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Cai J, Zhu Q. New advances in signal amplification strategies for DNA methylation detection in vitro. Talanta 2024; 273:125895. [PMID: 38508130 DOI: 10.1016/j.talanta.2024.125895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
5-methylcytosine (5 mC) DNA methylation is a prominent epigenetic modification ubiquitous in the genome. It plays a critical role in the regulation of gene expression, maintenance of genome stability, and disease control. The potential of 5 mC DNA methylation for disease detection, prognostic information, and prediction of response to therapy is enormous. However, the quantification of DNA methylation from clinical samples remains a considerable challenge due to its low abundance (only 1% of total bases). To overcome this challenge, scientists have recently developed various signal amplification strategies to enhance the sensitivity of DNA methylation biosensors. These strategies include isothermal nucleic acid amplification and enzyme-assisted target cycling amplification, among others. This review summarizes the applications, advantages, and limitations of these signal amplification strategies over the past six years (2018-2023). Our goal is to provide new insights into the selection and establishment of DNA methylation analysis. We hope that this review will offer valuable insights to researchers in the field and facilitate further advancements in this area.
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Affiliation(s)
- Jiajing Cai
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China
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Liu XW, Zhao NN, Yuan HM, Li DL, Liu M, Zhang CY. Demethylation-activated light-up dual-color RNA aptamersensor for label-free detection of multiple demethylases in lung tissues. Biosens Bioelectron 2024; 247:115966. [PMID: 38147719 DOI: 10.1016/j.bios.2023.115966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023]
Abstract
Methylation is one of the most prevalent epigenetic modifications in natural organisms, and the processes of methylation and demethylation are closely associated with cell growth, differentiation, gene transcription and expression. Abnormal methylation may lead to various human diseases including cancers. Simultaneous analysis of multiple DNA demethylases remains a huge challenge due to the requirement of diverse substrate probes and scarcity of proper signal transduction strategies. Herein, we propose a sensitive and label-free method for simultaneous monitoring of multiple DNA demethylases on the basis of demethylation-activated light-up dual-color RNA aptamers. The presence of targets AlkB homologue-3 (ALKBH3) and fat mass and obesity-associated enzyme (FTO) erases the methyl group in DNA substrate probes, activating the ligation-mediate bidirectional transcription amplification reaction to produce enormous Spinach and Mango aptamers. The resulting RNA aptamers (i.e., Spinach and Mango aptamers) can bind with their cognate nonfluorescent fluorogens (DFHBI and TO1-biotin) to significantly improve the fluorescence signals. This aptamersensor shows high specificity and sensitivity with a limit of detection (LOD) of 8.50 × 10-14 M for ALKBH3 and 6.80 × 10-14 M for FTO, and it can apply to screen DNA demethylase inhibitors, evaluate DNA demethylase kinetic parameters, and simultaneously measure multiple endogenous DNA demethylases in a single cell. Importantly, this aptamersensor can accurately discriminate the expressions of ALKBH3 and FTO between healthy tissues and non-small cell lung cancer (NSCLC) patient tissues, offering a powerful platform for clinical diagnosis and drug discovery.
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Affiliation(s)
- Xiao-Wen Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Ning-Ning Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Hui-Min Yuan
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Dong-Ling Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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Cheng W, Shan J, Ding J, Liu Y, Sun S, Xu L, Yu C. Therapeutic effects of Huayu Jiedu formula on endometriosis via downregulating GATA 6 expression. Heliyon 2024; 10:e23149. [PMID: 38187253 PMCID: PMC10767382 DOI: 10.1016/j.heliyon.2023.e23149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Background Endometriosis (EMs) is a common chronic inflammatory disease which is characterized by multiple clinical symptoms and high recurrence rate due to the absence of effective therapies. Huayu Jiedu Formula (HYJDF), is a traditional Chinese medicine prescription with five major herbs. It has been used as traditional medicine to treat EMs for more than twenty years and exerted a good therapeutic effect. However, the underlying mechanism is unclear. Here we aim to observe the effects of HYJDF on EMs and investigate the therapeutic mechanism. Methods The extract components of HYJDF were identified and quantified by an UHPLC-QE-MS method. Network pharmacology was used to obtain the core targets of HYJDF for the treatment of EMs and the specific biologic processes involved. A total of 68 EMs cases were randomly divided into control (gestrinone) and observation (HYJDF) groups. The overall effectiveness, pain scores, cyst-size changes, serum CA125 levels, quality-of-life scores, safety, and adverse events were evaluated before and after treatment. For the mechanism research, DNA methylation-chip analysis was performed to determine the differential genes. EMs mice models and human ectopic stromal cells (ESCs) were treated with HYJDF and its pharmaceutical serum, respectively. The ectopic