Reciprocal control of lncRNA-BCAT1 and β-catenin pathway reveals lncRNA-BCAT1 long non-coding RNA acts as a tumor suppressor in colorectal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28416735", "kind": "science-record", "revision": 8, "content_hash": "sha256:ac8b988024040fec26f188996e40b680beaccea66289f7a156bbf309b7a81bdb", "created_at": "2026-11-01T15:40:25Z", "updated_at": "2026-11-01T21:59:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Reciprocal control of lncRNA-BCAT1 and β-catenin pathway reveals lncRNA-BCAT1 long non-coding RNA acts as a tumor suppressor in colorectal cancer.", "doi": "10.18632/oncotarget.15466", "pmid": "28416735", "authors": ["Fei Xie", "Xudong Xiang", "Qionglin Huang", "Pengzhan Ran", "Yuncang Yuan", "Qian Li", "Guoxiang Qi", "Xiaopeng Guo", "Chunjie Xiao", "Shangyong Zheng"], "journal": "Oncotarget", "year": 2017, "abstract": "β-catenin plays a major role in tumor development and progression. The present study found that β-catenin was upregulated in 30 samples of colorectal cancer (CRC) tissue as compared to adjacent non-tumor tissues. Analysis of long non-coding RNA (lncRNA) expression profiles using the GSE18560 and GSE44097 datasets, which were generated via the Affymetrix plus 2.0 microarray platform and downloaded from the GEO database, revealed 20 differentially expressed lncRNAs following β-catenin knockdown. We focused on AK091631, a novel lncRNA, which we named lncRNA-β-catenin associated transcript 1 (LncRNA-BCAT1). lncRNA-BCAT1 expression was decreased in CRC tissues, and was negatively associated with β-catenin in both CRC tissues and cell lines. lncRNA-BCAT1 overexpression suppressed CRC cell growth and invasion by downregulating cyclin D1, c-Myc, and MMP-2. These results suggest that lncRNA-BCAT1 overexpression inhibits CRC cell growth and invasion via Wnt/β-catenin pathway blockade, and that lncRNA-BCAT1 is repressed by Wnt/β-catenin signaling. This evidence suggests that lncRNA-BCAT1 is a tumor suppressor and that lncRNA-BCAT1 may be an effective prognostic biomarker in CRC.", "claims": [{"id": "claim-method", "statement": "Differences between groups were calculated using Student's t test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28416735", "locator": "sections[19] \"Statistical analysis\" paragraph 2", "quote": "Differences between groups were calculated using Student's t test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw data from sets, GSE18560 and GSE44097, generated using the Affymetrix plus 2.0 microarray platform, were downloaded from the GEO database. For the GSE18560 dataset, which was produced using Ls1747 CRC cells, only the shRNA-mediated β-catenin knockdown arrays were used.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28416735", "locator": "sections[13] \"lncRNA profile mining from Affymatrix microarray data\" paragraph 2", "quote": "Raw data from sets, GSE18560 and GSE44097, generated using the Affymetrix plus 2.0 microarray platform, were downloaded from the GEO database. For the GSE18560 dataset, which was produced using Ls1747 CRC cells, only the shRNA-mediated β-catenin knockdown arrays were used."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used Student's t test for group comparisons, with P<0.05 (two-tailed) considered significant. Its public expression-profile source data comprised the GSE18560 and GSE44097 Affymetrix Plus 2.0 datasets downloaded from GEO; raw CEL files were analyzed in R using lncRNA chip-definition files and the Affy package.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "All statistical analyses were carried out using the SPSS 18.0 statistical software package. Continuous variables were expressed as means ± SEM. Differences between groups were calculated using Student's t test. P<0.05 (two-tailed) was considered statistically significant."}, "evidence": [{"asset": "source:pmid:28416735", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "These results suggest that lncRNA-BCAT1 overexpression inhibits CRC cell growth and invasion via Wnt/β-catenin pathway blockade, and that lncRNA-BCAT1 is repressed by Wnt/β-catenin signaling."}, {"asset": "source:pmid:28416735", "locator": "sections[7] \"Effect of lncRNA-BCAT1 on CRC cell proliferation\" paragraph 3", "quote": "The data were subjected to Student's t-test."}, {"asset": "source:pmid:28416735", "locator": "sections[19] \"Statistical analysis\" paragraph 2", "quote": "All statistical analyses were carried out using the SPSS 18.0 statistical software package. Continuous variables were expressed as means ± SEM. Differences between groups were calculated using Student's t test. P<0.05 (two-tailed) was considered statistically significant."}, {"asset": "source:pmid:28416735", "locator": "sections[13] \"lncRNA profile mining from Affymatrix microarray data\" paragraph 2", "quote": "Raw data from sets, GSE18560 and GSE44097, generated using the Affymetrix plus 2.0 microarray platform, were downloaded from the GEO database."}, {"asset": "source:pmid:28416735", "locator": "sections[13] \"lncRNA profile mining from Affymatrix microarray data\" paragraph 2", "quote": "lncRNA expression profiles were analyzed from the raw CEL files in R with the lncRNA CDFs and Affy packages."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study used Student's t test for group comparisons, with P<0.05 (two-tailed) considered significant. Its public expression-profile source data comprised the GSE18560 and GSE44097 Affymetrix Plus 2.0 datasets downloaded from GEO; raw CEL files were analyzed in R using lncRNA chip-definition files and the Affy package.", "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:28416735"], "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:GSE18560"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE18560"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28416735", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.15466", "sha256": "sha256:b7f45071580bcfdf7375e7703b0cb15dca45c20522c2a469066714133a347d5a", "bytes": 23330, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/oncotarget.15466", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5410332", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE18560", "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=GSE18560", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE18560", "version": null, "note": "Raw data from sets, GSE18560 and GSE44097, generated using the Affymetrix plus 2.0 microarray platform, were downloaded from the GEO database. 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We focused on AK091631, a novel lncRNA, whi"], "order_basis": "paper_text_order:590", "id": "assay:2"}, {"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": ["ture Collection (ATCC). SW480 and SW620 were cultured in Leibovitz's L-15 medium (Thermo Fisher Scien", "s, Grand Island, USA). HCT-116 and LoVo were cultured in Ham's F12K medium (Thermo Fisher Scientific,", "and Island, USA). 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