← All .science files
pmid:41117854
Microglia-Derived Extracellular Vesicles Enhance Oligodendrocyte Maturation by Transcriptionally Regulating Mitochondrial Molecular Pathways.
Stefano Raffaele · Marta Lombardi · Davide Marangon · Maria P Abbracchio · Davide Lecca · Claudia Verderio · Marta Fumagalli
Cellular and molecular neurobiology · 2025 doi:10.1007/s10571-025-01612-7
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 7 items
claims array · 3 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 12 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 4 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 4 items
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] object · 11 fields
required_operations array · 4 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41117854", "kind": "science-record", "revision": 4, "content_hash": "sha256:9086d1a22c4a935cdc1bb71dbca9610c5d50cf2c02a20e420a8e0dc754296646", "created_at": "2026-11-01T20:31:10Z", "updated_at": "2026-11-01T22:57:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Microglia-Derived Extracellular Vesicles Enhance Oligodendrocyte Maturation by Transcriptionally Regulating Mitochondrial Molecular Pathways.", "doi": "10.1007/s10571-025-01612-7", "pmid": "41117854", "authors": ["Stefano Raffaele", "Marta Lombardi", "Davide Marangon", "Maria P Abbracchio", "Davide Lecca", "Claudia Verderio", "Marta Fumagalli"], "journal": "Cellular and molecular neurobiology", "year": 2025, "abstract": "Degeneration of myelinating oligodendrocytes and the resulting breakdown of the myelin sheath are key drivers of neurodegeneration and disability across numerous central nervous system pathologies. Thus, a compelling strategy to preserve neuronal function is to promote endogenous myelin repair by oligodendrocyte precursor cells (OPCs). Extracellular vesicles (EVs) secreted by pro-regenerative microglia have been shown to enhance OPC maturation and remyelination across different experimental models. Yet, the mechanisms by which microglia-derived EVs exert their beneficial effects on OPCs are not fully understood. In this study, we performed transcriptomic profiling of primary murine OPCs treated during differentiation with EVs obtained from donor microglia following stimulation with pro-inflammatory cytokines (i-EVs), interleukin-4 (IL4-EVs), or mesenchymal stem cells in the presence of the inflammatory cocktail (MSC-EVs; GEO accession number: GSE304130). Compared to controls, IL4-EVs and MSC-EVs induced robust changes in gene expression, whereas i-EVs elicited far fewer alterations. Using bioinformatic analyses, we identified the molecular pathways significantly modulated by microglial EVs, revealing a large overlap between IL4-EV and MSC-EV targets. Notably, many of these shared pathways centered on mitochondrial function and bioenergetic metabolism. Upstream regulatory network inference further pinpointed candidate transcription factors and kinases that may drive EV-induced transcriptional reprogramming in OPCs. Hence, our findings indicate that rewiring mitochondria-associated pathways is a core mechanism underlying the pro-differentiation effects of microglial EVs on OPCs. Elucidating these intracellular circuits will open new avenues for developing EV-based or mitochondria-targeted remyelinating therapies.", "claims": [{"id": "claim-method", "statement": "For each gene, a one-way ANOVA was performed across the groups (CTRL, i-EVs, IL4-EVs, MSC-EVs), and the resulting p values were adjusted for multiple testing using the Benjamini–Hochberg false discovery rate (FDR) method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41117854", "locator": "sections[9] \"Transcriptomics\" paragraph 7", "quote": "For each gene, a one-way ANOVA was performed across the groups (CTRL, i-EVs, IL4-EVs, MSC-EVs), and the resulting p values were adjusted for multiple testing using the Benjamini–Hochberg false discovery rate (FDR) method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Microarray raw data are available in the GEO database (accession number: GSE304130). Further information and data that support the findings of this study are available from the corresponding authors upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41117854", "locator": "sections[23] \"notes\" paragraph 1", "quote": "Microarray raw data are available in the GEO database (accession number: GSE304130). Further information and data that support the findings of this study are available from the corresponding authors upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Rewiring mitochondria-associated pathways is a core mechanism underlying the pro-differentiation effects of microglial EVs on OPCs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41117854", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Hence, our findings indicate that rewiring mitochondria-associated pathways is a core mechanism underlying the pro-differentiation effects of microglial EVs on OPCs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Rewiring mitochondria-associated pathways is a core mechanism underlying the pro-differentiation effects of microglial EVs on OPCs.", "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:41117854"], "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:GSE304130"], "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:GSE304130"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41117854", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s10571-025-01612-7", "sha256": "sha256:acdf5734a13d8390cd4724d168c07e115f14c82d155f92323cbdcbef885c0dca", "bytes": 44578, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s10571-025-01612-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12540241", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE304130", "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=GSE304130", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE304130", "version": null, "note": "Microarray raw data are available in the GEO database (accession number: GSE304130). Further information and data that support the findings of this study are available from the corresponding authors upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray raw data are available in the GEO database (accession number: GSE304130). Further information and data that support the findings of this study are available from the corresponding authors upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM9144183", "GSM9144184", "GSM9144185", "GSM9144186", "GSM9144187", "GSM9144188", "GSM9144189", "GSM9144190", "GSM9144191", "GSM9144192", "GSM9144193", "GSM9144194"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "20775", "taxon": "Mus musculus", "title": "Transcriptomics of mouse oligodendrocyte precursor cells treated with microglia-derived extracellular vesicles", "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:GSE304130 not downloaded", "asset:data:geo:GSE304130 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": "For each gene, a one-way ANOVA was performed across the groups (CTRL, i-EVs, IL4-EVs, MSC-EVs), and the resulting p values were adjusted for multiple testing using the Benjamini–Hochberg false discovery rate (FDR) method."}}], "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": ["GSE304130"], "resolved_accessions": ["GSE304130"], "statements": ["Microarray raw data are available in the GEO database (accession number: GSE304130). Further information and data that support the findings of this study are available from the corresponding authors upon reasonable request."], "basis": "The paper names GSE304130 in 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:41117854", "data:geo:GSE304130"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE304130"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:03:32Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11706, "completion_tokens": 1239, "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:41117854", "type": "paper", "label": "pmid:41117854"}, {"id": "source:pmid:41117854", "type": "manuscript", "label": "PMID 41117854 full text"}, {"id": "data:geo:GSE304130", "type": "dataset", "label": "GEO GSE304130"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41117854", "type": "paper", "label": "pmid:41117854"}, {"id": "source:pmid:41117854", "type": "manuscript", "label": "PMID 41117854 full text"}, {"id": "data:geo:GSE304130", "type": "dataset", "label": "GEO GSE304130"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41117854", "type": "extraction", "used": ["source:pmid:41117854"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE304130", "type": "accession_resolution", "used": ["data:geo:GSE304130"], "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:41117854", "parent_hash": "sha256:0cacad1693e5db605e1aa7e2334c53bad95b3b7f418a12695f4013a139a85ddf", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE304130 licence not read", "asset:data:geo:GSE304130 not downloaded", "execution.not_run", "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": 0.69, "evidence": ["ully understood. In this study, we performed transcriptomic profiling of primary murine OPCs treated dur"], "order_basis": "paper_text_order:745", "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": 0.77, "evidence": ["erformed transcriptomic profiling of primary murine OPCs treated during differentiation with EVs"], "order_basis": "paper_text_order:781", "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": ["For each gene, a one-way ANOVA was performed across the groups (CTRL, i-EVs, IL4-EVs, MSC-EVs), and the resulting p values were adjusted for multiple testing using the Benjamini–Hochberg false discovery rate (FDR) method."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}