1
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Berndt D, Glaap D, Jennings T, Dose C, Werz DB, Reckert DNH. Water-Soluble Fluorescent Polymer Dyes with Tunable Emission Spectra for Flow Cytometry Applications. Angew Chem Int Ed Engl 2024; 63:e202402616. [PMID: 38488317 DOI: 10.1002/anie.202402616] [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: 02/05/2024] [Indexed: 04/04/2024]
Abstract
The application of spectrally unique, bright, and water-soluble fluorescent dyes is indispensable for the analysis of biological systems. Multiparameter flow cytometry is a powerful tool for characterization of mixed cell populations. To discriminate the different cell populations, they are typically stained by a set of fluorescent reagents, e.g., antibody-fluorophore conjugates. The number of parameters which can be studied simultaneously strongly depends on the availability of reagents which can be differentiated by their spectral properties. In this study a series of fluorescent polymer dyes was developed, that can be excited with a single violet laser (405 nm) but distinguished by their unique emission spectra. The polyfluorene-based polymers can be used on their own, or in combination with covalently bound small-molecule dyes to generate energy transfer constructs to red-shift the emission wavelength based on Förster resonance energy transfer (FRET). The polymer dyes were utilized in a biological flow cytometry assay by conjugating several of them to antibodies, demonstrating their effectiveness as reagents. This report represents the first systematic investigation of structure-property relationships for this type of fluorescent dyes.
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Affiliation(s)
- Daniel Berndt
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
- DFG Cluster of Excellence livMatS @FIT and Albert-Ludwigs-Universität Freiburg, Institut für Organische Chemie, Albertstraße 21, 79104, Freiburg, Germany
| | - Dorina Glaap
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
| | - Travis Jennings
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
| | - Christian Dose
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
| | - Daniel B Werz
- DFG Cluster of Excellence livMatS @FIT and Albert-Ludwigs-Universität Freiburg, Institut für Organische Chemie, Albertstraße 21, 79104, Freiburg, Germany
| | - Dirk N H Reckert
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
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2
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Kare AJ, Nichols L, Zermeno R, Raie MN, Tumbale SK, Ferrara KW. OMIP-095: 40-Color spectral flow cytometry delineates all major leukocyte populations in murine lymphoid tissues. Cytometry A 2023; 103:839-850. [PMID: 37768325 PMCID: PMC10843696 DOI: 10.1002/cyto.a.24788] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/26/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023]
Abstract
High-dimensional immunoprofiling is essential for studying host response to immunotherapy, infection, and disease in murine model systems. However, the difficulty of multiparameter panel design combined with a lack of existing murine tools has prevented the comprehensive study of all major leukocyte phenotypes in a single assay. Herein, we present a 40-color flow cytometry panel for deep immunophenotyping of murine lymphoid tissues, including the spleen, blood, Peyer's patches, inguinal lymph nodes, bone marrow, and thymus. This panel uses a robust set of surface markers capable of differentiating leukocyte subsets without the use of intracellular staining, thus allowing for the use of cells in downstream functional experiments or multiomic analyses. Our panel classifies T cells, B cells, natural killer cells, innate lymphoid cells, monocytes, macrophages, dendritic cells, basophils, neutrophils, eosinophils, progenitors, and their functional subsets by using a series of co-stimulatory, checkpoint, activation, migration, and maturation markers. This tool has a multitude of systems immunology applications ranging from serial monitoring of circulating blood signatures to complex endpoint analysis, especially in pre-clinical settings where treatments can modulate leukocyte abundance and/or function. Ultimately, this 40-color panel resolves a diverse array of immune cells on the axes of time, tissue, and treatment, filling the niche for a modern tool dedicated to murine immunophenotyping.
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Affiliation(s)
- Aris J. Kare
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Lisa Nichols
- Stanford Shared FACS Facility, Stanford University, Stanford, CA 94305, USA
| | - Ricardo Zermeno
- Stanford Shared FACS Facility, Stanford University, Stanford, CA 94305, USA
| | - Marina N. Raie
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
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3
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Sadighi Akha AA, Csomós K, Ujházi B, Walter JE, Kumánovics A. Evolving Approach to Clinical Cytometry for Immunodeficiencies and Other Immune Disorders. Clin Lab Med 2023; 43:467-483. [PMID: 37481324 DOI: 10.1016/j.cll.2023.05.002] [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: 07/24/2023]
Abstract
Primary immunodeficiencies were initially identified on the basis of recurrent, severe or unusual infections. Subsequently, it was noted that these diseases can also manifest with autoimmunity, autoinflammation, allergy, lymphoproliferation and malignancy, hence a conceptual change and their renaming as inborn errors of immunity. Ongoing advances in flow cytometry provide the opportunity to expand or modify the utility and scope of existing laboratory tests in this field to mirror this conceptual change. Here we have used the B cell subset, variably known as CD21low B cells, age-associated B cells and T-bet+ B cells, as an example to demonstrate this possibility.
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Affiliation(s)
- Amir A Sadighi Akha
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Krisztián Csomós
- Division of Pediatric Allergy/Immunology, University of South Florida, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
| | - Boglárka Ujházi
- Division of Pediatric Allergy/Immunology, University of South Florida, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
| | - Jolán E Walter
- Division of Pediatric Allergy/Immunology, University of South Florida, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
| | - Attila Kumánovics
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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4
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Bruce-Tagoe TA, Danquah MK. Bioaffinity Nanoprobes for Foodborne Pathogen Sensing. MICROMACHINES 2023; 14:1122. [PMID: 37374709 DOI: 10.3390/mi14061122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Bioaffinity nanoprobes are a type of biosensor that utilize the specific binding properties of biological molecules, such as antibodies, enzymes, and nucleic acids, for the detection of foodborne pathogens. These probes serve as nanosensors and can provide highly specific and sensitive detection of pathogens in food samples, making them an attractive option for food safety testing. The advantages of bioaffinity nanoprobes include their ability to detect low levels of pathogens, rapid analysis time, and cost-effectiveness. However, limitations include the need for specialized equipment and the potential for cross-reactivity with other biological molecules. Current research efforts focus on optimizing the performance of bioaffinity probes and expanding their application in the food industry. This article discusses relevant analytical methods, such as surface plasmon resonance (SPR) analysis, Fluorescence Resonance Energy Transfer (FRET) measurements, circular dichroism, and flow cytometry, that are used to evaluate the efficacy of bioaffinity nanoprobes. Additionally, it discusses advances in the development and application of biosensors in monitoring foodborne pathogens.
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Affiliation(s)
- Tracy Ann Bruce-Tagoe
- Department of Chemical Engineering, University of Tennessee, Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
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5
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Catitti G, De Fabritiis S, Brocco D, Simeone P, De Bellis D, Vespa S, Veschi S, De Lellis L, Tinari N, Verginelli F, Marchisio M, Cama A, Patruno A, Lanuti P. Flow Cytometry Detection of Anthracycline-Treated Breast Cancer Cells: An Optimized Protocol. Curr Issues Mol Biol 2022; 45:164-174. [PMID: 36661499 PMCID: PMC9857732 DOI: 10.3390/cimb45010013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
The use of anthracycline derivatives was approved for the treatment of a broad spectrum of human tumors (i.e., breast cancer). The need to test these drugs on cancer models has pushed the basic research to apply many types of in vitro assays, and, among them, the study of anthracycline-induced apoptosis was mainly based on the application of flow cytometry protocols. However, the chemical structure of anthracycline derivatives gives them a strong autofluorescence effect that must be considered when flow cytometry is used. Unfortunately, the guidelines on the analysis of anthracycline effects through flow cytometry are lacking. Therefore, in this study, we optimized the flow cytometry detection of doxorubicin and epirubicin-treated breast cancer cells. Their autofluorescence was assessed both by using conventional and imaging flow cytometry; we found that all the channels excited by the 488 nm laser were affected. Anthracycline-induced apoptosis was then measured via flow cytometry using the optimized setting. Consequently, we established a set of recommendations that enable the development of optimized flow cytometry settings when the in vitro assays of anthracycline effects are analyzed, with the final aim to reveal a new perspective on the use of those in vitro tests for the further implementation of precision medicine strategies in cancer.
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Affiliation(s)
- Giulia Catitti
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Department of Neurology, Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Simone De Fabritiis
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Davide Brocco
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Pasquale Simeone
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Domenico De Bellis
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Simone Vespa
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Serena Veschi
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Laura De Lellis
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Nicola Tinari
- Department of Medical, Oral & Biotechnological Sciences, University “G. d’Annunzio” Chieti-Pescara, 66100 Chieti, Italy
| | - Fabio Verginelli
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Marco Marchisio
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Alessandro Cama
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Antonia Patruno
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Correspondence:
| | - Paola Lanuti
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
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6
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Nolan JP. The evolution of spectral flow cytometry. Cytometry A 2022; 101:812-817. [PMID: 35567367 DOI: 10.1002/cyto.a.24566] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 01/27/2023]
Abstract
This special issue of Cytometry marks the transition of spectral flow cytometry from an emerging technology into a transformative force that will shape the fields of cytometry and single-cell analysis for some time to come. Tracing its roots to the earliest years of flow cytometry, spectral flow cytometry has evolved from the domain of individual researchers pushing the limits of hardware, reagents, and software to the mainstream, where it is being harnessed and adapted to meet the analytical challenges presented by modern biomedical research. In particular, the current form of spectral flow technology has arisen to address the needs of multiparameter immunophenotyping of immune cells in basic and translational research, and much of the current instrumentation and software reflects the needs of those applications. Yet, the possibilities enabled by high-resolution analysis of the spectral properties of optical absorbance, scatter, and emission have only begun to be exploited. In this brief review, the author highlights the origins and early milestones of single-cell spectral analysis, assesses the current state of instrumentation and software, and speculates as to future directions of spectral flow cytometry technology and applications.
