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Hassan JJ, Lieske A, Dörpmund N, Klatt D, Hoffmann D, Kleppa MJ, Kustikova OS, Stahlhut M, Schwarzer A, Schambach A, Maetzig T. A Multiplex CRISPR-Screen Identifies PLA2G4A as Prognostic Marker and Druggable Target for HOXA9 and MEIS1 Dependent AML. Int J Mol Sci 2021; 22:ijms22179411. [PMID: 34502319 PMCID: PMC8431012 DOI: 10.3390/ijms22179411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/03/2022] Open
Abstract
HOXA9 and MEIS1 are frequently upregulated in acute myeloid leukemia (AML), including those with MLL-rearrangement. Because of their pivotal role in hemostasis, HOXA9 and MEIS1 appear non-druggable. We, thus, interrogated gene expression data of pre-leukemic (overexpressing Hoxa9) and leukemogenic (overexpressing Hoxa9 and Meis1; H9M) murine cell lines to identify cancer vulnerabilities. Through gene expression analysis and gene set enrichment analyses, we compiled a list of 15 candidates for functional validation. Using a novel lentiviral multiplexing approach, we selected and tested highly active sgRNAs to knockout candidate genes by CRISPR/Cas9, and subsequently identified a H9M cell growth dependency on the cytosolic phospholipase A2 (PLA2G4A). Similar results were obtained by shRNA-mediated suppression of Pla2g4a. Remarkably, pharmacologic inhibition of PLA2G4A with arachidonyl trifluoromethyl ketone (AACOCF3) accelerated the loss of H9M cells in bulk cultures. Additionally, AACOCF3 treatment of H9M cells reduced colony numbers and colony sizes in methylcellulose. Moreover, AACOCF3 was highly active in human AML with MLL rearrangement, in which PLA2G4A was significantly higher expressed than in AML patients without MLL rearrangement, and is sufficient as an independent prognostic marker. Our work, thus, identifies PLA2G4A as a prognostic marker and potential therapeutic target for H9M-dependent AML with MLL-rearrangement.
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MESH Headings
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- CRISPR-Cas Systems
- Cell Proliferation
- Gene Expression Regulation, Neoplastic
- Group IV Phospholipases A2/antagonists & inhibitors
- Group IV Phospholipases A2/genetics
- High-Throughput Screening Assays
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Myeloid Ecotropic Viral Integration Site 1 Protein/genetics
- Myeloid Ecotropic Viral Integration Site 1 Protein/metabolism
- Tumor Cells, Cultured
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Affiliation(s)
- Jacob Jalil Hassan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Anna Lieske
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Nicole Dörpmund
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Denise Klatt
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Dirk Hoffmann
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Marc-Jens Kleppa
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Olga S. Kustikova
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Maike Stahlhut
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Adrian Schwarzer
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Tobias Maetzig
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
- Correspondence:
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2
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Lieske A, Ha TC, Schambach A, Maetzig T. An improved lentiviral fluorescent genetic barcoding approach distinguishes hematopoietic stem cell properties in multiplexed in vivo experiments. Hum Gene Ther 2021; 32:1280-1294. [PMID: 34139894 DOI: 10.1089/hum.2021.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hematopoietic stem cells (HSC) represent a rare cell population of particular interest for biomedical research and regenerative medicine. Various marker combinations enable the isolation of HSCs but fail to reach purity in transplantation assays. To reduce animal consumption, we developed a multiplexing system based on lentiviral fluorescent genetic barcoding (FGB) to enable the parallel characterization of multiple HSC samples within single animals. While previous FGB-mediated HSC multiplexing experiments achieved high in vitro gene marking rates, in vivo persistence of transduced cells remained sub-optimal. Thus, we aimed to optimize vector design and gene transfer protocols to demonstrate the applicability of FGB for functional characterization of two highly similar HSC populations in a reduced number of mice. We developed a set of 6 new lentiviral FGB vectors, utilizing individual and combinatorial expression of Azami Green, mCherry, and YFP derivatives. Gene transfer rates were optimized by overnight transduction of pre-stimulated HSCs with titrated vector doses. Populations for competitive transplantation experiments were identified by immunophenotyping