101
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Ramon Y Cajal S, Castellvi J, Hümmer S, Peg V, Pelletier J, Sonenberg N. Beyond molecular tumor heterogeneity: protein synthesis takes control. Oncogene 2018; 37:2490-2501. [PMID: 29463861 PMCID: PMC5945578 DOI: 10.1038/s41388-018-0152-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/15/2017] [Accepted: 01/02/2018] [Indexed: 01/04/2023]
Abstract
One of the daunting challenges facing modern medicine lies in the understanding and treatment of tumor heterogeneity. Most tumors show intra-tumor heterogeneity at both genomic and proteomic levels, with marked impacts on the responses of therapeutic targets. Therapeutic target-related gene expression pathways are affected by hypoxia and cellular stress. However, the finding that targets such as eukaryotic initiation factor (eIF) 4E (and its phosphorylated form, p-eIF4E) are generally homogenously expressed throughout tumors, regardless of the presence of hypoxia or other cellular stress conditions, opens the exciting possibility that malignancies could be treated with therapies that combine targeting of eIF4E phosphorylation with immune checkpoint inhibitors or chemotherapy.
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Affiliation(s)
- Santiago Ramon Y Cajal
- Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain. .,Pathology Department, Vall d'Hebron Hospital, 08035, Barcelona, Spain. .,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain.
| | - Josep Castellvi
- Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Pathology Department, Vall d'Hebron Hospital, 08035, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | - Stefan Hümmer
- Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | - Vicente Peg
- Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Pathology Department, Vall d'Hebron Hospital, 08035, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | - Jerry Pelletier
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
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102
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Inde Z, Dixon SJ. The impact of non-genetic heterogeneity on cancer cell death. Crit Rev Biochem Mol Biol 2018; 53:99-114. [PMID: 29250983 PMCID: PMC6089072 DOI: 10.1080/10409238.2017.1412395] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 12/22/2022]
Abstract
The goal of cancer chemotherapy is to induce homogeneous cell death within the population of targeted cancer cells. However, no two cells are exactly alike at the molecular level, and sensitivity to drug-induced cell death, therefore, varies within a population. Genetic alterations can contribute to this variability and lead to selection for drug resistant clones. However, there is a growing appreciation for the role of non-genetic variation in producing drug-tolerant cellular states that exhibit reduced sensitivity to cell death for extended periods of time, from hours to weeks. These cellular states may result from individual variation in epigenetics, gene expression, metabolism, and other processes that impact drug mechanism of action or the execution of cell death. Such population-level non-genetic heterogeneity may contribute to treatment failure and provide a cellular "substrate" for the emergence of genetic alterations that confer frank drug resistance.
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Affiliation(s)
- Zintis Inde
- a Cancer Biology Program , Stanford University School of Medicine , Stanford , CA , USA
| | - Scott J Dixon
- a Cancer Biology Program , Stanford University School of Medicine , Stanford , CA , USA
- b Department of Biology , Stanford University , Stanford , CA , USA
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103
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Mondal M, Liao R, Guo J. Highly Multiplexed Single-Cell Protein Analysis. Chemistry 2018; 24:7083-7091. [PMID: 29194810 DOI: 10.1002/chem.201705014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Indexed: 12/17/2022]
Abstract
Single-cell proteomic analysis is crucial to advance our understanding of normal physiology and disease pathogenesis. The comprehensive protein profiling in individual cells of a heterogeneous sample can provide new insights into many important biological issues, such as the regulation of inter- and intracellular signaling pathways or the varied cellular compositions of normal and diseased tissues. With highly multiplexed molecular imaging of many different protein biomarkers in patient biopsies, diseases can be accurately diagnosed to guide the selection of the ideal treatment. In this Minireview, we will describe the recent technological advances of single-cell proteomic assays, discuss their advantages and limitations, highlight their applications in biology and precision medicine, and present the current challenges and potential solutions.
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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
| | - Jia Guo
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona, 85287, USA
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104
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Abstract
In their native environment, cells are immersed in a complex milieu of biochemical and biophysical cues. These cues may include growth factors, the extracellular matrix, cell-cell contacts, stiffness, and topography, and they are responsible for regulating cellular behaviors such as adhesion, proliferation, migration, apoptosis, and differentiation. The decision-making process used to convert these extracellular inputs into actions is highly complex and sensitive to changes both in the type of individual cue (e.g., growth factor dose/level, timing) and in how these individual cues are combined (e.g., homotypic/heterotypic combinations). In this review, we highlight recent advances in the development of engineering-based approaches to study the cellular decision-making process. Specifically, we discuss the use of biomaterial platforms that enable controlled and tailored delivery of individual and combined cues, as well as the application of computational modeling to analyses of the complex cellular decision-making networks.
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Affiliation(s)
- Pamela K Kreeger
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , .,Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health , Madison, Wisconsin 53705, USA.,Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, USA.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792, USA
| | - Laura E Strong
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; ,
| | - Kristyn S Masters
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , .,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792, USA.,Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792, USA
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105
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Earl DC, Ferrell PB, Leelatian N, Froese JT, Reisman BJ, Irish JM, Bachmann BO. Discovery of human cell selective effector molecules using single cell multiplexed activity metabolomics. Nat Commun 2018; 9:39. [PMID: 29295987 PMCID: PMC5750220 DOI: 10.1038/s41467-017-02470-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 12/01/2017] [Indexed: 01/06/2023] Open
Abstract
Discovering bioactive metabolites within a metabolome is challenging because there is generally little foreknowledge of metabolite molecular and cell-targeting activities. Here, single-cell response profiles and primary human tissue comprise a response platform used to discover novel microbial metabolites with cell-type-selective effector properties in untargeted metabolomic inventories. Metabolites display diverse effector mechanisms, including targeting protein synthesis, cell cycle status, DNA damage repair, necrosis, apoptosis, or phosphoprotein signaling. Arrayed metabolites are tested against acute myeloid leukemia patient bone marrow and molecules that specifically targeted blast cells or nonleukemic immune cell subsets within the same tissue biopsy are revealed. Cell-targeting polyketides are identified in extracts from biosynthetically prolific bacteria, including a previously unreported leukemia blast-targeting anthracycline and a polyene macrolactam that alternates between targeting blasts or nonmalignant cells by way of light-triggered photochemical isomerization. High-resolution cell profiling with mass cytometry confirms response mechanisms and is used to validate initial observations.
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Affiliation(s)
- David C Earl
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA
| | - P Brent Ferrell
- Department of Medicine, Vanderbilt University Medical Center, 1161 21st Avenue South, D-3100 Medical Center North, Nashville, TN, 37232, USA
| | - Nalin Leelatian
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37232, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2220 Pierce Avenue, Nashville, TN, 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, D-2220 Medical Center North, Nashville, TN, 37232, USA
| | - Jordan T Froese
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA
| | - Benjamin J Reisman
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37232, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2220 Pierce Avenue, Nashville, TN, 37232, USA.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, D-2220 Medical Center North, Nashville, TN, 37232, USA.
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA.
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106
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Caen O, Schütz S, Jammalamadaka MSS, Vrignon J, Nizard P, Schneider TM, Baret JC, Taly V. High-throughput multiplexed fluorescence-activated droplet sorting. MICROSYSTEMS & NANOENGINEERING 2018; 4:33. [PMID: 31057921 PMCID: PMC6220162 DOI: 10.1038/s41378-018-0033-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/05/2018] [Accepted: 07/05/2018] [Indexed: 05/02/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) is one of the most important features provided by droplet-based microfluidics. However, to date, it does not allow to compete with the high-throughput multiplexed sorting capabilities offered by flow cytometery. Here, we demonstrate the use of a dielectrophoretic-based FADS, allowing to sort up to five different droplet populations simultaneously. Our system provides means to select droplets of different phenotypes in a single experimental run to separate initially heterogeneous populations. Our experimental results are rationalized with the help of a numerical model of the actuation of droplets in electric fields providing guidelines for the prediction of sorting designs for upscaled or downscaled microsystems.
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Affiliation(s)
- Ouriel Caen
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Simon Schütz
- Emergent Complexity in Physical Systems Laboratory (ECPS), Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - M. S. Suryateja Jammalamadaka
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Jérémy Vrignon
- CNRS, University Bordeaux, CRPP, UMR 5031, 115 Avenue Schweitzer, 33600 Pessac, France
| | - Philippe Nizard
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Tobias M. Schneider
- Emergent Complexity in Physical Systems Laboratory (ECPS), Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jean-Christophe Baret
- CNRS, University Bordeaux, CRPP, UMR 5031, 115 Avenue Schweitzer, 33600 Pessac, France
| | - Valérie Taly
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
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107
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Fong LE, Sulistijo ES, Miller-Jensen K. Systems analysis of latent HIV reversal reveals altered stress kinase signaling and increased cell death in infected T cells. Sci Rep 2017; 7:16179. [PMID: 29170390 PMCID: PMC5701066 DOI: 10.1038/s41598-017-15532-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/27/2017] [Indexed: 11/13/2022] Open
Abstract
Viral latency remains the most significant obstacle to HIV eradication. Clinical strategies aim to purge the latent CD4+ T cell reservoir by activating viral expression to induce death, but are undercut by the inability to target latently infected cells. Here we explored the acute signaling response of latent HIV-infected CD4+ T cells to identify dynamic phosphorylation signatures that could be targeted for therapy. Stimulation with CD3/CD28, PMA/ionomycin, or latency reversing agents prostratin and SAHA, yielded increased phosphorylation of IκBα, ERK, p38, and JNK in HIV-infected cells across two in vitro latency models. Both latent infection and viral protein expression contributed to changes in perturbation-induced signaling. Data-driven statistical models calculated from the phosphorylation signatures successfully classified infected and uninfected cells and further identified signals that were functionally important for regulating cell death. Specifically, the stress kinase pathways p38 and JNK were modified in latently infected cells, and activation of p38 and JNK signaling by anisomycin resulted in increased cell death independent of HIV reactivation. Our findings suggest that altered phosphorylation signatures in infected T cells provide a novel strategy to more selectively target the latent reservoir to enhance eradication efforts.
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Affiliation(s)
- Linda E Fong
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Endah S Sulistijo
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Kathryn Miller-Jensen
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA. .,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.
