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Lohrer MF, Liu Y, Hanna DM, Wang KH, Liu FT, Laurence TA, Liu GY. Determination of the Maturation Status of Dendritic Cells by Applying Pattern Recognition to High-Resolution Images. J Phys Chem B 2020; 124:8540-8548. [DOI: 10.1021/acs.jpcb.0c06437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Michael F. Lohrer
- Department of Electrical and Computer Engineering, Oakland University, Rochester, Michigan 48309, United States
| | - Yang Liu
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Darrin M. Hanna
- Department of Electrical and Computer Engineering, Oakland University, Rochester, Michigan 48309, United States
| | - Kang-Hsin Wang
- Department of Chemistry, University of California, Davis, California 95616, United States
- Department of Dermatology, University of California, Davis Medical Center, Sacramento, California 95817, United States
| | - Fu-Tong Liu
- Department of Dermatology, University of California, Davis Medical Center, Sacramento, California 95817, United States
| | - Ted A. Laurence
- Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Gang-yu Liu
- Department of Chemistry, University of California, Davis, California 95616, United States
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Liu L, Yang J, Men K, He Z, Luo M, Qian Z, Wei X, Wei Y. Current Status of Nonviral Vectors for Gene Therapy in China. Hum Gene Ther 2018; 29:110-120. [PMID: 29320893 DOI: 10.1089/hum.2017.226] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Li Liu
- Laboratory for Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Jingyun Yang
- Laboratory for Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Ke Men
- Laboratory for Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Zhiyao He
- Laboratory for Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Min Luo
- Laboratory for Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Zhiyong Qian
- Laboratory for Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Xiawei Wei
- Laboratory for Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Yuquan Wei
- Laboratory for Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
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Lohrer MF, Hanna DM, Liu Y, Wang KH, Liu FT, Laurence TA, Liu GY. Applying Pattern Recognition to High-Resolution Images to Determine Cellular Signaling Status. IEEE Trans Nanobioscience 2017; 16:438-446. [PMID: 28644811 PMCID: PMC5633003 DOI: 10.1109/tnb.2017.2717871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Two frequently used tools to acquire high- resolution images of cells are scanning electron microscopy (SEM) and atomic force microscopy (AFM). The former provides a nanometer resolution view of cellular features rapidly and with high throughput, while the latter enables visualizing hydrated and living cells. In current practice, these images are viewed by eye to determine cellular status, e.g., activated versus resting. Automatic and quantitative data analysis is lacking. This paper develops an algorithm of pattern recognition that works very effectively for AFM and SEM images. Using rat basophilic leukemia cells, our approach creates a support vector machine to automatically classify resting and activated cells. Ten-fold cross-validation with cells that are known to be activated or resting gives a good estimate of the generalized classification results. The pattern recognition of AFM images achieves 100% accuracy, while SEM reaches 95.4% for our images as well as images published in prior literature. This outcome suggests that our methodology could become an important and frequently used tool for researchers utilizing AFM and SEM for structural characterization as well as determining cellular signaling status and function.
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Affiliation(s)
- Michael F. Lohrer
- Department of Electrical and Computer Engineering, Oakland University, Rochester MI 48309, USA
| | - Darrin M. Hanna
- Department of Electrical and Computer Engineering, Oakland University, Rochester MI 48309, USA
| | - Yang Liu
- Department of chemistry, University of California, Davis, CA 95616 USA
| | - Kang-Hsin Wang
- Department of chemistry, University of California, Davis, CA 95616 USA
| | - Fu-Tong Liu
- Department of Dermatology, University of California, Davis Medical Center, Sacramento, CA 95817, USA
| | - Ted A. Laurence
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Gang-Yu Liu
- Department of chemistry, University of California, Davis, CA 95616 USA
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4
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Deciphering the interaction of bovine heart cystatin with ZnO nanoparticles: Spectroscopic and thermodynamic approach. Int J Biol Macromol 2017; 95:1056-1063. [DOI: 10.1016/j.ijbiomac.2016.10.095] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/18/2016] [Accepted: 10/24/2016] [Indexed: 12/21/2022]
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Karsai A, Slack TJ, Malekan H, Khoury F, Lin WF, Tran V, Cox D, Toney M, Chen X, Liu GY. Local Mechanical Perturbation Provides an Effective Means to Regulate the Growth and Assembly of Functional Peptide Fibrils. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:6407-6415. [PMID: 27689936 DOI: 10.1002/smll.201601657] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/30/2016] [Indexed: 06/06/2023]
Abstract
Mucin 1 (MUC1) peptide fused with Q11 (MUC1-Q11) having 35 residues has previously been shown to form amyloid fibrils. Using time-dependent and high-resolution atomic force microscopy (AFM) imaging, it is revealed that the formation of individual MUC1-Q11 fibrils entails nucleation and extension at both ends. This process can be altered by local mechanical perturbations using AFM probes. This work reports two specific perturbations and outcomes. First, by increasing load while maintaining tip-surface contact, the fibrils are cut during the scan due to shearing. Growth of fibrils occurs at the newly exposed termini, following similar mechanism of the MUC1-Q11 nucleation growth. As a result, branched fibrils are seen on the surface whose orientation and length can be controlled by the nuclei orientation and reaction time. In contrast to the "one-time-cut", fibrils can be continuously fragmented by modulation at sufficiently high amplitude. As a result, short and highly branched fibrils accumulate and pile on surfaces. Since the fibril formation and assembly of MUC1-Q11 can be impacted by local mechanical force, this approach offers a nonchemical and label-free means to control the presentation of MUC1 epitopes, and has promising application in MUC1 fibril-based immunotherapy.
