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Li Y, Jiang G, Wan Y, Dauda SAA, Pi F. Tailoring strategies of SERS tags-based sensors for cellular molecules detection and imaging. Talanta 2024; 276:126283. [PMID: 38776777 DOI: 10.1016/j.talanta.2024.126283] [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: 02/17/2024] [Revised: 05/02/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
As an emerging nanoprobe, surface enhanced Raman scattering (SERS) tags hold significant promise in sensing and bioimaging applications due to their attractive merits of anti-photobleaching ability, high sensitivity and specificity, multiplex, and low background capabilities. Recently, several reviews have proposed the application of SERS tags in different fields, however, the specific sensing strategies of SERS tags-based sensors for cellular molecules have not yet been systematically summarized. To provide beneficial and comprehensive insights into the advanced SERS tags technique at the cellular level, this review systematically elaborated on the latest advances in SERS tags-based sensors for cellular molecules detection and imaging. The general SERS tags-based sensing strategies for biomolecules and ions were first introduced according to molecular classes. Then, aiming at such molecules located in the extracellular, cellular membrane and intracellular regions, the tailored strategies by designing and manipulating SERS tags were summarized and explored through several key examples. Finally, the challenges and perspectives of developing high performance of advanced SERS tags were briefly discussed to provide effective guidance for further development and extended applications.
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Affiliation(s)
- Yu Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Guoyong Jiang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yuqi Wan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Sa-Adu Abiola Dauda
- School of Allied Health Sciences, University for Development Studies, P.O. Box 1883, Tamale, Ghana
| | - Fuwei Pi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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2
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Stollmann A, Garcia-Guirado J, Hong JS, Rüedi P, Im H, Lee H, Ortega Arroyo J, Quidant R. Molecular fingerprinting of biological nanoparticles with a label-free optofluidic platform. Nat Commun 2024; 15:4109. [PMID: 38750038 PMCID: PMC11096335 DOI: 10.1038/s41467-024-48132-4] [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: 09/22/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Label-free detection of multiple analytes in a high-throughput fashion has been one of the long-sought goals in biosensing applications. Yet, for all-optical approaches, interfacing state-of-the-art label-free techniques with microfluidics tools that can process small volumes of sample with high throughput, and with surface chemistry that grants analyte specificity, poses a critical challenge to date. Here, we introduce an optofluidic platform that brings together state-of-the-art digital holography with PDMS microfluidics by using supported lipid bilayers as a surface chemistry building block to integrate both technologies. Specifically, this platform fingerprints heterogeneous biological nanoparticle populations via a multiplexed label-free immunoaffinity assay with single particle sensitivity. First, we characterise the robustness and performance of the platform, and then apply it to profile four distinct ovarian cell-derived extracellular vesicle populations over a panel of surface protein biomarkers, thus developing a unique biomarker fingerprint for each cell line. We foresee that our approach will find many applications where routine and multiplexed characterisation of biological nanoparticles are required.
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Affiliation(s)
- Alexia Stollmann
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Jose Garcia-Guirado
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Jae-Sang Hong
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Pascal Rüedi
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Jaime Ortega Arroyo
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland.
| | - Romain Quidant
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland.
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3
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Jiang L, Guo K, Chen Y, Xiang N. Droplet Microfluidics for Current Cancer Research: From Single-Cell Analysis to 3D Cell Culture. ACS Biomater Sci Eng 2024; 10:1335-1354. [PMID: 38420753 DOI: 10.1021/acsbiomaterials.3c01866] [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: 03/02/2024]
Abstract
Cancer is the second leading cause of death worldwide. Differences in drug resistance and treatment response caused by the heterogeneity of cancer cells are the primary reasons for poor cancer therapy outcomes in patients. In addition, current in vitro anticancer drug-screening methods rely on two-dimensional monolayer-cultured cancer cells, which cannot accurately predict drug behavior in vivo. Therefore, a powerful tool to study the heterogeneity of cancer cells and produce effective in vitro tumor models is warranted to leverage cancer research. Droplet microfluidics has become a powerful platform for the single-cell analysis of cancer cells and three-dimensional cell culture of in vitro tumor spheroids. In this review, we discuss the use of droplet microfluidics in cancer research. Droplet microfluidic technologies, including single- or double-emulsion droplet generation and passive- or active-droplet manipulation, are concisely discussed. Recent advances in droplet microfluidics for single-cell analysis of cancer cells, circulating tumor cells, and scaffold-free/based 3D cell culture of tumor spheroids have been systematically introduced. Finally, the challenges that must be overcome for the further application of droplet microfluidics in cancer research are discussed.
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Affiliation(s)
- Lin Jiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Kefan Guo
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Yao Chen
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Nan Xiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
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4
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Li Y, Li W, Chen J, Qiu S, Liu Y, Xu L, Tian T, Li JP. Deciphering single-cell protein secretion and gene expressions by constructing cell-antibody conjugates. Bioorg Chem 2024; 143:106987. [PMID: 38039927 DOI: 10.1016/j.bioorg.2023.106987] [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: 10/12/2023] [Revised: 11/13/2023] [Accepted: 11/19/2023] [Indexed: 12/03/2023]
Abstract
Secreted proteins play critical roles in regulating immune responses, exerting cytotoxic effects on tumor cells, promoting inflammatory processes, and influencing cellular metabolism. Deciphering the intricate relationship between the heterogeneity of secreted proteins and their transcriptional states is pivotal in the study of cellular heterogeneity. Here we proposed a cell-antibody conjugate-based sequencing methodology (Cellab-seq) for joint characterization of secreted proteins and transcriptome. Cellab-seq utilizes a chemoenzymatic strategy to construct cell-antibody conjugates, which enables the capture of secreted proteins and their signal transduction with the incorporation of barcode detection antibodies. We applied Cellab-seq to investigate how gene expression influences the activity of secreted proteins in NK cells. Altogether, this strategy facilitates a nuanced understanding of cellular dynamics under diverse physiological conditions, ultimately contributing to the prevention, diagnosis and treatment of diseases.
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Affiliation(s)
- Yachao Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Wannan Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Jiashang Chen
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Shuang Qiu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Yilong Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Lingjie Xu
- Vazyme Biotech, Red Maple Hi-tech Industry Park, Kechuang Road, Qixia District, Nanjing, Jiangsu 210023, China
| | - Tian Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China.
| | - Jie P Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China.
