Gene Expression Changes Associated with Dedifferentiation in Liposarcoma Predict Overall Survival.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34207401", "kind": "science-record", "revision": 6, "content_hash": "sha256:cc99cef24498c9b8055790c66690d703ad4bb3dc764014678ddbad3cfe3e4258", "created_at": "2026-11-01T15:41:41Z", "updated_at": "2026-11-01T21:25:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene Expression Changes Associated with Dedifferentiation in Liposarcoma Predict Overall Survival.", "doi": "10.3390/cancers13123049", "pmid": "34207401", "authors": ["Nicholas Brian Shannon", "Qiu Xuan Tan", "Joey Wee-Shan Tan", "Josephine Hendrikson", "Wai Har Ng", "Gillian Ng", "Ying Liu", "Grace Hwei Ching Tan", "Jolene Si Min Wong", "Khee Chee Soo", "Melissa Ching Ching Teo", "Claramae Shulyn Chia", "Chin-Ann Johnny Ong"], "journal": "Cancers", "year": 2021, "abstract": "Up to 10% of well-differentiated liposarcoma (WDLS) progress to dedifferentiated liposarcoma (DDLS). We aimed to identify gene expression changes associated with dedifferentiation and whether these were informative of tumour biology of DDLS. We analysed datasets from the Gene Expression Omnibus (GEO, ID = GSE30929) database to identify differentially expressed genes between WDLS (n = 52) and DDLS (n = 39). We validated the signature on whole and laser-capture microdissected samples from patients with tumours consisting of mixed WDLS and DDLS components. A subset of this signature was applied to an independent dataset from The Cancer Genome Atlas (TCGA, n = 58 DDLS) database to segregate samples based on gene expression and compared for recurrence and overall survival (OS). A 15-gene signature consisting of genes with increased expression in DDLS compared to WDLS was generated. This signature segregated WDLS and DDLS samples from patients with mixed component tumours and across multiple recurrences. A further subset of this signature, consisting of five genes (AQP7, ACACB, FZD4, GPD1, LEP), segregated DDLS in a TCGA cohort with a significant difference in OS (p = 0.019) and recurrence-free survival (RFS) (p = 0.061). The five-gene model stratified DDLS into prognostic groups and outperformed clinical factors in existing models in retroperitoneal DDLS.", "claims": [{"id": "claim-method", "statement": "Univariate analysis was performed utilising Fisher’s exact test and multivariate analysis of significant factors was performed using a factorial logistic regression model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34207401", "locator": "sections[5] \"2.3. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE30929"], "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:GSE30929"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34207401", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cancers13123049", "sha256": "sha256:b5bc26631fc9b8da6c0546225224f4ab12563fc3a3b9fbb9bfeda76de39a3e59", "bytes": 28561, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cancers13123049", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8235385", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE30929", "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=GSE30929", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30929", "version": null, "note": "The data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM766533", "GSM766534", "GSM766535", "GSM766536", "GSM766537", "GSM766538", "GSM766539", "GSM766540", "GSM766541", "GSM766542", "GSM766543", "GSM766544", "GSM766545", "GSM766546", "GSM766547", "GSM766548", "GSM766549", "GSM766550", "GSM766551", "GSM766552", "GSM766553", "GSM766554", "GSM766555", "GSM766556", "GSM766557", "GSM766558", "GSM766559", "GSM766560", "GSM766561", "GSM766562", "GSM766563", "GSM766564", "GSM766565", "GSM766566", "GSM766567", "GSM766568", "GSM766569", "GSM766570", "GSM766571", "GSM766572", "GSM766573", "GSM766574", "GSM766575", "GSM766576", "GSM766577", "GSM766578", "GSM766579", "GSM766580", "GSM766581", "GSM766582", "GSM766583", "GSM766584", "GSM766585", "GSM766586", "GSM766587", "GSM766588", "GSM766589", "GSM766590", "GSM766591", "GSM766592", "GSM766593", "GSM766594", "GSM766595", "GSM766596", "GSM766597", "GSM766598", "GSM766599", "GSM766600", "GSM766601", "GSM766602", "GSM766603", "GSM766604", "GSM766605", "GSM766606", "GSM766607", "GSM766608", "GSM766609", "GSM766610", "GSM766611", "GSM766612", "GSM766613", "GSM766614", "GSM766615", "GSM766616", "GSM766617", "GSM766618", "GSM766619", "GSM766620", "GSM766621", "GSM766622", "GSM766623", "GSM766624", "GSM766625", "GSM766626", "GSM766627", "GSM766628", "GSM766629", "GSM766630", "GSM766631", "GSM766632", "GSM766633", "GSM766634", "GSM766635", "GSM766636", "GSM766637", "GSM766638", "GSM766639", "GSM766640", "GSM766641", "GSM766642", "GSM766643", "GSM766644", "GSM766645", "GSM766646", "GSM766647", "GSM766648", "GSM766649", "GSM766650", "GSM766651", "GSM766652", "GSM766653", "GSM766654", "GSM766655", "GSM766656", "GSM766657", "GSM766658", "GSM766659", "GSM766660", "GSM766661", "GSM766662", "GSM766663", "GSM766664", "GSM766665", "GSM766666", "GSM766667", "GSM766668", "GSM766669", "GSM766670", "GSM766671", "GSM766672"], "sample_count": 140, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Whole-transcript expression data for liposarcoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34207401:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d02c0b32214599d09f3cc8e6c1a0caeb23f4ff17f139dcc5955b6e1dda1aee5d", "bytes": 468, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#cancers-13-03049-t001", "version": null, "note": "Transcriptomics datasets analysed as part of the study.", "structure": {"pmcid": "PMC8235385", "section_index": 3, "section_title": "2.1. External Datasets", "row_count": 3, "column_count": 4}, "table": {"label": "Table 1", "caption": "Transcriptomics datasets analysed as part of the study.", "rows": [["ID", "First Author", "Published", "Samples; of Which Liposarcoma"], ["GSE30929", "Gobble", "Cancer Res 2011 [9]", "140; WDLS (n = 52), DDLS (n = 30), MLS (n = 17), RCLS (n = 12), PLS (n = 20)"], ["TCGA-SARC", "CGARN", "Cell 2017 [3]", "259; DDLS (n = 58)"]], "row_count": 3, "column_count": 4, "numeric_cells": 5, "header_rows": 1, "locator": "section[3]/table-wrap[1]#cancers-13-03049-t001"}}, {"id": "asset:table:pmid:34207401:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d531d79d9d88a4619825ad44e8fd8517c7fba608ee89c065efad9b57c3337741", "bytes": 773, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#cancers-13-03049-t002", "version": null, "note": "Multivariate comparison of model prediction and clinical factors. W = width, L = length, R2 = gross positive margin, R1 = microscopically positive margin, R0 = negative margin.", "structure": {"pmcid": "PMC8235385", "section_index": 10, "section_title": "3.4. Comparison to Clinical Information", "row_count": 8, "column_count": 5}, "table": {"label": "Table 2", "caption": "Multivariate comparison of model prediction and clinical factors. 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