murine HSCs. This identified an LSK-SLAM- (Lin-Sca-1+cKit+CD48-CD150+EPCR-) cell subpopulation that lacks EPCR expression and exhibits prospectively reduced self-renewal potential compared with prototypical ESLAM (CD45+EPCR+CD48-CD150+) HSCs. We monitored 30 data points per HSC-subpopulation in two independent experiments (each n=5) after co-transplantation of 3 uniquely color-coded ESLAM and LSK-SLAM- samples per recipient. While the first experiment was hampered by data fluctuations, increasing cell numbers and exchange of the internal promoter in the second experiment led to 74.4% chimerism, with 87.1% of fluorescent cells derived from ESLAM HSCs. Furthermore, ESLAM-derived cells produced 88.1% of myeloid cells, which is indicative of their origin from long-term repopulating HSCs. This work verifies the importance of EPCR for long-term repopulating HSCs and demonstrates the applicability of our optimized FGB-driven multiplexing approach for the efficient characterization of blood cell populations in biomedical research.
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Affiliation(s)
- Anna Lieske
- Hannover Medical School, Institute of Experimental Hematology, Hannover, Germany.,Hannover Medical School, Clinic for Pediatric Hematology and Oncology, Hannover, Germany.,Hannover Medical School, 9177, REBIRTH Cluster of Excellence, Hannover, Germany;
| | - Teng-Cheong Ha
- Hannover Medical School, 9177, Institute of Experimental Hematology, Hannover, State..., Germany.,Hannover Medical School, 9177, REBIRTH Cluster of Excellence, Hannover, Germany;
| | - Axel Schambach
- Hannover Medical School, Institute of Experimental Hematology, Hannover, Germany.,Hannover Medical School, 9177, REBIRTH Cluster of Excellence, Hannover, Germany.,Harvard Medical School, 1811, Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, United States;
| | - Tobias Maetzig
- Hannover Medical School, Insitute of Experimental Hematology, Hannover, Germany.,Hannover Medical School, Clinic for Pediatric Hematology and Oncology, Hannover, Germany.,Hannover Medical School, 9177, REBIRTH Cluster of Excellence, Hannover, Germany;
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3
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Abstract
Flow cytometry (FCM) is a sophisticated technique that works on the principle of light scattering and fluorescence emission by the specific fluorescent probe-labeled cells as they pass through a laser beam. It offers several unique advantages as it allows fast, relatively quantitative, multiparametric analysis of cell populations at the single cell level. In addition, it also enables physical sorting of the cells to separate the subpopulations based on different parameters. In this constantly evolving field, innovative technologies such as imaging FCM, mass cytometry and Raman FCM are being developed in order to address limitations of traditional FCM. This review explains the general principles, main applications and recent advances in the field of FCM.
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4
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Meng H, Warden A, Zhang L, Zhang T, Li Y, Tan Z, Wang B, Li H, Jiang H, Shen G, Hong Y, Ding X. A Mass-Ratiometry-Based CD45 Barcoding Method for Mass Cytometry Detection. SLAS Technol 2019; 24:408-419. [PMID: 30856358 DOI: 10.1177/2472630319834057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Mass cytometry (CyTOF) is a critical cell profiling tool in acquiring multiparameter proteome data at the single-cell level. A major challenge in CyTOF analysis is sample-to-sample variance arising from the pipetting process, staining variation, and instrument sensitivity. To reduce such variations, cell barcoding strategies that enable the combination of individual samples prior to antibody staining and data acquisition on CyTOF are often utilized. The most prevalent barcoding strategy is based on a binary scheme that cross-examines the existence or nonexistence of certain mass signals; however, it is limited by low barcoding efficiency and high cost, especially for large sample size. Herein, we present a novel barcoding method for CyTOF application based on mass ratiometry. Different mass tags with specific fixed ratios are used to label CD45 antibody to achieve sample barcoding. The presented method exponentially increases the number of possible barcoded samples with the same amount of mass tags compared with conventional methods. It also reduces the overall time for the labeling process to 40 min and avoids the need for expensive commercial barcoding buffer reagents. Moreover, unlike the conventional barcoding process, this strategy does not pre-permeabilize cells before the barcoding procedure, which offers additional benefits in preserving surface biomarker signals.