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5
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Zheng D, Zhang J, Jiang W, Xu Y, Meng H, Poh CL, Chen CH. Graphene oxide aptasensor droplet assay for detection of metabolites secreted by single cells applied to synthetic biology. LAB ON A CHIP 2023; 24:137-147. [PMID: 38054213 DOI: 10.1039/d3lc00959a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Synthetic biology harnesses the power of natural microbes by re-engineering metabolic pathways to manufacture desired compounds. Droplet technology has emerged as a high-throughput tool to screen single cells for synthetic biology, while the challenges in sensitive flexible single-cell secretion assay for bioproduction of high-value chemicals remained. Here, a novel droplet modifiable graphene oxide (GO) aptasensor was developed, enabling sensitive flexible detection of different target compounds secreted from single cells. Fluorophore-labeled aptamers were stably anchored on GO through π-π stacking interactions to minimize the non-specific interactions for low-background detection of target compounds with high signal-to-noise ratios. The assay's versatility was exhibited by adapting aptamer sequences to measure metabolic secretions like ATP and naringenin. To show the case, engineered E. coli were constructed for the bioproduction of naringenin. The high signal-to-noise ratio assay (∼2.72) was approached to precisely measure the naringenins secreted from single E. coli in the droplets. Consequently, secretory cells (Gib) were clearly distinguished from wild-type (WT) cells, with a low overlap in cell populations (∼0%) for bioproduction.
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Affiliation(s)
- Dan Zheng
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Jingyun Zhang
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Wenxin Jiang
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Ying Xu
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Haixu Meng
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Chueh Loo Poh
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
- City University of Hong Kong Shenzhen Research Institute, Shenzhen Virtual University Park, Shenzhen, China
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6
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Zhu Y, Zhang M, Guo S, Xu H, Jie Z, Tao SC. CRISPR-based diagnostics of different biomolecules from nucleic acids, proteins, and small molecules to exosomes. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1539-1550. [PMID: 37528660 PMCID: PMC10577475 DOI: 10.3724/abbs.2023134] [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: 04/26/2023] [Accepted: 06/29/2023] [Indexed: 08/03/2023] Open
Abstract
CRISPR-based detection technologies have been widely explored for molecular diagnostics. However, the challenge lies in converting the signal of different biomolecules, such as nucleic acids, proteins, small molecules, exosomes, and ions, into a CRISPR-based nucleic acid detection signal. Understanding the detection of different biomolecules using CRISPR technology can aid in the development of practical and promising detection approaches. Unfortunately, existing reviews rarely provide an overview of CRISPR-based molecular diagnostics from the perspective of different biomolecules. Herein, we first introduce the principles and characteristics of various CRISPR nucleases for molecular diagnostics. Then, we focus on summarizing and evaluating the latest advancements in CRISPR-based detection of different biomolecules. Through a comparison of different methods of amplification and signal readout, we discuss how general detection methods can be integrated with CRISPR. Finally, we conclude by identifying opportunities for the improvement of CRISPR in quantitative, amplification-free, multiplex, all-in-one, and point-of-care testing (POCT) purposes.
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Affiliation(s)
- Yuanshou Zhu
- Shanghai Center for Systems BiomedicineKey Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Jiao Tong UniversityShanghai200240China
- School of Biomedical EngineeringMed-X Research InstituteShanghai Jiao Tong UniversityShanghai200030China
| | - Meng Zhang
- Department of Pulmonary and Critical Care MedicineShanghai Fifth People’s HospitalFudan UniversityShanghai200240China
| | - Shujuan Guo
- Shanghai Center for Systems BiomedicineKey Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Jiao Tong UniversityShanghai200240China
| | - Hong Xu
- School of Biomedical EngineeringMed-X Research InstituteShanghai Jiao Tong UniversityShanghai200030China
| | - Zhijun Jie
- Department of Pulmonary and Critical Care MedicineShanghai Fifth People’s HospitalFudan UniversityShanghai200240China
- Center of Community-Based Health ResearchFudan UniversityShanghai200240China
| | - Sheng-ce Tao
- Shanghai Center for Systems BiomedicineKey Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Jiao Tong UniversityShanghai200240China
- School of Biomedical EngineeringMed-X Research InstituteShanghai Jiao Tong UniversityShanghai200030China
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7
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Kang YA, Paik H, Zhang SY, Chen JJ, Olson OC, Mitchell CA, Collins A, Swann JW, Warr MR, Fan R, Passegué E. Secretory MPP3 reinforce myeloid differentiation trajectory and amplify myeloid cell production. J Exp Med 2023; 220:214059. [PMID: 37115584 PMCID: PMC10140385 DOI: 10.1084/jem.20230088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/25/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
Hematopoietic stem cells (HSC) and downstream lineage-biased multipotent progenitors (MPP) tailor blood production and control myelopoiesis on demand. Recent lineage tracing analyses revealed MPPs to be major functional contributors to steady-state hematopoiesis. However, we still lack a precise resolution of myeloid differentiation trajectories and cellular heterogeneity in the MPP compartment. Here, we found that myeloid-biased MPP3 are functionally and molecularly heterogeneous, with a distinct subset of myeloid-primed secretory cells with high endoplasmic reticulum (ER) volume and FcγR expression. We show that FcγR+/ERhigh MPP3 are a transitional population serving as a reservoir for rapid production of granulocyte/macrophage progenitors (GMP), which directly amplify myelopoiesis through inflammation-triggered secretion of cytokines in the local bone marrow (BM) microenvironment. Our results identify a novel regulatory function for a secretory MPP3 subset that controls myeloid differentiation through lineage-priming and cytokine production and acts as a self-reinforcing amplification compartment in inflammatory stress and disease conditions.
