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Zhang C, Yu M, Hepperla AJ, Zhang Z, Raj R, Zhong H, Zhou J, Hu L, Fang J, Liu H, Liang Q, Jia L, Liao C, Xi S, Simon JM, Xu K, Liu Z, Nam Y, Kapur P, Zhang Q. Von Hippel Lindau tumor suppressor controls m6A-dependent gene expression in renal tumorigenesis. J Clin Invest 2024; 134:e175703. [PMID: 38618952 PMCID: PMC11014668 DOI: 10.1172/jci175703] [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: 09/11/2023] [Accepted: 03/01/2024] [Indexed: 04/16/2024] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant posttranscriptional modification, and its contribution to cancer evolution has recently been appreciated. Renal cancer is the most common adult genitourinary cancer, approximately 85% of which is accounted for by the clear cell renal cell carcinoma (ccRCC) subtype characterized by VHL loss. However, it is unclear whether VHL loss in ccRCC affects m6A patterns. In this study, we demonstrate that VHL binds and promotes METTL3/METTL14 complex formation while VHL depletion suppresses m6A modification, which is distinctive from its canonical E3 ligase role. m6A RNA immunoprecipitation sequencing (RIP-Seq) coupled with RNA-Seq allows us to identify a selection of genes whose expression may be regulated by VHL-m6A signaling. Specifically, PIK3R3 is identified to be a critical gene whose mRNA stability is regulated by VHL in a m6A-dependent but HIF-independent manner. Functionally, PIK3R3 depletion promotes renal cancer cell growth and orthotopic tumor growth while its overexpression leads to decreased tumorigenesis. Mechanistically, the VHL-m6A-regulated PIK3R3 suppresses tumor growth by restraining PI3K/AKT activity. Taken together, we propose a mechanism by which VHL regulates m6A through modulation of METTL3/METTL14 complex formation, thereby promoting PIK3R3 mRNA stability and protein levels that are critical for regulating ccRCC tumorigenesis.
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Affiliation(s)
- Cheng Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Miaomiao Yu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Austin J. Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Department of Genetics, Neuroscience Center and
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, UNC, Chapel Hill, North Carolina, USA
| | - Zhao Zhang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Rishi Raj
- Department of Biochemistry, Department of Biophysics, Simmons Comprehensive Cancer Center and
| | - Hua Zhong
- Department of Pathology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jin Zhou
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lianxin Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jun Fang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Hongyi Liu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Qian Liang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Liwei Jia
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sichuan Xi
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeremy M. Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Department of Genetics, Neuroscience Center and
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, UNC, Chapel Hill, North Carolina, USA
| | - Kexin Xu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Yunsun Nam
- Department of Biochemistry, Department of Biophysics, Simmons Comprehensive Cancer Center and
| | - Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, Department of Urology
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Blanchard MW, Sigmon JS, Brennan J, Ahulamibe C, Allen ME, Baric RS, Bell TA, Farrington J, Ciavatta D, Cruz Cisneros M, Drushal M, Ferris MT, Fry R, Gaines C, Gu B, Heise MT, Hodges RA, Kafri T, Lynch R, Magnuson T, Miller D, Murphy CEY, Nguyen DT, Noll KE, Proulx M, Sassetti C, Shaw GD, Simon JM, Smith C, Styblo M, Tarantino L, Woo J, Pardo Manuel de Villena F. The Updated Mouse Universal Genotyping Array Bioinformatic Pipeline Improves Genetic QC in Laboratory Mice. bioRxiv 2024:2024.02.29.582794. [PMID: 38464063 PMCID: PMC10925293 DOI: 10.1101/2024.02.29.582794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The MiniMUGA genotyping array is a popular tool for genetic QC of laboratory mice and genotyping of samples from most types of experimental crosses involving laboratory strains, particularly for reduced complexity crosses. The content of the production version of the MiniMUGA array is fixed; however, there is the opportunity to improve array's performance and the associated report's usefulness by leveraging thousands of samples genotyped since the initial description of MiniMUGA in 2020. Here we report our efforts to update and improve marker annotation, increase the number and the reliability of the consensus genotypes for inbred strains and increase the number of constructs that can reliably be detected with MiniMUGA. In addition, we have implemented key changes in the informatics pipeline to identify and quantify the contribution of specific genetic backgrounds to the makeup of a given sample, remove arbitrary thresholds, include the Y Chromosome and mitochondrial genome in the ideogram, and improve robust detection of the presence of commercially available substrains based on diagnostic alleles. Finally, we have made changes to the layout of the report, to simplify the interpretation and completeness of the analysis and added a table summarizing the ideogram. We believe that these changes will be of general interest to the mouse research community and will be instrumental in our goal of improving the rigor and reproducibility of mouse-based biomedical research.
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Souroullas GP, Jeck WR, Parker JS, Simon JM, Liu JY, Paulk J, Xiong J, Clark KS, Fedoriw Y, Qi J, Burd CE, Bradner JE, Sharpless NE. Author Correction: An oncogenic Ezh2 mutation induces tumors through global redistribution of histone 3 lysine 27 trimethylation. Nat Med 2024:10.1038/s41591-024-02867-1. [PMID: 38383796 DOI: 10.1038/s41591-024-02867-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Affiliation(s)
- George P Souroullas
- Department of Genetics, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - William R Jeck
- Department of Genetics, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jeremy M Simon
- Department of Genetics, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jie-Yu Liu
- Department of Genetics, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jessie Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Kelly S Clark
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Yuri Fedoriw
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Christin E Burd
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio, USA
- Department of Molecular Virology, Immunology and Medical Genetics, Ohio State University, Columbus, Ohio, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Norman E Sharpless
- Department of Genetics, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
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4
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Williams BN, Draper A, Lang PF, Lewis TR, Smith AL, Mayerl SJ, Rougié M, Simon JM, Arshavsky VY, Greenwald SH, Gamm DM, Pinilla I, Philpot BD. Heterogeneity in the progression of retinal pathologies in mice harboring patient mimicking Impg2 mutations. Hum Mol Genet 2024; 33:448-464. [PMID: 37975905 PMCID: PMC10877459 DOI: 10.1093/hmg/ddad199] [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: 06/02/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
Biallelic mutations in interphotoreceptor matrix proteoglycan 2 (IMPG2) in humans cause retinitis pigmentosa (RP) with early macular involvement, albeit the disease progression varies widely due to genetic heterogeneity and IMPG2 mutation type. There are currently no treatments for IMPG2-RP. To aid preclinical studies toward eventual treatments, there is a need to better understand the progression of disease pathology in appropriate animal models. Toward this goal, we developed mouse models with patient mimicking homozygous frameshift (T807Ter) or missense (Y250C) Impg2 mutations, as well as mice with a homozygous frameshift mutation (Q244Ter) designed to completely prevent IMPG2 protein expression, and characterized the trajectory of their retinal pathologies across postnatal development until late adulthood. We found that the Impg2T807Ter/T807Ter and Impg2Q244Ter/Q244Ter mice exhibited early onset gliosis, impaired photoreceptor outer segment maintenance, appearance of subretinal deposits near the optic disc, disruption of the outer retina, and neurosensorial detachment, whereas the Impg2Y250C/Y250C mice exhibited minimal retinal pathology. These results demonstrate the importance of mutation type in disease progression in IMPG2-RP and provide a toolkit and preclinical data for advancing therapeutic approaches.
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Affiliation(s)
- Brittany N Williams
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Adam Draper
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Patrick F Lang
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Tylor R Lewis
- Department of Ophthalmology, Duke University, Durham, NC 27705, United States
| | - Audrey L Smith
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Steven J Mayerl
- Department of Ophthalmology and Visual Sciences, McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Marie Rougié
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Jeremy M Simon
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University, Durham, NC 27705, United States
| | | | - David M Gamm
- Department of Ophthalmology and Visual Sciences, McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Isabel Pinilla
- Department of Ophthalmology, Lozano Blesa University Hospital, Zaragoza 50009, Spain
- Aragón Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
- Department of Surgery, University of Zaragoza, Zaragoza 50009, Spain
| | - Benjamin D Philpot
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, United States
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5
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Boschen KE, Dragicevich CJ, Fish EW, Hepperla AJ, Simon JM, Parnell SE. Gastrulation-stage alcohol exposure induces similar rates of craniofacial malformations in male and female C57BL/6J mice. Birth Defects Res 2024; 116:e2292. [PMID: 38116840 PMCID: PMC10872400 DOI: 10.1002/bdr2.2292] [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: 07/31/2023] [Revised: 11/18/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Prenatal alcohol exposure during gastrulation (embryonic day [E] 7 in mice, ~3rd week of human pregnancy) impairs eye, facial, and cortical development, recapitulating birth defects characteristic of Fetal Alcohol Syndrome (FAS). However, it is not known whether the prevalence or severity of craniofacial features associated with FAS is affected by biological sex. METHODS The current study administered either alcohol (2.9 g/kg, two i.p. doses, 4 hr apart) or vehicle to pregnant C57BL/6J females on E7, prior to gonadal sex differentiation, and assessed fetal morphology at E17. RESULTS Whereas sex did not affect fetal size in controls, alcohol-exposed females were smaller than both control females and alcohol-treated males. Alcohol exposure increased the incidence of eye defects to a similar degree in males and females. Together, these data suggest that females might be more sensitive to the general developmental effects of alcohol, but not effects specific to the craniofacies. Whole transcriptomic analysis of untreated E7 embryos found 214 differentially expressed genes in females vs. males, including those in pathways related to cilia and mitochondria, histone demethylase activity, and pluripotency. CONCLUSION Gastrulation-stage alcohol induces craniofacial malformations in male and female mouse fetuses at similar rates and severity, though growth deficits are more prevalent females. These findings support the investigation of biological sex as a contributing factor in prenatal alcohol studies.
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Affiliation(s)
- Karen E. Boschen
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Constance J. Dragicevich
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eric W. Fish
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Austin J. Hepperla
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy M. Simon
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott E. Parnell
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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6
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Peterson JJ, Lewis CA, Burgos SD, Manickam A, Xu Y, Rowley AA, Clutton G, Richardson B, Zou F, Simon JM, Margolis DM, Goonetilleke N, Browne EP. A histone deacetylase network regulates epigenetic reprogramming and viral silencing in HIV-infected cells. Cell Chem Biol 2023; 30:1617-1633.e9. [PMID: 38134881 PMCID: PMC10754471 DOI: 10.1016/j.chembiol.2023.11.009] [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: 05/16/2022] [Revised: 08/23/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023]
Abstract
A long-lived latent reservoir of HIV-1-infected CD4 T cells persists with antiretroviral therapy and prevents cure. We report that the emergence of latently infected primary CD4 T cells requires the activity of histone deacetylase enzymes HDAC1/2 and HDAC3. Data from targeted HDAC molecules, an HDAC3-directed PROTAC, and CRISPR-Cas9 knockout experiments converge on a model where either HDAC1/2 or HDAC3 targeting can prevent latency, whereas all three enzymes must be targeted to achieve latency reversal. Furthermore, HDACi treatment targets features of memory T cells that are linked to proviral latency and persistence. Latency prevention is associated with increased H3K9ac at the proviral LTR promoter region and decreased H3K9me3, suggesting that this epigenetic switch is a key proviral silencing mechanism that depends on HDAC activity. These findings support further mechanistic work on latency initiation and eventual clinical studies of HDAC inhibitors to interfere with latency initiation.
