201
|
Håland TW, Boye E, Stokke T, Grallert B, Syljuåsen RG. Simultaneous measurement of passage through the restriction point and MCM loading in single cells. Nucleic Acids Res 2015; 43:e150. [PMID: 26250117 PMCID: PMC4678840 DOI: 10.1093/nar/gkv744] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/12/2015] [Indexed: 12/14/2022] Open
Abstract
Passage through the Retinoblastoma protein (RB1)-dependent restriction point and the loading of minichromosome maintenance proteins (MCMs) are two crucial events in G1-phase that help maintain genome integrity. Deregulation of these processes can cause uncontrolled proliferation and cancer development. Both events have been extensively characterized individually, but their relative timing and inter-dependence remain less clear. Here, we describe a novel method to simultaneously measure MCM loading and passage through the restriction point. We exploit that the RB1 protein is anchored in G1-phase but is released when hyper-phosphorylated at the restriction point. After extracting cells with salt and detergent before fixation we can simultaneously measure, by flow cytometry, the loading of MCMs onto chromatin and RB1 binding to determine the order of the two events in individual cells. We have used this method to examine the relative timing of the two events in human cells. Whereas in BJ fibroblasts released from G0-phase MCM loading started mainly after the restriction point, in a significant fraction of exponentially growing BJ and U2OS osteosarcoma cells MCMs were loaded in G1-phase with RB1 anchored, demonstrating that MCM loading can also start before the restriction point. These results were supported by measurements in synchronized U2OS cells.
Collapse
Affiliation(s)
- T W Håland
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0310 Oslo, Norway Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - E Boye
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0310 Oslo, Norway Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - T Stokke
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0310 Oslo, Norway
| | - B Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0310 Oslo, Norway
| | - R G Syljuåsen
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0310 Oslo, Norway
| |
Collapse
|
202
|
Zhang H, Wu Q, Berezin MY. Fluorescence anisotropy (polarization): from drug screening to precision medicine. Expert Opin Drug Discov 2015; 10:1145-61. [PMID: 26289575 DOI: 10.1517/17460441.2015.1075001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Fluorescence anisotropy (FA) is one of the major established methods accepted by industry and regulatory agencies for understanding the mechanisms of drug action and selecting drug candidates utilizing a high-throughput format. AREAS COVERED This review covers the basics of FA and complementary methods, such as fluorescence lifetime anisotropy and their roles in the drug discovery process. The authors highlight the factors affecting FA readouts, fluorophore selection and instrumentation. Furthermore, the authors describe the recent development of a successful, commercially valuable FA assay for long QT syndrome drug toxicity to illustrate the role that FA can play in the early stages of drug discovery. EXPERT OPINION Despite the success in drug discovery, the FA-based technique experiences competitive pressure from other homogeneous assays. That being said, FA is an established yet rapidly developing technique, recognized by academic institutions, the pharmaceutical industry and regulatory agencies across the globe. The technical problems encountered in working with small molecules in homogeneous assays are largely solved, and new challenges come from more complex biological molecules and nanoparticles. With that, FA will remain one of the major work-horse techniques leading to precision (personalized) medicine.
Collapse
Affiliation(s)
- Hairong Zhang
- a 1 Washington University School of Medicine, Department of Radiology , St. Louis 63110, USA
| | - Qian Wu
- a 1 Washington University School of Medicine, Department of Radiology , St. Louis 63110, USA
| | - Mikhail Y Berezin
- a 1 Washington University School of Medicine, Department of Radiology , St. Louis 63110, USA.,b 2 Washington University School of Medicine, Institute of Materials Science and Engineering, Department of Radiology , 510 S. Kingshighway, Barnard Bldg, 6th floor, 6604A, St. Louis, MO, USA +1 314 747 0701 ; +1 314 747 5191 ;
| |
Collapse
|
203
|
von Palffy S, Bulaeva E, Babovic S, Kannan N, Knapp DJ, Wei L, Eaves CJ, Beer PA. Dominant-negative IKAROS enhances IL-3-stimulated signaling in wild-type but not BCR-ABL1+ mouse BA/F3 cells. Exp Hematol 2015; 43:514-23.e1-2. [DOI: 10.1016/j.exphem.2015.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 02/08/2023]
|
204
|
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.
Collapse
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
| |
Collapse
|
205
|
Robinson JP, Li N, Narayanan PK. High Throughput-Based Mitochondrial Function Assays by Multi-Parametric Flow Cytometry. ACTA ACUST UNITED AC 2015; 73:9.48.1-9.48.9. [PMID: 26132178 DOI: 10.1002/0471142956.cy0948s73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mitochondrial dysfunction has been increasingly implicated as an important mechanism for chemical-induced toxicity. In the present unit, we describe a multi-parametric flow cytometry assay to assess the effects of drug or chemical-induced mitochondrial dysfunction in cells. Cells are cultured in a glucose-supplemented medium and exposed to increasing concentrations of various chemicals. Several key mitochondrial/cellular parameters known to be directly impacted by mitochondrial dysfunction, such as mitochondrial membrane potential (MMP), mitochondrial reactive oxygen species (ROS) production, intracellular reduced glutathione (GSH) level, and cell viability, are simultaneously measured by flow cytometry.
Collapse
Affiliation(s)
- J Paul Robinson
- Purdue University Cytometry Laboratories, West Lafayette, Indiana
| | | | | |
Collapse
|
206
|
Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene transcription dynamics. Methods 2015; 85:12-21. [PMID: 26079925 DOI: 10.1016/j.ymeth.2015.06.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 06/06/2015] [Accepted: 06/08/2015] [Indexed: 11/21/2022] Open
Abstract
The production and degradation of RNA transcripts is inherently subject to biological noise that arises from small gene copy numbers in individual cells. As a result, cellular RNA levels can exhibit large fluctuations over time and from one cell to the next. This article presents a range of precise single-molecule experimental techniques, based upon RNA fluorescence in situ hybridization, which can be used to measure the fluctuations of RNA at the single-cell level. A class of models for gene activation and deactivation is postulated in order to capture complex stochastic effects of chromatin modifications or transcription factor interactions. A computational tool, known as the finite state projection approach, is introduced to accurately and efficiently analyze these models in order to predict how probability distributions of RNA change over time in response to changing environmental conditions. These single-molecule experiments, discrete stochastic models, and computational analyses are systematically integrated to identify models of gene regulation dynamics. To illustrate the power and generality of our integrated experimental and computational approach, we explore cases that include different models for three different RNA types (sRNA, mRNA and nascent RNA), three different experimental techniques and three different biological species (bacteria, yeast and human cells).
Collapse
|
207
|
Magnussen GI, Emilsen E, Giller Fleten K, Engesæter B, Nähse-Kumpf V, Fjær R, Slipicevic A, Flørenes VA. Combined inhibition of the cell cycle related proteins Wee1 and Chk1/2 induces synergistic anti-cancer effect in melanoma. BMC Cancer 2015; 15:462. [PMID: 26054341 PMCID: PMC4460948 DOI: 10.1186/s12885-015-1474-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 05/26/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Malignant melanoma has an increasing incidence rate and the metastatic disease is notoriously resistant to standard chemotherapy. Loss of cell cycle checkpoints is frequently found in many cancer types and makes the cells reliant on compensatory mechanisms to control progression. This feature may be exploited in therapy, and kinases involved in checkpoint regulation, such as Wee1 and Chk1/2, have thus become attractive therapeutic targets. METHODS In the present study we combined a Wee1 inhibitor (MK1775) with Chk1/2 inhibitor (AZD7762) in malignant melanoma cell lines grown in vitro (2D and 3D cultures) and in xenografts models. RESULTS Our in vitro studies showed that combined inhibition of Wee1 and Chk1/2 synergistically decreased viability and increased apoptosis (cleavage of caspase 3 and PARP), which may be explained by accumulation of DNA-damage (increased expression of γ-H2A.X)--and premature mitosis of S-phase cells. Compared to either inhibitor used as single agents, combined treatment reduced spheroid growth and led to greater tumour growth inhibition in melanoma xenografts. CONCLUSIONS These data provide a rationale for further evaluation of the combination of Wee1 and Chk1/2 inhibitors in malignant melanoma.
