1
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Noll A, Myers C, Biery MC, Meechan M, Tahiri S, Rajendran A, Berens ME, Paine D, Byron S, Zhang J, Winter C, Pakiam F, Leary SES, Cole BL, Jackson ER, Dun MD, Foster JB, Evans MK, Pattwell SS, Olson JM, Vitanza NA. Therapeutic HDAC inhibition in hypermutant diffuse intrinsic pontine glioma. Neoplasia 2023; 43:100921. [PMID: 37603953 PMCID: PMC10465940 DOI: 10.1016/j.neo.2023.100921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Received: 03/16/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/23/2023]
Abstract
Constitutional mismatch repair deficiency (CMMRD) is a cancer predisposition syndrome associated with the development of hypermutant pediatric high-grade glioma, and confers a poor prognosis. While therapeutic histone deacetylase (HDAC) inhibition of diffuse intrinsic pontine glioma (DIPG) has been reported; here, we use a clinically relevant biopsy-derived hypermutant DIPG model (PBT-24FH) and a CRISPR-Cas9 induced genetic model to evaluate the efficacy of HDAC inhibition against hypermutant DIPG. We screened PBT-24FH cells for sensitivity to a panel of HDAC inhibitors (HDACis) in vitro, identifying two HDACis associated with low nanomolar IC50s, quisinostat (27 nM) and romidepsin (2 nM). In vivo, quisinostat proved more efficacious, inducing near-complete tumor regression in a PBT-24FH flank model. RNA sequencing revealed significant quisinostat-driven changes in gene expression, including upregulation of neural and pro-inflammatory genes. To validate the observed potency of quisinostat in vivo against additional hypermutant DIPG models, we tested quisinostat in genetically-induced mismatch repair (MMR)-deficient DIPG flank tumors, demonstrating that loss of MMR function increases sensitivity to quisinostat in vivo. Here, we establish the preclinical efficacy of quisinostat against hypermutant DIPG, supporting further investigation of epigenetic targeting of hypermutant pediatric cancers with the potential for clinical translation. These findings support further investigation of HDAC inhibitors against pontine high-grade gliomas, beyond only those with histone mutations, as well as against other hypermutant central nervous system tumors.
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Affiliation(s)
- Alyssa Noll
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Molecular and Cellular Biology Graduate Program and Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Carrie Myers
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Matthew C Biery
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael Meechan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sophie Tahiri
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Molecular Mechanisms of Disease Graduate Program, University of Washington, Seattle, WA, USA
| | - Asmitha Rajendran
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Biomedical Informatics and Medical Education Graduate Program, University of Washington, Seattle, WA, USA
| | - Michael E Berens
- Cancer & Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Danyelle Paine
- Cancer & Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Sara Byron
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Jiaming Zhang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Conrad Winter
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Fiona Pakiam
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sarah E S Leary
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - Bonnie L Cole
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Evangeline R Jackson
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Matthew D Dun
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia; Paediatric Program, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
| | - Jessica B Foster
- Division of Oncology, The Children's Hospital of Philadelphia, Philidelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Myron K Evans
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - Siobhan S Pattwell
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - James M Olson
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - Nicholas A Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA.
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2
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Vitanza NA, Wilson AL, Huang W, Seidel K, Brown C, Gustafson JA, Yokoyama JK, Johnson AJ, Baxter BA, Koning RW, Reid AN, Meechan M, Biery MC, Myers C, Rawlings-Rhea SD, Albert CM, Browd SR, Hauptman JS, Lee A, Ojemann JG, Berens ME, Dun MD, Foster JB, Crotty EE, Leary SE, Cole BL, Perez FA, Wright JN, Orentas RJ, Chour T, Newell EW, Whiteaker JR, Zhao L, Paulovich AG, Pinto N, Gust J, Gardner RA, Jensen MC, Park JR. Intraventricular B7-H3 CAR T Cells for Diffuse Intrinsic Pontine Glioma: Preliminary First-in-Human Bioactivity and Safety. Cancer Discov 2023; 13:114-131. [PMID: 36259971 PMCID: PMC9827115 DOI: 10.1158/2159-8290.cd-22-0750] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [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] [Received: 07/13/2022] [Revised: 09/13/2022] [Accepted: 10/13/2022] [Indexed: 01/16/2023]
Abstract