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Affiliation(s)
- Jackson J Peterson
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Catherine A Lewis
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Samuel D Burgos
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Ashokkumar Manickam
- University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Yinyan Xu
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Allison A Rowley
- University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Genevieve Clutton
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Brian Richardson
- Department of Biostatistics, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Fei Zou
- Department of Biostatistics, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Jeremy M Simon
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC 27514, USA; UNC Neuroscience Center, UNC School of Medicine, Chapel Hill, NC 27514, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - David M Margolis
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA; Department of Medicine, UNC School of Medicine, Chapel Hill, NC 27514, USA; Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC 27514, USA
| | - Nilu Goonetilleke
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA
| | - Edward P Browne
- Department of Microbiology and Immunology, University of North Carolina (UNC) School of Medicine, Chapel Hill, NC 27514, USA; University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, Chapel Hill, NC 27514, USA.
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7
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Necarsulmer JC, Simon JM, Evangelista BA, Chen Y, Tian X, Nafees S, Marquez AB, Jiang H, Wang P, Ajit D, Nikolova VD, Harper KM, Ezzell JA, Lin FC, Beltran AS, Moy SS, Cohen TJ. RNA-binding deficient TDP-43 drives cognitive decline in a mouse model of TDP-43 proteinopathy. eLife 2023; 12:RP85921. [PMID: 37819053 PMCID: PMC10567115 DOI: 10.7554/elife.85921] [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: 10/13/2023] Open
Abstract
TDP-43 proteinopathies including frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) are neurodegenerative disorders characterized by aggregation and mislocalization of the nucleic acid-binding protein TDP-43 and subsequent neuronal dysfunction. Here, we developed endogenous models of sporadic TDP-43 proteinopathy based on the principle that disease-associated TDP-43 acetylation at lysine 145 (K145) alters TDP-43 conformation, impairs RNA-binding capacity, and induces downstream mis-regulation of target genes. Expression of acetylation-mimic TDP-43K145Q resulted in stress-induced nuclear TDP-43 foci and loss of TDP-43 function in primary mouse and human-induced pluripotent stem cell (hiPSC)-derived cortical neurons. Mice harboring the TDP-43K145Q mutation recapitulated key hallmarks of FTLD, including progressive TDP-43 phosphorylation and insolubility, TDP-43 mis-localization, transcriptomic and splicing alterations, and cognitive dysfunction. Our study supports a model in which TDP-43 acetylation drives neuronal dysfunction and cognitive decline through aberrant splicing and transcription of critical genes that regulate synaptic plasticity and stress response signaling. The neurodegenerative cascade initiated by TDP-43 acetylation recapitulates many aspects of human FTLD and provides a new paradigm to further interrogate TDP-43 proteinopathies.
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Affiliation(s)
- Julie C Necarsulmer
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Jeremy M Simon
- UNC Neuroscience Center, University of North CarolinaChapel HillUnited States
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Genetics, University of North CarolinaChapel HillUnited States
| | - Baggio A Evangelista
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Youjun Chen
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Xu Tian
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Sara Nafees
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Ariana B Marquez
- Human Pluripotent Stem Cell Core, University of North CarolinaChapel HillUnited States
| | - Huijun Jiang
- Department of Biostatistics, University of North CarolinaChapel HillUnited States
| | - Ping Wang
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Deepa Ajit
- Department of Neurology, University of North CarolinaChapel HillUnited States
| | - Viktoriya D Nikolova
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - Kathryn M Harper
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - J Ashley Ezzell
- Department of Cell Biology & Physiology, Histology Research Core Facility, University of North CarolinaChapel HillUnited States
| | - Feng-Chang Lin
- Department of Biostatistics, University of North CarolinaChapel HillUnited States
| | - Adriana S Beltran
- Department of Genetics, University of North CarolinaChapel HillUnited States
- Human Pluripotent Stem Cell Core, University of North CarolinaChapel HillUnited States
- Department of Pharmacology, University of North CarolinaChapel HillUnited States
| | - Sheryl S Moy
- Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
- Department of Psychiatry, The University of North CarolinaChapel HillUnited States
| | - Todd J Cohen
- Department of Cell Biology and Physiology, University of North CarolinaChapel HillUnited States
- Department of Neurology, University of North CarolinaChapel HillUnited States
- UNC Neuroscience Center, University of North CarolinaChapel HillUnited States
- Department of Biochemistry and Biophysics, University of North CarolinaChapel HillUnited States
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8
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Baker BH, Zhang S, Simon JM, McLarnan SM, Chung WK, Pearson BL. Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders. Front Neurosci 2023; 17:1106573. [PMID: 37599994 PMCID: PMC10435087 DOI: 10.3389/fnins.2023.1106573] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction De novo mutations contribute to a large proportion of sporadic psychiatric and developmental disorders, yet the potential role of environmental carcinogens as drivers of causal de novo mutations in neurodevelopmental disorders is poorly studied. Methods To explore environmental mutation vulnerability of disease-associated gene sets, we analyzed publicly available whole genome sequencing datasets of mutations in human induced pluripotent stem cell clonal lines exposed to 12 classes of environmental carcinogens, and human lung cancers from individuals living in highly polluted regions. We compared observed rates of exposure-induced mutations in disease-related gene sets with the expected rates of mutations based on control genes randomly sampled from the genome using exact binomial tests. To explore the role of sequence characteristics in mutation vulnerability, we modeled the effects of sequence length, gene expression, and percent GC content on mutation rates of entire genes and gene coding sequences using multivariate Quasi-Poisson regressions. Results We demonstrate that several mutagens, including radiation and polycyclic aromatic hydrocarbons, disproportionately mutate genes related to neurodevelopmental disorders including autism spectrum disorders, schizophrenia, and attention deficit hyperactivity disorder. Other disease genes including amyotrophic lateral sclerosis, Alzheimer's disease, congenital heart disease, orofacial clefts, and coronary artery disease were generally not mutated more than expected. Longer sequence length was more strongly associated with elevated mutations in entire genes compared with mutations in coding sequences. Increased expression was associated with decreased coding sequence mutation rate, but not with the mutability of entire genes. Increased GC content was associated with increased coding sequence mutation rates but decreased mutation rates in entire genes. Discussion Our findings support the possibility that neurodevelopmental disorder genetic etiology is partially driven by a contribution of environment-induced germ line and somatic mutations.
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Affiliation(s)
- Brennan H. Baker
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Shaoyi Zhang
- Master of Public Health Program, Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Jeremy M. Simon
- Department of Genetics and Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sarah M. McLarnan
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Wendy K. Chung
- Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Brandon L. Pearson
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
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9
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Xing L, Simon JM, Ptacek TS, Yi JJ, Loo L, Mao H, Wolter JM, McCoy ES, Paranjape SR, Taylor-Blake B, Zylka MJ. Autism-linked UBE3A gain-of-function mutation causes interneuron and behavioral phenotypes when inherited maternally or paternally in mice. Cell Rep 2023; 42:112706. [PMID: 37389991 PMCID: PMC10530456 DOI: 10.1016/j.celrep.2023.112706] [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: 08/17/2022] [Revised: 04/15/2023] [Accepted: 06/12/2023] [Indexed: 07/02/2023] Open
Abstract
The E3 ubiquitin ligase Ube3a is biallelically expressed in neural progenitors and glial cells, suggesting that UBE3A gain-of-function mutations might cause neurodevelopmental disorders irrespective of parent of origin. Here, we engineered a mouse line that harbors an autism-linked UBE3AT485A (T503A in mouse) gain-of-function mutation and evaluated phenotypes in animals that inherited the mutant allele paternally, maternally, or from both parents. We find that paternally and maternally expressed UBE3AT503A results in elevated UBE3A activity in neural progenitors and glial cells. Expression of UBE3AT503A from the maternal allele, but not the paternal one, leads to a persistent elevation of UBE3A activity in neurons. Mutant mice display behavioral phenotypes that differ by parent of origin. Expression of UBE3AT503A, irrespective of its parent of origin, promotes transient embryonic expansion of Zcchc12 lineage interneurons. Phenotypes of Ube3aT503A mice are distinct from Angelman syndrome model mice. Our study has clinical implications for a growing number of disease-linked UBE3A gain-of-function mutations.
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Affiliation(s)
- Lei Xing
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Campus Box #7255, Chapel Hill, NC 27599, USA; Department of Genetics, The University of North Carolina at Chapel Hill, Campus Box #7264, Chapel Hill, NC 27599, USA
| | - Travis S Ptacek
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Campus Box #7255, Chapel Hill, NC 27599, USA
| | - Jason J Yi
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Campus Box #7255, Chapel Hill, NC 27599, USA
| | - Lipin Loo
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hanqian Mao
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Campus Box #7255, Chapel Hill, NC 27599, USA
| | - Justin M Wolter
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Campus Box #7255, Chapel Hill, NC 27599, USA; Department of Genetics, The University of North Carolina at Chapel Hill, Campus Box #7264, Chapel Hill, NC 27599, USA
| | - Eric S McCoy
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Smita R Paranjape
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bonnie Taylor-Blake
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark J Zylka
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Campus Box #7255, Chapel Hill, NC 27599, USA.
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10
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Dardis GJ, Wang J, Simon JM, Wang GG, Baldwin AS. An EZH2-NF-κB regulatory axis drives expression of pro-oncogenic gene signatures in triple negative breast cancer. iScience 2023; 26:107115. [PMID: 37416481 PMCID: PMC10319845 DOI: 10.1016/j.isci.2023.107115] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/10/2023] [Accepted: 06/09/2023] [Indexed: 07/08/2023] Open
Abstract
The histone methyltransferase EZH2 has been studied most extensively in the context of PRC2-dependent gene repression. Accumulating evidence indicates non-canonical functions for EZH2 in cancer contexts including promoting paradoxical gene expression through interactions with transcription factors, including NF-κB in triple negative breast cancer (TNBC). We profile EZH2 and NF-κB factor co-localization and positive gene regulation genome-wide, and define a subset of NF-κB targets and genes associated with oncogenic functions in TNBC that is enriched in patient datasets. We demonstrate interaction between EZH2 and RelA requiring the recently identified transactivation domain (TAD) which mediates EZH2 recruitment to, and activation of certain NF-κB-dependent genes, and supports downstream migration and stemness phenotypes in TNBC cells. Interestingly, EZH2-NF-κB positive regulation of genes and stemness does not require PRC2. This study provides new insight into pro-oncogenic regulatory functions for EZH2 in breast cancer through PRC2-independent, and NF-κB-dependent regulatory mechanisms.
