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Wang Y, Wang Y, Wang X, Sun W, Yang F, Yao X, Pan T, Li B, Chu J. Label-free active single-cell encapsulation enabled by microvalve-based on-demand droplet generation and real-time image processing. Talanta 2024; 276:126299. [PMID: 38788384 DOI: 10.1016/j.talanta.2024.126299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/01/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]
Abstract
Droplet microfluidics-based single-cell encapsulation is a critical technology that enables large-scale parallel single-cell analysis by capturing and processing thousands of individual cells. As the efficiency of passive single-cell encapsulation is limited by Poisson distribution, active single-cell encapsulation has been developed to theoretically ensure that each droplet contains one cell. However, existing active single-cell encapsulation technologies still face issues related to fluorescence labeling and low throughput. Here, we present an active single-cell encapsulation technique by using microvalve-based drop-on-demand technology and real-time image processing to encapsulate single cells with high throughput in a label-free manner. Our experiments demonstrated that the single-cell encapsulation system can encapsulate individual polystyrene beads with 96.3 % efficiency and HeLa cells with 94.9 % efficiency. The flow speed of cells in this system can reach 150 mm/s, resulting in a corresponding theoretical encapsulation throughput of 150 Hz. This technology has significant potential in various biomedical applications, including single-cell omics, secretion detection, and drug screening.
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Affiliation(s)
- Yiming Wang
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China
| | - Yousu Wang
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China
| | - Xiaojie Wang
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China
| | - Wei Sun
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China
| | - Fengrui Yang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Xuebiao Yao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Tingrui Pan
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
| | - Baoqing Li
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China.
| | - Jiaru Chu
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China
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2
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Chen L, Chen A, Zhang XD, Saenz Robles MT, Han HS, Xiao Y, Xiao G, Pipas JM, Weitz DA. Targeted whole-genome recovery of single viral species in a complex environmental sample. Proc Natl Acad Sci U S A 2024; 121:e2404727121. [PMID: 39052829 PMCID: PMC11295033 DOI: 10.1073/pnas.2404727121] [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: 03/06/2024] [Accepted: 06/07/2024] [Indexed: 07/27/2024] Open
Abstract
Characterizing unknown viruses is essential for understanding viral ecology and preparing against viral outbreaks. Recovering complete genome sequences from environmental samples remains computationally challenging using metagenomics, especially for low-abundance species with uneven coverage. We present an experimental method for reliably recovering complete viral genomes from complex environmental samples. Individual genomes are encapsulated into droplets and amplified using multiple displacement amplification. A unique gene detection assay, which employs an RNA-based probe and an exonuclease, selectively identifies droplets containing the target viral genome. Labeled droplets are sorted using a microfluidic sorter, and genomes are extracted for sequencing. We demonstrate this method's efficacy by spiking two known viral genomes, Simian virus 40 (SV40, 5,243 bp) and Human Adenovirus 5 (HAd5, 35,938 bp), into a sewage sample with a final abundance in the droplets of around 0.1% and 0.015%, respectively. We achieve 100% recovery of the complete sequence of the spiked-in SV40 genome with uniform coverage distribution. For the larger HAd5 genome, we cover approximately 99.4% of its sequence. Notably, genome recovery is achieved with as few as one sorted droplet, which enables the recovery of any desired genomes in complex environmental samples, regardless of their abundance. This method enables single-genome whole-genome amplification and targeting characterizations of rare viral species and will facilitate our ability to access the mutational profile in single-virus genomes and contribute to an improved understanding of viral ecology.