Diffuse intrinsic pontine glioma (DIPG) remains a fatal brainstem tumor demanding innovative therapies. As B7-H3 (CD276) is expressed on central nervous system (CNS) tumors, we designed B7-H3-specific chimeric antigen receptor (CAR) T cells, confirmed their preclinical efficacy, and opened BrainChild-03 (NCT04185038), a first-in-human phase I trial administering repeated locoregional B7-H3 CAR T cells to children with recurrent/refractory CNS tumors and DIPG. Here, we report the results of the first three evaluable patients with DIPG (including two who enrolled after progression), who received 40 infusions with no dose-limiting toxicities. One patient had sustained clinical and radiographic improvement through 12 months on study. Patients exhibited correlative evidence of local immune activation and persistent cerebrospinal fluid (CSF) B7-H3 CAR T cells. Targeted mass spectrometry of CSF biospecimens revealed modulation of B7-H3 and critical immune analytes (CD14, CD163, CSF-1, CXCL13, and VCAM-1). Our data suggest the feasibility of repeated intracranial B7-H3 CAR T-cell dosing and that intracranial delivery may induce local immune activation. SIGNIFICANCE This is the first report of repeatedly dosed intracranial B7-H3 CAR T cells for patients with DIPG and includes preliminary tolerability, the detection of CAR T cells in the CSF, CSF cytokine elevations supporting locoregional immune activation, and the feasibility of serial mass spectrometry from both serum and CSF. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Nicholas A. Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Corresponding Author: Nicholas A. Vitanza, Seattle Children's Research Institute, M/S JMB-8, 1900 9th Avenue, Seattle, WA 98101. Phone: 206-884-4084; E-mail:
| | | | - Wenjun Huang
- Seattle Children's Therapeutics, Seattle, Washington
| | - Kristy Seidel
- Seattle Children's Therapeutics, Seattle, Washington
| | - Christopher Brown
- Seattle Children's Therapeutics, Seattle, Washington.,Therapeutic Cell Production Core, Seattle Children's Research Institute, Seattle, Washington
| | | | | | | | | | | | | | - Michael Meechan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | - Matthew C. Biery
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | - Carrie Myers
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | | | - Catherine M. Albert
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Samuel R. Browd
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Jason S. Hauptman
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Amy Lee
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Jeffrey G. Ojemann
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Michael E. Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Matthew D. Dun
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, Callaghan, Australia.,Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Jessica B. Foster
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Erin E. Crotty
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Sarah E.S. Leary
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Bonnie L. Cole
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Francisco A. Perez
- Department of Radiology, Seattle Children's Hospital, Seattle, Washington
| | - Jason N. Wright
- Department of Radiology, Seattle Children's Hospital, Seattle, Washington
| | - Rimas J. Orentas
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Tony Chour
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Evan W. Newell
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Navin Pinto
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Juliane Gust
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington.,Division of Pediatric Neurology, Department of Neurology, University of Washington, Seattle, Washington
| | - Rebecca A. Gardner
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Seattle Children's Therapeutics, Seattle, Washington
| | | | - Julie R. Park
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Seattle Children's Therapeutics, Seattle, Washington
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Vignali M, Armour CD, Chen J, Morrison R, Castle JC, Biery MC, Bouzek H, Moon W, Babak T, Fried M, Raymond CK, Duffy PE. NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children. J Clin Invest 2011; 121:1119-29. [PMID: 21317536 DOI: 10.1172/jci43457] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 12/15/2010] [Indexed: 11/17/2022] Open
Abstract
Malaria caused by Plasmodium falciparum results in approximately 1 million annual deaths worldwide, with young children and pregnant mothers at highest risk. Disease severity might be related to parasite virulence factors, but expression profiling studies of parasites to test this hypothesis have been hindered by extensive sequence variation in putative virulence genes and a preponderance of host RNA in clinical samples. We report here the application of RNA sequencing to clinical isolates of P. falciparum, using not-so-random (NSR) primers to successfully exclude human ribosomal RNA and globin transcripts and enrich for parasite transcripts. Using NSR-seq, we confirmed earlier microarray studies showing upregulation of a distinct subset of genes in parasites infecting pregnant women, including that encoding the well-established pregnancy malaria vaccine candidate var2csa. We also describe a subset of parasite transcripts that distinguished parasites infecting children from those infecting pregnant women and confirmed this observation using quantitative real-time PCR and mass spectrometry proteomic analyses. Based on their putative functional properties, we propose that these proteins could have a role in childhood malaria pathogenesis. Our study provides proof of principle that NSR-seq represents an approach that can be used to study clinical isolates of parasites causing severe malaria syndromes as well other blood-borne pathogens and blood-related diseases.
