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Labora A, Creech A, Lee H, Tabornal E, Radu C, Donahue T. Establishing a mouse model of lung metastases using ultrasound-guided right heart ventricle injection. STAR Protoc 2023; 4:102698. [PMID: 37925631 PMCID: PMC10652205 DOI: 10.1016/j.xpro.2023.102698] [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] [Received: 06/18/2023] [Revised: 09/10/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023] Open
Abstract
We report a technique to generate a murine model of lung metastases by selectively injecting tumor cells into the right heart ventricle under ultrasound guidance. First, we describe cell preparation and reference animal preparation as previously described. We then detail the technique using a previously described 3D-printed instrument stabilization device. Finally, we describe tumor growth surveillance using bioluminescent imaging. For complete details on the use and execution of this protocol, please refer to Labora et al.1.
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Affiliation(s)
- Amanda Labora
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Amanda Creech
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hailey Lee
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Erin Tabornal
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Caius Radu
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy Donahue
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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2
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Labora A, Lee H, Chan C, Tabornal E, Le T, Rashid K, Abt E, Yamao T, Mandl H, Creech A, Premji A, Li L, Link J, Wu N, Radu C, Donahue T. Generation of liver metastases in a mouse model using ultrasound-guided intravenous injection. STAR Protoc 2023; 4:102163. [PMID: 36930646 PMCID: PMC10036864 DOI: 10.1016/j.xpro.2023.102163] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/25/2023] [Accepted: 02/15/2023] [Indexed: 03/18/2023] Open
Abstract
Here, we present a protocol to generate a murine model of liver metastasis by directly injecting tumor cells into the portal vein under ultrasound guidance. We describe steps for animal and cell preparation and two techniques for injecting tumor cells. One technique is freehand, while the other technique is device-assisted using a 3D-printed prototype device. Finally, we describe tumor surveillance with bioluminescent imaging.
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Affiliation(s)
- Amanda Labora
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Hailey Lee
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Charlotte Chan
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Erin Tabornal
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Thuc Le
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Khalid Rashid
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Evan Abt
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Takanobu Yamao
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hanna Mandl
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amanda Creech
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alykhan Premji
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Luyi Li
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jason Link
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nanping Wu
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Caius Radu
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy Donahue
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Ibarrola J, Kim SK, Lu Q, DuPont JJ, Creech A, Sun Z, Hill MA, Jaffe JD, Jaffe IZ. Smooth muscle mineralocorticoid receptor as an epigenetic regulator of vascular ageing. Cardiovasc Res 2023; 118:3386-3400. [PMID: 35020830 PMCID: PMC10060709 DOI: 10.1093/cvr/cvac007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/07/2022] [Indexed: 01/25/2023] Open
Abstract
AIMS Vascular stiffness increases with age and independently predicts cardiovascular disease risk. Epigenetic changes, including histone modifications, accumulate with age but the global pattern has not been elucidated nor are the regulators known. Smooth muscle cell-mineralocorticoid receptor (SMC-MR) contributes to vascular stiffness in ageing mice. Thus, we investigated the regulatory role of SMC-MR in vascular epigenetics and stiffness. METHODS AND RESULTS Mass spectrometry-based proteomic profiling of all histone modifications completely distinguished 3 from 12-month-old mouse aortas. Histone-H3 lysine-27 (H3K27) methylation (me) significantly decreased in ageing vessels and this was attenuated in SMC-MR-KO littermates. Immunoblotting revealed less H3K27-specific methyltransferase EZH2 with age in MR-intact but not SMC-MR-KO vessels. These ageing changes were examined in primary human aortic (HA)SMC from adult vs. aged donors. MR, H3K27 acetylation (ac), and stiffness gene (connective tissue growth factor, integrin-α5) expression significantly increased, while H3K27me and EZH2 decreased, with age. MR inhibition reversed these ageing changes in HASMC and the decline in stiffness genes was prevented by EZH2 blockade. Atomic force microscopy revealed that MR antagonism decreased intrinsic stiffness and the probability of fibronectin adhesion of aged HASMC. Conversely, ageing induction in young HASMC with H2O2; increased MR, decreased EZH2, enriched H3K27ac and MR at stiffness gene promoters by chromatin immunoprecipitation, and increased stiffness gene expression. In 12-month-old mice, MR antagonism increased aortic EZH2 and H3K27 methylation, increased EZH2 recruitment and decreased H3K27ac at stiffness genes promoters, and prevented ageing-induced vascular stiffness and fibrosis. Finally, in human aortic tissue, age positively correlated with MR and stiffness gene expression and negatively correlated with H3K27me3 while MR and EZH2 are negatively correlated. CONCLUSION These data support a novel vascular ageing model with rising MR in human SMC suppressing EZH2 expression thereby decreasing H3K27me, promoting MR recruitment and H3K27ac at stiffness gene promoters to induce vascular stiffness and suggests new targets for ameliorating ageing-associated vascular disease.
