miR-624-5p promoted tumorigenesis and metastasis by suppressing hippo signaling through targeting PTPRB in osteosarcoma cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31829261", "kind": "science-record", "revision": 8, "content_hash": "sha256:586105c7a189b9bde52956f19f0443e4512755794bbf09291bb6ac4c77e59c6a", "created_at": "2026-11-01T15:40:53Z", "updated_at": "2026-11-01T22:44:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "miR-624-5p promoted tumorigenesis and metastasis by suppressing hippo signaling through targeting PTPRB in osteosarcoma cells.", "doi": "10.1186/s13046-019-1491-6", "pmid": "31829261", "authors": ["Yongjun Luo", "Wei Liu", "Pengyu Tang", "Dongdong Jiang", "Changjiang Gu", "Yumin Huang", "Fangyi Gong", "Yuluo Rong", "Dingfei Qian", "Jian Chen", "Zheng Zhou", "Shujie Zhao", "Jiaxing Wang", "Tao Xu", "Yongzhong Wei", "Guoyong Yin", "Jin Fan", "Weihua Cai"], "journal": "Journal of experimental & clinical cancer research : CR", "year": 2019, "abstract": "BACKGROUND: Accumulating evidence indicates that aberrant microRNA (miRNA) expression contributes to osteosarcoma progression. This study aimed to elucidate the association between miR-624-5p expression and osteosarcoma (OS) development and to investigate its underlying mechanism.\nMETHODS: We analyzed GSE65071 from the GEO database and found miR-624-5p was the most upregulated miRNA. The expression of miR-624-5p and its specific target gene were determined in human OS specimens and cell lines by RT-PCR and western blot. The effects of miR-624-5p depletion or ectopic expression on OS proliferation, migration and invasion were evaluated in vitro using CCK-8 proliferation assay, colony formation assay, transwell assay, would-healing assay and 3D spheroid BME cell invasion assay respectively. We investigated in vivo effects of miR-624-5p using a mouse tumorigenicity model. Besides, luciferase reporter assays were employed to identify interactions between miR-624-5p and its specific target gene.\nRESULTS: miR-624-5p expression was upregulated in OS cells and tissues, and overexpressing miR-624-5p led to a higher malignant level of OS, including cell proliferation, migration and invasion in vitro and in vivo. Protein tyrosine phosphatase receptor type B (PTPRB) was negatively correlated with miR-624-5p expression in OS tissues. Using the luciferase reporter assay and Western blotting, PTPRB was confirmed as a downstream target of miR-624-5p. PTPRB restored the effects of miR-624-5p on OS migration and invasion. The Hippo signaling pathway was identified as being involved in the miR-624-5p/PTPRB axis.\nCONCLUSIONS: In conclusion, our results suggest that miR-624-5p is a negative regulator of PTPRB and a risk factor for tumor metastasis in OS progression.", "claims": [{"id": "claim-method", "statement": "The χ2 test was used to analyze the association of miR-624-5p expression level with clinicopathological features. Independent t-tests were used to compare differences between the two groups. A paired t-test was used to analyze miR-624-5p and PTPRB mRNA levels in tissue samples. One-way or two-way ANOVA with Bonferroni post hoc test was used for multivariate analysis. Correlations were determined by Pearson’s correlation analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31829261", "locator": "sections[16] \"Statistical analysis\" paragraph 2", "quote": "The χ2 test was used to analyze the association of miR-624-5p expression level with clinicopathological features. Independent t-tests were used to compare differences between the two groups. A paired t-test was used to analyze miR-624-5p and PTPRB mRNA levels in tissue samples. One-way or two-way ANOVA with Bonferroni post hoc test was used for multivariate analysis. Correlations were determined by Pearson’s correlation analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Most of the datasets supporting the conclusions of this article are included within this article and the additional files. The datasets used or analyzed during the current study are available on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31829261", "locator": "sections[34] \"Availability of data and materials\" paragraph 2", "quote": "Most of the datasets supporting the conclusions of this article are included within this article and the additional files. The datasets used or analyzed during the current study are available on reasonable request."}], "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:31829261"], "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:GSE65071"], "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:GSE65071"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31829261", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13046-019-1491-6", "sha256": "sha256:c6d531f1de8f8e8593267db15a07f019de62f8effaecd80445046e158bb413a5", "bytes": 52131, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13046-019-1491-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6907337", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE65071", "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=GSE65071", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65071", "version": null, "note": "Most of the datasets supporting the conclusions of this article are included within this article and the additional files. The datasets used or analyzed during the current study are available on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Most of the datasets supporting the conclusions of this article are included within this article and the additional files. The datasets used or analyzed during the current study are available on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1586740", "GSM1586741", "GSM1586742", "GSM1586743", "GSM1586744", "GSM1586745", "GSM1586746", "GSM1586747", "GSM1586748", "GSM1586749", "GSM1586750", "GSM1586751", "GSM1586752", "GSM1586753", "GSM1586754", "GSM1586755", "GSM1586756", "GSM1586757", "GSM1586758", "GSM1586759", "GSM1586760", "GSM1586761", "GSM1586762", "GSM1586763", "GSM1586764", "GSM1586765", "GSM1586766", "GSM1586767", "GSM1586768", "GSM1586769", "GSM1586770", "GSM1586771", "GSM1586772", "GSM1586773", "GSM1586774"], "sample_count": 