foci was measured via H&E staining while the expressions of the target genes were verified by real-time PCR and Western blot analysis. The inflammatory cytokine levels in the peritoneal fluid of mice were detected by ELISA. The proliferative potential of cells was analyzed by MTS whereas the apoptosis and cell cycle were determined through flow analysis. Results The total number of components detected in positive and negative ion modes was 839 and 597, respectively. Network pharmacology suggested that HYJDF treated EMs through DNA methylation. We found that HYJDF and gestrinone exerted good therapeutic effect with no obvious difference, but the HYJDF treatment group had fewer side effects. GATA 6, which was hypomethylated and abundant in endometriotic cells, potently induced inflammatory response. This finding indicated the important role of GATA 6 in EMs development. Moreover, HYJDF ameliorated inflammatory response (i.e., reduced the levels of IL-1β and PGE2 in peritoneal fluid), suppressed ESCs proliferation, and increased cell apoptosis by down-regulating GATA 6 expression. Conclusion We demonstrated that HYJDF has anti-inflammation activity and increased cell apoptosis through the reduction of GATA 6 expression in ectopic tissues, which showed good therapeutic effect without any obvious side effects. These findings suggest that HYJDF may be a new and efficient traditional Chinese medicine for the treatment of EMs.
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Affiliation(s)
- Wen Cheng
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Department of Gynecology of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China
| | - Jing Shan
- Department of Gynecology of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China
| | - Jie Ding
- Department of Gynecology of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China
| | - Yiqun Liu
- Department of Gynecology of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China
| | - Shuai Sun
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Department of Gynecology of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China
| | - Lianwei Xu
- Department of Gynecology of Traditional Chinese Medicine, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Chaoqin Yu
- Department of Gynecology of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China
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Ge QQ, Han Q, Han Y, Ma F, Li CZ, Zhang CY. A multi-cycle signal amplification-mediated single quantum dot nanosensor for PIWI-interacting RNA detection. Chem Commun (Camb) 2024; 60:408-411. [PMID: 38084051 DOI: 10.1039/d3cc05639b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
We construct a single quantum dot-based nanosensor for piRNA detection based on ligation-mediated multi-cycle signal amplification. This nanosensor is homogenous, selective, and sensitive with a detection limit of 0.104 fM. Moreover, it can detect the endogenous piRNA level in different cell lines, and discriminate cancer tissues from normal tissues.
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Affiliation(s)
- Qi-Qin Ge
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Qian Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Yun Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Chen-Zhong Li
- Biomedical Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
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Peng S, Zhang X, Wu Y. Potential applications of DNA methylation testing technology in female tumors and screening methods. Biochim Biophys Acta Rev Cancer 2023; 1878:188941. [PMID: 37329994 DOI: 10.1016/j.bbcan.2023.188941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/19/2023]
Abstract
DNA methylation is a common epigenetic modification, and the current commonly used methods for DNA methylation detection include methylation-specific PCR, methylation-sensitive restriction endonuclease-PCR, and methylation-specific sequencing. DNA methylation plays an important role in genomic and epigenomic studies, and combining DNA methylation with other epigenetic modifications, such as histone modifications, may lead to better DNA methylation. DNA methylation also plays an important role in the development of disease, and analyzing changes in individual DNA methylation patterns can provide individualized diagnostic and therapeutic solutions. Liquid biopsy techniques are also increasingly well established in clinical practice and may provide new methods for early cancer screening. It is important to find new screening methods that are easy to perform, minimally invasive, patient-friendly, and affordable. DNA methylation mechanisms are thought to have an important role in cancer and have potential applications in the diagnosis and treatment of female tumors. This review discussed early detection targets and screening methods for common female tumors such as breast, ovarian, and cervical cancers and discussed advances in the study of DNA methylation in these tumors. Although existing screening, diagnostic, and treatment modalities exist, the high morbidity and mortality rates of these tumors remain challenging.
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Affiliation(s)
- Shixuan Peng
- Graduate Collaborative Training Base of The First People's Hospital of Xiangtan City, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China
| | - Xinwen Zhang
- Graduate Collaborative Training Base of The First People's Hospital of Xiangtan City, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China
| | - Yongjun Wu
- Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China.
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