The LncRNA lnc-POTEM-4:14 promotes HCC progression by interacting with FOXK1.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40044876", "kind": "science-record", "revision": 4, "content_hash": "sha256:2e6fb6cb29ffac30269b19e7ddc4bff08f714d43ca223f6b2cf09e00932d7c3e", "created_at": "2026-11-01T20:30:15Z", "updated_at": "2026-11-01T22:56:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The LncRNA lnc-POTEM-4:14 promotes HCC progression by interacting with FOXK1.", "doi": "10.1038/s41598-025-92614-4", "pmid": "40044876", "authors": ["Bo Peng", "Zhipeng Quan", "Lixing Liang", "Mingjiang Liu", "Kai Hu", "Shilian Chen", "Qiuli Xie", "Jing Qin", "Jingzhao Chen", "Lijuan Liao", "Songqing He", "Zeyuan Li"], "journal": "Scientific reports", "year": 2025, "abstract": "Hepatocellular carcinoma (HCC) is one of the most common malignant tumours of the digestive tract and poses a serious threat to human life. This study first analysed two GEO datasets (GSE166705 and GSE115018) to screen for differentially expressed lncRNAs between HCC and adjacent tissues. The lncRNA lnc-POTEM-4:14 was determined via a series of methods to be closely related to liver cancer. Further research was subsequently performed to investigate the role of the lncRNA lnc-POTEM-4:14 in the progression of HCC. The lncRNA lnc-POTEM-4:14 is localized primarily within the nucleus and is highly expressed in liver cancer tissues. We established lnc-POTEM-4:14 knockdown and overexpression cell lines to analyse the role of lnc-POTEM-4:14 in liver cancer through functional experiments such as qPCR and WB. We identified FOXK1 as an RNA-binding protein (RBP) of lnc-POTEM-4:14 that participates in MAPK signal activation and cell cycle progression by regulating the activation or expression levels of the downstream target protein TAB1 as a transcription factor. The restoration of FOXK1 can rescue the limited proliferation and increased apoptosis caused by lnc-POTEM-4:14 knockdown. Finally, we validated our hypothesis in a nude mouse tumour-bearing model. In conclusion, lnc-POTEM-4:14 affects the progression of HCC through the FOXK1/TAB1/NLK axis, suggesting that lnc-POTEM-4:14 has potential as a therapeutic target for treating this aggressive malignancy.", "claims": [{"id": "claim-method", "statement": "Differences between two groups were analysed via unpaired Student’s t tests. Comparisons among multiple groups were performed by means of one-way analysis of variance (ANOVA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40044876", "locator": "sections[16] \"Statistical analysis\" paragraph 2", "quote": "Differences between two groups were analysed via unpaired Student’s t tests. Comparisons among multiple groups were performed by means of one-way analysis of variance (ANOVA)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data will be available upon reasonable requests from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40044876", "locator": "sections[28] \"Data availability\" paragraph 2", "quote": "Data will be available upon reasonable requests from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "lnc-POTEM-4:14 affects the progression of HCC through the FOXK1/TAB1/NLK axis, suggesting that lnc-POTEM-4:14 has potential as a therapeutic target for treating this aggressive malignancy.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40044876", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In conclusion, lnc-POTEM-4:14 affects the progression of HCC through the FOXK1/TAB1/NLK axis, suggesting that lnc-POTEM-4:14 has potential as a therapeutic target for treating this aggressive malignancy."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "lnc-POTEM-4:14 affects the progression of HCC through the FOXK1/TAB1/NLK axis, suggesting that lnc-POTEM-4:14 has potential as a therapeutic target for treating this aggressive malignancy.", "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:40044876"], "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:GSE115018"], "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:GSE115018"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40044876", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-92614-4", "sha256": "sha256:fb372072a6b3bf8db2bdd1271672c691033f9bc223e7f2360f23edab4ac31af5", "bytes": 47021, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-92614-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11882843", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE115018", "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=GSE115018", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE115018", "version": null, "note": "Data will be available upon reasonable requests from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data will be available upon reasonable requests