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Dong Z, Su R, Fu Y, Wang Y, Chang L. Recent Progress in DNA Biosensors for Detecting Biomarkers in Living Cells. ACS Biomater Sci Eng 2024; 10:5595-5608. [PMID: 39143919 DOI: 10.1021/acsbiomaterials.4c01339] [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] [Indexed: 08/16/2024]
Abstract
Analysis of biomarkers in living cells is crucial for deciphering the dynamics of cells as well as for precise diagnosis of diseases. DNA biosensors employ DNA sequences as probes to offer insights into living cells, and drive progress in disease diagnosis and drug development. In this review, we present recent advances in DNA biosensors for detecting biomarkers in living cells. The basic structural components of DNA biosensors and the signal output method are presented. The strategies of DNA biosensors crossing the cell membrane are also described, including coincubation, nanocarriers, and nanoelectroporation techniques. Based on biomarker categorization, we detail recent applications of DNA biosensors for detecting small molecules, RNAs, proteins, and integrated targets in living cells. Furthermore, the future development directions of DNA biosensors are summarized to encourage further research in this growing field.
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Affiliation(s)
- Zaizai Dong
- School of Engineering Medicine, Beihang University, Beijing 100191, China
| | - Rongtai Su
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yao Fu
- School of Engineering Medicine, Beihang University, Beijing 100191, China
| | - Yupei Wang
- Gansu Provincial Maternity and Child-Care Hospital (Gansu Provincial Central Hospital), Lanzhou 730050, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
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Zhu X, Shi Z, Mao Y, Lächelt U, Huang R. Cell Membrane Perforation: Patterns, Mechanisms and Functions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310605. [PMID: 38344881 DOI: 10.1002/smll.202310605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/21/2023] [Indexed: 02/21/2024]
Abstract
Cell membrane is crucial for the cellular activities, and any disruption to it may affect the cells. It is demonstrated that cell membrane perforation is associated with some biological processes like programmed cell death (PCD) and infection of pathogens. Specific developments make it a promising technique to perforate the cell membrane controllably and precisely. The pores on the cell membrane provide direct pathways for the entry and exit of substances, and can also cause cell death, which means reasonable utilization of cell membrane perforation is able to assist intracellular delivery, eliminate diseased or cancerous cells, and bring about other benefits. This review classifies the patterns of cell membrane perforation based on the mechanisms into 1) physical patterns, 2) biological patterns, and 3) chemical patterns, introduces the characterization methods and then summarizes the functions according to the characteristics of reversible and irreversible pores, with the aim of providing a comprehensive summary of the knowledge related to cell membrane perforation and enlightening broad applications in biomedical science.
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Affiliation(s)
- Xinran Zhu
- Key Laboratory of Smart Drug Delivery (Ministry of Education), Huashan Hospital, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhifeng Shi
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 201203, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 201203, China
| | - Ulrich Lächelt
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, 1090, Austria
| | - Rongqin Huang
- Key Laboratory of Smart Drug Delivery (Ministry of Education), Huashan Hospital, School of Pharmacy, Fudan University, Shanghai, 201203, China
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3
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Dong Z, Wang Y, Xu G, Liu B, Wang Y, Reboud J, Jajesniak P, Yan S, Ma P, Liu F, Zhou Y, Jin Z, Yang K, Huang Z, Zhuo M, Jia B, Fang J, Zhang P, Wu N, Yang M, Cooper JM, Chang L. Genetic and phenotypic profiling of single living circulating tumor cells from patients with microfluidics. Proc Natl Acad Sci U S A 2024; 121:e2315168121. [PMID: 38683997 PMCID: PMC11087790 DOI: 10.1073/pnas.2315168121] [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: 09/11/2023] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
Accurate prediction of the efficacy of immunotherapy for cancer patients through the characterization of both genetic and phenotypic heterogeneity in individual patient cells holds great promise in informing targeted treatments, and ultimately in improving care pathways and clinical outcomes. Here, we describe the nanoplatform for interrogating living cell host-gene and (micro-)environment (NICHE) relationships, that integrates micro- and nanofluidics to enable highly efficient capture of circulating tumor cells (CTCs) from blood samples. The platform uses a unique nanopore-enhanced electrodelivery system that efficiently and rapidly integrates stable multichannel fluorescence probes into living CTCs for in situ quantification of target gene expression, while on-chip coculturing of CTCs with immune cells allows for the real-time correlative quantification of their phenotypic heterogeneities in response to immune checkpoint inhibitors (ICI). The NICHE microfluidic device provides a unique ability to perform both gene expression and phenotypic analysis on the same single cells in situ, allowing us to generate a predictive index for screening patients who could benefit from ICI. This index, which simultaneously integrates the heterogeneity of single cellular responses for both gene expression and phenotype, was validated by clinically tracing 80 non-small cell lung cancer patients, demonstrating significantly higher AUC (area under the curve) (0.906) than current clinical reference for immunotherapy prediction.