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Affiliation(s)
- Gabrielle J. Dardis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jeremy M. Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Albert S. Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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11
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da Silva GCQ, Simon JM, Salazar JM. When less is more: does more Na +-cations mean more adsorption sites for toluene in faujasites? Phys Chem Chem Phys 2023; 25:8028-8042. [PMID: 36876505 DOI: 10.1039/d2cp04644j] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The unique properties of zeolites make them an interesting material to be used in separation processes. The possibility of tailoring some of their characteristics, like the Si/Al ratio, allows optimizing their synthesis for a given task. Concerning the adsorption of toluene by faujasites an understanding of the effect of cations is necessary to foster the elaboration of new materials, which can capture molecules with a high degree of selectivity and sensitivity. Undoubtedly, this knowledge is relevant for a wide range of applications going from the elaboration of technologies for improving the air-quality to diagnostic procedures to prevent health risks. The studies reported here using Grand Canonical Monte Carlo simulations elucidate the role of Na-cations in the adsorption of toluene by faujasites with different Si/Al ratios. They detail how the location of the cations inhibits or enhances the adsorption. The cations located at site II are shown to be those enhancing the adsorption of toluene on faujasites. Interestingly, the cations located at site III generate a hindrance at high loading. This becomes an impediment for the organization of toluene molecules inside faujasites.
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Affiliation(s)
- G C Q da Silva
- Laboratoire ICB UMR 6303, Université Bourgogne Franche-Comté, 21078 Dijon, France.
| | - J M Simon
- Laboratoire ICB UMR 6303, Université Bourgogne Franche-Comté, 21078 Dijon, France.
| | - J Marcos Salazar
- Laboratoire ICB UMR 6303, Université Bourgogne Franche-Comté, 21078 Dijon, France.
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12
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Salzler HR, Vandadi V, McMichael BD, Brown JC, Boerma SA, Leatham-Jensen MP, Adams KM, Meers MP, Simon JM, Duronio RJ, McKay DJ, Matera AG. Distinct roles for canonical and variant histone H3 lysine-36 in Polycomb silencing. Sci Adv 2023; 9:eadf2451. [PMID: 36857457 PMCID: PMC9977188 DOI: 10.1126/sciadv.adf2451] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/31/2023] [Indexed: 05/26/2023]
Abstract
Polycomb complexes regulate cell type-specific gene expression programs through heritable silencing of target genes. Trimethylation of histone H3 lysine 27 (H3K27me3) is essential for this process. Perturbation of H3K36 is thought to interfere with H3K27me3. We show that mutants of Drosophila replication-dependent (H3.2K36R) or replication-independent (H3.3K36R) histone H3 genes generally maintain Polycomb silencing and reach later stages of development. In contrast, combined (H3.3K36RH3.2K36R) mutants display widespread Hox gene misexpression and fail to develop past the first larval stage. Chromatin profiling revealed that the H3.2K36R mutation disrupts H3K27me3 levels broadly throughout silenced domains, whereas these regions are mostly unaffected in H3.3K36R animals. Analysis of H3.3 distributions showed that this histone is enriched at presumptive Polycomb response elements located outside of silenced domains but relatively depleted from those inside. We conclude that H3.2 and H3.3 K36 residues collaborate to repress Hox genes using different mechanisms.
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Affiliation(s)
- Harmony R. Salzler
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Vasudha Vandadi
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Benjamin D. McMichael
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - John C. Brown
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Sally A. Boerma
- Department of Biology, Carleton College, Northfield, MN, USA
| | - Mary P. Leatham-Jensen
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kirsten M. Adams
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Michael P. Meers
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeremy M. Simon
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Robert J. Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel J. McKay
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - A. Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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13
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Boschen KE, Steensen MC, Simon JM, Parnell SE. Short-term transcriptomic changes in the mouse neural tube induced by an acute alcohol exposure. Alcohol 2023; 106:1-9. [PMID: 36202274 DOI: 10.1016/j.alcohol.2022.09.001] [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: 04/01/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 01/28/2023]
Abstract
Alcohol exposure during the formation and closure of the neural tube, or neurulation (embryonic day [E] 8-10 in mice; ∼4th week of human pregnancy), perturbs development of midline brain structures and significantly disrupts gene expression in the rostroventral neural tube (RVNT). Previously, alcohol exposure during neurulation was found to alter gene pathways related to cell proliferation, p53 signaling, ribosome biogenesis, immune signaling, organogenesis, and cell migration 6 or 24 h after administration. Our current study expands upon this work by investigating short-term gene expression changes in the RVNT following a single binge-like alcohol exposure during neurulation. Female C57BL/6J mice were administered a single dose of 2.9 g/kg alcohol or vehicle on E9.0 to target mid-neurulation. The RVNTs of stage-matched embryos were collected 2 or 4 h after exposure and processed for RNA-seq. Functional profiling was performed with g:Profiler, as well as with the CiliaCarta and DisGeNet databases. Two hours following E9.0 alcohol exposure, 650 genes in the RVNT were differentially expressed. Functional enrichment analysis revealed that pathways related to cellular metabolism, gene expression, cell cycle, organogenesis, and Hedgehog signaling were down-regulated, and pathways related to cellular stress response, p53 signaling, and hypoxia were up-regulated by alcohol. Four hours after alcohol exposure, 225 genes were differentially expressed. Biological processes related to metabolism, RNA binding, ribosome biogenesis, and methylation were down-regulated, while protein localization and binding, autophagy, and intracellular signaling pathways were up-regulated. Two hours after alcohol exposure, the differentially expressed genes were associated with disease terms related to eye and craniofacial development and anoxia. These data provide further information regarding the biological functions targeted by alcohol exposure during neurulation in regions of the neural tube that give rise to alcohol-sensitive midline brain structures. Disruption of these gene pathways contributes to the craniofacial and brain malformations associated with prenatal alcohol exposure.
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Affiliation(s)
- Karen E Boschen
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Melina C Steensen
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeremy M Simon
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Scott E Parnell
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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14
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Zhu Z, Zhou X, Du H, Cloer EW, Zhang J, Mei L, Wang Y, Tan X, Hepperla AJ, Simon JM, Cook JG, Major MB, Dotti G, Liu P. STING Suppresses Mitochondrial VDAC2 to Govern RCC Growth Independent of Innate Immunity. Adv Sci (Weinh) 2023; 10:e2203718. [PMID: 36445063 PMCID: PMC9875608 DOI: 10.1002/advs.202203718] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/10/2022] [Indexed: 05/02/2023]
Abstract
STING is an innate immune sensor for immune surveillance of viral/bacterial infection and maintenance of an immune-friendly microenvironment to prevent tumorigenesis. However, if and how STING exerts innate immunity-independent function remains elusive. Here, the authors report that STING expression is increased in renal cell carcinoma (RCC) patients and governs tumor growth through non-canonical innate immune signaling involving mitochondrial ROS maintenance and calcium homeostasis. Mitochondrial voltage-dependent anion channel VDAC2 is identified as a new STING binding partner. STING depletion potentiates VDAC2/GRP75-mediated MERC (mitochondria-ER contact) formation to increase mitochondrial ROS/calcium levels, impairs mitochondria function, and suppresses mTORC1/S6K signaling leading to RCC growth retardation. STING interaction with VDAC2 occurs through STING-C88/C91 palmitoylation and inhibiting STING palmitoyl-transferases ZDHHCs by 2-BP significantly impedes RCC cell growth alone or in combination with sorafenib. Together, these studies reveal an innate immunity-independent function of STING in regulating mitochondrial function and growth in RCC, providing a rationale to target the STING/VDAC2 interaction in treating RCC.
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Affiliation(s)
- Zhichuan Zhu
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Xin Zhou
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Microbiology and ImmunologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Hongwei Du
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Microbiology and ImmunologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Erica W. Cloer
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Jiaming Zhang
- Department of Oral MedicineInfection and ImmunityHarvard School of Dental MedicineBostonMA02115USA
| | - Liu Mei
- Department of Biochemistry and BiophysicsThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Ying Wang
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Xianming Tan
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of BiostatisticsThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Austin J. Hepperla
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Carolina Institute for Developmental DisabilitiesThe University of North Carolina at Chapel HillChapel HillNC27599USA
- UNC Neuroscience CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Jeremy M. Simon
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Carolina Institute for Developmental DisabilitiesThe University of North Carolina at Chapel HillChapel HillNC27599USA
- UNC Neuroscience CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of GeneticsThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Jeanette Gowen Cook
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Michael B. Major
- Department of Cell Biology and PhysiologyDepartment of OtolaryngologyWashington University in St. LouisSt. LouisMO63130USA
| | - Gianpietro Dotti
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Microbiology and ImmunologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Pengda Liu
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsThe University of North Carolina at Chapel HillChapel HillNC27599USA
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15
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Fish EW, Mendoza-Romero HN, Love CA, Dragicevich CJ, Cannizzo MD, Boschen KE, Hepperla A, Simon JM, Parnell SE. The pro-apoptotic Bax gene modifies susceptibility to craniofacial dysmorphology following gastrulation-stage alcohol exposure. Birth Defects Res 2022; 114:1229-1243. [PMID: 35396933 PMCID: PMC10103739 DOI: 10.1002/bdr2.2009] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/11/2022] [Accepted: 03/23/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND During early development, alcohol exposure causes apoptotic cell death in discrete regions of the embryo which are associated with distinctive patterns of later-life abnormalities. In gastrulation, which occurs during the third week of human pregnancy, alcohol targets the ectoderm, the precursor of the eyes, face, and brain. This midline tissue loss leads to the craniofacial dysmorphologies, such as microphthalmia and a smooth philtrum, which define fetal alcohol syndrome (FAS). An important regulator of alcohol-induced cell death is the pro-apoptotic protein Bax. The current study determines if mice lacking the Bax gene are less susceptible to the pathogenic effects of gastrulation-stage alcohol exposure. METHODS Male and female Bax+/- mice mated to produce embryos with full (-/- ) or partial (+/- ) Bax deletions, or Bax+/+ wild-type controls. On Gestational Day 7 (GD 7), embryos received two alcohol (2.9 g/kg, 4 hr apart), or control exposures. A subset of embryos was collected 12 hr later and examined for the presence of apoptotic cell death, while others were examined on GD 17 for the presence of FAS-like facial features. RESULTS Full Bax deletion reduced embryonic apoptotic cell death and the incidence of fetal eye and face malformations, indicating that Bax normally facilitates the development of alcohol-induced defects. An RNA-seq analysis of GD 7 Bax+/+ and Bax-/- embryos revealed 63 differentially expressed genes, some of which may interact with the Bax deletion to further protect against apoptosis. CONCLUSIONS Overall, these experiments identify that Bax is a primary teratogenic mechanism of gastrulation-stage alcohol exposure.