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Affiliation(s)
- Hongu Meng
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Antony Warden
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Lulu Zhang
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ting Zhang
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yiyang Li
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ziyang Tan
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Boqian Wang
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hongxia Li
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hui Jiang
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Guangxia Shen
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yifan Hong
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xianting Ding
- 1 Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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5
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Fluorescent genetic barcoding for cellular multiplex analyses. Exp Hematol 2018; 67:10-17. [DOI: 10.1016/j.exphem.2018.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022]
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6
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Lekishvili T, Campbell JJ. Rapid comparative immunophenotyping of human mesenchymal stromal cells by a modified fluorescent cell barcoding flow cytometric assay. Cytometry A 2017; 93:905-915. [DOI: 10.1002/cyto.a.23248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/30/2017] [Accepted: 09/02/2017] [Indexed: 12/15/2022]
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7
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Maetzig T, Ruschmann J, Sanchez Milde L, Lai CK, von Krosigk N, Humphries RK. Lentiviral Fluorescent Genetic Barcoding for Multiplex Fate Tracking of Leukemic Cells. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 6:54-65. [PMID: 28664166 PMCID: PMC5480982 DOI: 10.1016/j.omtm.2017.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/28/2017] [Indexed: 02/06/2023]
Abstract
Tracking the behavior of leukemic samples both in vitro and in vivo plays an increasingly large role in efforts to better understand the leukemogenic processes and the effects of potential new therapies. Such work can be accelerated and made more efficient by methodologies enabling the characterization of leukemia samples in multiplex assays. We recently developed three sets of lentiviral fluorescent genetic barcoding (FGB) vectors that create 26, 14, and 6 unique immunophenotyping-compatible color codes from GFP-, yellow fluorescent protein (YFP)-, and monomeric kusabira orange 2 (mKO2)-derived fluorescent proteins. These vectors allow for labeling and tracking of individual color-coded cell populations in mixed samples by real-time flow cytometry. Using the prototypical Hoxa9/Meis1 murine model of acute myeloid leukemia, we describe the application of the 6xFGB vector system for assessing leukemic cell characteristics in multiplex assays. By transplanting color-coded cell mixes, we investigated the competitive growth behavior of individual color-coded populations, determined leukemia-initiating cell frequencies, and assessed the dose-dependent potential of cells exposed to the histone deacetylase inhibitor Entinostat for bone marrow homing. Thus, FGB provides a useful tool for the multiplex characterization of leukemia samples in a wide variety of applications with a concomitant reduction in workload, processing times, and mouse utilization.
