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Chakkarappan SR, Umadharshini KV, Dhamodharan S, Rose MM, Gopu G, Murugan AK, Inoue I, Munirajan AK. Super enhancer loci of EGFR regulate EGFR variant 8 through enhancer RNA and strongly associate with survival in HNSCCs. Mol Genet Genomics 2024; 299:3. [PMID: 38236481 DOI: 10.1007/s00438-023-02089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/21/2023] [Indexed: 01/19/2024]
Abstract
Epidermal growth factor receptor (EGFR) has been shown to be overexpressed in human cancers due to mutation, amplification, and epigenetic hyperactivity, which leads to deregulated transcriptional mechanism. Among the eight different EGFR isoforms, the mechanism of regulation of full-length variant 1 is well-known, no studies have examined the function & factors regulating the expression of variant 8. This study aimed to understand the function of EGFR super-enhancer loci and its associated transcription factors regulating the expression of EGFR variant 8. Our study shows that overexpression of variant 8 and its transcription was more prevalent than variant 1 in many cancers and positively correlated with the EGFR-AS1 expression in oral cancer and HNSCC. Notably, individuals overexpressing variant 8 showed shorter overall survival and had a greater connection with other clinical traits than patients with overexpression of variant 1. In this study, TCGA enhancer RNA profiling on the constituent enhancer (CE1 and CE2) region revealed that the multiple enhancer RNAs formed from CE2 by employing CE1 as a promoter. Our bioinformatic analysis further supports the enrichment of enhancer RNA specific chromatin marks H3K27ac, H3K4me1, POL2 and H2AZ on CE2. GeneHancer and 3D chromatin capture analysis showed clustered interactions between CE1, CE2 loci and this interaction may regulates expression of both EGFR-eRNA and variant 8. Moreover, increased expression of SNAI2 and its close relationship to EGFR-AS1 and variant 8 suggest that SNAI2 could regulates variant 8 overexpression by building a MegaTrans complex with both EGFR-eRNA and EGFR-AS1. Our findings show that EGFR variant 8 and its transcriptional regulation & chromatin modification by eRNAs may provide a rationale for targeting RNA splicing in combination with targeted EGFR therapies in cancer.
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Affiliation(s)
- Sundaram Reddy Chakkarappan
- Department of Health Research, Multi Disciplinary Research Unit (DHR-MRU), Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | | | - Shankar Dhamodharan
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | - Mathew Maria Rose
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | - Govindasamy Gopu
- Department of Surgical Oncology, Rajiv Gandhi Government General Hospital, Madras Medical College, Chennai, 600003, India
| | - Avaniyapuram Kannan Murugan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Arasambattu Kannan Munirajan
- Department of Health Research, Multi Disciplinary Research Unit (DHR-MRU), Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India.
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India.
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Zhang Z, Leng Z, Fang K, Sun M, Li Z, Kang L, Chen T, Xu M. Global research trend of esophageal squamous cell carcinoma from 2012 to 2022: a bibliometric analysis. Front Oncol 2022; 12:977935. [PMID: 36033465 PMCID: PMC9403081 DOI: 10.3389/fonc.2022.977935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 07/27/2022] [Indexed: 11/15/2022] Open
Abstract
Background Esophageal cancer is currently a worldwide health problem. Esophageal squamous cell carcinoma (ESCC) is the most common pathological type of esophageal cancer, and its treatment methods and therapeutic effects are relatively limited, so it also requires the unremitting efforts of basic and clinical researchers to overcome difficulties. Bibliometric analysis can help sort out global research trends and hotspots, but no bibliometric analysis of ESCC has been reported. Therefore, we performed this study to analyze the global trends and potential hotspots of ESCC to indicate future research directions. Methods The articles related to ESCC research were collected from the WoS Core Collection SCI-EXPANDED database from 2012 to 2022. The article information was analyzed by BiblioShiny and VOSviewer. Results were presented as bar and network visualization to describe the current trend of ESCC research. This was a retrospective study evaluating data that is publicly available online and at libraries and institutional review board approval, as such, was not demanded. Results The global publication trend illustrated a strong growth in the ESCC research field (annual growth rate of 11.4%) and the citation trend increased from an average of 2.98 citations per article per year in 2012 to an average of 3.84 citations per article per year in 2019. With the corresponding author’s country, China contributed the largest number (5,063 articles). The scholars from China and USA had the most collaboration (427 times). China had the largest number of institutions conducting ESCC research. Oncotarget, Oncology Letters, and Annals of Surgical Oncology published the most articles, while Cancer Research, International Journal of Cancer, and Journal of Clinical Oncology had the most local citations. Furthermore, the clinical research hotspots involved in the treatment of ESCC and the basic research hotspots involved in tumor malignant phenotype have received the most attention in recent years. Conclusion Our study demonstrated that the research of ESCC has developed rapidly in recent years, and the academic institutions in China have played a decisive role in this field. The global research purpose is to find effective therapies against ESCC, so some emerging hotspots related to ESCC treatment, such as endoscopic therapy, chemoradiotherapy, immunotherapy, tumor microenvironment, and the epithelial-mesenchymal transition will receive more attention and develop rapidly in the future.