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108
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Forthun RB, Aasebø E, Rasinger JD, Bedringaas SL, Berven F, Selheim F, Bruserud Ø, Gjertsen BT. Phosphoprotein DIGE profiles reflect blast differentiation, cytogenetic risk stratification, FLT3/NPM1 mutations and therapy response in acute myeloid leukaemia. J Proteomics 2017; 173:32-41. [PMID: 29175091 DOI: 10.1016/j.jprot.2017.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 09/30/2017] [Accepted: 11/18/2017] [Indexed: 12/12/2022]
Abstract
Acute myeloid leukaemia (AML) is an aggressive blood cancer characterized by a distinct block in differentiation of myeloid progenitors, recurrent chromosomal translocations and gene mutations of which >50% involve signal transduction through dysregulated kinases and phosphatases. In search for novel protein biomarkers for disease stratification we investigated the phosphoproteome in leukaemic cells from 62 AML patients at time of diagnosis using immobilized metal-affinity chromatography, protein separation by two-dimensional differential gel electrophoresis (2D-DIGE) and mass spectrometry before validation by selected reaction monitoring (SRM). Unsupervised clustering found 27 phosphoproteins significantly discriminating patients according to leukaemic cell differentiation (French-American-British (FAB) classification), cytogenetic and mutational (FLT3, NPM1) status or response to chemotherapy. Monocytic differentiation (FAB M4-M5) correlated with enrichment of proteins involved in apoptosis (MOES, ANXA5 and EFHD2). TALDO, a protein associated with thrombocytopenia if down-regulated, was elevated in patients with wild type NPM1 compared to patients with NPM1 mutation. This study demonstrates the potential of quantitative proteomics in AML classification and risk stratification. BIOLOGICAL SIGNIFICANCE Patients diagnosed with AML are currently categorized according to cellular morphology, cytogenetic alterations and mutations, although the majority of these cellular and genetic alterations have no or unsolved impact on therapy selection or prognosis. We therefore explored the phosphoproteome for abundance changes associated with traditional classifiers to unravel patterns that could stratify patients at the protein level. MOES, ANXA5 and EFHD2 were confirmed by SRM to be correlated to monocytic differentiation, whilst TALDO was elevated in NPM1 wild type patients.
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Affiliation(s)
- Rakel Brendsdal Forthun
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Elise Aasebø
- Department of Biomedicine, Proteomic Unit, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway; Department of Clinical Science, Leukemia Research Group, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | | | - Siv Lise Bedringaas
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Frode Berven
- Department of Biomedicine, Proteomic Unit, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Frode Selheim
- Department of Biomedicine, Proteomic Unit, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Øystein Bruserud
- Department of Clinical Science, Leukemia Research Group, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway; Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
| | - Bjørn Tore Gjertsen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway; Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway.
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109
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Tyner JW. Integrating functional genomics to accelerate mechanistic personalized medicine. Cold Spring Harb Mol Case Stud 2017; 3:a001370. [PMID: 28299357 PMCID: PMC5334473 DOI: 10.1101/mcs.a001370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The advent of deep sequencing technologies has resulted in the deciphering of tremendous amounts of genetic information. These data have led to major discoveries, and many anecdotes now exist of individual patients whose clinical outcomes have benefited from novel, genetically guided therapeutic strategies. However, the majority of genetic events in cancer are currently undrugged, leading to a biological gap between understanding of tumor genetic etiology and translation to improved clinical approaches. Functional screening has made tremendous strides in recent years with the development of new experimental approaches to studying ex vivo and in vivo drug sensitivity. Numerous discoveries and anecdotes also exist for translation of functional screening into novel clinical strategies; however, the current clinical application of functional screening remains largely confined to small clinical trials at specific academic centers. The intersection between genomic and functional approaches represents an ideal modality to accelerate our understanding of drug sensitivities as they relate to specific genetic events and further understand the full mechanisms underlying drug sensitivity patterns.
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Affiliation(s)
- Jeffrey W Tyner
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
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110
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Snijder B, Vladimer GI, Krall N, Miura K, Schmolke AS, Kornauth C, Lopez de la Fuente O, Choi HS, van der Kouwe E, Gültekin S, Kazianka L, Bigenzahn JW, Hoermann G, Prutsch N, Merkel O, Ringler A, Sabler M, Jeryczynski G, Mayerhoefer ME, Simonitsch-Klupp I, Ocko K, Felberbauer F, Müllauer L, Prager GW, Korkmaz B, Kenner L, Sperr WR, Kralovics R, Gisslinger H, Valent P, Kubicek S, Jäger U, Staber PB, Superti-Furga G. Image-based ex-vivo drug screening for patients with aggressive haematological malignancies: interim results from a single-arm, open-label, pilot study. LANCET HAEMATOLOGY 2017; 4:e595-e606. [PMID: 29153976 PMCID: PMC5719985 DOI: 10.1016/s2352-3026(17)30208-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/13/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023]
Abstract
Background Patients with refractory or relapsed haematological malignancies have few treatment options and short survival times. Identification of effective therapies with genomic-based precision medicine is hampered by intratumour heterogeneity and incomplete understanding of the contribution of various mutations within specific cancer phenotypes. Ex-vivo drug-response profiling in patient biopsies might aid effective treatment identification; however, proof of its clinical utility is limited. Methods We investigated the feasibility and clinical impact of multiparametric, single-cell, drug-response profiling in patient biopsies by immunofluorescence, automated microscopy, and image analysis, an approach we call pharmacoscopy. First, the ability of pharmacoscopy to separate responders from non-responders was evaluated retrospectively for a cohort of 20 newly diagnosed and previously untreated patients with acute myeloid leukaemia. Next, 48 patients with aggressive haematological malignancies were prospectively evaluated for pharmacoscopy-guided treatment, of whom 17 could receive the treatment. The primary endpoint was progression-free survival in pharmacoscopy-treated patients, as compared with their own progression-free survival for the most recent regimen on which they had progressive disease. This trial is ongoing and registered with ClinicalTrials.gov, number NCT03096821. Findings Pharmacoscopy retrospectively predicted the clinical response of 20 acute myeloid leukaemia patients to initial therapy with 88·1% accuracy. In this interim analysis, 15 (88%) of 17 patients receiving pharmacoscopy-guided treatment had an overall response compared with four (24%) of 17 patients with their most recent regimen (odds ratio 24·38 [95% CI 3·99–125·4], p=0·0013). 12 (71%) of 17 patients had a progression-free survival ratio of 1·3 or higher, and median progression-free survival increased by four times, from 5·7 (95% CI 4·1–12·1) weeks to 22·6 (7·4–34·0) weeks (hazard ratio 3·14 [95% CI 1·37–7·22], p=0·0075). Interpretation Routine clinical integration of pharmacoscopy for treatment selection is technically feasible, and led to improved treatment of patients with aggressive refractory haematological malignancies in an initial patient cohort, warranting further investigation. Funding Austrian Academy of Sciences; European Research Council; Austrian Science Fund; Austrian Federal Ministry of Science, Research and Economy; National Foundation for Research, Technology and Development; Anniversary Fund of the Austrian National Bank; MPN Research Foundation; European Molecular Biology Organization; and Swiss National Science Foundation.
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Affiliation(s)
- Berend Snijder
- CeMM Research Center for Molecular Medicine, Vienna, Austria; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Gregory I Vladimer
- CeMM Research Center for Molecular Medicine, Vienna, Austria; Allcyte, Vienna, Austria
| | - Nikolaus Krall
- CeMM Research Center for Molecular Medicine, Vienna, Austria
| | - Katsuhiro Miura
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Ann-Sofie Schmolke
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Christoph Kornauth
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | | | - Hye-Soo Choi
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Emiel van der Kouwe
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Sinan Gültekin
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Lukas Kazianka
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | | | - Gregor Hoermann
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Nicole Prutsch
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Olaf Merkel
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Anna Ringler
- CeMM Research Center for Molecular Medicine, Vienna, Austria; Christian Doppler Laboratory for Chemical Epigenetics and Anti-Infectives, Vienna, Austria
| | - Monika Sabler
- CeMM Research Center for Molecular Medicine, Vienna, Austria
| | - Georg Jeryczynski
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Marius E Mayerhoefer
- Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | | | - Katharina Ocko
- Pharmacy Department, Vienna General Hospital, Vienna, Austria
| | - Franz Felberbauer
- Division of General Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Leonhard Müllauer
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Gerald W Prager
- Department of Internal Medicine I, Division of Oncology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Belgin Korkmaz
- Division of General Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Lukas Kenner
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria; Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria; Unit of Laboratory Animal Pathology, University of Veterinary Medicine, Vienna, Austria
| | - Wolfgang R Sperr
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria; Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria
| | | | - Heinz Gisslinger
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria; Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine, Vienna, Austria; Christian Doppler Laboratory for Chemical Epigenetics and Anti-Infectives, Vienna, Austria
| | - Ulrich Jäger
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Philipp B Staber
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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111
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Gupta SD, Sachs Z. Novel single-cell technologies in acute myeloid leukemia research. Transl Res 2017; 189:123-135. [PMID: 28802867 PMCID: PMC6584944 DOI: 10.1016/j.trsl.2017.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022]
Abstract
Acute myeloid leukemia (AML) is a lethal malignancy because patients who initially respond to chemotherapy eventually relapse with treatment refractory disease. Relapse is caused by leukemia stem cells (LSCs) that reestablish the disease through self-renewal. Self-renewal is the ability of a stem cell to produce copies of itself and give rise to progeny cells. Therefore, therapeutic strategies eradicating LSCs are essential to prevent relapse and achieve long-term remission in AML. AML is a heterogeneous disease both at phenotypic and genotypic levels, and this heterogeneity extends to LSCs. Classical studies in AML have aimed at characterization of the bulk tumor population, thereby masking cellular heterogeneity. Single-cell approaches provide a novel opportunity to elucidate molecular mechanisms in heterogeneous diseases such as AML. In recent years, major advancements in single-cell measurement systems have revolutionized our understanding of the pathophysiology of AML and enabled the characterization of LSCs. Identifying the molecular mechanisms critical to AML LSCs will aid in the development of targeted therapeutic strategies to combat this deadly disease.
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Affiliation(s)
- Soumyasri Das Gupta
- Division of Hematology, Oncology, and Transplantation, Department Medicine, University of Minnesota, Minneapolis, Minn
| | - Zohar Sachs
- Division of Hematology, Oncology, and Transplantation, Department Medicine, University of Minnesota, Minneapolis, Minn; Masonic Cancer Center, University of Minnesota, Minneapolis, Minn.
