651
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Mondal M, Liao R, Xiao L, Eno T, Guo J. Highly Multiplexed Single-Cell In Situ Protein Analysis with Cleavable Fluorescent Antibodies. Angew Chem Int Ed Engl 2017; 56:2636-2639. [PMID: 28128531 DOI: 10.1002/anie.201611641] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 12/24/2016] [Indexed: 01/23/2023]
Abstract
Limitations on the number of proteins that can be quantified in single cells in situ impede advances in our deep understanding of normal cell physiology and disease pathogenesis. Herein, we present a highly multiplexed single-cell in situ protein analysis approach that is based on chemically cleavable fluorescent antibodies. In this method, antibodies tethered to fluorophores through a novel azide-based cleavable linker are utilized to detect their protein targets. After fluorescence imaging and data storage, the fluorophores coupled to the antibodies are efficiently cleaved without loss of protein target antigenicity. Upon continuous cycles of target recognition, fluorescence imaging, and fluorophore cleavage, this approach has the potential to quantify over 100 different proteins in individual cells at optical resolution. This single-cell in situ protein profiling technology will have wide applications in signaling network analysis, molecular diagnosis, and cellular targeted therapies.
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Affiliation(s)
- Manas Mondal
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, 85287, USA
| | - Renjie Liao
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, 85287, USA
| | - Lu Xiao
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, 85287, USA
| | - Taylor Eno
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, 85287, USA
| | - Jia Guo
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, 85287, USA
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652
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Abstract
Hematopoiesis is probably the best-understood stem cell differentiation system; hematopoietic stem cell (HSC) transplantation represents the most widely used regenerative therapy. The classical view of lineage hierarchy in hematopoiesis is built on cell type definition system by a group of cell surface markers. However, the traditional model is facing increasing challenges, as many classical cell types are proved to be heterogeneous. Recently, the developments of new technologies allow genome, transcriptome, proteome, and epigenome analysis at the single-cell level. For the first time, we can study hematopoietic system at single-cell resolution on a multi-omic scale. Here, we review recent technical advances in single-cell analysis technology, as well as their current applications. We will also discuss the impact of single-cell technologies on both basic research and clinical application in hematology.
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653
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Burns TJ, Frei AP, Gherardini PF, Bava FA, Batchelder JE, Yoshiyasu Y, Yu JM, Groziak AR, Kimmey SC, Gonzalez VD, Fantl WJ, Nolan GP. High-throughput precision measurement of subcellular localization in single cells. Cytometry A 2017; 91:180-189. [PMID: 28094900 DOI: 10.1002/cyto.a.23054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/13/2016] [Accepted: 12/28/2016] [Indexed: 01/21/2023]
Abstract
To quantify visual and spatial information in single cells with a throughput of thousands of cells per second, we developed Subcellular Localization Assay (SLA). This adaptation of Proximity Ligation Assay expands the capabilities of flow cytometry to include data relating to localization of proteins to and within organelles. We used SLA to detect the nuclear import of transcription factors across cell subsets in complex samples. We further measured intranuclear re-localization of target proteins across the cell cycle and upon DNA damage induction. SLA combines multiple single-cell methods to bring about a new dimension of inquiry and analysis in complex cell populations. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- Tyler J Burns
- Department of Cancer Biology, Stanford University School of Medicine, Stanford, California
| | - Andreas P Frei
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Pier F Gherardini
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Felice A Bava
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Jake E Batchelder
- Immunology and Microbial Pathogenesis, Joan and Sanford I. Weill Medical College of Cornell University, New York, New York
| | - Yuki Yoshiyasu
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Julie M Yu
- Department of Biological Sciences, University of California Berkeley, Berkeley, California
| | | | - Samuel C Kimmey
- Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Veronica D Gonzalez
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Wendy J Fantl
- Stanford Comprehensive Cancer Institute and Department of Obstetrics and Gynecology, Stanford University, Stanford, California
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, California
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654
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Buckle T, van der Wal S, van Malderen SJ, Müller L, Kuil J, van Unen V, Peters RJ, van Bemmel ME, McDonnell LA, Velders AH, Koning F, Vanhaeke F, van Leeuwen FWB. Hybrid Imaging Labels: Providing the Link Between Mass Spectrometry-Based Molecular Pathology and Theranostics. Theranostics 2017; 7:624-633. [PMID: 28255355 PMCID: PMC5327638 DOI: 10.7150/thno.17484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/16/2016] [Indexed: 01/28/2023] Open
Abstract
Background: Development of theranostic concepts that include inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS (LA-ICP-MS) imaging can be hindered by the lack of a direct comparison to more standardly used methods for in vitro and in vivo evaluation; e.g. fluorescence or nuclear medicine. In this study a bimodal (or rather, hybrid) tracer that contains both a fluorescent dye and a chelate was used to evaluate the existence of a direct link between mass spectrometry (MS) and in vitro and in vivo molecular imaging findings using fluorescence and radioisotopes. At the same time, the hybrid label was used to determine whether the use of a single isotope label would allow for MS-based diagnostics. Methods: A hybrid label that contained both a DTPA chelate (that was coordinated with either 165Ho or 111In) and a Cy5 fluorescent dye was coupled to the chemokine receptor 4 (CXCR4) targeting peptide Ac-TZ14011 (hybrid-Cy5-Ac-TZ4011). This receptor targeting tracer was used to 1) validate the efficacy of (165Ho-based) mass-cytometry in determining the receptor affinity via comparison with fluorescence-based flow cytometry (Cy5), 2) evaluate the microscopic binding pattern of the tracer in tumor cells using both fluorescence confocal imaging (Cy5) and LA-ICP-MS-imaging (165Ho), 3) compare in vivo biodistribution patterns obtained with ICP-MS (165Ho) and radiodetection (111In) after intravenous administration of hybrid-Cy5-Ac-TZ4011 in tumor-bearing mice. Finally, LA-ICP-MS-imaging (165Ho) was linked to fluorescence-based analysis of excised tissue samples (Cy5). Results: Analysis with both mass-cytometry and flow cytometry revealed a similar receptor affinity, respectively 352 ± 141 nM and 245 ± 65 nM (p = 0.08), but with a much lower detection sensitivity for the first modality. In vitro LA-ICP-MS imaging (165Ho) enabled clear discrimination between CXCR4 positive and negative cells, but fluorescence microscopy was required to determine the intracellular distribution. In vivo biodistribution patterns obtained with ICP-MS (165Ho) and radiodetection (111In) of the hybrid peptide were shown to be similar. Assessment of tracer distribution in excised tissues revealed the location of tracer uptake with both LA-ICP-MS-imaging and fluorescence imaging. Conclusion: Lanthanide-isotope chelation expands the scope of fluorescent/radioactive hybrid tracers to include MS-based analytical tools such as mass-cytometry, ICP-MS and LA-ICP-MS imaging in molecular pathology. In contradiction to common expectations, MS detection using a single chelate imaging agent was shown to be feasible, enabling a direct link between nuclear medicine-based imaging and theranostic methods.
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655
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Abstract
Technology development in biological research often aims to either increase the number of cellular features that can be surveyed simultaneously or enhance the resolution at which such observations are possible. For decades, flow cytometry has balanced these goals to fill a critical need by enabling the measurement of multiple features in single cells, commonly to examine complex or hierarchical cellular systems. Recently, a format for flow cytometry has been developed that leverages the precision of mass spectrometry. This fusion of the two technologies, termed mass cytometry, provides measurement of over 40 simultaneous cellular parameters at single-cell resolution, significantly augmenting the ability of cytometry to evaluate complex cellular systems and processes. In this Primer, we review the current state of mass cytometry, providing an overview of the instrumentation, its present capabilities, and methods of data analysis, as well as thoughts on future developments and applications.
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656
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Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla C, Schurdak ME, Haney SA, Taylor DL. Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS DISCOVERY 2017; 22:213-237. [PMID: 28231035 DOI: 10.1177/2472555216682725] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications, including basic biomedical research, drug discovery, diagnostics, and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high-throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell-level data, as well as the need for standard metrics of the spatial, temporal, and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high-throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics, and the design of optimal therapeutic strategies for individual patients.
