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Liu W, Xu Y, Bai S, Liao L. Bioinformatics analysis of key biomarkers for bladder cancer. Biomed Rep 2022; 18:14. [PMID: 36643693 PMCID: PMC9813473 DOI: 10.3892/br.2022.1596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
Bladder cancer (BC) is one of the most prevalent genitourinary cancers. Despite the growing research interest in BC, the molecular mechanisms underlying its carcinogenesis remain poorly understood. The microarray datasets GSE38264 and GSE61615 obtained from the Gene Expression Omnibus (GEO) database were analyzed and differentially expressed genes (DEGs) were identified, which were then verified using a dataset from The Cancer Genome Atlas (TCGA). By taking the intersection of the two microarray datasets, the common DEGs were identified and these were selected as candidate genes associated with BC. The DEGs were further subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and the protein-protein interaction network was constructed. Further module analysis was performed using STRING and Cytoscape. A total of 362 DEGs were identified, including 13 hub genes, and the GO analysis revealed that these genes were mainly enriched in extracellular matrix organization, positive regulation of cell proliferation, angiogenesis and peptidyl-tyrosine phosphorylation. The expression changes of PTPRC, PDGFRA, CASQ2, TGFBI, KLRD1 and MT1X in the different datasets indicated that these genes were involved in the development of BC. Next, the differential expression of these genes was verified in the TCGA dataset, and ultimately, these 13 genes were determined to be related to the occurrence and development of BC. Finally, the cancer tissues and adjacent tissues of patients with BC were collected and subjected to reverse transcription-quantitative PCR, the results of which were consistent with the bioinformatics prediction. The present findings provide several vital genes for the clinical diagnosis and treatment of BC.
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Affiliation(s)
- Wentao Liu
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China
| | - Yuxin Xu
- Disease Surveillance Department, Center for Disease Control and Prevention, Western Theater Command, Lanzhou, Gansu 730020, P.R. China
| | - Shengbin Bai
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China,Correspondence to: Professor Shengbin Bai or Professor Libin Liao, Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, 393 Xinyi Road, High Tech Zone, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China NULL
| | - Libin Liao
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China,Correspondence to: Professor Shengbin Bai or Professor Libin Liao, Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, 393 Xinyi Road, High Tech Zone, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China NULL
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t(4;12)(q12;p13) ETV6-rearranged AML without eosinophilia does not involve PDGFRA: relevance for imatinib insensitivity. Blood Adv 2021; 6:818-827. [PMID: 34587239 PMCID: PMC8945303 DOI: 10.1182/bloodadvances.2021005280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/14/2021] [Indexed: 11/20/2022] Open
Abstract
Apparent ETV6-PDGFRA fusions identified by FISH analysis in t(4;12)(q12;p13) AML should be confirmed by sequencing. Sequence-confirmed ETV6-PDGFRA fusions have not been identified in patients with t(4;12)(q12;p13) AML without eosinophilia.
Acute myeloid leukemia (AML) with t(4;12)(q12;p13) translocation is rare and often associated with an aggressive clinical course and poor prognosis. Previous reports based on fluorescence in situ hybridization (FISH) analysis have suggested that ETV6::PDGFRA fusions are present in these patients, despite the absence of eosinophilia, which is typically found in other hematopoietic malignancies with PDGFRA-containing fusions. We first detected an ETV6-SCFD2 fusion by targeted RNA sequencing in a patient with t(4;12)(q12;p13) who had been diagnosed with an ETV6-PDGFRA fusion by FISH analysis but failed to respond to imatinib. We then retrospectively identified 4 additional patients with AML and t(4;12)(q12;p13) with apparent ETV6-PDGFRA fusions using chromosome and FISH analysis and applied targeted RNA sequencing to archival material. We again detected rearrangements between ETV6 and non-PDGFRA 4q12 genes, including SCFD2, CHIC2, and GSX2. None of the 3 patients who received imatinib based on the incorrect assumption of an ETV6-PDGFRA fusion responded. Our findings highlight the importance of using a sequencing-based assay to confirm the presence of targetable gene fusions, particularly in genomic regions, such as 4q12, with many clinically relevant genes that are too close to resolve by chromosome or FISH analysis. Finally, combining our data and review of the literature, we show that sequence-confirmed ETV6-PDGFRA fusions are typically found in eosinophilic disorders (3/3 cases), and patients with t(4;12)(q12;p13) without eosinophilia are found to have other 4q12 partners on sequencing (17/17 cases).
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