Function of hsa_circ_0006646 as a competing endogenous RNA to promote progression in gastric cancer by regulating the miR-665-HMGB1 axis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37435216", "kind": "science-record", "revision": 5, "content_hash": "sha256:b332ee6baeea2e8a74275e8811d0eb07f771636bb7b2f5079abf30de8a851b4d", "created_at": "2026-11-01T19:02:12Z", "updated_at": "2026-11-01T22:52:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Function of hsa_circ_0006646 as a competing endogenous RNA to promote progression in gastric cancer by regulating the miR-665-HMGB1 axis.", "doi": "10.21037/jgo-23-240", "pmid": "37435216", "authors": ["Jing Qin", "Shuman Zhen", "Jiali Wang", "Wei Lv", "Yan Zhao", "Yuqing Duan", "Tianxu Liu", "Lei Feng", "Guiying Wang", "Lihua Liu"], "journal": "Journal of gastrointestinal oncology", "year": 2023, "abstract": "Background: Mounting evidences indicate that circular RNAs (circRNAs) are a novel class of non-coding RNAs and play vital roles in the tumorigenesis and aggressiveness including gastric cancer (GC). Nevertheless, the precise functions and underlying mechanisms of circRNAs in GC remain largely unknown.\nMethods: The Gene Expression Omnibus (GEO) data set GSE163416 was analyzed to screen the key circRNAs in GC. hsa_circ_0006646 was chosen for further study. GC tissues and matched adjacent normal gastric mucosal epithelial tissues were obtained from the Fourth Hospital of Hebei Medical University. The expressions of hsa_circ_0006646 was detected using quantitative real-time polymerase chain reaction (qRT-PCR). hsa_circ_0006646 was knocked down to identify its effects on GC cells. Bioinformatics algorithms were analyzed to predict the microRNA (miRNAs) potentially sponged by hsa_circ_0006646 and its target genes. Fluorescence in situ hybridization (FISH) was conducted to determine the subcellular location of hsa_circ_0006646 and the predicted miRNA. Then, qRT-PCR, luciferase reporter assay, radioimmunoprecipitation assay, Western blotting, and miRNA rescue experiments were used to confirm the hsa_circ_0006646-related regulatory axis in GC. Cell Counting Kit-8 (CCK-8), colony formation, wound healing, and Transwell experiments were performed to determine the effect of the hsa_circ_0006646-related regulatory axis on GC cells' malignant behaviors in vitro. The xenograft tumor mouse model was established to evaluate the effect of hsa_circ_0006646 in vivo.\nResults: hsa_circ_0006646 exhibited a high expression in GC tissues as compared to corresponding adjacent normal gastric mucosal epithelial tissues and its high expression was positively correlated with TNM stage, lymph node invasion and poor prognosis (P<0.05). Knockdown of hsa_circ_0006646 suppressed the proliferation, colony formation, migration, and invasion in GC cells (all P<0.05). hsa_circ_0006646 upregulated high mobility group box 1 (HMGB1) by sponging miR-665 in GC cells (P<0.05). The hsa_circ_0006646-miR-665-HMGB1 axis promoted malignant behaviors and epithelial-mesenchymal transition (EMT) in GC cells by activating the Wnt/β-catenin pathway (P<0.05). The existence of hsa_circ_0006646-miR-665-HMGB1 axis was confirmed in GC specimens (P<0.05). Consequently, down-regulated hsa_circ_0006646 inhibited the progression and EMT of GC cells in vivo (P<0.05).\nConclusions: For the first time, we demonstrated that hsa_circ_0006646-miR-665-HMGB1 axis exerted its tumor-promoting effects in GC, which suggested that hsa_circ_0006646 could be potentially targeted for GC treatment.", "claims": [{"id": "claim-method", "statement": "The high throughput sequencing dates were analyzed by using the “limma” package in R software (The R Foundation for Statistical Computing).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37435216", "locator": "sections[4] \"Bioinformatic analysis\" paragraph 2", "quote": "The high throughput sequencing dates were analyzed by using the “limma” package in R software (The R Foundation for Statistical Computing)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Sharing Statement: Available at https://jgo.amegroups.com/article/view/10.21037/jgo-23-240/dss", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37435216", "locator": "sections[36] \"fn-group\" paragraph 1", "quote": "Data Sharing Statement: Available at https://jgo.amegroups.com/article/view/10.21037/jgo-23-240/dss"}], "state": "complete"}, {"id": "claim-target-result", "statement": "As shown in Figure 1A, hsa_circ_0006646 exhibited the most significant upregulation, among all candidate circRNAs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37435216", "locator": "sections[26] \"hsa_circ_0006646 was found to be a circRNA exhibiting high expression in GC and positively correlated with poor prognosis\" paragraph 2", "quote": "As shown in Figure 1A, hsa_circ_0006646 exhibited the most significant upregulation, among all candidate circRNAs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "As shown in Figure 1A, hsa_circ_0006646 exhibited the most significant upregulation, among all candidate