Identification of Regulatory RNA-Binding Genes in Spermatogonial Stem Cell Reprogramming to ES-like Cells Using Machine Learning-Integrated Transcriptomic and Network Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41148847", "kind": "science-record", "revision": 3, "content_hash": "sha256:6a4b8bd4caacd82ec542f3c14b9886d976d80262482f1b5107cad654a25b3487", "created_at": "2026-11-01T20:31:12Z", "updated_at": "2026-11-01T22:14:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Regulatory RNA-Binding Genes in Spermatogonial Stem Cell Reprogramming to ES-like Cells Using Machine Learning-Integrated Transcriptomic and Network Analysis.", "doi": "10.3390/cells14201632", "pmid": "41148847", "authors": ["Ali Shakeri Abroudi", "Hossein Azizi", "Hewa Khalid Abdullah", "Marwa Fadhil Alsaffar", "Thomas Skutella"], "journal": "Cells", "year": 2025, "abstract": "Spermatogonial stem cells (SSCs) are unipotent germline cells with emerging pluripotent potential under specific in vitro conditions. Understanding their capacity for reprogramming and the molecular mechanisms involved offers valuable insights into regenerative medicine and fertility preservation. SSCs were isolated from Oct4-GFP C57BL/6 transgenic mice using enzymatic digestion and cultured in defined media. Under these conditions, ES-like colonies emerged expressing pluripotency markers. These cells were characterized by immunocytochemistry, teratoma assays, and transcriptomic analyses using bulk and single-cell RNA sequencing datasets. Gene expression profiles were compared with ESCs and SSCs using datasets from GEO (GSE43850, GSE38776, GSE149512). Protein-protein interaction (PPI) networks and co-expression modules were explored through STRING, Cytoscape, and WGCNA. ES-like cells derived from SSCs exhibited strong expression of OCT4, DAZL, and VASA. Transcriptomic analysis revealed key differentially expressed genes and shared regulatory networks with ESCs. WGCNA identified key co-expression modules and hub regulatory RNA binding genes (Ctdsp1, Rest, and Stra8) potentially responsible for the reprogramming process. Teratoma assays confirmed pluripotency, and single-cell RNA-seq validated expression of critical markers in cultured SSCs. This study demonstrates that SSCs can acquire pluripotency features and be reprogrammed into ES-like cells. The integration of transcriptomic and network-based analyses reveals novel insights into the molecular drivers of SSC reprogramming, highlighting their potential utility in stem cell-based therapies and male fertility preservation.", "claims": [{"id": "claim-method", "statement": "We used the WGCNA R [17] program to construct gene co-expression networks using hSSC gene expression data profiles.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41148847", "locator": "sections[11] \"2.9. Identification of Key Co-Expression Modules Using WGCNA\" paragraph 2", "quote": "We used the WGCNA R [17] program to construct gene co-expression networks using hSSC gene expression data profiles."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in this research are included in the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41148847", "locator": "sections[35] \"notes\" paragraph 1", "quote": "The original contributions presented in this research are included in the article."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:41148847"], "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:GSE149512"], "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:GSE149512"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41148847", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cells14201632", "sha256": "sha256:337d450791674274d376412c27b48b774781c1956e300528ff8cab1ad0c969d6", "bytes": 51017, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cells14201632", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12562428", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE149512", "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=GSE149512", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE149512", "version": null, "note": "The original contributions presented in this research are included in the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in this research are included in the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4504181", "GSM4504182", "GSM4504183", "GSM4504184", "GSM4504185", "GSM4504186", "GSM4504187", "GSM4504188", "GSM4504189", "GSM4504190", "GSM4504191", "GSM4504192", "GSM4504193", "GSM4504194", "GSM4504195", "GSM4504196", "GSM4504197"], "sample_count": 17, "group_sizes": null, "group_sizes_basis": null, "platform": "24676;27644", "taxon": "Homo sapiens", "title": "Single-cell analysis of developing and azoospermia human testicles reveals central role of Sertoli cells", "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:GSE38776", "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=GSE38776", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38776", "version": null, "note": "The original contributions presented in this research are included in the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in this research are included in the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM949357", "GSM949358", "GSM949359", "GSM949360", "GSM949361", "GSM949362"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "6887", "taxon": "Mus musculus", "title": "Genomic profiling of