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Affiliation(s)
- Liyin Chen
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Anqi Chen
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Xinge Diana Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | | | - Hee-Sun Han
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Yi Xiao
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Gao Xiao
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - James M. Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA15260
| | - David A. Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
- Department of Physics, Harvard University, Cambridge, MA02138
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3
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Sharkey C, White R, Finocchiaro M, Thomas J, Estevam J, Konry T. Advancing Point-of-Care Applications with Droplet Microfluidics: From Single-Cell to Multicellular Analysis. Annu Rev Biomed Eng 2024; 26:119-139. [PMID: 38316063 DOI: 10.1146/annurev-bioeng-110222-102142] [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: 02/07/2024]
Abstract
Recent advances in single-cell and multicellular microfluidics technology have provided powerful tools for studying cancer biology and immunology. The ability to create controlled microenvironments, perform high-throughput screenings, and monitor cellular interactions at the single-cell level has significantly advanced our understanding of tumor biology and immune responses. We discuss cutting-edge multicellular and single-cell microfluidic technologies and methodologies utilized to investigate cancer-immune cell interactions and assess the effectiveness of immunotherapies. We explore the advantages and limitations of the wide range of 3D spheroid and single-cell microfluidic models recently developed, highlighting the various approaches in device generation and applications in immunotherapy screening for potential opportunities for point-of-care approaches.
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Affiliation(s)
- Christina Sharkey
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
- Department of Surgery, Division of Urology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Rachel White
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
| | - Michael Finocchiaro
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
| | - Judene Thomas
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Jose Estevam
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
| | - Tania Konry
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
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4
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Armani-Tourret M, Bone B, Tan TS, Sun W, Bellefroid M, Struyve T, Louella M, Yu XG, Lichterfeld M. Immune targeting of HIV-1 reservoir cells: a path to elimination strategies and cure. Nat Rev Microbiol 2024; 22:328-344. [PMID: 38337034 PMCID: PMC11131351 DOI: 10.1038/s41579-024-01010-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Successful approaches for eradication or cure of HIV-1 infection are likely to include immunological mechanisms, but remarkably little is known about how human immune responses can recognize and interact with the few HIV-1-infected cells that harbour genome-intact viral DNA, persist long term despite antiretroviral therapy and represent the main barrier to a cure. For a long time regarded as being completely shielded from host immune responses due to viral latency, these cells do, on closer examination with single-cell analytic techniques, display discrete footprints of immune selection, implying that human immune responses may be able to effectively engage and target at least some of these cells. The failure to eliminate rebound-competent virally infected cells in the majority of persons likely reflects the evolution of a highly selected pool of reservoir cells that are effectively camouflaged from immune recognition or rely on sophisticated approaches for resisting immune-mediated killing. Understanding the fine-tuned interplay between host immune responses and viral reservoir cells will help to design improved interventions that exploit the immunological vulnerabilities of HIV-1 reservoir cells.
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Affiliation(s)
- Marie Armani-Tourret
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Benjamin Bone
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Toong Seng Tan
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Weiwei Sun
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Maxime Bellefroid
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Tine Struyve
- HIV Cure Research Center, Ghent University, Ghent, Belgium
| | - Michael Louella
- Community Advisory Board, Delaney AIDS Research Enterprise (DARE), San Francisco, CA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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5
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Pan S, Zhang T, Zhang C, Liao N, Zhang M, Zhao T. Fabrication of a high performance flexible capacitive porous GO/PDMS pressure sensor based on droplet microfluidic technology. LAB ON A CHIP 2024; 24:1668-1675. [PMID: 38304936 DOI: 10.1039/d4lc00021h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Porous structures are an effective way to improve the performance of flexible capacitive sensors, but the pore size uniformity of porous structures is not easily controlled by current methods, which may affect the inconsistent performance of different batches of sensors. In this paper, a high performance capacitive flexible porous GO/PDMS pressure sensor was prepared based on droplet microfluidic technology. By testing the performance of the sensor, we found that the sensor with a flow rate ratio of 1 : 3 has relatively good performance, with a degree of hysteresis (DH) of 8.64% and a coefficient of variation (CV) of 5.2%. Therefore, we studied the sensor performance based on this process. The result shows that the sensitivity of the flexible capacitive porous GO/PDMS pressure sensor reached 0.627 kPa-1 at low pressure (0-3 kPa), which is significantly higher than that of the pure PDMS thin film sensor (about 0.031 kPa-1) and the porous PDMS pressure sensor (0.263 kPa-1). At the same time, the sensor has a large range with a fast response time of 240 ms and a relaxation time of 300 ms at 30 kPa and an ultra-low detection limit (70 Pa). It can maintain stable operation under continuous force loading/unloading cycles and can respond well to different pressure step changes, so the sensor can be used to detect the movement process of each finger, knee, foot and other joints of the human body. In conclusion, the droplet microfluidic technology can effectively prepare high-performance capacitive flexible porous GO/PDMS pressure sensors.