Collapse
Affiliation(s)
- Gry Irene Magnussen
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, N-0310, Oslo, Norway.
| | - Elisabeth Emilsen
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, N-0310, Oslo, Norway.
| | - Karianne Giller Fleten
- Department of Tumour Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo, Norway.
| | - Birgit Engesæter
- Department of Tumour Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo, Norway.
| | - Viola Nähse-Kumpf
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo, Norway.
| | - Roar Fjær
- Department of Medical Genetics, Ullevål University Hospital, Oslo, Norway.
| | - Ana Slipicevic
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, N-0310, Oslo, Norway.
| | - Vivi Ann Flørenes
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, N-0310, Oslo, Norway.
| |
Collapse
|
208
|
Janzen WP. Screening technologies for small molecule discovery: the state of the art. ACTA ACUST UNITED AC 2015; 21:1162-70. [PMID: 25237860 DOI: 10.1016/j.chembiol.2014.07.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 01/24/2023]
Abstract
Screening, high-throughput screening, and ultra-high-throughput screening are all really just points on a spectrum that represent differing applications of the same process: the creation of biologically relevant assays that are relevant, reproducible, reliable, and robust. Whether the discovery program is developing a pharmaceutical, an academic probe, cosmetics, pesticides, or a toxicity monitoring assay, the development of a screen focuses on generating a method that will reliably deliver reproducible results over a period of weeks, months, or years and that will generate consistent results for every test along the way. This review provides both historical perspective on how this unique scientific discipline evolved and commentary on the current state of the art technologies and techniques.
Collapse
Affiliation(s)
- William P Janzen
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|
209
|
Smurthwaite CA, Williams W, Fetsko A, Abbadessa D, Stolp ZD, Reed CW, Dharmawan A, Wolkowicz R. Genetic barcoding with fluorescent proteins for multiplexed applications. J Vis Exp 2015:52452. [PMID: 25938804 PMCID: PMC4541556 DOI: 10.3791/52452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Fluorescent proteins, fluorescent dyes and fluorophores in general have revolutionized the field of molecular cell biology. In particular, the discovery of fluorescent proteins and their genes have enabled the engineering of protein fusions for localization, the analysis of transcriptional activation and translation of proteins of interest, or the general tracking of individual cells and cell populations. The use of fluorescent protein genes in combination with retroviral technology has further allowed the expression of these proteins in mammalian cells in a stable and reliable manner. Shown here is how one can utilize these genes to give cells within a population of cells their own biosignature. As the biosignature is achieved with retroviral technology, cells are barcoded 'indefinitely'. As such, they can be individually tracked within a mixture of barcoded cells and utilized in more complex biological applications. The tracking of distinct populations in a mixture of cells is ideal for multiplexed applications such as discovery of drugs against a multitude of targets or the activation profile of different promoters. The protocol describes how to elegantly develop and amplify barcoded mammalian cells with distinct genetic fluorescent markers, and how to use several markers at once or one marker at different intensities. Finally, the protocol describes how the cells can be further utilized in combination with cell-based assays to increase the power of analysis through multiplexing.
Collapse
|
210
|
Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJL, Furman D, Shen-Orr S, Dekker CL, Swan GE, Butte AJ, Maecker HT, Davis MM. Variation in the human immune system is largely driven by non-heritable influences. Cell 2015; 160:37-47. [PMID: 25594173 DOI: 10.1016/j.cell.2014.12.020] [Citation(s) in RCA: 702] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/20/2014] [Accepted: 11/14/2014] [Indexed: 12/31/2022]
Abstract
There is considerable heterogeneity in immunological parameters between individuals, but its sources are largely unknown. To assess the relative contribution of heritable versus non-heritable factors, we have performed a systems-level analysis of 210 healthy twins between 8 and 82 years of age. We measured 204 different parameters, including cell population frequencies, cytokine responses, and serum proteins, and found that 77% of these are dominated (>50% of variance) and 58% almost completely determined (>80% of variance) by non-heritable influences. In addition, some of these parameters become more variable with age, suggesting the cumulative influence of environmental exposure. Similarly, the serological responses to seasonal influenza vaccination are also determined largely by non-heritable factors, likely due to repeated exposure to different strains. Lastly, in MZ twins discordant for cytomegalovirus infection, more than half of all parameters are affected. These results highlight the largely reactive and adaptive nature of the immune system in healthy individuals.
Collapse
Affiliation(s)
- Petter Brodin
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institutet, 17121 Solna, Sweden; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tianxiang Gao
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sanchita Bhattacharya
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Cesar J Lopez Angel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - David Furman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Shai Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Gary E Swan
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Atul J Butte
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA; Center for Pediatric Bioinformatics, Lucille Packard Children's Hospital, Stanford University, Stanford, CA 94304, USA
| | - Holden T Maecker
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA; Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94304, USA.
| |
Collapse
|
211
|
Tárnok A. Stardust memories. Cytometry A 2015; 87:283-4. [DOI: 10.1002/cyto.a.22660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 02/05/2015] [Accepted: 03/02/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Attila Tárnok
- Department of Pediatric Cardiology; Heart Centre Leipzig; Leipzig Germany
- Translational Centre for Regenerative Medicine (TRM); University of Leipzig; Leipzig Germany
| |
Collapse
|
212
|
Lai L, Ong R, Li J, Albani S. A CD45-based barcoding approach to multiplex mass-cytometry (CyTOF). Cytometry A 2015; 87:369-74. [PMID: 25645694 PMCID: PMC4670699 DOI: 10.1002/cyto.a.22640] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/07/2014] [Accepted: 01/13/2015] [Indexed: 01/15/2023]
Abstract
CyTOF enables the study of the immune system with a complexity, depth, and multidimensionality never achieved before. However, the full potential of using CyTOF can be limited by scarce cell samples. Barcoding strategies developed based on direct labeling of cells using maleimido-monoamide-DOTA (m-DOTA) provide a very useful tool. However, using m-DOTA has some inherent problems, mainly associated with signal intensity. This may be a source of uncertainty when samples are multiplexed. As an alternative or complementary approach to m-DOTA, conjugating an antibody, specific for a membrane protein present on most immune cells, with different isotopes could address the issues of stability and signal intensity needed for effective barcoding. We chose for this purpose CD45, and designed experiments to address different types of cultures and the ability to detect extra- and intra-cellular targets. We show here that our approach provides an useful alternative to m-DOTA in terms of sensitivity, specificity, flexibility, and user-friendliness. Our manuscript provides details to effectively barcode immune cells, overcoming limitations in current technology and enabling the use of CyTOF with scarce samples (for instance precious clinical samples). © 2015 The Authors. Published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Liyun Lai
- SingHealth Translational Immunology and Inflammation Centre, Singapore Health Services Pte Ltd, Singapore
| | | | | | | |
Collapse
|
213
|
Castellarnau M, Szeto GL, Su HW, Tokatlian T, Love JC, Irvine DJ, Voldman J. Stochastic particle barcoding for single-cell tracking and multiparametric analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:489-98. [PMID: 25180800 PMCID: PMC4303509 DOI: 10.1002/smll.201401369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 07/29/2014] [Indexed: 05/04/2023]
Abstract
This study presents stochastic particle barcoding (SPB), a method for tracking cell identity across bioanalytical platforms. In this approach, single cells or small collections of cells are co-encapsulated within an enzymatically-degradable hydrogel block along with a random collection of fluorescent beads, whose number, color, and position encode the identity of the cell, enabling samples to be transferred in bulk between single-cell assay platforms without losing the identity of individual cells. The application of SPB is demonstrated for transferring cells from a subnanoliter protein secretion/phenotyping array platform into a microtiter plate, with re-identification accuracies in the plate assay of 96±2%. Encapsulated cells are recovered by digesting the hydrogel, allowing subsequent genotyping and phenotyping of cell lysates. Finally, a model scaling is developed to illustrate how different parameters affect the accuracy of SPB and to motivate scaling of the method to thousands of unique blocks.