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Affiliation(s)
- Eric W Fish
- Bowles Center for Alcohol Studies, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Haley N Mendoza-Romero
- Bowles Center for Alcohol Studies, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Charlotte A Love
- Bowles Center for Alcohol Studies, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Constance J Dragicevich
- Bowles Center for Alcohol Studies, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michael D Cannizzo
- Bowles Center for Alcohol Studies, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Karen E Boschen
- Bowles Center for Alcohol Studies, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Austin Hepperla
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, North Carolina, USA.,Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jeremy M Simon
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, North Carolina, USA.,Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Scott E Parnell
- Bowles Center for Alcohol Studies, University of North Carolina, Chapel Hill, North Carolina, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina, USA
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16
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Evin C, Eude Y, Jacob J, Jenny C, Bourdais R, Mathon B, Valery CA, Clausse E, Simon JM, Maingon P, Feuvret L. Hypofractionated postoperative stereotactic radiotherapy for large resected brain metastases. Cancer Radiother 2022; 27:87-95. [PMID: 36075831 DOI: 10.1016/j.canrad.2022.07.006] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/10/2022] [Accepted: 07/16/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE The aim of the present retrospective study was to report outcomes after hypofractionated stereotactic radiotherapy (HSRT) for resected brain metastases (BM). PATIENTS AND METHODS We reviewed results of patients with resected BM treated with postoperative HSRT (3×7.7Gy to the prescription isodose 70%) between May 2013 and June 2020. Local control (LC), distant brain control (DBC), overall survival (OS), leptomeningeal disease relapse (LMDR), and radiation necrosis (RN) occurrence were reported. RESULTS Twenty-two patients with 23 brain cavities were included. Karnofsky Performance status (KPS) was≥70 in 77.3%. Median preoperative diameter was 37mm [21.0-75.0] and median planning target volume (PTV) was 23 cm3 [9.9-61.6]. Median time from surgery to SRT was 69 days [7-101] and 48% of patients had a local relapse on pre-SRT imaging. Median follow-up was 17.5 months [1.6-95.9]. One and two-year LC rates were 60.9 and 52.2% respectively. One and 2-year DBC rates were 45.5 and 40.9%. Median OS was 16.5 months. Four patients (18.2%) presented LMDR during follow-up. RN occurred in 6 patients (27.2%). Three factors were associated with OS: ECOG-PS (P=0.009), KPS (P=0.04), and cystic metastasis before surgery (P=0.037). Several factors were related to RN occurrence: PTV diameter and volume, Normal brain V21, V21 and V24 isodoses volumes. CONCLUSION HSRT is the most widely used scheme for larger brain cavities after surgery. The optimal dose and scheme remain to be defined as well as the optimal delay between postoperative SRT and surgery. Dose escalation may be necessary, especially in case of subtotal resection.
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Affiliation(s)
- C Evin
- Service d'oncologie radiothérapie, hôpitaux universitaires Pitié-Salpêtrière - Charles-Foix, Assistance publique-Hôpitaux de Paris, 47-83, boulevard de l'Hôpital, 75651 Paris cedex 13, France.
| | - Y Eude
- Service d'ophtalmologie, Hôtel-Dieu, centre hospitalier universitaire de Nantes, 1, place Alexis-Ricordeau, 44000 Nantes France
| | - J Jacob
- Service d'oncologie radiothérapie, hôpitaux universitaires Pitié-Salpêtrière - Charles-Foix, Assistance publique-Hôpitaux de Paris, 47-83, boulevard de l'Hôpital, 75651 Paris cedex 13, France
| | - C Jenny
- Service d'oncologie radiothérapie, hôpitaux universitaires Pitié-Salpêtrière - Charles-Foix, Assistance publique-Hôpitaux de Paris, 47-83, boulevard de l'Hôpital, 75651 Paris cedex 13, France
| | - R Bourdais
- Service d'oncologie radiothérapie, hôpitaux universitaires Pitié-Salpêtrière - Charles-Foix, Assistance publique-Hôpitaux de Paris, 47-83, boulevard de l'Hôpital, 75651 Paris cedex 13, France
| | - B Mathon
- Service de neurochirurgie, groupe Pitié-Salpêtrière, Assistance publique-Hôpitaux de Paris, 47-83, boulevard de l'Hôpital, 75651 Paris cedex 13, France
| | - C A Valery
- Service de neurochirurgie, groupe Pitié-Salpêtrière, Assistance publique-Hôpitaux de Paris, 47-83, boulevard de l'Hôpital, 75651 Paris cedex 13, France
| | - E Clausse
- Service d'oncologie radiothérapie, hôpitaux universitaires Pitié-Salpêtrière - Charles-Foix, Assistance publique-Hôpitaux de Paris, 47-83, boulevard de l'Hôpital, 75651 Paris cedex 13, France
| | - J M Simon
- Service d'oncologie radiothérapie, hôpitaux universitaires Pitié-Salpêtrière - Charles-Foix, Assistance publique-Hôpitaux de Paris, 47-83, boulevard de l'Hôpital, 75651 Paris cedex 13, France
| | - P Maingon
- Service d'oncologie radiothérapie, hôpitaux universitaires Pitié-Salpêtrière - Charles-Foix, Assistance publique-Hôpitaux de Paris, 47-83, boulevard de l'Hôpital, 75651 Paris cedex 13, France
| | - L Feuvret
- Service d'oncologie radiothérapie, hôpitaux universitaires Pitié-Salpêtrière - Charles-Foix, Assistance publique-Hôpitaux de Paris, 47-83, boulevard de l'Hôpital, 75651 Paris cedex 13, France
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Hamad SH, Montgomery SA, Simon JM, Bowman BM, Spainhower KB, Murphy RM, Knudsen ES, Fenton SE, Randell SH, Holt JR, Hayes DN, Witkiewicz AK, Oliver TG, Major MB, Weissman BE. Correction: TP53, CDKN2A/P16, and NFE2L2/NRF2 regulate the incidence of pure- and combined-small cell lung cancer in mice. Oncogene 2022; 41:4485. [PMID: 36002660 DOI: 10.1038/s41388-022-02442-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Samera H Hamad
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Brittany M Bowman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Kyle B Spainhower
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Ryan M Murphy
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Erik S Knudsen
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Suzanne E Fenton
- Division of National Toxicology Program, NIEHS/NIH, Research Triangle Park, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jeremiah R Holt
- University of Tennessee Health Science Center for Cancer Research, Department of Medicine, Division of Hematology and Oncology, University of Tennessee, Memphis, TN, USA
| | - D Neil Hayes
- University of Tennessee Health Science Center for Cancer Research, Department of Medicine, Division of Hematology and Oncology, University of Tennessee, Memphis, TN, USA
| | | | - Trudy G Oliver
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - M Ben Major
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Bernard E Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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18
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Zhou J, Simon JM, Liao C, Zhang C, Hu L, Zurlo G, Liu X, Fan C, Hepperla A, Jia L, Tcheuyap VT, Zhong H, Elias R, Ye J, Henne WM, Kapur P, Nijhawan D, Brugarolas J, Zhang Q. An oncogenic JMJD6-DGAT1 axis tunes the epigenetic regulation of lipid droplet formation in clear cell renal cell carcinoma. Mol Cell 2022; 82:3030-3044.e8. [PMID: 35764091 PMCID: PMC9391320 DOI: 10.1016/j.molcel.2022.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 10/12/2021] [Revised: 03/15/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022]
Abstract
Characterized by intracellular lipid droplet accumulation, clear cell renal cell carcinoma (ccRCC) is resistant to cytotoxic chemotherapy and is a lethal disease. Through an unbiased siRNA screen of 2-oxoglutarate (2-OG)-dependent enzymes, which play a critical role in tumorigenesis, we identified Jumonji domain-containing 6 (JMJD6) as an essential gene for ccRCC tumor development. The downregulation of JMJD6 abolished ccRCC colony formation in vitro and inhibited orthotopic tumor growth in vivo. Integrated ChIP-seq and RNA-seq analyses uncovered diacylglycerol O-acyltransferase 1 (DGAT1) as a critical JMJD6 effector. Mechanistically, JMJD6 interacted with RBM39 and co-occupied DGAT1 gene promoter with H3K4me3 to induce DGAT1 expression. JMJD6 silencing reduced DGAT1, leading to decreased lipid droplet formation and tumorigenesis. The pharmacological inhibition (or depletion) of DGAT1 inhibited lipid droplet formation in vitro and ccRCC tumorigenesis in vivo. Thus, the JMJD6-DGAT1 axis represents a potential new therapeutic target for ccRCC.
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Affiliation(s)
- Jin Zhou
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Genetics, Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cheng Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lianxin Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Giada Zurlo
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xijuan Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Austin Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Genetics, Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Liwei Jia
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vanina Toffessi Tcheuyap
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hua Zhong
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Roy Elias
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jin Ye
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Mike Henne
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Deepak Nijhawan
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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19
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Hamad S, Montgomery SA, Simon JM, Bowman BM, Spainhower KB, Murphy RM, Witkiewicz A, Fenton SE, Randell SH, Hayes N, Knudsen E, Oliver TG, Major B, Weissman BE. Abstract 921: The Nrf2E79Q activating mutation accelerates growth of pure-small cell lung cancer but not combined small cell lung cancer Tp53floxed/floxed/Cdkn2afloxed/floxed mice. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
Inactivating mutations in TP53/P16 are found in most types of non-small cell lung cancer while RB1/P16 losspredominates in small cell lung cancer (SCLC). NRF2 activating mutations are also found frequently in lungcancer, especially in lung squamous cell carcinoma. However, how concurrent mutations in these genes maycontribute to lung cancer development is not fully understood. To address this problem, we compared lung tumordevelopment in a genetically-engineered mouse model (GEMM) with dual Trp53/p16 deficiency, +/- expressionof one of the most common mutations in NRF2 found in human tumors, Nrf2E79Q/+. Surprisingly, both groups,Nrf2E79Q/+ and Nrf2+/+, developed combined-SCLC (C-SCLC): a mixture of SCLC and large cell neuroendocrine(NE) carcinoma along with pure-SCLC (P-SCLC). The appearance of C-SCLC implicates Trp53/p16 double lossin the development of this type of lung cancer. Both groups developed C-SCLC at the same penetrance andincidence; all tumors labeled positive for NE-markers by immunohistochemistry (IHC) including ASCL1, SYP andINSM1. However, C-SCLCs developed by Nrf2E79Q/+ mice did not show NRF2 labeling by IHC, despiterecombination of the Nrf2E79Q/+ allele. In contrast, the Nrf2E79Q/+ mice showed significantly higher incidence of P-SCLC compared to Nrf2+/+ mice. All P-SCLC from Nrf2E79Q/+ mice were NRF2-positive by IHC, while the fewtumors developed by Nrf2+/+ mice were negative. All P-SCLC lesions labeled positive for NE-markers includingASCL1, CGRP & SYP. Both C-SCLCs & P-SCLCs were positive for NKX1.2 (lung cancer-marker) and negativefor P63 (squamous cell-marker). Interestingly, phospho-RB1 was positive for both C-SCLCs & P-SCLCs,suggesting the loss of p16 in our GEMM inactivates Rb1 through loss of inhibition of the cyclin dependent kinases4/6 (CDK4/6). This is the first study showing that the concurrent inactivation of Trp53/p16 in mice drivesdevelopment of C-SCLC. Our study also implicated activation of NRF2 signaling in the progression of SCLC.Our next studies will dissect the mechanisms by which NRF2 activation contributes to the development of SCLCdevelopment.