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Affiliation(s)
- Yoon-A Kang
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University , New York, NY, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Medicine, Hem/Onc Division, University of California, San Francisco , San Francisco, CA, USA
| | - Hyojung Paik
- Center for Applied Scientific Computing, Korea Institute of Science and Technology Information, and University of Science and Technology , Daejeon, South Korea
| | - Si Yi Zhang
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Medicine, Hem/Onc Division, University of California, San Francisco , San Francisco, CA, USA
| | - Jonathan J Chen
- Department of Biomedical Engineering, Yale University , New Haven, CT, USA
| | - Oakley C Olson
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University , New York, NY, USA
| | - Carl A Mitchell
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University , New York, NY, USA
| | - Amelie Collins
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University , New York, NY, USA
| | - James W Swann
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University , New York, NY, USA
| | - Matthew R Warr
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Medicine, Hem/Onc Division, University of California, San Francisco , San Francisco, CA, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University , New Haven, CT, USA
| | - Emmanuelle Passegué
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University , New York, NY, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Medicine, Hem/Onc Division, University of California, San Francisco , San Francisco, CA, USA
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8
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Ansaryan S, Liu YC, Li X, Economou AM, Eberhardt CS, Jandus C, Altug H. High-throughput spatiotemporal monitoring of single-cell secretions via plasmonic microwell arrays. Nat Biomed Eng 2023:10.1038/s41551-023-01017-1. [PMID: 37012313 PMCID: PMC10365996 DOI: 10.1038/s41551-023-01017-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/02/2023] [Indexed: 04/05/2023]
Abstract
Methods for the analysis of cell secretions at the single-cell level only provide semiquantitative endpoint readouts. Here we describe a microwell array for the real-time spatiotemporal monitoring of extracellular secretions from hundreds of single cells in parallel. The microwell array incorporates a gold substrate with arrays of nanometric holes functionalized with receptors for a specific analyte, and is illuminated with light spectrally overlapping with the device's spectrum of extraordinary optical transmission. Spectral shifts in surface plasmon resonance resulting from analyte-receptor bindings around a secreting cell are recorded by a camera as variations in the intensity of the transmitted light while machine-learning-assisted cell tracking eliminates the influence of cell movements. We used the microwell array to characterize the antibody-secretion profiles of hybridoma cells and of a rare subset of antibody-secreting cells sorted from human donor peripheral blood mononuclear cells. High-throughput measurements of spatiotemporal secretory profiles at the single-cell level will aid the study of the physiological mechanisms governing protein secretion.
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Affiliation(s)
- Saeid Ansaryan
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Yen-Cheng Liu
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Xiaokang Li
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Agora Center, Lausanne, Switzerland
| | | | - Christiane Sigrid Eberhardt
- Center for Vaccinology, University Hospitals Geneva and University of Geneva, Geneva, Switzerland
- Division of General Pediatrics, Department of Woman, Child and Adolescent Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Camilla Jandus
- Ludwig Institute for Cancer Research, Lausanne Branch, Agora Center, Lausanne, Switzerland
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Hatice Altug
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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Armakolas A, Kotsari M, Koskinas J. Liquid Biopsies, Novel Approaches and Future Directions. Cancers (Basel) 2023; 15:1579. [PMID: 36900369 PMCID: PMC10000663 DOI: 10.3390/cancers15051579] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Cancer is among the leading causes of death worldwide. Early diagnosis and prognosis are vital to improve patients' outcomes. The gold standard of tumor characterization leading to tumor diagnosis and prognosis is tissue biopsy. Amongst the constraints of tissue biopsy collection is the sampling frequency and the incomplete representation of the entire tumor bulk. Liquid biopsy approaches, including the analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating miRNAs, and tumor-derived extracellular vesicles (EVs), as well as certain protein signatures that are released in the circulation from primary tumors and their metastatic sites, present a promising and more potent candidate for patient diagnosis and follow up monitoring. The minimally invasive nature of liquid biopsies, allowing frequent collection, can be used in the monitoring of therapy response in real time, allowing the development of novel approaches in the therapeutic management of cancer patients. In this review we will describe recent advances in the field of liquid biopsy markers focusing on their advantages and disadvantages.
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Affiliation(s)
- Athanasios Armakolas
- Physiology Laboratory, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- B' Department of Medicine, Hippokration Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Maria Kotsari
- Physiology Laboratory, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - John Koskinas
- B' Department of Medicine, Hippokration Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
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10
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Cedillo-Alcantar DF, Rodriguez-Moncayo R, Maravillas-Montero JL, Garcia-Cordero JL. On-Chip Analysis of Protein Secretion from Single Cells Using Microbead Biosensors. ACS Sens 2023; 8:655-664. [PMID: 36710459 DOI: 10.1021/acssensors.2c02148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The profiling of the effector functions of single immune cells─including cytokine secretion─can lead to a deeper understanding of how the immune system operates and to potential diagnostics and therapeutical applications. Here, we report a microfluidic device that pairs single cells and antibody-functionalized microbeads in hydrodynamic traps to quantitate cytokine secretion. The device contains 1008 microchambers, each with a volume of ∼500 pL, divided into six different sections individually addressed to deliver an equal number of chemical stimuli. Integrating microvalves allowed us to isolate cell/bead pairs, preventing cross-contamination with factors secreted by adjacent cells. We implemented a fluorescence sandwich immunoassay on the biosensing microbeads with a limit of detection of 9 pg/mL and were able to detect interleukin-8 (IL-8) secreted by single blood-derived human monocytes in response to different concentrations of LPS. Finally, our platform allowed us to observe a significant decrease in the number of IL-8-secreting monocytes when paracrine signaling becomes disrupted. Overall, our platform could have a variety of applications for which the analysis of cellular function heterogeneity is necessary, such as cancer research, antibody discovery, or rare cell screening.
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Affiliation(s)
- Diana F Cedillo-Alcantar
- Laboratory of Microtechnologies for Biomedicine, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Monterrey 66628, Nuevo León Mexico
| | - Roberto Rodriguez-Moncayo
- Laboratory of Microtechnologies for Biomedicine, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Monterrey 66628, Nuevo León Mexico
| | - Jose L Maravillas-Montero
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico
| | - Jose L Garcia-Cordero
- Laboratory of Microtechnologies for Biomedicine, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Monterrey 66628, Nuevo León Mexico.,Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel 4058, Switzerland
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11
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Jiang L, Yang H, Cheng W, Ni Z, Xiang N. Droplet microfluidics for CTC-based liquid biopsy: a review. Analyst 2023; 148:203-221. [PMID: 36508171 DOI: 10.1039/d2an01747d] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Circulating tumor cells (CTCs) are important biomarkers of liquid biopsy. The number and heterogeneity of CTCs play an important role in cancer diagnosis and personalized medicine. However, owing to the low-abundance biomarkers of CTCs, conventional assays are only able to detect CTCs at the population level. Therefore, there is a pressing need for a highly sensitive method to analyze CTCs at the single-cell level. As an important branch of microfluidics, droplet microfluidics is a high-throughput and sensitive single-cell analysis platform for the quantitative detection and heterogeneity analysis of CTCs. In this review, we focus on the quantitative detection and heterogeneity analysis of CTCs using droplet microfluidics. Technologies that enable droplet microfluidics, particularly high-throughput droplet generation and high-efficiency droplet manipulation, are first discussed. Then, recent advances in detecting and analyzing CTCs using droplet microfluidics from the different aspects of nucleic acids, proteins, and metabolites are introduced. The purpose of this review is to provide guidance for the continued study of droplet microfluidics for CTC-based liquid biopsy.