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Affiliation(s)
- Arpad Karsai
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Teri Jo Slack
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Hamed Malekan
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Fadi Khoury
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Wei-Feng Lin
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Victoria Tran
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Daniel Cox
- Department of Physics, University of California, Davis, CA, 95616, USA
| | - Michael Toney
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Gang-Yu Liu
- Department of Chemistry, University of California, Davis, CA, 95616, USA
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Li JR, Ross SS, Liu Y, Liu YX, Wang KH, Chen HY, Liu FT, Laurence TA, Liu GY. Engineered Nanostructures of Haptens Lead to Unexpected Formation of Membrane Nanotubes Connecting Rat Basophilic Leukemia Cells. ACS NANO 2015; 9:6738-6746. [PMID: 26057701 PMCID: PMC4758354 DOI: 10.1021/acsnano.5b02270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A recent finding reports that co-stimulation of the high-affinity immunoglobulin E (IgE) receptor (FcεRI) and the chemokine receptor 1 (CCR1) triggered formation of membrane nanotubes among bone-marrow-derived mast cells. The co-stimulation was attained using corresponding ligands: IgE binding antigen and macrophage inflammatory protein 1α (MIP1 α), respectively. However, this approach failed to trigger formation of nanotubes among rat basophilic leukemia (RBL) cells due to the lack of CCR1 on the cell surface (Int. Immunol. 2010, 22 (2), 113-128). RBL cells are frequently used as a model for mast cells and are best known for antibody-mediated activation via FcεRI. This work reports the successful formation of membrane nanotubes among RBLs using only one stimulus, a hapten of 2,4-dinitrophenyl (DNP) molecules, which are presented as nanostructures with our designed spatial arrangements. This observation underlines the significance of the local presentation of ligands in the context of impacting the cellular signaling cascades. In the case of RBL, certain DNP nanostructures suppress antigen-induced degranulation and facilitate the rearrangement of the cytoskeleton to form nanotubes. These results demonstrate an important scientific concept; engineered nanostructures enable cellular signaling cascades, where current technologies encounter great difficulties. More importantly, nanotechnology offers a new platform to selectively activate and/or inhibit desired cellular signaling cascades.
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Affiliation(s)
- Jie-Ren Li
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Shailise S. Ross
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Yang Liu
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Ying X. Liu
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Kang-hsin Wang
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Huan-Yuan Chen
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, California 95817, United States
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Fu-Tong Liu
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, California 95817, United States
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Ted A. Laurence
- Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Gang-yu Liu
- Department of Chemistry, University of California, Davis, California 95616, United States
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Pi F, Dillard P, Limozin L, Charrier A, Sengupta K. Nanometric protein-patch arrays on glass and polydimethylsiloxane for cell adhesion studies. NANO LETTERS 2013; 13:3372-8. [PMID: 23808889 DOI: 10.1021/nl401696m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We present a simple cost-effective benchtop protocol to functionalize glass and polydimethylsiloxane (PDMS) with nanometric protein patches for cell adhesion studies. Evaporation masks, covering macroscopic areas on glass, were made using improved strategies for self-assembly of colloidal microbeads which then served as templates for creating the protein patch arrays via the intermediate steps of organo-aminosilane deposition and polyethylene-glycol grafting. The diameter of the patches could be varied down to about 80 nm. The glass substrates were used for advanced optical imaging of T-lymphocytes to explore adhesion by reflection interference contrast microscopy and the possible colocalization of T-cell receptor microclusters and the activating protein patches by total internal reflection fluorescence microscopy. The selectively functionalized glass could also serve as template for transferring the protein nanopatches to the surface of a soft elastomer. We demonstrated successful reverse contact printing onto the surface of thin layers of PDMS with stiffness ranging from 30 KPa to 3 MPa.
