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Cao C, Li A, Xu C, Wu B, Yao L, Liu Y. Engineering artificial non-coding RNAs for targeted protein degradation. Nat Chem Biol 2024:10.1038/s41589-024-01719-w. [PMID: 39215101 DOI: 10.1038/s41589-024-01719-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Targeted protein degradation has become a notable drug development strategy, but its application has been limited by the dependence on protein-based chimeras with restricted genetic manipulation capabilities. The use of long non-coding RNAs (lncRNAs) has emerged as a viable alternative, offering interactions with cellular proteins to modulate pathways and enhance degradation capabilities. Here we introduce a strategy employing artificial lncRNAs (alncRNAs) for precise targeted protein degradation. By integrating RNA aptamers and sequences from the lncRNA HOTAIR, our alncRNAs specifically target and facilitate the ubiquitination and degradation of oncogenic transcription factors and tumor-related proteins, such as c-MYC, NF-κB, ETS-1, KRAS and EGFR. These alncRNAs show potential in reducing malignant phenotypes in cells, both in vitro and in vivo, offering advantages in efficiency, adaptability and versatility. This research enhances knowledge of lncRNA-driven protein degradation and presents an effective method for targeted therapies.
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Affiliation(s)
- Congcong Cao
- Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Synthetic Biology Research Center, Health Science Center, Shenzhen University, Shenzhen, China
| | - Aolin Li
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Chaojie Xu
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Baorui Wu
- Department of Urology, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Beijing, China.
| | - Yuchen Liu
- Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Synthetic Biology Research Center, Health Science Center, Shenzhen University, Shenzhen, China.
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Li Z, Fu X, Huang J, Zeng P, Huang Y, Chen X, Liang C. Advances in Screening and Development of Therapeutic Aptamers Against Cancer Cells. Front Cell Dev Biol 2021; 9:662791. [PMID: 34095130 PMCID: PMC8170048 DOI: 10.3389/fcell.2021.662791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/21/2021] [Indexed: 01/10/2023] Open
Abstract
Cancer has become the leading cause of death in recent years. As great advances in medical treatment, emerging therapies of various cancers have been developed. Current treatments include surgery, radiotherapy, chemotherapy, immunotherapy, and targeted therapy. Aptamers are synthetic ssDNA or RNA. They can bind tightly to target molecules due to their unique tertiary structure. It is easy for aptamers to be screened, synthesized, programmed, and chemically modified. Aptamers are emerging targeted drugs that hold great potentials, called therapeutic aptamers. There are few types of therapeutic aptamers that have already been approved by the US Food and Drug Administration (FDA) for disease treatment. Now more and more therapeutic aptamers are in the stage of preclinical research or clinical trials. This review summarized the screening and development of therapeutic aptamers against different types of cancer cells.
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Affiliation(s)
- Zheng Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xuekun Fu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jie Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Peiyuan Zeng
- Department of Biochemistry, University of Victoria, Victoria, BC, Canada
| | - Yuhong Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xinxin Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Chao Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
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Xie H, Ma K, Zhang K, Zhou J, Li L, Yang W, Gong Y, Cai L, Gong K. Cell-cycle arrest and senescence in TP53-wild type renal carcinoma by enhancer RNA-P53-bound enhancer regions 2 (p53BER2) in a p53-dependent pathway. Cell Death Dis 2021; 12:1. [PMID: 33414393 PMCID: PMC7791070 DOI: 10.1038/s41419-020-03229-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/24/2022]
Abstract
TP53 is a classic tumor suppressor, but its role in kidney cancer remains unclear. In our study, we tried to explain the role of p53 in kidney cancer through the p53-related enhancer RNA pathway. Functional experiments were used to explore whether P53-bound enhancer regions 2 (p53BER2) has a role in the cell cycle and senescence response of TP53-wild type (WT) renal cancer cells in vitro or vivo. RNA-sequencing was used to identify the potential target of p53BER2. The results showed that the expression level of P53BER2 was downregulated in renal cancer tissues and cell lines, further dual-luciferase experiments and APR-256-reactivated experiments showed p53BER2 expresses in a p53-dependent way. Moreover, knockdown p53BER2 could reverse nutlin-3-induced cytotoxic effect in TP53-WT cell lines. Further exploration showed the downregulation of p53BER2 could reverse nutlin-3-induced G1-arrest and senescence in TP53-WT cell lines. What is more, the knockdown of p53BER2 showed resistance to nutlin-3 treatment in vivo. Additionally, we found BRCA2 could be regulated by p53BER2 in vitro and vivo; further experiment showed p53BER2 could induce cell-cycle arrest and DNA repair by mediating BRCA2. In summary, the p53-associated enhancer RNA-p53BER2 mediates the cell cycle and senescence of p53 in TP53-WT renal cancer cells.