Citation Format: Samera Hamad, Stephanie A. Montgomery, Jeremy M. Simon, Brittany M. Bowman, Kyle B. Spainhower, Ryan M. Murphy, Agnieszka Witkiewicz, Suzanne E. Fenton, Scott H. Randell, Neil Hayes, Erik Knudsen, Trudy G. Oliver, Ben Major, Bernard E. Weissman. The Nrf2E79Q activating mutation accelerates growth of pure-small cell lung cancer but not combined small cell lung cancer Tp53floxed/floxed/Cdkn2afloxed/floxed mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 921.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Neil Hayes
- 7University of Tennessee Health Science Center for Cancer Research, Memphis, TN
| | - Erik Knudsen
- 4Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | - Ben Major
- 1UNC-Lineberger Cancer Center, Chapel Hill, NC
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20
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Hamad SH, Montgomery SA, Simon JM, Bowman BM, Spainhower KB, Murphy RM, Knudsen ES, Fenton SE, Randell SH, Holt JR, Hayes DN, Witkiewicz AK, Oliver TG, Major MB, Weissman BE. TP53, CDKN2A/P16, and NFE2L2/NRF2 regulate the incidence of pure- and combined-small cell lung cancer in mice. Oncogene 2022; 41:3423-3432. [PMID: 35577980 PMCID: PMC10039451 DOI: 10.1038/s41388-022-02348-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 06/07/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 12/11/2022]
Abstract
Studies have shown that Nrf2E79Q/+ is one of the most common mutations found in human tumors. To elucidate how this genetic change contributes to lung cancer, we compared lung tumor development in a genetically-engineered mouse model (GEMM) with dual Trp53/p16 loss, the most common mutations found in human lung tumors, in the presence or absence of Nrf2E79Q/+. Trp53/p16-deficient mice developed combined-small cell lung cancer (C-SCLC), a mixture of pure-SCLC (P-SCLC) and large cell neuroendocrine carcinoma. Mice possessing the LSL-Nrf2E79Q mutation showed no difference in the incidence or latency of C-SCLC compared with Nrf2+/+ mice. However, these tumors did not express NRF2 despite Cre-induced recombination of the LSL-Nrf2E79Q allele. Trp53/p16-deficient mice also developed P-SCLC, where activation of the NRF2E79Q mutation associated with a higher incidence of this tumor type. All C-SCLCs and P-SCLCs were positive for NE-markers, NKX1-2 (a lung cancer marker) and negative for P63 (a squamous cell marker), while only P-SCLC expressed NRF2 by immunohistochemistry. Analysis of a consensus NRF2 pathway signature in human NE+-lung tumors showed variable activation of NRF2 signaling. Our study characterizes the first GEMM that develops C-SCLC, a poorly-studied human cancer and implicates a role for NRF2 activation in SCLC development.
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Affiliation(s)
- Samera H Hamad
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Brittany M Bowman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Kyle B Spainhower
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Ryan M Murphy
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Erik S Knudsen
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Suzanne E Fenton
- Division of National Toxicology Program, NIEHS/NIH, Research Triangle Park, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jeremiah R Holt
- University of Tennessee Health Science Center for Cancer Research, Department of Medicine, Division of Hematology and Oncology, University of Tennessee, Memphis, TN, USA
| | - D Neil Hayes
- University of Tennessee Health Science Center for Cancer Research, Department of Medicine, Division of Hematology and Oncology, University of Tennessee, Memphis, TN, USA
| | | | - Trudy G Oliver
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - M Ben Major
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Bernard E Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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21
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Kim H, Gao EB, Draper A, Berens NC, Vihma H, Zhang X, Higashi-Howard A, Ritola KD, Simon JM, Kennedy AJ, Philpot BD. Rescue of behavioral and electrophysiological phenotypes in a Pitt-Hopkins syndrome mouse model by genetic restoration of Tcf4 expression. eLife 2022; 11:72290. [PMID: 35535852 PMCID: PMC9090324 DOI: 10.7554/elife.72290] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 07/18/2021] [Accepted: 04/19/2022] [Indexed: 12/14/2022] Open
Abstract
Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder caused by monoallelic mutation or deletion in the transcription factor 4 (TCF4) gene. Individuals with PTHS typically present in the first year of life with developmental delay and exhibit intellectual disability, lack of speech, and motor incoordination. There are no effective treatments available for PTHS, but the root cause of the disorder, TCF4 haploinsufficiency, suggests that it could be treated by normalizing TCF4 gene expression. Here, we performed proof-of-concept viral gene therapy experiments using a conditional Tcf4 mouse model of PTHS and found that postnatally reinstating Tcf4 expression in neurons improved anxiety-like behavior, activity levels, innate behaviors, and memory. Postnatal reinstatement also partially corrected EEG abnormalities, which we characterized here for the first time, and the expression of key TCF4-regulated genes. Our results support a genetic normalization approach as a treatment strategy for PTHS, and possibly other TCF4-linked disorders.
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Affiliation(s)
- Hyojin Kim
- Department of Cell Biology and Physiology, University of North Carolina at Chapel HillChapel HillUnited States
- Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
| | - Eric B Gao
- Department of Cell Biology and Physiology, University of North Carolina at Chapel HillChapel HillUnited States
- Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
| | - Adam Draper
- Department of Cell Biology and Physiology, University of North Carolina at Chapel HillChapel HillUnited States
- Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
| | - Noah C Berens
- Department of Biology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Hanna Vihma
- Department of Cell Biology and Physiology, University of North Carolina at Chapel HillChapel HillUnited States
- Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
| | - Xinyuan Zhang
- Department of Chemistry and Biochemistry, Bates CollegeLewistonUnited States
| | | | | | - Jeremy M Simon
- Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel HilChapel HillUnited States
| | - Andrew J Kennedy
- Department of Chemistry and Biochemistry, Bates CollegeLewistonUnited States
| | - Benjamin D Philpot
- Department of Cell Biology and Physiology, University of North Carolina at Chapel HillChapel HillUnited States
- Neuroscience Center, University of North Carolina at Chapel HillChapel HillUnited States
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel HilChapel HillUnited States
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22
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Lu D, Foley CA, Birla SV, Hepperla AJ, Simon JM, James LI, Hathaway NA. Bioorthogonal Chemical Epigenetic Modifiers Enable Dose-Dependent CRISPR Targeted Gene Activation in Mammalian Cells. ACS Synth Biol 2022; 11:1397-1407. [PMID: 35302756 PMCID: PMC9048219 DOI: 10.1021/acssynbio.1c00606] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CRISPR-Cas9 systems have been developed to regulate gene expression by using either fusions to epigenetic regulators or, more recently, through the use of chemically mediated strategies. These approaches have armed researchers with new tools to examine the function of proteins by intricately controlling expression levels of specific genes. Here we present a CRISPR-based chemical approach that uses a new chemical epigenetic modifier (CEM) to hone to a gene targeted with a catalytically inactive Cas9 (dCas9) bridged to an FK506-binding protein (FKBP) in mammalian cells. One arm of the bifunctional CEM recruits BRD4 to the target site, and the other arm is composed of a bumped ligand that binds to a mutant FKBP with a compensatory hole at F36V. This bump-and-hole strategy allows for activation of target genes in a dose-dependent and reversible fashion with increased specificity and high efficacy, providing a new synthetic biology approach to answer important mechanistic questions in the future.
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Affiliation(s)
- Dongbo Lu
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Caroline A. Foley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shama V. Birla
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Austin J. Hepperla
- Department of Genetics, UNC Neuroscience Center, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, United States
| | - Jeremy M. Simon
- Department of Genetics, UNC Neuroscience Center, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nathaniel A. Hathaway
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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23
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Hoffner O’Connor M, Berglind A, Kennedy Ng MM, Keith BP, Lynch ZJ, Schaner MR, Steinbach EC, Herzog J, Trad OK, Jeck WR, Arthur JC, Simon JM, Sartor RB, Furey TS, Sheikh SZ. BET Protein Inhibition Regulates Macrophage Chromatin Accessibility and Microbiota-Dependent Colitis. Front Immunol 2022; 13:856966. [PMID: 35401533 PMCID: PMC8988134 DOI: 10.3389/fimmu.2022.856966] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/16/2022] [Indexed: 01/14/2023] Open
Abstract
Introduction In colitis, macrophage functionality is altered compared to normal homeostatic conditions. Loss of IL-10 signaling results in an inappropriate chronic inflammatory response to bacterial stimulation. It remains unknown if inhibition of bromodomain and extra-terminal domain (BET) proteins alters usage of DNA regulatory elements responsible for driving inflammatory gene expression. We determined if the BET inhibitor, (+)-JQ1, could suppress inflammatory activation of macrophages in Il10-/- mice. Methods We performed ATAC-seq and RNA-seq on Il10-/- bone marrow-derived macrophages (BMDMs) cultured in the presence and absence of lipopolysaccharide (LPS) with and without treatment with (+)-JQ1 and evaluated changes in chromatin accessibility and gene expression. Germ-free Il10-/- mice were treated with (+)-JQ1, colonized with fecal slurries and underwent histological and molecular evaluation 14-days post colonization. Results Treatment with (+)-JQ1 suppressed LPS-induced changes in chromatin at distal regulatory elements associated with inflammatory genes, particularly in regions that contain motifs for AP-1 and IRF transcription factors. This resulted in attenuation of inflammatory gene expression. Treatment with (+)-JQ1 in vivo resulted in a mild reduction in colitis severity as compared with vehicle-treated mice. Conclusion We identified the mechanism of action associated with a new class of compounds that may mitigate aberrant macrophage responses to bacteria in colitis.