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Affiliation(s)
- John P Nolan
- Scintillon Institute, San Diego, California, USA
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7
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Burke PEP, Strange A, Monk E, Thompson B, Amato CM, Woods DM. PhenoComb: a discovery tool to assess complex phenotypes in high-dimensional single-cell datasets. BIOINFORMATICS ADVANCES 2022; 2:vbac052. [PMID: 36699375 PMCID: PMC9710698 DOI: 10.1093/bioadv/vbac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/28/2022] [Accepted: 07/28/2022] [Indexed: 02/01/2023]
Abstract
Motivation High-dimensional cytometry assays can simultaneously measure dozens of markers, enabling the investigation of complex phenotypes. However, as manual gating relies on previous biological knowledge, few marker combinations are often assessed. This results in complex phenotypes with the potential for biological relevance being overlooked. Here, we present PhenoComb, an R package that allows agnostic exploration of phenotypes by assessing all combinations of markers. PhenoComb uses signal intensity thresholds to assign markers to discrete states (e.g. negative, low, high) and then counts the number of cells per sample from all possible marker combinations in a memory-safe manner. Time and disk space are the only constraints on the number of markers evaluated. PhenoComb also provides several approaches to perform statistical comparisons, evaluate the relevance of phenotypes and assess the independence of identified phenotypes. PhenoComb allows users to guide analysis by adjusting several function arguments, such as identifying parent populations of interest, filtering of low-frequency populations and defining a maximum complexity of phenotypes to evaluate. We have designed PhenoComb to be compatible with a local computer or server-based use. Results In testing of PhenoComb's performance on synthetic datasets, computation on 16 markers was completed in the scale of minutes and up to 26 markers in hours. We applied PhenoComb to two publicly available datasets: an HIV flow cytometry dataset (12 markers and 421 samples) and the COVIDome CyTOF dataset (40 markers and 99 samples). In the HIV dataset, PhenoComb identified immune phenotypes associated with HIV seroconversion, including those highlighted in the original publication. In the COVID dataset, we identified several immune phenotypes with altered frequencies in infected individuals relative to healthy individuals. Collectively, PhenoComb represents a powerful discovery tool for agnostically assessing high-dimensional single-cell data. Availability and implementation The PhenoComb R package can be downloaded from https://github.com/SciOmicsLab/PhenoComb. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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8
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Chen Q, Wang X, Chen J, Xiang Y, Xiao M, Pei H, Li L. Multiple-Aptamer-Integrated DNA-Origami-Based Chemical Nose Sensors for Accurate Identification of Cancer Cells. Anal Chem 2022; 94:10192-10197. [PMID: 35786864 DOI: 10.1021/acs.analchem.2c01646] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Developing simple, rapid, and accurate methods for cancer cell identification could facilitate early cancer diagnosis and tumor metastasis research. Herein, we develop a novel chemical nose sensor that employs the collective recognition abilities of a set of multiple-aptamer-integrated DNA origami (MADO) probes for discriminative identification of cancer cells. By controlling the types and/or copies of aptamers assembled on the DNA origami nanostructure, we constructed five MADO probes with differential binding affinities (ranging from 3.08 to 78.92 nM) to five types of cells (HeLa, MDA-MB-468, MCF-7, HepG2, and MCF-10A). We demonstrate the utility of the MADO-based chemical nose sensor in the identification of blinded unknown cell samples with a 95% accuracy. This sensing platform holds great potential for applications in medical diagnostics.
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Affiliation(s)
- Qiaoji Chen
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
| | - Xiwei Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
| | - Jing Chen
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
| | - Ying Xiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
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9
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Rodriguez-Esteban R, Duarte J, Teixeira PC, Richard F, Koltsova S, So WV. Prediction of standard cell types and functional markers from textual descriptions of flow cytometry gating definitions using machine learning. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2022; 102:220-227. [PMID: 35253974 DOI: 10.1002/cyto.b.22065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND A key step in clinical flow cytometry data analysis is gating, which involves the identification of cell populations. The process of gating produces a set of reportable results, which are typically described by gating definitions. The non-standardized, non-interpreted nature of gating definitions represents a hurdle for data interpretation and data sharing across and within organizations. Interpreting and standardizing gating definitions for subsequent analysis of gating results requires a curation effort from experts. Machine learning approaches have the potential to help in this process by predicting expert annotations associated with gating definitions. METHODS We created a gold-standard dataset by manually annotating thousands of gating definitions with cell type and functional marker annotations. We used this dataset to train and test a machine learning pipeline able to predict standard cell types and functional marker genes associated with gating definitions. RESULTS The machine learning pipeline predicted annotations with high accuracy for both cell types and functional marker genes. Accuracy was lower for gating definitions from assays belonging to laboratories from which limited or no prior data was available in the training. Manual error review ensured that resulting predicted annotations could be reused subsequently as additional gold-standard training data. CONCLUSIONS Machine learning methods are able to consistently predict annotations associated with gating definitions from flow cytometry assays. However, a hybrid automatic and manual annotation workflow would be recommended to achieve optimal results.
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Affiliation(s)
- Raul Rodriguez-Esteban
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - José Duarte
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Priscila C Teixeira
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Fabien Richard
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Svetlana Koltsova
- Curation Department, Rancho BioSciences LLC, San Diego, California, USA
| | - W Venus So
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center New York, New York, USA
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10
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Xiao Z, Darwish GH, Susumu K, Medintz IL, Algar WR. Prototype Smartphone-Based Device for Flow Cytometry with Immunolabeling via Supra-nanoparticle Assemblies of Quantum Dots. ACS MEASUREMENT SCIENCE AU 2022; 2:57-66. [PMID: 36785592 PMCID: PMC9838726 DOI: 10.1021/acsmeasuresciau.1c00033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Methods for the detection, enumeration, and typing of cells are important in many areas of research and healthcare. In this context, flow cytometers are a widely used research and clinical tool but are also an example of a large and expensive instrument that is limited to specialized laboratories. Smartphones have been shown to have excellent potential to serve as portable and lower-cost platforms for analyses that would normally be done in a laboratory. Here, we developed a prototype smartphone-based flow cytometer (FC). This compact 3D-printed device incorporated a laser diode and a microfluidic flow cell and used the built-in camera of a smartphone to track immunofluorescently labeled cells in suspension and measure their color. This capability was enabled by high-brightness supra-nanoparticle assemblies of colloidal semiconductor quantum dots (SiO2@QDs) as well as a support vector machine (SVM) classification algorithm. The smartphone-based FC device detected and enumerated target cells against a background of other cells, simultaneously and selectively counted two different cell types in a mixture, and used multiple colors of SiO2@QD-antibody conjugates to screen for and identify a particular cell type. The potential limits of multicolor detection are discussed alongside ideas for further development. Our results suggest that innovations in materials and engineering should enable eventual smartphone-based FC assays for clinical applications.
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Affiliation(s)
- Zhujun Xiao
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ghinwa H. Darwish
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Kimihiro Susumu
- Jacobs
Corporation, Hanover, Maryland 21076, United
States
- Optical
Sciences Division, Code 5600, U.S. Naval
Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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11
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Algar WR, Massey M, Rees K, Higgins R, Krause KD, Darwish GH, Peveler WJ, Xiao Z, Tsai HY, Gupta R, Lix K, Tran MV, Kim H. Photoluminescent Nanoparticles for Chemical and Biological Analysis and Imaging. Chem Rev 2021; 121:9243-9358. [PMID: 34282906 DOI: 10.1021/acs.chemrev.0c01176] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Research related to the development and application of luminescent nanoparticles (LNPs) for chemical and biological analysis and imaging is flourishing. Novel materials and new applications continue to be reported after two decades of research. This review provides a comprehensive and heuristic overview of this field. It is targeted to both newcomers and experts who are interested in a critical assessment of LNP materials, their properties, strengths and weaknesses, and prospective applications. Numerous LNP materials are cataloged by fundamental descriptions of their chemical identities and physical morphology, quantitative photoluminescence (PL) properties, PL mechanisms, and surface chemistry. These materials include various semiconductor quantum dots, carbon nanotubes, graphene derivatives, carbon dots, nanodiamonds, luminescent metal nanoclusters, lanthanide-doped upconversion nanoparticles and downshifting nanoparticles, triplet-triplet annihilation nanoparticles, persistent-luminescence nanoparticles, conjugated polymer nanoparticles and semiconducting polymer dots, multi-nanoparticle assemblies, and doped and labeled nanoparticles, including but not limited to those based on polymers and silica. As an exercise in the critical assessment of LNP properties, these materials are ranked by several application-related functional criteria. Additional sections highlight recent examples of advances in chemical and biological analysis, point-of-care diagnostics, and cellular, tissue, and in vivo imaging and theranostics. These examples are drawn from the recent literature and organized by both LNP material and the particular properties that are leveraged to an advantage. Finally, a perspective on what comes next for the field is offered.
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Affiliation(s)
- W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Melissa Massey
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kelly Rees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Rehan Higgins
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Katherine D Krause
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Ghinwa H Darwish
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - William J Peveler
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Zhujun Xiao
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hsin-Yun Tsai
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Rupsa Gupta
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kelsi Lix
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Michael V Tran
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hyungki Kim
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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12
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Cappellano G, Raineri D, Rolla R, Giordano M, Puricelli C, Vilardo B, Manfredi M, Cantaluppi V, Sainaghi PP, Castello L, De Vita N, Scotti L, Vaschetto R, Dianzani U, Chiocchetti A. Circulating Platelet-Derived Extracellular Vesicles Are a Hallmark of Sars-Cov-2 Infection. Cells 2021; 10:cells10010085. [PMID: 33430260 PMCID: PMC7825711 DOI: 10.3390/cells10010085] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/29/2020] [Accepted: 01/03/2021] [Indexed: 12/26/2022] Open
Abstract
Sars-Cov-2 infection causes fever and cough that may rapidly lead to acute respiratory distress syndrome (ARDS). Few biomarkers have been identified but, unfortunately, these are individually poorly specific, and novel biomarkers are needed to better predict patient outcome. The aim of this study was to evaluate the diagnostic performance of circulating platelets (PLT)-derived extracellular vesicles (EVs) as biomarkers for Sars-Cov-2 infection, by setting a rapid and reliable test on unmanipulated blood samples. PLT-EVs were quantified by flow cytometry on two independent cohorts of Sars-CoV-2+ (n = 69), Sars-Cov-2- (n = 62) hospitalized patients, and healthy controls. Diagnostic performance of PLT-EVs was evaluated by receiver operating characteristic (ROC) curve. PLT-EVs count were higher in Sars-Cov-2+ compared to Sars-Cov-2- patients or HC. ROC analysis of the combined cohorts showed an AUC = 0.79 and an optimal cut-off value of 1472 EVs/μL, with 75% sensitivity and 74% specificity. These data suggest that PLT-EVs might be an interesting biomarker deserving further investigations to test their predictive power.