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Affiliation(s)
- Zehua Zhang
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhuyun Leng
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Kang Fang
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Mingchuang Sun
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhaoxing Li
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Le Kang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Tao Chen
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Meidong Xu, ; Tao Chen,
| | - Meidong Xu
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Meidong Xu, ; Tao Chen,
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Jiao P, Zhang M, Wang Z, Liang G, Xie X, Zhang Y, Chen Z, Jiang Q, Loor JJ. Circ003429 Regulates Unsaturated Fatty Acid Synthesis in the Dairy Goat Mammary Gland by Interacting with miR-199a-3p, Targeting the YAP1 Gene. Int J Mol Sci 2022; 23:ijms23074068. [PMID: 35409428 PMCID: PMC8999533 DOI: 10.3390/ijms23074068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 02/01/2023] Open
Abstract
Fatty acid composition is a key factor affecting the flavor and quality of goat milk. CircRNAs are now recognized as important regulators of transcription, and they play an important role in the control of fatty acid synthesis. Thus, understanding the regulatory mechanisms controlling this process in ruminant mammary glands is of great significance. In the present study, mammary tissue from dairy goats during early lactation and the dry period (nonlactating) were collected and used for high-throughput sequencing. Compared to levels during the dry period, the expression level of circ003429 during early lactation was lower (12.68-fold downregulated). In isolated goat mammary epithelial cells, circ003429 inhibited the synthesis of triglycerides (TAG) and decreased the content of unsaturated fatty acids (C16:1, C18:1, and C18:2), indicating that this circRNA plays an important role in regulating lipid synthesis. A binding site for miR-199a-3p in the circ003429 sequence was detected, and a dual-luciferase reporter system revealed that circ003429 targets miR-199a-3p. Overexpression of circ003429 (pcDNA-circ003429) downregulated the abundance of miR-199a-3p. In contrast, overexpression of miR-199a-3p increased TAG content and decreased mRNA abundance of Yes-associated protein 1 (YAP1) (a target gene of miR-199a-3p), and TAG content was decreased and mRNA abundance was increased in response to overexpression of circ003429. These results indicate that circ003429 alleviates the inhibitory effect of miR-199a-3p on the mRNA abundance of YAP1 by binding miR-199a-3p, resulting in subsequent regulation of the synthesis of TAG and unsaturated fatty acids.
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Affiliation(s)
- Peixin Jiao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (P.J.); (M.Z.); (Z.W.); (G.L.); (X.X.); (Y.Z.)
| | - Meimei Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (P.J.); (M.Z.); (Z.W.); (G.L.); (X.X.); (Y.Z.)
| | - Ziwei Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (P.J.); (M.Z.); (Z.W.); (G.L.); (X.X.); (Y.Z.)
| | - Gege Liang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (P.J.); (M.Z.); (Z.W.); (G.L.); (X.X.); (Y.Z.)
| | - Xiaolai Xie
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (P.J.); (M.Z.); (Z.W.); (G.L.); (X.X.); (Y.Z.)
| | - Yonggen Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (P.J.); (M.Z.); (Z.W.); (G.L.); (X.X.); (Y.Z.)
| | - Zhi Chen
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Z.C.); (J.J.L.)
| | - Qianming Jiang
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA;
| | - Juan J. Loor
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA;
- Correspondence: (Z.C.); (J.J.L.)
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Lin Y, Chen Y, Shen R, Chen D, Lin Y. MicroRNA-148a-3p suppresses cell proliferation and migration of esophageal carcinoma by targeting CEP55. Cell Mol Biol Lett 2021; 26:54. [PMID: 34952571 PMCID: PMC8903601 DOI: 10.1186/s11658-021-00298-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
This study evaluated microRNA-148a-3p in esophageal carcinoma cells. The prediction of bioinformatics analysis revealed that microRNA-148a-3p may target CEP55. qRT-PCR and western blot showed that CEP55 level in esophageal carcinoma cells and tissue was dramatically higher than that of normal cells and tissue, while microRNA-148a-3p was the opposite. Forced expression of microRNA-148a-3p restrained cell malignant behaviors of esophageal carcinoma, and repression of microRNA-148a-3p resulted in the converse results in terms of cell function. Dual-luciferase assay confirmed that microRNA-148a-3p targeted CEP55. CEP55 attenuated the suppressive effect of microRNA-148a-3p on proliferation and migration of esophageal carcinoma cells, demonstrating that microRNA-148a-3p regulated function of esophageal carcinoma cells via decreasing CEP55 level. Microscopy observation indicated that cell morphology was also affected by the microRNA-148a-3p/CEP55 axis. Furthermore, western blot analysis revealed that the PI3K/AKT signaling pathway could be suppressed by activating the microRNA-148a-3p/CEP55 axis. Finally, in vivo experiments confirmed the effects of microRNA-148a-3p on tumorigenesis. Thus, microRNA-148a-3p could act as a repressor in esophageal carcinoma via binding to CEP55.
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Affiliation(s)
- Yong Lin
- Department of Cardiothoracic Surgery, Zhangzhou Affiliated Hospital of Fujian Medical University, No. 59 Shengli West Road, Zhangzhou, Fujian, 363000, People's Republic of China
| | - Yushan Chen
- Department of Radiology, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, Fujian, 363000, People's Republic of China
| | - Rongqiang Shen
- Department of Cardiothoracic Surgery, Zhangzhou Affiliated Hospital of Fujian Medical University, No. 59 Shengli West Road, Zhangzhou, Fujian, 363000, People's Republic of China
| | - Dingzhu Chen
- Department of Cardiothoracic Surgery, Zhangzhou Affiliated Hospital of Fujian Medical University, No. 59 Shengli West Road, Zhangzhou, Fujian, 363000, People's Republic of China
| | - Yimin Lin
- Department of Cardiothoracic Surgery, Zhangzhou Affiliated Hospital of Fujian Medical University, No. 59 Shengli West Road, Zhangzhou, Fujian, 363000, People's Republic of China.
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