Development and validation of novel prognostic models for zinc finger proteins-related genes in soft tissue sarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37100454", "kind": "science-record", "revision": 3, "content_hash": "sha256:0b4b4932f526912eea841d5f42e068bab39f5ca8e5840b640b15e22775cb9171", "created_at": "2026-11-01T19:01:46Z", "updated_at": "2026-11-01T22:09:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development and validation of novel prognostic models for zinc finger proteins-related genes in soft tissue sarcoma.", "doi": "10.18632/aging.204682", "pmid": "37100454", "authors": ["Junqing Li", "Quan Zhou", "Changsheng Zhang", "Huimin Zhu", "Jie Yao", "Meng Zhang"], "journal": "Aging", "year": 2023, "abstract": "As the most common transcriptional regulators, zinc finer proteins (ZNFs) play vital roles in occurrence and progression of malignant tumors. Whereas, information regarding the roles of ZNFs in soft tissue sarcomas (STS) remains scarce. In this study, a comprehensive bioinformatics analysis investigating roles of ZNFs in STS was performed. Initially, we extracted raw datasets of differentially expressed ZNFs from GSE2719. Using a sequence of bioinformatics methods, we then investigated the prognostic significance, function, and molecular subtype of these differentially expressed ZNFs. In addition, CCK8 and plate clone formation assays were used to explore the effect of ZNF141 on STS cells. A total of 110 differentially expressed ZNFs were identified. Nine ZNFs (HLTF, ZNF292, ZNF141, LDB3, PHF14, ZNF322, PDLIM1, NR3C2, and LIMS2) were selected to establish an overall survival (OS) prediction model, and seven ZNFs (ZIC1, ZNF141, ZHX2, ZNF281, ZNHIT2, NR3C2, and LIMS2) were used to develop a progression-free survival (PFS) prediction model. Compared with patients with low-risk in the TCGA training and testing cohorts, as well as the GEO validation cohorts, patients with high-risk had poorer OS and PFS. Using nomograms constructed with the identified ZNFs predicting OS and PFS, we established a clinically useful model. Four distinct molecular subtypes with different prognostic and immune infiltration characteristics were identified. In vitro experiments showed that ZNF141 promoted the proliferation and viability of STS cells. In conclusion, ZNF-related models are useful as prognostic biomarkers, suggesting their potentials as therapeutic targets in STS. These findings will enable us to develop novel strategies treating STS, which will potentially improve outcomes of patients with STS.", "claims": [{"id": "claim-method", "statement": "Then factors confirmed by the univariate Cox regression analysis to be significantly associated with prognosis were subsequently incorporated into the LASSO-penalized Cox regression analysis to establish prognostic models.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37100454", "locator": "sections[4] \"Construction and validation of prognostic models\" paragraph 3", "quote": "Then factors confirmed by the univariate Cox regression analysis to be significantly associated with prognosis were subsequently incorporated into the LASSO-penalized Cox regression analysis to establish prognostic models."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets presented in this study are included in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37100454", "locator": "sections[12] \"Data availability statement\" paragraph 2", "quote": "All datasets presented in this study are included in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Nine ZNFs (HLTF, ZNF292, ZNF141, LDB3, PHF14, ZNF322, PDLIM1, NR3C2, and LIMS2) were selected to establish an overall survival (OS) prediction model, and seven ZNFs (ZIC1, ZNF141, ZHX2, ZNF281, ZNHIT2, NR3C2, and LIMS2) were used to develop a progression-free survival (PFS) prediction model.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37100454", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Nine ZNFs (HLTF, ZNF292, ZNF141, LDB3, PHF14, ZNF322, PDLIM1, NR3C2, and LIMS2) were selected to establish an overall survival (OS) prediction model, and seven ZNFs (ZIC1, ZNF141, ZHX2, ZNF281, ZNHIT2, NR3C2, and LIMS2) were used to develop a progression-free survival (PFS) prediction model."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Nine ZNFs (HLTF, ZNF292, ZNF141, LDB3, PHF14, ZNF322, PDLIM1, NR3C2, and LIMS2) were selected to establish an overall survival (OS) prediction model, and seven ZNFs (ZIC1, ZNF141, ZHX2, ZNF281, ZNHIT2, NR3C2, and LIMS2) were used to develop a progression-free survival (PFS) prediction model.", "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:37100454"], "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. 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In addition, CCK8 and plate clone formation assays were used t"], "order_basis": "paper_text_order:678", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["re constructed using the “pheatmap” package. RNA-seq data and clinical information of patients di", "ormatics and statistical analyses, including RNA-seq data normalization and transformation, DEG a"], "order_basis": "paper_text_order:2522", "id": "assay:2"}, {"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": ["ZNFs on human chromosomes. Cell culture and transfection A673 and SW982 cell lines were purchased fro", "MAX (Invitrogen, Carlsbad, CA, USA). Then we transfected ZNF141-overexpression-promoting plasmid (GV-", "bovine serum (Biological Industries). ZNF141 siRNA and negative control siRNA oligonucleotides", "dustries). ZNF141 siRNA and negative control siRNA oligonucleotides were designed and synthesiz"], "order_basis": "paper_text_order:3051", "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": 0.77, "evidence": ["(Shanghai, China). A673 and SW982 cells were cultured in DMEM (Biological Industries, Shanghai, China"], "order_basis": "paper_text_order:3203", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Then factors confirmed by the univariate Cox regression analysis to be significantly associated with prognosis were subsequently incorporated into the LASSO-penalized Cox regression analysis to establish prognostic models."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}