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Affiliation(s)
- Albert Gough
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Andrew M Stern
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - John Maier
- 3 Department of Family Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy Lezon
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Tong-Ying Shun
- 2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Chakra Chennubhotla
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Mark E Schurdak
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Steven A Haney
- 5 Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - D Lansing Taylor
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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657
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Affiliation(s)
- Lucas Armbrecht
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
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658
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Veith L, Vennemann A, Breitenstein D, Engelhard C, Wiemann M, Hagenhoff B. Detection of SiO2 nanoparticles in lung tissue by ToF-SIMS imaging and fluorescence microscopy. Analyst 2017; 142:2631-2639. [DOI: 10.1039/c7an00399d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We demonstrate the suitability of the ToF-SIMS technique for the detection of SiO2 nanoparticles in lung tissue sections by a comparison to fluorescence microscopy.
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Affiliation(s)
- Lothar Veith
- Tascon GmbH
- D-48149 Münster
- Germany
- University of Siegen
- Department of Chemistry & Biology
| | | | | | - Carsten Engelhard
- University of Siegen
- Department of Chemistry & Biology
- D-57076 Siegen
- Germany
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659
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Mansfield JR. Phenotyping Multiple Subsets of Immune Cells In Situ in FFPE Tissue Sections: An Overview of Methodologies. Methods Mol Biol 2017; 1546:75-99. [PMID: 27896758 DOI: 10.1007/978-1-4939-6730-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The recent clinical success of new cancer immunotherapy agents and methods is driving the need to understand the role of immune cells in solid tissues, especially tumors. Immune cell phenotyping via flow cytometry, while a cornerstone of immunology, is not spatially resolved and cannot analyze immune cell subsets in situ in clinical biopsy sections or to determine their interrelationships. To address this problem, a number of methodologies have been developed in attempts to phenotype immune and other cells in images acquired from tissue sections and to assess their organization in the tumor and its microenvironment. This chapter review the staining and multiplex image analysis methods that have been developed for phenotyping immune and other cells in formalin-fixed, paraffin-embedded (FFPE) tissue sections.
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660
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Moysi E, Estes JD, Petrovas C. Novel Imaging Methods for Analysis of Tissue Resident Cells in HIV/SIV. Curr HIV/AIDS Rep 2016; 13:38-43. [PMID: 26830285 DOI: 10.1007/s11904-016-0300-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The use of advanced tissue-imaging methodologies has greatly facilitated the study of molecular mechanisms and cellular interactions in humans and animal models of disease. Particularly, in HIV research, there is an ever-increasing demand for a comprehensive analysis of immune cell dynamics at tissue level stemming from the need to advance our understanding of those interactions that regulate the generation of adaptive antigen-specific immune responses. The latter is critical for the development of vaccines to elicit broadly neutralizing antibodies as well as for the discovery of novel targets for immuno-therapies to strengthen the cytolytic arm of the immune system at local level. In this review, we focus on current and emerging imaging technologies, discuss their strengths and limitations, and examine how such technologies can inform the development of new treatments and vaccination strategies. We also present some perspective on the future of the technology development.
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Affiliation(s)
- Eirini Moysi
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, 33136-1013, USA
| | - Jacob D Estes
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Constantinos Petrovas
- Immunology Laboratory, Vaccine Research Center, NIAID, National Institutes of Health, Building 40, 40 Convent Drive, Bethesda, MD, 20892-3005, USA.
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661
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Abstract
Jia-Ren Lin from the Laboratory of Systems Pharmacology at Harvard Medical School was awarded best poster at the annual Society of Biomolecular Imaging and Informatics meeting held in Boston, September 2016. His work focuses on single-cell imaging, especially on developing new methods for simultaneously detecting many antigens, named cyclic immunofluorescence (CycIF). This method could be applied in different stages of drug development, from discovery phase, preclinical research to clinical research. The current works and future directions of CycIF method are summarized in the following overview.
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Affiliation(s)
- Jia-Ren Lin
- Laboratory of Systems Pharmacology, HMS LINCS Center , Harvard Medical School Boston, Boston, Massachusetts
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662
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Angelo M. Highly multiplexed IHC in clinical tissue biopsies using multiplexed ion beam imaging. J Histotechnol 2016. [DOI: 10.1080/01478885.2016.1233749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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663
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Lin JR, Fallahi-Sichani M, Chen JY, Sorger PK. Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging. ACTA ACUST UNITED AC 2016; 8:251-264. [PMID: 27925668 DOI: 10.1002/cpch.14] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cyclic Immunofluorescence (CycIF) is a public-domain method for performing highly multiplexed immunofluorescence imaging using a conventional epifluorescence microscope. It uses simple reagents and existing antibodies to construct images with up to 30 channels by sequential 4- to 6-channel imaging followed by fluorophore inactivation. Three variant methods are described, the most generally useful of which involves staining fixed cells with antibodies directly conjugated to Alexa Fluor dyes and imaging in four colors, inactivating fluorophores using a mild base in the presence of hydrogen peroxide and light, and then performing another round of staining and imaging. Cell morphology is preserved through multiple rounds of CycIF, and signal-to-noise ratios appear to increase. Unlike antibody-stripping methods, CycIF is gentle and optimized for monolayers of cultured cells. A second protocol involves indirect immunofluorescence and a third enables chemical inactivation of genetically encoded fluorescent proteins, allowing multiplex immunofluorescence to be combined with live-cell analysis of cells expressing fluorescent reporter proteins. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jia-Ren Lin
- HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Mohammad Fallahi-Sichani
- HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Jia-Yun Chen
- HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Peter K Sorger
- HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
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664
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Harryman WL, Hinton JP, Rubenstein CP, Singh P, Nagle RB, Parker SJ, Knudsen BS, Cress AE. The Cohesive Metastasis Phenotype in Human Prostate Cancer. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1866:221-231. [PMID: 27678419 PMCID: PMC5534328 DOI: 10.1016/j.bbcan.2016.09.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/27/2016] [Accepted: 09/23/2016] [Indexed: 12/21/2022]
Abstract
A critical barrier for the successful prevention and treatment of recurrent prostate cancer is detection and eradication of metastatic and therapy-resistant disease. Despite the fall in diagnoses and mortality, the reported incidence of metastatic disease has increased 72% since 2004. Prostate cancer arises in cohesive groups as intraepithelial neoplasia, migrates through muscle and leaves the gland via perineural invasion for hematogenous dissemination. Current technological advances have shown cohesive-clusters of tumor (also known as microemboli) within the circulation. Circulating tumor cell (CTC) profiles are indicative of disseminated prostate cancer, and disseminated tumor cells (DTC) are found in cohesive-clusters, a phenotypic characteristic of both radiation- and drug-resistant tumors. Recent reports in cell biology and informatics, coupled with mass spectrometry, indicate that the integrin adhesome network provides an explanation for the biophysical ability of cohesive-clusters of tumor cells to invade thorough muscle and nerve microenvironments while maintaining adhesion-dependent therapeutic resistance. Targeting cohesive-clusters takes advantage of the known ability of extracellular matrix (ECM) adhesion to promote tumor cell survival and represents an approach that has the potential to avoid the progression to drug- and radiotherapy-resistance. In the following review we will examine the evidence for development and dissemination of cohesive-clusters in metastatic prostate cancer.
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Affiliation(s)
- William L Harryman
- The University of Arizona Cancer Center, 1515 N. Campbell Ave., Tucson, AZ, 85724, USA
| | - James P Hinton
- Cancer Biology Graduate Program, The University of Arizona Cancer Center, 1515 N. Campbell Ave., Tucson, AZ, 85724, USA
| | - Cynthia P Rubenstein
- Cancer Biology Graduate Program, The University of Arizona Cancer Center, 1515 N. Campbell Ave., Tucson, AZ, 85724, USA
| | - Parminder Singh
- The University of Arizona Cancer Center, 1515 N. Campbell Ave., Tucson, AZ, 85724, USA
| | - Raymond B Nagle
- The University of Arizona Cancer Center, 1515 N. Campbell Ave., Tucson, AZ, 85724, USA
| | - Sarah J Parker
- Cedars Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, United States
| | - Beatrice S Knudsen
- Cedars Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, United States
| | - Anne E Cress
- The University of Arizona Cancer Center, 1515 N. Campbell Ave., Tucson, AZ, 85724, USA.