Collapse
Affiliation(s)
- Marc Castellarnau
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - Gregory L. Szeto
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - Hao-Wei Su
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - Talar Tokatlian
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - J. Christopher Love
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - Darrell J. Irvine
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - Joel Voldman
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| |
Collapse
|
214
|
Zunder ER, Finck R, Behbehani GK, Amir EAD, Krishnaswamy S, Gonzalez VD, Lorang CG, Bjornson Z, Spitzer MH, Bodenmiller B, Fantl WJ, Pe'er D, Nolan GP. Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. Nat Protoc 2015; 10:316-33. [PMID: 25612231 DOI: 10.1038/nprot.2015.020] [Citation(s) in RCA: 379] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mass-tag cell barcoding (MCB) labels individual cell samples with unique combinatorial barcodes, after which they are pooled for processing and measurement as a single multiplexed sample. The MCB method eliminates variability between samples in antibody staining and instrument sensitivity, reduces antibody consumption and shortens instrument measurement time. Here we present an optimized MCB protocol. The use of palladium-based labeling reagents expands the number of measurement channels available for mass cytometry and reduces interference with lanthanide-based antibody measurement. An error-detecting combinatorial barcoding scheme allows cell doublets to be identified and removed from the analysis. A debarcoding algorithm that is single cell-based rather than population-based improves the accuracy and efficiency of sample deconvolution. This debarcoding algorithm has been packaged into software that allows rapid and unbiased sample deconvolution. The MCB procedure takes 3-4 h, not including sample acquisition time of ∼1 h per million cells.
Collapse
Affiliation(s)
- Eli R Zunder
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Rachel Finck
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Gregory K Behbehani
- 1] Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA. [2] Divisions of Hematology and Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - El-Ad D Amir
- Department of Biological Sciences, Department of Systems Biology, Columbia University, New York, New York, USA
| | - Smita Krishnaswamy
- Department of Biological Sciences, Department of Systems Biology, Columbia University, New York, New York, USA
| | - Veronica D Gonzalez
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Cynthia G Lorang
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Zach Bjornson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew H Spitzer
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Bernd Bodenmiller
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Wendy J Fantl
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Dana Pe'er
- Department of Biological Sciences, Department of Systems Biology, Columbia University, New York, New York, USA
| | - Garry P Nolan
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| |
Collapse
|
215
|
Mei HE, Leipold MD, Schulz AR, Chester C, Maecker HT. Barcoding of live human peripheral blood mononuclear cells for multiplexed mass cytometry. THE JOURNAL OF IMMUNOLOGY 2015; 194:2022-31. [PMID: 25609839 DOI: 10.4049/jimmunol.1402661] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mass cytometry is developing as a means of multiparametric single-cell analysis. In this study, we present an approach to barcoding separate live human PBMC samples for combined preparation and acquisition on a cytometry by time of flight instrument. Using six different anti-CD45 Ab conjugates labeled with Pd104, Pd106, Pd108, Pd110, In113, and In115, respectively, we barcoded up to 20 samples with unique combinations of exactly three different CD45 Ab tags. Cell events carrying more than or less than three different tags were excluded from analyses during Boolean data deconvolution, allowing for precise sample assignment and the electronic removal of cell aggregates. Data from barcoded samples matched data from corresponding individually stained and acquired samples, at cell event recoveries similar to individual sample analyses. The approach greatly reduced technical noise and minimizes unwanted cell doublet events in mass cytometry data, and it reduces wet work and Ab consumption. It also eliminates sample-to-sample carryover and the requirement of instrument cleaning between samples, thereby effectively reducing overall instrument runtime. Hence, CD45 barcoding facilitates accuracy of mass cytometric immunophenotyping studies, thus supporting biomarker discovery efforts, and it should be applicable to fluorescence flow cytometry as well.
Collapse
Affiliation(s)
- Henrik E Mei
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305; and
| | - Michael D Leipold
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305; and
| | - Axel Ronald Schulz
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305; and
| | - Cariad Chester
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305; and Department of Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Holden T Maecker
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305; and
| |
Collapse
|
216
|
The Applications of Upconversion Nanoparticles in Bioassay. PHOTON UPCONVERSION NANOMATERIALS 2015. [DOI: 10.1007/978-3-662-45597-5_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
217
|
Ellinger B, Silber J, Prashar A, Landskron J, Weber J, Rehermann S, Müller FJ, Smith S, Wrigley S, Taskén K, Gribbon P, Labes A, Imhoff JF. A phenotypic screening approach to identify anticancer compounds derived from marine fungi. Assay Drug Dev Technol 2014; 12:162-75. [PMID: 24735443 DOI: 10.1089/adt.2013.564] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
This study covers the isolation, testing, and identification of natural products with anticancer properties. Secondary metabolites were isolated from fungal strains originating from a variety of marine habitats. Strain culture protocols were optimized with respect to growth media composition and fermentation conditions. From these producers, isolated compounds were screened for their effect on the viability and proliferation of a subset of the NCI60 panel of cancer cell lines. Active compounds of interest were identified and selected for detailed assessments and structural elucidation using nuclear magnetic resonance. This revealed the majority of fungal-derived compounds represented known anticancer chemotypes, confirming the integrity of the process and the ability to identify suitable compounds. Examination of effects of selected compounds on cancer-associated cell signaling pathways used phospho flow cytometry in combination with 3D fluorescent cell barcoding. In parallel, the study addressed the logistical aspects of maintaining multiple cancer cell lines in culture simultaneously. A potential solution involving microbead-based cell culture was investigated (BioLevitator, Hamilton). Selected cell lines were cultured in microbead and 2D methods and cell viability tests showed comparable compound inhibition in both methods (R2=0.95). In a further technology assessment, an image-based assay system was investigated for its utility as a possible complement to ATP-based detection for quantifying cell growth and viability in a label-free manner.
Collapse
|
218
|
Rapid determination of il-6 specific activity by flow cytometry. J Immunol Methods 2014; 415:63-5. [DOI: 10.1016/j.jim.2014.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 09/22/2014] [Accepted: 09/27/2014] [Indexed: 01/22/2023]
|
219
|
O’Connor JE, Herrera G, Martínez-Romero A, de Oyanguren FS, Díaz L, Gomes A, Balaguer S, Callaghan RC. Systems Biology and immune aging. Immunol Lett 2014; 162:334-45. [DOI: 10.1016/j.imlet.2014.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
|
220
|
Bernardo SM, Allen CP, Waller A, Young SM, Oprea T, Sklar LA, Lee SA. An automated high-throughput cell-based multiplexed flow cytometry assay to identify novel compounds to target Candida albicans virulence-related proteins. PLoS One 2014; 9:e110354. [PMID: 25350399 PMCID: PMC4211665 DOI: 10.1371/journal.pone.0110354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/18/2014] [Indexed: 11/19/2022] Open
Abstract
Although three major classes of systemic antifungal agents are clinically available, each is characterized by important limitations. Thus, there has been considerable ongoing effort to develop novel and repurposed agents for the therapy of invasive fungal infections. In an effort to address these needs, we developed a novel high-throughput, multiplexed screening method that utilizes small molecules to probe candidate drug targets in the opportunistic fungal pathogen Candida albicans. This method is amenable to high-throughput automated screening and is based upon detection of changes in GFP levels of individually tagged target proteins. We first selected four GFP-tagged membrane-bound proteins associated with virulence or antifungal drug resistance in C. albicans. We demonstrated proof-of-principle that modulation of fluorescence intensity can be used to assay the expression of specific GFP-tagged target proteins to inhibitors (and inducers), and this change is measurable within the HyperCyt automated flow cytometry sampling system. Next, we generated a multiplex of differentially color-coded C. albicans strains bearing C-terminal GFP-tags of each gene encoding candidate drug targets incubated in the presence of small molecules from the Prestwick Chemical Library in 384-well microtiter plate format. Following incubation, cells were sampled through the HyperCyt system and modulation of protein levels, as indicated by changes in GFP-levels of each strain, was used to identify compounds of interest. The hit rate for both inducers and inhibitors identified in the primary screen did not exceed 1% of the total number of compounds in the small-molecule library that was probed, as would be expected from a robust target-specific, high-throughput screening campaign. Secondary assays for virulence characteristics based on null mutant strains were then used to further validate specificity. In all, this study presents a method for the identification and verification of new antifungal drugs targeted to fungal virulence proteins using C. albicans as a model fungal pathogen.