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112
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Tong J, Helmy M, Cavalli FMG, Jin L, St-Germain J, Karisch R, Taylor P, Minden MD, Taylor MD, Neel BG, Bader GD, Moran MF. Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome, and tyrosine-phosphatome in acute myeloid leukemia. Proteomics 2017; 17. [PMID: 28176486 DOI: 10.1002/pmic.201600361] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/21/2016] [Accepted: 02/06/2017] [Indexed: 12/22/2022]
Abstract
Reversible protein-tyrosine phosphorylation is catalyzed by the antagonistic actions of protein-tyrosine kinases (PTKs) and phosphatases (PTPs), and represents a major form of cell regulation. Acute myeloid leukemia (AML) is an aggressive hematological malignancy that results from the acquisition of multiple genetic alterations, which in some instances are associated with deregulated protein-phosphotyrosine (pY) mediated signaling networks. However, although individual PTKs and PTPs have been linked to AML and other malignancies, analysis of protein-pY networks as a function of activated PTKs and PTPs has not been done. In this study, MS was used to characterize AML proteomes, and phospho-proteome-subsets including pY proteins, PTKs, and PTPs. AML proteomes resolved into two groups related to high or low degrees of maturation according to French-American-British classification, and reflecting differential expression of cell surface antigens. AML pY proteomes reflect canonical, spatially organized signaling networks, unrelated to maturation, with heterogeneous expression of activated receptor and nonreceptor PTKs. We present the first integrated analysis of the pY-proteome, activated PTKs, and PTPs. Every PTP and most PTKs have both positive and negative associations with the pY-proteome. pY proteins resolve into groups with shared PTK and PTP correlations. These findings highlight the importance of pY turnover and the PTP phosphatome in shaping the pY-proteome in AML.
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Affiliation(s)
- Jiefei Tong
- Program in Cell Biology, Hospital for Sick Children, Toronto, Canada.,Peter Gilgan Centre for Research and Learning, Hospital For Sick Children, Toronto, Canada
| | - Mohamed Helmy
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Florence M G Cavalli
- Peter Gilgan Centre for Research and Learning, Hospital For Sick Children, Toronto, Canada.,Program in Developmental & Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
| | - Lily Jin
- Program in Cell Biology, Hospital for Sick Children, Toronto, Canada.,Peter Gilgan Centre for Research and Learning, Hospital For Sick Children, Toronto, Canada
| | | | - Robert Karisch
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Paul Taylor
- Program in Cell Biology, Hospital for Sick Children, Toronto, Canada.,Peter Gilgan Centre for Research and Learning, Hospital For Sick Children, Toronto, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Michael D Taylor
- Peter Gilgan Centre for Research and Learning, Hospital For Sick Children, Toronto, Canada.,Program in Developmental & Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Benjamin G Neel
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada.,Departmet of Medicine, NYU School of Medicine, New York, NY, USA
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael F Moran
- Program in Cell Biology, Hospital for Sick Children, Toronto, Canada.,Peter Gilgan Centre for Research and Learning, Hospital For Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
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113
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Tan M, Rong Y, Su Q, Chen Y. Artesunate induces apoptosis via inhibition of STAT3 in THP-1 cells. Leuk Res 2017; 62:98-103. [PMID: 29031126 DOI: 10.1016/j.leukres.2017.09.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 10/18/2022]
Abstract
OBJECTIVE Our objective was to explore STAT3 expression in patients with acute myeloid leukaemia (AML), assess the anti-proliferative effects of artesunate (ART) on THP-1 cells in vivo and in vitro, and investigate the underlying mechanisms. METHODS In this study, we examined 30 patients with acute myeloid leukaemia diagnosed in our hospital from January 2015 to January 2016. The 20 control group patients had non-haematological diseases and were hospitalized for the same period. We extracted 2ml bone marrow, separated the mononuclear cells, obtained total proteins, and detected STAT3 protein levels with Western blot analyses. The THP-1 cells were treated with different concentrations of ART(0, 10, 25, 50, 100, 200μM). Then, THP-1 cell viability was detected with CCK-8 assays, apoptosis was measured with flow cytometry, and the STAT3, caspase-3 and caspase-8 protein levels were assessed using Western blot analyses. THP-1 cells in logarithmic growth phase were subcutaneously injected into the necks of 5-week-old nude mice. The control group was subcutaneously injected with 0.1ml PBS. After the nude mouse tumours grew, the mice were divided into the control group and drug intervention groups (ART 100μM group, ART 200μM group). The mice in the intervention groups were intraperitoneally injected with ART, and the control group was injected with the same amount of normal saline. Then, changes in the tumours were observed. After the drug intervention, the total protein was extracted, and STAT3 expression was detected by Western blot analysis. RESULTS Compared with the control group, the AML patients had significantly increased STAT3 protein levels (P<0.01). ART significantly inhibited the proliferation of THP-1 cells in a dose-dependent and time-dependent manner. ART also increased THP-1cell apoptosis. After treatment with ART, STAT3 protein was significantly down-regulated, and apoptosis of the cells was induced by the activation of caspase-3 and caspse-8. CONCLUSION AML patients had higher expression of STAT3 than that of the controls. ART induced apoptosis in THP-1 cells and inhibited the growth of xenografts in nude mice, and we also observed that ART down-regulated the expression of STAT3 and activated the caspase-3 and caspase-8. We speculated that the effect of ART on THP-1 cells may be related to inhibition of STAT3 and activation of caspase3 and caspase-8.
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Affiliation(s)
- Mei Tan
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China
| | - Ying Rong
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China
| | - Qiong Su
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China
| | - Yan Chen
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China.
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114
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Tevis KM, Colson YL, Grinstaff MW. Embedded Spheroids as Models of the Cancer Microenvironment. ADVANCED BIOSYSTEMS 2017; 1:1700083. [PMID: 30221187 PMCID: PMC6135264 DOI: 10.1002/adbi.201700083] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
To more accurately study the complex mechanisms behind cancer invasion, progression, and response to treatment, researchers require models that replicate both the multicellular nature and 3D stromal environment present in an in vivo tumor. Multicellular aggregates (i.e., spheroids) embedded in an extracellular matrix mimic are a prevalent model. Recently, quantitative metrics that fully utilize the capability of spheroids are described along with conventional experiments, such as invasion into a matrix, to provide additional details and insights into the underlying cancer biology. The review begins with a discussion of the salient features of the tumor microenvironment, introduces the early work on non-embedded spheroids as tumor models, and then concentrates on the successes achieved with the study of embedded spheroids. Examples of studies include cell movement, drug response, tumor cellular heterogeneity, stromal effects, and cancer progression. Additionally, new methodologies and those borrowed from other research fields (e.g., vascularization and tissue engineering) are highlighted that expand the capability of spheroids to aid future users in designing their cancer-related experiments. The convergence of spheroid research among the various fields catalyzes new applications and leads to a natural synergy. Finally, the review concludes with a reflection and future perspectives for cancer spheroid research.
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Affiliation(s)
- Kristie M. Tevis
- Departments of Biomedical Engineering, Chemistry, and Medicine, Metcalf Center for Science and Engineering, Boston University, Boston, MA 02215
| | - Yolonda L. Colson
- Division of Thoracic Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MA 02215
| | - Mark W. Grinstaff
- Departments of Biomedical Engineering, Chemistry, and Medicine, Metcalf Center for Science and Engineering, Boston University, Boston, MA 02215
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115
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Hanif S, Liu HL, Ahmed SA, Yang JM, Zhou Y, Pang J, Ji LN, Xia XH, Wang K. Nanopipette-Based SERS Aptasensor for Subcellular Localization of Cancer Biomarker in Single Cells. Anal Chem 2017; 89:9911-9917. [PMID: 28825473 DOI: 10.1021/acs.analchem.7b02147] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single cell analysis is essential for understanding the heterogeneity, behaviors of cells, and diversity of target analyte in different subcellular regions. Nucleolin (NCL) is a multifunctional protein that is markedly overexpressed in most of the cancer cells. The variant expression levels of NCL in subcellular regions have a marked influence on cancer proliferation and treatments. However, the specificity of available methods to identify the cancer biomarkers is limited because of the high level of subcellular matrix effect. Herein, we proposed a novel technique to increase both the molecular and spectral specificity of cancer diagnosis by using aptamers affinity based portable nanopipette with distinctive surface-enhanced Raman scattering (SERS) activities. The aptamers-functionalized gold-coated nanopipette was used to capture target, while p-mercaptobenzonitrile (MBN) and complementary DNA modified Ag nanoparticles (AgNPs) worked as Raman reporter to produce SERS signal. The SERS signal of Raman nanotag was lost upon NCL capturing via modified DNA aptamers on nanoprobe, which further helped to verify the specificity of nanoprobe. For proof of concept, NCL protein was specifically extracted from different cell lines by aptamers modified SERS active nanoprobe. The nanoprobes manifested specifically good affinity for NCL with a dissociation constant Kd of 36 nM and provided a 1000-fold higher specificity against other competing proteins. Furthermore, the Raman reporter moiety has a vibrational frequency in the spectroscopically silent region (1800-2300 cm-1) with a negligible matrix effect from cell analysis. The subcellular localization and spatial distribution of NCL were successfully achieved in various types of cells, including MCF-7A, HeLa, and MCF-10A cells. This type of probing technique for single cell analysis could lead to the development of a new perspective in cancer diagnosis and treatment at the cellular level.
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Affiliation(s)
- Sumaira Hanif
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, and ‡State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Hai-Ling Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, and ‡State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Saud Asif Ahmed
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, and ‡State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Jin-Mei Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, and ‡State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Yue Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, and ‡State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Jie Pang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, and ‡State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, and ‡State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, and ‡State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, and ‡State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023, China
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116
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Li X, Fan B, Cao S, Chen D, Zhao X, Men D, Yue W, Wang J, Chen J. A microfluidic flow cytometer enabling absolute quantification of single-cell intracellular proteins. LAB ON A CHIP 2017; 17:3129-3137. [PMID: 28805868 DOI: 10.1039/c7lc00546f] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Quantification of single-cell proteomics provides key insights into cellular heterogeneity while conventional flow cytometry cannot provide absolute quantification of intracellular proteins of single cells due to the lack of calibration approaches. This paper presents a constriction channel (with a cross sectional area smaller than cells) based microfluidic flow cytometer, capable of collecting copy numbers of specific intracellular proteins. In this platform, single cells stained with fluorescence labelled antibodies were forced to squeeze through the constriction channel with the fluorescence intensities quantified and since cells fully filled the constriction channel during the squeezing process, solutions with fluorescence labelled antibodies were flushed into the constriction channel to obtain calibration curves. By combining raw fluorescence data and calibration curves, absolute quantification of intracellular proteins was realized. As a demonstration, copy numbers of beta-actin of single tumour cells were quantified to be 0.90 ± 0.30 μM (A549, ncell = 14 228), 2.34 ± 0.70 μM (MCF 10A, ncell = 2455), and 0.98 ± 0.65 μM (Hep G2, ncell = 6945). The travelling time for individual cells was quantified to be roughly 10 ms and thus a throughput of 100 cells per s can be achieved. This microfluidic system can be used to quantify the copy numbers of intracellular proteins in a high-throughput manner, which may function as an enabling technique in the field of single-cell proteomics.