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665
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Abstract
The invention of the microscope has been fundamental for the understanding of tissue architecture and subcellular structures. With the advancement of higher magnification microscopes came the development of various molecular biology tools such as Förster resonance energy transfer (FRET) and in situ proximity ligation assay (in situ PLA) to monitor protein interactions. Microscopy has become a commonly used method for the investigation of molecular events within the cell, for the identification of key players in signaling networks, and the activation of these pathways. Multiple approaches are available for functional analyses in single cells. They provide information not only on the localization of proteins at a given time point, but also on their expression levels and activity states, allowing us to pinpoint hallmarks of different cellular identities within tissues in health and disease. Clever solutions to increase the sensitivity of molecular tools, the possibilities for multiplexing, as well as image resolution have recently been introduced; however, these methods have their pros and cons. Therefore, one needs to carefully consider the biological question of interest along with the nature of the sample before choosing the most suitable method or combination of methods. Herein, we review a few of the most exciting microscopy-based molecular techniques for proteomic analysis and cover the benefits as well as the disadvantages of their use.
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666
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Rocha B, Ruiz-Romero C, Blanco FJ. Mass spectrometry imaging: a novel technology in rheumatology. Nat Rev Rheumatol 2016; 13:52-63. [DOI: 10.1038/nrrheum.2016.184] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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667
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Masucci GV, Cesano A, Hawtin R, Janetzki S, Zhang J, Kirsch I, Dobbin KK, Alvarez J, Robbins PB, Selvan SR, Streicher HZ, Butterfield LH, Thurin M. Validation of biomarkers to predict response to immunotherapy in cancer: Volume I - pre-analytical and analytical validation. J Immunother Cancer 2016; 4:76. [PMID: 27895917 PMCID: PMC5109744 DOI: 10.1186/s40425-016-0178-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022] Open
Abstract
Immunotherapies have emerged as one of the most promising approaches to treat patients with cancer. Recently, there have been many clinical successes using checkpoint receptor blockade, including T cell inhibitory receptors such as cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death-1 (PD-1). Despite demonstrated successes in a variety of malignancies, responses only typically occur in a minority of patients in any given histology. Additionally, treatment is associated with inflammatory toxicity and high cost. Therefore, determining which patients would derive clinical benefit from immunotherapy is a compelling clinical question. Although numerous candidate biomarkers have been described, there are currently three FDA-approved assays based on PD-1 ligand expression (PD-L1) that have been clinically validated to identify patients who are more likely to benefit from a single-agent anti-PD-1/PD-L1 therapy. Because of the complexity of the immune response and tumor biology, it is unlikely that a single biomarker will be sufficient to predict clinical outcomes in response to immune-targeted therapy. Rather, the integration of multiple tumor and immune response parameters, such as protein expression, genomics, and transcriptomics, may be necessary for accurate prediction of clinical benefit. Before a candidate biomarker and/or new technology can be used in a clinical setting, several steps are necessary to demonstrate its clinical validity. Although regulatory guidelines provide general roadmaps for the validation process, their applicability to biomarkers in the cancer immunotherapy field is somewhat limited. Thus, Working Group 1 (WG1) of the Society for Immunotherapy of Cancer (SITC) Immune Biomarkers Task Force convened to address this need. In this two volume series, we discuss pre-analytical and analytical (Volume I) as well as clinical and regulatory (Volume II) aspects of the validation process as applied to predictive biomarkers for cancer immunotherapy. To illustrate the requirements for validation, we discuss examples of biomarker assays that have shown preliminary evidence of an association with clinical benefit from immunotherapeutic interventions. The scope includes only those assays and technologies that have established a certain level of validation for clinical use (fit-for-purpose). Recommendations to meet challenges and strategies to guide the choice of analytical and clinical validation design for specific assays are also provided.
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Affiliation(s)
- Giuseppe V Masucci
- Department of Oncology-Pathology, Karolinska Institutet, 171 76 Stockholm, Sweden
| | | | - Rachael Hawtin
- Nodality, Inc, 170 Harbor Way, South San Francisco, 94080 CA USA
| | - Sylvia Janetzki
- ZellNet Consulting, Inc, 555 North Avenue, Fort Lee, 07024 NJ USA
| | - Jenny Zhang
- Covaris Inc, 14 Gill St, Woburn, MA 01801 USA
| | - Ilan Kirsch
- Adaptive Biotechnologies, Inc, 1551 Eastlake Ave. E, Seattle, WA 98102 USA
| | - Kevin K Dobbin
- Department of Epidemiology and Biostatistics, College of Public Health, The University of Georgia, 101 Buck Road, Athens, 30602 GA USA
| | - John Alvarez
- Janssen Research & Development, LLC, Spring House, PA 19477 USA
| | | | - Senthamil R Selvan
- Omni Array Biotechnology, 15601 Crabbs Branch Way, Rockville, 20855 MD USA
| | - Howard Z Streicher
- National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, 20892 MD USA
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Magdalena Thurin
- National Cancer Institute, Cancer Diagnosis Program, DCTD, National Institutes of Health, 9609 Medical Center Drive, Bethesda, 20892 MD USA ; Adaptive Biotechnologies, Inc, 1551 Eastlake Ave. E, Seattle, WA 98102 USA
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668
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Kompauer M, Heiles S, Spengler B. Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution. Nat Methods 2016; 14:90-96. [PMID: 27842060 DOI: 10.1038/nmeth.4071] [Citation(s) in RCA: 373] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/28/2016] [Indexed: 02/07/2023]
Abstract
We report an atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) setup with a lateral resolution of 1.4 μm, a mass resolution greater than 100,000, and accuracy below ±2 p.p.m. We achieved this by coupling a focusing objective with a numerical aperture (NA) of 0.9 at 337 nm and a free working distance of 18 mm in coaxial geometry to an orbitrap mass spectrometer and optimizing the matrix application. We demonstrate improvement in image contrast, lateral resolution, and ion yield per unit area compared with a state-of-the-art commercial MSI source. We show that our setup can be used to detect metabolites, lipids, and small peptides, as well as to perform tandem MS experiments with 1.5-μm2 sampling areas. To showcase these capabilities, we identified subcellular lipid, metabolite, and peptide distributions that differentiate, for example, cilia and oral groove in Paramecium caudatum.
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Affiliation(s)
- Mario Kompauer
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
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669
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In-Field, In Situ, and In Vivo 3-Dimensional Elemental Mapping for Plant Tissue and Soil Analysis Using Laser-Induced Breakdown Spectroscopy. SENSORS 2016; 16:s16101764. [PMID: 27782074 PMCID: PMC5087548 DOI: 10.3390/s16101764] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/16/2022]
Abstract
Sensing and mapping element distributions in plant tissues and its growth environment has great significance for understanding the uptake, transport, and accumulation of nutrients and harmful elements in plants, as well as for understanding interactions between plants and the environment. In this study, we developed a 3-dimensional elemental mapping system based on laser-induced breakdown spectroscopy that can be deployed in- field to directly measure the distribution of multiple elements in living plants as well as in the soil. Mapping is performed by a fast scanning laser, which ablates a micro volume of a sample to form a plasma. The presence and concentration of specific elements are calculated using the atomic, ionic, and molecular spectral characteristics of the plasma emission spectra. Furthermore, we mapped the pesticide residues in maize leaves after spraying to demonstrate the capacity of this method for trace elemental mapping. We also used the system to quantitatively detect the element concentrations in soil, which can be used to further understand the element transport between plants and soil. We demonstrate that this method has great potential for elemental mapping in plant tissues and soil with the advantages of 3-dimensional and multi-elemental mapping, in situ and in vivo measurement, flexible use, and low cost.
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670
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Cannoodt R, Saelens W, Saeys Y. Computational methods for trajectory inference from single-cell transcriptomics. Eur J Immunol 2016; 46:2496-2506. [DOI: 10.1002/eji.201646347] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/30/2016] [Accepted: 09/26/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Robrecht Cannoodt
- Data Mining and Modelling for Biomedicine group; VIB Inflammation Research Center; Ghent Belgium
- Department of Internal Medicine; Ghent University; Ghent Belgium
- Center for Medical Genetics; Ghent University; Ghent Belgium
- Cancer Research Institute Ghent (CRIG); Ghent Belgium
| | - Wouter Saelens
- Data Mining and Modelling for Biomedicine group; VIB Inflammation Research Center; Ghent Belgium
- Department of Internal Medicine; Ghent University; Ghent Belgium
| | - Yvan Saeys
- Data Mining and Modelling for Biomedicine group; VIB Inflammation Research Center; Ghent Belgium
- Department of Internal Medicine; Ghent University; Ghent Belgium
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671
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Sapiezynski J, Taratula O, Rodriguez-Rodriguez L, Minko T. Precision targeted therapy of ovarian cancer. J Control Release 2016; 243:250-268. [PMID: 27746277 DOI: 10.1016/j.jconrel.2016.10.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/09/2016] [Accepted: 10/12/2016] [Indexed: 10/20/2022]
Abstract
The review is aimed at describing modern approaches to detection as well as precision and personalized treatment of ovarian cancer. Modern methods and future directions of nanotechnology-based targeted and personalized therapy are discussed.