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Affiliation(s)
- Giuseppe Cappellano
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases—IRCAD, Università del Piemonte Orientale, 28100 Novara, Italy; (G.C.); (D.R.); (R.R.); (M.G.); (B.V.); (U.D.); (A.C.)
- Center for Translational Research on Autoimmune and Allergic Disease—CAAD, Università del Piemonte Orientale, 28100 Novara, Italy; (M.M.); (V.C.); (P.P.S.)
| | - Davide Raineri
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases—IRCAD, Università del Piemonte Orientale, 28100 Novara, Italy; (G.C.); (D.R.); (R.R.); (M.G.); (B.V.); (U.D.); (A.C.)
- Center for Translational Research on Autoimmune and Allergic Disease—CAAD, Università del Piemonte Orientale, 28100 Novara, Italy; (M.M.); (V.C.); (P.P.S.)
| | - Roberta Rolla
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases—IRCAD, Università del Piemonte Orientale, 28100 Novara, Italy; (G.C.); (D.R.); (R.R.); (M.G.); (B.V.); (U.D.); (A.C.)
- Clinical Chemistry Unit, “Maggiore della Carità” University Hospital, 28100 Novara, Italy;
| | - Mara Giordano
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases—IRCAD, Università del Piemonte Orientale, 28100 Novara, Italy; (G.C.); (D.R.); (R.R.); (M.G.); (B.V.); (U.D.); (A.C.)
- Clinical Chemistry Unit, “Maggiore della Carità” University Hospital, 28100 Novara, Italy;
| | - Chiara Puricelli
- Clinical Chemistry Unit, “Maggiore della Carità” University Hospital, 28100 Novara, Italy;
| | - Beatrice Vilardo
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases—IRCAD, Università del Piemonte Orientale, 28100 Novara, Italy; (G.C.); (D.R.); (R.R.); (M.G.); (B.V.); (U.D.); (A.C.)
- Center for Translational Research on Autoimmune and Allergic Disease—CAAD, Università del Piemonte Orientale, 28100 Novara, Italy; (M.M.); (V.C.); (P.P.S.)
| | - Marcello Manfredi
- Center for Translational Research on Autoimmune and Allergic Disease—CAAD, Università del Piemonte Orientale, 28100 Novara, Italy; (M.M.); (V.C.); (P.P.S.)
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (L.C.); (N.D.V.); (L.S.)
| | - Vincenzo Cantaluppi
- Center for Translational Research on Autoimmune and Allergic Disease—CAAD, Università del Piemonte Orientale, 28100 Novara, Italy; (M.M.); (V.C.); (P.P.S.)
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (L.C.); (N.D.V.); (L.S.)
- Nephrology and Kidney Transplantation Unit, “Maggiore della Carità” University Hospital, 28100 Novara, Italy
| | - Pier Paolo Sainaghi
- Center for Translational Research on Autoimmune and Allergic Disease—CAAD, Università del Piemonte Orientale, 28100 Novara, Italy; (M.M.); (V.C.); (P.P.S.)
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (L.C.); (N.D.V.); (L.S.)
- Immunorheumatology Unit, Division of Internal Medicine, “Maggiore della Carità” Univerisity Hospital, 28100 Novara, Italy
| | - Luigi Castello
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (L.C.); (N.D.V.); (L.S.)
- Emergency Department, “Maggiore della Carità” University Hospital, 28100 Novara, Italy
| | - Nello De Vita
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (L.C.); (N.D.V.); (L.S.)
| | - Lorenza Scotti
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (L.C.); (N.D.V.); (L.S.)
| | - Rosanna Vaschetto
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy; (L.C.); (N.D.V.); (L.S.)
- Correspondence: ; Tel.: +39-032-1373-3406
| | - Umberto Dianzani
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases—IRCAD, Università del Piemonte Orientale, 28100 Novara, Italy; (G.C.); (D.R.); (R.R.); (M.G.); (B.V.); (U.D.); (A.C.)
- Clinical Chemistry Unit, “Maggiore della Carità” University Hospital, 28100 Novara, Italy;
| | - Annalisa Chiocchetti
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases—IRCAD, Università del Piemonte Orientale, 28100 Novara, Italy; (G.C.); (D.R.); (R.R.); (M.G.); (B.V.); (U.D.); (A.C.)
- Center for Translational Research on Autoimmune and Allergic Disease—CAAD, Università del Piemonte Orientale, 28100 Novara, Italy; (M.M.); (V.C.); (P.P.S.)
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Marchisio M, Simeone P, Bologna G, Ercolino E, Pierdomenico L, Pieragostino D, Ventrella A, Antonini F, Del Zotto G, Vergara D, Celia C, Di Marzio L, Del Boccio P, Fontana A, Bosco D, Miscia S, Lanuti P. Flow Cytometry Analysis of Circulating Extracellular Vesicle Subtypes from Fresh Peripheral Blood Samples. Int J Mol Sci 2020; 22:ijms22010048. [PMID: 33374539 PMCID: PMC7793062 DOI: 10.3390/ijms22010048] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 01/04/2023] Open
Abstract
Extracellular vesicles (EVs) are released by shedding during different physiological processes and are increasingly thought to be new potential biomarkers. However, the impact of pre-analytical processing phases on the final measurement is not predictable and for this reason, the translation of basic research into clinical practice has been precluded. Here we have optimized a simple procedure in combination with polychromatic flow cytometry (PFC), to identify, classify, enumerate, and separate circulating EVs from different cell origins. This protocol takes advantage of a lipophilic cationic dye (LCD) able to probe EVs. Moreover, the application of the newly optimized PFC protocol here described allowed the obtainment of repeatable EVs counts. The translation of this PFC protocol to fluorescence-activated cell sorting allowed us to separate EVs from fresh peripheral blood samples. Sorted EVs preparations resulted particularly suitable for proteomic analyses, which we applied to study their protein cargo. Here we show that LCD staining allowed PFC detection and sorting of EVs from fresh body fluids, avoiding pre-analytical steps of enrichment that could impact final results. Therefore, LCD staining is an essential step towards the assessment of EVs clinical significance.
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Affiliation(s)
- Marco Marchisio
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
| | - Pasquale Simeone
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
| | - Giuseppina Bologna
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
| | - Eva Ercolino
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
| | - Laura Pierdomenico
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
| | - Damiana Pieragostino
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
- Department of Innovative Technologies in Medicine & Dentistry, University G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy
| | - Alessia Ventrella
- Department of Pharmacy, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (A.V.); (C.C.); (L.D.M.); (A.F.)
| | - Francesca Antonini
- Department of Research and Diagnostics, IRCCS Giannina Gaslini, 16147 Genova, Italy; (F.A.); (G.D.Z.)
| | - Genny Del Zotto
- Department of Research and Diagnostics, IRCCS Giannina Gaslini, 16147 Genova, Italy; (F.A.); (G.D.Z.)
| | - Daniele Vergara
- Laboratory of Clinical Proteomics, “Giovanni Paolo II” Hospital, 73100 ASL-Lecce, Italy;
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Christian Celia
- Department of Pharmacy, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (A.V.); (C.C.); (L.D.M.); (A.F.)
| | - Luisa Di Marzio
- Department of Pharmacy, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (A.V.); (C.C.); (L.D.M.); (A.F.)
| | - Piero Del Boccio
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
- Department of Pharmacy, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (A.V.); (C.C.); (L.D.M.); (A.F.)
| | - Antonella Fontana
- Department of Pharmacy, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (A.V.); (C.C.); (L.D.M.); (A.F.)
| | - Domenico Bosco
- Department of Biomorphological Science, Molecular Genetic Institute, Italian National Research Council, 66100 Chieti, Italy;
| | - Sebastiano Miscia
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
- Correspondence: ; Tel.: +39-0871541391
| | - Paola Lanuti
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
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14
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Bares AJ, Mejooli MA, Pender MA, Leddon SA, Tilley S, Lin K, Dong J, Kim M, Fowell DJ, Nishimura N, Schaffer CB. Hyperspectral multiphoton microscopy for in vivo visualization of multiple, spectrally overlapped fluorescent labels. OPTICA 2020; 7:1587-1601. [PMID: 33928182 PMCID: PMC8081374 DOI: 10.1364/optica.389982] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 09/30/2020] [Indexed: 05/17/2023]
Abstract
The insensitivity of multiphoton microscopy to optical scattering enables high-resolution, high-contrast imaging deep into tissue, including in live animals. Scattering does, however, severely limit the use of spectral dispersion techniques to improve spectral resolution. In practice, this limited spectral resolution together with the need for multiple excitation wavelengths to excite different fluorophores limits multiphoton microscopy to imaging a few, spectrally-distinct fluorescent labels at a time, restricting the complexity of biological processes that can be studied. Here, we demonstrate a hyperspectral multiphoton microscope that utilizes three different wavelength excitation sources together with multiplexed fluorescence emission detection using angle-tuned bandpass filters. This microscope maintains scattering insensitivity, while providing high enough spectral resolution on the emitted fluorescence and capitalizing on the wavelength-dependent nonlinear excitation of fluorescent dyes to enable clean separation of multiple, spectrally overlapping labels, in vivo. We demonstrated the utility of this instrument for spectral separation of closely-overlapped fluorophores in samples containing ten different colors of fluorescent beads, live cells expressing up to seven different fluorescent protein fusion constructs, and in multiple in vivo preparations in mouse cortex and inflamed skin with up to eight different cell types or tissue structures distinguished.
