CCNB1 may as a biomarker for the adipogenic differentiation of adipose-derived stem cells in the postoperative fat transplantation of breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38323233", "kind": "science-record", "revision": 4, "content_hash": "sha256:b34d363de37ecf494e218174ea0e0bc408208374abcea4e5a7ab0031a2e79428", "created_at": "2026-11-01T19:20:16Z", "updated_at": "2026-11-01T22:53:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CCNB1 may as a biomarker for the adipogenic differentiation of adipose-derived stem cells in the postoperative fat transplantation of breast cancer.", "doi": "10.21037/gs-23-493", "pmid": "38323233", "authors": ["Zheng-Hui Wang", "Jing-Hui Peng", "Yin-Cheng Liu", "Quan-Hua Zhu", "Chang Sun", "Hui Xie", "Shui Wang"], "journal": "Gland surgery", "year": 2024, "abstract": "Background: Adipose-derived stem cells (ADSCs) are closely associated with the survival rate of transplanted fat in breast reconstruction after breast cancer surgery. Nevertheless, the intrinsic mechanisms regulating ADSCs adipogenic differentiation remain ambiguous. The aim of our study was to explore the relevant genes and pathways to elucidate the potential mechanisms of adipogenic differentiation in ADSCs.\nMethods: The Gene Expression Omnibus (GEO) dataset GSE61302 was downloaded and analyzed to identify differentially expressed genes (DEGs). Key genes and signaling pathways were obtained through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional and enrichment analysis. Protein-protein interaction (PPI) network and hub gene analyses were performed with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database and Cytoscape software. Finally, the transcription levels of hub genes in the adipogenic differentiated group and undifferentiated group of ADSCs were compared via real-time quantitative polymerase chain reaction (RT-qPCR).\nResults: In total, 1,091 DEGs were identified through bioinformatics analysis of the adipogenic differentiated group and undifferentiated group. If was then found that the 10 downregulated key genes, CCNB1, NUSAP1, DLGAP5, TTK, CCNB2, KIF23, BUB1B, CDC20, CDCA8, and KIF11 may play important roles in the adipogenic differentiation of ADSCs. Subsequent in vitro experimental verification also revealed that the messenger RNA (mRNA) expression levels of cyclin B1 in adipogenic differentiated cells and undifferentiated cells were significantly different at the early stage (P<0.05), but there was no significant difference at the late stage (P>0.05).\nConclusions: As a key gene, CCNB1 might be a potential biomarker in the adipogenic differentiation of ADSCs at the early stage.", "claims": [{"id": "claim-method", "statement": "The “limma” package in R was subsequently used for removing batch effects and identifying DEGs, with those with a log2fold change (log2FC) >1 or <−1 and a P value <0.05 being considered significant. Statistical analysis with the paired Student t-test was performed with GraphPad Prism 9.0 software (GraphPad Software, La Jolla, CA, USA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38323233", "locator": "sections[6] \"Identification of DEGs\" paragraph 2", "quote": "The “limma” package in R was subsequently used for removing batch effects and identifying DEGs, with those with a log2fold change (log2FC) >1 or <−1 and a P value <0.05 being considered significant."}, {"asset": "source:pmid:38323233", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "Statistical analysis with the paired Student t-test was performed with GraphPad Prism 9.0 software (GraphPad Software, La Jolla, CA, USA)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Sharing Statement: Available at https://gs.amegroups.com/article/view/10.21037/gs-23-493/dss", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38323233", "locator": "sections[26] \"Footnotes\" paragraph 2", "quote": "Data Sharing Statement: Available at https://gs.amegroups.com/article/view/10.21037/gs-23-493/dss"}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 1,091 differentially expressed genes were identified between adipogenic differentiated and undifferentiated ADSCs, comprising 382 upregulated and 709 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38323233", "locator": "sections[15] \"Identification of DEGs\" paragraph 2", "quote": "A total of 1,091 DEGs were screened according to the criteria of false discovery rate (FDR) <0.05 and log2FC >1 or < −1. Among these genes, 382 genes were upregulated and 709 downregulated, as shown in the volcano plot in Figure 1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A total of 1,091 differentially expressed genes were identified between adipogenic differentiated and undifferentiated ADSCs, comprising 382 upregulated and 709 downregulated genes.", "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:38323233"], "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:GSE61302"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE61302"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38323233", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/gs-23-493", "sha256": "sha256:386985c01efe0a84466645f4ff4e944725175fcdb418872fe1ad5b82cdc840e1", "bytes": 42387, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/gs-23-493", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10839700", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE61302", "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=GSE61302", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE61302", "version": null, "note": "Data Sharing Statement: Available at https://gs.amegroups.com/article/view/10.21037/gs-23-493/dss", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Sharing Statement: Available at https://gs.amegroups.com/article/view/10.21037/gs-23-493/dss", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1501795", "GSM1501796", "GSM1501797", "GSM1501798", "GSM1501799", "GSM1501800", "GSM1501801", "GSM1501802", "GSM1501803", "GSM1501804", "GSM1501805", "GSM1501806", "GSM1501807", "GSM1501808", "GSM1501809"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression Analysis of Human Adipose-Derived Stem Cells During In Vitro Differentiation to an Adipocyte Lineage", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE61302 not downloaded", "asset:data:geo:GSE61302 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The “limma” package in R was subsequently used for removing batch effects and identifying DEGs, with those with a log2fold change (log2FC) >1 or <−1 and a P value <0.05 being considered significant. 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