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Affiliation(s)
- Fuwei Pi
- Aix-Marseille Université , CNRS, CINaM UMR 7325, 13288 Marseille, France
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Delcassian D, Depoil D, Rudnicka D, Liu M, Davis DM, Dustin ML, Dunlop IE. Nanoscale ligand spacing influences receptor triggering in T cells and NK cells. NANO LETTERS 2013; 13:5608-14. [PMID: 24125583 PMCID: PMC4288448 DOI: 10.1021/nl403252x] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Bioactive nanoscale arrays were constructed to ligate activating cell surface receptors on T cells (the CD3 component of the TCR complex) and natural killer (NK) cells (CD16). These arrays are formed from biofunctionalized gold nanospheres with controlled interparticle spacing in the range 25-104 nm. Responses to these nanoarrays were assessed using the extent of membrane-localized phosphotyrosine in T cells stimulated with CD3-binding nanoarrays and the size of cell contact area for NK cells stimulated with CD16-binding nanoarrays. In both cases, the strength of response decreased with increasing spacing, falling to background levels by 69 nm in the T cell/anti-CD3 system and 104 nm for the NK cell/anti-CD16 system. These results demonstrate that immune receptor triggering can be influenced by the nanoscale spatial organization of receptor/ligand interactions.
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MESH Headings
- CD3 Complex/chemistry
- CD3 Complex/immunology
- Humans
- Killer Cells, Natural/chemistry
- Killer Cells, Natural/immunology
- Nanoparticles/chemistry
- Nanotechnology
- Receptor-CD3 Complex, Antigen, T-Cell/chemistry
- Receptor-CD3 Complex, Antigen, T-Cell/immunology
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/immunology
- Receptors, IgG/chemistry
- Receptors, IgG/immunology
- Receptors, Natural Killer Cell/chemistry
- Receptors, Natural Killer Cell/immunology
- T-Lymphocytes/chemistry
- T-Lymphocytes/immunology
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Affiliation(s)
- Derfogail Delcassian
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - David Depoil
- Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, New York, NY10016 USA
| | - Dominika Rudnicka
- Division of Cell and Molecular Biology, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Mengling Liu
- Department of Biostatistics, NYU School of Medicine, New York, New York, NY10016 USA
| | - Daniel M. Davis
- Division of Cell and Molecular Biology, Imperial College London, Exhibition Road, London SW7 2AZ, UK
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Grafton Street, Manchester M13 9NT, UK
| | - Michael L. Dustin
- Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, New York, NY10016 USA
- Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus, Oxford, OX3 7FY, UK
| | - Iain E. Dunlop
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, UK
- To whom correspondence should be addressed:
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Li JR, Shi L, Deng Z, Lo SH, Liu GY. Nanostructures of designed geometry and functionality enable regulation of cellular signaling processes. Biochemistry 2012; 51:5876-93. [PMID: 22783801 PMCID: PMC4041195 DOI: 10.1021/bi200880p] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Extracellular matrices (ECM) triggered cellular signaling processes often begin with the clustering of the cellular receptors such as integrin and FcεRI. The sizes of these initial protein complexes or clusters are tens to 100 nm in dimension; therefore, engineered nanostructures could provide effective mimics of ECM for investigation and control of the initial and downstream specific signaling processes. This current topic discusses recent advances in nanotechnology in the context of design and production of matching chemical functionality and geometry for control of specific cellular signaling processes. Two investigations are reported to demonstrate this concept: (a) how the presentation of antigen at the nanometer scale would influence the aggregation of FcεRI, which would impact the formation of activation complexes, leading to the rearrangement of actin in cytoskeleton and degranulation or activation of mast cells; (b) how the engineered nanostructure could guide the initial integrin clustering, which would impact the formation of focal adhesion and downstream cell signaling cascades, leading to polarization, migration, and morphological changes. Complementary to engineered ECMs using synthetic ligands or peptides, or topographic control at the micrometer scale, nanostructures of designed geometry and chemical functionality provide new and effective biochemical cues for regulation of cellular signaling processes and downstream behaviors.
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Affiliation(s)
- Jie-Ren Li
- Department of Chemistry, University of California, Davis, California 95616
| | - Lifang Shi
- Department of Chemistry, University of California, Davis, California 95616
| | - Zhao Deng
- Department of Chemistry, University of California, Davis, California 95616
| | - Su Hao Lo
- Department of Biochemistry and Molecular Medicine, Center for Tissue Regeneration and Repair, University of California-Davis, Medical Center, Sacramento, California 95817
| | - Gang-yu Liu
- Department of Chemistry, University of California, Davis, California 95616
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