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Affiliation(s)
- Tobias Maetzig
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Jens Ruschmann
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Lea Sanchez Milde
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Courteney K Lai
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Niklas von Krosigk
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - R Keith Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
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8
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Hawley TS, Hawley RG, Telford WG. Fluorescent Proteins for Flow Cytometry. ACTA ACUST UNITED AC 2017; 80:9.12.1-9.12.20. [PMID: 28369764 DOI: 10.1002/cpcy.17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fluorescent proteins have become standard tools for cell and molecular biologists. The color palette of fluorescent proteins spans the ultraviolet, visible, and near-infrared spectrum. Utility of fluorescent proteins has been greatly facilitated by the availability of compact and affordable solid state lasers capable of providing various excitation wavelengths. In theory, the plethora of fluorescent proteins and lasers make it easy to detect multiple fluorescent proteins simultaneously. However, in practice, heavy spectral overlap due to broad excitation and emission spectra presents a challenge. In conventional flow cytometry, careful selection of excitation wavelengths and detection filters is necessary. Spectral flow cytometry, an emerging methodology that is not confined by the "one color, one detector" paradigm, shows promise in the facile detection of multiple fluorescent proteins. This chapter provides a synopsis of fluorescent protein development, a list of commonly used fluorescent proteins, some practical considerations and strategies for detection, and examples of applications. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Teresa S Hawley
- Flow Cytometry Core Facility, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Robert G Hawley
- Department of Anatomy and Regenerative Biology, George Washington University School of Medicine and Health Sciences, Washington, D.C
| | - William G Telford
- Flow Cytometry Core Facility, Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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9
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Mohme M, Maire CL, Riecken K, Zapf S, Aranyossy T, Westphal M, Lamszus K, Fehse B. Optical Barcoding for Single-Clone Tracking to Study Tumor Heterogeneity. Mol Ther 2017; 25:621-633. [PMID: 28109958 PMCID: PMC5363186 DOI: 10.1016/j.ymthe.2016.12.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/10/2016] [Accepted: 12/12/2016] [Indexed: 11/29/2022] Open
Abstract
Intratumoral heterogeneity has been identified as one of the strongest drivers of treatment resistance and tumor recurrence. Therefore, investigating the complex clonal architecture of tumors over time has become a major challenge in cancer research. We developed a new fluorescent "optical barcoding" technique that allows fast tracking, identification, and quantification of live cell clones in vitro and in vivo using flow cytometry (FC). We optically barcoded two cell lines derived from malignant glioma, an exemplary heterogeneous brain tumor. In agreement with mathematical combinatorics, we demonstrate that up to 41 clones can unambiguously be marked using six fluorescent proteins and a maximum of three colors per clone. We show that optical barcoding facilitates sensitive, precise, rapid, and inexpensive analysis of clonal composition kinetics of heterogeneous cell populations by FC. We further assessed the quantitative contribution of multiple clones to glioblastoma growth in vivo and we highlight the potential to recover individual viable cell clones by fluorescence-activated cell sorting. In summary, we demonstrate that optical barcoding is a powerful technique for clonal cell tracking in vitro and in vivo, rendering this approach a potent tool for studying the heterogeneity of complex tissues, in particular, cancer.
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Affiliation(s)
- Malte Mohme
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Cecile L Maire
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Svenja Zapf
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Tim Aranyossy
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Manfred Westphal
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Katrin Lamszus
- Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
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10
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Maetzig T, Ruschmann J, Lai CK, Ngom M, Imren S, Rosten P, Norddahl GL, von Krosigk N, Sanchez Milde L, May C, Selich A, Rothe M, Dhillon I, Schambach A, Humphries RK. A Lentiviral Fluorescent Genetic Barcoding System for Flow Cytometry-Based Multiplex Tracking. Mol Ther 2017; 25:606-620. [PMID: 28253481 DOI: 10.1016/j.ymthe.2016.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 11/25/2022] Open
Abstract
Retroviral integration site analysis and barcoding have been instrumental for multiplex clonal fate mapping, although their use imposes an inherent delay between sample acquisition and data analysis. Monitoring of multiple cell populations in real time would be advantageous, but multiplex assays compatible with flow cytometric tracking of competitive growth behavior are currently limited. We here describe the development and initial validation of three generations of lentiviral fluorescent genetic barcoding (FGB) systems that allow the creation of 26, 14, or 6 unique labels. Color-coded populations could be tracked in multiplex in vitro assays for up to 28 days by flow cytometry using all three vector systems. Those involving lower levels of multiplexing eased color-code generation and the reliability of vector expression and enabled functional in vitro and in vivo studies. In proof-of-principle experiments, FGB vectors facilitated in vitro multiplex screening of microRNA (miRNA)-induced growth advantages, as well as the in vivo recovery of color-coded progeny of murine and human hematopoietic stem cells. This novel series of FGB vectors provides new tools for assessing comparative growth properties in in vitro and in vivo multiplexing experiments, while simultaneously allowing for a reduction in sample numbers by up to 26-fold.