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Affiliation(s)
- Amanda J. Bares
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Menansili A. Mejooli
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Mitchell A. Pender
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Scott A. Leddon
- Center for Vaccine Biology and Immunology, Dept. of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Steven Tilley
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Karen Lin
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Jingyuan Dong
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Minsoo Kim
- Center for Vaccine Biology and Immunology, Dept. of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Deborah J. Fowell
- Center for Vaccine Biology and Immunology, Dept. of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Nozomi Nishimura
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Chris B. Schaffer
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
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15
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Gao Q, Zhao Y, Xu K, Zhang C, Ma Q, Qi L, Chao D, Zheng T, Yang L, Miao Y, Han D. Highly Specific, Single-step Cancer Cell Isolation with Multi-Aptamer-Mediated Proximity Ligation on Live Cell Membranes. Angew Chem Int Ed Engl 2020; 59:23564-23568. [PMID: 32896066 DOI: 10.1002/anie.202011198] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Indexed: 12/24/2022]
Abstract
A single-step method for isolation of specific cells based on multiple surface markers will have unique advantages because of its scalability, efficacy, and mildness. Herein, we developed multi-aptamer-mediated proximity ligation method on live cell membranes that leverages a multi-receptor co-recognition design for enhanced specificity, as well as a robust in situ signal amplification design for improved sensitivity of cell isolation. We demonstrated the promising efficacy of our method on differentiating tumor cell subtypes in both cell mixtures and clinical samples. Owing to its simple and fast operation with excellent cell isolation sensitivity and accuracy, this approach will have broad applications in biological science, biomedical engineering, and personalized medicine.
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Affiliation(s)
- Qianqian Gao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yumeng Zhao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Kangli Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Chao Zhang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Qian Ma
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Liqing Qi
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Dandan Chao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Tingting Zheng
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Linlin Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yanyan Miao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Da Han
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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16
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Gao Q, Zhao Y, Xu K, Zhang C, Ma Q, Qi L, Chao D, Zheng T, Yang L, Miao Y, Han D. Highly Specific, Single‐step Cancer Cell Isolation with Multi‐Aptamer‐Mediated Proximity Ligation on Live Cell Membranes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011198] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Qianqian Gao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yumeng Zhao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Kangli Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Chao Zhang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Qian Ma
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Liqing Qi
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Dandan Chao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Tingting Zheng
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Linlin Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yanyan Miao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Da Han
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
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17
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Ding M, Baker D. Recent advances in high-throughput flow cytometry for drug discovery. Expert Opin Drug Discov 2020; 16:303-317. [PMID: 33054417 DOI: 10.1080/17460441.2021.1826433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION High-throughput flow cytometry (HTFC) has proven to be an important technology in drug discovery. The use of HTFC enables multi-parametric screening of suspension cells containing heterogenous cell populations and coated particles for screening proteins of interest. Novel targets, novel cell markers and compound clusters for drug development have been identified from HTFC screens. AREAS COVERED In this article, the authors focus on reviewing the recent HTFC applications reported during the last 5-6 years, including drug discovery screens and studies for immune, immune-oncology, infectious and inflammatory diseases. The main HTFC approaches, development of HTFC systems, and automated sample preparation systems for HTFC are also discussed. EXPERT OPINION The advance of HTFC technology coupled with automated sample acquisition and sample preparation has demonstrated its utility in screening large numbers of compounds using suspension cells, facilitated screening of disease-relevant human primary cells, and enabled deep understanding of mechanism of action by analyzing multiple parameters. The authors see HTFC as a very valuable tool in immune, immune-oncology, infectious and inflammatory diseases where immune cells play essential roles.
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Affiliation(s)
- Mei Ding
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - David Baker
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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18
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Marmelstein AM, Lobba MJ, Mogilevsky CS, Maza JC, Brauer DD, Francis MB. Tyrosinase-Mediated Oxidative Coupling of Tyrosine Tags on Peptides and Proteins. J Am Chem Soc 2020; 142:5078-5086. [PMID: 32093466 DOI: 10.1021/jacs.9b12002] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Oxidative coupling (OC) through o-quinone intermediates has been established as an efficient and site-selective way to modify protein N-termini and the unnatural amino acid p-aminophenylalanine (paF). Recently, we reported that the tyrosinase-mediated oxidation of phenol-tagged cargo molecules is a particularly convenient method of generating o-quinones in situ. The coupling partners can be easily prepared and stored, the reaction takes place under mild conditions (phosphate buffer, pH 6.5, 4 to 23 °C), and dissolved oxygen is the only oxidant required. Here, we show an important extension of this chemistry for the activation of tyrosine residues that project into solution from the N or C-termini of peptide and protein substrates. Generating the o-quinone electrophiles from tyrosine allows greater flexibility in choosing the nucleophilic coupling partner and expands the scope of the reaction to include C-terminal positions. We also introduce a new bacterial tyrosinase enzyme that shows improved activation for some tyrosine substrates. The efficacy of several secondary amines and aniline derivatives was evaluated in the coupling reactions, providing important information for coupling partner design. This strategy was used to modify the C-termini of an antibody scFv construct and of Protein L, a human IgG kappa light chain binding protein. The use of the modified proteins as immunolabeling agents was also demonstrated.
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Affiliation(s)
- Alan M Marmelstein
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Marco J Lobba
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Casey S Mogilevsky
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Johnathan C Maza
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Daniel D Brauer
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Matthew B Francis
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
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19
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Matsumoto N, Taniguchi M, Lindsey JS. Bioconjugatable synthetic chlorins rendered water-soluble with three PEG-12 groups via click chemistry. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s1088424619501219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Chlorins provide many ideal features for use as red-region fluorophores but require molecular tailoring for solubilization in aqueous solution. A chlorin building-block bearing 18,18-dimethyl, 15-bromo and 10-[2,4,6-tris(propargyloxy)phenyl] substituents has been transformed via click chemistry with CH3(OCH2CH[Formula: see text]-N3 followed by Suzuki coupling with 3-(4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl)propanoic acid, thereby installing a water-solubilization motif and a bioconjugatable handle, respectively. In toluene, [Formula: see text]-dimethylformamide (DMF) or water, the resulting facially encumbered free base chlorin exhibits characteristic chlorin absorption ([Formula: see text] [Formula: see text]412, 643 nm) and fluorescence ([Formula: see text] [Formula: see text]645 nm) spectra with only modest variation in fluorescence quantum yield ([Formula: see text] values (0.24, 0.25 and 0.19, respectively). The zinc chlorin derived therefrom exhibits similar spectral constancy ([Formula: see text] [Formula: see text]414 and 613 nm, [Formula: see text] [Formula: see text]616 nm) and [Formula: see text] 0.094, 0.10 and 0.086 in the three solvents. The results together indicate the viability of the molecular design and synthetic methodology to create red-region fluorophores for use in diverse applications.
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Affiliation(s)
- Nobuyuki Matsumoto
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Masahiko Taniguchi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Jonathan S. Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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20
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Annunziata J, Miller ML, Park DC, Vlad G, Bhagat G, Alobeid B. Detection of Nonhematologic Neoplasms by Routine Flow Cytometry Analysis. Am J Clin Pathol 2020; 153:99-104. [PMID: 31587038 DOI: 10.1093/ajcp/aqz138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES We investigated the ability of routine flow cytometry (FC) to detect nonhematologic neoplasms (non-HN) using antibody panels routinely used for the diagnosis of hematologic neoplasms. METHODS FC analyses of 4,000 various diagnostic samples were retrospectively reviewed to identify cases in which an aberrant, viable CD45-negative, nonhematologic neoplastic population was detected by FC panels designed to evaluate hematologic neoplasms. RESULTS A total of 57 (1.4%) diverse non-HNs were identified, representing neuroendocrine tumors (33/57) and carcinomas (9/57), as well as other malignancies (15/57) such as sarcoma and melanoma. The majority of neoplasms were positive for at least one antibody, typically CD56 (43/51, 84.3%), followed by CD117 (15/34, 44.1%) and CD138 (6/33, 18.2%). CONCLUSIONS Our findings highlight the importance of carefully inspecting CD45-negative events to identify non-HNs by routine FC analysis. This can help expedite further downstream immunophenotypic analysis of specimens and triage samples for appropriate genetic and molecular studies.
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Affiliation(s)
- Joseph Annunziata
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- New York-Presbyterian Hospital/Columbia University Irving Medical Center, New York, NY
| | - Michael L Miller
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- New York-Presbyterian Hospital/Columbia University Irving Medical Center, New York, NY
| | - David C Park
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- New York-Presbyterian Hospital/Columbia University Irving Medical Center, New York, NY
| | - George Vlad
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- New York-Presbyterian Hospital/Columbia University Irving Medical Center, New York, NY
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- New York-Presbyterian Hospital/Columbia University Irving Medical Center, New York, NY
| | - Bachir Alobeid
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- New York-Presbyterian Hospital/Columbia University Irving Medical Center, New York, NY
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21
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Kalina T, Lundsten K, Engel P. Relevance of Antibody Validation for Flow Cytometry. Cytometry A 2019; 97:126-136. [DOI: 10.1002/cyto.a.23895] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/10/2019] [Accepted: 08/22/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Tomas Kalina
- CLIP‐Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Medical SchoolCharles University and University Hospital Motol Prague Czech Republic
| | | | - Pablo Engel
- Department of Biomedical SciencesFaculty of Medicine and Health Sciences, University of Barcelona Barcelona Spain
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22
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Manglani M, Gossa S, McGavern DB. Leukocyte Isolation from Brain, Spinal Cord, and Meninges for Flow Cytometric Analysis. ACTA ACUST UNITED AC 2019; 121:e44. [PMID: 30040211 DOI: 10.1002/cpim.44] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A continual dialogue exists between the central nervous system (CNS) and immune system that contributes to neural homeostasis as well as protection from microbes, repair following damage, autoimmune disease, and neurodegeneration. Characterization of resident and peripherally derived leukocyte populations within the central nervous system can provide valuable information regarding how these cells contribute to steady-state and inflammatory conditions. Flow cytometry provides a method to conduct detailed multi-parameter analyses of immune cells isolated from various tissues. This protocol provides a method to isolate leukocytes from brain, spinal cord, and meninges for flow cytometric analysis and provides a basic framework for phenotyping these cells. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Monica Manglani
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland.,Medical Scientist Training Program, Penn State College of Medicine, Hershey, Pennsylvania
| | - Selamawit Gossa
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Dorian B McGavern
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
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23
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24
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Gong Y, Fan N, Yang X, Peng B, Jiang H. New advances in microfluidic flow cytometry. Electrophoresis 2018; 40:1212-1229. [PMID: 30242856 DOI: 10.1002/elps.201800298] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/07/2018] [Accepted: 09/15/2018] [Indexed: 01/22/2023]
Abstract
In recent years, researchers are paying the increasing attention to the development of portable microfluidic diagnostic devices including microfluidic flow cytometry for the point-of-care testing. Microfluidic flow cytometry, where microfluidics and flow cytometry work together to realize novel functionalities on the microchip, provides a powerful tool for measuring the multiple characteristics of biological samples. The development of a portable, low-cost, and compact flow cytometer can benefit the health care in underserved areas such as Africa or Asia. In this article, we review recent advancements of microfluidics including sample pumping, focusing and sorting, novel detection approaches, and data analysis in the field of flow cytometry. The challenge of microfluidic flow cytometry is also examined briefly.
