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Ling M, Cardle II, Song K, Yan AJ, Kacherovsky N, Jensen MC, Pun SH. Aptamer-Based Chromatographic Methods for Efficient and Economical Separation of Leukocyte Populations. ACS Biomater Sci Eng 2023; 9:5062-5071. [PMID: 37467493 PMCID: PMC11016351 DOI: 10.1021/acsbiomaterials.3c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
The manufacturing process of chimeric antigen receptor T cell therapies includes isolation systems that provide pure T cells. Current magnetic-activated cell sorting and immunoaffinity chromatography methods produce desired cells with high purity and yield but require expensive equipment and reagents and involve time-consuming incubation steps. Here, we demonstrate that aptamers can be employed in a continuous-flow resin platform for both depletion of monocytes and selection of CD8+ T cells from peripheral blood mononuclear cells at low cost with high purity and throughput. Aptamer-mediated cell selection could potentially enable fully synthetic, traceless isolations of leukocyte subsets from a single isolation system.
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Affiliation(s)
- Melissa Ling
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195
| | - Ian I. Cardle
- Department of Bioengineering, University of Washington, Seattle, WA 98195
- Seattle Children’s Therapeutics, Seattle, WA 98101
| | - Kefan Song
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Alexander J. Yan
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | | | - Suzie H. Pun
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of Washington, Seattle, WA 98195
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2
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Yang LF, Ling M, Kacherovsky N, Pun SH. Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations. Chem Sci 2023; 14:4961-4978. [PMID: 37206388 PMCID: PMC10189874 DOI: 10.1039/d3sc00439b] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Aptamers are single-stranded nucleic acids that bind and recognize targets much like antibodies. Recently, aptamers have garnered increased interest due to their unique properties, including inexpensive production, simple chemical modification, and long-term stability. At the same time, aptamers possess similar binding affinity and specificity as their protein counterpart. In this review, we discuss the aptamer discovery process as well as aptamer applications to biosensors and separations. In the discovery section, we describe the major steps of the library selection process for aptamers, called systematic evolution of ligands by exponential enrichment (SELEX). We highlight common approaches and emerging strategies in SELEX, from starting library selection to aptamer-target binding characterization. In the applications section, we first evaluate recently developed aptamer biosensors for SARS-CoV-2 virus detection, including electrochemical aptamer-based sensors and lateral flow assays. Then we discuss aptamer-based separations for partitioning different molecules or cell types, especially for purifying T cell subsets for therapeutic applications. Overall, aptamers are promising biomolecular tools and the aptamer field is primed for expansion in biosensing and cell separation.
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Affiliation(s)
- Lucy F Yang
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Melissa Ling
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Nataly Kacherovsky
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
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3
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Abstract
In both biomedical research and clinical cell therapy manufacturing, there is a need for cell isolation systems that recover purified cells in the absence of any selection agent. Reported traceless cell isolation methods using engineered antigen-binding fragments or aptamers have been limited to processing a single cell type at a time. There remains an unmet need for cell isolation processes that rapidly sort multiple target cell types. Here, we utilized two aptamers along with their designated complementary strands (reversal agents) to tracelessly isolate two cell types from a mixed cell population with one aptamer-labeling step and two sequential cell elution steps with reversal agents. We engineered a CD71-binding aptamer (rvCD71apt) and a reversal agent pair to be used simultaneously with our previously reported traceless purification approach using the CD8 aptamer (rvCD8apt) and its reversal agent. We verified the compatibility of the two aptamer displacement mechanisms by flow cytometry and the feasibility of incorporating rvCD71apt with a magnetic solid state. We then combined rvCD71apt with rvCD8apt to isolate activated CD4+ T cells and resting CD8+ cells by eluting these target cells into separate fractions with orthogonal strand displacements. This is the first demonstration of isolating different cell types using two aptamers and reversal agents at the same time. Potentially, different or more aptamers can be included in this traceless multiplexed isolation system for diverse applications with a shortened operation time and a lower production cost.
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Affiliation(s)
- Emmeline L Cheng
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
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Yang LF, Kacherovsky N, Liang J, Salipante SJ, Pun SH. SCORe: SARS-CoV-2 Omicron Variant RBD-Binding DNA Aptamer for Multiplexed Rapid Detection and Pseudovirus Neutralization. Anal Chem 2022; 94:12683-12690. [PMID: 35972202 PMCID: PMC9397568 DOI: 10.1021/acs.analchem.2c01993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/03/2022] [Indexed: 01/18/2023]
Abstract
During the COVID-19 (coronavirus disease 2019) pandemic, several SARS-CoV-2 variants of concern emerged, including the Omicron variant, which has enhanced infectivity and immune invasion. Many antibodies and aptamers that bind the spike (S) of previous strains of SARS-CoV-2 either do not bind or bind with low affinity to Omicron S. In this study, we report a high-affinity SARS-CoV-2 Omicron RBD-binding aptamer (SCORe) that binds Omicron BA.1 and BA.2 RBD with nanomolar KD1. We employ aptamers SCORe.50 and SNAP4.74 in a multiplexed lateral flow assay (LFA) to distinguish between Omicron and wild-type S at concentrations as low as 100 pM. Finally, we show that SCORe.50 and its dimerized form SCOReD can neutralize Omicron S-pseudotyped virus infection of ACE2-overexpressing cells by >70%. SCORe therefore has potential applications in COVID-19 rapid diagnostics as well as in viral neutralization.