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Affiliation(s)
- Marissa Vignali
- Seattle Biomedical Research Institute, Seattle, Washington, USA
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4
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Georges SA, Biery MC, Kim SY, Schelter JM, Guo J, Chang AN, Jackson AL, Carleton MO, Linsley PS, Cleary MA, Chau BN. Coordinated regulation of cell cycle transcripts by p53-Inducible microRNAs, miR-192 and miR-215. Cancer Res 2009; 68:10105-12. [PMID: 19074876 DOI: 10.1158/0008-5472.can-08-1846] [Citation(s) in RCA: 273] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cell cycle arrest in response to DNA damage is an important antitumorigenic mechanism. MicroRNAs (miRNAs) were recently shown to play key regulatory roles in cell cycle progression. For example, miR-34a is induced in response to p53 activation and mediates G(1) arrest by down-regulating multiple cell cycle-related transcripts. Here we show that genotoxic stress promotes the p53-dependent up-regulation of the homologous miRNAs miR-192 and miR-215. Like miR-34a, activation of miR-192/215 induces cell cycle arrest, suggesting that multiple miRNA families operate in the p53 network. Furthermore, we define a downstream gene expression signature for miR-192/215 expression, which includes a number of transcripts that regulate G(1) and G(2) checkpoints. Of these transcripts, 18 transcripts are direct targets of miR-192/215, and the observed cell cycle arrest likely results from a cooperative effect among the modulations of these genes by the miRNAs. Our results showing a role for miR-192/215 in cell proliferation combined with recent observations that these miRNAs are underexpressed in primary cancers support the idea that miR-192 and miR-215 function as tumor suppressors.
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Affiliation(s)
- Sara A Georges
- Rosetta Inpharmatics LLC, Seattle, Washington WA 98109, USA.
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5
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Kumar A, Seringhaus M, Biery MC, Sarnovsky RJ, Umansky L, Piccirillo S, Heidtman M, Cheung KH, Dobry CJ, Gerstein MB, Craig NL, Snyder M. Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Res 2004; 14:1975-86. [PMID: 15466296 PMCID: PMC524422 DOI: 10.1101/gr.2875304] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We present here an unbiased and extremely versatile insertional library of yeast genomic DNA generated by in vitro mutagenesis with a multipurpose element derived from the bacterial transposon Tn7. This mini-Tn7 element has been engineered such that a single insertion can be used to generate a lacZ fusion, gene disruption, and epitope-tagged gene product. Using this transposon, we generated a plasmid-based library of approximately 300,000 mutant alleles; by high-throughput screening in yeast, we identified and sequenced 9032 insertions affecting 2613 genes (45% of the genome). From analysis of 7176 insertions, we found little bias in Tn7 target-site selection in vitro. In contrast, we also sequenced 10,174 Tn3 insertions and found a markedly stronger preference for an AT-rich 5-base pair target sequence. We further screened 1327 insertion alleles in yeast for hypersensitivity to the chemotherapeutic cisplatin. Fifty-one genes were identified, including four functionally uncharacterized genes and 25 genes involved in DNA repair, replication, transcription, and chromatin structure. In total, the collection reported here constitutes the largest plasmid-based set of sequenced yeast mutant alleles to date and, as such, should be singularly useful for gene and genome-wide functional analysis.
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Affiliation(s)
- Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
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6
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Castano I, Kaur R, Pan S, Cregg R, Penas ADL, Guo N, Biery MC, Craig NL, Cormack BP. Tn7-based genome-wide random insertional mutagenesis of Candida glabrata. Genome Res 2003; 13:905-15. [PMID: 12695329 PMCID: PMC430877 DOI: 10.1101/gr.848203] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [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: 11/24/2022]
Abstract
We describe and characterize a method for insertional mutagenesis of the yeast pathogen Candida glabrata using the bacterial transposon Tn7. Tn7 was used to mutagenize a C. glabrata genomic fosmid library. Pools of random Tn7 insertions in individual fosmids were recovered by transformation into Escherichia coli. Subsequently, these were introduced by recombination into the C. glabrata genome. We found that C. glabrata genomic fragments carrying a Tn7 insertion could integrate into the genome by nonhomologous recombination, by single crossover (generating a duplication of the insertionally mutagenized locus), and by double crossover, yielding an allele replacement. We were able to generate a highly representative set of approximately 10(4) allele replacements in C. glabrata, and an initial characterization of these shows that a wide diversity of genes were targeted in the mutagenesis. Because the identity of disrupted genes for any mutant of interest can be rapidly identified, this method should be of general utility in functional genomic characterization of this important yeast pathogen. In addition, the method might be broadly applicable to mutational analysis of other organisms.