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Affiliation(s)
- Yanli Gong
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, P. R. China
| | - Na Fan
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, P. R. China
| | - Xu Yang
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, P. R. China
| | - Bei Peng
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, P. R. China
| | - Hai Jiang
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, P. R. China
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25
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Joseph MM, Narayanan N, Nair JB, Karunakaran V, Ramya AN, Sujai PT, Saranya G, Arya JS, Vijayan VM, Maiti KK. Exploring the margins of SERS in practical domain: An emerging diagnostic modality for modern biomedical applications. Biomaterials 2018; 181:140-181. [PMID: 30081304 DOI: 10.1016/j.biomaterials.2018.07.045] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/16/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022]
Abstract
Excellent multiplexing capability, molecular specificity, high sensitivity and the potential of resolving complex molecular level biological compositions augmented the diagnostic modality of surface-enhanced Raman scattering (SERS) in biology and medicine. While maintaining all the merits of classical Raman spectroscopy, SERS provides a more sensitive and selective detection and quantification platform. Non-invasive, chemically specific and spatially resolved analysis facilitates the exploration of SERS-based nano probes in diagnostic and theranostic applications with improved clinical outcomes compared to the currently available so called state-of-art technologies. Adequate knowledge on the mechanism and properties of SERS based nano probes are inevitable in utilizing the full potential of this modality for biomedical applications. The safety and efficiency of metal nanoparticles and Raman reporters have to be critically evaluated for the successful translation of SERS in to clinics. In this context, the present review attempts to give a comprehensive overview about the selected medical, biomedical and allied applications of SERS while highlighting recent and relevant outcomes ranging from simple detection platforms to complicated clinical applications.
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Affiliation(s)
- Manu M Joseph
- Chemical Sciences and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Pappanamcode, Thiruvananthapuram, Kerala 695019, India
| | - Nisha Narayanan
- Chemical Sciences and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Pappanamcode, Thiruvananthapuram, Kerala 695019, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST, Pappanamcode, Thiruvananthapuram, Kerala 695019, India
| | - Jyothi B Nair
- Chemical Sciences and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Pappanamcode, Thiruvananthapuram, Kerala 695019, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST, Pappanamcode, Thiruvananthapuram, Kerala 695019, India
| | - Varsha Karunakaran
- Chemical Sciences and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Pappanamcode, Thiruvananthapuram, Kerala 695019, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST, Pappanamcode, Thiruvananthapuram, Kerala 695019, India
| | - Adukkadan N Ramya
- Chemical Sciences and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Pappanamcode, Thiruvananthapuram, Kerala 695019, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST, Pappanamcode, Thiruvananthapuram, Kerala 695019, India
| | - Palasseri T Sujai
- Chemical Sciences and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Pappanamcode, Thiruvananthapuram, Kerala 695019, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST, Pappanamcode, Thiruvananthapuram, Kerala 695019, India
| | - Giridharan Saranya
- Chemical Sciences and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Pappanamcode, Thiruvananthapuram, Kerala 695019, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST, Pappanamcode, Thiruvananthapuram, Kerala 695019, India
| | - Jayadev S Arya
- Chemical Sciences and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Pappanamcode, Thiruvananthapuram, Kerala 695019, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST, Pappanamcode, Thiruvananthapuram, Kerala 695019, India
| | - Vineeth M Vijayan
- Chemical Sciences and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Pappanamcode, Thiruvananthapuram, Kerala 695019, India
| | - Kaustabh Kumar Maiti
- Chemical Sciences and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Pappanamcode, Thiruvananthapuram, Kerala 695019, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST, Pappanamcode, Thiruvananthapuram, Kerala 695019, India.
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26
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Wilson AC, Moutsatsos IK, Yu G, Pineda JJ, Feng Y, Auld DS. A Scalable Pipeline for High-Throughput Flow Cytometry. SLAS DISCOVERY 2018; 23:708-718. [PMID: 29768981 DOI: 10.1177/2472555218774770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Flow cytometry (FC) provides high-content data for a variety of applications, including phenotypic analysis of cell surface and intracellular markers, characterization of cell supernatant or lysates, and gene expression analysis. Historically, sample preparation, acquisition, and analysis have presented as a bottleneck for running such types of assays at scale. This article will outline the solutions that have been implemented at Novartis which have allowed high-throughput FC to be successfully conducted and analyzed for a variety of cell-based assays. While these experiments were generally conducted to measure phenotypic responses from a well-characterized and information-rich small molecular probe library known as the Mechanism-of-Action (MoA) Box, they are broadly applicable to any type of test sample. The article focuses on application of automated methods for FC sample preparation in 384-well assay plates. It also highlights a pipeline for analyzing large volumes of FC data, covering a visualization approach that facilitates review of screen-level data by dynamically embedding FlowJo (FJ) workspace images for each sample into a Spotfire file, directly linking them to the metric being observed. Finally, an application of these methods to a screen for MHC-I expression upregulators is discussed.
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Affiliation(s)
- Aaron C Wilson
- 1 Novartis Institutes of Biomedical Research, Cambridge, MA, USA
| | | | - Gary Yu
- 1 Novartis Institutes of Biomedical Research, Cambridge, MA, USA
| | - Javier J Pineda
- 2 Department Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Yan Feng
- 1 Novartis Institutes of Biomedical Research, Cambridge, MA, USA
| | - Douglas S Auld
- 1 Novartis Institutes of Biomedical Research, Cambridge, MA, USA
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27
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Apichitsopa N, Jaffe A, Voldman J. Multiparameter cell-tracking intrinsic cytometry for single-cell characterization. LAB ON A CHIP 2018; 18:1430-1439. [PMID: 29687107 DOI: 10.1039/c8lc00240a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
An abundance of label-free microfluidic techniques for measuring cell intrinsic markers exists, yet these techniques are seldom combined because of integration complexity such as restricted physical space and incompatible modes of operation. We introduce a multiparameter intrinsic cytometry approach for the characterization of single cells that combines ≥2 label-free measurement techniques onto the same platform and uses cell tracking to associate the measured properties to cells. Our proof-of-concept implementation can measure up to five intrinsic properties including size, deformability, and polarizability at three frequencies. Each measurement module along with the integrated platform were validated and evaluated in the context of chemically induced changes in the actin cytoskeleton of cells. viSNE and machine learning classification were used to determine the orthogonality between and the contribution of the measured intrinsic markers for cell classification.
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Affiliation(s)
- N Apichitsopa
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 36-824, Cambridge, MA 02139, USA.
| | - A Jaffe
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 36-824, Cambridge, MA 02139, USA.
| | - J Voldman
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 36-824, Cambridge, MA 02139, USA.
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28
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Santilli F, Marchisio M, Lanuti P, Boccatonda A, Miscia S, Davì G. Microparticles as new markers of cardiovascular risk in diabetes and beyond. Thromb Haemost 2018; 116:220-34. [DOI: 10.1160/th16-03-0176] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/19/2016] [Indexed: 12/25/2022]
Abstract
SummaryThe term microparticle (MP) identifies a heterogeneous population of vesicles playing a relevant role in the pathogenesis of vascular diseases, cancer and metabolic diseases such as diabetes mellitus. MPs are released by virtually all cell types by shedding during cell growth, proliferation, activation, apoptosis or senescence processes. MPs, in particular platelet- and endothelial-derived MPs (PMPs and EMPs), are increased in a wide range of thrombotic disorders, with an interesting relationship between their levels and disease pathophysiology, activity or progression. EMP plasma levels have been associated with several cardiovascular diseases and risk factors. PMPs are also shown to be involved in the progressive formation of atherosclerotic plaque and development of arterial thrombosis, especially in diabetic patients. Indeed, diabetes is characterised by an increased procoagulant state and by a hyperreactive platelet phenotype, with enhanced adhesion, aggregation, and activation. Elevated MP levels, such as TF+ MPs, have been shown to be one of the procoagulant determinants in patients with type 2 diabetes mellitus. Atherosclerotic plaque constitutes an opulent source of sequestered MPs, called “plaque” MPs. Otherwise, circulating MPs represent a TF reservoir, named “blood-borne” TF, challenging the dogma that TF is a constitutive protein expressed in minute amounts. “Blood-borne” TF is mainly harboured by PMPs, and it can be trapped within the developing thrombus. MP detection and enumeration by polychromatic flow cytometry (PFC) have opened interesting perspectives in clinical settings, particularly for the evaluation of MP numbers and phenotypes as independent marker of cardiovascular risk, disease and outcome in diabetic patients.