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Affiliation(s)
- ShengYuan Pan
- College of Mechanical and Electrical Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Tao Zhang
- College of Mechanical and Electrical Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Cheng Zhang
- College of Mechanical and Electrical Engineering, Wenzhou University, Wenzhou 325035, China.
- Cangnan Research Institute of Wenzhou University, Wenzhou 325800, China
| | - Ningbo Liao
- College of Mechanical and Electrical Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Miao Zhang
- College of Mechanical and Electrical Engineering, Wenzhou University, Wenzhou 325035, China.
- Cangnan Research Institute of Wenzhou University, Wenzhou 325800, China
| | - Tianchen Zhao
- Key Laboratory of Air-driven Equipment Technology of Zhejiang Province, Quzhou University, Quzhou 324000, China
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Nan L, Zhang H, Weitz DA, Shum HC. Development and future of droplet microfluidics. LAB ON A CHIP 2024; 24:1135-1153. [PMID: 38165829 DOI: 10.1039/d3lc00729d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Over the past two decades, advances in droplet-based microfluidics have facilitated new approaches to process and analyze samples with unprecedented levels of precision and throughput. A wide variety of applications has been inspired across multiple disciplines ranging from materials science to biology. Understanding the dynamics of droplets enables optimization of microfluidic operations and design of new techniques tailored to emerging demands. In this review, we discuss the underlying physics behind high-throughput generation and manipulation of droplets. We also summarize the applications in droplet-derived materials and droplet-based lab-on-a-chip biotechnology. In addition, we offer perspectives on future directions to realize wider use of droplet microfluidics in industrial production and biomedical analyses.
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Affiliation(s)
- Lang Nan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Huidan Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
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7
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Rausch JW, Parvez S, Pathak S, Capoferri AA, Kearney MF. HIV Expression in Infected T Cell Clones. Viruses 2024; 16:108. [PMID: 38257808 PMCID: PMC10820123 DOI: 10.3390/v16010108] [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: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
The principal barrier to an HIV-1 cure is the persistence of infected cells harboring replication-competent proviruses despite antiretroviral therapy (ART). HIV-1 transcriptional suppression, referred to as viral latency, is foremost among persistence determinants, as it allows infected cells to evade the cytopathic effects of virion production and killing by cytotoxic T lymphocytes (CTL) and other immune factors. HIV-1 persistence is also governed by cellular proliferation, an innate and essential capacity of CD4+ T cells that both sustains cell populations over time and enables a robust directed response to immunological threats. However, when HIV-1 infects CD4+ T cells, this capacity for proliferation can enable surreptitious HIV-1 propagation without the deleterious effects of viral gene expression in latently infected cells. Over time on ART, the HIV-1 reservoir is shaped by both persistence determinants, with selective forces most often favoring clonally expanded infected cell populations harboring transcriptionally quiescent proviruses. Moreover, if HIV latency is incomplete or sporadically reversed in clonal infected cell populations that are replenished faster than they are depleted, such populations could both persist indefinitely and contribute to low-level persistent viremia during ART and viremic rebound if treatment is withdrawn. In this review, select genetic, epigenetic, cellular, and immunological determinants of viral transcriptional suppression and clonal expansion of HIV-1 reservoir T cells, interdependencies among these determinants, and implications for HIV-1 persistence will be presented and discussed.
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Affiliation(s)
- Jason W. Rausch
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (S.P.); (S.P.); (A.A.C.); (M.F.K.)