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Affiliation(s)
- Zaizai Dong
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing100191, China
- School of Engineering Medicine, Beihang University, Beijing100191, China
| | - Yusen Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing100191, China
| | - Gaolian Xu
- Shanghai Sci-Tech InnoCenter for Infection and Immunity, Shanghai200438, China
| | - Bing Liu
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing100142, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing100191, China
- School of Engineering Medicine, Beihang University, Beijing100191, China
| | - Julien Reboud
- Division of Biomedical Engineering, University of Glasgow, G12 8LTGlasgow, United Kingdom
| | - Pawel Jajesniak
- Division of Biomedical Engineering, University of Glasgow, G12 8LTGlasgow, United Kingdom
| | - Shi Yan
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing100142, China
| | - Pingchuan Ma
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing100191, China
| | - Feng Liu
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing100191, China
| | - Yuhao Zhou
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing100191, China
| | - Zhiyuan Jin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing100191, China
| | - Kuan Yang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing100191, China
| | - Zhaocun Huang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing100191, China
| | - Minglei Zhuo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital and Institute, Beijing100142, China
| | - Bo Jia
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital and Institute, Beijing100142, China
| | - Jian Fang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Oncology II, Peking University Cancer Hospital and Institute, Beijing100142, China
| | - Panpan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Oncology II, Peking University Cancer Hospital and Institute, Beijing100142, China
| | - Nan Wu
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Thoracic Surgery II, Peking University Cancer Hospital and Institute, Beijing100142, China
| | - Mingzhu Yang
- Beijing Research Institute of Mechanical Equipment, Beijing100143, China
| | - Jonathan M. Cooper
- Division of Biomedical Engineering, University of Glasgow, G12 8LTGlasgow, United Kingdom
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing100191, China
- School of Biomedical Engineering, Research and Engineering Center of Biomedical Materials, Anhui Medical University, Hefei230032, China
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Jin Z, Dong Z, Zhao X, Hang X, Lu Y, Zhang Q, Chen H, Huang Z, Wang Y, Zhou G, Chang L. Sensitive, rapid detection of NCOA4-m6A towards precisely quantifying radiation dosage on a Cas13a-Microdroplet platform. Biosens Bioelectron 2023; 242:115753. [PMID: 37839351 DOI: 10.1016/j.bios.2023.115753] [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: 08/08/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
Precise quantification of low-dose ionizing radiation is of great significance in protecting people from damage caused by clinical radiotherapy or environmental radiation. Traditional techniques for detecting radiation, however, remain extreme challenges to achieve high sensitivity and speed in quantifying radiation dosage. In this work, we report a Cas13a-Microdroplet platform that enables sensitive detection of ultra-low doses of radiation (0.5 Gy vs. 1 Gy traditional) within 1 h. The micro-platform adopts an ideal, specific radiation-sensitive marker, m6A on NCOA4 gene (NCOA4-m6A) that was first reported in our recent work. Microfluidics of the platform generate uniform microdroplets that encapsulate a CRISPR/Cas13a detection system and NCOA4-m6A target from the whole RNA extraction, achieving 10-fold enhancement in sensitivity and significantly reduced limit of detection (LOD). Systematic mouse models and clinical patient samples demonstrated its superior sensitivity and LOD (0.5 Gy) than traditional qPCR, which show wide potentials in radiation tracking and damage protection.
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Affiliation(s)
- Zhiyuan Jin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Zaizai Dong
- School of Engineering Medicine, Beihang University, Beijing, 100191, China.
| | - Xi Zhao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xinxin Hang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Yiming Lu
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 100850, China; School of Life Science, University of Hebei, Baoding, 071002, China
| | - Qi Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 100850, China; School of Medicine, University of South China, Hengyang, 421001, China
| | - Hongxia Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Zhaocun Huang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Yusen Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 100850, China; School of Life Science, University of Hebei, Baoding, 071002, China; School of Medicine, University of South China, Hengyang, 421001, China; Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China; School of Biomedical Engineering, Research and Engineering Center of Biomedical Materials, Anhui Medical University, Hefei, 230032, China.