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Affiliation(s)
- Justin Sapiezynski
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States
| | - Oleh Taratula
- Department of Pharmaceutical Sciences, Oregon State University, Portland, OR 97239, United States
| | - Lorna Rodriguez-Rodriguez
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, United States; Department of Obstetrics and Gynecology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, United States
| | - Tamara Minko
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, United States.
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672
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Simmons AJ, Scurrah CR, McKinley ET, Herring CA, Irish JM, Washington MK, Coffey RJ, Lau KS. Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks. Sci Signal 2016; 9:rs11. [PMID: 27729552 DOI: 10.1126/scisignal.aah4413] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cellular heterogeneity poses a substantial challenge to understanding tissue-level phenotypes and confounds conventional bulk analyses. To analyze signaling at the single-cell level in human tissues, we applied mass cytometry using cytometry time of flight to formalin-fixed, paraffin-embedded (FFPE) normal and diseased intestinal specimens. This technique, called FFPE-DISSECT (disaggregation for intracellular signaling in single epithelial cells from tissue), is a single-cell approach to characterizing signaling states in embedded tissue samples. We applied FFPE-DISSECT coupled to mass cytometry and found differential signaling by tumor necrosis factor-α in intestinal enterocytes, goblet cells, and enteroendocrine cells, implicating the downstream RAS-RAF-MEK pathway in determining goblet cell identity. Application of this technique and computational analyses to human colon specimens confirmed the reduced differentiation in colorectal cancer (CRC) compared to normal colon and revealed increased intratissue and intertissue heterogeneity in CRC with quantitative changes in the regulation of signaling pathways. Specifically, coregulation of the kinases p38 and ERK, the translation regulator 4EBP1, and the transcription factor CREB in proliferating normal colon cells was lost in CRC. Our data suggest that this single-cell approach, applied in conjunction with genomic annotation, enables the rapid and detailed characterization of cellular heterogeneity from clinical repositories of embedded human tissues. This technique can be used to derive cellular landscapes from archived patient samples (beyond CRC) and as a high-resolution tool for disease characterization and subtyping.
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Affiliation(s)
- Alan J Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Cherié R Scurrah
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Eliot T McKinley
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Charles A Herring
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Chemical and Physical Biology Program, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jonathan M Irish
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, TN 37232, USA
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Chemical and Physical Biology Program, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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673
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Lin XC, Wang XN, Liu L, Wen Q, Yu RQ, Jiang JH. Surface Enhanced Laser Desorption Ionization of Phospholipids on Gold Nanoparticles for Mass Spectrometric Immunoassay. Anal Chem 2016; 88:9881-9884. [DOI: 10.1021/acs.analchem.6b02733] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Xiang-Cheng Lin
- State Key Laboratory of Chemeo/Bio-Sensing
and Chemometrics, Institute of Chemical Biology and Nanomedicine,
College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Xiang-Nan Wang
- State Key Laboratory of Chemeo/Bio-Sensing
and Chemometrics, Institute of Chemical Biology and Nanomedicine,
College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Lan Liu
- State Key Laboratory of Chemeo/Bio-Sensing
and Chemometrics, Institute of Chemical Biology and Nanomedicine,
College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Qian Wen
- State Key Laboratory of Chemeo/Bio-Sensing
and Chemometrics, Institute of Chemical Biology and Nanomedicine,
College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemeo/Bio-Sensing
and Chemometrics, Institute of Chemical Biology and Nanomedicine,
College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemeo/Bio-Sensing
and Chemometrics, Institute of Chemical Biology and Nanomedicine,
College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
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674
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NanoSIMS chemical imaging combined with correlative microscopy for biological sample analysis. Curr Opin Biotechnol 2016; 41:130-135. [PMID: 27506876 DOI: 10.1016/j.copbio.2016.06.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/17/2016] [Accepted: 06/23/2016] [Indexed: 12/18/2022]
Abstract
Nano-scale Secondary Ion Mass Spectrometry (NanoSIMS) is one of the most powerful in situ elemental and isotopic analysis techniques available to biologists. The combination of stable isotope probing with NanoSIMS (nanoSIP) has opened up new avenues for biological studies over the past decade. However, due to limitations inherent with any analytical methodology, additional information from correlative techniques is usually required to address real biological questions. Here we review recent developments in correlative analysis applied to complex biological systems: first, high-resolution tracking of molecules (e.g. peptides, lipids) by correlation with electron microscopy and atomic force microscopy; second, identification of a specific microbial taxon with fluorescence in situ hybridization and quantification of its metabolic capacities; and, third, molecular specific imaging with new probes.
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675
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Tape CJ. Systems Biology Analysis of Heterocellular Signaling. Trends Biotechnol 2016; 34:627-637. [DOI: 10.1016/j.tibtech.2016.02.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
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676
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Zrazhevskiy P, Akilesh S, Tai W, Queitsch K, True LD, Fromm J, Wu D, Nelson P, Stamatoyannopoulos JA, Gao X. Cross-Platform DNA Encoding for Single-Cell Imaging of Gene Expression. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pavel Zrazhevskiy
- Department of Bioengineering; University of Washington; Seattle WA 98195 USA
| | - Shreeram Akilesh
- Department of Pathology; University of Washington; Seattle WA 98195 USA
| | - Wanyi Tai
- Department of Bioengineering; University of Washington; Seattle WA 98195 USA
| | - Konstantin Queitsch
- Department of Genome Sciences; University of Washington; Seattle WA 98195 USA
| | - Lawrence D. True
- Department of Pathology; University of Washington; Seattle WA 98195 USA
| | - Jonathan Fromm
- Department of Laboratory Medicine; University of Washington; Seattle WA 98195 USA
| | - David Wu
- Department of Laboratory Medicine; University of Washington; Seattle WA 98195 USA
| | - Peter Nelson
- Department of Medicine; University of Washington; Seattle WA 98195 USA
- Fred Hutchinson Cancer Research Center; Seattle WA 98109 USA
| | - John A. Stamatoyannopoulos
- Department of Genome Sciences; University of Washington; Seattle WA 98195 USA
- Department of Medicine; University of Washington; Seattle WA 98195 USA
| | - Xiaohu Gao
- Department of Bioengineering; University of Washington; Seattle WA 98195 USA
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677
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Abstract
Lanthanide complexes are of increasing importance in cancer diagnosis and therapy, owing to the versatile chemical and magnetic properties of the lanthanide-ion 4f electronic configuration. Following the first implementation of gadolinium(III)-based contrast agents in magnetic resonance imaging in the 1980s, lanthanide-based small molecules and nanomaterials have been investigated as cytotoxic agents and inhibitors, in photodynamic therapy, radiation therapy, drug/gene delivery, biosensing, and bioimaging. As the potential utility of lanthanides in these areas continues to increase, this timely review of current applications will be useful to medicinal chemists and other investigators interested in the latest developments and trends in this emerging field.
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Affiliation(s)
- Ruijie D. Teo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - John Termini
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Harry B. Gray
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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678
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Tumour heterogeneity: principles and practical consequences. Virchows Arch 2016; 469:371-84. [PMID: 27412632 DOI: 10.1007/s00428-016-1987-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/01/2016] [Accepted: 07/03/2016] [Indexed: 12/30/2022]
Abstract
Two major reasons compel us to study tumour heterogeneity: firstly, it represents the basis of acquired therapy resistance, and secondly, it may be one of the major sources of the low level of reproducibility in clinical cancer research. The present review focuses on the heterogeneity of neoplastic disease, both within the primary tumour and between primary tumour and metastases. We discuss different levels of heterogeneity and the current understanding of the phenomenon, as well as imminent developments relevant for clinical research and diagnostic pathology. It is necessary to develop new tools to study heterogeneity and new biomarkers for heterogeneity. Established and new in situ methods will be very useful. In future studies, not only clonal heterogeneity needs to be addressed but also non-clonal phenotypic heterogeneity which might be important for therapy resistance. We also review heterogeneity established in major tumour types, in order to explore potential similarities that might help to define new strategies for targeted therapy.
