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Zhu H, Shen W, Luo C, Liu F. An integrated microfluidic device for multiplexed imaging of spatial gene expression patterns of Drosophila embryos. LAB ON A CHIP 2022; 22:4081-4092. [PMID: 36165088 DOI: 10.1039/d2lc00514j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To reveal the underlying mechanism of the biological function of multicellular systems, it is important to obtain comprehensive spatial gene expression profiles. Among the emerging single-cell spatial-omics techniques, immunofluorescence (IF)-based iterative multiplexed imaging is a promising approach. However, the conventional method is usually costly, time-consuming, labor-intensive, and has low throughput. Moreover, it has yet to be demonstrated in intact multicellular organisms. Here, we developed an integrated microfluidic system to overcome these challenges for quantitatively measuring multiple protein profiles sequentially in situ in the same Drosophila embryo. We designed an array of hydrodynamic trapping sites to automatically capture over ten Drosophila embryos with orientation selectivity at more than 90% trapping rates. We also optimized the geometry of confinement and the on-chip IF protocol to achieve the same high signal-to-noise ratio as the off-chip traditional IF experiments. Moreover, we developed an efficient de-staining protocol by combining on-chip antibody stripping and fluorophore bleaching. Using the same secondary antibody to sequentially stain different genes, we confirmed that the de-stained genes have no detectable interference with the subsequently stained genes, and the gene expression profiles are preserved after multiple cycles of staining and de-staining processes. This preliminary test shows that our newly developed integrated microfluidic system can be a powerful tool for multiplexed imaging of Drosophila embryos. Our work opens a new avenue to design microfluidic chips for multicellular organisms and single-cell spatial-omics techniques.
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Affiliation(s)
- Hongcun Zhu
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China.
| | - Wenting Shen
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China.
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
| | - Feng Liu
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.
- Key Laboratory of Hebei Province for Molecular Biophysics, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300130, China
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Wang B, Park B. Microfluidic Sampling and Biosensing Systems for Foodborne Escherichia coli and Salmonella. Foodborne Pathog Dis 2022; 19:359-375. [PMID: 35713922 DOI: 10.1089/fpd.2021.0087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Developments of portable biosensors for field-deployable detections have been increasingly important to control foodborne pathogens in regulatory environment and in early stage of outbreaks. Conventional cultivation and gene amplification methods require sophisticated instruments and highly skilled professionals; while portable biosensing devices provide more freedom for rapid detections not only in research laboratories but also in the field; however, their sensitivity and specificity are limited. Microfluidic methods have the advantage of miniaturizing instrumental size while integrating multiple functions and high-throughput capability into one streamlined system at low cost. Minimal sample consumption is another advantage to detect samples in different sizes and concentrations, which is important for the close monitoring of pathogens at consumer end. They improve measurement or manipulation of bacteria by increasing the ratio of functional interface of the device to the targeted biospecies and in turn reducing background interference. This article introduces the major active and passive microfluidic devices that have been used for bacteria sampling and biosensing. The emphasis is on particle-based sorting/enrichment methods with or without external physical fields applied to the microfluidic devices and on various biosensing applications reported for bacteria sampling. Three major fabrication methods for microfluidics are briefly discussed with their advantages and limitations. The applications of these active and passive microfluidic sampling methods in the past 5 years have been summarized, with the focus on Escherichia coli and Salmonella. The current challenges to microfluidic bacteria sampling are caused by the small size and nonspherical shape of various bacterial cells, which can induce unpredictable deviations in sampling and biosensing processes. Future studies are needed to develop rapid prototyping methods for device manufacturing, which can facilitate rapid response to various foodborne pathogen outbreaks.