Collapse
Affiliation(s)
- Stella M. Bernardo
- Section of Infectious Diseases, New Mexico Veterans Healthcare System, Albuquerque, NM, United States of America
- Division of Infectious Diseases, University of New Mexico Health Science Center, Albuquerque, NM, United States of America
| | - Christopher P. Allen
- Center for Molecular Discovery, University of New Mexico, Albuquerque, NM, United States of America
| | - Anna Waller
- Center for Molecular Discovery, University of New Mexico, Albuquerque, NM, United States of America
| | - Susan M. Young
- Center for Molecular Discovery, University of New Mexico, Albuquerque, NM, United States of America
| | - Tudor Oprea
- Center for Molecular Discovery, University of New Mexico, Albuquerque, NM, United States of America
| | - Larry A. Sklar
- Center for Molecular Discovery, University of New Mexico, Albuquerque, NM, United States of America
| | - Samuel A. Lee
- Section of Infectious Diseases, New Mexico Veterans Healthcare System, Albuquerque, NM, United States of America
- Division of Infectious Diseases, University of New Mexico Health Science Center, Albuquerque, NM, United States of America
- * E-mail:
| |
Collapse
|
221
|
Behbehani GK, Thom C, Zunder ER, Finck R, Gaudilliere B, Fragiadakis GK, Fantl WJ, Nolan GP. Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining. Cytometry A 2014; 85:1011-9. [PMID: 25274027 DOI: 10.1002/cyto.a.22573] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/19/2014] [Accepted: 09/15/2014] [Indexed: 12/29/2022]
Abstract
Fluorescent cellular barcoding and mass-tag cellular barcoding are cytometric methods that enable high sample throughput, minimize inter-sample variation, and reduce reagent consumption. Previously employed barcoding protocols require that barcoding be performed after surface marker staining, complicating combining the technique with measurement of alcohol-sensitive surface epitopes. This report describes a method of barcoding fixed cells after a transient partial permeabilization with 0.02% saponin that results in efficient and consistent barcode staining with fluorescent or mass-tagged reagents while preserving surface marker staining. This approach simplifies barcoding protocols and allows direct comparison of surface marker staining of multiple samples without concern for variations in the antibody cocktail volume, antigen-antibody ratio, or machine sensitivity. Using this protocol, cellular barcoding can be used to reliably detect subtle differences in surface marker expression.
Collapse
Affiliation(s)
- Gregory K Behbehani
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California; Divisions of Hematology and Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | | | | | | | | | | | | | | |
Collapse
|
222
|
O'Connor JE, Herrera G, Martínez-Romero A, Oyanguren FSD, Díaz L, Gomes A, Balaguer S, Callaghan RC. WITHDRAWN: Systems Biology and Immune Aging. Immunol Lett 2014:S0165-2478(14)00197-7. [PMID: 25251659 DOI: 10.1016/j.imlet.2014.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of anarticle that has already been published, http://dx.doi.org/10.1016/j.imlet.2014.09.009. The duplicate article has therefore been withdrawn.
Collapse
Affiliation(s)
- José-Enrique O'Connor
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain.
| | - Guadalupe Herrera
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Alicia Martínez-Romero
- Cytometry Technological Service, Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Francisco Sala-de Oyanguren
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Laura Díaz
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Angela Gomes
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Susana Balaguer
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Robert C Callaghan
- Department of Pathology, Faculty of Medicine, The University of Valencia, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| |
Collapse
|
223
|
Liu R, Wu P, Yang L, Hou X, Lv Y. Inductively coupled plasma mass spectrometry-based immunoassay: a review. MASS SPECTROMETRY REVIEWS 2014; 33:373-393. [PMID: 24272753 DOI: 10.1002/mas.21391] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 05/15/2013] [Accepted: 05/29/2013] [Indexed: 06/02/2023]
Abstract
The last 10 years witnessed the emerging and growing up of inductively coupled plasma mass spectrometry (ICPMS)-based immunoassay. Its high sensitivity and multiplex potential have made ICPMS a revolutionary technique for bioanalyte quantification after element-tagged immunoassay. This review focuses on the major developments and the applications of ICPMS-based immunoassay, with emphasis on methodological innovations. The ICPMS-based immunoassay with elemental tags of metal ions, nanoparticles, and metal containing polymers was discussed in detail. The recent development of multiplex assay, mass cytometry, suspension array, and surface analysis demonstrated the versatility and great potential of this technique. ICPMS-based immunoassay has become one of the key methods in bioanalysis.
Collapse
Affiliation(s)
- Rui Liu
- College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, P.R. China; Mineral Resources Chemistry Key Laboratory of Sichuan Higher Education Institutions, College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, Sichuan, 610059, P.R. China
| | | | | | | | | |
Collapse
|
224
|
Di Palma S, Bodenmiller B. Unraveling cell populations in tumors by single-cell mass cytometry. Curr Opin Biotechnol 2014; 31:122-9. [PMID: 25123841 DOI: 10.1016/j.copbio.2014.07.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 07/22/2014] [Indexed: 11/26/2022]
Abstract
The development of new biotechnologies for the analysis of individual cells in heterogeneous populations is an important direction of life science research. This review provides a critical overview of relevant and recent advances in the field of single-cell mass cytometry, focusing on the latest applications in the study of cell heterogeneity. New approaches for multiparameter single-cell imaging, alongside advanced computational tools for deep mining of high-dimensional mass cytometric data, are facilitating the visualization of specific cell types and their interactions in complex cellular assemblies, such as tumors, potentially revealing new insights into cancer biology.
Collapse
Affiliation(s)
- Serena Di Palma
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.
| |
Collapse
|
225
|
T-cell co-stimulation through the CD2 and CD28 co-receptors induces distinct signalling responses. Biochem J 2014; 460:399-410. [PMID: 24665965 DOI: 10.1042/bj20140040] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Full T-cell activation critically depends on the engagement of the TCR (T-cell receptor) in conjunction with a second signal by co-stimulatory receptors that boost the immune response. In the present study we have compared signalling patterns induced by the two co-receptors CD2 and CD28 in human peripheral blood T-cells. These co-receptors were previously suggested to be redundant in function. By a combination of multi-parameter phosphoflow cytometry, phosphokinase arrays and Western blot analyses, we demonstrate that CD2 co-stimulation induces phosphorylation of the TCR-proximal signalling complex, whereas CD28 activates distal signalling molecules, including the transcription factors NF-κB (nuclear factor κB), ATF (activating transcription factor)-2, STAT3/5 (signal transducer and activator of transcription 3/5), p53 and c-Jun. These signalling patterns were conserved in both naïve and effector/memory T-cell subsets. We show that free intracellular Ca(2+) and signalling through the PI3K (phosphoinositide 3-kinase)/Akt pathway are required for proper CD28-induced NF-κB activation. The signalling patterns induced by CD2 and CD28 co-stimulation lead to distinct functional immune responses in T-cell proliferation and cytokine production. In conclusion, CD2 and CD28 co-stimulation induces distinct signalling responses and functional outcomes in T-cells.
Collapse
|
226
|
Zhu Z, Frey O, Franke F, Haandbæk N, Hierlemann A. Real-time monitoring of immobilized single yeast cells through multifrequency electrical impedance spectroscopy. Anal Bioanal Chem 2014; 406:7015-25. [PMID: 25012351 DOI: 10.1007/s00216-014-7955-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 05/30/2014] [Accepted: 06/05/2014] [Indexed: 11/24/2022]
Abstract
We present a microfluidic device, which enables single cells to be reliably trapped and cultivated while simultaneously being monitored by means of multifrequency electrical impedance spectroscopy (EIS) in the frequency range of 10 kHz-10 MHz. Polystyrene beads were employed to characterize the EIS performance inside the microfluidic device. The results demonstrate that EIS yields a low coefficient of variation in measuring the diameters of captured beads (~0.13%). Budding yeast, Saccharomyces cerevisiae, was afterwards used as model organism. Single yeast cells were immobilized and measured by means of EIS. The bud growth was monitored through EIS at a temporal resolution of 1 min. The size increment of the bud, which is difficult to determine optically within a short time period, can be clearly detected through EIS signals. The impedance measurements also reflect the changes in position or motion of single yeast cells in the trap. By analyzing the multifrequency EIS data, cell motion could be qualitatively discerned from bud growth. The results demonstrate that single-cell EIS can be used to monitor cell growth, while also detecting potential cell motion in real-time and label-free approach, and that EIS constitutes a sensitive tool for dynamic single-cell analysis.