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Affiliation(s)
- Irene Castano
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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7
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Affiliation(s)
- Nurjana Bachman
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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8
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Biery MC, Lopata M, Craig NL. A minimal system for Tn7 transposition: the transposon-encoded proteins TnsA and TnsB can execute DNA breakage and joining reactions that generate circularized Tn7 species. J Mol Biol 2000; 297:25-37. [PMID: 10704304 DOI: 10.1006/jmbi.2000.3558] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the presence of ATP and Mg(2+), the bacterial transposon Tn7 translocates via a cut and paste mechanism executed by the transposon-encoded proteins TnsA+TnsB+TnsC+TnsD. We report here that in the presence of Mn(2+), TnsA+TnsB alone can execute the DNA breakage and joining reactions of Tn7 recombination. ATP is not essential in this minimal system, revealing that this cofactor is not directly involved in the chemical steps of recombination. In both the TnsAB and TnsABC+D systems, recombination initiates with double-strand breaks at each transposon end that cut Tn7 away from flanking donor DNA. In the minimal system, breakage occurs predominantly at a single transposon end and the subsequent end-joining reactions are intramolecular, with the exposed 3' termini of a broken transposon end joining near the other end of the Tn7 element in the same donor molecule to form circular transposon species. In contrast, in TnsABC+D recombination, breaks occur at both ends of Tn7 and the two ends join to a target site on a different DNA molecule to form an intermolecular simple insertion. This demonstration of the capacity of TnsAB to execute breakage and joining reactions supports the view that these proteins form the Tn7 transposase.
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MESH Headings
- Bacterial Proteins/metabolism
- Base Sequence
- Cations, Divalent/pharmacology
- DNA Probes
- DNA Transposable Elements/genetics
- DNA Transposable Elements/physiology
- DNA, Circular/genetics
- DNA, Circular/isolation & purification
- DNA, Circular/metabolism
- DNA, Circular/ultrastructure
- DNA, Superhelical/genetics
- DNA, Superhelical/isolation & purification
- DNA, Superhelical/metabolism
- DNA, Superhelical/ultrastructure
- DNA-Binding Proteins/metabolism
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Escherichia coli Proteins
- Manganese/pharmacology
- Microscopy, Electron
- Molecular Weight
- Mutation/drug effects
- Mutation/genetics
- Nucleic Acid Conformation
- Nucleotides/genetics
- Recombination, Genetic/drug effects
- Recombination, Genetic/genetics
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Affiliation(s)
- M C Biery
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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9
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Biery MC, Stewart FJ, Stellwagen AE, Raleigh EA, Craig NL. A simple in vitro Tn7-based transposition system with low target site selectivity for genome and gene analysis. Nucleic Acids Res 2000; 28:1067-77. [PMID: 10666445 PMCID: PMC102592 DOI: 10.1093/nar/28.5.1067] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.0] [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: 11/13/2022] Open
Abstract
A robust Tn7-based in vitro transposition system is described that displays little target site selectivity, allowing the efficient recovery of many different transposon insertions in target DNAs ranging from small plasmids to cosmids to whole genomes. Two miniTn7 derivatives are described that are useful for the analysis of genes: one a derivative for making translational and transcriptional target gene fusions and the other a derivative that can generate 15 bp (5 amino acid) insertions in target DNAs (proteins).
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Affiliation(s)
- M C Biery
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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10
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Abstract
The bacterial transposon Tn7 uses a cut and paste mechanism to translocate between non-homologous insertion sites. In the first step of recombination, double-strand breaks at each transposon end disconnect the element from the donor backbone; in the second step, the now exposed 3' transposon ends join to the target DNA. To dissect the chemical steps in these reactions, we have used mutant transposons altered at and near their extreme termini. We find that the initiating double-strand breaks result from a collaboration of two distinct DNA strand processing activities, one mediating cleavages at the 3' ends of Tn7, which can be blocked by changes at the transposon tips, and another mediating cleavages at the 5' ends. The joining of exposed 3'transposon ends to the target DNA can be blocked by changing the transposon tips. Our results suggest that the target joining step occurs through two usually concerted, but actually separable, reactions in which individual 3' transposon ends are joined to separate strands of the target DNA. Thus Tn7 transposition involves several distinct DNA processing reactions: strand cleavage and strand transfer reactions at the 3' ends of the transposon, and separate strand cleavage reactions at the 5' ends of the transposon.
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Affiliation(s)
- P A Gary
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, John Hopkins Universtiy School of Medicine, Baltimore, MD 21205, USA
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11
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Abstract
Escherichia coli cells deficient in RecA protein frequently contain an abnormal number of chromosomes after completion of ongoing rounds of DNA replication. This suggests that RecA protein may be required for correct timing of initiation of DNA replication; however, we show here that initiation of DNA replication is properly timed in recA mutants. We also find that more than 10% of recA mutant cells contain no DNA. These anucleate cells appear to arise from partitioning of all the DNA into one daughter cell and no DNA into the other daughter cell. Based on these and previously published results, we propose that RecA protein is required for equal partitioning of chromosomes into the two daughter cells.
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Affiliation(s)
- J W Zyskind
- Department of Biology, San Diego State University, California 92182
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