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Affiliation(s)
- Tobias Maetzig
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany.
| | - Jens Ruschmann
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Courteney K Lai
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Mor Ngom
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Suzan Imren
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Patricia Rosten
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Gudmundur L Norddahl
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Niklas von Krosigk
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Lea Sanchez Milde
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Christopher May
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Anton Selich
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Ishpreet Dhillon
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - R Keith Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
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11
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Abbadessa D, Smurthwaite CA, Reed CW, Wolkowicz R. A Single-Cell Platform for Monitoring Viral Proteolytic Cleavage in Different Cellular Compartments. BIOCHEMISTRY INSIGHTS 2016; 8:23-31. [PMID: 27688710 PMCID: PMC5034881 DOI: 10.4137/bci.s30379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/17/2016] [Accepted: 08/19/2016] [Indexed: 11/08/2022]
Abstract
Infectious diseases affect human health despite advances in biomedical research and drug discovery. Among these, viruses are especially difficult to tackle due to the sudden transfer from animals to humans, high mutational rates, resistance to current treatments, and the intricacies of their molecular interactions with the host. As an example of these interactions, we describe a cell-based approach to monitor specific proteolytic events executed by either the viral-encoded protease or by host proteins on the virus. We then emphasize the significance of examining proteolysis within the subcellular compartment where cleavage occurs naturally. We show the power of stable expression, highlighting the usefulness of the cell-based multiplexed approach, which we have adapted to two independent assays previously developed to monitor (a) the activity of the HIV-1-encoded protease or (b) the cleavage of the HIV-1-encoded envelope protein by the host. Multiplexing was achieved by mixing cells each carrying a different assay or, alternatively, by engineering cells expressing two assays. Multiplexing relies on the robustness of the individual assays and their clear discrimination, further enhancing screening capabilities in an attempt to block proteolytic events required for viral infectivity and spread.
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Affiliation(s)
- Darin Abbadessa
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Connor W Reed
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Roland Wolkowicz
- Department of Biology, San Diego State University, San Diego, CA, USA
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12
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Edwards BS, Sklar LA. Flow Cytometry: Impact on Early Drug Discovery. JOURNAL OF BIOMOLECULAR SCREENING 2015; 20:689-707. [PMID: 25805180 PMCID: PMC4606936 DOI: 10.1177/1087057115578273] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/27/2015] [Indexed: 12/15/2022]
Abstract
Modern flow cytometers can make optical measurements of 10 or more parameters per cell at tens of thousands of cells per second and more than five orders of magnitude dynamic range. Although flow cytometry is used in most drug discovery stages, "sip-and-spit" sampling technology has restricted it to low-sample-throughput applications. The advent of HyperCyt sampling technology has recently made possible primary screening applications in which tens of thousands of compounds are analyzed per day. Target-multiplexing methodologies in combination with extended multiparameter analyses enable profiling of lead candidates early in the discovery process, when the greatest numbers of candidates are available for evaluation. The ability to sample small volumes with negligible waste reduces reagent costs, compound usage, and consumption of cells. Improved compound library formatting strategies can further extend primary screening opportunities when samples are scarce. Dozens of targets have been screened in 384- and 1536-well assay formats, predominantly in academic screening lab settings. In concert with commercial platform evolution and trending drug discovery strategies, HyperCyt-based systems are now finding their way into mainstream screening labs. Recent advances in flow-based imaging, mass spectrometry, and parallel sample processing promise dramatically expanded single-cell profiling capabilities to bolster systems-level approaches to drug discovery.