Collapse
Affiliation(s)
- Zhen Zhu
- Bio Engineering Laboratory (BEL), Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland,
| | | | | | | | | |
Collapse
|
227
|
Clark MA, Goheen MM, Spidale NA, Kasthuri RS, Fulford A, Cerami C. RBC barcoding allows for the study of erythrocyte population dynamics and P. falciparum merozoite invasion. PLoS One 2014; 9:e101041. [PMID: 24984000 PMCID: PMC4077748 DOI: 10.1371/journal.pone.0101041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/02/2014] [Indexed: 11/30/2022] Open
Abstract
Plasmodium falciparum invasion of host erythrocytes is essential for the propagation of the blood stage of malaria infection. Additionally, the brief extracellular merozoite stage of P. falciparum represents one of the rare windows during which the parasite is directly exposed to the host immune response. Therefore, efficient invasion of the host erythrocyte is necessary not only for productive host erythrocyte infection, but also for evasion of the immune response. Host traits, such as hemoglobinopathies and differential expression of erythrocyte invasion ligands, can protect individuals from malaria by impeding parasite erythrocyte invasion. Here we combine RBC barcoding with flow cytometry to study P. falciparum invasion. This novel high-throughput method allows for the (i) direct comparison of P. falciparum invasion into different erythrocyte populations and (ii) assessment of the impact of changing erythrocyte population dynamics on P. falciparum invasion.
Collapse
Affiliation(s)
- Martha A Clark
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Morgan M Goheen
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Nicholas A Spidale
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Raj S Kasthuri
- Division of Hematology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Anthony Fulford
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Carla Cerami
- Medical Research Council International Nutrition Group, London School of Hygiene and Tropical Medicine, London, United Kingdom & Medical Research Council Keneba, The Gambia
| |
Collapse
|
228
|
Pyne S, Lee SX, Wang K, Irish J, Tamayo P, Nazaire MD, Duong T, Ng SK, Hafler D, Levy R, Nolan GP, Mesirov J, McLachlan GJ. Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data. PLoS One 2014; 9:e100334. [PMID: 24983991 PMCID: PMC4077578 DOI: 10.1371/journal.pone.0100334] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/23/2014] [Indexed: 01/20/2023] Open
Abstract
In biomedical applications, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multivariate responses of a panel of markers such as from a signaling network. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While computational methods can identify cell populations in individual samples, without the ability to automatically match them across samples, it is difficult to compare and characterize the populations in typical experiments, such as those responding to various stimulations or distinctive of particular patients or time-points, especially when there are many samples. Joint Clustering and Matching (JCM) is a multi-level framework for simultaneous modeling and registration of populations across a cohort. JCM models every population with a robust multivariate probability distribution. Simultaneously, JCM fits a random-effects model to construct an overall batch template – used for registering populations across samples, and classifying new samples. By tackling systems-level variation, JCM supports practical biomedical applications involving large cohorts. Software for fitting the JCM models have been implemented in an R package EMMIX-JCM, available from http://www.maths.uq.edu.au/~gjm/mix_soft/EMMIX-JCM/.
Collapse
Affiliation(s)
- Saumyadipta Pyne
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, Hyderabad, Andhra Pradesh, India
| | - Sharon X. Lee
- Department of Mathematics, University of Queensland, St. Lucia, Queensland, Australia
| | - Kui Wang
- Department of Mathematics, University of Queensland, St. Lucia, Queensland, Australia
| | - Jonathan Irish
- Division of Oncology, Stanford Medical School, Stanford, California, United States of America
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, United States of America
- Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Pablo Tamayo
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Marc-Danie Nazaire
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Tarn Duong
- Molecular Mechanisms of Intracellular Transport, Unit Mixte de Recherche 144 Centre National de la Recherche Scientifique/Institut Curie, Paris, France
| | - Shu-Kay Ng
- School of Medicine, Griffith University, Meadowbrook, Queensland, Australia
| | - David Hafler
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Ronald Levy
- Division of Oncology, Stanford Medical School, Stanford, California, United States of America
| | - Garry P. Nolan
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, United States of America
| | - Jill Mesirov
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Geoffrey J. McLachlan
- Department of Mathematics, University of Queensland, St. Lucia, Queensland, Australia
- * E-mail:
| |
Collapse
|
229
|
Quah BJC, Wijesundara DK, Ranasinghe C, Parish CR. The use of fluorescent target arrays for assessment of T cell responses in vivo. J Vis Exp 2014:e51627. [PMID: 24998253 DOI: 10.3791/51627] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The ability to monitor T cell responses in vivo is important for the development of our understanding of the immune response and the design of immunotherapies. Here we describe the use of fluorescent target array (FTA) technology, which utilizes vital dyes such as carboxyfluorescein succinimidyl ester (CFSE), violet laser excitable dyes (CellTrace Violet: CTV) and red laser excitable dyes (Cell Proliferation Dye eFluor 670: CPD) to combinatorially label mouse lymphocytes into > 250 discernable fluorescent cell clusters. Cell clusters within these FTAs can be pulsed with major histocompatibility (MHC) class-I and MHC class-II binding peptides and thereby act as target cells for CD8(+) and CD4(+) T cells, respectively. These FTA cells remain viable and fully functional, and can therefore be administered into mice to allow assessment of CD8(+) T cell-mediated killing of FTA target cells and CD4(+) T cell-meditated help of FTA B cell target cells in real time in vivo by flow cytometry. Since > 250 target cells can be assessed at once, the technique allows the monitoring of T cell responses against several antigen epitopes at several concentrations and in multiple replicates. As such, the technique can measure T cell responses at both a quantitative (e.g. the cumulative magnitude of the response) and a qualitative (e.g. functional avidity and epitope-cross reactivity of the response) level. Herein, we describe how these FTAs are constructed and give an example of how they can be applied to assess T cell responses induced by a recombinant pox virus vaccine.
Collapse
Affiliation(s)
- Benjamin J C Quah
- Department of Immunology, John Curtin School of Medical Research, Australian National University;
| | - Danushka K Wijesundara
- Department of Immunology, John Curtin School of Medical Research, Australian National University
| | - Charani Ranasinghe
- Department of Immunology, John Curtin School of Medical Research, Australian National University
| | - Christopher R Parish
- Department of Immunology, John Curtin School of Medical Research, Australian National University
| |
Collapse
|
230
|
Association between latent proviral characteristics and immune activation in antiretrovirus-treated human immunodeficiency virus type 1-infected adults. J Virol 2014; 88:8629-39. [PMID: 24850730 DOI: 10.1128/jvi.01257-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
UNLABELLED Generalized immune activation during HIV infection is associated with an increased risk of cardiovascular disease, neurocognitive disease, osteoporosis, metabolic disorders, and physical frailty. The mechanisms driving this immune activation are poorly understood, particularly for individuals effectively treated with antiretroviral medications. We hypothesized that viral characteristics such as sequence diversity may play a role in driving HIV-associated immune activation. We therefore sequenced proviral DNA isolated from peripheral blood mononuclear cells from HIV-infected individuals on fully suppressive antiretroviral therapy. We performed phylogenetic analyses, calculated viral diversity and divergence in the env and pol genes, and determined coreceptor tropism and the frequency of drug resistance mutations. Comprehensive immune profiling included quantification of immune cell subsets, plasma cytokine levels, and intracellular signaling responses in T cells, B cells, and monocytes. These antiretroviral therapy-treated HIV-infected individuals exhibited a wide range of diversity and divergence in both env and pol genes. However, proviral diversity and divergence in env and pol, coreceptor tropism, and the level of drug resistance did not significantly correlate with markers of immune activation. A clinical history of virologic failure was also not significantly associated with levels of immune activation, indicating that a history of virologic failure does not inexorably lead to increased immune activation as long as suppressive antiretroviral medications are provided. Overall, this study demonstrates that latent viral diversity is unlikely to be a major driver of persistent HIV-associated immune activation. IMPORTANCE Chronic immune activation, which is associated with cardiovascular disease, neurologic disease, and early aging, is likely to be a major driver of morbidity and mortality in HIV-infected individuals. Although treatment of HIV with antiretroviral medications decreases the level of immune activation, levels do not return to normal. The factors driving this persistent immune activation, particularly during effective treatment, are poorly understood. In this study, we investigated whether characteristics of the latent, integrated HIV provirus that persists during treatment are associated with immune activation. We found no relationship between latent viral characteristics and immune activation in treated individuals, indicating that qualities of the provirus are unlikely to be a major driver of persistent inflammation. We also found that individuals who had previously failed treatment but were currently effectively treated did not have significantly increased levels of immune activation, providing hope that past treatment failures do not have a lifelong "legacy" impact.