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Affiliation(s)
- Xiufeng Li
- State Key Laboratory of Transducer Technology, Institute of Electronics, Chinese Academy of Sciences, Beijing, P.R. China.
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117
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Hydrogen bond based smart polymer for highly selective and tunable capture of multiply phosphorylated peptides. Nat Commun 2017; 8:461. [PMID: 28878229 PMCID: PMC5587758 DOI: 10.1038/s41467-017-00464-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 06/30/2017] [Indexed: 01/01/2023] Open
Abstract
Multisite phosphorylation is an important and common mechanism for finely regulating protein functions and subsequent cellular responses. However, this study is largely restricted by the difficulty to capture low-abundance multiply phosphorylated peptides (MPPs) from complex biosamples owing to the limitation of enrichment materials and their interactions with phosphates. Here we show that smart polymer can serve as an ideal platform to resolve this challenge. Driven by specific but tunable hydrogen bonding interactions, the smart polymer displays differential complexation with MPPs, singly phosphorylated and non-modified peptides. Importantly, MPP binding can be modulated conveniently and precisely by solution conditions, resulting in highly controllable MPP adsorption on material surface. This facilitates excellent performance in MPP enrichment and separation from model proteins and real biosamples. High enrichment selectivity and coverage, extraordinary adsorption capacities and recovery towards MPPs, as well as high discovery rates of unique phosphorylation sites, suggest its great potential in phosphoproteomics studies. Capture of low-abundance multiply phosphorylated peptides (MPPs) is difficult due to limitation of enrichment materials and their interactions with phosphates. Here the authors show, a smart polymer driven by specific but tunable hydrogen bonding interactions can differentially complex with MPPs, singly phosphorylated and non-modified peptides.
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118
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Molecularly targeted drug combinations demonstrate selective effectiveness for myeloid- and lymphoid-derived hematologic malignancies. Proc Natl Acad Sci U S A 2017; 114:E7554-E7563. [PMID: 28784769 DOI: 10.1073/pnas.1703094114] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Translating the genetic and epigenetic heterogeneity underlying human cancers into therapeutic strategies is an ongoing challenge. Large-scale sequencing efforts have uncovered a spectrum of mutations in many hematologic malignancies, including acute myeloid leukemia (AML), suggesting that combinations of agents will be required to treat these diseases effectively. Combinatorial approaches will also be critical for combating the emergence of genetically heterogeneous subclones, rescue signals in the microenvironment, and tumor-intrinsic feedback pathways that all contribute to disease relapse. To identify novel and effective drug combinations, we performed ex vivo sensitivity profiling of 122 primary patient samples from a variety of hematologic malignancies against a panel of 48 drug combinations. The combinations were designed as drug pairs that target nonoverlapping biological pathways and comprise drugs from different classes, preferably with Food and Drug Administration approval. A combination ratio (CR) was derived for each drug pair, and CRs were evaluated with respect to diagnostic categories as well as against genetic, cytogenetic, and cellular phenotypes of specimens from the two largest disease categories: AML and chronic lymphocytic leukemia (CLL). Nearly all tested combinations involving a BCL2 inhibitor showed additional benefit in patients with myeloid malignancies, whereas select combinations involving PI3K, CSF1R, or bromodomain inhibitors showed preferential benefit in lymphoid malignancies. Expanded analyses of patients with AML and CLL revealed specific patterns of ex vivo drug combination efficacy that were associated with select genetic, cytogenetic, and phenotypic disease subsets, warranting further evaluation. These findings highlight the heuristic value of an integrated functional genomic approach to the identification of novel treatment strategies for hematologic malignancies.
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119
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Stepanenko AA, Heng HH. Transient and stable vector transfection: Pitfalls, off-target effects, artifacts. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:91-103. [DOI: 10.1016/j.mrrev.2017.05.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 05/09/2017] [Accepted: 05/13/2017] [Indexed: 12/15/2022]
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120
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Gill R, McCabe MJ, Rosenspire AJ. Low level exposure to inorganic mercury interferes with B cell receptor signaling in transitional type 1 B cells. Toxicol Appl Pharmacol 2017; 330:22-29. [PMID: 28668464 DOI: 10.1016/j.taap.2017.06.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/09/2017] [Accepted: 06/27/2017] [Indexed: 01/11/2023]
Abstract
Mercury (Hg) has been implicated as a factor contributing to autoimmune disease in animal models and humans. However the mechanism by which this occurs has remained elusive. Since the discovery of B cells it has been appreciated by immunologists that during the normal course of B cell development, some immature B cells must be generated that produce immunoglobulin reactive to self-antigens (auto-antibodies). However in the course of normal development, the vast majority of immature auto-reactive B cells are prevented from maturing by processes collectively known as tolerance. Autoimmune disease arises when these mechanisms of tolerance are disrupted. In the B cell compartment, it is firmly established that tolerance depends in part upon negative selection of self-reactive immature (transitional type 1) B cells. In these cells negative selection depends upon signals generated by the B Cell Receptor (BCR), in the sense that those T1 B cells who's BCRs most strongly bind to, and so generate the strongest signals to self-antigens are neutralized. In this report we have utilized multicolor phosphoflow cytometry to show that in immature T1 B cells Hg attenuates signal generation by the BCR through mechanisms that may involve Lyn, a key tyrosine kinase in the BCR signal transduction pathway. We suggest that exposure to low, environmentally relevant levels of Hg, disrupts tolerance by interfering with BCR signaling in immature B cells, potentially leading to the appearance of mature auto-reactive B cells which have the ability to contribute to auto-immune disease.
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Affiliation(s)
- R Gill
- Department of Immunology, Microbiology and Biochemistry, Wayne State University, Detroit, MI, United States
| | - M J McCabe
- Department of Environmental Medicine, University of Rochester, Rochester, NY, United States
| | - A J Rosenspire
- Department of Immunology, Microbiology and Biochemistry, Wayne State University, Detroit, MI, United States; Center for Urban Responses to Environmental Stressors (CURES), Wayne State University, Detroit, MI, United States.
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121
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Matte-Martone C, Liu J, Zhou M, Chikina M, Green DR, Harty JT, Shlomchik WD. Differential requirements for myeloid leukemia IFN-γ conditioning determine graft-versus-leukemia resistance and sensitivity. J Clin Invest 2017; 127:2765-2776. [PMID: 28604385 DOI: 10.1172/jci85736] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/20/2017] [Indexed: 12/25/2022] Open
Abstract
The graft-versus-leukemia (GVL) effect in allogeneic hematopoietic stem cell transplantation (alloSCT) is potent against chronic phase chronic myelogenous leukemia (CP-CML), but blast crisis CML (BC-CML) and acute myeloid leukemias (AML) are GVL resistant. To understand GVL resistance, we studied GVL against mouse models of CP-CML, BC-CML, and AML generated by the transduction of mouse BM with fusion cDNAs derived from human leukemias. Prior work has shown that CD4+ T cell-mediated GVL against CP-CML and BC-CML required intact leukemia MHCII; however, stem cells from both leukemias were MHCII negative. Here, we show that CP-CML, BC-CML, and AML stem cells upregulate MHCII in alloSCT recipients. Using gene-deficient leukemias, we determined that BC-CML and AML MHC upregulation required IFN-γ stimulation, whereas CP-CML MHC upregulation was independent of both the IFN-γ receptor (IFN-γR) and the IFN-α/β receptor IFNAR1. Importantly, IFN-γR-deficient BC-CML and AML were completely resistant to CD4- and CD8-mediated GVL, whereas IFN-γR/IFNAR1 double-deficient CP-CML was fully GVL sensitive. Mouse AML and BC-CML stem cells were MHCI+ without IFN-γ stimulation, suggesting that IFN-γ sensitizes these leukemias to T cell killing by mechanisms other than MHC upregulation. Our studies identify the requirement of IFN-γ stimulation as a mechanism for BC-CML and AML GVL resistance, whereas independence from IFN-γ renders CP-CML more GVL sensitive, even with a lower-level alloimmune response.