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679
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Aoi T. Biology of lung cancer: genetic mutation, epithelial-mesenchymal transition, and cancer stem cells. Gen Thorac Cardiovasc Surg 2016; 64:517-23. [PMID: 27376535 DOI: 10.1007/s11748-016-0682-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/27/2016] [Indexed: 12/13/2022]
Abstract
At present, most cases of unresectable cancer cannot be cured. Genetic mutations, EMT, and cancer stem cells are three major issues linked to poor prognosis in such cases, all connected by inter- and intra-tumor heterogeneity. Issues on inter-/intra-tumor heterogeneity of genetic mutation could be resolved with recent and future technologies of deep sequencers, whereas, regarding such issues as the "same genome, different epigenome/phenotype", we expect to solve many of these problems in the future through further research in stem cell biology. We herein review and discuss the three major issues in the biology of cancers, especially from the standpoint of stem cell biology.
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Affiliation(s)
- Takashi Aoi
- Division of Advanced Medical Science, Graduate School of Science, Technology and Innovation, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan. .,Department of iPS cell Applications, Graduate School of Medicine, Kobe University, Kobe, Japan. .,Center for Human Resource Development for Regenerative Medicine, Kobe University Hospital, Kobe, Japan.
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680
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Greenplate AR, Johnson DB, Ferrell PB, Irish JM. Systems immune monitoring in cancer therapy. Eur J Cancer 2016; 61:77-84. [PMID: 27155446 PMCID: PMC4885747 DOI: 10.1016/j.ejca.2016.03.085] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 03/28/2016] [Indexed: 12/20/2022]
Abstract
Treatments that successfully modulate anti-cancer immunity have significantly improved outcomes for advanced stage malignancies and sparked intense study of the cellular mechanisms governing therapy response and resistance. These responses are governed by an evolving milieu of cancer and immune cell subpopulations that can be a rich source of biomarkers and biological insight, but it is only recently that research tools have developed to comprehensively characterize this level of cellular complexity. Mass cytometry is particularly well suited to tracking cells in complex tissues because >35 measurements can be made on each of hundreds of thousands of cells per sample, allowing all cells detected in a sample to be characterized for cell type, signalling activity, and functional outcome. This review focuses on mass cytometry as an example of systems level characterization of cancer and immune cells in human tissues, including blood, bone marrow, lymph nodes, and primary tumours. This review also discusses the state of the art in single cell tumour immunology, including tissue collection, technical and biological quality controls, computational analysis, and integration of different experimental and clinical data types. Ex vivo analysis of human tumour cells complements both in vivo monitoring, which generally measures far fewer features or lacks single cell resolution, and laboratory models, which incur cell type losses, signalling alterations, and genomic changes during establishment. Mass cytometry is on the leading edge of a new generation of cytomic tools that work with small tissue samples, such as a fine needle aspirates or blood draws, to monitor changes in rare or unexpected cell subsets during cancer therapy. This approach holds great promise for dissecting cellular microenvironments, monitoring how treatments affect tissues, revealing cellular biomarkers and effector mechanisms, and creating new treatments that productively engage the immune system to fight cancer and other diseases.
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Affiliation(s)
- Allison R Greenplate
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - P Brent Ferrell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan M Irish
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cancer Biology, Vanderbilt University, Nashville, TN, USA.
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681
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Newman AM, Alizadeh AA. High-throughput genomic profiling of tumor-infiltrating leukocytes. Curr Opin Immunol 2016; 41:77-84. [PMID: 27372732 DOI: 10.1016/j.coi.2016.06.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022]
Abstract
Tumors are complex ecosystems comprised of diverse cell types including malignant cells, mesenchymal cells, and tumor-infiltrating leukocytes (TILs). While TILs are well known to play important roles in many aspects of cancer biology, recent developments in immuno-oncology have spurred considerable interest in TILs, particularly in relation to their optimal engagement by emerging immunotherapies. Traditionally, the enumeration of TIL phenotypic diversity and composition in solid tumors has relied on resolving single cells by flow cytometry and immunohistochemical methods. However, advances in genome-wide technologies and computational methods are now allowing TILs to be profiled with increasingly high resolution and accuracy directly from RNA mixtures of bulk tumor samples. In this review, we highlight recent progress in the development of in silico tumor dissection methods, and illustrate examples of how these strategies can be applied to characterize TILs in human tumors to facilitate personalized cancer therapy.
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Affiliation(s)
- Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
| | - Ash A Alizadeh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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682
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Yedra L, Eswara S, Dowsett D, Wirtz T. In-situ Isotopic Analysis at Nanoscale using Parallel Ion Electron Spectrometry: A Powerful New Paradigm for Correlative Microscopy. Sci Rep 2016; 6:28705. [PMID: 27350565 PMCID: PMC4923888 DOI: 10.1038/srep28705] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/06/2016] [Indexed: 01/20/2023] Open
Abstract
Isotopic analysis is of paramount importance across the entire gamut of scientific research. To advance the frontiers of knowledge, a technique for nanoscale isotopic analysis is indispensable. Secondary Ion Mass Spectrometry (SIMS) is a well-established technique for analyzing isotopes, but its spatial-resolution is fundamentally limited. Transmission Electron Microscopy (TEM) is a well-known method for high-resolution imaging down to the atomic scale. However, isotopic analysis in TEM is not possible. Here, we introduce a powerful new paradigm for in-situ correlative microscopy called the Parallel Ion Electron Spectrometry by synergizing SIMS with TEM. We demonstrate this technique by distinguishing lithium carbonate nanoparticles according to the isotopic label of lithium, viz. 6Li and 7Li and imaging them at high-resolution by TEM, adding a new dimension to correlative microscopy.
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Affiliation(s)
- Lluís Yedra
- Advanced Instrumentation for Ion Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Santhana Eswara
- Advanced Instrumentation for Ion Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - David Dowsett
- Advanced Instrumentation for Ion Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Tom Wirtz
- Advanced Instrumentation for Ion Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
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683
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Remark R, Merghoub T, Grabe N, Litjens G, Damotte D, Wolchok JD, Merad M, Gnjatic S. In-depth tissue profiling using multiplexed immunohistochemical consecutive staining on single slide. Sci Immunol 2016; 1:aaf6925. [PMID: 28783673 PMCID: PMC10152404 DOI: 10.1126/sciimmunol.aaf6925] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/31/2016] [Indexed: 12/16/2022]
Abstract
Despite remarkable recent achievements of immunotherapy strategies in cancer treatment, clinical responses remain limited to subsets of patients. Predictive markers of disease course and response to immunotherapy are urgently needed. Recent results have revealed the potential predictive value of immune cell phenotype and spatial distribution at the tumor site, prompting the need for multidimensional immunohistochemical analyses of tumor tissues. To address this need, we developed a sample-sparing, highly multiplexed immunohistochemistry technique based on iterative cycles of tagging, image scanning, and destaining of chromogenic substrate on a single slide. This assay, in combination with a newly developed automated digital landscaping solution, democratizes access to high-dimensional immunohistochemical analyses by capturing the complexity of the immunome using routine pathology standards. Applications of the method extend beyond cancer to screen and validate comprehensive panels of tissue-based prognostic and predictive markers, perform in-depth in situ monitoring of therapies, and identify targets of disease.
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Affiliation(s)
- Romain Remark
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Taha Merghoub
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Niels Grabe
- Department of Medical Oncology at National Center for Tumor Diseases, University Hospital Heidelberg and Hamamatsu Tissue Imaging and Analysis Center, BIOQUANT, University of Heidelberg, Heidelberg, Germany
| | - Geert Litjens
- Department of Medical Oncology at National Center for Tumor Diseases, University Hospital Heidelberg and Hamamatsu Tissue Imaging and Analysis Center, BIOQUANT, University of Heidelberg, Heidelberg, Germany
| | - Diane Damotte
- INSERM U1138, Team "Cancer, Immune Control and Escape" Cordeliers Research Center, Paris, France.,Department of Pathology, Cochin Hospital, AP-HP, Paris, France
| | - Jedd D Wolchok
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Miriam Merad
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Sacha Gnjatic
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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684
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Zrazhevskiy P, Akilesh S, Tai W, Queitsch K, True LD, Fromm J, Wu D, Nelson P, Stamatoyannopoulos JA, Gao X. Cross-Platform DNA Encoding for Single-Cell Imaging of Gene Expression. Angew Chem Int Ed Engl 2016; 55:8975-8. [PMID: 27273345 DOI: 10.1002/anie.201603945] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Indexed: 12/16/2022]
Abstract
Integration of imaging data across different molecular target types can provide in-depth insight into cell physiology and pathology, but remains challenging owing to poor compatibility between target-type-specific labeling methods. We show that cross-platform imaging analysis can be readily achieved through DNA encoding of molecular targets, which translates the molecular identity of various target types into a uniform in situ array of ssDNA tags for subsequent labeling with complementary imaging probes. The concept was demonstrated through multiplexed imaging of mRNAs and their corresponding proteins with multicolor quantum dots. The results reveal heterogeneity of cell transfection with siRNA and outline disparity in RNA interference (RNAi) kinetics at the level of both the mRNA and the encoded protein.