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Affiliation(s)
- Lin Jiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Hang Yang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Weiqi Cheng
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Zhonghua Ni
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Nan Xiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
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12
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Zhang T, Chen X, Chen D, Wang J, Chen J. Development of constrictional microchannels and the recurrent neural network in single-cell protein analysis. Front Bioeng Biotechnol 2023; 11:1195940. [PMID: 37207125 PMCID: PMC10190128 DOI: 10.3389/fbioe.2023.1195940] [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: 03/29/2023] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
Introduction: As the golden approach of single-cell analysis, fluorescent flow cytometry can estimate single-cell proteins with high throughputs, which, however, cannot translate fluorescent intensities into protein numbers. Methods: This study reported a fluorescent flow cytometry based on constrictional microchannels for quantitative measurements of single-cell fluorescent levels and the recurrent neural network for data analysis of fluorescent profiles for high-accuracy cell-type classification. Results: As a demonstration, fluorescent profiles (e.g., FITC labeled β-actin antibody, PE labeled EpCAM antibody and PerCP labeled β-tubulin antibody) of individual A549 and CAL 27 cells were firstly measured and translated into protein numbers of 0.56 ± 0.43 × 104, 1.78 ± 1.06 × 106 and 8.11 ± 4.89 × 104 of A549 cells (ncell = 10232), and 3.47 ± 2.45 × 104, 2.65 ± 1.19 × 106 and 8.61 ± 5.25 × 104 of CAL 27 cells (ncell = 16376) based on the equivalent model of the constrictional microchannel. Then, the feedforward neural network was used to process these single-cell protein expressions, producing a classification accuracy of 92.0% for A549 vs. CAL 27 cells. In order to further increase the classification accuracies, as a key subtype of the recurrent neural network, the long short-term memory (LSTM) neural network was adopted to process fluorescent pulses sampled in constrictional microchannels directly, producing a classification accuracy of 95.5% for A549 vs. CAL 27 cells after optimization. Discussion: This fluorescent flow cytometry based on constrictional microchannels and recurrent neural network can function as an enabling tool of single-cell analysis and contribute to the development of quantitative cell biology.
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Affiliation(s)
- Ting Zhang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Deyong Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Junbo Wang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Junbo Wang, ; Jian Chen,
| | - Jian Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Junbo Wang, ; Jian Chen,
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13
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Mesoporous Silica Promotes Osteogenesis of Human Adipose-Derived Stem Cells Identified by a High-Throughput Microfluidic Chip Assay. Pharmaceutics 2022; 14:pharmaceutics14122730. [PMID: 36559224 PMCID: PMC9781822 DOI: 10.3390/pharmaceutics14122730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Silicon-derived biomaterials are conducive to regulating the fate of osteo-related stem cells, while their effects on the osteogenic differentiation of human adipose-derived stem cells (hADSCs) remain inconclusive. Mesoporous silica (mSiO2) is synthesized in a facile route that exhibited the capability of promoting osteogenic differentiation of hADSCs. The metabolism of SiO2 in cells is proposed according to the colocalization fluorescence analysis between lysosomes and nanoparticles. The released silicon elements promote osteogenic differentiation. The detection of secretory proteins through numerous parallel experiments performed via a microfluidic chip confirms the positive effect of SiO2 on the osteogenic differentiation of hADSCs. Moreover, constructed with superparamagnetic iron oxide (Fe3O4), the magnetic nanoparticles (MNPs) of Fe3O4@mSiO2 endow the cells with magnetic resonance imaging (MRI) properties. The MNP-regulated osteogenic differentiation of autologous adipose-derived stem cells provides considerable clinical application prospects for stem cell therapy of bone tissue repair with an effective reduction in immune rejection.
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14
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Zhao L, Wang X. 3D printed microfluidics for cell biological applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Liu Z, Li H, Dang Q, Weng S, Duo M, Lv J, Han X. Integrative insights and clinical applications of single-cell sequencing in cancer immunotherapy. Cell Mol Life Sci 2022; 79:577. [DOI: 10.1007/s00018-022-04608-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/03/2022]
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16
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Fang Y, Yan Y, Bi S, Wang Y, Chen Y, Xu P, Ju H, Liu Y. Screening T-Cell Activity via a Photodetachable DNA-Copolymer Nanocage and Its Therapeutic Application. Anal Chem 2022; 94:13205-13214. [PMID: 36095289 DOI: 10.1021/acs.analchem.2c02763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Screening T-cell activity and selecting active ones from large ex vivo-expanded populations before reinfusion is important for the success of T-cell therapy. Cytokine secretion is the evaluation criterion of cell immune activity. Cell membrane-anchored probes and microchamber-based techniques have been used to screen cytokine secretion at the single-cell level. However, they are either easily affected by nearby cells' secretion or lack of single-cell encapsulation efficiency. Here, we design a photodetachable DNA-copolymer nanocage on the cell membrane for screening the activities of ex vivo-expanded T cells by in-situ monitoring cytokine interferon-gamma (IFN-γ) secretion. The ones with good immune activity are selected for therapeutic application. DNA-copolymer nanocage is self-assembled on a cell membrane to encapsulate a single T cell. A self-quenched IFN-γ recognition aptamer is contained in the DNA-copolymer nanocage, which recovers fluorescence in response to IFN-γ secretion to indicate individual T-cell activity. The active T cells are collected after fluorescence-activated cell sorting, irradiated with 5 min UV light to detach nanocage from the cell membrane, and continuously cocultured with downstream cells. The selected Jurkat cells and CD19 CAR-T cells showed improved capabilities for downstream cell activation and cancer cell killing. The cell membrane-detachable DNA-copolymer nanocage-based T-cell activity screening and selection would have promising applications in T-cell therapy.
