← All .science files
pmid:36142823
GDF15 Contributes to Radioresistance by Mediating the EMT and Stemness of Breast Cancer Cells.
Xinrui Zhao · Xinglong Liu · Songling Hu · Yan Pan · Jianghong Zhang · Guomei Tai · Chunlin Shao
International journal of molecular sciences · 2022 doi:10.3390/ijms231810911
Paper
complete
Experiment
complete
Data
partial
Analysis
partial
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 · 2 items
[0] object · 6 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 · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 96 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 19 items
gaps array · 4 items
analysis object · 4 fields
methods array · 3 items
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
targets array · 0 items
gaps array · 1 item
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 · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 2 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 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 · 9 items
assays array · 4 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 · 4 items
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[3] object · 11 fields
required_operations array · 3 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:36142823", "kind": "science-record", "revision": 4, "content_hash": "sha256:3d3a904539e3ab2aa292ed88a0c303383f02d53ec5eeae98827f4cad3fab0d50", "created_at": "2026-11-01T18:15:25Z", "updated_at": "2026-11-01T22:07:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "GDF15 Contributes to Radioresistance by Mediating the EMT and Stemness of Breast Cancer Cells.", "doi": "10.3390/ijms231810911", "pmid": "36142823", "authors": ["Xinrui Zhao", "Xinglong Liu", "Songling Hu", "Yan Pan", "Jianghong Zhang", "Guomei Tai", "Chunlin Shao"], "journal": "International journal of molecular sciences", "year": 2022, "abstract": "Radiotherapy is one of the conventional methods for the clinical treatment of breast cancer. However, radioresistance has an adverse effect on the prognosis of breast cancer patients after radiotherapy. In this study, using bioinformatic analysis of GSE59732 and GSE59733 datasets in the Gene Expression Omnibus (GEO) database together with the prognosis database of breast cancer patients after radiotherapy, the GDF15 gene was screened out to be related to the poor prognosis of breast cancer after radiotherapy. Compared with radiosensitive parental breast cancer cells, breast cancer cells with acquired radioresistance exhibited a high level of GDF15 expression and enhanced epithelial-to-mesenchymal transition (EMT) properties of migration and invasion, as well as obvious stem-like traits, including the increases of mammosphere formation ability, the proportion of stem cells (CD44+ CD24- cells), and the expressions of stem cell-related markers (SOX2, NANOG). Moreover, knockdown of GDF15 sensitized the radioresistance cells to irradiation and significantly inhibited their EMT and stem-like traits, indicating that GDF15 promoted the radioresistance of breast cancer by enhancing the properties of EMT and stemness. Conclusively, GDF15 may be applicable as a novel prognosis-related biomarker and a potential therapeutic target for breast cancer radiotherapy.", "claims": [{"id": "claim-method", "statement": "A Student’s t-test was performed to compare the difference of independent groups, and the significant level was considered at p < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36142823", "locator": "sections[26] \"4.16. Statistical Analysis\" paragraph 2", "quote": "A Student’s t-test was performed to compare the difference of independent groups, and the significant level was considered at p < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data presented in this study are available on request from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36142823", "locator": "sections[31] \"Data Availability Statement\" paragraph 2", "quote": "The data presented in this study are available on request from the corresponding author upon reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper states no numerical result for the registered target in the specified sections.", "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:36142823"], "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:GSE59732"], "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:GSE59732"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36142823", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms231810911", "sha256": "sha256:c08ea29b2873bfd2c78e66433ae4e2de0bbe6fc4673b8edf1098a434f9dd1892", "bytes": 55527, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms231810911", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9504016", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE59732", "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=GSE59732", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59732", "version": null, "note": "The data presented in this study are available on request from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are available on request