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Affiliation(s)
- Bin Wang
- U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, USA
| | - Bosoon Park
- U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, USA
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Si H, Du D, Li W, Li Q, Li J, Zhao D, Li L, Tang B. Sputum-Based Tumor Fluid Biopsy: Isolation and High-Throughput Single-Cell Analysis of Exfoliated Tumor Cells for Lung Cancer Diagnosis. Anal Chem 2021; 93:10477-10486. [PMID: 34292723 DOI: 10.1021/acs.analchem.1c00833] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Timely and effective diagnosis is of great significance for improving the survival rate of lung cancer patients. Although histopathology is the main diagnostic tool among the existing methods for lung cancer diagnosis, it is not suitable for high-risk groups, early lung cancer patients, patients with advanced-stage disease, and other situations wherein tumor tissues cannot be obtained. In view of this, we proposed an innovative lung cancer diagnosis method employing for the first time a microfluidic technology for high-efficiency isolation and high-throughput single-cell analysis of exfoliated tumor cells (ETCs) in sputum. This method fully combines the advantages of traditional sputum cytology and microfluidic technology and realizes the diagnosis of lung cancer by using a small amount of repeatable ETCs instead of the tumor tissue. This method is expected to provide a practical strategy for the non-invasive detection of lung cancer patients and lung cancer screening for high-risk groups.
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Affiliation(s)
- Haibin Si
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Dexin Du
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Wenbo Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Qingling Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Jingxin Li
- Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, P. R. China
| | - Dongbo Zhao
- Department of Thoracic Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, P. R. China
| | - Lu Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
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Isolation of proliferating cells from whole blood using Human Transferrin Receptor in a two-stage separation system. Talanta 2019; 204:731-738. [DOI: 10.1016/j.talanta.2019.05.096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022]
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Shi X, Shao C, Luo C, Chu Y, Wang J, Meng Q, Yu J, Gao Z, Kang Y. Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics. mSystems 2019; 4:e00198-19. [PMID: 31117025 PMCID: PMC6589435 DOI: 10.1128/msystems.00198-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/04/2019] [Indexed: 01/13/2023] Open
Abstract
Dysbiosis of airway microbiomes has been found in various respiratory diseases, but its molecular details in terms of taxonomic profile, metabolic characteristics, defensive function, and inhabit adaption are far from clear. Shotgun metagenome sequencing provides detailed information for microbes, whereas its application is rather limited in airways due to host DNA contaminants that overwhelm a minute amount of microbial content. Here, we describe a microfluidics-based enrichment device and an emulsion-based whole-genome amplification procedure (MEEA) for the preparation of DNA from sputa for shotgun sequencing in a metagenomics study. The two protocols coupled in MEEA are first separately assayed with mock samples and are both promising in efficiency and bias. The efficiency and consistency of MEEA are further evaluated in six clinical sputum samples against direct sequencing without enrichment, and MEEA enables 2 to 14 times enrichment for microbial reads, which take 14.68% to 33.52% of total reads. The dominant pathogens detected in MEEA are in excellent agreement with those from clinical etiological tests. Meanwhile, MEEA presents much more microbiome complexity and genome information at a strain level than direct sequencing, exhibiting high sensitivity for identifying prophages and DNA viruses. MEEA provides better microbiome profiling than direct sequencing without a preference for specific microorganisms. The more detailed functional and taxonomic characterization of their species constituents, including both bacterium and virus, facilitates metagenomics studies on the pathogenesis of respiratory microbiomes.IMPORTANCE The airway microbial community, which takes important pathogenic roles for respiratory diseases, is far from clear in terms of taxonomy and gene functions. One of the critical reasons is the heavy contamination of host cell/DNA in airway samples, which hinders the subsequent sequencing of the whole genomic contents of the microbial community-the metagenome. Here, we describe a protocol for airway sample preparation which couples a microbe enrichment microfluidic device and a DNA amplification method performed in numerous droplets. When evaluated with mock and clinical sputum samples, the microfluidics-based enrichment device and emulsion-based whole-genome amplification (MEEA) procedure efficiently removes host cells, amplifies the microbial genome, and shows no obvious bias among microbes. The efficiency of MEEA makes it a promising method in research of respiratory microbial communities and their roles in diseases.
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Affiliation(s)
- Xing Shi
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, People's Republic of China
| | - Changjun Shao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, People's Republic of China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Yanan Chu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Qingren Meng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, People's Republic of China
| | - Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
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