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Affiliation(s)
- Yanyun Fang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yawei Yan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shiyi Bi
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yingfei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yue Chen
- Department of Hematology, Nanjing Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing 210093, China
| | - Peipei Xu
- Department of Hematology, Nanjing Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing 210093, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
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17
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Zhong Q, Huang X, Zhang R, Zhang K, Liu B. Optical Sensing Strategies for Probing Single-Cell Secretion. ACS Sens 2022; 7:1779-1790. [PMID: 35709496 DOI: 10.1021/acssensors.2c00474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Measuring cell secretion events is crucial to understand the fundamental cell biology that underlies cell-cell communication, migration, proliferation, and differentiation. Although strategies targeting cell populations have provided significant information about live cell secretion, they yield ensemble profiles that obscure intrinsic cell-to-cell variations. Innovation in single-cell analysis has made breakthroughs allowing accurate sensing of a wide variety of secretions and their release dynamics with high spatiotemporal resolution. This perspective focuses on the power of single-cell protocols to revolutionize cell-secretion analysis by allowing real-time and real-space measurements on single live cell resolution. We begin by discussing recent progress on single-cell bioanalytical techniques, specifically optical sensing strategies such as fluorescence-, surface plasmon resonance-, and surface-enhanced Raman scattering-based strategies, capable of in situ real-time monitoring of single-cell released ions, metabolites, proteins, and vesicles. Single-cell sensing platforms which allow for high-throughput high-resolution analysis with enough accuracy are highlighted. Furthermore, we discuss remaining challenges that should be addressed to get a more comprehensive understanding of secretion biology. Finally, future opportunities and potential breakthroughs in secretome analysis that will arise as a result of further development of single-cell sensing approaches are discussed.
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Affiliation(s)
- Qingmei Zhong
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Xuedong Huang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Rongrong Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Kun Zhang
- Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
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18
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Label-free nanofluidic scattering microscopy of size and mass of single diffusing molecules and nanoparticles. Nat Methods 2022; 19:751-758. [PMID: 35637303 PMCID: PMC9184284 DOI: 10.1038/s41592-022-01491-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 04/12/2022] [Indexed: 12/18/2022]
Abstract
Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species to bind to a surface to be visible, thereby leaving a large fraction of analytes undetected. Here, we present nanofluidic scattering microscopy (NSM), which overcomes these limitations by enabling label-free, real-time imaging of single biomolecules diffusing inside a nanofluidic channel. NSM facilitates accurate determination of molecular weight from the measured optical contrast and of the hydrodynamic radius from the measured diffusivity, from which information about the conformational state can be inferred. Furthermore, we demonstrate its applicability to the analysis of a complex biofluid, using conditioned cell culture medium containing extracellular vesicles as an example. We foresee the application of NSM to monitor conformational changes, aggregation and interactions of single biomolecules, and to analyze single-cell secretomes. Nanofluidic scattering microscopy enables label-free, quantitative measurements of the molecular weight and hydrodynamic radius of biological molecules and nanoparticles freely diffusing inside a nanofluidic channel.
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19
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de Rutte J, Dimatteo R, Archang MM, van Zee M, Koo D, Lee S, Sharrow AC, Krohl PJ, Mellody M, Zhu S, Eichenbaum JV, Kizerwetter M, Udani S, Ha K, Willson RC, Bertozzi AL, Spangler J, Damoiseaux R, Di Carlo D. Suspendable Hydrogel Nanovials for Massively Parallel Single-Cell Functional Analysis and Sorting. ACS NANO 2022; 16:7242-7257. [PMID: 35324146 PMCID: PMC9869715 DOI: 10.1021/acsnano.1c11420] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Techniques to analyze and sort single cells based on functional outputs, such as secreted products, have the potential to transform our understanding of cellular biology as well as accelerate the development of next-generation cell and antibody therapies. However, secreted molecules rapidly diffuse away from cells, and analysis of these products requires specialized equipment and expertise to compartmentalize individual cells and capture their secretions. Herein, we describe methods to fabricate hydrogel-based chemically functionalized microcontainers, which we call nanovials, and demonstrate their use for sorting single viable cells based on their secreted products at high-throughput using only commonly accessible laboratory infrastructure. These nanovials act as solid supports that facilitate attachment of a variety of adherent and suspension cell types, partition uniform aqueous compartments, and capture secreted proteins. Solutions can be exchanged around nanovials to perform fluorescence immunoassays on secreted proteins. Using this platform and commercial flow sorters, we demonstrate high-throughput screening of stably and transiently transfected producer cells based on relative IgG production. Chinese hamster ovary cells sorted based on IgG production regrew and maintained a high secretion phenotype over at least a week, yielding >40% increase in bulk IgG production rates. We also sorted hybridomas and B lymphocytes based on antigen-specific antibody production. Hybridoma cells secreting an antihen egg lysozyme antibody were recovered from background cells, enriching a population of ∼4% prevalence to >90% following sorting. Leveraging the high-speed sorting capabilities of standard sorters, we sorted >1 million events in <1 h. IgG secreting mouse B cells were also sorted and enriched based on antigen-specific binding. Successful sorting of antibody-secreting B cells combined with the ability to perform single-cell RT-PCR to recover sequence information suggests the potential to perform antibody discovery workflows. The reported nanovials can be easily stored and distributed among researchers, democratizing access to high-throughput functional cell screening.
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Affiliation(s)
- Joseph de Rutte
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
- Partillion Bioscience Corporation, Los Angeles, CA 90095, USA
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Maani M. Archang
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Mark van Zee
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Doyeon Koo
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Sohyung Lee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Allison C. Sharrow
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Patrick J. Krohl
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Michael Mellody
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Sheldon Zhu
- Partillion Bioscience Corporation, Los Angeles, CA 90095, USA
| | - James V. Eichenbaum
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Monika Kizerwetter
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Shreya Udani
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Kyung Ha
- Department of Mathematics, University of California, Los Angeles, CA 90095, USA
| | - Richard C. Willson
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Andrea L. Bertozzi
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA 90095, USA
- Department of Mathematics, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Jamie Spangler
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095, USA
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20
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de Rutte J, Dimatteo R, Zhu S, Archang MM, Di Carlo D. Sorting single-cell microcarriers using commercial flow cytometers. SLAS Technol 2022; 27:150-159. [PMID: 35058209 PMCID: PMC9018595 DOI: 10.1016/j.slast.2021.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The scale of biological discovery is driven by the vessels in which we can perform assays and analyze results, from multi-well plates to microfluidic compartments. We report on the compatibility of sub-nanoliter single-cell containers or "nanovials" with commercial fluorescence activated cell sorters (FACS). This recent lab on a particle approach utilizes 3D structured microparticles to isolate cells and perform single-cell assays at scale with existing lab equipment. Use of flow cytometry led to detection of fluorescently labeled protein with dynamic ranges spanning 2-3 log and detection limits down to ∼10,000 molecules per nanovial, which was the lowest amount tested. Detection limits were improved compared to fluorescence microscopy measurements using a 20X objective and a cooled CMOS camera. Nanovials with diameters between 35-85 µm could also be sorted with purity from 99-93% on different commercial instruments at throughputs up to 800 events/second. Cell-loaded nanovials were found to have unique forward and side (or back) scatter signatures that enabled gating of cell-containing nanovials using scatter metrics alone. The compatibility of nanovials with widely-available commercial FACS instruments promises to democratize single-cell assays used in discovery of antibodies and cell therapies, by enabling analysis of single cells based on secreted products and leveraging the unmatched analytical capabilities of flow cytometers to sort important clones.