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Affiliation(s)
- Haibiao Xie
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China.,Institute of Urology, Peking University, Beijing, People's Republic of China.,National Urological Cancer Center, Beijing, People's Republic of China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, People's Republic of China
| | - Kaifang Ma
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China.,Institute of Urology, Peking University, Beijing, People's Republic of China.,National Urological Cancer Center, Beijing, People's Republic of China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, People's Republic of China
| | - Kenan Zhang
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China.,Institute of Urology, Peking University, Beijing, People's Republic of China.,National Urological Cancer Center, Beijing, People's Republic of China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, People's Republic of China
| | - Jingcheng Zhou
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China.,Institute of Urology, Peking University, Beijing, People's Republic of China.,National Urological Cancer Center, Beijing, People's Republic of China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, People's Republic of China
| | - Lei Li
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China.,Institute of Urology, Peking University, Beijing, People's Republic of China.,National Urological Cancer Center, Beijing, People's Republic of China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, People's Republic of China
| | - Wuping Yang
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China.,Institute of Urology, Peking University, Beijing, People's Republic of China.,National Urological Cancer Center, Beijing, People's Republic of China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, People's Republic of China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China. .,Institute of Urology, Peking University, Beijing, People's Republic of China. .,National Urological Cancer Center, Beijing, People's Republic of China.
| | - Lin Cai
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China. .,Institute of Urology, Peking University, Beijing, People's Republic of China. .,National Urological Cancer Center, Beijing, People's Republic of China.
| | - Kan Gong
- Department of Urology, Peking University First Hospital, Beijing, People's Republic of China. .,Institute of Urology, Peking University, Beijing, People's Republic of China. .,National Urological Cancer Center, Beijing, People's Republic of China. .,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, People's Republic of China.
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Qi F, Tan B, Ma F, Zhu B, Zhang L, Liu X, Li H, Yang J, Cheng B. A Synthetic Light-switchable System based on CRISPR Cas13a Regulates the Expression of LncRNA MALAT1 and Affects the Malignant Phenotype of Bladder Cancer Cells. Int J Biol Sci 2019; 15:1630-1636. [PMID: 31360106 PMCID: PMC6643210 DOI: 10.7150/ijbs.33772] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/10/2019] [Indexed: 12/19/2022] Open
Abstract
DNA sequences drive their various functions through post-transcriptional processes, using mRNA or lncRNA (long non-coding RNA), and this accommodates the gene network by using various RNA types. However, the tools necessary to regulate RNA molecules are few. Likewise, RNA knockdown techniques that can be artificially controlled have not been extensively explored. Here, we investigated a novel light-inducible synthetic system based on CRISPR-Cas13a that can be used for RNA knockdown and binding in cancer cells. Based on the techniques of synthetic molecular biology, we constructed a light sensor, which efficiently induced Cas13a protein expression after blue light illumination. We also chose a lncRNA, Metastasis-associated Lung Adenocarcinoma Transcript 1 (MALAT1), as the functional target and detected it in bladder cancer 5637 and T24 cells in order to demonstrate the application of our synthetic system. Fluorescence reporter assays and real-time quantitative PCR (qRT-PCR) were used to detect the expression of the target gene. Phenotypic experiments were also used to test the effects of our synthetic system in bladder cancers. The results showed that our synthetic light-switchable system could inhibit the expression of MALAT1, and the fluorescence activity of enhanced green fluorescent protein. Our novel system provides a new technique to study RNA functions in gene networks and for precise tumor treatments.
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Affiliation(s)
- Fuming Qi
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Bo Tan
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Fujun Ma
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Bo Zhu
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Li Zhang
- Burn and Plastic surgery Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Xiaoyun Liu
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Honglei Li
- Medical Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Jinhui Yang
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Bo Cheng
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
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Gao Q, Liu Y, Xie H, Zhong Y, Liao X, Zhan H, Zhou Q, Ding M, Yang K, Li A, Liu Y, Mei H, Cai Z. Lentivirus-mediated shRNA targeting MUTYH inhibits malignant phenotypes of bladder cancer SW780 cells. Onco Targets Ther 2018; 11:6101-6109. [PMID: 30275714 PMCID: PMC6157993 DOI: 10.2147/ott.s174223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objectives MUTYH is a protein-coding gene that takes part in base excision repair. Many previous studies have reported that MUTYH is directly related to hereditary adenomatous polyposis and colorectal cancer and is also associated with other cancers. However, the relationship between MUTYH and bladder cancer (BC) is unknown. Materials and methods The expression of MUTYH and clinical characteristics of BC were collected from databases including The Cancer Genome Atlas and Cancer Cell Line Encyclopedia. RNA sequencing and quantitative real-time PCR were used to detect MUTYH expression in SW780 BC cells. The level of MUTYH was stably downregulated by lentivirus-mediated vector in SW780 cells. Cell proliferation was evaluated using Cell Counting Kit-8 assay and 5-ethynyl-20-deoxyuridine assay, migration was detected using scratch assay and Transwell assay, and apoptosis was determined using ELISA. Results MUTYH was upregulated in BC tissues and SW780 cells and its expression level was positively associated with the stage and grade of carcinomas. MUTYH was successfully downregulated in SW780 cells by transducing with a lentivirus-mediated shRNA targeting MUTYH. MUTYH knockdown inhibited the proliferation and migration and induced apoptosis in SW780 cells. Conclusion Our data suggest that MUTYH is a new participant in bladder urothelial carcinoma. MUTYH may play a role as a biomarker and therapeutic target in BC.
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Affiliation(s)
- Qunjun Gao
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Guangzhou Medical University, Guangzhou 511436, China, .,Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, , .,Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Yuhan Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, , .,Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Haibiao Xie
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, , .,Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Yucheng Zhong
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, , .,Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Xinhui Liao
- Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Hengji Zhan
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, , .,Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Qun Zhou
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, , .,Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Mengting Ding
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, , .,Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Kang Yang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, , .,Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Aolin Li
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, , .,Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, , .,Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Hongbing Mei
- Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
| | - Zhiming Cai
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Guangzhou Medical University, Guangzhou 511436, China, .,Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, , .,Department of Urology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China, ,
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