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Affiliation(s)
- Bruce S Edwards
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Larry A Sklar
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
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13
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Smurthwaite CA, Williams W, Fetsko A, Abbadessa D, Stolp ZD, Reed CW, Dharmawan A, Wolkowicz R. Genetic barcoding with fluorescent proteins for multiplexed applications. J Vis Exp 2015:52452. [PMID: 25938804 PMCID: PMC4541556 DOI: 10.3791/52452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Fluorescent proteins, fluorescent dyes and fluorophores in general have revolutionized the field of molecular cell biology. In particular, the discovery of fluorescent proteins and their genes have enabled the engineering of protein fusions for localization, the analysis of transcriptional activation and translation of proteins of interest, or the general tracking of individual cells and cell populations. The use of fluorescent protein genes in combination with retroviral technology has further allowed the expression of these proteins in mammalian cells in a stable and reliable manner. Shown here is how one can utilize these genes to give cells within a population of cells their own biosignature. As the biosignature is achieved with retroviral technology, cells are barcoded 'indefinitely'. As such, they can be individually tracked within a mixture of barcoded cells and utilized in more complex biological applications. The tracking of distinct populations in a mixture of cells is ideal for multiplexed applications such as discovery of drugs against a multitude of targets or the activation profile of different promoters. The protocol describes how to elegantly develop and amplify barcoded mammalian cells with distinct genetic fluorescent markers, and how to use several markers at once or one marker at different intensities. Finally, the protocol describes how the cells can be further utilized in combination with cell-based assays to increase the power of analysis through multiplexing.
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14
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Tárnok A. Stardust memories. Cytometry A 2015; 87:283-4. [DOI: 10.1002/cyto.a.22660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 02/05/2015] [Accepted: 03/02/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Attila Tárnok
- Department of Pediatric Cardiology; Heart Centre Leipzig; Leipzig Germany
- Translational Centre for Regenerative Medicine (TRM); University of Leipzig; Leipzig Germany
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15
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Stolp ZD, Smurthwaite CA, Reed C, Williams W, Dharmawan A, Djaballah H, Wolkowicz R. A Multiplexed Cell-Based Assay for the Identification of Modulators of Pre-Membrane Processing as a Target against Dengue Virus. ACTA ACUST UNITED AC 2015; 20:616-26. [PMID: 25724189 PMCID: PMC4438100 DOI: 10.1177/1087057115571247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/14/2015] [Indexed: 12/19/2022]
Abstract
The DenV pre-membrane protein (prM) is a crucial chaperone for the viral envelope protein, preventing premature fusion with vesicles during viral export. prM molecules in immature particles are cleaved by host proteases, leading to mature fusogenic virions. Blockade of prM cleavage would restrict fusion and represents a novel druggable opportunity against DenV. We have thus established a cell-based platform to monitor prM processing that relies on an engineered two-tag scaffold that travels to the cell surface through the secretory pathway. The assay discriminates between a single cell-surface tag when prM is cleaved and two tags when it is not, as detected through fluorescent-coupled antibodies by flow cytometry. The assay, miniaturized into a 96-well plate format, was multiplexed with the HIV-1 envelope boundary, also cleaved in the same pathway. A pilot screen against 1280 compounds was executed, leading to the identification of a potential active and corroborating the robustness of our assay for large-scale screening. We describe for the first time a cell-based assay that monitors DenV prM processing within the classical secretory pathway, which was exploited to identify a potential novel drug against DenV.
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Affiliation(s)
- Zachary D Stolp
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Connor Reed
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Wesley Williams
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Andre Dharmawan
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Roland Wolkowicz
- Department of Biology, San Diego State University, San Diego, CA, USA
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Tárnok A. The year of light for enlightening photonics and cytometry- start of new year's note. Cytometry A 2014; 87:1-2. [DOI: 10.1002/cyto.a.22606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/01/2014] [Indexed: 02/06/2023]
Affiliation(s)
- Attila Tárnok
- Department of Pediatric Cardiology; Heart Centre Leipzig, University of Leipzig; Leipzig Germany
- Translational Centre for Regenerative Medicine (TRM), University of Leipzig; Leipzig Germany
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