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Nahalka J. 1-L Transcription of SARS-CoV-2 Spike Protein S1 Subunit. Int J Mol Sci 2024; 25:4440. [PMID: 38674024 PMCID: PMC11049929 DOI: 10.3390/ijms25084440] [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: 02/29/2024] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
The COVID-19 pandemic prompted rapid research on SARS-CoV-2 pathogenicity. Consequently, new data can be used to advance the molecular understanding of SARS-CoV-2 infection. The present bioinformatics study discusses the "spikeopathy" at the molecular level and focuses on the possible post-transcriptional regulation of the SARS-CoV-2 spike protein S1 subunit in the host cell/tissue. A theoretical protein-RNA recognition code was used to check the compatibility of the SARS-CoV-2 spike protein S1 subunit with mRNAs in the human transcriptome (1-L transcription). The principle for this method is elucidated on the defined RNA binding protein GEMIN5 (gem nuclear organelle-associated protein 5) and RNU2-1 (U2 spliceosomal RNA). Using the method described here, it was shown that 45% of the genes/proteins identified by 1-L transcription of the SARS-CoV-2 spike protein S1 subunit are directly linked to COVID-19, 39% are indirectly linked to COVID-19, and 16% cannot currently be associated with COVID-19. The identified genes/proteins are associated with stroke, diabetes, and cardiac injury.
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Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska Cesta 9, SK-84538 Bratislava, Slovakia;
- Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovakia
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2
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Zhou Y, Petrovic J, Zhao J, Zhang W, Bigdeli A, Zhang Z, Berger SL, Pear WS, Faryabi RB. EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. Mol Cell 2022; 82:1003-1020.e15. [PMID: 35182476 PMCID: PMC8897266 DOI: 10.1016/j.molcel.2022.01.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/05/2021] [Accepted: 01/19/2022] [Indexed: 12/12/2022]
Abstract
Chromatin misfolding has been implicated in cancer pathogenesis; yet, its role in therapy resistance remains unclear. Here, we systematically integrated sequencing and imaging data to examine the spatial and linear chromatin structures in targeted therapy-sensitive and -resistant human T cell acute lymphoblastic leukemia (T-ALL). We found widespread alterations in successive layers of chromatin organization including spatial compartments, contact domain boundaries, and enhancer positioning upon the emergence of targeted therapy resistance. The reorganization of genome folding structures closely coincides with the restructuring of chromatin activity and redistribution of architectural proteins. Mechanistically, the derepression and repositioning of the B-lineage-determining transcription factor EBF1 from the heterochromatic nuclear envelope to the euchromatic interior instructs widespread genome refolding and promotes therapy resistance in leukemic T cells. Together, our findings suggest that lineage-determining transcription factors can instruct changes in genome topology as a driving force for epigenetic adaptations in targeted therapy resistance.
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Affiliation(s)
- Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jelena Petrovic
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jingru Zhao
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wu Zhang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ashkan Bigdeli
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zhen Zhang
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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Hu Z, Yang C, Guo S, Li Y, Li Y. LINC01615 activates ZEB2 through competitively binding with miR-3653-3p to promote the carcinogenesis of colon cancer cells. Cell Cycle 2022; 21:228-246. [PMID: 34965191 PMCID: PMC8855844 DOI: 10.1080/15384101.2021.2015670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
As a newly discovered cancer-related molecule, we explored the unreported mechanism of LINC01615 intervention in colon cancer.LINC01615 expression in clinical samples and cells were detected. Effects of LINC01615 silencing/overexpression on the malignant development of colon cancer cells were analyzed through cell function experiments. Changes at the level of molecular biology were detected by quantitative real-time polymerase chain reaction and Western blot. Bioinformatics analysis and dual luciferase reporter assay were involved in the display and verification of targeted binding sequences. The rescue tests and correlation analysis examined the relationship among LINC01615, miR-3653-3p and zinc finger E-box binding homeobox 2 (ZEB2) in colon cancer cells. The xenograft experiment and immunohistochemistry were performed to verify these results.TCGA suggested that LINC01615 was high-expressed in colon cancer, as verified in clinical and cell samples, and patients with LINC01615 overexpression suffered from a poor prognosis. Silent LINC01615 blocked the malignant development of colon cancer cells through regulating related genes expressions, while overexpressed LINC01615 had the opposite effect. LINC01615, which was targeted by miR-3653-3p, partially offset the inhibitory effect of miR-3653-3p on colon cancer cells. The downstream target gene ZEB2 of miR-3653-3p was high-expressed in colon cancer. MiR-3653-3p was negatively correlated with LINC01615 or ZEB2, while LINC01615 was positively correlated with ZEB2. Therefore, LINC01615 induced ZEB2 up-regulation, while miR-3653-3p reduced ZEB2 level. The results of in vivo studies were consistent with cell experiments.LINC01615 competitively binds with miR-3653-3p to regulate ZEB2 and promote canceration of colon cancer cells.