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8
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Moar P, Premeaux TA, Atkins A, Ndhlovu LC. The latent HIV reservoir: current advances in genetic sequencing approaches. mBio 2023; 14:e0134423. [PMID: 37811964 PMCID: PMC10653892 DOI: 10.1128/mbio.01344-23] [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] [Indexed: 10/10/2023] Open
Abstract
Multiple cellular HIV reservoirs in diverse anatomical sites can undergo clonal expansion and persist for years despite suppressive antiretroviral therapy, posing a major barrier toward an HIV cure. Commonly adopted assays to assess HIV reservoir size mainly consist of PCR-based measures of cell-associated total proviral DNA, intact proviruses and transcriptionally competent provirus (viral RNA), flow cytometry and microscopy-based methods to measure translationally competent provirus (viral protein), and quantitative viral outgrowth assay, the gold standard to measure replication-competent provirus; yet no assay alone can provide a comprehensive view of the total HIV reservoir or its dynamics. Furthermore, the detection of extant provirus by these measures does not preclude defects affecting replication competence. An accurate measure of the latent reservoir is essential for evaluating the efficacy of HIV cure strategies. Recent approaches have been developed, which generate proviral sequence data to create a more detailed profile of the latent reservoir. These sequencing approaches are valuable tools to understand the complex multicellular processes in a diverse range of tissues and cell types and have provided insights into the mechanisms of HIV establishment and persistence. These advancements over previous sequencing methods have allowed multiplexing and new assays have emerged, which can document transcriptional activity, chromosome accessibility, and in-depth cellular phenotypes harboring latent HIV, enabling the characterization of rare infected cells across restrictive sites such as the brain. In this manuscript, we provide a review of HIV sequencing-based assays adopted to address challenges in quantifying and characterizing the latent HIV reservoir.
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Affiliation(s)
- Preeti Moar
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Thomas A. Premeaux
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Andrew Atkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York City, New York, USA
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9
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Zhang Y, Lin Y, Hong X, Di C, Xin Y, Wang X, Qi S, Liu BF, Zhang Z, Du W. Demand-driven active droplet generation and sorting based on positive pressure-controlled fluid wall. Anal Bioanal Chem 2023; 415:5311-5322. [PMID: 37392212 DOI: 10.1007/s00216-023-04806-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 07/03/2023]
Abstract
Droplet microfluidics is a rapidly advancing area of microfluidic technology, which offers numerous advantages for cell analysis, such as isolation and accumulation of signals, by confining cells within droplets. However, controlling cell numbers in droplets is challenging due to the uncertainty of random encapsulation which result in many empty droplets. Therefore, more precise control techniques are needed to achieve efficient encapsulation of cells within droplets. Here, an innovative microfluidic droplet manipulation platform had been developed, which employed positive pressure as a stable and controllable driving force for manipulating fluid within chips. The air cylinder, electro-pneumatics proportional valve, and the microfluidic chip were connected through a capillary, which enabled the formation of a fluid wall by creating a difference in hydrodynamic resistance between two fluid streams at the channel junction. Lowering the pressure of the driving oil phase eliminates hydrodynamic resistance and breaks the fluid wall. Regulating the duration of the fluid wall breakage controls the volume of the introduced fluid. Several important droplet microfluidic manipulations were demonstrated on this microfluidic platform, such as sorting of cells/droplets, sorting of droplets co-encapsulated cells and hydrogels, and active generation of droplets encapsulated with cells in a responsive manner. The simple, on-demand microfluidic platform was featured with high stability, good controllability, and compatibility with other droplet microfluidic technologies.
