Circular RNA Circ_0000098 Elevates ALX4 Expression via Adsorbing miR-1204 to Inhibit the Progression of Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34900665", "kind": "science-record", "revision": 5, "content_hash": "sha256:5858dbe15a13274e30e1008a6bcb64137c1977c9a9932d4281ab5623091ed36c", "created_at": "2026-11-01T17:36:37Z", "updated_at": "2026-11-01T22:48:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Circular RNA Circ_0000098 Elevates ALX4 Expression via Adsorbing miR-1204 to Inhibit the Progression of Hepatocellular Carcinoma.", "doi": "10.3389/fonc.2021.696078", "pmid": "34900665", "authors": ["Ming Li", "Wenjing Yue", "Qiankun Li", "Wenyu Yu", "Yao Li", "Xiaoling Cao"], "journal": "Frontiers in oncology", "year": 2021, "abstract": "BACKGROUND: Circular RNAs (CircRNAs) feature prominently in the progression of various cancers. However, the biological functions of many circRNAs in hepatocellular carcinoma (HCC) are far from fully clarified. This work is performed to decipher the function of circ_0000098 (circSLC30A7) in modulating the progression of HCC and its molecular mechanism.\nMETHODS: Microarray data (GSE97332) were available from the Gene Expression Omnibus (GEO) database, and circRNA differentially expressed in HCC tissues was screened out by GEO2R tool. Circ_0000098, microRNA-1204 (miR-1204), and aristaless-like homeobox-4 (ALX4) mRNA expressions were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Cell counting kit-8 (CCK-8), scratch wound healing, and Transwell assays were adopted to determine proliferation, migration, and invasion of HCC cells. ALX4 protein, E-cadherin, N-cadherin, and Vimentin expressions were evaluated by Western blot. In addition, the targeting relationship between miR-1204 and circ_0000098 or ALX4 was studied with dual-luciferase reporter assay and RIP assay.\nRESULTS: Circ_0000098 expression level was markedly declined in HCC tissues and cells, and its underexpression was associated with larger tumor size of HCC patients. Knocking down circ_0000098 observably promoted the multiplication, migration, invasion, and epithelial-mesenchymal transition (EMT) of Huh7 and SMMC-7721 cells. Additionally, circ_0000098 was mainly distributed in the cytoplasm of HCC cells, and up-regulated ALX4 expression through competitively decoying miR-1204.\nCONCLUSION: Circ_0000098, as a competitive endogenous RNA (ceRNA) of miR-1204, upregulates ALX4 expression and suppresses the growth, migration, invasion, and EMT of HCC cells.", "claims": [{"id": "claim-method", "statement": "Fisher’s exact test was employed to analyze the relationship between circ_0000098 expression and clinicopathological features. Student’s t-test was used to analyze the difference between two groups. One-way ANOVA was used to analyze the differences among the multiple groups. Pearson correlation analysis was employed to study the correlation among circRNA, miRNA, and mRNA expressions.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34900665", "locator": "sections[16] \"Statistical Analysis\" paragraph 2", "quote": "Fisher’s exact test was employed to analyze the relationship between circ_0000098 expression and clinicopathological features. Student’s t-test was used to analyze the difference between two groups. One-way ANOVA was used to analyze the differences among the multiple groups. Pearson correlation analysis was employed to study the correlation among circRNA, miRNA, and mRNA expressions."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34900665", "locator": "sections[25] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Circ_0000098, as a competitive endogenous RNA (ceRNA) of miR-1204, upregulates ALX4 expression and suppresses the growth, migration, invasion, and EMT of HCC cells.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34900665", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Circ_0000098, as a competitive endogenous RNA (ceRNA) of miR-1204, upregulates ALX4 expression and suppresses the growth, migration, invasion, and EMT of HCC cells."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Circ_0000098, as a competitive endogenous RNA (ceRNA) of miR-1204, upregulates ALX4 expression and suppresses the growth, migration, invasion, and EMT of HCC cells.", "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:34900665"], "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:GSE97332"], "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:GSE97332"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34900665", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2021.696078", "sha256": "sha256:6391f4fcdd3171110e3b04e8ab18c08b9740041dd5a438d592ce35cefbb4eee4", "bytes": 37356, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2021.696078", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8662564", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE97332", "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=GSE97332", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE97332", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2561829", "GSM2561830", "GSM2561831", "GSM2561832", "GSM2561833", "GSM2561834", "GSM2561835", "GSM2561836", "GSM2561837", "GSM2561838", "GSM2561839", "GSM2561840", "GSM2561841", "GSM2561842"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "19978", "taxon": "Homo