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Affiliation(s)
- Lucy F. Yang
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Joey Liang
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | | | - Suzie H. Pun
- Department of Bioengineering, University of Washington, Seattle, WA 98195
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5
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Cheng EL, Cardle II, Kacherovsky N, Bansia H, Wang T, Zhou Y, Raman J, Yen A, Gutierrez D, Salipante SJ, des Georges A, Jensen MC, Pun SH. Discovery of a Transferrin Receptor 1-Binding Aptamer and Its Application in Cancer Cell Depletion for Adoptive T-Cell Therapy Manufacturing. J Am Chem Soc 2022; 144:13851-13864. [PMID: 35875870 PMCID: PMC10024945 DOI: 10.1021/jacs.2c05349] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The clinical manufacturing of chimeric antigen receptor (CAR) T cells includes cell selection, activation, gene transduction, and expansion. While the method of T-cell selection varies across companies, current methods do not actively eliminate the cancer cells in the patient's apheresis product from the healthy immune cells. Alarmingly, it has been found that transduction of a single leukemic B cell with the CAR gene can confer resistance to CAR T-cell therapy and lead to treatment failure. In this study, we report the identification of a novel high-affinity DNA aptamer, termed tJBA8.1, that binds transferrin receptor 1 (TfR1), a receptor broadly upregulated by cancer cells. Using competition assays, high resolution cryo-EM, and de novo model building of the aptamer into the resulting electron density, we reveal that tJBA8.1 shares a binding site on TfR1 with holo-transferrin, the natural ligand of TfR1. We use tJBA8.1 to effectively deplete B lymphoma cells spiked into peripheral blood mononuclear cells with minimal impact on the healthy immune cell composition. Lastly, we present opportunities for affinity improvement of tJBA8.1. As TfR1 expression is broadly upregulated in many cancers, including difficult-to-treat T-cell leukemias and lymphomas, our work provides a facile, universal, and inexpensive approach for comprehensively removing cancerous cells from patient apheresis products for safe manufacturing of adoptive T-cell therapies.
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Affiliation(s)
- Emmeline L Cheng
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Ian I Cardle
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States.,Seattle Children's Therapeutics, Seattle, Washington 98101, United States
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Harsh Bansia
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States
| | - Tong Wang
- Nanoscience Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States
| | - Yunshi Zhou
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Jai Raman
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Albert Yen
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Dominique Gutierrez
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York (CUNY), New York, New York 10016, United States
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195-7110, United States
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States.,Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.,Department of Chemistry and Biochemistry, City College of New York, New York, New York 10031, United States
| | - Michael C Jensen
- Seattle Children's Therapeutics, Seattle, Washington 98101, United States.,Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
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Yang LF, Kacherovsky N, Panpradist N, Wan R, Liang J, Zhang B, Salipante SJ, Lutz BR, Pun SH. Aptamer Sandwich Lateral Flow Assay (AptaFlow) for Antibody-Free SARS-CoV-2 Detection. Anal Chem 2022; 94:7278-7285. [PMID: 35532905 PMCID: PMC9112978 DOI: 10.1021/acs.analchem.2c00554] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/10/2022] [Indexed: 12/17/2022]
Abstract
The COVID-19 pandemic is among the greatest health and socioeconomic crises in recent history. Although COVID-19 vaccines are being distributed, there remains a need for rapid testing to limit viral spread from infected individuals. We previously identified the SARS-CoV-2 spike protein N-terminal domain (NTD) binding DNA aptamer 1 (SNAP1) for detection of SARS-CoV-2 virus by aptamer-antibody sandwich enzyme-linked immunoassay (ELISA) and lateral flow assay (LFA). In this work, we identify a new aptamer that also binds at the NTD, named SARS-CoV-2 spike protein NTD-binding DNA aptamer 4 (SNAP4). SNAP4 binds with high affinity (<30 nM) for the SARS-CoV-2 spike protein, a 2-fold improvement over SNAP1. Furthermore, we utilized both SNAP1 and SNAP4 in an aptamer sandwich LFA (AptaFlow), which detected SARS-CoV-2 UV-inactivated virus at concentrations as low as 106 copies/mL. AptaFlow costs <$1 per test to produce, provides results in <1 h, and detects SARS-CoV-2 at concentrations that indicate higher viral loads and a high probability of contagious transmission. AptaFlow is a potential approach for a low-cost, convenient antigen test to aid the control of the COVID-19 pandemic.