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29
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Balfe A, Lennon G, Lavelle A, Docherty NG, Coffey JC, Sheahan K, Winter DC, O'Connell PR. Isolation and gene expression profiling of intestinal epithelial cells: crypt isolation by calcium chelation from in vivo samples. Clin Exp Gastroenterol 2018; 11:29-37. [PMID: 29391821 PMCID: PMC5769583 DOI: 10.2147/ceg.s145224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim The epithelial layer within the colon represents a physical barrier between the luminal contents and its underlying mucosa. It plays a pivotal role in mucosal homeostasis, and both tolerance and anti-pathogenic immune responses. Identifying signals of inflammation initiation and responses to stimuli from within the epithelial layer is critical to understanding the molecular pathways underlying disease pathology. This study validated a method to isolate and analyze epithelial populations, enabling investigations of epithelial function and response in a variety of disease setting. Materials and methods Epithelial cells were isolated from whole mucosal biopsies harvested from healthy controls and patients with active ulcerative colitis by calcium chelation. The purity of isolated cells was assessed by flow cytometry. The expression profiles of a panel of epithelial functional genes were investigated by reverse transcription-polymerase chain reaction (PCR) in isolated epithelial cells and corresponding mucosal biopsies. The expression profiles of isolated cells and corresponding mucosal biopsies were evaluated and compared between healthy and inflamed colonic tissue. Results Flow cytometry identified 97% of cells isolated as intestinal epithelial cells (IECs). Comparisons of gene expression profiles between the mucosal biopsies and isolated IECs demonstrated clear differences in the gene expression signatures. Sixty percent of the examined genes showed contrasting trends of expression between sample types. Conclusion The calcium chelation isolation method provided a reliable method for the isolation of a pure population of cells with preservation of epithelial cell-specific gene expression. This demonstrates the importance of sample choice when investigating functions directly affecting the colonic epithelial layer.
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Affiliation(s)
- Aine Balfe
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin.,Centre for Colorectal Disease, St Vincent's University Hospital Dublin, Dublin
| | - Grainne Lennon
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin.,Centre for Colorectal Disease, St Vincent's University Hospital Dublin, Dublin
| | - Aonghus Lavelle
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin.,Centre for Colorectal Disease, St Vincent's University Hospital Dublin, Dublin
| | - Neil G Docherty
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin
| | - J Calvin Coffey
- Graduate Entry Medical School, University Hospital Limerick, 4i Centre for Interventions in Infection, Inflammation and Immunity, University of Limerick, Limerick
| | - Kieran Sheahan
- Histopathology Department, St. Vincent's University Hospital Dublin, Dublin, Ireland
| | - Desmond C Winter
- Centre for Colorectal Disease, St Vincent's University Hospital Dublin, Dublin
| | - P Ronan O'Connell
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin.,Centre for Colorectal Disease, St Vincent's University Hospital Dublin, Dublin
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30
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High-throughput flow cytometry for drug discovery: principles, applications, and case studies. Drug Discov Today 2017; 22:1844-1850. [DOI: 10.1016/j.drudis.2017.09.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/01/2017] [Accepted: 09/08/2017] [Indexed: 12/31/2022]
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31
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Ryherd M, Plassmeyer M, Alexander C, Eugenio I, Kleschenko Y, Badger A, Gupta R, Alpan O, Sønder SU. Improved panels for clinical immune phenotyping: Utilization of the violet laser. CYTOMETRY PART B-CLINICAL CYTOMETRY 2017; 94:671-679. [DOI: 10.1002/cyto.b.21532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/11/2017] [Accepted: 05/04/2017] [Indexed: 12/13/2022]
Affiliation(s)
| | | | | | | | | | | | - Raavi Gupta
- Amerimmune LLC; Fairfax Virginia
- Department of Pathology; SUNY; New York
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32
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Abstract
The composition and function of platelet-derived extracellular vesicles (EVs) in health and in disease are a major topic of investigation in biomedical research. However, efforts to delineate specific molecular repertoires and roles for different types of EVs in the circulation are limited not only by the lack of flow cytometers capable of analyzing submicron- and nano-materials across the full size spectrum of plasma EVs, but also by the lack of standardized methods and reference materials that would permit inter-laboratory reproducibility for these analyses. In this review, we summarize the flow cytometry of EVs, with a focus on platelet vesicles in plasma. In addition to delineating the basic principles that govern what precautions must be considered when using flow cytometry for the analysis of platelet vesicles, we provide an overview for how to standardize, control, annotate, and report EV flow cytometry data reproducibly, while looking forward to a next generation of high sensitivity instruments for the analysis of EVs and other submicron biomaterials in the circulation.
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Affiliation(s)
| | - Jennifer C Jones
- b Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda , MD , USA
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33
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Qiu P. Toward deterministic and semiautomated SPADE analysis. Cytometry A 2017; 91:281-289. [PMID: 28234411 DOI: 10.1002/cyto.a.23068] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/02/2016] [Accepted: 01/23/2017] [Indexed: 11/11/2022]
Abstract
SPADE stands for spanning-tree progression analysis for density-normalized events. It combines downsampling, clustering and a minimum-spanning tree to provide an intuitive visualization of high-dimensional single-cell data, which assists with the interpretation of the cellular heterogeneity underlying the data. SPADE has been widely used for analysis of high-content flow cytometry data and CyTOF data. The downsampling and clustering components of SPADE are both stochastic, which lead to stochasticity in the tree visualization it generates. Running SPADE twice on the same data may generate two different tree structures. Although they typically lead to the same biological interpretation of subpopulations present in the data, robustness of the algorithm can be improved. Another avenue of improvement is the interpretation of the SPADE tree, which involves visual inspection of multiple colored versions of the tree based on expression of measured markers. This is essentially manual gating on the SPADE tree and can benefit from automated algorithms. This article presents improvements of SPADE in both aspects above, leading to a deterministic SPADE algorithm and a software implementation for semiautomated interpretation. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
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34
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Burel JG, Qian Y, Lindestam Arlehamn C, Weiskopf D, Zapardiel-Gonzalo J, Taplitz R, Gilman RH, Saito M, de Silva AD, Vijayanand P, Scheuermann RH, Sette A, Peters B. An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry. THE JOURNAL OF IMMUNOLOGY 2017; 198:1748-1758. [PMID: 28069807 DOI: 10.4049/jimmunol.1601750] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/06/2016] [Indexed: 12/19/2022]
Abstract
In the context of large-scale human system immunology studies, controlling for technical and biological variability is crucial to ensure that experimental data support research conclusions. In this study, we report on a universal workflow to evaluate both technical and biological variation in multiparameter flow cytometry, applied to the development of a 10-color panel to identify all major cell populations and T cell subsets in cryopreserved PBMC. Replicate runs from a control donation and comparison of different gating strategies assessed the technical variability associated with each cell population and permitted the calculation of a quality control score. Applying our panel to a large collection of PBMC samples, we found that most cell populations showed low intraindividual variability over time. In contrast, certain subpopulations such as CD56 T cells and Temra CD4 T cells were associated with high interindividual variability. Age but not gender had a significant effect on the frequency of several populations, with a drastic decrease in naive T cells observed in older donors. Ethnicity also influenced a significant proportion of immune cell population frequencies, emphasizing the need to account for these covariates in immune profiling studies. We also exemplify the usefulness of our workflow by identifying a novel cell-subset signature of latent tuberculosis infection. Thus, our study provides a universal workflow to establish and evaluate any flow cytometry panel in systems immunology studies.
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Affiliation(s)
- Julie G Burel
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037;
| | - Yu Qian
- J. Craig Venter Institute, La Jolla, CA 92037
| | | | - Daniela Weiskopf
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | | | - Randy Taplitz
- Division of Infectious Diseases, University of California, San Diego, La Jolla, CA 92093
| | - Robert H Gilman
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205.,Universidad Peruana Caytano Hereida, Lima 15102, Peru
| | - Mayuko Saito
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205.,Universidad Peruana Caytano Hereida, Lima 15102, Peru.,Department of Virology, Tohoku University, Sendai 9808575, Japan
| | | | | | - Richard H Scheuermann
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037.,J. Craig Venter Institute, La Jolla, CA 92037.,Department of Pathology, University of California, San Diego, La Jolla, CA 92093
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
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35
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Abstract
Pregnancy complications such as preterm birth, miscarriage, maternal and/or neonatal morbidities, and mortality can be manifestations of underlying placental pathology. Hofbauer cells refer to a heterogeneous population of fetal macrophages that reside within the functional unit of the placenta known as the chorionic villus. Hofbauer cells can be detected within the connective tissue matrix of the placenta as early as 4 weeks post-conception and are present throughout pregnancy. These cells are implicated in a wide array of functions important for a successful pregnancy including placental morphogenesis, immune regulation, control of stromal water content, and the transfer of ions and serum proteins across the maternal-fetal barrier. Derangements in Hofbauer cell homeostasis are associated with placental pathologies involving infection, inflammation, and inadequate placental development. Despite a growing body of evidence that these cells are important, our knowledge about Hofbauer cell function in both normal and dysfunctional pregnancy is rudimentary. The goal of this chapter is to provide an overview of what is known about Hofbauer cell origins and their potential roles in normal and complicated pregnancy. We also review established and emerging methodologies available for the study of Hofbauer cells during in vitro and in vivo conditions.
