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pmid:35756612
Up-Regulation of TRIM32 Associated With the Poor Prognosis of Acute Myeloid Leukemia by Integrated Bioinformatics Analysis With External Validation.
Xiaoyan Xu · Jiaqian Qi · Jingyi Yang · Tingting Pan · Haohao Han · Meng Yang · Yue Han
Frontiers in oncology · 2022 doi:10.3389/fonc.2022.848395
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Experiment
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Complete file
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It is essential to clarify the molecular mechanisms of AML and develop targeted treatment strategies to improve patient prognosis.\nMethods: AML mRNA expression data and survival status were extracted from TCGA and GEO databases (GSE37642, GSE76009, GSE16432, GSE12417, GSE71014). Weighted gene co-expression network analysis (WGCNA) and differential gene expression analysis were performed. Functional enrichment analysis and protein-protein interaction (PPI) network were used to screen out hub genes. In addition, we validated the expression levels of hub genes as well as the prognostic value and externally validated TRIM32 with clinical data from our center. AML cell lines transfected with TRIM32 shRNA were also established to detect the proliferation in vitro.\nResults: A total of 2192 AML patients from TCGA and GEO datasets were included in this study and 20 differentially co-expressed genes were screened by WGCNA and differential gene expression analysis methods. These genes were mainly enriched in phospholipid metabolic processes (biological processes, BP), secretory granule membranes (cellular components, CC), and protein serine/threonine kinase activity (molecular functions, MF). In addition, the protein-protein interaction (PPI) network contains 15 nodes and 15 edges and 10 hub genes (TLE1, GLI2, HDAC9, MICALL2, DOCK1, PDPN, RAB27B, SIX3, TRIM32 and TBX1) were identified. The expression of 10 central genes, except TLE1, was associated with survival status in AML patients (p<0.05). High expression of TRIM32 was tightly associated with poor relapse-free survival (RFS) and overall survival (OS) in AML patients, which was verified in the bone marrow samples from our center. In vitro, knockdown of TRIM32 can inhibit the proliferation of AML cell lines.\nConclusion: TRIM32 was associated with the progression and prognosis of AML patients and could be a potential therapeutic target and biomarker for AML in the future.", "claims": [{"id": "claim-method", "statement": "Univariate Kaplan-Meier survival analysis was done with R package survival to identify the prognostic value of hub genes further.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35756612", "locator": "sections[8] \"Validation of the Expression Level and Prognostic Value of Hub Genes\" paragraph 2", "quote": "Univariate Kaplan-Meier survival analysis was done with R package survival to identify the prognostic value of hub genes further."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. 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"10105;10108;8654;8651;10106;8652;8650;10107;8653", "taxon": "Homo sapiens", "title": "Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE37642", "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=GSE37642", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37642", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. 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"blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE37642", "GSE76009", "GSE16432", "GSE12417", "GSE71014"], "resolved_accessions": ["GSE37642", "GSE76009", "GSE16432", "GSE12417", "GSE71014"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."], "basis": "The paper names GSE37642, GSE76009, GSE16432, GSE12417, GSE71014 in GEO and the accession resolves in the repository. 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AML cell lines transfected with TRIM32 shRNA were also established to d", "ne marrow samples from our center. In vitro, knockdown of TRIM32 can inhibit the proliferation of A", "nter. AML cell lines transfected with TRIM32 shRNA were also established to detect the prolifer"], "order_basis": "paper_text_order:878", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Univariate Kaplan-Meier survival analysis was done with R package survival to identify the prognostic value of hub genes further."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}