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Affiliation(s)
- Joseph de Rutte
- Department of Bioengineering, University of California, Los Angeles, United States; Partillion Bioscience Corporation, Los Angeles, CA, United States.
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, United States
| | - Sheldon Zhu
- Partillion Bioscience Corporation, Los Angeles, CA, United States
| | - Maani M Archang
- Department of Bioengineering, University of California, Los Angeles, United States
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, United States; Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, United States; California NanoSystems Institute, University of California, Los Angeles, United States; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, United States
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21
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Zhong Q, Zhang K, Huang X, Lu Y, Zhao J, He Y, Liu B. In situ ratiometric SERS imaging of intracellular protease activity for subtype discrimination of human breast cancer. Biosens Bioelectron 2022; 207:114194. [PMID: 35325718 DOI: 10.1016/j.bios.2022.114194] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022]
Abstract
Accurate discrimination between different cells at the molecular level is of fundamental importance for disease diagnosis. Endogenous proteases are such molecular candidates for cancer cell subtype study. But in situ probing their activity in live cells remains challenging for surface-enhanced Raman scattering (SERS). Here, we present a sensitive ratio-type SERS nanoprobe for imaging of matrix metalloproteinase-2 (MMP-2) in different cancer cells subtypes. The nanoprobe contained three components: a plasmon-active gold nanoparticle as the SERS enhancing matrix, Raman dye rhodamine B (Rh B)-labelled substrate peptides as the specific MMP-2 recognizer, and 2-naphthalenethiol (2-NT) as the internal standard. MMP-2-responsive cleavage of peptides from the nanoprobe surface results in decrease or even disappearance of SERS emission of Rh B, which was ratioed over the emission of 2-NT for the quantification of MMP-2 activity. Both in-tube assay and in-cell imaging results show that the MMP-responsive nanoprobe can work and serve to differentiate the normal breast cells from the tumorous ones, to differentiate two breast cancer cell subtypes with a different degree of malignancy. We believe that this SERS nanoprobe could find a wide application in the fields of tumor biology and accurate disease diagnosis.
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Affiliation(s)
- Qingmei Zhong
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | - Kun Zhang
- Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Xuedong Huang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | - Yanwei Lu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | - Jinzhi Zhao
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | - Ying He
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China.
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22
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Abstract
Alterations in DNAs could not reveal what happened in proteins. The accumulated alterations of DNAs would change the manifestation of proteins. Therefore, as is the case in cancer liquid biopsies, deep proteome profiling will likely provide invaluable and clinically relevant information in real-time throughout all stages of cancer progression. However, due to the great complexity of proteomes in liquid biopsy samples and the limitations of proteomic technologies compared to high-plex sequencing technologies, proteomic discoveries have yet lagged behind their counterpart, genomic technologies. Therefore, novel protein technologies are in urgent demand to fulfill the goals set out for biomarker discovery in cancer liquid biopsies.Notably, conventional and innovative technologies are being rapidly developed for proteomic analysis in cancer liquid biopsies. These advances have greatly facilitated early detection, diagnosis, prognosis, and monitoring of cancer evolution, adapted or adopted in response to therapeutic interventions. In this paper, we review the high-plex proteomics technologies that are capable of measuring at least hundreds of proteins simultaneously from liquid biopsy samples, ranging from traditional technologies based on mass spectrometry (MS) and antibody/antigen arrays to innovative technologies based on aptamer, proximity extension assay (PEA), and reverse phase protein arrays (RPPA).
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23
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Characterizing cell interactions at scale with made-to-order droplet ensembles (MODEs). Proc Natl Acad Sci U S A 2022; 119:2110867119. [PMID: 35074872 PMCID: PMC8812558 DOI: 10.1073/pnas.2110867119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 01/22/2023] Open
Abstract
The study of specific cell–cell interactions at scale would be a significant advancement in single-cell biology with clear utility in immuno-oncology. Our development of Droplet Assembly provides a tool for such studies by extending the benefits of single-cell droplet microfluidics to high-order cell analyses. This technology allows for the construction, sorting, and downstream processing of cell–cell interactions and is compatible with single-cell genomic readouts. Cell–cell interactions are important to numerous biological systems, including tissue microenvironments, the immune system, and cancer. However, current methods for studying cell combinations and interactions are limited in scalability, allowing just hundreds to thousands of multicell assays per experiment; this limited throughput makes it difficult to characterize interactions at biologically relevant scales. Here, we describe a paradigm in cell interaction profiling that allows accurate grouping of cells and characterization of their interactions for tens to hundreds of thousands of combinations. Our approach leverages high-throughput droplet microfluidics to construct multicellular combinations in a deterministic process that allows inclusion of programmed reagent mixtures and beads. The combination droplets are compatible with common manipulation and measurement techniques, including imaging, barcode-based genomics, and sorting. We demonstrate the approach by using it to enrich for chimeric antigen receptor (CAR)-T cells that activate upon incubation with target cells, a bottleneck in the therapeutic T cell engineering pipeline. The speed and control of our approach should enable valuable cell interaction studies.
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Khajvand T, Huang P, Li L, Zhang M, Zhu F, Xu X, Huang M, Yang C, Lu Y, Zhu Z. Interfacing droplet microfluidics with antibody barcodes for multiplexed single-cell protein secretion profiling. LAB ON A CHIP 2021; 21:4823-4830. [PMID: 34792068 DOI: 10.1039/d1lc00567g] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Multiplexed protein secretion analysis of single cells is important to understand the heterogeneity of cellular functions and processes in healthy and disease states. However, current single-cell platforms, such as microwell-, microchamber-, or droplet-based assays, suffer from low single-cell occupancy, waste of reagents, limited sensitivity, or inability to perform necessary operations, etc. To overcome these drawbacks, we present an integrated droplet microfluidic device that interfaces with spatially patterned antibody barcodes for multiplexed single-cell secretome analysis. The trapping array of 100 picoliter-sized isolation chambers could achieve >80% single-cell capture efficiency with >90% viability. The single-cell analysis microchip was validated by the detection of four-plexed cytokines, including IL-8, MCP-1, MIP-1b, and TNF-a/IL-10, from unstimulated and lipopolysaccharide (LPS)-stimulated individual human macrophages. We also successfully applied the platform to profile protein secretions of human tumor cell lines and primary/metastatic cancer cells dissociated from cancer patients to observe the secretion heterogeneity among cells. This unique microfluidic platform enables multiplexed secretion assays for static droplet microfluidics, provides a reliable and straightforward workflow for protein secretion assays based on a low number of single cells in a short incubation time (∼4 h), and could have widespread applications for studying secretion-mediated cellular heterogeneity.
