Osteoporosis and Advanced Age on Human Mesenchymal Stem Cells", "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:GSE35958", "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=GSE35958", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE35958", "version": null, "note": "Supplementary Material, GitHub.com, GWAS summary data, and the publication include the original contributions that were presented in the research. Kindly contact the corresponding author with any further questions.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Supplementary Material, GitHub.com, GWAS summary data, and the publication include the original contributions that were presented in the research. Kindly contact the corresponding author with any further questions.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM878100", "GSM878101", "GSM878102", "GSM878103", "GSM878104", "GSM878105", "GSM878106", "GSM878107", "GSM878108"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Effects of Primary Osteoporosis on Human Mesenchymal Stem Cells", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE35956 not downloaded", "asset:data:geo:GSE35956 licence not read", "asset:data:geo:GSE35958 not downloaded", "asset:data:geo:GSE35958 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The limma package was employed to assess variations in m6A regulators between high‐ and low‐Bone Mineral Density (BMD) samples."}}, {"id": "method-2", "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": "analysis of variance"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman rank correlation"}}, {"id": "method-4", "family": "genetic_association", "specific": "mendelian_randomisation", "label": "Genetic association (GWAS / linkage / MR)", "dsl_operations": ["mr_estimate"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["genotype_phenotype_table"], "evidence": {"score": 0.7, "band": "medium", "quote": "Mendelian randomization"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE35956", "GSE35958"], "resolved_accessions": ["GSE35956", "GSE35958"], "statements": ["Supplementary Material, GitHub.com, GWAS summary data, and the publication include the original contributions that were presented in the research. Kindly contact the corresponding author with any further questions."], "basis": "The paper names GSE35956, GSE35958 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:38658320", "data:geo:GSE35956"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE35956"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:16:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15603, "completion_tokens": 1671, "cached_tokens": 128}}, "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:38658320", "type": "paper", "label": "pmid:38658320"}, {"id": "source:pmid:38658320", "type": "manuscript", "label": "PMID 38658320 full text"}, {"id": "data:geo:GSE35956", "type": "dataset", "label": "GEO GSE35956"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38658320", "type": "paper", "label": "pmid:38658320"}, {"id": "source:pmid:38658320", "type": "manuscript", "label": "PMID 38658320 full text"}, {"id": "data:geo:GSE35956", "type": "dataset", "label": "GEO GSE35956"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38658320", "type": "extraction", "used": ["source:pmid:38658320"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE35956", "type": "accession_resolution", "used": ["data:geo:GSE35956"], "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:38658320", "parent_hash": "sha256:101eea225c5531c6ca6af3323ac5aa709ac5edea5e2fc789740a37e51b6edfc7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE35956 licence not read", "asset:data:geo:GSE35956 not downloaded", "asset:data:geo:GSE35958 licence not read", "asset:data:geo:GSE35958 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "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": ["bone formation ability. METHODS: We examined microarray datasets (GSE35956 and GSE35958) from the Ge"], "order_basis": "paper_text_order:559", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["assessment, and Mendelian randomization. Our in vivo and in vitro experiments validated the expre", "sociated with OP, we induced an osteoporotic mouse model through OVX. Trabecular bone imaging data de", "om the bone marrow mesenchymal stem cells of mouse data, including a total of 7585 cells. Furth", "sociated with OP, we induced an osteoporotic mouse model through OVX. Trabecular bone imaging d"], "order_basis": "paper_text_order:979", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["in bone volume in the OP group (Figure 5A). Western blot analysis showed a notable downregulation of"], "order_basis": "paper_text_order:5465", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": [", PCNA, and YTHDF3 (Figure 5F). Furthermore, immunofluorescence of the femur demonstrated that, compared to", "and YTHDF3 in SHAM and OVX mice (n = 3). (G) Immunofluorescence staining for YTHDF3 and RUNX2 in femurs of s", "Osterix, and YTHDF3 in OVX mice (Figure 5E). IHC analyses illustrated reduced expression of R", "and YTHDF3 in SHAM and OVX mice (n = 3). (F) IHC images showed the expression of RUNX2, Oster"], "order_basis": "paper_text_order:6382", "id": "assay:4"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The limma package was employed to assess variations in m6A regulators between high‐ and low‐Bone Mineral Density (BMD) samples."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}