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Affiliation(s)
- Lucy F. Yang
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
| | - Nataly Kacherovsky
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
| | - Nuttada Panpradist
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
| | - Ruixuan Wan
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Joey Liang
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
| | - Bo Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Stephen J. Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195
| | - Barry R. Lutz
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
| | - Suzie H. Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
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Kacherovsky N, Yang LF, Dang HV, Cheng EL, Cardle II, Walls AC, McCallum M, Sellers DL, DiMaio F, Salipante SJ, Corti D, Veesler D, Pun SH. Discovery and Characterization of Spike N‐Terminal Domain‐Binding Aptamers for Rapid SARS‐CoV‐2 Detection. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107730] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nataly Kacherovsky
- Department of Bioengineering University of Washington Seattle WA 98105 USA
| | - Lucy F. Yang
- Department of Bioengineering University of Washington Seattle WA 98105 USA
| | - Ha V. Dang
- Department of Biochemistry University of Washington Seattle WA 98105 USA
| | - Emmeline L. Cheng
- Department of Bioengineering University of Washington Seattle WA 98105 USA
| | - Ian I. Cardle
- Department of Bioengineering University of Washington Seattle WA 98105 USA
| | - Alexandra C. Walls
- Department of Biochemistry University of Washington Seattle WA 98105 USA
| | - Matthew McCallum
- Department of Biochemistry University of Washington Seattle WA 98105 USA
| | - Drew L. Sellers
- Department of Bioengineering University of Washington Seattle WA 98105 USA
| | - Frank DiMaio
- Department of Biochemistry University of Washington Seattle WA 98105 USA
| | | | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology 6500 Bellinzona Switzerland
| | - David Veesler
- Department of Biochemistry University of Washington Seattle WA 98105 USA
| | - Suzie H. Pun
- Department of Bioengineering University of Washington Seattle WA 98105 USA
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8
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Kacherovsky N, Yang LF, Dang HV, Cheng EL, Cardle II, Walls AC, McCallum M, Sellers DL, DiMaio F, Salipante SJ, Corti D, Veesler D, Pun SH. Discovery and Characterization of Spike N-Terminal Domain-Binding Aptamers for Rapid SARS-CoV-2 Detection. Angew Chem Int Ed Engl 2021; 60:21211-21215. [PMID: 34328683 PMCID: PMC8426805 DOI: 10.1002/anie.202107730] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 12/13/2022]
Abstract
The coronavirus disease 2019 (COVID‐19) pandemic has devastated families and disrupted healthcare, economies and societies across the globe. Molecular recognition agents that are specific for distinct viral proteins are critical components for rapid diagnostics and targeted therapeutics. In this work, we demonstrate the selection of novel DNA aptamers that bind to the SARS‐CoV‐2 spike glycoprotein with high specificity and affinity (<80 nM). Through binding assays and high resolution cryo‐EM, we demonstrate that SNAP1 (SARS‐CoV‐2 spike protein N‐terminal domain‐binding aptamer 1) binds to the S N‐terminal domain. We applied SNAP1 in lateral flow assays (LFAs) and ELISAs to detect UV‐inactivated SARS‐CoV‐2 at concentrations as low as 5×105 copies mL−1. SNAP1 is therefore a promising molecular tool for SARS‐CoV‐2 diagnostics.
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Affiliation(s)
- Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Lucy F Yang
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Ha V Dang
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Emmeline L Cheng
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Ian I Cardle
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Drew L Sellers
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98105, USA
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of, Vir Biotechnology, 6500, Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
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9
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Sylvestre M, Saxby CP, Kacherovsky N, Gustafson H, Salipante SJ, Pun SH. Identification of a DNA Aptamer That Binds to Human Monocytes and Macrophages. Bioconjug Chem 2020; 31:1899-1907. [PMID: 32589412 DOI: 10.1021/acs.bioconjchem.0c00247] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
As cancer strategies shift toward immunotherapy, the need for new binding ligands to target and isolate specific immune cell populations has soared. Based on prior work identifying a peptide specific for murine M2-like macrophages, we sought to identify an aptamer that could bind human M2-like macrophages. Tumor-associated macrophages (TAMs) adopt an M2-like phenotype and support tumor progression and dissemination. Here, we employed cell-SELEX to identify an aptamer ligand that targets this cell population over tissue resident (M0-like) or tumoricidal (M1-like) macrophages. Instead, we identified an aptamer that binds both human M0- and M2-like macrophages and monocytes, with highest binding affinity to M2-like macrophage (Kd ∼ 20 nM) and monocytes (Kd ∼ 45 nM) and minimal binding to other leukocytes. The aptamer binds to CD14+ but not CD16+ monocytes, and is rapidly internalized by these cells. We also demonstrate that this aptamer is able to bind human monocytes when both are administered in vivo to mice. Thus, binding to these cell populations (monocytes, M0-like and M2-like macrophages), this aptamer lends itself toward monocyte-specific applications, such as monocyte-targeted drug delivery or column selection.