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Affiliation(s)
- Tahereh Khajvand
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Peifeng Huang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Linmei Li
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.
| | - Mingxia Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Fengjiao Zhu
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.
| | - Xing Xu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Mengjiao Huang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
- Institute of Molecular Medicine, Department of Obstetrics and Gynecology, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yao Lu
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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25
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Shao X, Wang C, Wang C, Han L, Han Y, Nižetić D, Zhang Y, Han L. Mechanical Stress Induces a Transient Suppression of Cytokine Secretion in Astrocytes Assessed at the Single-Cell Level with a High-Throughput Microfluidic Chip. Adv Healthc Mater 2021; 10:e2100698. [PMID: 34549544 DOI: 10.1002/adhm.202100698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/27/2021] [Indexed: 11/11/2022]
Abstract
Brain cells are constantly subjected to mechanical signals. Astrocytes are the most abundant glial cells of the central nervous system (CNS), which display immunoreactivity and have been suggested as an emerging disease focus in the recent years. However, how mechanical signals regulate astrocyte immunoreactivity, and the cytokine release in particular, remains to be fully characterized. Here, human neural stem cells are used to induce astrocytes, from which the release of 15 types of cytokines are screened, and nine of them are detected using a protein microfluidic chip. When a gentle compressive force is applied, altered cell morphology and reinforced cytoskeleton are observed. The force induces a transient suppression of cytokine secretions including IL-6, MCP-1, and IL-8 in the early astrocytes. Further, using a multiplexed single-cell culture and protein detection microfluidic chip, the mechanical effects at a single-cell level are analyzed, which validates a concerted downregulation by force on IL-6 and MCP-1 secretions in the cells releasing both factors. This work demonstrates an original attempt of employing the protein detection microfluidic chips in the assessment of mechanical regulation on the brain cells at a single-cell resolution, offering novel approach and unique insights for the understanding of the CNS immune regulation.
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Affiliation(s)
- Xiaowei Shao
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
- Suzhou Research Institute Shandong University Suzhou 215123 China
- Lee Kong Chian School of Medicine Nanyang Technological University Singapore 308232
| | - Chunhua Wang
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Chao Wang
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Lei Han
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Yunrui Han
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Dean Nižetić
- Lee Kong Chian School of Medicine Nanyang Technological University Singapore 308232
- The Blizard Institute Barts and The London School of Medicine Queen Mary University of London London E1 2AT UK
| | - Yu Zhang
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Lin Han
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
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26
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Abstract
Measurement of biological systems containing biomolecules and bioparticles is a key task in the fields of analytical chemistry, biology, and medicine. Driven by the complex nature of biological systems and unprecedented amounts of measurement data, artificial intelligence (AI) in measurement science has rapidly advanced from the use of silicon-based machine learning (ML) for data mining to the development of molecular computing with improved sensitivity and accuracy. This review presents an overview of fundamental ML methodologies and discusses their applications in disease diagnostics, biomarker discovery, and imaging analysis. We next provide the working principles of molecular computing using logic gates and arithmetical devices, which can be employed for in situ detection, computation, and signal transduction for biological systems. This review concludes by summarizing the strengths and limitations of AI-involved biological measurement in fundamental and applied research.
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Affiliation(s)
- Chao Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
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27
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Ras-Carmona A, Gomez-Perosanz M, Reche PA. Prediction of unconventional protein secretion by exosomes. BMC Bioinformatics 2021; 22:333. [PMID: 34134630 PMCID: PMC8210391 DOI: 10.1186/s12859-021-04219-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/21/2021] [Indexed: 01/08/2023] Open
Abstract
MOTIVATION In eukaryotes, proteins targeted for secretion contain a signal peptide, which allows them to proceed through the conventional ER/Golgi-dependent pathway. However, an important number of proteins lacking a signal peptide can be secreted through unconventional routes, including that mediated by exosomes. Currently, no method is available to predict protein secretion via exosomes. RESULTS Here, we first assembled a dataset including the sequences of 2992 proteins secreted by exosomes and 2961 proteins that are not secreted by exosomes. Subsequently, we trained different random forests models on feature vectors derived from the sequences in this dataset. In tenfold cross-validation, the best model was trained on dipeptide composition, reaching an accuracy of 69.88% ± 2.08 and an area under the curve (AUC) of 0.76 ± 0.03. In an independent dataset, this model reached an accuracy of 75.73% and an AUC of 0.840. After these results, we developed ExoPred, a web-based tool that uses random forests to predict protein secretion by exosomes. CONCLUSION ExoPred is available for free public use at http://imath.med.ucm.es/exopred/ . Datasets are available at http://imath.med.ucm.es/exopred/datasets/ .
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Affiliation(s)
- Alvaro Ras-Carmona
- Laboratory of Immunomedicine, Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Pza Ramón y Cajal, s/n, 28040 Madrid, Spain
| | - Marta Gomez-Perosanz
- Laboratory of Immunomedicine, Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Pza Ramón y Cajal, s/n, 28040 Madrid, Spain
| | - Pedro A. Reche
- Laboratory of Immunomedicine, Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Pza Ramón y Cajal, s/n, 28040 Madrid, Spain
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28
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Choi JR, Lee JH, Xu A, Matthews K, Xie S, Duffy SP, Ma H. Monolithic hydrogel nanowells-in-microwells enabling simultaneous single cell secretion and phenotype analysis. LAB ON A CHIP 2020; 20:4539-4551. [PMID: 33201962 DOI: 10.1039/d0lc00965b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cytokine secretion is a form of cellular communication that regulates a wide range of biological processes. A common approach for measuring cytokine secretion from single cells is to confine individual cells in arrays of nanoliter wells (nanowells) fabricated using polydimethylsiloxane. However, this approach cannot be easily integrated in standard microwell plates in order to take advantage of high-throughput infrastructure for automated and multiplexed analysis. Here, we used laser micropatterning to fabricate monolithic hydrogel nanowells inside wells in a microwell plate (microwells) using polyethylene glycol diacrylate (PEGDA). This approach produces high-aspect ratio nanowells that retain cells and beads during reagent exchange, enabling simultaneous profiling of single cell secretion and phenotyping via immunostaining. To limit contamination between nanowells, we used methylcellulose as a media additive to reduce diffusion distance. Patterning nanowells monolithically in microwells also dramatically increases density, providing ∼1200 nanowells per microwell in a microwell plate. Using this approach, we profiled IL-8 secretion from single MDA-MB-231 cells, which showed significant heterogeneity. We further profiled the polarization of THP-1 cells into M1 and M2 macrophages, along with their associated IL-1β and CCL-22 secretion profiles. These results demonstrate the potential to use this approach for high-throughput secretion and phenotype analysis on single cells.