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Affiliation(s)
- Zhen Hu
- Department of Colorectal & Anal Surgery Shanxi Provincial People’s Hospital, Taiyuan, China
| | - Chong Yang
- Department of Colorectal & Anal Surgery Shanxi Provincial People’s Hospital, Taiyuan, China
| | - Shangqi Guo
- Department of Colorectal & Anal Surgery Shanxi Provincial People’s Hospital, Taiyuan, China
| | - Yiqun Li
- Department of Colorectal & Anal Surgery Shanxi Provincial People’s Hospital, Taiyuan, China
| | - Yaoping Li
- Department of Colorectal & Anal Surgery Shanxi Provincial People’s Hospital, Taiyuan, China,CONTACT Yaoping Li Department of Colorectal & Anal Surgery, Shanxi Provincial People’s Hospital, No 29 Shuangtasi Street, Taiyuan, Shanxi030012, China
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Chen W, Jiang W, Dong J, Wang J, Wang B. MiR-200b-3p induces the formation of insulin-producing cells from umbilical cord mesenchymal stem cells by targeting ZEB2. Crit Rev Eukaryot Gene Expr 2022; 32:33-46. [DOI: 10.1615/critreveukaryotgeneexpr.2022041822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Lv J, Zhu S, Chen H, Xu Y, Su Q, Yu G, Ma W. Paeonol inhibits human lung cancer cell viability and metastasis in vitro via miR-126-5p/ZEB2 axis. Drug Dev Res 2021; 83:432-446. [PMID: 34636432 DOI: 10.1002/ddr.21873] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/02/2021] [Accepted: 08/16/2021] [Indexed: 11/06/2022]
Abstract
Paeonol exerted an effect in lung cancer, but the underlying mechanism remained vague. In this research, we assessed the effects of Paeonol and microRNA (miR)-126-5p on the viability, migration, invasion, and epithelial-mesenchymal transition (EMT) of lung cancer cells. Lung cancer cells and BEAS-2B cells were treated with Paeonol, and viability was detected by 3-(4,5)-dimethylthiahiazo (-z-y1)-3,5-di- phenytetrazoliumromide (MTT) assay. The migration and invasion of lung cancer cells after treatment with Paeonol at 40 μg/mL or 80 μg/mL were detected by wound healing assay and Transwell assay, respectively. The effects of Paeonol on transforming growth factor-β1 (TGF-β1)-induced EMT and relative expressions of EMT-related proteins were determined using Western blot. The target gene of miR-126-5p and the binding sites between them were predicted by TargetScan, and confirmed using dual-luciferase reporter assay. Relative expressions of miR-126-5p, its target gene and EMT-related proteins were determined by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot. Rescue assay was performed to analyze the relation between Paeonol and miR-126-5p. Paeonol down-regulated cell viability and inhibited migration, invasion and TGF-β1-induced EMT while up-regulating miR-126-5p expression in lung cancer cells as the dose increased. However, miR-126-5p inhibitor could reverse the effect of Paeonol. ZEB2 was the target gene of miR-126-5p, and silencing ZEB2 expression reversed the effects of miR-126-5p downregulation. Paeonol also regulated the expression of ZEB2 in lung cancer cells, and this regulation depends on the regulation of miR-126-5p. Paeonol inhibits human lung cancer cell viability and metastasis via the miR-126-5p/ZEB2 axis, and could be adopted as a potential agent for lung cancer treatment.