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Affiliation(s)
- Meilyn Sylvestre
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher P Saxby
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Heather Gustafson
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Stephen J Salipante
- Laboratory Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
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10
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Kacherovsky N, Liu GW, Jensen MC, Pun SH. Multiplexed gene transfer to a human T-cell line by combining Sleeping Beauty transposon system with methotrexate selection. Biotechnol Bioeng 2015; 112:1429-36. [PMID: 25808830 DOI: 10.1002/bit.25538] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/30/2014] [Indexed: 11/06/2022]
Abstract
Engineered human T-cells are a promising therapeutic modality for cancer immunotherapy. T-cells expressing chimeric antigen receptors combined with additional genes to enhance T-cell proliferation, survival, or tumor targeting may further improve efficacy but require multiple stable gene transfer events. Methods are therefore needed to increase production efficiency for multiplexed engineered cells. In this work, we demonstrate multiplexed, non-viral gene transfer to a human T-cell line with efficient selection (∼ 50%) of cells expressing up to three recombinant open reading frames. The efficient introduction of multiple genes to T-cells was achieved using the Sleeping Beauty transposon system delivered in minicircles by nucleofection. We demonstrate rapid selection for engineered cells using methotrexate (MTX) and a mutant human dihydrofolate reductase resistant to methotrexate-induced metabolic inhibition. Preferential amplification of cells expressing multiple transgenes was achieved by two successive rounds of increasing MTX concentration. This non-viral gene transfer method with MTX step selection can potentially be used in the generation of clinical-grade T-cells housing multiplexed genetic modifications.
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Affiliation(s)
- Nataly Kacherovsky
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington
| | - Gary W Liu
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington
| | - Michael C Jensen
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington. .,Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington.
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11
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Kacherovsky N, Harkey MA, Blau CA, Giachelli CM, Pun SH. Combination of Sleeping Beauty transposition and chemically induced dimerization selection for robust production of engineered cells. Nucleic Acids Res 2012; 40:e85. [PMID: 22402491 PMCID: PMC3367214 DOI: 10.1093/nar/gks213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The main methods for producing genetically engineered cells use viral vectors for which safety issues and manufacturing costs remain a concern. In addition, selection of desired cells typically relies on the use of cytotoxic drugs with long culture times. Here, we introduce an efficient non-viral approach combining the Sleeping Beauty (SB) Transposon System with selective proliferation of engineered cells by chemically induced dimerization (CID) of growth factor receptors. Minicircles carrying a SB transposon cassette containing a reporter transgene and a gene for the F36VFGFR1 fusion protein were delivered to the hematopoietic cell line Ba/F3. Stably-transduced Ba/F3 cell populations with >98% purity were obtained within 1 week using this positive selection strategy. Copy number analysis by quantitative PCR (qPCR) revealed that CID-selected cells contain on average higher copy numbers of transgenes than flow cytometry-selected cells, demonstrating selective advantage for cells with multiple transposon insertions. A diverse population of cells is present both before and after culture in CID media, although site-specific qPCR of transposon junctions show that population diversity is significantly reduced after selection due to preferential expansion of clones with multiple integration events. This non-viral, positive selection approach is an attractive alternative for producing engineered cells.
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Affiliation(s)
- Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
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12
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Kacherovsky N, Tachibana C, Amos E, Fox D, Young ET. Promoter binding by the Adr1 transcriptional activator may be regulated by phosphorylation in the DNA-binding region. PLoS One 2008; 3:e3213. [PMID: 18791642 PMCID: PMC2527678 DOI: 10.1371/journal.pone.0003213] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 08/25/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Post-translational modification regulates promoter-binding by Adr1, a Zn-finger transcriptional activator of glucose-regulated genes. Support for this model includes the activation of an Adr1-dependent gene in the absence of Adr1 protein synthesis, and a requirement for the kinase Snf1 for Adr1 DNA-binding. A fusion protein with the Adr1 DNA-binding domain and a heterologous activation domain is glucose-regulated, suggesting that the DNA binding region is the target of regulation. METHODOLOGY/PRINCIPAL FINDINGS Peptide mapping identified serine 98 adjacent to the Zn-fingers as a phosphorylation site. An antibody specific for phosphorylated serine 98 on Adr1 showed that the level of phosphorylated Adr1 relative to the level of total Adr1 decreased with glucose derepression, in a Snf1-dependent manner. Relative phosphorylation decreased in a PHO85 mutant, and this mutant constitutively expressed an Adr1-dependent reporter. Pho85 did not phosphorylate Adr1 in vitro, suggesting that it affects Adr1 indirectly. Mutation of serine 98 to the phosphomimetic amino acid aspartate reduced in vitro DNA-binding of the recombinant Adr1 DNA-binding domain. Mutation to aspartate or alanine affected activation of a reporter by full-length Adr1, and in vivo promoter binding. CONCLUSIONS/SIGNIFICANCE Mutation of Adr1 serine 98 affects in vitro and in vivo DNA binding, and phosphorylation of serine 98 in vivo correlates with glucose availability, suggesting that Adr1 promoter-binding is regulated in part by serine 98 phosphorylation.