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Affiliation(s)
- Leticia Reyes
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, 2015 Linden Drive, Madison, WI, 53706, USA.
| | - Bryce Wolfe
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thaddeus Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
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36
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Bhagwat N, Carpenter EL. Flow Cytometric Methods for Circulating Tumor Cell Isolation and Molecular Analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 994:105-118. [DOI: 10.1007/978-3-319-55947-6_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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37
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Zhang N, Jiang J, Liu M, Taniguchi M, Mandal AK, Evans-Storms RB, Pitner JB, Bocian DF, Holten D, Lindsey JS. Bioconjugatable, PEGylated Hydroporphyrins for Photochemistry and Photomedicine. Narrow-Band, Near-Infrared-Emitting Bacteriochlorins. NEW J CHEM 2016; 40:7750-7767. [PMID: 28133433 DOI: 10.1039/c6nj01155a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Synthetic bacteriochlorins absorb in the near-infrared (NIR) region and are versatile analogues of natural bacteriochlorophylls. The utilization of these chromophores in energy sciences and photomedicine requires the ability to tailor their physicochemical properties, including the incorporation of units to impart water solubility. Herein, we report the synthesis, from two common bacteriochlorin building blocks, of five wavelength-tunable, bioconjugatable and water-soluble bacteriochlorins along with two non-bioconjugatable benchmarks. Each bacteriochlorin bears short polyethylene glycol (PEG) units as the water-solubilizing motif. The PEG groups are located at the 3,5-positions of aryl groups at the pyrrolic β-positions to suppress aggregation in aqueous media. A handle containing a single carboxylic acid is incorporated to allow bioconjugation. The seven water-soluble bacteriochlorins in water display Qy absorption into the NIR range (679-819 nm), sharp emission (21-36 nm full-width-at-half-maximum) and modest fluorescence quantum yield (0.017-0.13). Each bacteriochlorin is neutral (non-ionic) yet soluble in organic (e.g., CH2Cl2, DMF) and aqueous solutions. Water solubility was assessed using absorption spectroscopy by changing the concentration ∼1000-fold (190-690 µM to 0.19-0.69 µM) with a reciprocal change in pathlength (0.1-10 cm). All bacteriochlorins showed excellent solubility in water, except for a bacteriochlorin-imide that gave slight aggregation at higher concentrations. One bacteriochlorin was conjugated to a mouse polyclonal IgG antibody for use in flow cytometry with compensation beads for proof-of-principle. The antibody conjugate of B2-NHS displayed a sharp signal upon ultraviolet laser excitation (355 nm) with NIR emission measured with a 730/45 nm bandpass filter. Overall, the study gives access to a set of water-soluble bacteriochlorins with desirable photophysical properties for use in multiple fields.
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Affiliation(s)
- Nuonuo Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204
| | - Jianbing Jiang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204
| | - Mengran Liu
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204
| | - Masahiko Taniguchi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204
| | - Amit Kumar Mandal
- Department of Chemistry, Washington University, St. Louis, MO 63130-4889
| | | | | | - David F Bocian
- Department of Chemistry, University of California, Riverside, CA 92521-0403
| | - Dewey Holten
- Department of Chemistry, Washington University, St. Louis, MO 63130-4889
| | - Jonathan S Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204
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38
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Liu M, Chen CY, Mandal AK, Chandrashaker V, Evans-Storms RB, Pitner JB, Bocian DF, Holten D, Lindsey JS. Bioconjugatable, PEGylated Hydroporphyrins for Photochemistry and Photomedicine. Narrow-Band, Red-Emitting Chlorins. NEW J CHEM 2016; 40:7721-7740. [PMID: 28154477 DOI: 10.1039/c6nj01154c] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chromophores that absorb and emit in the red spectral region (600-700 nm), are water soluble, and bear a bioconjugatable tether are relatively rare yet would fulfill many applications in photochemistry and photomedicine. Here, three molecular designs have been developed wherein stable synthetic chlorins - analogues of chlorophylls - have been tailored with PEG groups for use in aqueous solution. The designs differ with regard to order of the installation (pre/post-formation of the chlorin macrocycle) and position of the PEG groups. Six PEGylated synthetic chlorins (three free bases, three zinc chelates) have been prepared, of which four are equipped with a bioconjugatable (carboxylic acid) tether. The most effective design for aqueous solubilization entails facial encumbrance where PEG groups project above and below the plane of the hydrophobic disk-like chlorin macrocycle. The chlorins possess strong absorption at ~400 nm (B band) and in the red region (Qy band); regardless of wavelength of excitation, emission occurs in the red region. Excitation in the ~400 nm region thus provides an effective Stokes shift of >200 nm. The four bioconjugatable water-soluble chlorins exhibit Qy absorption/emission in water at 613/614, 636/638, 698/700 and 706/710 nm. The spectral properties are essentially unchanged in DMF and water for the facially encumbered chlorins, which also exhibit narrow Qy absorption and emission bands (full-width-at-half maximum of each <25 nm). The water-solubility was assessed by absorption spectroscopy over the concentration range ~0.4 μM - 0.4 mM. One chlorin was conjugated to a mouse polyclonal IgG antibody for use in flow cytometry with compensation beads for proof-of-principle. The conjugate displayed a sharp signal when excited by a violet laser (405 nm) with emission in the 620-660 nm range. Taken together, the designs described herein augur well for development of a set of spectrally distinct chlorins with relatively sharp bands in the red region.
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Affiliation(s)
- Mengran Liu
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204
| | - Chih-Yuan Chen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204
| | - Amit Kumar Mandal
- Department of Chemistry, Washington University, St. Louis, MO 63130-4889
| | | | | | | | - David F Bocian
- Department of Chemistry, University of California, Riverside, CA 92521-0403
| | - Dewey Holten
- Department of Chemistry, Washington University, St. Louis, MO 63130-4889
| | - Jonathan S Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204
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39
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Circulating endothelial cells and serum visfatin are indicators of cardiovascular disease risk in psoriasis patients. DERMATOL SIN 2016. [DOI: 10.1016/j.dsi.2015.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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40
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Abstract
Naturally acquired immunity to the blood-stage of the malaria parasite develops slowly in areas of high endemicity, but is not sterilizing. It manifests as a reduction in parasite density and clinical symptoms. Immunity as a result of blood-stage vaccination has not yet been achieved in humans, although there are many animal models where vaccination has been successful. The development of a blood-stage vaccine has been complicated by a number of factors including limited knowledge of human-parasite interactions and which antigens and immune responses are critical for protection. Opinion is divided as to whether this vaccine should aim to accelerate the acquisition of responses acquired following natural exposure, or whether it should induce a different response. Animal and experimental human models suggest that cell-mediated immune responses can control parasite growth, but these responses can also contribute to significant immunopathology if unregulated. They are largely ignored in most blood-stage malaria vaccine development strategies. Here, we discuss key observations relating to cell-mediated immune responses in the context of experimental human systems and field studies involving naturally exposed individuals and how this may inform the development of a blood-stage malaria vaccine.
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41
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Burel JG, Apte SH, Doolan DL. Systems Approaches towards Molecular Profiling of Human Immunity. Trends Immunol 2016; 37:53-67. [DOI: 10.1016/j.it.2015.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/14/2015] [Accepted: 11/15/2015] [Indexed: 12/12/2022]
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42
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Jenkins P, Naivar MA, Houston JP. Toward the measurement of multiple fluorescence lifetimes in flow cytometry: maximizing multi-harmonic content from cells and microspheres. JOURNAL OF BIOPHOTONICS 2015; 8:908-17. [PMID: 25727072 PMCID: PMC4869968 DOI: 10.1002/jbio.201400115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/21/2014] [Accepted: 01/23/2015] [Indexed: 05/20/2023]
Abstract
Flow cytometry is a powerful means for in vitro cellular analyses where multi-fluorescence and multi-angle light scattering can indicate unique biochemical or morphological features of single cells. Yet, to date, flow cytometry systems have lacked the ability to capture complex fluorescence dynamics due to the transient nature of flowing cells. In this contribution we introduce a simple approach for measuring multiple fluorescence lifetimes from a single cytometric event. We leverage square wave modulation, Fourier analysis, and high frequency digitization and show the ability to resolve more than one fluorescence lifetime from fluorescently-labelled cells and microspheres. Illustration of a flow cytometer capable of capturing multiple fluorescence lifetime measurements; creating potential for multi-parametric, time-resolved signals to be captured for every color channel.
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Affiliation(s)
- Patrick Jenkins
- Department of Chemical Engineering, New Mexico State University, MSC 3805 P.O. Box 30001 Las Cruces, NM 88003-8001
| | | | - Jessica P. Houston
- Department of Chemical Engineering, New Mexico State University, MSC 3805 P.O. Box 30001 Las Cruces, NM 88003-8001
- Corresponding author: , Phone: 575-646-5563, Fax: 575-646-7706
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43
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Stoner SA, Duggan E, Condello D, Guerrero A, Turk JR, Narayanan PK, Nolan JP. High sensitivity flow cytometry of membrane vesicles. Cytometry A 2015; 89:196-206. [PMID: 26484737 DOI: 10.1002/cyto.a.22787] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 07/31/2015] [Accepted: 09/23/2015] [Indexed: 12/17/2022]
Abstract
Extracellular vesicles (EVs) are attracting attention as vehicles for inter-cellular signaling that may have value as diagnostic or therapeutic targets. EVs are released by many cell types and by different mechanisms, resulting in phenotypic heterogeneity that makes them a challenge to study. Flow cytometry is a popular tool for characterizing heterogeneous mixtures of particles such as cell types within blood, but the small size of EVs makes them difficult to measure using conventional flow cytometry. To address this limitation, a high sensitivity flow cytometer was constructed and EV measurement approaches that allowed them to enumerate and estimate the size of individual EVs, as well as measure the presence of surface markers to identify phenotypic subsets of EVs. Several fluorescent membrane probes were evaluated and it was found that the voltage sensing dye di-8-ANEPPS could produce vesicle fluorescence in proportion to vesicle surface area, allowing for accurate measurements of EV number and size. Fluorescence-labeled annexin V and anti-CD61 antibody was used to measure the abundance of these surface markers on EVs in rat plasma. It was shown that treatment of platelet rich plasma with calcium ionophore resulted in an increase in the fraction of annexin V and CD61-positive EVs. Vesicle flow cytometry using fluorescence-based detection of EVs has the potential to realize the potential of cell-derived membrane vesicles as functional biomarkers for a variety of applications.