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Affiliation(s)
- Pavel Zrazhevskiy
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Shreeram Akilesh
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Wanyi Tai
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Konstantin Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Lawrence D True
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Jonathan Fromm
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98195, USA
| | - David Wu
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Peter Nelson
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - John A Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.,Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Xiaohu Gao
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
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685
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Imaging of amyloid-β in Alzheimer's disease transgenic mouse brains with ToF-SIMS using immunoliposomes. Biointerphases 2016; 11:02A312. [DOI: 10.1116/1.4940215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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686
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Wargo JA, Reddy SM, Reuben A, Sharma P. Monitoring immune responses in the tumor microenvironment. Curr Opin Immunol 2016; 41:23-31. [PMID: 27240055 DOI: 10.1016/j.coi.2016.05.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/12/2016] [Indexed: 12/15/2022]
Abstract
Immune monitoring in the tumor microenvironment allows for important insights into immune mechanisms of response and resistance to various cancer treatments; however clinical challenges exist using current strategies. Significant questions remain regarding monitoring of archival versus fresh tissue, assessment of static versus dynamic markers, evaluation of limited tissue samples, and the translation of insights gained from immunologically 'hot' tumors such as melanoma to other 'cold' tumor microenvironments prevalent in other cancer types. Current and emerging immune monitoring strategies will be examined herein, and genomic-based assays complementing these techniques will also be discussed. Finally, host genomic and external environmental factors influencing anti-tumor immune responses will be considered, including the role of the gut microbiome. Though optimal immune monitoring techniques are in evolution, great promise exists in recent advances that will help guide patient selection as far as type, sequence, and combination of therapeutic regimens to enhance anti-tumor immunity and clinical responses.
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Affiliation(s)
- Jennifer A Wargo
- Department of Surgical Oncology, Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Sangeetha M Reddy
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Blvd, Unit 463, Houston, TX 77030, USA
| | - Alexandre Reuben
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1155 Pressler Street, Unit 1374, Houston, TX 77030, USA.
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687
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Liu R, Zhang S, Wei C, Xing Z, Zhang S, Zhang X. Metal Stable Isotope Tagging: Renaissance of Radioimmunoassay for Multiplex and Absolute Quantification of Biomolecules. Acc Chem Res 2016; 49:775-83. [PMID: 26990857 DOI: 10.1021/acs.accounts.5b00509] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The unambiguous quantification of biomolecules is of great significance in fundamental biological research as well as practical clinical diagnosis. Due to the lack of a detectable moiety, the direct and highly sensitive quantification of biomolecules is often a "mission impossible". Consequently, tagging strategies to introduce detectable moieties for labeling target biomolecules were invented, which had a long and significant impact on studies of biomolecules in the past decades. For instance, immunoassays have been developed with radioisotope tagging by Yalow and Berson in the late 1950s. The later languishment of this technology can be almost exclusively ascribed to the use of radioactive isotopes, which led to the development of nonradioactive tagging strategy-based assays such as enzyme-linked immunosorbent assay, fluorescent immunoassay, and chemiluminescent and electrochemiluminescent immunoassay. Despite great success, these strategies suffered from drawbacks such as limited spectral window capacity for multiplex detection and inability to provide absolute quantification of biomolecules. After recalling the sequences of tagging strategies, an apparent question is why not use stable isotopes from the start? A reasonable explanation is the lack of reliable means for accurate and precise quantification of stable isotopes at that time. The situation has changed greatly at present, since several atomic mass spectrometric measures for metal stable isotopes have been developed. Among the newly developed techniques, inductively coupled plasma mass spectrometry is an ideal technique to determine metal stable isotope-tagged biomolecules, for its high sensitivity, wide dynamic linear range, and more importantly multiplex and absolute quantification ability. Since the first published report by our group, metal stable isotope tagging has become a revolutionary technique and gained great success in biomolecule quantification. An exciting research highlight in this area is the development and application of the mass cytometer, which fully exploited the multiplexing potential of metal stable isotope tagging. It realized the simultaneous detection of dozens of parameters in single cells, accurate immunophenotyping in cell populations, through modeling of intracellular signaling network and undoubted discrimination of function and connection of cell subsets. Metal stable isotope tagging has great potential applications in hematopoiesis, immunology, stem cells, cancer, and drug screening related research and opened a post-fluorescence era of cytometry. Herein, we review the development of biomolecule quantification using metal stable isotope tagging. Particularly, the power of multiplex and absolute quantification is demonstrated. We address the advantages, applicable situations, and limitations of metal stable isotope tagging strategies and propose suggestions for future developments. The transfer of enzymatic or fluorescent tagging to metal stable isotope tagging may occur in many aspects of biological and clinical practices in the near future, just as the revolution from radioactive isotope tagging to fluorescent tagging happened in the past.
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Affiliation(s)
- Rui Liu
- Beijing
Key Laboratory for Microanalytical Methods and Instrumentation, Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
- Collaborative Innovation Center for Comprehensive Utilization of Panxi Strategic Mineral Resources, College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, P.R. China
| | - Shixi Zhang
- Beijing
Key Laboratory for Microanalytical Methods and Instrumentation, Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Chao Wei
- National Institute of Metrology, Beijing 100029, P.R. China
| | - Zhi Xing
- Beijing
Key Laboratory for Microanalytical Methods and Instrumentation, Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Sichun Zhang
- Beijing
Key Laboratory for Microanalytical Methods and Instrumentation, Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Xinrong Zhang
- Beijing
Key Laboratory for Microanalytical Methods and Instrumentation, Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
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688
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Sood A, Miller AM, Brogi E, Sui Y, Armenia J, McDonough E, Santamaria-Pang A, Carlin S, Stamper A, Campos C, Pang Z, Li Q, Port E, Graeber TG, Schultz N, Ginty F, Larson SM, Mellinghoff IK. Multiplexed immunofluorescence delineates proteomic cancer cell states associated with metabolism. JCI Insight 2016; 1:87030. [PMID: 27182557 DOI: 10.1172/jci.insight.87030] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The phenotypic diversity of cancer results from genetic and nongenetic factors. Most studies of cancer heterogeneity have focused on DNA alterations, as technologies for proteomic measurements in clinical specimen are currently less advanced. Here, we used a multiplexed immunofluorescence staining platform to measure the expression of 27 proteins at the single-cell level in formalin-fixed and paraffin-embedded samples from treatment-naive stage II/III human breast cancer. Unsupervised clustering of protein expression data from 638,577 tumor cells in 26 breast cancers identified 8 clusters of protein coexpression. In about one-third of breast cancers, over 95% of all neoplastic cells expressed a single protein coexpression cluster. The remaining tumors harbored tumor cells representing multiple protein coexpression clusters, either in a regional distribution or intermingled throughout the tumor. Tumor uptake of the radiotracer 18F-fluorodeoxyglucose was associated with protein expression clusters characterized by hormone receptor loss, PTEN alteration, and HER2 gene amplification. Our study demonstrates an approach to generate cellular heterogeneity metrics in routinely collected solid tumor specimens and integrate them with in vivo cancer phenotypes.