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Affiliation(s)
| | - Jinling Liu
- Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Meng Zhou
- Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Maria Chikina
- Department of Computational Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis Tennessee, USA
| | - John T Harty
- Department of Microbiology and Pathology, University of Iowa, Iowa City, Iowa, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Warren D Shlomchik
- Department of Medicine, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA.,Department of Microbiology and Pathology, University of Iowa, Iowa City, Iowa, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
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122
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Rahman MS, Kwon WS, Pang MG. Prediction of male fertility using capacitation-associated proteins in spermatozoa. Mol Reprod Dev 2017; 84:749-759. [DOI: 10.1002/mrd.22810] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/28/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Md Saidur Rahman
- Department of Animal Science and Technology; Chung-Ang University; Anseong Republic of Korea
| | - Woo-Sung Kwon
- Department of Animal Science and Technology; Chung-Ang University; Anseong Republic of Korea
| | - Myung-Geol Pang
- Department of Animal Science and Technology; Chung-Ang University; Anseong Republic of Korea
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123
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Gullaksen SE, Skavland J, Gavasso S, Tosevski V, Warzocha K, Dumrese C, Ferrant A, Gedde-Dahl T, Hellmann A, Janssen J, Labar B, Lang A, Majeed W, Mihaylov G, Stentoft J, Stenke L, Thaler J, Thielen N, Verhoef G, Voglova J, Ossenkoppele G, Hochhaus A, Hjorth-Hansen H, Mustjoki S, Sopper S, Giles F, Porkka K, Wolf D, Gjertsen BT. Single cell immune profiling by mass cytometry of newly diagnosed chronic phase chronic myeloid leukemia treated with nilotinib. Haematologica 2017; 102:1361-1367. [PMID: 28522574 PMCID: PMC5541871 DOI: 10.3324/haematol.2017.167080] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 05/08/2017] [Indexed: 12/27/2022] Open
Abstract
Monitoring of single cell signal transduction in leukemic cellular subsets has been proposed to provide deeper understanding of disease biology and prognosis, but has so far not been tested in a clinical trial of targeted therapy. We developed a complete mass cytometry analysis pipeline for characterization of intracellular signal transduction patterns in the major leukocyte subsets of chronic phase chronic myeloid leukemia. Changes in phosphorylated Bcr-Abl1 and the signaling pathways involved were readily identifiable in peripheral blood single cells already within three hours of the patient receiving oral nilotinib. The signal transduction profiles of healthy donors were clearly distinct from those of the patients at diagnosis. Furthermore, using principal component analysis, we could show that phosphorylated transcription factors STAT3 (Y705) and CREB (S133) within seven days reflected BCR-ABL1IS at three and six months. Analyses of peripheral blood cells longitudinally collected from patients in the ENEST1st clinical trial showed that single cell mass cytometry appears to be highly suitable for future investigations addressing tyrosine kinase inhibitor dosing and effect. (clinicaltrials.gov identifier: 01061177)
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Affiliation(s)
- Stein-Erik Gullaksen
- Centre of Cancer Biomarkers CCBIO, Department of Clinical Science, Precision Oncology Research Group, University of Bergen, Norway
| | - Jørn Skavland
- Centre of Cancer Biomarkers CCBIO, Department of Clinical Science, Precision Oncology Research Group, University of Bergen, Norway
| | - Sonia Gavasso
- Department of Clinical Medicine, University of Bergen, Norway.,Neuroimmunology Lab, Haukeland University Hospital, Bergen, Norway
| | - Vinko Tosevski
- Mass Cytometry Facility, University of Zurich, Switzerland
| | - Krzysztof Warzocha
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | | | - Augustin Ferrant
- Hematology Department, Cliniques Universitaires St Luc, Brussels, Belgium
| | | | | | - Jeroen Janssen
- Department of Hematology, VU University Medical Center, Amsterdam, the Netherlands
| | - Boris Labar
- Department of Hematology, University Hospital Center Rebro, Zagreb, Croatia
| | - Alois Lang
- Internal Medicine, Hospital Feldkirch, Austria
| | - Waleed Majeed
- Department of Hemato-Oncology, Stavanger University Hospital, Norway
| | | | | | - Leif Stenke
- Department of Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Josef Thaler
- Department of Internal Medicine IV, Wels-Grieskirchen Hospital, Wels, Austria
| | - Noortje Thielen
- Department of Hematology, VU University Medical Center, Amsterdam, the Netherlands
| | - Gregor Verhoef
- Department of Hematology, University Hospital Leuven, Belgium
| | - Jaroslava Voglova
- 4 Department of Internal Medicine - Hematology, University Hospital Hradec Kralove, Czech Republic
| | - Gert Ossenkoppele
- Department of Hematology, VU University Medical Center, Amsterdam, the Netherlands
| | - Andreas Hochhaus
- Department of Hematology and Medical Oncology, Universitätsklinikum Jena, Germany
| | - Henrik Hjorth-Hansen
- Department of Hematology, St Olavs Hospital, Trondheim, Norway.,IKM, NTNU, Trondheim, Norway
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Finland.,Department of Clinical Chemistry, University of Helsinki, Finland
| | - Sieghart Sopper
- Department of Hematology and Oncology, Innsbruck Medical University and Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Francis Giles
- NMDTI, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Kimmo Porkka
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Finland
| | - Dominik Wolf
- Department of Hematology and Oncology, Innsbruck Medical University and Tyrolean Cancer Research Institute, Innsbruck, Austria.,Medical Clinic 3, Oncology, Hematology and Rheumatology, University Hospital Bonn (UKB), Germany
| | - Bjørn Tore Gjertsen
- Centre of Cancer Biomarkers CCBIO, Department of Clinical Science, Precision Oncology Research Group, University of Bergen, Norway .,Department of Internal Medicine, Haukeland University Hospital, Bergen, Norway
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124
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Sepsis Patients Display a Reduced Capacity to Activate Nuclear Factor-κB in Multiple Cell Types. Crit Care Med 2017; 45:e524-e531. [PMID: 28240686 DOI: 10.1097/ccm.0000000000002294] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Sepsis is a complex clinical condition associated with high morbidity and mortality. A distinctive feature of sepsis is the reduced capacity of leukocytes to release proinflammatory cytokines in response to ex vivo stimulation. Cellular signaling events leading to immunosuppression in sepsis are not well defined. We investigated cell-specific signaling events underlying the immunosuppressed phenotype in sepsis. DESIGN Ex vivo study. SETTING ICU of an academic hospital. PATIENTS Nineteen patients with sepsis and 19 age-matched healthy controls. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS The phosphorylation state of p38 mitogen activated protein kinase and nuclear factor kappa-light-chain-enhancer of activated B cells were determined in ex vivo stimulated CD4 T cells, CD8 T cells, B cells, monocytes, and neutrophils. Messenger RNA expression levels of p38 mitogen activated protein kinase and nuclear factor kappa-light-chain-enhancer of activated B cells and negative regulators tumor necrosis factor-α-induced protein 3 (A20) and mitogen activated protein kinase phosphatase-1 were determined in neutrophils and peripheral blood mononuclear cells. Upon ex vivo stimulation, monocytes of sepsis patients were less capable in phosphorylating nuclear factor kappa-light-chain-enhancer of activated B cells. Sepsis was also associated with reduced phosphorylation of nuclear factor kappa-light-chain-enhancer of activated B cells in stimulated B cells, CD4 and CD8 T cells. Messenger RNA expression levels of nuclear factor kappa-light-chain-enhancer of activated B cells and A20 were diminished in peripheral blood mononuclear cells of sepsis patients, whereas p38 mitogen activated protein kinase messenger RNA was up-regulated. In neutrophils of sepsis patients, mitogen activated protein kinase phosphatase-1 messenger RNA levels were down-regulated. CONCLUSIONS Sepsis-induced immunosuppression associates with a defect in the capacity to phosphorylate nuclear factor kappa-light-chain-enhancer of activated B cells in lymphoid cells and monocytes.
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Abstract
Signaling networks mediate environmental information to the cell nucleus. To perform this task effectively they must be able to integrate multiple stimuli and distinguish persistent signals from transient environmental fluctuations. However, the ways in which signaling networks process environmental noise are not well understood. Here we outline a mathematical framework that relates a network’s structure to its capacity to process noise, and use this framework to dissect the noise-processing ability of signaling networks. We find that complex networks that are dense in directed paths are poor noise processors, while those that are sparse and strongly directional process noise well. These results suggest that while cross-talk between signaling pathways may increase the ability of signaling networks to integrate multiple stimuli, too much cross-talk may compromise the ability of the network to distinguish signal from noise. To illustrate these general results we consider the structure of the signalling network that maintains pluripotency in mouse embryonic stem cells, and find an incoherent feedforward loop structure involving Stat3, Tfcp2l1, Esrrb, Klf2 and Klf4 is particularly important for noise-processing. Taken together these results suggest that noise-processing is an important function of signaling networks and they may be structured in part to optimize this task.
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126
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Leelatian N, Doxie DB, Greenplate AR, Sinnaeve J, Ihrie RA, Irish JM. Preparing Viable Single Cells from Human Tissue and Tumors for Cytomic Analysis. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2017; 118:25C.1.1-25C.1.23. [PMID: 28369679 PMCID: PMC5518778 DOI: 10.1002/cpmb.37] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mass cytometry is a single-cell biology technique that samples >500 cells per second, measures >35 features per cell, and is sensitive across a dynamic range of >104 relative intensity units per feature. This combination of technical assets has powered a series of recent cytomic studies where investigators used mass cytometry to measure protein and phospho-protein expression in millions of cells, characterize rare cell types in healthy and diseased tissues, and reveal novel, unexpected cells. However, these advances largely occurred in studies of blood, lymphoid tissues, and bone marrow, since the cells in these tissues are readily obtained in single-cell suspensions. This unit establishes a primer for single-cell analysis of solid tumors and tissues, and has been tested with mass cytometry. The cells obtained from these protocols can be fixed for study, cryopreserved for long-term storage, or perturbed ex vivo to dissect responses to stimuli and inhibitors. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | | | | | | | - Rebecca A. Ihrie
- Department of Cancer Biology, Vanderbilt University
- Department of Neurological Surgery, Vanderbilt University School of Medicine
- Department of Cell and Developmental Biology, Vanderbilt University
| | - Jonathan M. Irish
- Department of Cancer Biology, Vanderbilt University
- Department of Pathology, Microbiology and Immunology, Vanderbilt University
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127
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Lu Y, Yang L, Wei W, Shi Q. Microchip-based single-cell functional proteomics for biomedical applications. LAB ON A CHIP 2017; 17:1250-1263. [PMID: 28280819 PMCID: PMC5459479 DOI: 10.1039/c7lc00037e] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cellular heterogeneity has been widely recognized but only recently have single cell tools become available that allow characterizing heterogeneity at the genomic and proteomic levels. We review the technological advances in microchip-based toolkits for single-cell functional proteomics. Each of these tools has distinct advantages and limitations, and a few have advanced toward being applied to address biological or clinical problems that traditional population-based methods fail to address. High-throughput single-cell proteomic assays generate high-dimensional data sets that contain new information and thus require developing new analytical frameworks to extract new biology. In this review article, we highlight a few biological and clinical applications in which microchip-based single-cell proteomic tools provide unique advantages. The examples include resolving functional heterogeneity and dynamics of immune cells, dissecting cell-cell interaction by creating a well-controlled on-chip microenvironment, capturing high-resolution snapshots of immune system functions in patients for better immunotherapy and elucidating phosphoprotein signaling networks in cancer cells for guiding effective molecularly targeted therapies.
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Affiliation(s)
- Yao Lu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Liu Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Wei Wei
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
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128
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Diggins KE, Greenplate AR, Leelatian N, Wogsland CE, Irish JM. Characterizing cell subsets using marker enrichment modeling. Nat Methods 2017; 14:275-278. [PMID: 28135256 PMCID: PMC5330853 DOI: 10.1038/nmeth.4149] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 12/22/2016] [Indexed: 12/21/2022]
Abstract
Learning cell identity from high-content single-cell data presently relies on human experts. We present marker enrichment modeling (MEM), an algorithm that objectively describes cells by quantifying contextual feature enrichment and reporting a human- and machine-readable text label. MEM outperforms traditional metrics in describing immune and cancer cell subsets from fluorescence and mass cytometry. MEM provides a quantitative language to communicate characteristics of new and established cytotypes observed in complex tissues.
