From unipotency to pluripotency: deciphering protein networks and signaling pathways in the generation of embryonic stem-like cells from murine spermatogonial stem cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40307702", "kind": "science-record", "revision": 4, "content_hash": "sha256:b0ab70561925f638810310bd13908dfe4e5efff07ca3fef9b45a85d0d4dc8382", "created_at": "2026-11-01T20:30:27Z", "updated_at": "2026-11-01T22:56:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "From unipotency to pluripotency: deciphering protein networks and signaling pathways in the generation of embryonic stem-like cells from murine spermatogonial stem cells.", "doi": "10.1186/s12864-025-11612-y", "pmid": "40307702", "authors": ["Nima Ghasemi", "Hossein Azizi", "Ali Qorbanee", "Thomas Skutella"], "journal": "BMC genomics", "year": 2025, "abstract": "With the significant challenges in using human embryonic stem cells (ESCs) for research and clinical applications, there is a growing impetus to seek alternative pluripotent cell sources. Embryonic stem-like (ES-like) cells emerge as a promising avenue in this pursuit. Our research demonstrates the potential for deriving ES-like cells from spermatogonial stem cells (SSCs) in a time-dependent manner under defined culture conditions. To better understand this process, we investigated the gene expression dynamics and underlying pathways associated with ES-like cell generation from SSCs. A deeper understanding of the signaling pathways underlying this biological process can lead us to refine protocols for ES-like cell generation, which could catalyze the development of more efficient and expedited methodologies inspired by the derivation pathway for future research in regenerative medicine. To identify differentially expressed genes (DEGs), we analyzed publicly available microarray data from murine cells obtained from the Gene Expression Omnibus (GEO). This analysis enabled the prediction of protein-protein interactions (PPIs), which were subsequently used for pathway enrichment analysis to identify biologically relevant pathways. Complementing these computational findings, we conducted in vitro experiments, including Fluidigm qPCR and immunostaining. These experiments serve as validation for our microarray data and the DEGs identified, providing reassurance about the reliability of our research. Among the identified enriched pathways in our investigation are the Toll-like receptor (TLR), GDNF/RET, interleukins (ILs), FGF/FGFR, and SMAD signaling pathway, along with the activation of NIMA kinases. Additionally, miR-410-3p, miRNA let-7e, Miat, and Xist are among some of the predicted non-coding RNAs.", "claims": [{"id": "claim-method", "statement": "Data was normalized using the Robust Multi-array Average (RMA) method, and differential gene expression was assessed through the empirical Bayes (eBayes) ANOVA method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40307702", "locator": "sections[10] \"Microarray data analysis and data normalization\" paragraph 2", "quote": "Data was normalized using the Robust Multi-array Average (RMA) method, and differential gene expression was assessed through the empirical Bayes (eBayes) ANOVA method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are available in the NCBI, GEO repository, GSE27043 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27043) and GSE43850 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43850).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40307702", "locator": "sections[32] \"notes\" paragraph 1", "quote": "The datasets analyzed during the current study are available in the NCBI, GEO repository, GSE27043 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27043) and GSE43850 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43850)."}], "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:40307702"], "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:GSE27043"], "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:GSE27043"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40307702", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12864-025-11612-y", "sha256": "sha256:d0277cfad8b3ff47994a9e85cc0a8fb838e19cbff3b83e484328504d56663801", "bytes": 55724, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12864-025-11612-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12042637", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE27043", "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=GSE27043", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27043", "version": null, "note": "The datasets analyzed during the current study are available in the NCBI, GEO repository, GSE27043 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27043) and GSE43850 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43850).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the NCBI, GEO repository, GSE27043 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27043) and GSE43850 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43850).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM666102", "GSM666103", "GSM666104", "GSM666105", "GSM666106", "GSM666107", "GSM666108", "GSM666109"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "6246", "taxon": "Mus musculus", "title": "Expression data from aged spermatogonial 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 datasets analyzed during the current study are available in the NCBI, GEO repository, GSE27043 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27043) and GSE43850 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43850).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the NCBI, GEO repository, GSE27043 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27043) and GSE43850 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43850).", "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:GSE27043 not downloaded", "asset:data:geo:GSE27043 licence not read", "asset:data:geo:GSE43850 not downloaded", "asset:data:geo:GSE43850 licence not read"]}, "analysis": {"state": "complete", "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": 1.0, "band": "verbatim", "quote": "Data was normalized using the Robust Multi-array Average (RMA) method, and differential gene expression was assessed through the empirical Bayes (eBayes) ANOVA method."}}, {"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": "PPI"}}, {"id": "method-3", "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": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [], "gaps": []}, "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": ["GSE27043", "GSE43850"], "resolved_accessions": ["GSE27043", "GSE43850"], "statements": ["The datasets analyzed during the current study are available in the NCBI, GEO repository, GSE27043 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27043) and GSE43850 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43850)."], "basis": "The paper names GSE27043, GSE43850 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:40307702", "data:geo:GSE27043"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE27043"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:51:28Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14122, "completion_tokens": 982, "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:40307702", "type": "paper", "label": "pmid:40307702"}, {"id": "source:pmid:40307702", "type": "manuscript", "label": "PMID 40307702 full text"}, {"id": "data:geo:GSE27043", "type": "dataset", "label": "GEO GSE27043"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40307702", "type": "paper", "label": "pmid:40307702"}, {"id": "source:pmid:40307702", "type": "manuscript", "label": "PMID 40307702 full text"}, {"id": "data:geo:GSE27043", "type": "dataset", "label": "GEO GSE27043"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40307702", "type": "extraction", "used": ["source:pmid:40307702"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE27043", "type": "accession_resolution", "used": ["data:geo:GSE27043"], "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:40307702", "parent_hash": "sha256:efd8a59f434f3d7918e7ab26775e17085b8251a7cba29507a831380d88278aa4", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE27043 licence not read", "asset:data:geo:GSE27043 not downloaded", "asset:data:geo:GSE43850 licence not read", "asset:data:geo:GSE43850 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ted in vitro experiments, including Fluidigm qPCR and immunostaining. These experiments serve"], "order_basis": "paper_text_order:1471", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["tro experiments, including Fluidigm qPCR and immunostaining. These experiments serve as validation for o"], "order_basis": "paper_text_order:1480", "id": "assay:2"}, {"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": 1.0, "evidence": ["Data was normalized using the Robust Multi-array Average (RMA) method, and differential gene expression was assessed through the empirical Bayes (eBayes) ANOVA method."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}