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Affiliation(s)
- Michelle Hoffner O’Connor
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ana Berglind
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Meaghan M. Kennedy Ng
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Benjamin P. Keith
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Zachary J. Lynch
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Matthew R. Schaner
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Erin C. Steinbach
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Medicine, Division of Rheumatology, Allergy, and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeremy Herzog
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Omar K. Trad
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - William R. Jeck
- Department of Pathology, Duke University, Durham, NC, United States
| | - Janelle C. Arthur
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeremy M. Simon
- Department of Genetics, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Carolina Institute for Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - R. Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Terrence S. Furey
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,*Correspondence: Terrence S. Furey, ; Shehzad Z. Sheikh,
| | - Shehzad Z. Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,*Correspondence: Terrence S. Furey, ; Shehzad Z. Sheikh,
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24
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Zhou M, Leung JY, Gessner KH, Hepperla AJ, Simon JM, Davis IJ, Kim WY. PBRM1 inactivation promotes upregulation of human endogenous retroviruses in a HIF-dependent manner. Cancer Immunol Res 2022; 10:285-290. [PMID: 35013001 DOI: 10.1158/2326-6066.cir-21-0480] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/05/2021] [Accepted: 01/05/2022] [Indexed: 11/16/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is considered an immunotherapy-responsive disease; however, the reasons for this remain unclear. Studies have variably implicated PBRM1 mutations as a predictive biomarker of immune checkpoint blockade (ICB) response, and separate studies demonstrate that expression of human endogenous retroviruses (hERVs) might be an important class of tumor-associated antigens. We sought to understand if specific mutations were associated with hERV expression. Two large, annotated genomic datasets, TCGA KIRC and IMmotion150, were used to correlate mutations and hERV expression. PBRM1 mutations were consistently associated with increased hERV expression in primary tumors. In vitro silencing of PBRM1, HIF1A and HIF2A followed by RNA-seq was performed in UMRC2 cells, confirming that PBRM1 regulates hERVs in a HIF1α- and HIF2α- dependent manner and that hERVs of the HERVERI superfamily are enriched in PBRM1-regulated hERVs. Our results uncover a role of PBRM1 in the negative regulation of hERVs in ccRCC. Moreover, the HIF-dependent nature of hERV expression explains the previously reported ccRCC-specific clinical associations of PBRM1 mutant ccRCC with both a good prognosis as well as improved clinical outcomes to ICB.
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Affiliation(s)
- Mi Zhou
- Medicine and Genetics, University of North Carolina at Chapel Hill
| | - Janet Y Leung
- Department of Medicine and Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill
| | | | - Austin J Hepperla
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill
| | - Jeremy M Simon
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill
| | - Ian J Davis
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill
| | - William Y Kim
- Medicine, Genetics, Pharmacology, and Urology, University of North Carolina at Chapel Hill
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25
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Fang W, Liao C, Shi R, Simon JM, Ptacek TS, Zurlo G, Ye Y, Han L, Fan C, Bao L, Ortiz CL, Lin HR, Manocha U, Luo W, Peng Y, Kim WY, Yang LW, Zhang Q. ZHX2 promotes HIF1α oncogenic signaling in triple-negative breast cancer. eLife 2021; 10:e70412. [PMID: 34779768 PMCID: PMC8673836 DOI: 10.7554/elife.70412] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 05/16/2021] [Accepted: 11/14/2021] [Indexed: 12/24/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive and highly lethal disease, which warrants the critical need to identify new therapeutic targets. We show that Zinc Fingers and Homeoboxes 2 (ZHX2) is amplified or overexpressed in TNBC cell lines and patients. Functionally, depletion of ZHX2 inhibited TNBC cell growth and invasion in vitro, orthotopic tumor growth, and spontaneous lung metastasis in vivo. Mechanistically, ZHX2 bound with hypoxia-inducible factor (HIF) family members and positively regulated HIF1α activity in TNBC. Integrated ChIP-seq and gene expression profiling demonstrated that ZHX2 co-occupied with HIF1α on transcriptionally active promoters marked by H3K4me3 and H3K27ac, thereby promoting gene expression. Among the identified ZHX2 and HIF1α coregulated genes, overexpression of AP2B1, COX20, KDM3A, or PTGES3L could partially rescue TNBC cell growth defect by ZHX2 depletion, suggested that these downstream targets contribute to the oncogenic role of ZHX2 in an accumulative fashion. Furthermore, multiple residues (R491, R581, and R674) on ZHX2 are important in regulating its phenotype, which correspond with their roles on controlling ZHX2 transcriptional activity in TNBC cells. These studies establish that ZHX2 activates oncogenic HIF1α signaling, therefore serving as a potential therapeutic target for TNBC.
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Affiliation(s)
- Wentong Fang
- Department of Pharmacy, The First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Rachel Shi
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
- Department of Genetics, Neuroscience Center; University of North Carolina School of MedicineChapel HillUnited States
| | - Travis S Ptacek
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North CarolinaChapel HillUnited States
| | - Giada Zurlo
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Youqiong Ye
- Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical SchoolHoustonUnited States
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Lei Bao
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Christopher Llynard Ortiz
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchuTaiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of ChemistryAcademia SinicaTaiwan
- Department of Chemistry, National Tsing-Hua UniversityHsinchuTaiwan
| | - Hong-Rui Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchuTaiwan
| | - Ujjawal Manocha
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Weibo Luo
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Yan Peng
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical CenterDallasUnited States
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina School of MedicineChapel hillUnited States
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchuTaiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of ChemistryAcademia SinicaTaiwan
- Physics Division, National Center for Theoretical SciencesHsinchuTaiwan
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
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26
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Judson MC, Shyng C, Simon JM, Davis CR, Punt AM, Salmon MT, Miller NW, Ritola KD, Elgersma Y, Amaral DG, Gray SJ, Philpot BD. Dual-isoform hUBE3A gene transfer improves behavioral and seizure outcomes in Angelman syndrome model mice. JCI Insight 2021; 6:144712. [PMID: 34676830 PMCID: PMC8564914 DOI: 10.1172/jci.insight.144712] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 09/28/2020] [Accepted: 09/02/2021] [Indexed: 12/23/2022] Open
Abstract
Loss of the maternal UBE3A allele causes Angelman syndrome (AS), a debilitating neurodevelopmental disorder. Here, we devised an AS treatment strategy based on reinstating dual-isoform expression of human UBE3A (hUBE3A) in the developing brain. Kozak sequence engineering of our codon-optimized vector (hUBE3Aopt) enabled translation of both short and long hUBE3A protein isoforms at a near-endogenous 3:1 (short/long) ratio, a feature that could help to support optimal therapeutic outcomes. To model widespread brain delivery and early postnatal onset of hUBE3A expression, we packaged the hUBE3Aopt vector into PHP.B capsids and performed intracerebroventricular injections in neonates. This treatment significantly improved motor learning and innate behaviors in AS mice, and it rendered them resilient to epileptogenesis and associated hippocampal neuropathologies induced by seizure kindling. hUBE3A overexpression occurred frequently in the hippocampus but was uncommon in the neocortex and other major brain structures; furthermore, it did not correlate with behavioral performance. Our results demonstrate the feasibility, tolerability, and therapeutic potential for dual-isoform hUBE3A gene transfer in the treatment of AS.
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Affiliation(s)
- Matthew C Judson
- Neuroscience Center.,Department of Cell Biology and Physiology.,Carolina Institute for Developmental Disabilities
| | - Charles Shyng
- Carolina Institute for Developmental Disabilities.,Gene Therapy Center, and
| | - Jeremy M Simon
- Neuroscience Center.,Carolina Institute for Developmental Disabilities.,Department of Genetics, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | | | - A Mattijs Punt
- Department of Clinical Genetics and.,Department of Neuroscience, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | | | - Noah W Miller
- Neuroscience Center.,Department of Cell Biology and Physiology
| | - Kimberly D Ritola
- Neuroscience Center.,Department of Pharmacology, UNC, Chapel Hill, North Carolina, USA.,Scientific Operations Manager-Viral Tools, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Ype Elgersma
- Department of Clinical Genetics and.,Department of Neuroscience, Erasmus MC University Medical Center, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - David G Amaral
- Department of Psychiatry and Behavioral Sciences, MIND Institute, and.,California National Primate Research Center, University of California, Davis, California, USA
| | - Steven J Gray
- Gene Therapy Center, and.,Department of Pediatrics and.,Eugene McDermott Center for Human Growth and Development, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Benjamin D Philpot
- Neuroscience Center.,Department of Cell Biology and Physiology.,Carolina Institute for Developmental Disabilities
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27
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Boschen KE, Ptacek TS, Berginski ME, Simon JM, Parnell SE. Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol. Dis Model Mech 2021; 14:dmm049012. [PMID: 34137816 PMCID: PMC8246266 DOI: 10.1242/dmm.049012] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/12/2021] [Indexed: 12/28/2022] Open
Abstract
Genetics are a known contributor to differences in alcohol sensitivity in humans with fetal alcohol spectrum disorders (FASDs) and in animal models. Our study profiled gene expression in gastrulation-stage embryos from two commonly used, genetically similar mouse substrains, C57BL/6J (6J) and C57BL/6NHsd (6N), that differ in alcohol sensitivity. First, we established normal gene expression patterns at three finely resolved time points during gastrulation and developed a web-based interactive tool. Baseline transcriptional differences across strains were associated with immune signaling. Second, we examined the gene networks impacted by alcohol in each strain. Alcohol caused a more pronounced transcriptional effect in the 6J versus 6N mice, matching the increased susceptibility of the 6J mice. The 6J strain exhibited dysregulation of pathways related to cell death, proliferation, morphogenic signaling and craniofacial defects, while the 6N strain showed enrichment of hypoxia and cellular metabolism pathways. These datasets provide insight into the changing transcriptional landscape across mouse gastrulation, establish a valuable resource that enables the discovery of candidate genes that may modify alcohol susceptibility that can be validated in humans, and identify novel pathogenic mechanisms of alcohol. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Karen E. Boschen
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Travis S. Ptacek
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew E. Berginski
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeremy M. Simon
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Scott E. Parnell
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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28
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DiFiore JV, Ptacek TS, Wang Y, Li B, Simon JM, Strahl BD. Unique and Shared Roles for Histone H3K36 Methylation States in Transcription Regulation Functions. Cell Rep 2021; 31:107751. [PMID: 32521276 DOI: 10.1016/j.celrep.2020.107751] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 02/19/2019] [Revised: 01/21/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
Set2 co-transcriptionally methylates lysine 36 of histone H3 (H3K36), producing mono-, di-, and trimethylation (H3K36me1/2/3). These modifications recruit or repel chromatin effector proteins important for transcriptional fidelity, mRNA splicing, and DNA repair. However, it was not known whether the different methylation states of H3K36 have distinct biological functions. Here, we use engineered forms of Set2 that produce different lysine methylation states to identify unique and shared functions for H3K36 modifications. Although H3K36me1/2 and H3K36me3 are functionally redundant in many SET2 deletion phenotypes, we found that H3K36me3 has a unique function related to Bur1 kinase activity and FACT (facilitates chromatin transcription) complex function. Further, during nutrient stress, either H3K36me1/2 or H3K36me3 represses high levels of histone acetylation and cryptic transcription that arises from within genes. Our findings uncover the potential for the regulation of diverse chromatin functions by different H3K36 methylation states.