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Affiliation(s)
- K. E. Diggins
- Department of Cancer Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - A. R. Greenplate
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - N. Leelatian
- Department of Cancer Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - C. E. Wogsland
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - J. M. Irish
- Department of Cancer Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
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129
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Utomo WK, de Vries M, Braat H, Bruno MJ, Parikh K, Comalada M, Peppelenbosch MP, van Goor H, Fuhler GM. Modulation of Human Peripheral Blood Mononuclear Cell Signaling by Medicinal Cannabinoids. Front Mol Neurosci 2017; 10:14. [PMID: 28174520 PMCID: PMC5258717 DOI: 10.3389/fnmol.2017.00014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/11/2017] [Indexed: 01/28/2023] Open
Abstract
Medical marijuana is increasingly prescribed as an analgesic for a growing number of indications, amongst which terminal cancer and multiple sclerosis. However, the mechanistic aspects and properties of cannabis remain remarkably poorly characterized. In this study we aimed to investigate the immune-cell modulatory properties of medical cannabis. Healthy volunteers were asked to ingest medical cannabis, and kinome profiling was used to generate comprehensive descriptions of the cannabis challenge on inflammatory signal transduction in the peripheral blood of these volunteers. Results were related to both short term and long term effects in patients experimentally treated with a medical marijuana preparation for suffering from abdominal pain as a result of chronic pancreatitis or other causes. The results reveal an immunosuppressive effect of cannabinoid preparations via deactivation of signaling through the pro-inflammatory p38 MAP kinase and mTOR pathways and a concomitant deactivation of the pro-mitogenic ERK pathway. However, long term cannabis exposure in two patients resulted in reversal of this effect. While these data provide a powerful mechanistic rationale for the clinical use of medical marijuana in inflammatory and oncological disease, caution may be advised with sustained use of such preparations.
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Affiliation(s)
- Wesley K Utomo
- Department of Gastroenterology and Hepatology, Erasmus MC, Erasmus University of Rotterdam Rotterdam, Netherlands
| | - Marjan de Vries
- Department of Surgery, Radboud University Medical Center Nijmegen, Netherlands
| | - Henri Braat
- Department of Gastroenterology and Hepatology, Erasmus MC, Erasmus University of Rotterdam Rotterdam, Netherlands
| | - Marco J Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC, Erasmus University of Rotterdam Rotterdam, Netherlands
| | - Kaushal Parikh
- Department of Cell Biology, University Medical Center Groningen Groningen, Netherlands
| | | | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC, Erasmus University of Rotterdam Rotterdam, Netherlands
| | - Harry van Goor
- Department of Surgery, Radboud University Medical Center Nijmegen, Netherlands
| | - Gwenny M Fuhler
- Department of Gastroenterology and Hepatology, Erasmus MC, Erasmus University of Rotterdam Rotterdam, Netherlands
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130
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Activation of the JAK-STAT Signaling Pathway after In Vitro Stimulation with IFNß in Multiple Sclerosis Patients According to the Therapeutic Response to IFNß. PLoS One 2017; 12:e0170031. [PMID: 28103257 PMCID: PMC5245989 DOI: 10.1371/journal.pone.0170031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/26/2016] [Indexed: 11/19/2022] Open
Abstract
Interferon beta (IFNß) is a common treatment used for multiple sclerosis (MS) which acts through the activation of the JAK-STAT pathway. However, this therapy is not always effective and currently there are no reliable biomarkers to predict therapeutic response. We postulate that the heterogeneity in the response to IFNß therapy could be related to differential activation patterns of the JAK-STAT signaling pathway. Our aim was to evaluate the basal levels and the short term activation of this pathway after IFNß stimulation in untreated and IFNß treated patients, as well as according to therapeutic response. Therefore, cell surface levels of IFNAR subunits (IFNAR1 and IFNAR2) and the activated forms of STAT1 and STAT2 were assessed in peripheral blood mononuclear cells from MS patients by flow cytometry. Basal levels of each of the markers strongly correlated with the expression of the others in untreated patients, but many of these correlations lost significance in treated patients and after short term activation with IFNß. Patients who had undergone IFNß treatment showed higher basal levels of IFNAR1 and pSTAT1, but a reduced response to in vitro exposure to IFNß. Conversely, untreated patients, with lower basal levels, showed a greater ability of short term activation of this pathway. Monocytes from responder patients had lower IFNAR1 levels (p = 0.039) and higher IFNAR2 levels (p = 0.035) than non-responders just after IFNß stimulation. A cluster analysis showed that levels of IFNAR1, IFNAR2 and pSTAT1-2 in monocytes grouped 13 out of 19 responder patients with a similar expression pattern, showing an association of this pattern with the phenotype of good response to IFNß (p = 0.013). Our findings suggest that an activation pattern of the IFNß signaling pathway in monocytes could be associated with a clinical phenotype of good response to IFNß treatment and that a differential modulation of the IFNAR subunits in monocytes could be related with treatment effectiveness.
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131
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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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132
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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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133
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Brumbaugh K, Liao WC, Houchins JP, Cooper J, Stoesz S. Phosphosite-Specific Antibodies: A Brief Update on Generation and Applications. Methods Mol Biol 2017; 1554:1-40. [PMID: 28185181 DOI: 10.1007/978-1-4939-6759-9_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Phosphate addition is a posttranslational modification of proteins, and this modification can affect the activity and other properties of intracellular proteins. Different animal species can be used to generate phosphosite-specific antibodies as either polyclonals or monoclonals, and each approach offers its own benefits and disadvantages. The validation of phosphosite-specific antibodies requires multiple techniques and tactics to demonstrate their specificity. These antibodies can be used in arrays, flow cytometry, and imaging platforms. The specificity of phosphosite-specific antibodies is vital for their use in proteomics and profiling of disease.
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Affiliation(s)
- Kathy Brumbaugh
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA.
| | - Wen-Chie Liao
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
| | - J P Houchins
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
| | - Jeff Cooper
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
| | - Steve Stoesz
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
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134
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Bandyopadhyay S, Fisher DAC, Malkova O, Oh ST. Analysis of Signaling Networks at the Single-Cell Level Using Mass Cytometry. Methods Mol Biol 2017; 1636:371-392. [PMID: 28730492 DOI: 10.1007/978-1-4939-7154-1_24] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass cytometry is a powerful technology that enables the measurement of >40 parameters at the single-cell level. The inherent spectral limitations of fluorescent flow cytometry are circumvented by the use of antibodies conjugated to metal isotope reporters, which are measured quantitatively using a CyTOF mass cytometer. The high dimensionality of mass cytometry is particularly useful for the analysis of cell signaling networks in complex biological samples. We describe here methods for cell preparation, antibody staining, data acquisition, and analysis of multidimensional data from a mass cytometry experiment.
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Affiliation(s)
- Shovik Bandyopadhyay
- Division of Hematology, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8125, St. Louis, MO, 63110, USA
| | - Daniel A C Fisher
- Division of Hematology, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8125, St. Louis, MO, 63110, USA
| | - Olga Malkova
- Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen T Oh
- Division of Hematology, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8125, St. Louis, MO, 63110, USA.
- Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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135
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Mass cytometry analysis reveals hyperactive NF Kappa B signaling in myelofibrosis and secondary acute myeloid leukemia. Leukemia 2016; 31:1962-1974. [PMID: 28008177 PMCID: PMC5540814 DOI: 10.1038/leu.2016.377] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 10/14/2016] [Accepted: 11/28/2016] [Indexed: 12/26/2022]
Abstract
Myeloproliferative neoplasms (MPNs) feature a malignant clone containing the JAK2 V617F mutation, or another mutation causing dysregulated JAK2 kinase activity. The multiple disease phenotypes of MPNs, and their tendency to transform phenotypically, suggest pathophysiologic heterogeneities beyond a common phenomenon of JAK2 hyperactivation. JAK2 has the potential to activate multiple other signaling molecules, either directly through downstream effectors, or indirectly through induction of target gene expression. We have interrogated myeloproliferative signaling in myelofibrosis (MF) and secondary acute myeloid leukemia (sAML) patient samples using mass cytometry, which allows the quantitative measurement of multiple signaling molecules simultaneously at the single cell level, in cell populations representing a nearly complete spectrum of hematopoiesis. MF and sAML malignant cells demonstrated a high prevalence of hyperactivation of the JAK-STAT, MAP kinase, PI3 kinase, and NFκB signaling pathways. Constitutive NFκB signaling was evident across MF and sAML patients. A supporting GSEA analysis of MF showed many NFκB target genes to be expressed above normal levels in MF patient CD34+ cells. NFκB inhibition suppressed colony formation from MF CD34+ cells. This study indicates that NFκB signaling contributes to human myeloproliferative disease and is abnormally activated in MF and sAML.
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136
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Distinct patterns of B-cell receptor signaling in non-Hodgkin lymphomas identified by single-cell profiling. Blood 2016; 129:759-770. [PMID: 28011673 DOI: 10.1182/blood-2016-05-718494] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022] Open
Abstract
Kinases downstream of B-cell antigen receptor (BCR) represent attractive targets for therapy in non-Hodgkin lymphoma (NHL). As clinical responses vary, improved knowledge regarding activation and regulation of BCR signaling in individual patients is needed. Here, using phosphospecific flow cytometry to obtain malignant B-cell signaling profiles from 95 patients representing 4 types of NHL revealed a striking contrast between chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) tumors. Lymphoma cells from diffuse large B-cell lymphoma patients had high basal phosphorylation levels of most measured signaling nodes, whereas follicular lymphoma cells represented the opposite pattern with no or very low basal levels. MCL showed large interpatient variability in basal levels, and elevated levels for the phosphorylated forms of AKT, extracellular signal-regulated kinase, p38, STAT1, and STAT5 were associated with poor outcome. CLL tumors had elevated basal levels for the phosphorylated forms of BCR-signaling nodes (Src family tyrosine kinase, spleen tyrosine kinase [SYK], phospholipase Cγ), but had low α-BCR-induced signaling. This contrasted MCL tumors, where α-BCR-induced signaling was variable, but significantly potentiated as compared with the other types. Overexpression of CD79B, combined with a gating strategy whereby signaling output was directly quantified per cell as a function of CD79B levels, confirmed a direct relationship between surface CD79B, immunoglobulin M (IgM), and IgM-induced signaling levels. Furthermore, α-BCR-induced signaling strength was variable across patient samples and correlated with BCR subunit CD79B expression, but was inversely correlated with susceptibility to Bruton tyrosine kinase (BTK) and SYK inhibitors in MCL. These individual differences in BCR levels and signaling might relate to differences in therapy responses to BCR-pathway inhibitors.
