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Wei Q. Bioinformatical identification of key genes regulated by IGF2BP2-mediated RNA N6-methyladenosine and prediction of prognosis in hepatocellular carcinoma. J Gastrointest Oncol 2021; 12:1773-1785. [PMID: 34532127 DOI: 10.21037/jgo-21-306] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/17/2021] [Indexed: 12/22/2022] Open
Abstract
Background The treatment of hepatocellular carcinoma (HCC), a malignant cancer with global spread, remains unsatisfactory, and novel prognostic biomarkers need to be identified. N6-methyladenosine (m6A) has been found to regulate tumor initiation and progression through different mechanisms. As a dynamic and reversible messenger RNA (mRNA) modification, m6A can be read by insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). IGF2BP2 targets thousands of mRNA transcripts, which may be involved in HCC progression. Methods In this study, we integrated 4 classes of datasets including The Cancer Genome Atlas (TCGA)-LICH, m6A-sequencing data of HepG2 cells, and RNA-sequencing data of IGF2BP2-knockdown HepG2 cells to explore the key genes regulated by IGF2BP2-mediated m6A in HCC. The expression and m6A modification of candidates were validation in independent microarray expression profile of HCC tissue and annotated m6A database RMBase. The relationship of immune cell infiltration and the genes expression was estimated by CIBERSORT and TIMER. Results A total of 89 candidate genes were filtered. Next, cluster analysis was performed base on functions and pathways to identify the enrichment pathways. By constructing a protein-protein interaction (PPI) network, we found 54 nodes. Ten significant genes were filtered from the PPI. These genes were validated in data of an independent microarray and an m6A database. We found that the upregulation of these 10 genes was associated with poor prognosis. In addition, we showed the expression of these 10 genes was associated with the infiltration of variety of immune cell and tumor purity. Conclusions These identified genes may provide novel insights and facilitate the development of potential biomarkers for HCC diagnosis, as well as provide clues for IGF2BP2 inhibition therapy in HCC.
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Affiliation(s)
- Qiang Wei
- Hepatological Surgery Department, Bethune International Peace Hospital of PLA, Shijiazhuang, China
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Singh AK, Verma S, Kushwaha PP, Prajapati KS, Shuaib M, Kumar S, Gupta S. Role of ZBTB7A zinc finger in tumorigenesis and metastasis. Mol Biol Rep 2021; 48:4703-4719. [PMID: 34014468 DOI: 10.1007/s11033-021-06405-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/08/2021] [Indexed: 02/08/2023]
Abstract
The zinc finger and BTB (broad-complex, tramtrack and bric a brac) domain containing protein 7A (ZBTB7A) is a pleiotropic transcription factor that plays an important role in various stages of cell proliferation, differentiation, and other developmental processes. ZBTB7A is a member of the POK family that directly and specifically binds to short DNA recognition sites located near their target genes thereby acting as transcriptional activator or repressor. ZBTB7A overexpression has been associated with tumorigenesis and metastasis in various human cancer types, including breast, prostate, lung, ovarian, and colon cancer. However in some instances downregulation of ZBTB7A results in tumor progression, suggesting its role as a tumor suppressor. ZBTB7A is involved with complicated regulatory networks which include protein-protein and protein-nucleic acid interactions. ZBTB7A involvement in cancer progression and metastasis is perhaps enabled through the regulation of various signaling pathways depending on the type and genetic context of cancer. The association of ZBTB7A with other proteins affects cancer aggressiveness, therapeutic resistance and clinical outcome. This review focuses on the involvement of ZBTB7A in various signaling pathways and its role in cancer progression. We will also review the literature on ZBTB7A and cancer which could be potentially explored for its therapeutic implications.
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Affiliation(s)
- Atul Kumar Singh
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Shiv Verma
- Department of Urology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.,Department of Urology, The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
| | - Prem Prakash Kushwaha
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Kumari Sunita Prajapati
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Mohd Shuaib
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Shashank Kumar
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India.
| | - Sanjay Gupta
- Department of Urology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA. .,Department of Urology, The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA. .,Department of Nutrition, Case Western Reserve University, Cleveland, OH, 44106, USA. .,Divison of General Medical Sciences, Case Comprehensive Cancer Center, Cleveland, OH, 44106, USA. .,Department of Urology, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, 44106, USA.
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El-Khazragy N, Khalifa MM, Salem AM, Swellam M, Hegazy M. Evaluation of Osteopontin and Pokémon genes expression in hepatitis C virus-associated hepatocellular carcinoma. J Cell Biochem 2019; 120:7439-7445. [PMID: 30417409 DOI: 10.1002/jcb.28018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/15/2018] [Indexed: 01/24/2023]
Abstract
Osteopontin and Pokémon genes may have an important role in the pathogenesis of different malignancies. Osteopontin is a glycoprotein of the extracellular matrix, and Pokémon is a regulator of transcription. Both have been hypothesized to be useful as therapeutic targets or diagnostic markers. We aim to assess the role of both in hepatocellular carcinoma and liver fibrosis due to hepatitis C virus (HCV) infection. We conducted our study on 50 patients and classified them into three groups-Group I: Patients with HCV-related hepatocellular carcinoma (HCC) (n = 30); Group II: Patients with hepatitis C cirrhosis (n = 10); and Group III: Patients with hepatitis C fibrosis (n = 10). We found high levels of Osteopontin and Pokémon gene expression in group I. Osteopontin levels were higher also in patients with liver fibrosis was correlated to high levels of parameters such as alpha fetoprotein and caspase. We conclude that HCC is associated with overexpression of both Osteopontin and Pokémon and that Osteopontin plays a significant role in liver fibrosis due to hepatitis C infection.
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Affiliation(s)
- Nashwa El-Khazragy
- Department of Clinical Pathology/Hematology, Faculty of Medicine, Ain Shams University, Cairo, Egypt.,Department of Medical Research, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mona M Khalifa
- Biochemistry Department, Faculty of Science and Arts, Jazan University, Jazan, Saudi Arabia
| | - Ahmed M Salem
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Menha Swellam
- High Throughput Molecular and Genetic laboratory, Center for Excellence for Advanced Sciences, Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre
| | - Marwa Hegazy
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
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