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Affiliation(s)
- Julia V DiFiore
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Travis S Ptacek
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yi Wang
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Bing Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jeremy M Simon
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
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29
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Swahari V, Nakamura A, Hollville E, Stroud H, Simon JM, Ptacek TS, Beck MV, Flowers C, Guo J, Plestant C, Liang J, Kurtz CL, Kanke M, Hammond SM, He YW, Anton ES, Sethupathy P, Moy SS, Greenberg ME, Deshmukh M. MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation. Cell Rep 2021; 35:108946. [PMID: 33826889 PMCID: PMC8103628 DOI: 10.1016/j.celrep.2021.108946] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 07/28/2020] [Revised: 12/09/2020] [Accepted: 03/14/2021] [Indexed: 11/27/2022] Open
Abstract
Although embryonic brain development and neurodegeneration have received considerable attention, the events that govern postnatal brain maturation are less understood. Here, we identify the miR-29 family to be strikingly induced during the late stages of brain maturation. Brain maturation is associated with a transient, postnatal period of de novo non-CG (CH) DNA methylation mediated by DNMT3A. We examine whether an important function of miR-29 during brain maturation is to restrict the period of CH methylation via its targeting of Dnmt3a. Deletion of miR-29 in the brain, or knockin mutations preventing miR-29 to specifically target Dnmt3a, result in increased DNMT3A expression, higher CH methylation, and repression of genes associated with neuronal activity and neuropsychiatric disorders. These mouse models also develop neurological deficits and premature lethality. Our results identify an essential role for miR-29 in restricting CH methylation in the brain and illustrate the importance of CH methylation regulation for normal brain maturation.
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Affiliation(s)
- Vijay Swahari
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.
| | - Ayumi Nakamura
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA
| | - Emilie Hollville
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Hume Stroud
- Department of Neurobiology, Harvard University, Boston, MA, USA
| | - Jeremy M Simon
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | - Travis S Ptacek
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew V Beck
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Cornelius Flowers
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jiami Guo
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jie Liang
- Department of Immunology, Duke University, Durham, NC, USA
| | - C Lisa Kurtz
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Matt Kanke
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Scott M Hammond
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - You-Wen He
- Department of Immunology, Duke University, Durham, NC, USA
| | - E S Anton
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | | | - Mohanish Deshmukh
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA.
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30
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Niehaus JK, Taylor-Blake B, Loo L, Simon JM, Zylka MJ. Spinal macrophages resolve nociceptive hypersensitivity after peripheral injury. Neuron 2021; 109:1274-1282.e6. [PMID: 33667343 DOI: 10.1016/j.neuron.2021.02.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [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: 07/08/2019] [Revised: 09/28/2020] [Accepted: 02/12/2021] [Indexed: 12/12/2022]
Abstract
Peripheral nerve injury induces long-term pro-inflammatory responses in spinal cord glial cells that facilitate neuropathic pain, but the identity of endogenous cells that resolve spinal inflammation has not been determined. Guided by single-cell RNA sequencing (scRNA-seq), we found that MRC1+ spinal cord macrophages proliferated and upregulated the anti-inflammatory mediator Cd163 in mice following superficial injury (SI; nerve intact), but this response was blunted in nerve-injured animals. Depleting spinal macrophages in SI animals promoted microgliosis and caused mechanical hypersensitivity to persist. Conversely, expressing Cd163 in spinal macrophages increased Interleukin 10 expression, attenuated micro- and astrogliosis, and enduringly alleviated mechanical and thermal hypersensitivity in nerve-injured animals. Our data indicate that MRC1+ spinal macrophages actively restrain glia to limit neuroinflammation and resolve mechanical pain following a superficial injury. Moreover, we show that spinal macrophages from nerve-injured animals mount a dampened anti-inflammatory response but can be therapeutically coaxed to promote long-lasting recovery of neuropathic pain.
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Affiliation(s)
- Jesse K Niehaus
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Curriculum, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bonnie Taylor-Blake
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lipin Loo
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark J Zylka
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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31
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Lee HM, Kuijer MB, Ruiz Blanes N, Clark EP, Aita M, Galiano Arjona L, Kokot A, Sciaky N, Simon JM, Bhatnagar S, Philpot BD, Cerase A. A small-molecule screen reveals novel modulators of MeCP2 and X-chromosome inactivation maintenance. J Neurodev Disord 2020; 12:29. [PMID: 33172406 PMCID: PMC7657357 DOI: 10.1186/s11689-020-09332-3] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/22/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in the X-linked methyl-CpG binding protein 2 (MeCP2) gene. While MeCP2 mutations are lethal in most males, females survive birth but show severe neurological defects. Because X-chromosome inactivation (XCI) is a random process, approximately 50% of the cells silence the wild-type (WT) copy of the MeCP2 gene. Thus, reactivating the silent WT copy of MeCP2 could provide therapeutic intervention for RTT. METHODS Toward this goal, we screened ~ 28,000 small-molecule compounds from several libraries using a MeCP2-luciferase reporter cell line and cortical neurons from a MeCP2-EGFP mouse model. We used gain/increase of luminescence or fluorescence as a readout of MeCP2 reactivation and tested the efficacy of these drugs under different drug regimens, conditions, and cellular contexts. RESULTS We identified inhibitors of the JAK/STAT pathway as XCI-reactivating agents, both by in vitro and ex vivo assays. In particular, we show that AG-490, a Janus Kinase 2 (JAK2) kinase inhibitor, and Jaki, a pan JAK/STAT inhibitor, are capable of reactivating MeCP2 from the inactive X chromosome, in different cellular contexts. CONCLUSIONS Our results suggest that inhibition of the JAK/STAT pathway is a new potential pathway to reinstate MeCP2 gene expression as an efficient RTT treatment.
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Affiliation(s)
- Hyeong-Min Lee
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Current Address: High-Throughput Bioscience Center, Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Bram Kuijer
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Ellen P Clark
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Megumi Aita
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Agnieszka Kokot
- Department of Biochemistry and Molecular Genetics, Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Noah Sciaky
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sanchita Bhatnagar
- Department of Biochemistry and Molecular Genetics, Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Benjamin D Philpot
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Andrea Cerase
- Blizard Institute, Queen Mary University of London, London, UK.
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32
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Nixon SJ, Zimmerman S, Simon JM, Souroullas GP. Abstract PO-08: Understanding the properties and oncogenic mechanisms of EZH2 Y641 mutations in lymphoma. Blood Cancer Discov 2020. [DOI: 10.1158/2643-3249.lymphoma20-po-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] Open
Abstract
Abstract
EZH2 (Enhancer of Zeste Homolog 2) is the catalytic component of the Polycomb Repressive Complex group 2 (PRC2), which establishes the repressive epigenetic mark histone 3 lysine 27 trimethylation (H3K27me3), resulting in silencing of gene expression. EZH2 was originally identified as a tumor suppressor since loss-of-function events were observed in myelodysplastic syndrome, acute myeloid, and T-cell leukemias. However, next-generation sequencing identified recurrent activating point mutations at tyrosine residue 641 (Y641) in 25% of germinal center diffuse large B-cell lymphoma and 15% of follicular lymphomas, suggesting that EZH2 also functions as an oncogene in a cell type-dependent manner. Using a faithful genetically engineered mouse model, we previously demonstrated that the Ezh2Y641F mutation drives formation of B-cell lymphoma as a single event and in cooperation with Bcl2 amplification or p53 loss. Unexpectedly, at the chromatin level, expression of Ezh2Y641F did not monotonically increase abundance of global H3K27me3 but rather resulted in redistribution of this mark across the genome, exhibiting loss of H3K27me3 at many loci, with direct effects on transcription. Others have shown that EZH2 mediates germinal center proliferation via repression of p21 and cooperation with Bcl6; however, given the global effect of Ezh2Y641F on chromatin, the oncogenic mechanisms of these mutations remain underexplored. These include the timing of the mutation during hematopoietic development, its role during differentiation, and the oncogenic activity of downstream targets. In order to investigate the effect of Ezh2Y641 mutations on hematopoietic development and differentiation, we used Cre alleles to drive expression of the mutant protein at different stages of hematopoietic development. Our data demonstrate that expression of Ezh2Y641 in early B cells is sufficient to drive oncogenic transformation. However, expression of Ezh2Y641 in hematopoietic stem cell (HSC) is not sufficient to drive oncogenic transformation despite the presence of mature healthy B cells. Additionally, expression of Ezh2Y641F in HSCs results in loss of self-renewal, differentiation bias towards the lymphoid lineages, and a partial block at the pre-pro B-cell stage. With regards to direct downstream targets, we identified upregulation of several HoxC cluster genes in Ezh2Y641F-mutant B cells prior to transformation. Upregulation of these genes is mediated via loss of H3K27me3 at the HoxC cluster and focal gains of H3K27 acetylation (H3K27ac). Overall, our findings underline the complicated biology and oncogenic activity of EZH2Y641 mutations in lymphoma, shed light on the effect of these mutations during hematopoietic development, and underscore some of the consequences of the paradoxical loss of H3K27me3 at certain loci.
Citation Format: Samantha J. Nixon, Sarah Zimmerman, Jeremy M. Simon, George P. Souroullas. Understanding the properties and oncogenic mechanisms of EZH2 Y641 mutations in lymphoma [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-08.
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Affiliation(s)
| | | | - Jeremy M. Simon
- 2University of North Carolina in Chapel Hill, Chapel Hill, NC
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Wolter JM, Mao H, Fragola G, Simon JM, Krantz JL, Bazick HO, Oztemiz B, Stein JL, Zylka MJ. Cas9 gene therapy for Angelman syndrome traps Ube3a-ATS long non-coding RNA. Nature 2020; 587:281-284. [PMID: 33087932 PMCID: PMC8020672 DOI: 10.1038/s41586-020-2835-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [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: 10/11/2019] [Accepted: 07/28/2020] [Indexed: 12/15/2022]
Abstract
Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by a mutation or deletion of the maternally inherited UBE3A allele. In neurons, the paternally inherited UBE3A allele is silenced in cis by a long non-coding RNA called UBE3A-ATS. Here, as part of a systematic screen, we found that Cas9 can be used to activate ('unsilence') paternal Ube3a in cultured mouse and human neurons when targeted to Snord115 genes, which are small nucleolar RNAs that are clustered in the 3' region of Ube3a-ATS. A short Cas9 variant and guide RNA that target about 75 Snord115 genes were packaged into an adeno-associated virus and administered to a mouse model of AS during the embryonic and early postnatal stages, when the therapeutic benefit of restoring Ube3a is predicted to be greatest1,2. This early treatment unsilenced paternal Ube3a throughout the brain for at least 17 months and rescued anatomical and behavioural phenotypes in AS mice. Genomic integration of the adeno-associated virus vector into Cas9 target sites caused premature termination of Ube3a-ATS at the vector-derived polyA cassette, or when integrated in the reverse orientation, by transcriptional collision with the vector-derived Cas9 transcript. Our study shows that targeted genomic integration of a gene therapy vector can restore the function of paternally inherited UBE3A throughout life, providing a path towards a disease-modifying treatment for a syndromic neurodevelopmental disorder.