Collapse
|
231
|
Nolan JP. Knowing the code. Cytometry A 2014; 85:10-1. [PMID: 24591112 DOI: 10.1002/cyto.a.22419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 11/01/2013] [Indexed: 11/08/2022]
Affiliation(s)
- John P Nolan
- La Jolla Bioengineering Institute, La Jolla, California
| |
Collapse
|
232
|
Lin G, Baraban L, Han L, Karnaushenko D, Makarov D, Cuniberti G, Schmidt OG. Magnetoresistive emulsion analyzer. Sci Rep 2014; 3:2548. [PMID: 23989504 PMCID: PMC3757360 DOI: 10.1038/srep02548] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 08/06/2013] [Indexed: 12/04/2022] Open
Abstract
We realize a magnetoresistive emulsion analyzer capable of detection, multiparametric analysis and sorting of ferrofluid-containing nanoliter-droplets. The operation of the device in a cytometric mode provides high throughput and quantitative information about the dimensions and magnetic content of the emulsion. Our method offers important complementarity to conventional optical approaches involving ferrofluids, and paves the way to the development of novel compact tools for diagnostics and nanomedicine including drug design and screening.
Collapse
Affiliation(s)
- Gungun Lin
- Institute for Integrative Nanosciences, IFW Dresden, Helmholtzstrasse 20, Dresden, Germany
| | | | | | | | | | | | | |
Collapse
|
233
|
Abstract
Oxidative metabolism is one of the central physiological processes that regulate multiple functions in a cell including cell death and survival, proliferation, gene transcription, and protein modification. There are multitudes of techniques that are used to evaluate oxidative activity. Here, we summarize how to measure oxidative activity by flow cytometry. This versatile technique allows the evaluation of the level of oxidative activity within heterogeneous populations of cells and in cell culture. Flow cytometry is a quick method that yields highly reproducible results with small sample volumes. Therefore, it is an ideal technique for evaluating changes in oxidative activity in samples from mice.
Collapse
|
234
|
Frick A, Suzuki O, Butz N, Chan E, Wiltshire T. In vitro and in vivo mouse models for pharmacogenetic studies. Methods Mol Biol 2014; 1015:263-78. [PMID: 23824862 DOI: 10.1007/978-1-62703-435-7_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The identification of causative genes underlying biomedically relevant phenotypes, particularly complex multigenic traits, is of vital interest to modern medicine. Using genome-wide association analysis, many studies have successfully identified thousands of loci (called quantitative trait loci or QTL), some of these associating with drug response phenotypes. However, the determination and validation of putative genes has been much more challenging. The actions of drugs, both efficacious and deleterious, are complex phenotypes that are controlled or influenced in part by genetic mechanisms.Investigation for genetic correlates of complex traits and pharmacogenetic traits is often difficult to perform in human studies due to cost, availability of relevant sample population, and limited ability to control for environmental effects. These challenges can be circumvented with the use of mouse models for pharmacogenetic studies. In addition, the mouse can be treated at sub- and supratherapeutic doses and subjected to invasive procedures, which can facilitate measures of drug response phenotypes, making identification of pharmacogenetically relevant genes more feasible. The availability of multiple mouse genetic and phenotypic resources is an additional benefit to using the mouse for pharmacogenetic studies.Here, we describe the contribution of animal models, specifically the mouse, towards the field of pharmacogenetics. In this chapter, we describe different mouse models, including the knockout mouse, recombinant mouse inbred strains, in vitro mouse cell-based assays, as well as novel experimental approaches like the Collaborative Cross recombinant mouse inbred panel, which can be applied to preclinical pharmacogenetics research. These approaches can be used to assess drug response phenotypes that are difficult to model in humans, thereby facilitating drug discovery, development, and application.
Collapse
Affiliation(s)
- Amber Frick
- Division of Pharmacotherapy and Experimental Therapeutics, Institute for Pharmacogenomics and Individualized Therapy, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | | |
Collapse
|
235
|
Chattopadhyay PK, Gierahn TM, Roederer M, Love JC. Single-cell technologies for monitoring immune systems. Nat Immunol 2014; 15:128-35. [PMID: 24448570 PMCID: PMC4040085 DOI: 10.1038/ni.2796] [Citation(s) in RCA: 275] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 11/25/2013] [Indexed: 12/12/2022]
Abstract
The complex heterogeneity of cells, and their interconnectedness with each other, are major challenges to identifying clinically relevant measurements that reflect the state and capability of the immune system. Highly multiplexed, single-cell technologies may be critical for identifying correlates of disease or immunological interventions as well as for elucidating the underlying mechanisms of immunity. Here we review limitations of bulk measurements and explore advances in single-cell technologies that overcome these problems by expanding the depth and breadth of functional and phenotypic analysis in space and time. The geometric increases in complexity of data make formidable hurdles for exploring, analyzing and presenting results. We summarize recent approaches to making such computations tractable and discuss challenges for integrating heterogeneous data obtained using these single-cell technologies.
Collapse
Affiliation(s)
- Pratip K Chattopadhyay
- ImmunoTechnology Section, Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, Maryland, USA
| | - Todd M Gierahn
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, Maryland, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
236
|
Wong DJL, Rao A, Avramis E, Matsunaga DR, Komatsubara KM, Atefi MS, Escuin-Ordinas H, Chodon T, Koya RC, Ribas A, Comin-Anduix B. Exposure to a histone deacetylase inhibitor has detrimental effects on human lymphocyte viability and function. Cancer Immunol Res 2014; 2:459-68. [PMID: 24795358 DOI: 10.1158/2326-6066.cir-13-0188] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Histone deacetylase inhibitors (HDACi) have been reported to increase tumor antigen expression, and have been successfully tested as adjuvants for melanoma immunotherapy in mouse models. In this work, we tested the effects of a pan-HDACi on human lymphocytes and melanoma cell lines. Effects of the pan-HDACi panobinostat (LBH589) on cell viability, cell cycle, apoptosis, and DNA damage were determined in peripheral blood mononuclear cells (PBMC) from 2 healthy donors, 13 patients with metastatic melanoma, 2 bone marrow samples from patients with different malignances, and 12 human melanoma cell lines. Intracellular signaling in lymphocytes, with or without cytokine stimulation, was analyzed by phospho-flow cytometry in one of each type. The IC50 in PBMCs was <20 nmol/L compared with >600 nmol/L in melanoma cell lines; >40% apoptotic cell death in PBMCs versus <10% in melanoma cell lines was seen at the same concentration. Phospho-histone variant H2A.X (pH2A.X) increased 2-fold in healthy donor PBMCs at 1 nmol/L, whereas the same effect in the melanoma cell line M229 required 10 nmol/L. pH2A.X was inhibited slightly in the PBMCs of 3 patients with metastatic melanoma at 1 nmol/L and in the melanoma cell line M370 at 10 nmol/L. Panobinostat inhibited phospho-STAT1/3/5/6, -p38, -ERK, -p53, -cyclin D3, and -histone H3 in flow cytometry-gated healthy donor B and T cells, whereas it induced up to 6-fold activation in patients with metastatic melanoma and bone marrow samples. In human lymphocytes, panobinostat alters key lymphocyte activation signaling pathways and is cytotoxic at concentrations much lower than those required for melanoma antitumor activity, resulting in an adverse therapeutic window.
