miR-30d Induced Apoptosis by Targeting Sox4 to Inhibit the Proliferation, Invasion and Migration of Nephroblastoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32821117", "kind": "science-record", "revision": 9, "content_hash": "sha256:cf532ca21fe4351e06553068c514b5c1f40f19fdf10c77281e1a6db76008ff00", "created_at": "2026-11-01T15:41:08Z", "updated_at": "2026-11-01T22:45:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "miR-30d Induced Apoptosis by Targeting Sox4 to Inhibit the Proliferation, Invasion and Migration of Nephroblastoma.", "doi": "10.2147/OTT.S251714", "pmid": "32821117", "authors": ["Shi Zong", "Jia Zhao", "Ling Liu"], "journal": "OncoTargets and therapy", "year": 2020, "abstract": "BACKGROUND: Wilms tumor (WT) is an embryonic malignant tumor, and its related mechanism is still unclear. microRNA (miR), as a short-chain non-coding RNA, has low expression in various tumors. In this study, WT differential miR was screened by multi-chip in GEO database and its mechanism was explored to provide potential therapeutic targets and ideas for clinic.\nMETHODS: We logged into GEO database and downloaded GSE57370 and GSE48137 chip matrix files to analyze potential differences in miR. TargetScan, miRDB, miRTarBase and starBase were applied to predict the target genes of miR with significant differences. qRT-PCR was applied to determine the expression of miR-30d and Sox4 in WT tissue and cell line (G401). The interaction of miR-30d with Sox4 was confirmed by qRT-PCR, Western blot and luciferase assay, respectively. CCK-8, Transwell and flow cytometry were applied to determine the proliferation, invasion, migration and apoptosis of cells.\nRESULTS: We found that miR-30d was low expressed in two chips. qRT-PCR showed that miR-30d was down-regulated and SOX4 was up-regulated in WT tissues and cells. The online target gene prediction software showed there was a targeted binding site between Sox4 and miR-30d. Sox4 was negatively controlled by miR-30d. Subsequent studies found that over-expression of miR-30d inhibited the proliferation, invasion, migration and induced apoptosis of C64 and WiT49 cells. In addition, Sox4 could reverse the proliferation, invasion and migration of C64 and WiT49 induced by miR-30d and induce apoptosis.\nCONCLUSION: miR-30d is poorly expressed in WT and can induce apoptosis and inhibit proliferation, invasion and migration by mediating Sox4.", "claims": [{"id": "claim-method", "statement": "The processed data were analyzed for differences using limma package", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32821117", "locator": "sections[3] \"GEO Database Data Analysis\" paragraph 2", "quote": "The processed data were analyzed for differences using limma package"}], "state": "complete"}, {"id": "claim-data-access", "statement": "We logged into GEO database (https://www.ncbi.nlm.nih.gov/gds) to search Wilms tumor and microRNA related chips. Finally, we selected GSE57370 and GSE48137 chips, downloaded matrix file Series Matrix File (s)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32821117", "locator": "sections[3] \"GEO Database Data Analysis\" paragraph 2", "quote": "We logged into GEO database (https://www.ncbi.nlm.nih.gov/gds) to search Wilms tumor and microRNA related chips. Finally, we selected GSE57370 and GSE48137 chips, downloaded matrix file Series Matrix File (s)"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32821117"], "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:GSE48137"], "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:GSE48137"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32821117", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S251714", "sha256": "sha256:2ee544abbb15fe8838b0083d0e3d0818cc87f0b388084d6729d2356e7d9f589c", "bytes": 27468, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/OTT.S251714", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7419636", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE48137", "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=GSE48137", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48137", "version": null, "note": "We logged into GEO database (https://www.ncbi.nlm.nih.gov/gds) to search Wilms tumor and microRNA related chips. 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["", "≥2 years old (n=13)", "6", "7"], ["", "<2 years old (n=17)", "9", "8"], ["Gender", "", "", "", "0.273"], ["", "Male (n=15)", "6", "9"], ["", "Female (n=15)", "9", "6"], ["Histopathological type", "", "", "", "0.028"], ["", "Favorable (FH) (n=16)", "5", "11"], ["", "Unfavorable (UH) (n=14)", "10", "4"], ["NWTS stage", "", "", "", "0.003"], ["", "I+II (n=16)", "4", "12"], ["", "III+IV (n=14)", "11", "3"], ["Lymphatic metastasis", "", "", "", "0.031"], ["", "Transferred (n=7)", "6", "1"], ["", "Non-transferred (n=23)", "9", "14"]], "row_count": 17, "column_count": 5, "numeric_cells": 38, "header_rows": 2, "locator": "section[17]/table-wrap[1]#T0003"}}], "gaps": ["asset:data:geo:GSE48137 not downloaded", "asset:data:geo:GSE48137 licence not read", "asset:data:geo:GSE57370 not downloaded", "asset:data:geo:GSE57370 licence not read", "asset:data:geo:GSE66405 not downloaded", "asset:data:geo:GSE66405 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32821117", "data:geo:GSE48137", "asset:table:pmid:32821117:1", "asset:table:pmid:32821117:2", "asset:table:pmid:32821117:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE48137"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:58Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 23773, "completion_tokens": 1894, "cached_tokens": 784}}, "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:32821117", "type": "paper", "label": "pmid:32821117"}, {"id": "source:pmid:32821117", "type": "manuscript", "label": "PMID 32821117 full text"}, {"id": "data:geo:GSE48137", "type": "dataset", "label": "GEO GSE48137"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32821117", "type": "paper", "label": "pmid:32821117"}, {"id": "source:pmid:32821117", "type": "manuscript", "label": "PMID 32821117 full text"}, {"id": "data:geo:GSE48137", "type": "dataset", "label": "GEO GSE48137"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32821117", "type": "extraction", "used": ["source:pmid:32821117"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE48137", "type": "accession_resolution", "used": ["data:geo:GSE48137"], "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:32821117", "parent_hash": "sha256:fc27a7da2be1ba0842cf7a5268e3164104af8d40a048807790b1c7bd2726793c", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE48137 licence not read", "asset:data:geo:GSE48137 not downloaded", "asset:data:geo:GSE57370 licence not read", "asset:data:geo:GSE57370 not downloaded", "asset:data:geo:GSE66405 licence not read", "asset:data:geo:GSE66405 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["miR-30d Induced Apoptosis by Targeting Sox4 to Inhibit the Proliferati", "e the proliferation, invasion, migration and apoptosis of cells. RESULTS: We found that miR-30d was", "oliferation, invasion, migration and induced apoptosis of C64 and WiT49 cells. In addition, Sox4 co", "C64 and WiT49 induced by miR-30d and induce apoptosis. CONCLUSION: miR-30d is poorly expressed in"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["miR-30d with Sox4 was confirmed by qRT-PCR, Western blot and luciferase assay, respectively. CCK-8, T"], "order_basis": "paper_text_order:857", "id": "assay:2"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["se assay, respectively. CCK-8, Transwell and flow cytometry were applied to determine the proliferation,"], "order_basis": "paper_text_order:926", "id": "assay:3"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The processed data were analyzed for differences using limma package"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}