circRNAs.", "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:37435216"], "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:GSE163416"], "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:GSE163416"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37435216", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/jgo-23-240", "sha256": "sha256:3bbc72612fff34bc50bdeff6fc6986084ba3c6ddf8317ffd1aea7d5918bff83f", "bytes": 51895, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/jgo-23-240", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10331750", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE163416", "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=GSE163416", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE163416", "version": null, "note": "Data Sharing Statement: Available at https://jgo.amegroups.com/article/view/10.21037/jgo-23-240/dss", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Sharing Statement: Available at https://jgo.amegroups.com/article/view/10.21037/jgo-23-240/dss", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4978621", "GSM4978622", "GSM4978623", "GSM4978624", "GSM4978625", "GSM4978626", "GSM4978627", "GSM4978628", "GSM4978629", "GSM4978630", "GSM4978631", "GSM4978632"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "20795", "taxon": "Homo sapiens", "title": "Expression profiles in the progression of the gastric cancer (mRNA+lncRNA+circRNA)", "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:GSE163416 not downloaded", "asset:data:geo:GSE163416 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The high throughput sequencing dates were analyzed by using the “limma” package in R software (The R Foundation for Statistical Computing)."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman rank correlation"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE163416"], "resolved_accessions": ["GSE163416"], "statements": ["Data Sharing Statement: Available at https://jgo.amegroups.com/article/view/10.21037/jgo-23-240/dss"], "basis": "The paper names GSE163416 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:37435216", "data:geo:GSE163416"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE163416"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:46:44Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15349, "completion_tokens": 1274, "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:37435216", "type": "paper", "label": "pmid:37435216"}, {"id": "source:pmid:37435216", "type": "manuscript", "label": "PMID 37435216 full text"}, {"id": "data:geo:GSE163416", "type": "dataset", "label": "GEO GSE163416"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37435216", "type": "paper", "label": "pmid:37435216"}, {"id": "source:pmid:37435216", "type": "manuscript", "label": "PMID 37435216 full text"}, {"id": "data:geo:GSE163416", "type": "dataset", "label": "GEO GSE163416"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37435216", "type": "extraction", "used": ["source:pmid:37435216"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE163416", "type": "accession_resolution", "used": ["data:geo:GSE163416"], "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:37435216", "parent_hash": "sha256:220d7b5c8e8c2125fafe16950043cff37abbaf475d901eb764512504733a8878", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE163416 licence not read", "asset:data:geo:GSE163416 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": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["orter assay, radioimmunoprecipitation assay, Western blotting, and miRNA rescue experiments were used to c"], "order_basis": "paper_text_order:1228", "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": 0.93, "evidence": ["regulatory axis in GC. Cell Counting Kit-8 (CCK-8), colony formation, wound healing, and Trans"], "order_basis": "paper_text_order:1370", "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": ["nant behaviors in vitro. The xenograft tumor mouse model was established to evaluate the effect of hs", "d to evaluate the effect of hsa_circ_0006646 in vivo. Results: hsa_circ_0006646 exhibited a high", "nhibited the progression and EMT of GC cells in vivo (P<0.05). Conclusions: For the first time, w", "nant behaviors in vitro. The xenograft tumor mouse model was established to evaluate the effect"], "order_basis": "paper_text_order:1586", "id": "assay:3"}, {"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": ["h node invasion and poor prognosis (P<0.05). Knockdown of hsa_circ_0006646 suppressed the prolifera"], "order_basis": "paper_text_order:1929", "id": "assay:4"}, {"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": ["tific, Waltham, MA, USA), while the other GC cell lines were cultured in RPMI-1640 (Gibco, USA) medium supplemente", "f Hebei Medical University. GES-1 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibc", "MA, USA), while the other GC cell lines were cultured in RPMI-1640 (Gibco, USA) medium supplemented w"], "order_basis": "paper_text_order:3065", "id": "assay:5"}, {"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 high throughput sequencing dates were analyzed by using the “limma” package in R software (The R Foundation for Statistical Computing)."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}