Collapse
Affiliation(s)
- Deborah J L Wong
- Authors' Affiliations: Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
237
|
Chowdhury I, Fisher AB, Christofidou-Solomidou M, Gao L, Tao JQ, Sorokina EM, Lien YC, Bates SR, Feinstein SI. Keratinocyte growth factor and glucocorticoid induction of human peroxiredoxin 6 gene expression occur by independent mechanisms that are synergistic. Antioxid Redox Signal 2014; 20:391-402. [PMID: 23815338 PMCID: PMC3894679 DOI: 10.1089/ars.2012.4634] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AIMS Peroxiredoxin 6 (Prdx6), a 1-cys Prdx has both peroxidase and phospholipase A2 activities, protecting against oxidative stress and regulating pulmonary surfactant phospholipid metabolism. This study determined the mechanism by which keratinocyte growth factor (KGF) and the glucocorticoid analogue, dexamethasone (Dex), induce increased Prdx6 expression. RESULTS Transcriptional activation by KGF in both A549 lung adenocarcinoma cells and rat lung alveolar epithelial type II (ATII) cells utilizes an antioxidant response element (ARE), located between 357 and 349 nucleotides before the PRDX6 translational start, that is also necessary for upregulation of the human PRDX6 promoter in response to oxidative stress. Activation is mediated by binding of the transcription factor, Nrf2, to the ARE as shown by experiments using siRNA against Nrf2 and by transfecting ATII cells isolated from lungs of Nrf2 null mice. KGF triggers the migration of Nrf2 from cytoplasm to nucleus where it binds to the PRDX6 promoter as shown by chromatin immunoprecipitation assays. Activation of transcription by Dex occurs through a glucocorticoid response element located about 750 nucleotides upstream of the PRDX6 translational start. INNOVATION This study demonstrates that KGF can activate an ARE in a promoter without reactive oxygen species involvement and that KGF and Dex can synergistically activate the PRDX6 promoter and protect cells from oxidative stress. CONCLUSION These two different activators work through different DNA elements. Their combined effect on transcription of the reporter gene is synergistic; however, at the protein level, the combined effect is additive and protects cells from oxidative damage.
Collapse
Affiliation(s)
- Ibrul Chowdhury
- 1 Institute for Environmental Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | | | | | | | | | | | | | | | | |
Collapse
|
238
|
Abstract
Mass cytometry is a form of flow cytometry based on single-cell mass spectrometry that uses monoisotopic elemental labels to probe individual cells. Reduced cross talk between channels and an ability to measure >30 independent cellular parameters make this an attractive approach for high-dimensional analysis of cellular phenotypes and function. Here, methods of using this approach for the analysis of human T cell surface markers and intracellular cytokines are described.
Collapse
Affiliation(s)
- Evan W Newell
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A-STAR), 8A Biomedical Grove, Immunos #03-06, Singapore, 138648, Singapore,
| | | |
Collapse
|
239
|
Moraga I, Spangler J, Mendoza JL, Garcia KC. Multifarious determinants of cytokine receptor signaling specificity. Adv Immunol 2014; 121:1-39. [PMID: 24388212 DOI: 10.1016/b978-0-12-800100-4.00001-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cytokines play crucial roles in regulating immune homeostasis. Two important characteristics of most cytokines are pleiotropy, defined as the ability of one cytokine to exhibit diverse functionalities, and redundancy, defined as the ability of multiple cytokines to exert overlapping activities. Identifying the determinants for unique cellular responses to cytokines in the face of shared receptor usage, pleiotropy, and redundancy will be essential in order to harness the potential of cytokines as therapeutics. Here, we discuss the biophysical (ligand-receptor geometry and affinity) and cellular (receptor trafficking and intracellular abundance of signaling molecules) parameters that contribute to the specificity of cytokine bioactivities. Whereas the role of extracellular ternary complex geometry in cytokine-induced signaling is still not completely elucidated, cytokine-receptor affinity is known to impact signaling through modulation of the stability and kinetics of ternary complex formation. Receptor trafficking also plays an important and likely underappreciated role in the diversification of cytokine bioactivities but it has been challenging to experimentally probe trafficking effects. We also review recent efforts to quantify levels of intracellular signaling components, as second messenger abundance can affect cytokine-induced bioactivities both quantitatively and qualitatively. We conclude by discussing the application of protein engineering to develop therapeutically relevant cytokines with reduced pleiotropy and redirected biological functionalities.
Collapse
Affiliation(s)
- Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jamie Spangler
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Juan L Mendoza
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA; Program in Immunology, Stanford University School of Medicine, Stanford, California, USA.
| |
Collapse
|
240
|
Wolpaw AJ, Stockwell BR. Multidimensional profiling in the investigation of small-molecule-induced cell death. Methods Enzymol 2014; 545:265-302. [PMID: 25065894 DOI: 10.1016/b978-0-12-801430-1.00011-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Numerous morphological variations of cell death have been described. These processes depend on a complex and overlapping cellular signaling network, making molecular definition of the pathways challenging. This review describes one solution to this problem for small-molecule-induced death, the creation of high-dimensionality profiles for compounds that can be used to define and compare pathways. Such profiles have been assembled from gene expression measurements, protein quantification, chemical-genetic interactions, chemical combination interactions, cancer cell line sensitivity profiling, quantitative imaging, and modulatory profiling. We discuss the advantages and limitations of these techniques in the study of cell death.
Collapse
Affiliation(s)
- Adam J Wolpaw
- Residency Program in Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York, USA; Department of Chemistry, Columbia University, New York, USA; Howard Hughes Medical Institute, Columbia University, New York, USA.
| |
Collapse
|
241
|
Abstract
Cancer cells are distinguished from each other and from healthy cells by features that drive clonal evolution and therapy resistance. New advances in high-dimensional flow cytometry make it possible to systematically measure mechanisms of tumor initiation, progression, and therapy resistance on millions of cells from human tumors. Here we describe flow cytometry techniques that enable a "single-cell " view of cancer. High-dimensional techniques like mass cytometry enable multiplexed single-cell analysis of cell identity, clinical biomarkers, signaling network phospho-proteins, transcription factors, and functional readouts of proliferation, cell cycle status, and apoptosis. This capability pairs well with a signaling profiles approach that dissects mechanism by systematically perturbing and measuring many nodes in a signaling network. Single-cell approaches enable study of cellular heterogeneity of primary tissues and turn cell subsets into experimental controls or opportunities for new discovery. Rare populations of stem cells or therapy-resistant cancer cells can be identified and compared to other types of cells within the same sample. In the long term, these techniques will enable tracking of minimal residual disease (MRD) and disease progression. By better understanding biological systems that control development and cell-cell interactions in healthy and diseased contexts, we can learn to program cells to become therapeutic agents or target malignant signaling events to specifically kill cancer cells. Single-cell approaches that provide deep insight into cell signaling and fate decisions will be critical to optimizing the next generation of cancer treatments combining targeted approaches and immunotherapy.
Collapse
|
242
|
Arnandis-Chover T, Morais S, González-Martínez MÁ, Puchades R, Maquieira Á. High density MicroArrays on Blu-ray discs for massive screening. Biosens Bioelectron 2014; 51:109-14. [DOI: 10.1016/j.bios.2013.07.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/19/2013] [Accepted: 07/22/2013] [Indexed: 12/01/2022]
|
243
|
Haselgrübler T, Haider M, Ji B, Juhasz K, Sonnleitner A, Balogi Z, Hesse J. High-throughput, multiparameter analysis of single cells. Anal Bioanal Chem 2013; 406:3279-96. [PMID: 24292433 DOI: 10.1007/s00216-013-7485-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/04/2013] [Accepted: 11/04/2013] [Indexed: 12/23/2022]
Abstract
Heterogeneity of cell populations in various biological systems has been widely recognized, and the highly heterogeneous nature of cancer cells has been emerging with clinical relevance. Single-cell analysis using a combination of high-throughput and multiparameter approaches is capable of reflecting cell-to-cell variability, and at the same time of unraveling the complexity and interdependence of cellular processes in the individual cells of a heterogeneous population. In this review, analytical methods and microfluidic tools commonly used for high-throughput, multiparameter single-cell analysis of DNA, RNA, and proteins are discussed. Applications and limitations of currently available technologies for cancer research and diagnostics are reviewed in the light of the ultimate goal to establish clinically applicable assays.
Collapse
Affiliation(s)
- Thomas Haselgrübler
- Center for Advanced Bioanalysis GmbH, Gruberstraße 40-42, 4020, Linz, Austria,
| | | | | | | | | | | | | |
Collapse
|
244
|
Ladanov M, Cheemalapati S, Pyayt A. Optimization of light delivery by a nanowire-based single cell optical endoscope. OPTICS EXPRESS 2013; 21:28001-28009. [PMID: 24514313 DOI: 10.1364/oe.21.028001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Here we present a new design and FDTD simulations of light delivery by a nanowire-based intracellular endoscope. Nanowires can be used for minimally invasive and very local light delivery inside cells. One of the main challenges is coupling of light into the nanowire. We propose a new plasmonic coupler interface between cleaved optical fiber and a nanowire, and optimize light coupling efficiency and contrast.
