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Wang L, Zhang Z, Ma HZ. Prognostic value of PEA3 subfamily gene expression in cholangiocarcinoma. World J Gastrointest Oncol 2024; 16:4014-4027. [DOI: 10.4251/wjgo.v16.i9.4014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/19/2024] [Accepted: 07/30/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is a lethal malignancy with limited treatment options and poor prognosis. The PEA3 subfamily of E26 transformation specific genes: ETV1, ETV4, and ETV5 are known to play significant roles in various cancers by influencing cell proliferation, invasion, and metastasis.
AIM To analyze PEA3 subfamily gene expression levels in CCA and their correlation with clinical parameters to determine their prognostic value for CCA.
METHODS The expression levels of PEA3 subfamily genes in pan-cancer and CCA data in the cancer genome atlas and genotype-tissue expression project databases were analyzed with R language software. Survival curve and receiver operating characteristic analyses were performed using the SurvMiner, Survival, and Procr language packages. The gene expression profiling interactive analysis 2.0 database was used to analyze the expression levels of PEA3 subfamily genes in different subtypes and stages of CCA. Web Gestalt was used to perform the gene ontology/ Kyoto encyclopedia of genes and genomes (GO/KEGG) analysis, and STRING database analysis was used to determine the genes and proteins related to PEA3 subfamily genes.
RESULTS ETV1, ETV4, and ETV5 expression levels were significantly increased in CCA. There were significant differences in ETV1, ETV4, and ETV5 expression levels among the different subtypes of CCA, and predictive analysis revealed that only high ETV1 and ETV4 expression levels were significantly associated with shorter overall survival in patients with CCA. GO/KEGG analysis revealed that PEA3 subfamily genes were closely related to transcriptional misregulation in cancer. In vitro and in vivo experiments revealed that PEA3 silencing inhibited the invasion and metastasis of CCA cells.
CONCLUSION The expression level of ETV4 may be a predictive biomarker of survival in patients with CCA.
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Affiliation(s)
- Li Wang
- Department of Emergency, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
| | - Zhe Zhang
- Department of Emergency Medicine, The First People’s Hospital of Linping District Hangzhou, Hangzhou 311100, Zhejiang Province, China
| | - Hai-Zhang Ma
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan 250000, Shandong Province, China
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Iori S, D'Onofrio C, Laham-Karam N, Mushimiyimana I, Lucatello L, Lopparelli RM, Gelain ME, Capolongo F, Pauletto M, Dacasto M, Giantin M. Establishment and characterization of cytochrome P450 1A1 CRISPR/Cas9 Knockout Bovine Foetal Hepatocyte Cell Line (BFH12). Cell Biol Toxicol 2024; 40:18. [PMID: 38528259 DOI: 10.1007/s10565-024-09856-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/21/2024] [Indexed: 03/27/2024]
Abstract
The cytochrome P450 1A (CYP1A) subfamily of xenobiotic metabolizing enzymes (XMEs) consists of two different isoforms, namely CYP1A1 and CYP1A2, which are highly conserved among species. These two isoenzymes are involved in the biotransformation of many endogenous compounds as well as in the bioactivation of several xenobiotics into carcinogenic derivatives, thereby increasing the risk of tumour development. Cattle (Bos taurus) are one of the most important food-producing animal species, being a significant source of nutrition worldwide. Despite daily exposure to xenobiotics, data on the contribution of CYP1A to bovine hepatic metabolism are still scarce. The CRISPR/Cas9-mediated knockout (KO) is a useful method for generating in vivo and in vitro models for studying xenobiotic biotransformations. In this study, we applied the ribonucleoprotein (RNP)-complex approach to successfully obtain the KO of CYP1A1 in a bovine foetal hepatocyte cell line (BFH12). After clonal expansion and selection, CYP1A1 excision was confirmed at the DNA, mRNA and protein level. Therefore, RNA-seq analysis revealed significant transcriptomic changes associated with cell cycle regulation, proliferation, and detoxification processes as well as on iron, lipid and mitochondrial homeostasis. Altogether, this study successfully generates a new bovine CYP1A1 KO in vitro model, representing a valuable resource for xenobiotic metabolism studies in this important farm animal species.
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Affiliation(s)
- Silvia Iori
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Caterina D'Onofrio
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Nihay Laham-Karam
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, Neulaniementie 2, 70211, Kuopio, Finland
| | - Isidore Mushimiyimana
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, Neulaniementie 2, 70211, Kuopio, Finland
| | - Lorena Lucatello
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Rosa Maria Lopparelli
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Maria Elena Gelain
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Francesca Capolongo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy.