spermatogonial stem cells and embryonic stem cells", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE43850", "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=GSE43850", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43850", "version": null, "note": "The original contributions presented in this research are included in the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in this research are included in the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1072226", "GSM1072227", "GSM1072228", "GSM1072229", "GSM1072230", "GSM1072231", "GSM1072232", "GSM1072233", "GSM1072234", "GSM1072235", "GSM1072236", "GSM1072237", "GSM1072238", "GSM1072239", "GSM1072240", "GSM1072241", "GSM1072242", "GSM1072243", "GSM1072244", "GSM1072245", "GSM1072246", "GSM1072247", "GSM1072248", "GSM1072249", "GSM1072250", "GSM1072251", "GSM1072252", "GSM1072253", "GSM1072254", "GSM1072255", "GSM1072256", "GSM1072257", "GSM1072258", "GSM1072259", "GSM1072260", "GSM1072261", "GSM1072262", "GSM1072263", "GSM1072264", "GSM1072265", "GSM1072266", "GSM1072267", "GSM1072268", "GSM1072269", "GSM1072270", "GSM1072271"], "sample_count": 46, "group_sizes": null, "group_sizes_basis": null, "platform": "6246", "taxon": "Mus musculus", "title": "Gene expression profiles of induced multipotent germline stem cells and other pluripotent stem cells", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE149512 not downloaded", "asset:data:geo:GSE149512 licence not read", "asset:data:geo:GSE38776 not downloaded", "asset:data:geo:GSE38776 licence not read", "asset:data:geo:GSE43850 not downloaded", "asset:data:geo:GSE43850 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": "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-3", "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": "We used the WGCNA R [17] program to construct gene co-expression networks using hSSC gene expression data profiles."}}], "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": ["GSE43850", "GSE38776", "GSE149512"], "resolved_accessions": ["GSE43850", "GSE38776", "GSE149512"], "statements": ["The original contributions presented in this research are included in the article."], "basis": "The paper names GSE43850, GSE38776, GSE149512 in NCBI Gene Expression Omnibus (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:41148847", "data:geo:GSE149512"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE149512"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:04:03Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13494, "completion_tokens": 1082, "cached_tokens": 256}}, "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:41148847", "type": "paper", "label": "pmid:41148847"}, {"id": "source:pmid:41148847", "type": "manuscript", "label": "PMID 41148847 full text"}, {"id": "data:geo:GSE149512", "type": "dataset", "label": "GEO GSE149512"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41148847", "type": "paper", "label": "pmid:41148847"}, {"id": "source:pmid:41148847", "type": "manuscript", "label": "PMID 41148847 full text"}, {"id": "data:geo:GSE149512", "type": "dataset", "label": "GEO GSE149512"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41148847", "type": "extraction", "used": ["source:pmid:41148847"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE149512", "type": "accession_resolution", "used": ["data:geo:GSE149512"], "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:41148847", "parent_hash": "sha256:070005a03c250510b895a1f47925dcf41058c65c8e73eebc37a84b2dc8d9c8b2", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE149512 licence not read", "asset:data:geo:GSE149512 not downloaded", "asset:data:geo:GSE38776 licence not read", "asset:data:geo:GSE38776 not downloaded", "asset:data:geo:GSE43850 licence not read", "asset:data:geo:GSE43850 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["like Cells Using Machine Learning-Integrated Transcriptomic and Network Analysis.", "by immunocytochemistry, teratoma assays, and transcriptomic analyses using bulk and single-cell RNA sequ", "d strong expression of OCT4, DAZL, and VASA. Transcriptomic analysis revealed key differentially express", "ammed into ES-like cells. The integration of transcriptomic and network-based analyses reveals novel ins"], "order_basis": "paper_text_order:95", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ransgenic mice using enzymatic digestion and cultured in defined media. Under these conditions, ES-li"], "order_basis": "paper_text_order:518", "id": "assay:2"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": [", and transcriptomic analyses using bulk and single-cell RNA sequencing datasets. Gene expression profiles were comp", "Teratoma assays confirmed pluripotency, and single-cell RNA-seq validated expression of critical markers in"], "order_basis": "paper_text_order:742", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": [". Analysis of Gene Expression Using Fluidigm qPCR Fluidigm dynamic array chips were used for g", "er RNA (mRNA), amplified before using TaqMan qPCR for quantification. Two technical and three"], "order_basis": "paper_text_order:1908", "id": "assay:4"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["r to quantify SSCs, ES-like cells, and MEFs (Mouse Embryonic Fibroblasts, a control group). Exa"], "order_basis": "paper_text_order:2033", "id": "assay:5"}, {"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:6"}]}