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Affiliation(s)
- Nataly Kacherovsky
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Christine Tachibana
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Emily Amos
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - David Fox
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Elton T. Young
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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13
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Voronkova V, Kacherovsky N, Tachibana C, Yu D, Young ET. Snf1-dependent and Snf1-independent pathways of constitutive ADH2 expression in Saccharomyces cerevisiae. Genetics 2006; 172:2123-38. [PMID: 16415371 PMCID: PMC1456411 DOI: 10.1534/genetics.105.048231] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The transcription factor Adr1 directly activates the expression of genes encoding enzymes in numerous pathways that are upregulated after the exhaustion of glucose in the yeast Saccharomyces cerevisiae. ADH2, encoding the alcohol dehydrogenase isozyme required for ethanol oxidation, is a highly glucose-repressed, Adr1-dependent gene. Using a genetic screen we isolated >100 mutants in 12 complementation groups that exhibit ADR1-dependent constitutive ADH2 expression on glucose. Temperature-sensitive alleles are present among the new constitutive mutants, indicating that essential genes play a role in ADH2 repression. Among the genes we cloned is MOT1, encoding a repressor that inhibits TBP binding to the promoter, thus linking glucose repression with TBP access to chromatin. Two genes encoding proteins involved in vacuolar function, FAB1 and VPS35, and CDC10, encoding a nonessential septin, were also uncovered in the search, suggesting that vacuolar function and the cytoskeleton have previously unknown roles in regulating gene expression. Constitutive activation of ADH2 expression by Adr1 is SNF1-dependent in a strain with a defective MOT1 gene, whereas deletion of SNF1 did not affect constitutive ADH2 expression in the mutants affecting vacuolar or septin function. Thus, the mutant search revealed previously unknown Snf1-dependent and -independent pathways of ADH2 expression.
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Affiliation(s)
- Valentina Voronkova
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7350, USA
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Tachibana C, Yoo JY, Tagne JB, Kacherovsky N, Lee TI, Young ET. Combined global localization analysis and transcriptome data identify genes that are directly coregulated by Adr1 and Cat8. Mol Cell Biol 2005; 25:2138-46. [PMID: 15743812 PMCID: PMC1061606 DOI: 10.1128/mcb.25.6.2138-2146.2005] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Saccharomyces cerevisiae, glucose depletion causes a profound alteration in metabolism, mediated in part by global transcriptional changes. Many of the transcription factors that regulate these changes act combinatorially. We have analyzed combinatorial regulation by Adr1 and Cat8, two transcription factors that act during glucose depletion, by combining genome-wide expression and genome-wide binding data. We identified 32 genes that are directly activated by Adr1, 28 genes that are directly activated by Cat8, and 14 genes that are directly regulated by both. Our analysis also uncovered promoters that Adr1 binds but does not regulate and promoters that are indirectly regulated by Cat8, stressing the advantage of combining global expression and global localization analysis to find directly regulated targets. At most of the coregulated promoters, the in vivo binding of one factor is independent of the other, but Adr1 is required for optimal Cat8 binding at two promoters with a poor match to the Cat8 binding consensus. In addition, Cat8 is required for Adr1 binding at promoters where Adr1 is not required for transcription. These data provide a comprehensive analysis of the direct, indirect, and combinatorial requirements for these two global transcription factors.
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Affiliation(s)
- Christine Tachibana
- Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350, USA
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Dombek KM, Kacherovsky N, Young ET. The Reg1-interacting proteins, Bmh1, Bmh2, Ssb1, and Ssb2, have roles in maintaining glucose repression in Saccharomyces cerevisiae. J Biol Chem 2004; 279:39165-74. [PMID: 15220335 DOI: 10.1074/jbc.m400433200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In Saccharomyces cerevisiae, a type 1 protein phosphatase complex composed of the Glc7 catalytic subunit and the Reg1 regulatory subunit represses expression of many glucose-regulated genes. Here we show that the Reg1-interacting proteins Bmh1, Bmh2, Ssb1, and Ssb2 have roles in glucose repression. Deleting both BMH genes causes partially constitutive ADH2 expression without significantly increasing the level of Adr1 protein, the major activator of ADH2 expression. Adr1 and Bcy1, the regulatory subunit of cAMP-dependent protein kinase, are both required for this effect indicating that constitutive expression in Deltabmh1Deltabmh2 cells uses the same activation pathway that operates in Deltareg1 cells. Deletion of both BMH genes and REG1 causes a synergistic relief from repression, suggesting that Bmh proteins also act independently of Reg1 during glucose repression. A two-hybrid interaction with the Bmh proteins was mapped to amino acids 187-232, a region of Reg1 that is conserved in different classes of fungi. Deleting this region partially releases SUC2 from glucose repression. This indicates a role for the Reg1-Bmh interaction in glucose repression and also suggests a broad role for Bmh proteins in this process. An in vivo Reg1-Bmh interaction was confirmed by copurification of Bmh proteins with HA(3)-TAP-tagged Reg1. The nonconventional heat shock proteins Ssb1 and Ssb2 are also copurified with HA(3)-TAP-tagged Reg1. Deletion of both SSB genes modestly decreases repression of ADH2 expression in the presence of glucose, suggesting that Ssb proteins, perhaps through their interaction with Reg1, play a minor role in glucose repression.