sapiens", "title": "circRNA expression in HCC and matched non-tumor tissues", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE97332 not downloaded", "asset:data:geo:GSE97332 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": "Fisher’s exact test was employed to analyze the relationship between circ_0000098 expression and clinicopathological features. Student’s t-test was used to analyze the difference between two groups. One-way ANOVA was used to analyze the differences among the multiple groups. Pearson correlation analysis was employed to study the correlation among circRNA, miRNA, and mRNA expressions."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}], "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": ["GSE97332"], "resolved_accessions": ["GSE97332"], "statements": ["The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE97332 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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:34900665", "data:geo:GSE97332"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE97332"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:11:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11514, "completion_tokens": 1609, "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:34900665", "type": "paper", "label": "pmid:34900665"}, {"id": "source:pmid:34900665", "type": "manuscript", "label": "PMID 34900665 full text"}, {"id": "data:geo:GSE97332", "type": "dataset", "label": "GEO GSE97332"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34900665", "type": "paper", "label": "pmid:34900665"}, {"id": "source:pmid:34900665", "type": "manuscript", "label": "PMID 34900665 full text"}, {"id": "data:geo:GSE97332", "type": "dataset", "label": "GEO GSE97332"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34900665", "type": "extraction", "used": ["source:pmid:34900665"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE97332", "type": "accession_resolution", "used": ["data:geo:GSE97332"], "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:34900665", "parent_hash": "sha256:306bacc00bf8a9be52c06f194b0856fe49cef3f57380e661ae01ac48460a4189", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE97332 licence not read", "asset:data:geo:GSE97332 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["of HCC and its molecular mechanism. METHODS: Microarray data (GSE97332) were available from the Gene"], "order_basis": "paper_text_order:449", "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": ["ain reaction (qRT-PCR). Cell counting kit-8 (CCK-8), scratch wound healing, and Transwell assay", "of circ_0000098 overexpression plasmid. (B) CCK-8 assay was used to detect cell proliferation", "nhibitor or co-transfected with si-ALX4. (B) CCK-8 assay was used to detect the proliferation o"], "order_basis": "paper_text_order:817", "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": [", and Vimentin expressions were evaluated by Western blot. In addition, the targeting relationship bet", "ion of circ_0000098 (Scale bar, 250 μm). (F) Western blot assay was used to detect the expression leve", "-1204-in+si-NC, and miR-1204-in+si-ALX4. (A) Western blot assay was used to detect the protein level o", "hibitor or co-transfection with si-ALX4. (F) Western blot assay was used to detect the expression leve"], "order_basis": "paper_text_order:1029", "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": ["ces (Shanghai, China). All of the cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Si", "d Methods Cell Culture Human HCC cell lines (HepG2, SNU423, and SNU475) were obtained from Amer"], "order_basis": "paper_text_order:1904", "id": "assay:4"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["000098 in Huh7 and SMMC-7721 cells after the transfection of circ_0000098 overexpression plasmid. (B)", ", invasion, and EMT via ALX4. HCC cells were transfected with miR-in, miR-1204-in, miR-1204-in+si-NC,", "in level of ALX4 in Huh7 and SMMC-7721 cells transfected with miR-1204 inhibitor or co-transfected wi", "ls transfected with miR-1204 inhibitor or co-transfected with si-ALX4. (B) CCK-8 assay was used to de"], "order_basis": "paper_text_order:3459", "id": "assay:5"}, {"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": ["Fisher’s exact test was employed to analyze the relationship between circ_0000098 expression and clinicopathological features. Student’s t-test was used to analyze the difference between two groups. One-way ANOVA was used to analyze the differences among the multiple groups. Pearson correlation analysis was employed to study the correlation among circRNA, miRNA, and mRNA expressions."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}