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Affiliation(s)
- Jaime Ibarrola
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington Street, Box 80, Boston, MA 02111, USA
| | - Seung Kyum Kim
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington Street, Box 80, Boston, MA 02111, USA
- Department of Sports Science, Seoul National University of Science and Technology, 232 Gongneung-ro, Nowon-gu, 01811 Republic of Korea, Seoul, South Korea
| | - Qing Lu
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington Street, Box 80, Boston, MA 02111, USA
| | - Jennifer J DuPont
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington Street, Box 80, Boston, MA 02111, USA
| | - Amanda Creech
- Broad Institute, Proteomics Platform, Cambridge, MA 02142, USA
| | - Zhe Sun
- Department of Medical Pharmacology and Physiology, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65203, USA
| | - Michael A Hill
- Department of Medical Pharmacology and Physiology, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65203, USA
| | - Jacob D Jaffe
- Broad Institute, Proteomics Platform, Cambridge, MA 02142, USA
| | - Iris Z Jaffe
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington Street, Box 80, Boston, MA 02111, USA
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4
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Bandopadhayay P, Piccioni F, O'Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, Pages M, Balboni Iniguez A, Paolella BR, Meng A, Sinai C, Roti G, Dharia NV, Creech A, Tanenbaum B, Khadka P, Tracy A, Tiv HL, Hong AL, Coy S, Rashid R, Lin JR, Cowley GS, Lam FC, Goodale A, Lee Y, Schoolcraft K, Vazquez F, Hahn WC, Tsherniak A, Bradner JE, Yaffe MB, Milde T, Pfister SM, Qi J, Schenone M, Carr SA, Ligon KL, Kieran MW, Santagata S, Olson JM, Gokhale PC, Jaffe JD, Root DE, Stegmaier K, Johannessen CM, Beroukhim R. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun 2019; 10:2400. [PMID: 31160565 PMCID: PMC6546744 DOI: 10.1038/s41467-019-10307-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 10/19/2018] [Accepted: 04/25/2019] [Indexed: 12/26/2022] Open
Abstract
BET-bromodomain inhibition (BETi) has shown pre-clinical promise for MYC-amplified medulloblastoma. However, the mechanisms for its action, and ultimately for resistance, have not been fully defined. Here, using a combination of expression profiling, genome-scale CRISPR/Cas9-mediated loss of function and ORF/cDNA driven rescue screens, and cell-based models of spontaneous resistance, we identify bHLH/homeobox transcription factors and cell-cycle regulators as key genes mediating BETi's response and resistance. Cells that acquire drug tolerance exhibit a more neuronally differentiated cell-state and expression of lineage-specific bHLH/homeobox transcription factors. However, they do not terminally differentiate, maintain expression of CCND2, and continue to cycle through S-phase. Moreover, CDK4/CDK6 inhibition delays acquisition of resistance. Therefore, our data provide insights about the mechanisms underlying BETi effects and the appearance of resistance and support the therapeutic use of combined cell-cycle inhibitors with BETi in MYC-amplified medulloblastoma.
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Affiliation(s)
- Pratiti Bandopadhayay
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | - Ryan O'Rourke
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Patricia Ho
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Elizabeth M Gonzalez
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Graham Buchan
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Kenin Qian
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Gabrielle Gionet
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Emily Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Margo Coxon
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | | | - Lisa Brenan
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Frank Dubois
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Ofer Shapira
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Noah F Greenwald
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, USA
| | - Melanie Pages
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Amanda Balboni Iniguez
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Brenton R Paolella
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Alice Meng
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Claire Sinai
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Giovanni Roti
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine and Surgery, Hematology and BMT, University of Parma, Parma, Italy
| | - Neekesh V Dharia
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | | | - Prasidda Khadka
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Adam Tracy
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Hong L Tiv
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Boston, USA
| | - Andrew L Hong
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Shannon Coy
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - Rumana Rashid
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, USA
| | - Glenn S Cowley
- Broad Institute of MIT and Harvard, Cambridge, USA
- Discovery Science, Janssen Research and Development (Johnson & Johnson), Spring House, PA, USA
| | - Fred C Lam
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Yenarae Lee
- Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
| | | | - James E Bradner
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Michael B Yaffe
- Broad Institute of MIT and Harvard, Cambridge, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Center for Child and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jun Qi
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pathology, Boston Children's Hospital, Boston, USA
| | - Mark W Kieran
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Sandro Santagata
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Prafulla C Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Boston, USA
| | | | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Kimberly Stegmaier
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | - Rameen Beroukhim
- Broad Institute of MIT and Harvard, Cambridge, USA.
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA.
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA.
- Department of Medicine, Harvard Medical School, Boston, USA.