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Affiliation(s)
- Samuel A Stoner
- La Jolla Bioengineering Institute, La Jolla, California, 92037
| | - Erika Duggan
- La Jolla Bioengineering Institute, La Jolla, California, 92037.,Scintillon Institute, San Diego, California, 92121
| | - Danilo Condello
- La Jolla Bioengineering Institute, La Jolla, California, 92037.,Scintillon Institute, San Diego, California, 92121
| | - Abraham Guerrero
- Comparative Biology and Safety Sciences, Amgen Inc, Seattle, Washington
| | - James R Turk
- Comparative Biology and Safety Sciences, Amgen Inc, Seattle, Washington
| | - Padma K Narayanan
- Comparative Biology and Safety Sciences, Amgen Inc, Seattle, Washington
| | - John P Nolan
- La Jolla Bioengineering Institute, La Jolla, California, 92037.,Scintillon Institute, San Diego, California, 92121
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44
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DiGiuseppe JA, Tadmor MD, Pe’er D. Detection of minimal residual disease in B lymphoblastic leukemia using viSNE. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2015; 88:294-304. [PMID: 25974871 PMCID: PMC5981136 DOI: 10.1002/cyto.b.21252] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/03/2015] [Accepted: 05/11/2015] [Indexed: 11/05/2022]
Abstract
BACKGROUND Minimal residual disease (MRD) following treatment is a robust prognostic marker in B lymphoblastic leukemia. However, the detection of MRD by flow cytometric immunophenotyping is technically challenging, and an automated method to detect MRD is therefore desirable. viSNE, a recently developed computational tool based on the t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm, has been shown to be capable of detecting synthetic "MRD-like" populations of leukemic cells created in vitro, but whether viSNE can facilitate the immunophenotypic detection of MRD in clinical samples has not been evaluated. METHODS We applied viSNE retrospectively to 8-color flow cytometric immunophenotyping data from normal bone marrow samples, and samples from B lymphoblastic leukemia patients with or without suspected MRD on the basis of conventional manual gating. RESULTS In each of 14 bone marrow specimens containing MRD or suspected MRD, viSNE identified a putative MRD population; an abnormal composite immunophenotype was confirmed for the putative MRD in each case. MRD populations were not identified by viSNE in control bone marrow samples from patients with increased normal B-cell precursors, or in post-treatment samples from B lymphoblastic leukemia patients who did not have detectable MRD by manual gating. CONCLUSION viSNE shows promise as an automated method to facilitate immunophenotypic MRD detection in patients treated for B lymphoblastic leukemia.
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Affiliation(s)
- Joseph A. DiGiuseppe
- Department of Pathology & Laboratory Medicine, Hartford Hospital, Hartford, Connecticut
| | - Michelle D. Tadmor
- Department of Biological Sciences, Columbia University, New York, New York
- Department of Systems Biology, Columbia University, New York, New York
| | - Dana Pe’er
- Department of Biological Sciences, Columbia University, New York, New York
- Department of Systems Biology, Columbia University, New York, New York
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45
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Sternebring O, Alifrangis L, Christensen TF, Ji H, Hegelund AC, Högerkorp CM. A weighted method for estimation of receptor occupancy for pharmacodynamic measurements in drug development. CYTOMETRY PART B-CLINICAL CYTOMETRY 2015. [DOI: 10.1002/cyto.b.21277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ola Sternebring
- Department of Development DMPK; Novo Nordisk A/S; DK-2760 Maaloev Denmark
| | - Lene Alifrangis
- Department of Development DMPK; Novo Nordisk A/S; DK-2760 Maaloev Denmark
| | - Toke Folke Christensen
- Department of Quantitative Clinical Pharmacology; Novo Nordisk A/S; DK-2860 Soeborg Denmark
| | - Hong Ji
- Department of Pharmacodynamics; Novo Nordisk A/S; DK-2760 Maaloev Denmark
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46
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Lane LA, Qian X, Nie S. SERS Nanoparticles in Medicine: From Label-Free Detection to Spectroscopic Tagging. Chem Rev 2015; 115:10489-529. [DOI: 10.1021/acs.chemrev.5b00265] [Citation(s) in RCA: 607] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Lucas A. Lane
- Departments
of Biomedical Engineering and Chemistry, Emory University and Georgia Institute of Technology, Health Sciences Research Building,
Room E116, 1760 Haygood Drive, Atlanta, Georgia 30322, United States
| | - Ximei Qian
- Departments
of Biomedical Engineering and Chemistry, Emory University and Georgia Institute of Technology, Health Sciences Research Building,
Room E116, 1760 Haygood Drive, Atlanta, Georgia 30322, United States
| | - Shuming Nie
- Departments
of Biomedical Engineering and Chemistry, Emory University and Georgia Institute of Technology, Health Sciences Research Building,
Room E116, 1760 Haygood Drive, Atlanta, Georgia 30322, United States
- College
of Engineering and Applied Sciences, Nanjing University, 22 Hankou
Road, Nanjing, Jiangsu Province 210093, China
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47
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Computational and experimental single cell biology techniques for the definition of cell type heterogeneity, interplay and intracellular dynamics. Curr Opin Biotechnol 2015; 34:9-15. [DOI: 10.1016/j.copbio.2014.10.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/21/2014] [Accepted: 10/22/2014] [Indexed: 12/31/2022]
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48
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Qiu P. Computational prediction of manually gated rare cells in flow cytometry data. Cytometry A 2015; 87:594-602. [PMID: 25755118 PMCID: PMC4483162 DOI: 10.1002/cyto.a.22654] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 02/16/2015] [Accepted: 02/18/2015] [Indexed: 01/03/2023]
Abstract
Rare cell identification is an interesting and challenging question in flow cytometry data analysis. In the literature, manual gating is a popular approach to distill flow cytometry data and drill down to the rare cells of interest, based on prior knowledge of measured protein markers and visual inspection of the data. Several computational algorithms have been proposed for rare cell identification. To compare existing algorithms and promote new developments, FlowCAP-III put forward one computational challenge that focused on this question. The challenge provided flow cytometry data for 202 training samples and two manually gated rare cell types for each training sample, roughly 0.02 and 0.04% of the cells, respectively. In addition, flow cytometry data for 203 testing samples were provided, and participants were invited to computationally identify the rare cells in the testing samples. Accuracy of the identification results was evaluated by comparing to manual gating of the testing samples. We participated in the challenge, and developed a method that combined the Hellinger divergence, a downsampling trick and the ensemble SVM. Our method achieved the highest accuracy in the challenge.
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Affiliation(s)
- Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, U.S.A., Telephone: 404-385-1656
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49
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Edwards BS, Sklar LA. Flow Cytometry: Impact on Early Drug Discovery. JOURNAL OF BIOMOLECULAR SCREENING 2015; 20:689-707. [PMID: 25805180 PMCID: PMC4606936 DOI: 10.1177/1087057115578273] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/27/2015] [Indexed: 12/15/2022]
Abstract
Modern flow cytometers can make optical measurements of 10 or more parameters per cell at tens of thousands of cells per second and more than five orders of magnitude dynamic range. Although flow cytometry is used in most drug discovery stages, "sip-and-spit" sampling technology has restricted it to low-sample-throughput applications. The advent of HyperCyt sampling technology has recently made possible primary screening applications in which tens of thousands of compounds are analyzed per day. Target-multiplexing methodologies in combination with extended multiparameter analyses enable profiling of lead candidates early in the discovery process, when the greatest numbers of candidates are available for evaluation. The ability to sample small volumes with negligible waste reduces reagent costs, compound usage, and consumption of cells. Improved compound library formatting strategies can further extend primary screening opportunities when samples are scarce. Dozens of targets have been screened in 384- and 1536-well assay formats, predominantly in academic screening lab settings. In concert with commercial platform evolution and trending drug discovery strategies, HyperCyt-based systems are now finding their way into mainstream screening labs. Recent advances in flow-based imaging, mass spectrometry, and parallel sample processing promise dramatically expanded single-cell profiling capabilities to bolster systems-level approaches to drug discovery.
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Affiliation(s)
- Bruce S Edwards
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Larry A Sklar
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
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50
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Zaunders J, Jing J, Leipold M, Maecker H, Kelleher AD, Koch I. Computationally efficient multidimensional analysis of complex flow cytometry data using second order polynomial histograms. Cytometry A 2015; 89:44-58. [PMID: 26097104 DOI: 10.1002/cyto.a.22704] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 04/07/2015] [Accepted: 05/18/2015] [Indexed: 12/29/2022]
Abstract
Many methods have been described for automated clustering analysis of complex flow cytometry data, but so far the goal to efficiently estimate multivariate densities and their modes for a moderate number of dimensions and potentially millions of data points has not been attained. We have devised a novel approach to describing modes using second order polynomial histogram estimators (SOPHE). The method divides the data into multivariate bins and determines the shape of the data in each bin based on second order polynomials, which is an efficient computation. These calculations yield local maxima and allow joining of adjacent bins to identify clusters. The use of second order polynomials also optimally uses wide bins, such that in most cases each parameter (dimension) need only be divided into 4-8 bins, again reducing computational load. We have validated this method using defined mixtures of up to 17 fluorescent beads in 16 dimensions, correctly identifying all populations in data files of 100,000 beads in <10 s, on a standard laptop. The method also correctly clustered granulocytes, lymphocytes, including standard T, B, and NK cell subsets, and monocytes in 9-color stained peripheral blood, within seconds. SOPHE successfully clustered up to 36 subsets of memory CD4 T cells using differentiation and trafficking markers, in 14-color flow analysis, and up to 65 subpopulations of PBMC in 33-dimensional CyTOF data, showing its usefulness in discovery research. SOPHE has the potential to greatly increase efficiency of analysing complex mixtures of cells in higher dimensions.
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Affiliation(s)
- John Zaunders
- St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Darlinghurst, New South Wales, 2010, Australia.,Kirby Institute, UNSW Australia, Kensington, New South Wales, 2052, Australia
| | - Junmei Jing
- Centre for Bioinformatics Science, Mathematical Science Institute, Australia National University, Canberra, Australian Capital Territory, 2600, Australia
| | - Michael Leipold
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, 94305
| | - Holden Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, 94305
| | - Anthony D Kelleher
- St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Darlinghurst, New South Wales, 2010, Australia.,Kirby Institute, UNSW Australia, Kensington, New South Wales, 2052, Australia
| | - Inge Koch
- School of Mathematical Sciences, University of Adelaide, South Australia, 5005, Australia
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