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Affiliation(s)
- Yiwei Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yiwei Lin
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xianzhe Hong
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Chao Di
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yuelai Xin
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xinru Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shuhong Qi
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhihong Zhang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wei Du
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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10
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Zhong J, Liang M, Ai Y. DUPLETS: Deformability-Assisted Dual-Particle Encapsulation Via Electrically Activated Sorting. SMALL METHODS 2023; 7:e2300089. [PMID: 37246250 DOI: 10.1002/smtd.202300089] [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: 01/24/2023] [Revised: 04/12/2023] [Indexed: 05/30/2023]
Abstract
Co-encapsulation of bead carriers and biological cells in microfluidics has become a powerful technique for various biological assays in single-cell genomics and drug screening because of its distinct capability of single-cell confinement. However, current co-encapsulation approaches exist a trade-off between cell/bead pairing rate and probability of multiple cells in individual droplets, significantly limiting the effective throughput of single-paired cell-bead droplets production. Deformability-assisted dUal-Particle encapsuLation via Electrically acTivated Sorting (DUPLETS) system is reported to overcome this problem. The DUPLETS can differentiate the encapsulated content in individual droplets and sort out targeted droplets via a combined screening of mechanical and electrical characteristics of single droplets in label-free manners and with the highest effective throughput in comparison to current commercial platforms. The DUPLETS has been demonstrated to enrich single-paired cell-bead droplets to over 80% (above eightfold higher than current co-encapsulation techniques). It eliminates multicell droplets to 0.1% whereas up to ≈24% in 10× Chromium. It is believed that merging DUPLETS into the current co-encapsulation platforms can meaningfully elevate sample quality in terms of high purity of single-paired cell-bead droplets, low fraction of multicell droplets, and high cell viability, which can benefit a multitude of biological assay applications.
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Affiliation(s)
- Jianwei Zhong
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Minhui Liang
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
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11
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Zhao W, Zhou Y, Feng YZ, Niu X, Zhao Y, Zhao J, Dong Y, Tan M, Xianyu Y, Chen Y. Computer Vision-Based Artificial Intelligence-Mediated Encoding-Decoding for Multiplexed Microfluidic Digital Immunoassay. ACS NANO 2023; 17:13700-13714. [PMID: 37458511 DOI: 10.1021/acsnano.3c02941] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Digital immunoassays with multiplexed capacity, ultrahigh sensitivity, and broad affordability are urgently required in clinical diagnosis, food safety, and environmental monitoring. In this work, a multidimensional digital immunoassay has been developed through microparticle-based encoding and artificial intelligence-based decoding, enabling multiplexed detection with high sensitivity and convenient operation. The information encoded in the features of microspheres, including their size, number, and color, allows for the simultaneous identification and accurate quantification of multiple targets. Computer vision-based artificial intelligence can analyze the microscopy images for information decoding and output identification results visually. Moreover, the optical microscopy imaging can be well integrated with the microfluidic platform, allowing for encoding-decoding through the computer vision-based artificial intelligence. This microfluidic digital immunoassay can simultaneously analyze multiple inflammatory markers and antibiotics within 30 min with high sensitivity and a broad detection range from pg/mL to μg/mL, which holds great promise as an intelligent bioassay for next-generation multiplexed biosensing.
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Affiliation(s)
- Weiqi Zhao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei China
| | - Yang Zhou
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei China
- College of Engineering, Huazhong Agricultural University, Wuhan, 430070, Hubei China
| | - Yao-Ze Feng
- College of Engineering, Huazhong Agricultural University, Wuhan, 430070, Hubei China
| | - Xiaohu Niu
- College of Engineering, Huazhong Agricultural University, Wuhan, 430070, Hubei China
| | - Yongkun Zhao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei China
- College of Engineering, Huazhong Agricultural University, Wuhan, 430070, Hubei China
| | - Junpeng Zhao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei China
| | - Yongzhen Dong
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei China
| | - Mingqian Tan
- Academy of Food Interdisciplinary Science, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, Liaoning China
| | - Yunlei Xianyu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, Zhejiang China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei China
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12
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Cardoso BD, Castanheira EMS, Lanceros-Méndez S, Cardoso VF. Recent Advances on Cell Culture Platforms for In Vitro Drug Screening and Cell Therapies: From Conventional to Microfluidic Strategies. Adv Healthc Mater 2023; 12:e2202936. [PMID: 36898671 DOI: 10.1002/adhm.202202936] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/27/2023] [Indexed: 03/12/2023]
Abstract
The clinical translations of drugs and nanomedicines depend on coherent pharmaceutical research based on biologically accurate screening approaches. Since establishing the 2D in vitro cell culture method, the scientific community has improved cell-based drug screening assays and models. Those advances result in more informative biochemical assays and the development of 3D multicellular models to describe the biological complexity better and enhance the simulation of the in vivo microenvironment. Despite the overall dominance of conventional 2D and 3D cell macroscopic culture methods, they present physicochemical and operational challenges that impair the scale-up of drug screening by not allowing a high parallelization, multidrug combination, and high-throughput screening. Their combination and complementarity with microfluidic platforms enable the development of microfluidics-based cell culture platforms with unequivocal advantages in drug screening and cell therapies. Thus, this review presents an updated and consolidated view of cell culture miniaturization's physical, chemical, and operational considerations in the pharmaceutical research scenario. It clarifies advances in the field using gradient-based microfluidics, droplet-based microfluidics, printed-based microfluidics, digital-based microfluidics, SlipChip, and paper-based microfluidics. Finally, it presents a comparative analysis of the performance of cell-based methods in life research and development to achieve increased precision in the drug screening process.