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Affiliation(s)
- Anup Sood
- Diagnostic Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, USA
| | | | | | - Yunxia Sui
- Diagnostic Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, USA
| | | | - Elizabeth McDonough
- Diagnostic Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, USA
| | - Alberto Santamaria-Pang
- Diagnostic Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, USA
| | | | | | | | - Zhengyu Pang
- Diagnostic Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, USA
| | - Qing Li
- Diagnostic Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, USA
| | - Elisa Port
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California, USA
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program.,Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Fiona Ginty
- Diagnostic Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, USA
| | | | - Ingo K Mellinghoff
- Department of Neurology.,Human Oncology and Pathogenesis Program.,Department of Pharmacology, Weill Cornell Medical School, New York, New York, USA
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689
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Bodenmiller B. Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications. Cell Syst 2016; 2:225-38. [PMID: 27135535 DOI: 10.1016/j.cels.2016.03.008] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/10/2016] [Indexed: 12/15/2022]
Abstract
The study of organs and tissues on a molecular level is necessary as we seek an understanding of health and disease. Over the last few years, powerful highly multiplexed epitope-based imaging approaches that rely on the serial imaging of tissues with fluorescently labeled antibodies and the simultaneous analysis using metal-labeled antibodies have emerged. These techniques enable analysis of dozens of epitopes in thousands of cells in a single experiment providing a systems level view of normal and disease processes at the single-cell level with spatial resolution in tissues. In this Review, I discuss, first, the highly multiplexed epitope-based imaging approaches and the generated data. Second, I describe challenges that must be overcome to implement these imaging methods from bench to bedside, including issues with tissue processing and analyses of the large amounts of data generated. Third, I discuss how these methods can be integrated with readouts of genome, transcriptome, metabolome, and live cell information, and fourth, the novel applications possible in tissue biology, drug development, and biomarker discovery. I anticipate that highly multiplexed epitope-based imaging approaches will broadly complement existing imaging methods and will become a cornerstone of tissue biology and biomedical research and of precision medical applications.
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Affiliation(s)
- Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland.
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690
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Laurinavicius A, Plancoulaine B, Herlin P, Laurinaviciene A. Comprehensive Immunohistochemistry: Digital, Analytical and Integrated. Pathobiology 2016; 83:156-63. [PMID: 27101138 DOI: 10.1159/000442389] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Immunohistochemistry (IHC) is widely used in contemporary pathology as a diagnostic and, increasingly, as a prognostic and predictive tool. The main value of the method today comes from a sensitive and specific detection of a protein of interest in the context of tissue architecture and cell populations. One of the major limitations of conventional IHC is related to the fact that the results are usually obtained by visual qualitative or semiquantitative evaluation. While this is sufficient for diagnostic purposes, measurement of prognostic and predictive biomarkers requires better accuracy and reproducibility. Also, objective evaluation of the spatial heterogeneity of biomarker expression as well as the development of combined/integrated biomarkers are in great demand. On the other end of the scale, the rapid development of tissue proteomics accounting for 2D spatial aspects has led to a disruptive concept of next-generation IHC, promising high multiplexing and broad dynamic range quantitative/spatial data on tissue protein expression. This 'evolutionary gap' between conventional and next-generation IHC can be filled by comprehensive IHC based on digital technologies (empowered by quantification and spatial and multiparametric analytics) and integrated into the pathology workflow and information systems. In this paper, we share our perspectives on a comprehensive IHC road map as a multistep development process.
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691
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Saadatpour A, Lai S, Guo G, Yuan GC. Single-Cell Analysis in Cancer Genomics. Trends Genet 2016; 31:576-586. [PMID: 26450340 DOI: 10.1016/j.tig.2015.07.003] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/26/2015] [Accepted: 07/20/2015] [Indexed: 02/04/2023]
Abstract
Genetic changes and environmental differences result in cellular heterogeneity among cancer cells within the same tumor, thereby complicating treatment outcomes. Recent advances in single-cell technologies have opened new avenues to characterize the intra-tumor cellular heterogeneity, identify rare cell types, measure mutation rates, and, ultimately, guide diagnosis and treatment. In this paper we review the recent single-cell technological and computational advances at the genomic, transcriptomic, and proteomic levels, and discuss their applications in cancer research.
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Affiliation(s)
- Assieh Saadatpour
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shujing Lai
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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692
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Murray E, Cho JH, Goodwin D, Ku T, Swaney J, Kim SY, Choi H, Park YG, Park JY, Hubbert A, McCue M, Vassallo S, Bakh N, Frosch MP, Wedeen VJ, Seung HS, Chung K. Simple, Scalable Proteomic Imaging for High-Dimensional Profiling of Intact Systems. Cell 2016; 163:1500-14. [PMID: 26638076 DOI: 10.1016/j.cell.2015.11.025] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/09/2015] [Accepted: 11/10/2015] [Indexed: 01/25/2023]
Abstract
Combined measurement of diverse molecular and anatomical traits that span multiple levels remains a major challenge in biology. Here, we introduce a simple method that enables proteomic imaging for scalable, integrated, high-dimensional phenotyping of both animal tissues and human clinical samples. This method, termed SWITCH, uniformly secures tissue architecture, native biomolecules, and antigenicity across an entire system by synchronizing the tissue preservation reaction. The heat- and chemical-resistant nature of the resulting framework permits multiple rounds (>20) of relabeling. We have performed 22 rounds of labeling of a single tissue with precise co-registration of multiple datasets. Furthermore, SWITCH synchronizes labeling reactions to improve probe penetration depth and uniformity of staining. With SWITCH, we performed combinatorial protein expression profiling of the human cortex and also interrogated the geometric structure of the fiber pathways in mouse brains. Such integrated high-dimensional information may accelerate our understanding of biological systems at multiple levels.
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Affiliation(s)
- Evan Murray
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jae Hun Cho
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel Goodwin
- Simons Center for Data Analysis, 160 Fifth Avenue, 8th Floor, New York, NY 10010, USA
| | - Taeyun Ku
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Justin Swaney
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sung-Yon Kim
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heejin Choi
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Young-Gyun Park
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jeong-Yoon Park
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Austin Hubbert
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Margaret McCue
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sara Vassallo
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Naveed Bakh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew P Frosch
- C.S. Kubik Laboratory of Neuropathology, Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Van J Wedeen
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - H Sebastian Seung
- Simons Center for Data Analysis, 160 Fifth Avenue, 8th Floor, New York, NY 10010, USA; Princeton Neuroscience Institute and Computer Science Department, Princeton University, Princeton, NJ 08544, USA
| | - Kwanghun Chung
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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693
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Lyons J, Herring CA, Banerjee A, Simmons AJ, Lau KS. Multiscale analysis of the murine intestine for modeling human diseases. Integr Biol (Camb) 2016; 7:740-57. [PMID: 26040649 DOI: 10.1039/c5ib00030k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
When functioning properly, the intestine is one of the key interfaces between the human body and its environment. It is responsible for extracting nutrients from our food and excreting our waste products. It provides an environment for a host of healthful microbes and serves as a first defense against pathogenic ones. These processes require tight homeostatic controls, which are provided by the interactions of a complex mix of epithelial, stromal, neural and immune cells, as well as the resident microflora. This homeostasis can be disrupted by invasive microbes, genetic lesions, and carcinogens, resulting in diseases such Clostridium difficile infection, inflammatory bowel disease (IBD) and cancer. Enormous strides have been made in understanding how this important organ functions in health and disease using everything from cell culture systems to animal models to human tissue samples. This has resulted in better therapies for all of these diseases, but there is still significant room for improvement. In the United States alone, 14,000 people per year die of C. difficile, up to 1.6 million people suffer from IBD, and more than 50,000 people die every year from colon cancer. Because these and other intestinal diseases arise from complex interactions between the different components of the gut ecosystem, we propose that systems approaches that address this complexity in an integrative manner may eventually lead to improved therapeutics that deliver lasting cures. This review will discuss the use of systems biology for studying intestinal diseases in vivo with particular emphasis on mouse models. Additionally, it will focus on established experimental techniques that have been used to drive this systems-level analysis, and emerging techniques that will push this field forward in the future.
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Affiliation(s)
- Jesse Lyons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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694
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Janes KA. Single-cell states versus single-cell atlases - two classes of heterogeneity that differ in meaning and method. Curr Opin Biotechnol 2016; 39:120-125. [PMID: 27042975 DOI: 10.1016/j.copbio.2016.03.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 03/04/2016] [Accepted: 03/20/2016] [Indexed: 12/30/2022]
Abstract
Recent advances have created new opportunities to dissect cellular heterogeneity at the omics level. The enthusiasm for deep single-cell profiling has obscured a discussion of different types of heterogeneity and the most-appropriate techniques for studying each type. Here, I distinguish heterogeneity in regulation from heterogeneity in lineage. Snapshots of lineage heterogeneity provide a cell atlas that catalogs cellular diversity within complex tissues. Profiles of regulatory heterogeneity seek to interrogate one lineage deeply to capture an ensemble of single-cell states. Single-cell atlases require molecular signatures from many cells at a throughput afforded by mass cytometry-based, microfluidic-based, and microencapsulation-based methods. Single-cell states are more dependent on time, microenvironment, and low-abundance transcripts, emphasizing in situ methods that stress depth of profiling and quantitative accuracy.