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Affiliation(s)
- Jane Ru Choi
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada
| | - Jeong Hyun Lee
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada
| | - Alec Xu
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada
| | - Kerryn Matthews
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada
| | - Shuyong Xie
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada
| | - Simon P Duffy
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada and British Columbia Institute of Technology, Canada
| | - Hongshen Ma
- Department of Mechanical Engineering, University of British Columbia, Canada. and Centre for Blood Research, University of British Columbia, Canada and School of Biomedical Engineering, University of British Columbia, Canada and Vancouver Prostate Centre, Vancouver General Hospital, Canada
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29
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Belanger MC, Anbaei P, Dunn AF, Kinman AW, Pompano RR. Spatially Resolved Analytical Chemistry in Intact, Living Tissues. Anal Chem 2020; 92:15255-15262. [PMID: 33201681 PMCID: PMC7864589 DOI: 10.1021/acs.analchem.0c03625] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tissues are an exciting frontier for bioanalytical chemistry, one in which spatial distribution is just as important as total content. Intact tissue preserves the native cellular and molecular organization and the cell-cell contacts found in vivo. Live tissue, in particular, offers the potential to analyze dynamic events in a spatially resolved manner, leading to fundamental biological insights and translational discoveries. In this Perspective, we provide a tutorial on the four fundamental challenges for the bioanalytical chemist working in living tissue samples as well as best practices for mitigating them. The challenges include (i) the complexity of the sample matrix, which contributes myriad interfering species and causes nonspecific binding of reagents; (ii) hindered delivery and mixing; (iii) the need to maintain physiological conditions; and (iv) tissue reactivity. This framework is relevant to a variety of methods for spatially resolved chemical analysis, including optical imaging, inserted sensors and probes such as electrodes, and surface analyses such as sensing arrays. The discussion focuses primarily on ex vivo tissues, though many considerations are relevant in vivo as well. Our goal is to convey the exciting potential of analytical chemistry to contribute to understanding the functions of live, intact tissues.
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Affiliation(s)
- Maura C. Belanger
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Parastoo Anbaei
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Austin F. Dunn
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Andrew W.L. Kinman
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Rebecca R. Pompano
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
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30
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Abstract
The immune system is composed of heterogeneous populations of immune cells that regulate physiological processes and protect organisms against diseases. Single cell technologies have been used to assess immune cell responses at the single cell level, which are crucial for identifying the causes of diseases and elucidating underlying biological mechanisms to facilitate medical therapy. In the present review we first discuss the most recent advances in the development of single cell technologies to investigate cell signaling, cell-cell interactions and cell migration. Each technology's advantages and limitations and its applications in immunology are subsequently reviewed. The latest progress toward commercialization, the remaining challenges and future perspectives for single cell technologies in immunology are also briefly discussed.
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Affiliation(s)
- Jane Ru Choi
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.,Department of Mechanical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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31
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Yang L, George J, Wang J. Deep Profiling of Cellular Heterogeneity by Emerging Single-Cell Proteomic Technologies. Proteomics 2020; 20:e1900226. [PMID: 31729152 PMCID: PMC7225074 DOI: 10.1002/pmic.201900226] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/14/2019] [Indexed: 12/20/2022]
Abstract
The ability to comprehensively profile cellular heterogeneity in functional proteome is crucial in advancing the understanding of cell behavior, organism development, and disease mechanisms. Conventional bulk measurement by averaging the biological responses across a population often loses the information of cellular variations. Single-cell proteomic technologies are becoming increasingly important to understand and discern cellular heterogeneity. The well-established methods for single-cell protein analysis based on flow cytometry and fluorescence microscopy are limited by the low multiplexing ability owing to the spectra overlap of fluorophores for labeling antibodies. Recent advances in mass spectrometry (MS), microchip, and reiterative staining-based techniques for single-cell proteomics have enabled the evaluation of cellular heterogeneity with high throughput, increased multiplexity, and improved sensitivity. In this review, the principles, developments, advantages, and limitations of these advanced technologies in analysis of single-cell proteins, along with their biological applications to study cellular heterogeneity, are described. At last, the remaining challenges, possible strategies, and future opportunities that will facilitate the improvement and broad applications of single-cell proteomic technologies in cell biology and medical research are discussed.
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Affiliation(s)
- Liwei Yang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
| | - Justin George
- Department of Chemistry, State University of New York, University at Albany, Albany, NY 12222
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
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32
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Liu L, Chen D, Wang J, Chen J. Advances of Single-Cell Protein Analysis. Cells 2020; 9:E1271. [PMID: 32443882 PMCID: PMC7290353 DOI: 10.3390/cells9051271] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
Proteins play a significant role in the key activities of cells. Single-cell protein analysis provides crucial insights in studying cellular heterogeneities. However, the low abundance and enormous complexity of the proteome posit challenges in analyzing protein expressions at the single-cell level. This review summarizes recent advances of various approaches to single-cell protein analysis. We begin by discussing conventional characterization approaches, including fluorescence flow cytometry, mass cytometry, enzyme-linked immunospot assay, and capillary electrophoresis. We then detail the landmark advances of microfluidic approaches for analyzing single-cell protein expressions, including microfluidic fluorescent flow cytometry, droplet-based microfluidics, microwell-based assay (microengraving), microchamber-based assay (barcoding microchips), and single-cell Western blotting, among which the advantages and limitations are compared. Looking forward, we discuss future research opportunities and challenges for multiplexity, analyte, throughput, and sensitivity of the microfluidic approaches, which we believe will prompt the research of single-cell proteins such as the molecular mechanism of cell biology, as well as the clinical applications for tumor treatment and drug development.
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Affiliation(s)
- Lixing Liu
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deyong Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junbo Wang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
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33
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Chen P, Chen D, Li S, Ou X, Liu BF. Microfluidics towards single cell resolution protein analysis. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.06.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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