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Affiliation(s)
- Beatriz D Cardoso
- Physics Centre of Minho and Porto Universities (CF-UM-UP), Campus de Gualtar, University of Minho, Braga, 4710-057, Portugal
- LaPMET-Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057, Braga, Portugal
- Center for MicroElectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058, Guimarães, Portugal
- LABBELS-Associate Laboratory in Biotechnology and Bioengineering and Microelectromechanical Systems, University of Minho, Braga/Guimarães, Portugal
| | - Elisabete M S Castanheira
- Physics Centre of Minho and Porto Universities (CF-UM-UP), Campus de Gualtar, University of Minho, Braga, 4710-057, Portugal
- LaPMET-Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057, Braga, Portugal
| | - Senentxu Lanceros-Méndez
- Physics Centre of Minho and Porto Universities (CF-UM-UP), Campus de Gualtar, University of Minho, Braga, 4710-057, Portugal
- LaPMET-Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057, Braga, Portugal
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, Leioa, 48940, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48009, Spain
| | - Vanessa F Cardoso
- Center for MicroElectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058, Guimarães, Portugal
- LABBELS-Associate Laboratory in Biotechnology and Bioengineering and Microelectromechanical Systems, University of Minho, Braga/Guimarães, Portugal
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13
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Abstract
Acquired immunodeficiency syndrome (AIDS), caused by the human immunodeficiency virus (HIV), has become a heavy burden of disease and an important public health problem in the world. Although current antiretroviral therapy (ART) is effective at suppressing the virus in the blood, HIV still remains in two different types of reservoirs-the latently infected cells (represented by CD4+ T cells) and the tissues containing those cells, which may block access to ART, HIV-neutralizing antibodies and latency-reversing agents. The latter is the focus of our review, as blood viral load drops below detectable levels after ART, a deeper and more systematic understanding of the HIV tissue reservoirs is imperative. In this review, we take the lymphoid system (including lymph nodes, gut-associated lymphoid tissue, spleen and bone marrow), nervous system, respiratory system, reproductive system (divided into male and female), urinary system as the order, focusing on the particularity and importance of each tissue in HIV infection, the infection target cell types of each tissue, the specific infection situation of each tissue quantified by HIV DNA or HIV RNA and the evidence of compartmentalization and pharmacokinetics. In summary, we found that the present state of HIV in different tissues has both similarities and differences. In the future, the therapeutic principle we need to follow is to respect the discrepancy on the basis of grasping the commonality. The measures taken to completely eliminate the virus in the whole body cannot be generalized. It is necessary to formulate personalized treatment strategies according to the different characteristics of the HIV in the various tissues, so as to realize the prospect of curing AIDS as soon as possible.