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Affiliation(s)
- Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908 USA.
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695
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Lavin Y, Mortha A, Rahman A, Merad M. Regulation of macrophage development and function in peripheral tissues. Nat Rev Immunol 2016; 15:731-44. [PMID: 26603899 DOI: 10.1038/nri3920] [Citation(s) in RCA: 428] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Macrophages are immune cells of haematopoietic origin that provide crucial innate immune defence and have tissue-specific functions in the regulation and maintenance of organ homeostasis. Recent studies of macrophage ontogeny, as well as transcriptional and epigenetic identity, have started to reveal the decisive role of the tissue stroma in the regulation of macrophage function. These findings suggest that most macrophages seed the tissues during embryonic development and functionally specialize in response to cytokines and metabolites that are released by the stroma and drive the expression of unique transcription factors. In this Review, we discuss how recent insights into macrophage ontogeny and macrophage-stroma interactions contribute to our understanding of the crosstalk that shapes macrophage function and the maintenance of organ integrity.
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Affiliation(s)
- Yonit Lavin
- Department of Oncological Sciences, Tisch Cancer Institute and the Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York 10029, USA
| | - Arthur Mortha
- Department of Oncological Sciences, Tisch Cancer Institute and the Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York 10029, USA
| | - Adeeb Rahman
- Department of Oncological Sciences, Tisch Cancer Institute and the Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York 10029, USA
| | - Miriam Merad
- Department of Oncological Sciences, Tisch Cancer Institute and the Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York 10029, USA
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696
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Kaznatcheev A, Scott JG, Basanta D. Edge effects in game-theoretic dynamics of spatially structured tumours. J R Soc Interface 2016; 12:20150154. [PMID: 26040596 DOI: 10.1098/rsif.2015.0154] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cancer dynamics are an evolutionary game between cellular phenotypes. A typical assumption in this modelling paradigm is that the probability of a given phenotypic strategy interacting with another depends exclusively on the abundance of those strategies without regard for local neighbourhood structure. We address this limitation by using the Ohtsuki-Nowak transform to introduce spatial structure to the go versus grow game. We show that spatial structure can promote the invasive (go) strategy. By considering the change in neighbourhood size at a static boundary--such as a blood vessel, organ capsule or basement membrane--we show an edge effect that allows a tumour without invasive phenotypes in the bulk to have a polyclonal boundary with invasive cells. We present an example of this promotion of invasive (epithelial-mesenchymal transition-positive) cells in a metastatic colony of prostate adenocarcinoma in bone marrow. Our results caution that pathologic analyses that do not distinguish between cells in the bulk and cells at a static edge of a tumour can underestimate the number of invasive cells. Although we concentrate on applications in mathematical oncology, we expect our approach to extend to other evolutionary game models where interaction neighbourhoods change at fixed system boundaries.
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Affiliation(s)
- Artem Kaznatcheev
- School of Computer Science and Department of Psychology, McGill University, Montreal, Quebec, Canada Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jacob G Scott
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - David Basanta
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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697
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Abstract
Imaging reveals complex structures and dynamic interactive processes, located deep inside the body, that are otherwise difficult to decipher. Numerous imaging modalities harness every last inch of the energy spectrum. Clinical modalities include magnetic resonance imaging (MRI), X-ray computed tomography (CT), ultrasound, and light-based methods [endoscopy and optical coherence tomography (OCT)]. Research modalities include various light microscopy techniques (confocal, multiphoton, total internal reflection, superresolution fluorescence microscopy), electron microscopy, mass spectrometry imaging, fluorescence tomography, bioluminescence, variations of OCT, and optoacoustic imaging, among a few others. Although clinical imaging and research microscopy are often isolated from one another, we argue that their combination and integration is not only informative but also essential to discovering new biology and interpreting clinical datasets in which signals invariably originate from hundreds to thousands of cells per voxel.
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698
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Ahmed Raza SE, Langenkämper D, Sirinukunwattana K, Epstein D, Nattkemper TW, Rajpoot NM. Robust normalization protocols for multiplexed fluorescence bioimage analysis. BioData Min 2016; 9:11. [PMID: 26949415 PMCID: PMC4779207 DOI: 10.1186/s13040-016-0088-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/02/2016] [Indexed: 12/18/2022] Open
Abstract
study of mapping and interaction of co-localized proteins at a sub-cellular level is important for understanding complex biological phenomena. One of the recent techniques to map co-localized proteins is to use the standard immuno-fluorescence microscopy in a cyclic manner (Nat Biotechnol 24:1270–8, 2006; Proc Natl Acad Sci 110:11982–7, 2013). Unfortunately, these techniques suffer from variability in intensity and positioning of signals from protein markers within a run and across different runs. Therefore, it is necessary to standardize protocols for preprocessing of the multiplexed bioimaging (MBI) data from multiple runs to a comparable scale before any further analysis can be performed on the data. In this paper, we compare various normalization protocols and propose on the basis of the obtained results, a robust normalization technique that produces consistent results on the MBI data collected from different runs using the Toponome Imaging System (TIS). Normalization results produced by the proposed method on a sample TIS data set for colorectal cancer patients were ranked favorably by two pathologists and two biologists. We show that the proposed method produces higher between class Kullback-Leibler (KL) divergence and lower within class KL divergence on a distribution of cell phenotypes from colorectal cancer and histologically normal samples.
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Affiliation(s)
- Shan E Ahmed Raza
- Department of Computer Science, University of Warwick, Coventry, CV4 7AL UK
| | | | | | - David Epstein
- Mathematics Institute, University of Warwick, Coventry, CV4 7AL UK
| | | | - Nasir M Rajpoot
- Department of Computer Science, University of Warwick, Coventry, CV4 7AL UK ; Department of Computer Science and Engineering, Qatar University, Doha, Qatar
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699
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Heath JR, Ribas A, Mischel PS. Single-cell analysis tools for drug discovery and development. Nat Rev Drug Discov 2016; 15:204-16. [PMID: 26669673 PMCID: PMC4883669 DOI: 10.1038/nrd.2015.16] [Citation(s) in RCA: 336] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The genetic, functional or compositional heterogeneity of healthy and diseased tissues presents major challenges in drug discovery and development. Such heterogeneity hinders the design of accurate disease models and can confound the interpretation of biomarker levels and of patient responses to specific therapies. The complex nature of virtually all tissues has motivated the development of tools for single-cell genomic, transcriptomic and multiplex proteomic analyses. Here, we review these tools and assess their advantages and limitations. Emerging applications of single cell analysis tools in drug discovery and development, particularly in the field of oncology, are discussed.
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Affiliation(s)
- James R Heath
- California Institute of Technology Division of Chemistry and Chemical Engineering, MC 127-72, 1200 East California Boulevard, Pasadena, California 91125, USA
| | - Antoni Ribas
- Department of Medicine, University of California, Los Angeles, 10833 Le Conte Avenue, Los Angeles, California 90095, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research San Diego, Department of Pathology and Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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Li J, Zrazhevskiy P, Gao X. Eliminating Size-Associated Diffusion Constraints for Rapid On-Surface Bioassays with Nanoparticle Probes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:1035-1043. [PMID: 26749053 PMCID: PMC4815929 DOI: 10.1002/smll.201503101] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/30/2015] [Indexed: 05/21/2023]
Abstract
Nanoparticle probes enable implementation of advanced on-surface assay formats, but impose often underappreciated size-associated constraints, in particular on assay kinetics and sensitivity. The present study highlights substantially slower diffusion-limited assay kinetics due to the rapid development of a nanoprobe depletion layer next to the surface, which static incubation and mixing of bulk solution employed in conventional assay setups often fail to disrupt. In contrast, cyclic solution draining and replenishing yields reaction-limited assay kinetics irrespective of the probe size. Using common surface bioassays, enzyme-linked immunosorbent assays and immunofluorescence, this study shows that this conceptually distinct approach effectively "erases" size-dependent diffusion constraints, providing a straightforward route to rapid on-surface bioassays employing bulky probes and procedures involving multiple labeling cycles, such as multicycle single-cell molecular profiling. For proof-of-concept, the study demonstrates that the assay time can be shortened from hours to minutes with the same probe concentration and, at a typical incubation time, comparable target labeling can be achieved with up to eight times lower nanoprobe concentration. The findings are expected to enable realization of novel assay formats and stimulate development of rapid on-surface bioassays with nanoparticle probes.
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Affiliation(s)
- Junwei Li
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Pavel Zrazhevskiy
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Xiaohu Gao
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
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