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Affiliation(s)
- Kenneth M Dombek
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350, USA.
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Abstract
The yeast transcriptional activator Adr1 controls the expression of genes required for ethanol, glycerol, and fatty acid utilization. We show that Adr1 acts directly on the promoters of ADH2, ACS1, GUT1, CTA1, and POT1 using chromatin immunoprecipitation assays. The yeast homolog of the AMP-activated protein kinase, Snf1, promotes Adr1 chromatin binding in the absence of glucose, and the protein phosphatase complex, Glc7.Reg1, represses its binding in the presence of glucose. A post-translational process is implicated in the regulation of Adr1 binding activity. Chromatin binding by Adr1 is not the only step in ADH2 transcription that is regulated by glucose repression. Adr1 can bind to chromatin in repressed conditions in the presence of hyperacetylated histones. To study steps subsequent to promoter binding we utilized miniAdr1 transcription factors to characterize Adr1-dependent transcription in vitro. Yeast nuclear extracts prepared from glucose-repressed and glucose-derepressed cells are equally capable of supporting miniAdr1-dependent transcription and pre-initiation complex formation. Nuclear extracts prepared from a snf1 mutant support miniAdr1-dependent transcription but are partially defective in the formation of pre-initiation complexes with Mediator components being particularly depleted. We conclude that Snf1 regulates Adr1-dependent transcription primarily at the level of chromatin binding.
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Affiliation(s)
- Elton T Young
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350, USA.
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Verdone L, Wu J, Riper KV, Kacherovsky N, Vogelauer M, Young ET, Grunstein M, Mauro ED, Caserta M. Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions. EMBO J 2002; 21:1101-11. [PMID: 11867538 PMCID: PMC125900 DOI: 10.1093/emboj/21.5.1101] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report that in vivo increased acetylation of the repressed Saccharomyces cerevisiae ADH2 promoter chromatin, as obtained by disrupting the genes for the two deacetylases HDA1 and RPD3, destabilizes the structure of the TATA box-containing nucleosome. This acetylation-dependent chromatin remodeling is not sufficient to allow the binding of the TATA box-binding protein, but facilitates the recruitment of the transcriptional activator Adr1 and induces faster kinetics of mRNA accumulation when the cells are shifted to derepressing conditions.
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Affiliation(s)
- Loredana Verdone
- Fondazione Istituto Pasteur-Fondazione Cenci Bolognetti and Centro di Studio per gli Acidi Nucleici, CNR, c/o Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, I-00185 Rome, Italy, Department of Biological Chemistry, UCLA School of Medicine and Molecular Biology Institute, University of California, Los Angeles, CA 90095 and Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350, USA Corresponding author e-mail:
| | - Jiansheng Wu
- Fondazione Istituto Pasteur-Fondazione Cenci Bolognetti and Centro di Studio per gli Acidi Nucleici, CNR, c/o Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, I-00185 Rome, Italy, Department of Biological Chemistry, UCLA School of Medicine and Molecular Biology Institute, University of California, Los Angeles, CA 90095 and Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350, USA Corresponding author e-mail:
| | - Kristen van Riper
- Fondazione Istituto Pasteur-Fondazione Cenci Bolognetti and Centro di Studio per gli Acidi Nucleici, CNR, c/o Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, I-00185 Rome, Italy, Department of Biological Chemistry, UCLA School of Medicine and Molecular Biology Institute, University of California, Los Angeles, CA 90095 and Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350, USA Corresponding author e-mail:
| | - Nataly Kacherovsky
- Fondazione Istituto Pasteur-Fondazione Cenci Bolognetti and Centro di Studio per gli Acidi Nucleici, CNR, c/o Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, I-00185 Rome, Italy, Department of Biological Chemistry, UCLA School of Medicine and Molecular Biology Institute, University of California, Los Angeles, CA 90095 and Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350, USA Corresponding author e-mail:
| | - Maria Vogelauer
- Fondazione Istituto Pasteur-Fondazione Cenci Bolognetti and Centro di Studio per gli Acidi Nucleici, CNR, c/o Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, I-00185 Rome, Italy, Department of Biological Chemistry, UCLA School of Medicine and Molecular Biology Institute, University of California, Los Angeles, CA 90095 and Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350, USA Corresponding author e-mail:
| | - Elton T. Young
- Fondazione Istituto Pasteur-Fondazione Cenci Bolognetti and Centro di Studio per gli Acidi Nucleici, CNR, c/o Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, I-00185 Rome, Italy, Department of Biological Chemistry, UCLA School of Medicine and Molecular Biology Institute, University of California, Los Angeles, CA 90095 and Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350, USA Corresponding author e-mail:
| | - Michael Grunstein