35, "group_sizes": null, "group_sizes_basis": null, "platform": "19631", "taxon": "Homo sapiens", "title": "Plasma profiling of miRNAs in human specimens from osteosarcoma patients.", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31829261:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:aa956ecf4fac08d1ce556929bf3ce414719235aff6098042b54f9e5040db3485", "bytes": 1011, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Expression of miR-624-5p and PTPRB according to patients’ clinical features", "structure": {"pmcid": "PMC6907337", "section_index": 3, "section_title": "Tissue samples and cell lines", "row_count": 20, "column_count": 8}, "table": {"label": "Table 1", "caption": "Expression of miR-624-5p and PTPRB according to patients’ clinical features", "rows": [["", "", "miR-624-5p expression", "", "PTPRB expression", ""], ["Characteristics", "Number", "High group", "Low group", "P value", "High group", "Low group", "P value"], ["Age(y)"], ["< 18", "29", "14", "15", "0.70", "15", "14", "0.96"], ["≥ 18", "21", "9", "12", "", "11", "10", ""], ["Gender"], ["Female", "23", "13", "10", "0.39", "12", "11", "0.61"], ["Male", "27", "12", "15", "", "16", "11", ""], ["Location"], ["Femur/Tibia", "39", "18", "21", "0.96", "20", "19", "0.47"], ["Elsewhere", "11", "5", "6", "", "7", "4", ""], ["TNM stage"], ["I", "23", "11", "12", "0.028a", "15", "8", "0.012a"], ["II/III", "27", "21", "6", "", "8", "19", ""], ["Tumor size (cm)"], ["< 5", "28", "12", "16", "0.014a", "17", "11", "0.042a"], ["≥ 5", "22", "17", "5", "", "7", "15", ""], ["Lung metastasis"], ["Yes", "21", "18", "3", "0.012a", "6", "15", "0.01a"], ["No", "29", "15", "14", "", "19", "10", ""]], "row_count": 20, "column_count": 8, "numeric_cells": 77, "header_rows": 2, "locator": "section[3]/table-wrap[1]#Tab1"}}], "gaps": ["asset:data:geo:GSE65071 not downloaded", "asset:data:geo:GSE65071 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": "The χ2 test was used to analyze the association of miR-624-5p expression level with clinicopathological features. Independent t-tests were used to compare differences between the two groups. A paired t-test was used to analyze miR-624-5p and PTPRB mRNA levels in tissue samples. One-way or two-way ANOVA with Bonferroni post hoc test was used for multivariate analysis. Correlations were determined by Pearson’s correlation analysis."}}, {"id": "method-2", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "χ2"}}], "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": ["GSE65071"], "resolved_accessions": ["GSE65071"], "statements": ["Most of the datasets supporting the conclusions of this article are included within this article and the additional files. The datasets used or analyzed during the current study are available on reasonable request."], "basis": "The paper names GSE65071 in GEO database 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:31829261", "data:geo:GSE65071", "asset:table:pmid:31829261:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE65071"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:17:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 45556, "completion_tokens": 1510, "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:31829261", "type": "paper", "label": "pmid:31829261"}, {"id": "source:pmid:31829261", "type": "manuscript", "label": "PMID 31829261 full text"}, {"id": "data:geo:GSE65071", "type": "dataset", "label": "GEO GSE65071"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31829261", "type": "paper", "label": "pmid:31829261"}, {"id": "source:pmid:31829261", "type": "manuscript", "label": "PMID 31829261 full text"}, {"id": "data:geo:GSE65071", "type": "dataset", "label": "GEO GSE65071"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31829261", "type": "extraction", "used": ["source:pmid:31829261"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE65071", "type": "accession_resolution", "used": ["data:geo:GSE65071"], "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:31829261", "parent_hash": "sha256:3d94ff3b437c951a8b4fedfaf9972cd41b15a0a2bdfd1203a9ae0c051e805663", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE65071 licence not read", "asset:data:geo:GSE65071 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["an OS specimens and cell lines by RT-PCR and western blot. The effects of miR-624-5p depletion or ecto", "ues. Using the luciferase reporter assay and Western blotting, PTPRB was confirmed as a downstream target"], "order_basis": "paper_text_order:594", "id": "assay:1"}, {"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": ["n and invasion were evaluated in vitro using CCK-8 proliferation assay, colony formation assay,", "proliferation. A–B. The Cell Counting Kit-8 (CCK-8) assay and colony formation analysis reveal"], "order_basis": "paper_text_order:740", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["invasion assay respectively. We investigated in vivo effects of miR-624-5p using a mouse tumorige", "eration, migration and invasion in vitro and in vivo. Protein tyrosine phosphatase receptor type", "igated in vivo effects of miR-624-5p using a mouse tumorigenicity model. Besides, luciferase re", "anjing University (Nanjing, China). The nude mice were randomly divided into four groups (n = 5 per"], "order_basis": "paper_text_order:898", "id": "assay:3"}, {"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": ["ll culture The human OS cell lines including U2OS, MG63, SW1353, HOS, and Saos-2 and the norma", "ntly increased proliferation of the MG63 and U2OS cells (C, n = 4; D, n = 4)."], "order_basis": "paper_text_order:2594", "id": "assay:4"}, {"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": ["The χ2 test was used to analyze the association of miR-624-5p expression level with clinicopathological features. Independent t-tests were used to compare differences between the two groups. A paired t-test was used to analyze miR-624-5p and PTPRB mRNA levels in tissue samples. One-way or two-way ANOVA with Bonferroni post hoc test was used for multivariate analysis. Correlations were determined by Pearson’s correlation analysis."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}