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Affiliation(s)
- Kangpeng Li
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Bo Liu
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Rui Ma
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Qiang Zhang
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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14
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Zhou Y, Zhao W, Feng Y, Niu X, Dong Y, Chen Y. Artificial Intelligence-Assisted Digital Immunoassay Based on a Programmable-Particle-Decoding Technique for Multitarget Ultrasensitive Detection. Anal Chem 2023; 95:1589-1598. [PMID: 36571573 DOI: 10.1021/acs.analchem.2c04703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The development of a multitarget ultrasensitive immunoassay is significant to fields such as medical research, clinical diagnosis, and food safety inspection. In this study, an artificial intelligence (AI)-assisted programmable-particle-decoding technique (APT)-based digital immunoassay system was developed to perform multitarget ultrasensitive detection. Multitarget was encoded by programmable polystyrene (PS) microspheres with different characteristics (particle size and number), and subsequent visible signals were recorded under an optical microscope after the immune reaction. The resultant images were further analyzed using a customized, AI-based computer vision technique to decode the intrinsic properties of polystyrene microspheres and to reveal the types and concentrations of targets. Our strategy has successfully detected multiple inflammatory markers in clinical serum and antibiotics with a broad detection range from pg/mL to μg/mL without extra signal amplification and conversion. An AI-based digital immunoassay system exhibits great potential to be used for the next generation of multitarget detection in disease screening for candidate patients.
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Affiliation(s)
- Yang Zhou
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.,College of Engineering, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Weiqi Zhao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yaoze Feng
- College of Engineering, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xiaohu Niu
- College of Engineering, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yongzhen Dong
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.,Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518120, Guangdong, China
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15
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Ferreira RC, Wong E, Poon AFY. bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression. Virus Evol 2022; 9:veac120. [PMID: 36632480 PMCID: PMC9825830 DOI: 10.1093/ve/veac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/03/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
The composition of the latent human immunodeficiency virus 1 (HIV-1) reservoir is shaped by when proviruses integrated into host genomes. These integration dates can be estimated by phylogenetic methods like root-to-tip (RTT) regression. However, RTT does not accommodate variation in the number of mutations over time, uncertainty in estimating the molecular clock, or the position of the root in the tree. To address these limitations, we implemented a Bayesian extension of RTT as an R package (bayroot), which enables the user to incorporate prior information about the time of infection and start of antiretroviral therapy. Taking an unrooted maximum likelihood tree as input, we use a Metropolis-Hastings algorithm to sample from the joint posterior distribution of three parameters (the rate of sequence evolution, i.e., molecular clock; the location of the root; and the time associated with the root). Next, we apply rejection sampling to this posterior sample of model parameters to simulate integration dates for HIV proviral sequences. To validate this method, we use the R package treeswithintrees (twt) to simulate time-scaled trees relating samples of actively and latently infected T cells from a single host. We find that bayroot yields significantly more accurate estimates of integration dates than conventional RTT under a range of model settings.
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Affiliation(s)
| | - Emmanuel Wong
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 5C1, Canada
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16
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Abstract
Microfluidics has enabled a new era of cellular and molecular assays due to the small length scales, parallelization, and the modularity of various analysis and actuation functions. Droplet microfluidics, in particular, has been instrumental in providing new tools for biology with its ability to quickly and reproducibly generate drops that act as individual reactors. A notable beneficiary of this technology has been single-cell RNA sequencing, which has revealed new heterogeneities and interactions for the fundamental unit of life. However, viruses far surpass the diversity of cellular life, affect the dynamics of all ecosystems, and are a chronic source of global health crises. Despite their impact on the world, high-throughput and high-resolution viral profiling has been difficult, with conventional methods being limited to population-level averaging, large sample volumes, and few cultivable hosts. Consequently, most viruses have not been identified and studied. Droplet microfluidics holds the potential to address many of these limitations and offers new levels of sensitivity and throughput for virology. This Feature highlights recent efforts that have applied droplet microfluidics to the detection and study of viruses, including for diagnostics, virus-host interactions, and cell-independent virus assays. In combination with traditional virology methods, droplet microfluidics should prove a potent tool toward achieving a better understanding of the most abundant biological species on Earth.
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Affiliation(s)
- Wenyang Jing
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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