Collapse
|
245
|
Simard C, Cloutier M, Néron S. Feasibility study: Phosphospecific flow cytometry enabling rapid functional analysis of bone marrow samples from patients with multiple myeloma. CYTOMETRY PART B-CLINICAL CYTOMETRY 2013; 86:139-44. [DOI: 10.1002/cyto.b.21142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 09/13/2013] [Accepted: 10/18/2013] [Indexed: 01/11/2023]
Affiliation(s)
- Carl Simard
- Héma-Québec, Ingénierie cellulaire, Recherche et Développement; 1070 avenue des Sciences-de-la-vie; Québec G1V 5C3 Canada
| | - Marc Cloutier
- Héma-Québec, Ingénierie cellulaire, Recherche et Développement; 1070 avenue des Sciences-de-la-vie; Québec G1V 5C3 Canada
| | - Sonia Néron
- Héma-Québec, Ingénierie cellulaire, Recherche et Développement; 1070 avenue des Sciences-de-la-vie; Québec G1V 5C3 Canada
- Université Laval, Faculté des sciences et de génie; Département de Biochimie, de Microbiologie et de Bio-informatique; 1045 avenue de la Médecine Québec G1V 0A6 Canada
| |
Collapse
|
246
|
Nishi H, Mathäs R, Fürst R, Winter G. Label-free flow cytometry analysis of subvisible aggregates in liquid IgG1 antibody formulations. J Pharm Sci 2013; 103:90-9. [PMID: 24218205 DOI: 10.1002/jps.23782] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/08/2013] [Accepted: 10/18/2013] [Indexed: 01/13/2023]
Abstract
The objective of this study was to characterize and quantify label-free subvisible antibody particles in different formulations based on their size and physical properties by flow cytometry. Protein subvisible particles were prepared under various stress conditions and analyzed by applying different analytical techniques [light obscuration (LO), microflow imaging (MFI), and flow cytometry (FACS)] for the detection of aggregates. The capability of the FACS method to detect and count subvisible particles was evaluated and benchmarked against conventional techniques. FACS can analyze particles down to 500 nm reducing the gap between size-exclusion chromatography and LO. The applied methods of FACS, LO, and MFI displayed a proportional correlation between the total particle counts, however, FACS can provide additional information on the structural characteristics of such aggregated particles.
Collapse
Affiliation(s)
- Hirotaka Nishi
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig Maximilian University Munich, Munich, 81377, Germany
| | | | | | | |
Collapse
|
247
|
Smurthwaite CA, Hilton BJ, O'Hanlon R, Stolp ZD, Hancock BM, Abbadessa D, Stotland A, Sklar LA, Wolkowicz R. Fluorescent genetic barcoding in mammalian cells for enhanced multiplexing capabilities in flow cytometry. Cytometry A 2013; 85:105-13. [DOI: 10.1002/cyto.a.22406] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/01/2013] [Accepted: 10/04/2013] [Indexed: 01/19/2023]
Affiliation(s)
| | - Brett J. Hilton
- Department of Biology; San Diego State University; San Diego California 92182
| | - Ryan O'Hanlon
- Department of Biology; San Diego State University; San Diego California 92182
| | - Zachary D. Stolp
- Department of Biology; San Diego State University; San Diego California 92182
| | - Bryan M. Hancock
- Department of Biology; San Diego State University; San Diego California 92182
| | - Darin Abbadessa
- Department of Biology; San Diego State University; San Diego California 92182
| | - Aleksandr Stotland
- Department of Biology; San Diego State University; San Diego California 92182
| | - Larry A. Sklar
- UNM Center for Molecular Discovery; University of New Mexico School of Medicine; Albuquerque New Mexico 87131
- Department of Pathology; University of New Mexico School of Medicine; Albuquerque New Mexico 87131
| | - Roland Wolkowicz
- Department of Biology; San Diego State University; San Diego California 92182
| |
Collapse
|
248
|
Xu W, Narayanan P, Kang N, Clayton S, Ohne Y, Shi P, Herve MC, Balderas R, Picard C, Casanova JL, Gorvel JP, Oh S, Pascual V, Banchereau J. Human plasma cells express granzyme B. Eur J Immunol 2013; 44:275-84. [PMID: 24114594 DOI: 10.1002/eji.201343711] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/29/2013] [Accepted: 09/17/2013] [Indexed: 11/06/2022]
Abstract
While studying the plasma cell (PC) compartment in human tonsils, we identified that immunoglobulin kappa or lambda chain-expressing PCs are the main cells expressing granzyme B (GrzB). In vitro studies revealed that activated B cells differentiated into GrzB-expressing PCs when co-cultured with macrophages and follicular helper T cells. This effect could be reproduced on combined stimulation of IL-15 (produced by macrophages) and IL-21 (produced by T follicular helper cells) in a STAT3-dependent manner. Whereas IL-21 triggers the transcription of mRNA of GrzB, IL-15 synergizes the translation of GrzB proteins. The precise role of GrzB in PC biology remains to be understood and studies in mice will not help as their PCs do not express GrzB.
Collapse
Affiliation(s)
- Wei Xu
- Baylor Institute for Immunology Research, Dallas, TX, USA; Pharma Research and Early Development, Roche Glycart, Schlieren, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
249
|
Wang X, Wang G, Li W, Zhao B, Xing B, Leng Y, Dou H, Sun K, Shen L, Yuan X, Li J, Sun K, Han J, Xiao H, Li Y, Huang P, Chen X. NIR-emitting quantum dot-encoded microbeads through membrane emulsification for multiplexed immunoassays. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3327-3335. [PMID: 23463727 DOI: 10.1002/smll.201203156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/21/2013] [Indexed: 06/01/2023]
Abstract
NIR-emitting CdSeTe/CdS/ZnS core/shell/shell QD-encoded microbeads are combined with common flow cytometry with one laser for multiplexed detection of hepatitis B virus (HBV). A facile one-pot synthetic route is developed to prepare CdSeTe/CdS/ZnS core/shell/shell QDs with high photoluminescence quantum yield and excellent stability in liquid paraffin, and a Shirasu porous glass (SPG) membrane emulsification technique is applied to incorporate the QDs into polystyrene-maleic anhydride (PSMA) microbeads to obtain highly fluorescent QD-encoded microbeads. The relatively wide NIR photoluminescence full width half maximum of the CdSeTe/CdS/ZnS QDs is used to develop a 'single wavelength' encoding method to obtain different optical codes by changing the wavelengh and emission intensity of the QDs incorporated into the microbeads. Moreover, a detection platform combining NIR-emitting CdSeTe/CdS/ZnS QD-encoded microbeads and Beckman Coulter FC 500 flow cytometry with one laser of 488 nm is successfully used to conduct a 2-plex hybridization assay for hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), and a 3-plex hybridization assay for hepatitis B surface antibody (HBsAb), hepatitis B e antibody (HBeAb), and hepatitis B core antibody (HBcAb), which suggests the promising application of NIR QD-encoded microbeads for multiplex immunoassays.
Collapse
Affiliation(s)
- Xiebing Wang
- State Key Lab of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
250
|
Genomic and systems approaches to translational biomarker discovery in immunological diseases. Drug Discov Today 2013; 19:133-9. [PMID: 24126144 DOI: 10.1016/j.drudis.2013.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 09/13/2013] [Accepted: 10/04/2013] [Indexed: 02/07/2023]
Abstract
The high failure rate of new therapeutic mechanisms tested in clinical development has spurred an upsurge in research dedicated to discovering biomarker readouts that can improve decision-making. Increasingly, systems biology and genomic technologies, such as transcriptional profiling, are being leveraged to aid in the discovery of biomarker readouts. For inflammatory and immunological diseases, such as rheumatoid arthritis (RA) and asthma, progress has been made in developing biomarkers to monitor disease activity, prediction of response to therapy, and pharmacodynamic (PD) measurements. In this review, we discuss recent successes and challenges in these endeavors, highlighting the importance of human clinical studies of standard-of-care treatments in control subjects and patients with disease as the most direct path toward identifying useful translational biomarkers for clinical development.
Collapse
|