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Zhao D, Qin J, An J, Zhang H, Li J, Wang H, Du R, He Y. Optimization of piggyBac Transposon System Electrotransfection in Sheep Fibroblasts. Mol Biotechnol 2023; 65:1585-1597. [PMID: 36705779 DOI: 10.1007/s12033-023-00659-5] [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: 10/09/2022] [Accepted: 01/08/2023] [Indexed: 01/28/2023]
Abstract
Electroporation is a non-viral mediated transfection technique, which has the advantages of being harmless, easy to operate, and less expensive. This transfection method can be used for almost all cell types and has gradually become the preferred transfection method for mammalian gene editing. However, further improvements are needed in electroporation efficiency. There is no universal standard electrotransfection step for different types of cells, and the inappropriate electroporation parameters will result in a low transfection efficiency and high cell mortality. Here, we systematically optimized the electrotransfection parameters of piggyBac transposon system into sheep fetal fibroblasts for the first time. We found that the cell transfection efficiency and cell viability could be improved by using traditional cell culture medium DMEM/F12 as an electroporation buffer, and simultaneously using the square-wave pulsing program of 200 V, 2 pulses, 20 ms length, and 20 μg DNA (3 μg/μL) in 4 mm cuvette, and the transfection efficiency and cell viability could eventually reach 78.0% and 40.9%, respectively. The purpose of this study is to provide a method reference and theoretical basis for the plasmid electrotransfection in mammal cells.
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Affiliation(s)
- Dipeng Zhao
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- School of Life Science and Engineering, Foshan University, Foshan, 528000, Guangdong, China
| | - Jian Qin
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- College of Life Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- Center of Experiment Teaching, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Jie An
- College of Life Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Hao Zhang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Junling Li
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Hejie Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Rong Du
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| | - Yongming He
- School of Life Science and Engineering, Foshan University, Foshan, 528000, Guangdong, China.
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Wan F, Dong Z, Liu B, Yan S, Wu N, Yang M, Chang L. Sensitive Interrogation of Enhancer Activity in Living Cells on a Nanoelectroporation-Probing Platform. ACS Sens 2022; 7:3671-3681. [PMID: 36410738 DOI: 10.1021/acssensors.2c01187] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Enhancers involved in the upregulation of multiple oncogenes play a fundamental role in tumorigenesis and immortalization. Exploring the activity of enhancers in living cells has emerged as a critical path to a deep understanding of cancer properties, further providing important clues to targeted therapy. However, identifying enhancer activity in living cells is challenging due to the double biological barriers of a cell cytoplasmic membrane and a nuclear membrane, limiting the sensitivity and responsiveness of conventional probing methods. In this work, we developed a nanoelectroporation-probing (NP) platform, which enables intranuclear probe delivery for sensitive interrogation of enhancer activity in living cells. The nanoelectroporation biochip achieved highly focused perforation of the cell cytoplasmic membrane and brought about additional driving force to expedite the delivery of probes into the nucleus. The probes targeting enhancer activity (named "PH probe") are programmed with a cyclic amplification strategy and enable an increase in the fluorescence signals over 100-fold within 1 h. The platform was leveraged to detect the activity of CCAT1 enhancers (CCAT1, colon cancer-associated transcript-1, a long noncoding RNA that functions in tumor invasion and metastasis) in cell samples from clinical lung cancer patients, as well as reveal the heterogeneity of enhancers among different patients. The observations may extend the linkages between enhancers and cancer cells while validating the robustness and reliability of the platform for the assay of enhancer activity. This platform will be a promising toolbox with wide applicable potential for the intranuclear study of living cells.
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Affiliation(s)
- Fengqi Wan
- Key Laboratory of Biomechanics and Mechanobiology (Ministry of Education), Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.,Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - Zaizai Dong
- Key Laboratory of Biomechanics and Mechanobiology (Ministry of Education), Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Bing Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Shi Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Mingzhu Yang
- Key Laboratory of Biomechanics and Mechanobiology (Ministry of Education), Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Lingqian Chang
- Key Laboratory of Biomechanics and Mechanobiology (Ministry of Education), Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.,School of Biomedical Engineering, Research and Engineering Center of Biomedical Materials, Anhui Medical University, Hefei 230032, China
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