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Affiliation(s)
- Jing Lv
- Department of Traditional Chinese Medicine, Zhejiang Chinese Medicine and Western Medicine Integrated Hospital, Hangzhou, China
| | - Shibing Zhu
- Department of Traditional Chinese Medicine, Zhejiang Chinese Medicine and Western Medicine Integrated Hospital, Hangzhou, China
| | - Huiping Chen
- Department of Endocrinology, Zhe Jiang Chinese Medicine and Western Medicine Integrated Hospital, Hangzhou, China
| | - Ying Xu
- Department of Special Medical Treatment, Zhejiang Chinese Medicine and Western Medicine Integrated Hospital, Hangzhou, China
| | - Qingyu Su
- ICU, Zhejiang Chinese Medicine and Western Medicine Integrated Hospital, Hangzhou, China
| | - Guofen Yu
- Special Needs Ward, Zhejiang Chinese Medicine and Western Medicine Integrated Hospital, Hangzhou, China
| | - Wei Ma
- Department of Emergency, Zhejiang Chinese Medicine and Western Medicine Integrated Hospital, Hangzhou, China
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Shayimu P, Yusufu A, Rehemutula A, Redati D, Jiapaer R, Tuerdi R. MTBP promoted the proliferation, migration and invasion of colon cancer cells by activating the expression of ZEB2. Anim Cells Syst (Seoul) 2021; 25:152-160. [PMID: 34262658 PMCID: PMC8253212 DOI: 10.1080/19768354.2021.1938218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Colon cancer is a malignant tumor that seriously affects human health. Recently, studies revealed that the expression of MTBP enhanced the proliferation and metastasis of many types of cancer cells. And the data also showed that MTBP has the potential to regulate the expression of ZEB2. However, it is unclear whether MTBP can affect the proliferation, migration and invasion of colon cancer cells by modulating the expression of ZEB2. In this study, we established the MTBP overexpression and knockdown colon cancer cells with the transfection. Next, CCK-8 and transwell assays were carried out to determine the changes of the proliferation and invasion of colon cancer cells, respectively. After that, we overexpressed the ZEB2 in these MTBP knockdown colon cancer cells. Finally, the invasion and migration of these cells were detected with the same methods. We revealed that overexpression of MTBP enhanced the proliferation and invasion of colon cancer cells. Moreover, suppression of MTBP repressed the proliferation, migration and invasion of colon cancer cells. Furthermore, MTBP promoted the expression of ZEB2. The overexpression of ZEB2 abolished the MTBP knockdown induced inhibition of the migration and invasion of colon cancer cells. These results implied that MTBP enhanced the proliferation, migration and invasion of colon cancer cells by activating the expression of ZEB2.
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Affiliation(s)
- Paerhati Shayimu
- Department of Gastrointestinal Surgery, Cancer Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Aikeremu Yusufu
- Department of Gastrointestinal Surgery, Cancer Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Aizimaiti Rehemutula
- Department of Gastrointestinal Surgery, Cancer Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Darebai Redati
- B-Ultrasound Room, Cancer Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Rexida Jiapaer
- Department of Gastrointestinal Surgery, Cancer Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Rousidan Tuerdi
- Central Laboratory, Xinjiang Medical University, Urumqi, People's Republic of China
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Intrinsic Balance between ZEB Family Members Is Important for Melanocyte Homeostasis and Melanoma Progression. Cancers (Basel) 2020; 12:cancers12082248. [PMID: 32796736 PMCID: PMC7465899 DOI: 10.3390/cancers12082248] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 02/07/2023] Open
Abstract
It has become clear that cellular plasticity is a main driver of cancer therapy resistance. Consequently, there is a need to mechanistically identify the factors driving this process. The transcription factors of the zinc-finger E-box-binding homeobox family, consisting of ZEB1 and ZEB2, are notorious for their roles in epithelial-to-mesenchymal transition (EMT). However, in melanoma, an intrinsic balance between ZEB1 and ZEB2 seems to determine the cellular state by modulating the expression of the master regulator of melanocyte homeostasis, microphthalmia-associated transcription factor (MITF). ZEB2 drives MITF expression and is associated with a differentiated/proliferative melanoma cell state. On the other hand, ZEB1 is correlated with low MITF expression and a more invasive, stem cell-like and therapy-resistant cell state. This intrinsic balance between ZEB1 and ZEB2 could prove to be a promising therapeutic target for melanoma patients. In this review, we will summarise what is known on the functional mechanisms of these transcription factors. Moreover, we will look specifically at their roles during melanocyte-lineage development and homeostasis. Finally, we will overview the current literature on ZEB1 and ZEB2 in the melanoma context and link this to the 'phenotype-switching' model of melanoma cellular plasticity.
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Epithelial to Mesenchymal Transition: A Mechanism that Fuels Cancer Radio/Chemoresistance. Cells 2020; 9:cells9020428. [PMID: 32059478 PMCID: PMC7072371 DOI: 10.3390/cells9020428] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/27/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022] Open
Abstract
Epithelial to mesenchymal transition (EMT) contributes to tumor progression, cancer cell invasion, and therapy resistance. EMT is regulated by transcription factors such as the protein products of the SNAI gene family, which inhibits the expression of epithelial genes. Several signaling pathways, such as TGF-beta1, IL-6, Akt, and Erk1/2, trigger EMT responses. Besides regulatory transcription factors, RNA molecules without protein translation, micro RNAs, and long non-coding RNAs also assist in the initialization of the EMT gene cluster. A challenging novel aspect of EMT research is the investigation of the interplay between tumor microenvironments and EMT. Several microenvironmental factors, including fibroblasts and myofibroblasts, as well as inflammatory, immune, and endothelial cells, induce EMT in tumor cells. EMT tumor cells change their adverse microenvironment into a tumor friendly neighborhood, loaded with stromal regulatory T cells, exhausted CD8+ T cells, and M2 (protumor) macrophages. Several EMT inhibitory mechanisms are instrumental in reversing EMT or targeting EMT cells. Currently, these mechanisms are also significant for clinical use.
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