from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1444557", "GSM1444558", "GSM1444559", "GSM1444560", "GSM1444561", "GSM1444562", "GSM1444563", "GSM1444564", "GSM1444565", "GSM1444566", "GSM1444567", "GSM1444568", "GSM1444569", "GSM1444570", "GSM1444571", "GSM1444572", "GSM1444573", "GSM1444574", "GSM1444575", "GSM1444576", "GSM1444577", "GSM1444578", "GSM1444579", "GSM1444580", "GSM1444581", "GSM1444582", "GSM1444583", "GSM1444584", "GSM1444585", "GSM1444586", "GSM1444587", "GSM1444588", "GSM1444589", "GSM1444590", "GSM1444591", "GSM1444592", "GSM1444593", "GSM1444594", "GSM1444595", "GSM1444596", "GSM1444597", "GSM1444598", "GSM1444599", "GSM1444600", "GSM1444601", "GSM1444602", "GSM1444603", "GSM1444604", "GSM1444605", "GSM1444606", "GSM1444607", "GSM1444608", "GSM1444609", "GSM1444610", "GSM1444611", "GSM1444612", "GSM1444613", "GSM1444614", "GSM1444615", "GSM1444616", "GSM1444617", "GSM1444618", "GSM1444619", "GSM1444620", "GSM1444621", "GSM1444622", "GSM1444623", "GSM1444624", "GSM1444625", "GSM1444626", "GSM1444627", "GSM1444628", "GSM1444629", "GSM1444630", "GSM1444631", "GSM1444632", "GSM1444633", "GSM1444634", "GSM1444635", "GSM1444636", "GSM1444637", "GSM1444638", "GSM1444639", "GSM1444640", "GSM1444641", "GSM1444642", "GSM1444643", "GSM1444644", "GSM1444645", "GSM1444646", "GSM1444647", "GSM1444648", "GSM1444649", "GSM1444650", "GSM1444651", "GSM1444652"], "sample_count": 96, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Gene expression profiling in response to radiation treatment in breast cancer [cell lines]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE59733", "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=GSE59733", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59733", "version": null, "note": "The data presented in this study are available on request from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are available on request from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1444653", "GSM1444654", "GSM1444655", "GSM1444656", "GSM1444657", "GSM1444658", "GSM1444659", "GSM1444660", "GSM1444661", "GSM1444662", "GSM1444663", "GSM1444664", "GSM1444665", "GSM1444666", "GSM1444667", "GSM1444668", "GSM1444669", "GSM1444670", "GSM1444671"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "18990", "taxon": "Homo sapiens", "title": "Gene expression profiling in response to radiation treatment in breast cancer [patient samples]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE59732 not downloaded", "asset:data:geo:GSE59732 licence not read", "asset:data:geo:GSE59733 not downloaded", "asset:data:geo:GSE59733 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": 0.8, "band": "high", "quote": "PPI"}}, {"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": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "Student’s t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A Student’s t-test was performed to compare the difference of independent groups, and the significant level was considered at p < 0.05."}}], "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": ["GSE59732", "GSE59733"], "resolved_accessions": ["GSE59732", "GSE59733"], "statements": ["The data presented in this study are available on request from the corresponding author upon reasonable request."], "basis": "The paper names GSE59732, GSE59733 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:36142823", "data:geo:GSE59732"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE59732"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:06:37Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 17237, "completion_tokens": 2308, "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:36142823", "type": "paper", "label": "pmid:36142823"}, {"id": "source:pmid:36142823", "type": "manuscript", "label": "PMID 36142823 full text"}, {"id": "data:geo:GSE59732", "type": "dataset", "label": "GEO GSE59732"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36142823", "type": "paper", "label": "pmid:36142823"}, {"id": "source:pmid:36142823", "type": "manuscript", "label": "PMID 36142823 full text"}, {"id": "data:geo:GSE59732", "type": "dataset", "label": "GEO GSE59732"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36142823", "type": "extraction", "used": ["source:pmid:36142823"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE59732", "type": "accession_resolution", "used": ["data:geo:GSE59732"], "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:36142823", "parent_hash": "sha256:f4b4e0ddb76393e02f5dc9d7f858a25199680aa1fc5aeb450f1c3ec30b368b10", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE59732 licence not read", "asset:data:geo:GSE59732 not downloaded", "asset:data:geo:GSE59733 licence not read", "asset:data:geo:GSE59733 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["ell-related markers (SOX2, NANOG). Moreover, knockdown of GDF15 sensitized the radioresistance cell"], "order_basis": "paper_text_order:1030", "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": 0.99, "evidence": ["10% FBS and 1% penicillin/streptomycin. All cell lines were maintained in a humidified atmosphere containing 5% CO2", "d, NY, USA). MCF-7 and MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) su", "treptomycin. T-47D and MDA-MB-468 cells were cultured in RPMI-1640 medium containing 10% FBS and 1% p", "above 585 DEGs. (C) Venn diagrams of DEGs in MCF-7 and ZR751 cell lines from GSE59732 dataset a"], "order_basis": "paper_text_order:2951", "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": 0.99, "evidence": ["dividual cancer stages of breast cancer. (G) Western blot assay of the GDF15 protein expression in MCF", "7D, MDA-MB-23, MDA-MB-468). Judging from the Western blot assay, the expression of GDF15 was obviously"], "order_basis": "paper_text_order:7432", "id": "assay:3"}, {"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": 0.8, "evidence": ["PPI"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}