from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3163056", "GSM3163057", "GSM3163058", "GSM3163059", "GSM3163060", "GSM3163061", "GSM3163062", "GSM3163063", "GSM3163064", "GSM3163065", "GSM3163066", "GSM3163067", "GSM3163068", "GSM3163069", "GSM3163070", "GSM3163071", "GSM3163072", "GSM3163073", "GSM3163074", "GSM3163075", "GSM3163076", "GSM3163077", "GSM3163078", "GSM3163079"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "20115", "taxon": "Homo sapiens", "title": "Simultaneous control of non-coding RNA on the G2/M phase of the cell cycle in hepatocellular carcinoma [lncRNA and mRNA]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE166705", "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=GSE166705", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE166705", "version": null, "note": "Data will be available upon reasonable requests from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data will be available upon reasonable requests from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5079353", "GSM5079354", "GSM5079355", "GSM5079356", "GSM5079357", "GSM5079358", "GSM5079359", "GSM5079360", "GSM5079361", "GSM5079362"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "19615", "taxon": "Homo sapiens", "title": "Human liver tissues: cancer vs. control", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE115018 not downloaded", "asset:data:geo:GSE115018 licence not read", "asset:data:geo:GSE166705 not downloaded", "asset:data:geo:GSE166705 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": "Differences between two groups were analysed via unpaired Student’s t tests. Comparisons among multiple groups were performed by means of one-way analysis of variance (ANOVA)."}}], "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": ["GSE166705", "GSE115018"], "resolved_accessions": ["GSE166705", "GSE115018"], "statements": ["Data will be available upon reasonable requests from the corresponding author."], "basis": "The paper names GSE166705, GSE115018 in 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:40044876", "data:geo:GSE115018"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE115018"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:47:29Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14260, "completion_tokens": 1301, "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:40044876", "type": "paper", "label": "pmid:40044876"}, {"id": "source:pmid:40044876", "type": "manuscript", "label": "PMID 40044876 full text"}, {"id": "data:geo:GSE115018", "type": "dataset", "label": "GEO GSE115018"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40044876", "type": "paper", "label": "pmid:40044876"}, {"id": "source:pmid:40044876", "type": "manuscript", "label": "PMID 40044876 full text"}, {"id": "data:geo:GSE115018", "type": "dataset", "label": "GEO GSE115018"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40044876", "type": "extraction", "used": ["source:pmid:40044876"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE115018", "type": "accession_resolution", "used": ["data:geo:GSE115018"], "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:40044876", "parent_hash": "sha256:3f7946dc8d541724b6409e4a06c015d069c762214dfaf237d3498f85f1af75ef", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE115018 licence not read", "asset:data:geo:GSE115018 not downloaded", "asset:data:geo:GSE166705 licence not read", "asset:data:geo:GSE166705 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["ancer tissues. We established lnc-POTEM-4:14 knockdown and overexpression cell lines to analyse the", "increased apoptosis caused by lnc-POTEM-4:14 knockdown. Finally, we validated our hypothesis in a n", "he Declaration of Helsinki. Cell culture and transfection The human HCC cell lines LM3, Huh-7, MHCC97H", "io, China) and plasmids (IGEbio, China) were transfected into cells using Lipofectamine 3000 reagent"], "order_basis": "paper_text_order:698", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ancer through functional experiments such as qPCR and WB. We identified FOXK1 as an RNA-bindin"], "order_basis": "paper_text_order:831", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["scue the limited proliferation and increased apoptosis caused by lnc-POTEM-4:14 knockdown. Finally,"], "order_basis": "paper_text_order:1176", "id": "assay:3"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["nally, we validated our hypothesis in a nude mouse tumour-bearing model. In conclusion, lnc-POT"], "order_basis": "paper_text_order:1269", "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": 0.77, "evidence": ["pe Culture Collection (ATCC). The cells were cultured in DMEM or RPMI 1640 (Gibco, USA) supplemented"], "order_basis": "paper_text_order:2637", "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": ["Differences between two groups were analysed via unpaired Student’s t tests. Comparisons among multiple groups were performed by means of one-way analysis of variance (ANOVA)."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}