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137
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Conversion to Once-Daily Tacrolimus Results in Increased p38MAPK Phosphorylation in T Lymphocytes of Kidney Transplant Recipients. Ther Drug Monit 2016; 38:280-4. [PMID: 26606072 DOI: 10.1097/ftd.0000000000000264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND The once-daily formulation of tacrolimus (TAC(OD)) has been developed to overcome adherence problems. Conversion from the twice-daily TAC (TAC(BID)) formulation to TAC(OD) on a 1:1 basis, however, often leads to a decrease of TAC predose concentrations, which averages ∼15%. Switching between the two TAC formulations may thus influence drug efficacy and necessitates therapeutic drug monitoring. As an additional tool in transplantation diagnostics, phospho-specific flow cytometry was used to study the biological effects of conversion on p38MAPK phosphorylation, a kinase involved in T-lymphocyte activation. METHODS Stable renal transplant recipients (n = 12), at least 1 year after their transplantation, were converted from TAC(BID) to TAC(OD) on 1:1 mg for mg base. Comedication consisted of mycophenolate mofetil (n = 10) and prednisolone (n = 3). TAC whole-blood predose concentrations were determined by immunoassay before and 3 months after conversion. P38MAPK phosphorylation was measured in T lymphocytes by whole-blood phospho-specific flow cytometry. RESULTS Three months after conversion, no significant decreases in TAC predose concentrations (C0) were found (P = 0.54), whereas p38MAPK phosphorylation increased with 11.4% (P < 0.05) in CD4 and with 15.6% (P < 0.05) in CD8 T lymphocytes. The TAC C0 during treatment with TAC(BID) correlated inversely with p38MAPK phosphorylation in T lymphocytes (rs = -0.638; P < 0.05). CONCLUSIONS These results suggest that the measurement of p38MAPK phosphorylation status in T lymphocytes is a sensitive method to determine the biological effects of TAC before and after conversion from TAC(BID) to TAC(OD). This method could be a more sensitive tool for therapeutic drug monitoring of TAC.
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138
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Cavallini C, Visco C, Putta S, Rossi D, Mimiola E, Purvis N, Lovato O, Perbellini O, Falisi E, Facco M, Trentin L, Romanelli MG, Semenzato G, Ambrosetti A, Gaidano G, Pizzolo G, Cesano A, Scupoli MT. Integration of B-cell receptor-induced ERK1/2 phosphorylation and mutations of SF3B1 gene refines prognosis in treatment-naïve chronic lymphocytic leukemia. Haematologica 2016; 102:e144-e147. [PMID: 27927769 DOI: 10.3324/haematol.2016.154450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
| | - Carlo Visco
- Department of Cell Therapy and Hematology, San Bortolo Hospital, Vicenza, Italy
| | | | - Davide Rossi
- Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Elda Mimiola
- Department of Medicine, Section of Hematology, University of Verona, Italy
| | | | | | - Omar Perbellini
- Department of Cell Therapy and Hematology, San Bortolo Hospital, Vicenza, Italy
| | - Erika Falisi
- Department of Cell Therapy and Hematology, San Bortolo Hospital, Vicenza, Italy
| | - Monica Facco
- Department of Medicine, Hematology and Clinical Immunology Branch, University of Padua, Italy
| | - Livio Trentin
- Department of Medicine, Hematology and Clinical Immunology Branch, University of Padua, Italy
| | - Maria G Romanelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Italy
| | - Gianpietro Semenzato
- Department of Medicine, Hematology and Clinical Immunology Branch, University of Padua, Italy
| | - Achille Ambrosetti
- Department of Medicine, Section of Hematology, University of Verona, Italy
| | - Gianluca Gaidano
- Department of Translational Medicine, Division of Hematology, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Giovanni Pizzolo
- Department of Medicine, Section of Hematology, University of Verona, Italy
| | | | - Maria T Scupoli
- Research Center LURM, University of Verona, Italy .,Department of Medicine, Section of Hematology, University of Verona, Italy
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139
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Spagnolo DM, Gyanchandani R, Al-Kofahi Y, Stern AM, Lezon TR, Gough A, Meyer DE, Ginty F, Sarachan B, Fine J, Lee AV, Taylor DL, Chennubhotla SC. Pointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers. J Pathol Inform 2016; 7:47. [PMID: 27994939 PMCID: PMC5139455 DOI: 10.4103/2153-3539.194839] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 08/09/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Measures of spatial intratumor heterogeneity are potentially important diagnostic biomarkers for cancer progression, proliferation, and response to therapy. Spatial relationships among cells including cancer and stromal cells in the tumor microenvironment (TME) are key contributors to heterogeneity. METHODS We demonstrate how to quantify spatial heterogeneity from immunofluorescence pathology samples, using a set of 3 basic breast cancer biomarkers as a test case. We learn a set of dominant biomarker intensity patterns and map the spatial distribution of the biomarker patterns with a network. We then describe the pairwise association statistics for each pattern within the network using pointwise mutual information (PMI) and visually represent heterogeneity with a two-dimensional map. RESULTS We found a salient set of 8 biomarker patterns to describe cellular phenotypes from a tissue microarray cohort containing 4 different breast cancer subtypes. After computing PMI for each pair of biomarker patterns in each patient and tumor replicate, we visualize the interactions that contribute to the resulting association statistics. Then, we demonstrate the potential for using PMI as a diagnostic biomarker, by comparing PMI maps and heterogeneity scores from patients across the 4 different cancer subtypes. Estrogen receptor positive invasive lobular carcinoma patient, AL13-6, exhibited the highest heterogeneity score among those tested, while estrogen receptor negative invasive ductal carcinoma patient, AL13-14, exhibited the lowest heterogeneity score. CONCLUSIONS This paper presents an approach for describing intratumor heterogeneity, in a quantitative fashion (via PMI), which departs from the purely qualitative approaches currently used in the clinic. PMI is generalizable to highly multiplexed/hyperplexed immunofluorescence images, as well as spatial data from complementary in situ methods including FISSEQ and CyTOF, sampling many different components within the TME. We hypothesize that PMI will uncover key spatial interactions in the TME that contribute to disease proliferation and progression.
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Affiliation(s)
- Daniel M Spagnolo
- Program in Computational Biology, Joint Carnegie Mellon University-University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rekha Gyanchandani
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yousef Al-Kofahi
- GE Global Research Center, Diagnostics, Imaging and Biomedical Technologies, Niskayuna, NY, USA
| | - Andrew M Stern
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Timothy R Lezon
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Albert Gough
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Dan E Meyer
- GE Global Research Center, Diagnostics, Imaging and Biomedical Technologies, Niskayuna, NY, USA
| | - Fiona Ginty
- GE Global Research Center, Diagnostics, Imaging and Biomedical Technologies, Niskayuna, NY, USA
| | - Brion Sarachan
- GE Global Research Center, Software Science and Analytics Organization, Niskayuna, NY, USA
| | - Jeffrey Fine
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adrian V Lee
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - D Lansing Taylor
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania; University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - S Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
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140
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Altunbek M, Kuku G, Culha M. Gold Nanoparticles in Single-Cell Analysis for Surface Enhanced Raman Scattering. Molecules 2016; 21:E1617. [PMID: 27897986 PMCID: PMC6273107 DOI: 10.3390/molecules21121617] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/17/2016] [Accepted: 11/22/2016] [Indexed: 01/24/2023] Open
Abstract
The need for new therapeutic approaches in the treatment of challenging diseases such as cancer, which often consists of a highly heterogeneous and complex population of cells, brought up the idea of analyzing single cells. The development of novel techniques to analyze single cells has been intensively studied to fully understand specific alternations inducing abnormalities in cellular function. One of the techniques used for single cell analysis is surface-enhanced Raman spectroscopy (SERS) in which a noble metal nanoparticle is used to enhance Raman scattering. Due to its low toxicity and biocompatibility, gold nanoparticles (AuNPs) are commonly preferred as SERS substrates in single cell analysis. The intracellular uptake, localization and toxicity issues of AuNPs are the critical points for interpretation of data since the obtained SERS signals originate from molecules in close vicinity to AuNPs that are taken up by the cells. In this review, the AuNP-living cell interactions, cellular uptake and toxicity of AuNPs in relation to their physicochemical properties, and surface-enhanced Raman scattering from single cells are discussed.
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Affiliation(s)
- Mine Altunbek
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Atasehir, Istanbul 34755, Turkey.
| | - Gamze Kuku
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Atasehir, Istanbul 34755, Turkey.
| | - Mustafa Culha
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Atasehir, Istanbul 34755, Turkey.
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141
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Yang L, Wang Z, Deng Y, Li Y, Wei W, Shi Q. Single-Cell, Multiplexed Protein Detection of Rare Tumor Cells Based on a Beads-on-Barcode Antibody Microarray. Anal Chem 2016; 88:11077-11083. [PMID: 27644430 PMCID: PMC5519775 DOI: 10.1021/acs.analchem.6b03086] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Circulating tumor cells (CTCs) shed from tumor sites and represent the molecular characteristics of the tumor. Besides genetic and transcriptional characterization, it is important to profile a panel of proteins with single-cell precision for resolving CTCs' phenotype, organ-of-origin, and drug targets. We describe a new technology that enables profiling multiple protein markers of extraordinarily rare tumor cells at the single-cell level. This technology integrates a microchip consisting of 15000 60 pL-sized microwells and a novel beads-on-barcode antibody microarray (BOBarray). The BOBarray allows for multiplexed protein detection by assigning two independent identifiers (bead size and fluorescent color) of the beads to each protein. Four bead sizes (1.75, 3, 4.5, and 6 μm) and three colors (blue, green, and yellow) are utilized to encode up to 12 different proteins. The miniaturized BOBarray can fit an array of 60 pL-sized microwells that isolate single cells for cell lysis and the subsequent detection of protein markers. An enclosed 60 pL-sized microchamber defines a high concentration of proteins released from lysed single cells, leading to single-cell resolution of protein detection. The protein markers assayed in this study include organ-specific markers and drug targets that help to characterize the organ-of-origin and drug targets of isolated rare tumor cells from blood samples. This new approach enables handling a very small number of cells and achieves single-cell, multiplexed protein detection without loss of rare but clinically important tumor cells.
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Affiliation(s)
- Liu Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Zhihua Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yuliang Deng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yan Li
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Wei Wei
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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142
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Hu P, Zhang W, Xin H, Deng G. Single Cell Isolation and Analysis. Front Cell Dev Biol 2016; 4:116. [PMID: 27826548 PMCID: PMC5078503 DOI: 10.3389/fcell.2016.00116] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/07/2016] [Indexed: 02/05/2023] Open
Abstract
Individual cell heterogeneity within a population can be critical to its peculiar function and fate. Subpopulations studies with mixed mutants and wild types may not be as informative regarding which cell responds to which drugs or clinical treatments. Cell to cell differences in RNA transcripts and protein expression can be key to answering questions in cancer, neurobiology, stem cell biology, immunology, and developmental biology. Conventional cell-based assays mainly analyze the average responses from a population of cells, without regarding individual cell phenotypes. To better understand the variations from cell to cell, scientists need to use single cell analyses to provide more detailed information for therapeutic decision making in precision medicine. In this review, we focus on the recent developments in single cell isolation and analysis, which include technologies, analyses and main applications. Here, we summarize the historical background, limitations, applications, and potential of single cell isolation technologies.