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5
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Chakraborty AA, Nakamura E, Qi J, Creech A, Jaffe JD, Paulk J, Novak JS, Nagulapalli K, McBrayer SK, Cowley GS, Pineda J, Song J, Wang YE, Carr SA, Root DE, Signoretti S, Bradner JE, Kaelin WG. HIF activation causes synthetic lethality between the VHL tumor suppressor and the EZH1 histone methyltransferase. Sci Transl Med 2017; 9:eaal5272. [PMID: 28701475 PMCID: PMC6039096 DOI: 10.1126/scitranslmed.aal5272] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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] [Received: 12/05/2016] [Accepted: 06/10/2017] [Indexed: 12/13/2022]
Abstract
Inactivation of the von Hippel-Lindau tumor suppressor protein (pVHL) is the signature lesion in the most common form of kidney cancer, clear cell renal cell carcinoma (ccRCC). pVHL loss causes the transcriptional activation of hypoxia-inducible factor (HIF) target genes, including many genes that encode histone lysine demethylases. Moreover, chromatin regulators are frequently mutated in this disease. We found that ccRCC displays increased H3K27 acetylation and a shift toward mono- or unmethylated H3K27 caused by an HIF-dependent increase in H3K27 demethylase activity. Using a focused short hairpin RNA library, as well as CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) and a pharmacological inhibitor, we discovered that pVHL-defective ccRCC cells are hyperdependent on the H3K27 methyltransferase EZH1 for survival. Therefore, targeting EZH1 could be therapeutically useful in ccRCC.
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Affiliation(s)
- Abhishek A Chakraborty
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Eijiro Nakamura
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Amanda Creech
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jacob D Jaffe
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Jesse S Novak
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kshithija Nagulapalli
- Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Samuel K McBrayer
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Glenn S Cowley
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Javier Pineda
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Jiaxi Song
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yaoyu E Wang
- Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Steven A Carr
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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6
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Sholder G, Creech A, Loechler EL. How Y-Family DNA polymerase IV is more accurate than Dpo4 at dCTP insertion opposite an N2-dG adduct of benzo[a]pyrene. DNA Repair (Amst) 2015; 35:144-53. [PMID: 26523515 DOI: 10.1016/j.dnarep.2015.09.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/11/2015] [Accepted: 09/11/2015] [Indexed: 12/11/2022]
Abstract
To bypass DNA damage, cells have Y-Family DNA polymerases (DNAPs). One Y-Family-class includes DNAP κ and DNAP IV, which accurately insert dCTP opposite N(2)-dG adducts, including from the carcinogen benzo[a]pyrene (BP). Another class includes DNAP η and DNAP V, which insert accurately opposite UV-damage, but inaccurately opposite BP-N(2)-dG. To investigate structural differences between Y-Family-classes, regions are swapped between DNAP IV (a κ/IV-class-member) and Dpo4 (a η/V-class-member); the kinetic consequences are evaluated via primer-extension studies with a BP-N(2)-dG-containing template. Four key structural elements are revealed. (1) Y-Family DNAPs have discreet non-covalent contacts between their little finger-domain (LF-Domain) and their catalytic core-domain (CC-Domain), which we call "non-covalent bridges" (NCBs). Arg37 and Arg38 in DNAP IV's CC-Domain near the active site form a non-covalent bridge (AS-NCB) by interacting with Glu251 and Asp252, respectively, in DNAP IV's LF-Domain. Without these interactions dATP/dGTP/dTTP misinsertions increase. DNAP IV's AS-NCB suppresses misinsertions better than Dpo4's equivalent AS-NCB. (2) DNAP IV also suppresses dATP/dGTP/dTTP misinsertions via a second non-covalent bridge, which is ∼8Å from the active site (Distal-NCB). Dpo4 has no Distal-NCB, rendering it inferior at dATP/dGTP/dTTP suppression. (3) dCTP insertion is facilitated by the larger minor groove opening near the active site in DNAP IV versus Dpo4, which is sensible given that Watson/Crick-like [dCTP:BP-N(2)-dG] pairing requires the BP-moiety to be in the minor groove. (4) Compared to Dpo4, DNAP IV has a smaller major groove opening, which suppresses dGTP misinsertion, implying BP-N(2)-dG bulk in the major groove during Hoogsteen syn-adduct-dG:dGTP pairing. In summary, DNAP IV has a large minor groove opening to enhance dCTP insertion, a plugged major groove opening to suppress dGTP misinsertion, and two non-covalent bridges (near and distal to the active site) to suppress dATP/dGTP/dTTP misinsertions; collectively these four structural features enhance DNAP IV's dNTP insertion fidelity opposite a BP-N(2)-dG adduct compared to Dpo4.
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Affiliation(s)
- Gabriel Sholder
- Biology Department, Boston University, Boston, MA 02215, USA
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