- Fondazione Istituto Pasteur-Fondazione Cenci Bolognetti and Centro di Studio per gli Acidi Nucleici, CNR, c/o Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, I-00185 Rome, Italy, Department of Biological Chemistry, UCLA School of Medicine and Molecular Biology Institute, University of California, Los Angeles, CA 90095 and Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350, USA Corresponding author e-mail:
| | - Ernesto Di Mauro
- Fondazione Istituto Pasteur-Fondazione Cenci Bolognetti and Centro di Studio per gli Acidi Nucleici, CNR, c/o Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, I-00185 Rome, Italy, Department of Biological Chemistry, UCLA School of Medicine and Molecular Biology Institute, University of California, Los Angeles, CA 90095 and Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350, USA Corresponding author e-mail:
| | - Micaela Caserta
- Fondazione Istituto Pasteur-Fondazione Cenci Bolognetti and Centro di Studio per gli Acidi Nucleici, CNR, c/o Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, I-00185 Rome, Italy, Department of Biological Chemistry, UCLA School of Medicine and Molecular Biology Institute, University of California, Los Angeles, CA 90095 and Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195-7350, USA Corresponding author e-mail:
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Young ET, Kacherovsky N, Cheng C. An accessory DNA binding motif in the zinc finger protein Adr1 assists stable binding to DNA and can be replaced by a third finger. Biochemistry 2000; 39:567-74. [PMID: 10642181 DOI: 10.1021/bi992049r] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The DNA binding domain of Adr1, the protein derived from alcohol dehydrogenase regulatory gene 1, is unusual for zinc finger proteins in that it consists of two classical Cys2His2 zinc fingers and an amino-terminal proximal accessory region termed PAR. PAR is unstructured in the free protein and becomes structured in the DNA-bound form. We investigated the role of PAR in DNA binding using molecular and biochemical approaches, and its importance for activation in vivo, using Adr1-dependent reporter genes. PAR was unimportant for DNA binding when a third finger was added to Adr1, and its importance was diminished but not eliminated by mutations in finger two that increased DNA binding affinity. The kinetic rate constants for three Adr1 proteins containing or lacking PAR were determined by surface plasmon resonance. PAR increased the on rate and decreased the off rate for specific DNA sites for Adr1 containing wild-type fingers one and two. Surprisingly, PAR had no significant effect on the kinetic rate constants when a third finger was present, or when single-stranded DNA was used as the substrate for DNA binding. A mutant form of Adr1-F1F2 in which finger 2 makes three base-specific contacts with DNA had a higher affinity for DNA than Adr1 containing three fingers, yet the mutant protein still depended on PAR for optimal binding affinity. The ability to activate transcription in vivo was correlated with a low dissociation rate, suggesting that stabilizing an activator at the promoter might be rate-limiting for transcription in vivo. PAR may have evolved to lend additional stability to DNA-Adr1 complexes encompassing short binding sites. In addition, PAR may have a role in transcription at a step after DNA binding since deletion of PAR from Adr1 with three fingers decreased activation in vivo but had no effect on DNA binding kinetics.
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Affiliation(s)
- E T Young
- Department of Biochemistry, Box 357350, University of Washington, Seattle, Washington 98195-7350, USA.
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Young ET, Saario J, Kacherovsky N, Chao A, Sloan JS, Dombek KM. Characterization of a p53-related activation domain in Adr1p that is sufficient for ADR1-dependent gene expression. J Biol Chem 1998; 273:32080-7. [PMID: 9822683 DOI: 10.1074/jbc.273.48.32080] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The yeast transcriptional activator Adr1p controls expression of the glucose-repressible alcohol dehydrogenase gene (ADH2), genes involved in glycerol metabolism, and genes required for peroxisome biogenesis and function. Previous data suggested that promoter-specific activation domains might contribute to expression of the different types of ADR1-dependent genes. By using gene fusions encoding the Gal4p DNA binding domain and portions of Adr1p, we identified a single, strong acidic activation domain spanning amino acids 420-462 of Adr1p. Both acidic and hydrophobic amino acids within this activation domain were important for its function. The critical hydrophobic residues are in a motif previously identified in p53 and related acidic activators. A mini-Adr1 protein consisting of the DNA binding domain of Adr1p fused to this 42-residue activation domain carried out all of the known functions of wild-type ADR1. It conferred stringent glucose repression on the ADH2 locus and on UAS1-containing reporter genes. The putative inhibitory region of Adr1p encompassing the protein kinase A phosphorylation site at Ser-230 is thus not essential for glucose repression mediated by ADR1. Mini-ADR1 allowed efficient derepression of gene expression. In addition it complemented an ADR1-null allele for growth on glycerol and oleate media, indicating efficient activation of genes required for glycerol metabolism and peroxisome biogenesis. Thus, a single activation domain can activate all ADR1-dependent promoters.