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Affiliation(s)
- Ping Hu
- The Center for Biotechnology and Biopharmaceutics, Institute of Translational Medicine, Nanchang University Nanchang, China
| | - Wenhua Zhang
- Laboratory of Fear and Anxiety Disorders, Institute of Life Science, Nanchang University Nanchang, China
| | - Hongbo Xin
- The Center for Biotechnology and Biopharmaceutics, Institute of Translational Medicine, Nanchang University Nanchang, China
| | - Glenn Deng
- The Center for Biotechnology and Biopharmaceutics, Institute of Translational Medicine, Nanchang UniversityNanchang, China; Yichang Research Center for Biomedical Industry and Central Laboratory of Yichang Central Hospital, Medical School, China Three Gorges UniversityYichang, China; Division of Surgical Oncology, Stanford University School of MedicineStanford, CA, USA
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143
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Park SM, Lee JY, Hong S, Lee SH, Dimov IK, Lee H, Suh S, Pan Q, Li K, Wu AM, Mumenthaler SM, Mallick P, Lee LP. Dual transcript and protein quantification in a massive single cell array. LAB ON A CHIP 2016; 16:3682-8. [PMID: 27546183 PMCID: PMC5221609 DOI: 10.1039/c6lc00762g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Recently, single-cell molecular analysis has been leveraged to achieve unprecedented levels of biological investigation. However, a lack of simple, high-throughput single-cell methods has hindered in-depth population-wide studies with single-cell resolution. We report a microwell-based cytometric method for simultaneous measurements of gene and protein expression dynamics in thousands of single cells. We quantified the regulatory effects of transcriptional and translational inhibitors on cMET mRNA and cMET protein in cell populations. We studied the dynamic responses of individual cells to drug treatments, by measuring cMET overexpression levels in individual non-small cell lung cancer (NSCLC) cells with induced drug resistance. Across NSCLC cell lines with a given protein expression, distinct patterns of transcript-protein correlation emerged. We believe this platform is applicable for interrogating the dynamics of gene expression, protein expression, and translational kinetics at the single-cell level - a paradigm shift in life science and medicine toward discovering vital cell regulatory mechanisms.
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Affiliation(s)
- Seung-Min Park
- Department of Bioengineering, University of California, Berkeley, California, USA.
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144
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Liu J, Yin D, Wang S, Chen HY, Liu Z. Probing Low-Copy-Number Proteins in a Single Living Cell. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608237] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jia Liu
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Danyang Yin
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Shuangshou Wang
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
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145
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Liu J, Yin D, Wang S, Chen HY, Liu Z. Probing Low-Copy-Number Proteins in a Single Living Cell. Angew Chem Int Ed Engl 2016; 55:13215-13218. [DOI: 10.1002/anie.201608237] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Jia Liu
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Danyang Yin
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Shuangshou Wang
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; 163 Xianlin Avenue Nanjing 210023 China
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146
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Dichotomy of cellular inhibition by small-molecule inhibitors revealed by single-cell analysis. Nat Commun 2016; 7:12428. [PMID: 27687249 PMCID: PMC5056434 DOI: 10.1038/ncomms12428] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/30/2016] [Indexed: 12/15/2022] Open
Abstract
Despite progress in drug development, a quantitative and physiological understanding of how small-molecule inhibitors act on cells is lacking. Here, we measure the signalling and proliferative response of individual primary T-lymphocytes to a combination of antigen, cytokine and drug. We uncover two distinct modes of signalling inhibition: digital inhibition (the activated fraction of cells diminishes upon drug treatment, but active cells appear unperturbed), versus analogue inhibition (the activated fraction is unperturbed whereas activation response is diminished). We introduce a computational model of the signalling cascade that accounts for such inhibition dichotomy, and test the model predictions for the phenotypic variability of cellular responses. Finally, we demonstrate that the digital/analogue dichotomy of cellular response as revealed on short (signal transduction) timescales, translates into similar dichotomy on longer (proliferation) timescales. Our single-cell analysis of drug action illustrates the strength of quantitative approaches to translate in vitro pharmacology into functionally relevant cellular settings. Many drugs are small molecule inhibitors of cell signalling. Through single cell analysis and mathematical modelling here the authors show that cell-to-cell variability diversifies inhibition response into digital and analogue, and that the two translate into distinct long-term functional responses.
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147
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Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M. Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows. J Proteomics 2016; 145:214-225. [DOI: 10.1016/j.jprot.2016.03.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/23/2016] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
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148
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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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149
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Boros K, Puissant A, Back M, Alexe G, Bassil CF, Sinha P, Tholouli E, Stegmaier K, Byers RJ, Rodig SJ. Increased SYK activity is associated with unfavorable outcome among patients with acute myeloid leukemia. Oncotarget 2016; 6:25575-87. [PMID: 26315286 PMCID: PMC4694851 DOI: 10.18632/oncotarget.4669] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/29/2015] [Indexed: 01/19/2023] Open
Abstract
Recent discoveries have led to the testing of novel targeted therapies for the treatment of acute myeloid leukemia (AML). To better inform the results of clinical trials, there is a need to identify and systematically assess biomarkers of response and pharmacodynamic markers of successful target engagement. Spleen tyrosine kinase (SYK) is a candidate therapeutic target in AML. Small-molecule inhibitors of SYK induce AML differentiation and impair leukemia progression in preclinical studies. However, tools to predict response to SYK inhibition and to routinely evaluate SYK activation in primary patient samples have been lacking. In this study we quantified phosphorylated SYK (P-SYK) in AML cell lines and establish that increasing levels of baseline P-SYK are correlated with an increasing sensitivity to small-molecule inhibitors targeting SYK. In addition, we found that pharmacological inhibition of SYK activity extinguishes P-SYK expression as detected by an immunohistochemical (IHC) test. Quantitative analysis of P-SYK expression by the IHC test in a series of 70 primary bone marrow biopsy specimens revealed a spectrum of P-SYK expression across AML cases and that high P-SYK expression is associated with unfavourable outcome independent of age, cytogenetics, and white blood cell count. This study thus establishes P-SYK as a critical biomarker in AML that identifies tumors sensitive to SYK inhibition, identifies an at-risk patient population, and allows for the monitoring of target inhibition during treatment.
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Affiliation(s)
- Katalin Boros
- Department of Histopathology, Manchester Royal Infirmary, Manchester, UK
| | - Alexandre Puissant
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA.,INSERM U1065, Team 2, C3M, Nice, France
| | - Morgan Back
- The Medical School, The University of Manchester, Manchester, UK
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Christopher F Bassil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Papiya Sinha
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Eleni Tholouli
- Department of Haematology, Manchester Royal Infirmary, Manchester, UK
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Richard J Byers
- Institute of Cancer Sciences, The University of Manchester, Manchester, UK
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
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150
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Sachs Z, Been RA, DeCoursin KJ, Nguyen HT, Mohd Hassan NA, Noble-Orcutt KE, Eckfeldt CE, Pomeroy EJ, Diaz-Flores E, Geurts JL, Diers MD, Hasz DE, Morgan KJ, MacMillan ML, Shannon KM, Largaespada DA, Wiesner SM. Stat5 is critical for the development and maintenance of myeloproliferative neoplasm initiated by Nf1 deficiency. Haematologica 2016; 101:1190-1199. [PMID: 27418650 DOI: 10.3324/haematol.2015.136002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 06/15/2016] [Indexed: 11/09/2022] Open
Abstract
Juvenile myelomonocytic leukemia is a rare myeloproliferative neoplasm characterized by hyperactive RAS signaling. Neurofibromin1 (encoded by the NF1 gene) is a negative regulator of RAS activation. Patients with neurofibromatosis type 1 harbor loss-of-function mutations in NF1 and have a 200- to 500-fold increased risk of juvenile myelomonocytic leukemia. Leukemia cells from patients with juvenile myelomonocytic leukemia display hypersensitivity to certain cytokines, such as granulocyte-macrophage colony-stimulating factor. The granulocyte-macrophage colony-stimulating factor receptor utilizes pre-associated JAK2 to initiate signals after ligand binding. JAK2 subsequently activates STAT5, among other downstream effectors. Although STAT5 is gaining recognition as an important mediator of growth factor signaling in myeloid leukemias, the contribution of STAT5 to the development of hyperactive RAS-initiated myeloproliferative disease has not been well described. In this study, we investigated the consequence of STAT5 attenuation via genetic and pharmacological approaches in Nf1-deficient murine models of juvenile myelomonocytic leukemia. We found that homozygous Stat5 deficiency extended the lifespan of Nf1-deficient mice and eliminated the development of myeloproliferative neoplasm associated with Nf1 gene loss. Likewise, we found that JAK inhibition with ruxolitinib attenuated myeloproliferative neoplasm in Nf1-deficient mice. Finally, we found that primary cells from a patient with KRAS-mutant juvenile myelomonocytic leukemia displayed reduced colony formation in response to JAK2 inhibition. Our findings establish a central role for STAT5 activation in the pathogenesis of juvenile myelomonocytic leukemia and suggest that targeting this pathway may be of clinical utility in these patients.
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Affiliation(s)
- Zohar Sachs
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Raha A Been
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA College of Veterinary Medicine and Department of Comparative and Molecular Biosciences, University of Minnesota, St. Paul, MN, USA
| | | | - Hanh T Nguyen
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | - Klara E Noble-Orcutt
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Craig E Eckfeldt
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Emily J Pomeroy
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Ernesto Diaz-Flores
- Department of Pediatrics, University of California, San Francisco, CA, USA Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Jennifer L Geurts
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Miechaleen D Diers
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Diane E Hasz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Kelly J Morgan
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Margaret L MacMillan
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA Blood and Marrow Transplantation Program, University of Minnesota, Minneapolis, MN, USA
| | - Kevin M Shannon
- Department of Pediatrics, University of California, San Francisco, CA, USA Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - David A Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA Blood and Marrow Transplantation Program, University of Minnesota, Minneapolis, MN, USA
| | - Stephen M Wiesner
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA Center for Allied Health Programs, University of Minnesota, Minneapolis, MN, USA
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