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Shen D, Hong Y, Feng Z, Chen X, Cai Y, Peng Q, Tu J. Development of dynamical network biomarkers for regulation in Epstein-Barr virus positive peripheral T cell lymphoma unspecified type. Front Genet 2022; 13:966247. [PMID: 36544484 PMCID: PMC9760704 DOI: 10.3389/fgene.2022.966247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: This study was performed to identify key regulatory network biomarkers including transcription factors (TFs), miRNAs and lncRNAs that may affect the oncogenesis of EBV positive PTCL-U. Methods: GSE34143 dataset was downloaded and analyzed to identify differentially expressed genes (DEGs) between EBV positive PTCL-U and normal samples. Gene ontology and pathway enrichment analyses were performed to illustrate the potential function of the DEGs. Then, key regulators including TFs, miRNAs and lncRNAs involved in EBV positive PTCL-U were identified by constructing TF-mRNA, lncRNA-miRNA-mRNA, and EBV encoded miRNA-mRNA regulatory networks. Results: A total of 96 DEGs were identified between EBV positive PTCL-U and normal tissues, which were related to immune responses, B cell receptor signaling pathway, chemokine activity. Pathway analysis indicated that the DEGs were mainly enriched in cytokine-cytokine receptor interaction and chemokine signaling pathway. Based on the TF network, hub TFs were identified regulate the target DEGs. Afterwards, a ceRNA network was constructed, in which miR-181(a/b/c/d) and lncRNA LINC01744 were found. According to the EBV-related miRNA regulatory network, CXCL10 and CXCL11 were found to be regulated by EBV-miR-BART1-3p and EBV-miR-BHRF1-3, respectively. By integrating the three networks, some key regulators were found and may serve as potential network biomarkers in the regulation of EBV positive PTCL-U. Conclusion: The network-based approach of the present study identified potential biomarkers including transcription factors, miRNAs, lncRNAs and EBV-related miRNAs involved in EBV positive PTCL-U, assisting us in understanding the molecular mechanisms that underlie the carcinogenesis and progression of EBV positive PTCL-U.
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Affiliation(s)
- Dan Shen
- Department of Oncology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yin Hong
- Department of Cardiothoracic Surgery, Suzhou BenQ Hospital, Suzhou, China
| | - Zhengyang Feng
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiangying Chen
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuxing Cai
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Qiliang Peng
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China,*Correspondence: Jian Tu, ; Qiliang Peng,
| | - Jian Tu
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, China,*Correspondence: Jian Tu, ; Qiliang Peng,
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Matjašič A, Zupan A, Boštjančič E, Pižem J, Popović M, Kolenc D. A novel PTPRZ1-ETV1 fusion in gliomas. Brain Pathol 2019; 30:226-234. [PMID: 31381204 DOI: 10.1111/bpa.12776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 07/26/2019] [Indexed: 12/17/2022] Open
Abstract
The aggressive nature of malignant gliomas and their genetic and clinical heterogeneity present a major challenge in their diagnosis and treatment. Development of targeted therapy brought attention on detecting novel gene fusions, since they represent promising therapeutic targets (eg, TRK inhibitors in NTRK fusion-positive tumors). Using targeted next-generation sequencing, we prospectively analyzed 205 primary brain tumors and detected a novel PTPRZ1-ETV1 fusion transcript in 11 of 191 (5.8%) gliomas, including nine glioblastomas, one anaplastic oligodendroglioma and one pilocytic astrocytoma. PTPRZ1-ETV1 fusion was confirmed by RT-PCR followed by Sanger sequencing, and in-silico analysis predicted a potential driver role. The newly detected fusion consists of the PTPRZ1 promoter in frame with the highly conserved DNA-binding domain of ETV1 transcription factor. The ETV1 and PTPRZ1 genes are known oncogenes, involved in processes of tumor development. ETV1 is a member of the ETS family of transcription factors, already known oncogenic drivers in Ewing sarcoma, prostate cancer and gastrointestinal stromal tumors, but not in gliomas. Its overexpression contributes to tumor growth and more aggressive tumor behavior. PTPRZ1 is already considered to be a tumor growth promoting oncogene in gliomas. In 8%-16% of gliomas, PTPRZ1 is fused to the MET oncogene, resulting in a PTPRZ1-MET fusion, which is associated with poorer prognosis but is also a positive predictive biomarker for treatment with kinase inhibitors. In view of the oncogenic role that the two fusion partners, PTPRZ1 and ETV1, exhibit in other malignancies, PTPRZ1-ETV1 fusion might present a novel potential therapeutic target in gliomas. Although histopathological examination of PTPRZ1-ETV1 fusion-positive gliomas did not reveal any specific or unique pathological features, and the follow-up period was too short to assess prognostic value of the fusion, careful monitoring of patients and their response to therapy might provide additional insights into the prognostic and predictive value of this novel fusion.
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Affiliation(s)
- Alenka Matjašič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Andrej Zupan
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Emanuela Boštjančič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jože Pižem
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mara Popović
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Danijela Kolenc
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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