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Affiliation(s)
- E T Young
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350, USA.
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Donoviel MS, Kacherovsky N, Young ET. Synergistic activation of ADH2 expression is sensitive to upstream activation sequence 2 (UAS2) orientation, copy number and UAS1-UAS2 helical phasing. Mol Cell Biol 1995; 15:3442-9. [PMID: 7760841 PMCID: PMC230579 DOI: 10.1128/mcb.15.6.3442] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The alcohol dehydrogenase 2 (ADH2) gene of Saccharomyces cerevisiae is under stringent glucose repression. Two cis-acting upstream activation sequences (UAS) that function synergistically in the derepression of ADH2 gene expression have been identified. UAS1 is the binding site for the transcriptional regulator Adr1p. UAS2 has been shown to be important for ADH2 expression and confers glucose-regulated, ADR1-independent activity to a heterologous reporter gene. An analysis of point mutations within UAS2, in the context of the entire ADH2 upstream regulatory region, showed that the specific sequence of UAS2 is important for efficient derepression of ADH2, as would be expected if UAS2 were the binding site for a transcriptional regulatory protein. In the context of the ADH2 upstream regulatory region, including UAS1, working in concert with the ADH2 basal promoter elements, UAS2-dependent gene activation was dependent on orientation, copy number, and helix phase. Multimerization of UAS2, or its presence in reversed orientation, resulted in a decrease in ADH2 expression. In contrast, UAS2-dependent expression of a reporter gene containing the ADH2 basal promoter and coding sequence was enhanced by multimerization of UAS2 and was independent of UAS2 orientation. The reduced expression caused by multimerization of UAS2 in the native promoter was observed only in the presence of ADR1. Inhibition of UAS2-dependent gene expression by Adr1p was also observed with a UAS2-dependent ADH2 reporter gene. This inhibition increased with ADR1 copy number and required the DNA-binding activity of Adr1p. Specific but low-affinity binding of Adr1p to UAS2 in vitro was demonstrated, suggesting that the inhibition of UAS2-dependent gene expression observed in vivo could be a direct effect due to Adr1p binding to UAS2.
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Affiliation(s)
- M S Donoviel
- Department of Biochemistry, University of Washington, Seattle 98195, USA
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Cheng C, Kacherovsky N, Dombek KM, Camier S, Thukral SK, Rhim E, Young ET. Identification of potential target genes for Adr1p through characterization of essential nucleotides in UAS1. Mol Cell Biol 1994; 14:3842-52. [PMID: 8196627 PMCID: PMC358751 DOI: 10.1128/mcb.14.6.3842-3852.1994] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Adr1p is a regulatory protein in the yeast Saccharomyces cerevisiae that binds to and activates transcription from two sites in a perfect 22-bp inverted repeat, UAS1, in the ADH2 promoter. Binding requires two C2H2 zinc fingers and a region amino terminal to the fingers. The importance for DNA binding of each position within UAS1 was deduced from two types of assays. Both methods led to an identical consensus sequence containing only four essential base pairs: GG(A/G)G. The preferred sequence, TTGG(A/G)GA, is found in both halves of the inverted repeat. The region of Adr1p amino terminal to the fingers is important for phosphate contacts in the central region of UAS1. However, no base-specific contacts in this portion of UAS1 are important for DNA binding or for ADR1-dependent transcription in vivo. When the central 6 bp were deleted, only a single monomer of Adr1p was able to bind in vitro and activation in vivo was severely reduced. On the basis of these results and previous knowledge about the DNA binding site requirements, including constraints on the spacing and orientation of sites that affect activation in vivo, a consensus binding site for Adr1p was derived. By using this consensus site, potential Adr1p binding sites were located in the promoters of genes known to show ADR1-dependent expression. In addition, this consensus allowed the identification of new potential target genes for Adr1p.
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Affiliation(s)
- C Cheng
- Department of Biochemistry, University of Washington, Seattle 98195
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Abstract
A second-site mutation that restored DNA binding to ADR1 mutants altered at different positions in the two zinc fingers was identified. This mutation (called IS1) was a conservative change of arginine 91 to lysine in a region amino terminal to the two zinc fingers and known from previous experiments to be necessary for DNA binding. IS1 increased binding to the UAS1 sequence two- to sevenfold for various ADR1 mutants and twofold for wild-type ADR1. The change of arginine 91 to glycine decreased binding twofold, suggesting that this arginine is involved in DNA binding in the wild-type protein. The increase in binding by IS1 did not involve protein-protein interactions between the two ADR1 monomers, nor did it require the presence of the sequences flanking UAS1. However, the effect of IS1 was influenced by the sequence of the first finger, suggesting that interactions between the region amino terminal to the fingers and the fingers themselves could exist. A model for the role of the amino-terminal region based on these results and sequence homologies with other DNA-binding motifs is proposed.
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Affiliation(s)
- S Camier
- Department of Biochemistry, University of Washington, Seattle 98195
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