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Affiliation(s)
- Justin M Wolter
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hanqian Mao
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Giulia Fragola
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - James L Krantz
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hannah O Bazick
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Baris Oztemiz
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason L Stein
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark J Zylka
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Jiménez JA, Ptacek TS, Tuttle AH, Schmid RS, Moy SS, Simon JM, Zylka MJ. Chd8 haploinsufficiency impairs early brain development and protein homeostasis later in life. Mol Autism 2020; 11:74. [PMID: 33023670 PMCID: PMC7537101 DOI: 10.1186/s13229-020-00369-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 04/28/2020] [Accepted: 08/07/2020] [Indexed: 12/26/2022] Open
Abstract
Background Chromodomain helicase DNA-binding protein 8 (Chd8) is a high-confidence risk gene for autism spectrum disorder (ASD). However, how Chd8 haploinsufficiency impairs gene expression in the brain and impacts behavior at different stages of life is unknown. Methods We generated a mutant mouse line with an ASD-linked loss-of-function mutation in Chd8 (V986*; stop codon mutation). We examined the behavior of Chd8 mutant mice along with transcriptional changes in the cerebral cortex as a function of age, with a focus on one embryonic (E14.5) and three postnatal ages (1, 6, and 12 months). Results Chd8V986*/+ mutant mice displayed macrocephaly, reduced rearing responses and reduced center time in the open field, and enhanced social novelty preference. Behavioral phenotypes were more evident in Chd8V986*/+ mutant mice at 1 year of age. Pup survival was reduced in wild-type x Chd8V986*/+ crosses when the mutant parent was female. Transcriptomic analyses indicated that pathways associated with synaptic and neuronal projections and sodium channel activity were reduced in the cortex of embryonic Chd8V986*/+ mice and then equalized relative to wild-type mice in the postnatal period. At 12 months of age, expression of genes associated with endoplasmic reticulum (ER) stress, chaperone-mediated protein folding, and the unfolded protein response (UPR) were reduced in Chd8V986*/+ mice, whereas genes associated with the c-MET signaling pathway were increased in expression. Limitations It is unclear whether the transcriptional changes observed with age in Chd8V986*/+ mice reflect a direct effect of CHD8-regulated gene expression, or if CHD8 indirectly affects the expression of UPR/ER stress genes in adult mice as a consequence of neurodevelopmental abnormalities. Conclusions Collectively, these data suggest that UPR/ER stress pathways are reduced in the cerebral cortex of aged Chd8V986*/+ mice. Our study uncovers neurodevelopmental and age-related phenotypes in Chd8V986*/+ mice and highlights the importance of controlling for age when studying Chd8 haploinsufficient mice.
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Affiliation(s)
- Jessica A Jiménez
- Curriculum in Toxicology & Environmental Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Travis S Ptacek
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alex H Tuttle
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ralf S Schmid
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sheryl S Moy
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Psychiatry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Campus Box #7264, Chapel Hill, NC, 27599, USA
| | - Mark J Zylka
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Bowman BM, Montgomery SA, Schrank TP, Simon JM, Ptacek TS, Tamir TY, Mulvaney KM, Weir SJ, Nguyen TT, Murphy RM, Makowski L, Hayes DN, Chen XL, Randell SH, Weissman BE, Major MB. A conditional mouse expressing an activating mutation in NRF2 displays hyperplasia of the upper gastrointestinal tract and decreased white adipose tissue. J Pathol 2020; 252:125-137. [PMID: 32619021 DOI: 10.1002/path.5504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/04/2020] [Accepted: 06/24/2020] [Indexed: 12/23/2022]
Abstract
Activation of the nuclear factor (erythroid-derived 2)-like 2 (NFE2L2 or NRF2) transcription factor is a critical and evolutionarily conserved cellular response to oxidative stress, metabolic stress, and xenobiotic insult. Deficiency of NRF2 results in hypersensitivity to a variety of stressors, whereas its aberrant activation contributes to several cancer types, most commonly squamous cell carcinomas of the esophagus, oral cavity, bladder, and lung. Between 10% and 35% of patients with squamous cell carcinomas display hyperactive NRF2 signaling, harboring activating mutations and copy number amplifications of the NFE2L2 oncogene or inactivating mutations or deletions of KEAP1 or CUL3, the proteins of which co-complex to ubiquitylate and degrade NRF2 protein. To better understand the role of NRF2 in tumorigenesis and more broadly in development, we engineered the endogenous Nfe2l2 genomic locus to create a conditional mutant LSL-Nrf2E79Q mouse model. The E79Q mutation, one of the most commonly observed NRF2-activating mutations in human squamous cancers, codes for a mutant protein that does not undergo KEAP1/CUL3-dependent degradation, resulting in its constitutive activity. Expression of NRF2 E79Q protein in keratin 14 (KRT14)-positive murine tissues resulted in hyperplasia of squamous cell tissues of the tongue, forestomach, and esophagus, a stunted body axis, decreased weight, and decreased visceral adipose depots. RNA-seq profiling and follow-up validation studies of cultured NRF2E79Q murine esophageal epithelial cells revealed known and novel NRF2-regulated transcriptional programs, including genes associated with squamous cell carcinoma (e.g. Myc), lipid and cellular metabolism (Hk2, Ppard), and growth factors (Areg, Bmp6, Vegfa). These data suggest that in addition to decreasing adipogenesis, KRT14-restricted NRF2 activation drives hyperplasia of the esophagus, forestomach, and tongue, but not formation of squamous cell carcinoma. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Brittany M Bowman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Travis P Schrank
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.,Department of Otolaryngology/Head and Neck Surgery, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Travis S Ptacek
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tigist Y Tamir
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | | | - Seth J Weir
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Tuong T Nguyen
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Ryan M Murphy
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Liza Makowski
- University of Tennessee Health Science Center for Cancer Research, Department of Medicine, Division of Hematology and Oncology, University of Tennessee, Memphis, TN, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee, Memphis, TN, USA
| | - D Neil Hayes
- University of Tennessee Health Science Center for Cancer Research, Department of Medicine, Division of Hematology and Oncology, University of Tennessee, Memphis, TN, USA
| | - Xiaoxin L Chen
- Cancer Research Program, Julius L Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, USA.,Center for Esophageal Disease and Swallowing, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott H Randell
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Bernard E Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Michael B Major
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.,Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
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Liao C, Zhang Y, Fan C, Herring LE, Liu J, Locasale JW, Takada M, Zhou J, Zurlo G, Hu L, Simon JM, Ptacek TS, Andrianov VG, Loza E, Peng Y, Yang H, Perou CM, Zhang Q. Identification of BBOX1 as a Therapeutic Target in Triple-Negative Breast Cancer. Cancer Discov 2020; 10:1706-1721. [PMID: 32690540 PMCID: PMC7642036 DOI: 10.1158/2159-8290.cd-20-0288] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/15/2020] [Accepted: 07/15/2020] [Indexed: 11/16/2022]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive and highly lethal disease. Because of its heterogeneity and lack of hormone receptors or HER2 expression, targeted therapy is limited. Here, by performing a functional siRNA screening for 2-OG-dependent enzymes, we identified gamma-butyrobetaine hydroxylase 1 (BBOX1) as an essential gene for TNBC tumorigenesis. BBOX1 depletion inhibits TNBC cell growth while not affecting normal breast cells. Mechanistically, BBOX1 binds with the calcium channel inositol-1,4,5-trisphosphate receptor type 3 (IP3R3) in an enzymatic-dependent manner and prevents its ubiquitination and proteasomal degradation. BBOX1 depletion suppresses IP3R3-mediated endoplasmic reticulum calcium release, therefore impairing calcium-dependent energy-generating processes including mitochondrial respiration and mTORC1-mediated glycolysis, which leads to apoptosis and impaired cell-cycle progression in TNBC cells. Therapeutically, genetic depletion or pharmacologic inhibition of BBOX1 inhibits TNBC tumor growth in vitro and in vivo. Our study highlights the importance of targeting the previously uncharacterized BBOX1-IP3R3-calcium oncogenic signaling axis in TNBC. SIGNIFICANCE: We provide evidence from unbiased screens that BBOX1 is a potential therapeutic target in TNBC and that genetic knockdown or pharmacologic inhibition of BBOX1 leads to decreased TNBC cell fitness. This study lays the foundation for developing effective BBOX1 inhibitors for treatment of this lethal disease.This article is highlighted in the In This Issue feature, p. 1611.
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Affiliation(s)
- Chengheng Liao
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yang Zhang
- Department of Biochemistry, Duke University, Durham, North Carolina
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Laura E Herring
- Department of Pharmacology and UNC Proteomics Core Facility, University of North Carolina, Chapel Hill, North Carolina
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Mamoru Takada
- Department of General Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Jin Zhou
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Giada Zurlo
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lianxin Hu
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,Department of Genetics, Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina.,UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, North Carolina
| | - Travis S Ptacek
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, North Carolina
| | | | - Einars Loza
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Yan Peng
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Huanghe Yang
- Department of Biochemistry, Duke University, Durham, North Carolina
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Qing Zhang
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas.
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Boschen KE, Ptacek TS, Simon JM, Parnell SE. Transcriptome-Wide Regulation of Key Developmental Pathways in the Mouse Neural Tube by Prenatal Alcohol Exposure. Alcohol Clin Exp Res 2020; 44:1540-1550. [PMID: 32557641 DOI: 10.1111/acer.14389] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/02/2020] [Accepted: 05/31/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Early gestational alcohol exposure is associated with severe craniofacial and CNS dysmorphologies and behavioral abnormalities during adolescence and adulthood. Alcohol exposure during the formation of the neural tube (gestational day [GD] 8 to 10 in mice; equivalent to4th week of human pregnancy) disrupts development of ventral midline brain structures such as the pituitary, septum, and ventricles. This study identifies transcriptomic changes in the rostroventral neural tube (RVNT), the region of the neural tube that gives rise to the midline structures sensitive to alcohol exposure during neurulation. METHODS Female C57BL/6J mice were administered 2 doses of alcohol (2.9 g/kg) or vehicle 4 hours apart on GD 9.0. The RVNTs of embryos were collected 6 or 24 hours after the first dose and processed for RNA-seq. RESULTS Six hours following GD 9.0 alcohol exposure (GD 9.25), over 2,300 genes in the RVNT were determined to be differentially regulated by alcohol. Enrichment analysis determined that PAE affected pathways related to cell proliferation, p53 signaling, ribosome biogenesis, and immune activation. In addition, over 100 genes involved in primary cilia formation and function and regulation of morphogenic pathways were altered 6 hours after alcohol exposure. The changes to gene expression were largely transient, as only 91 genes identified as differentially regulated by prenatal alcohol at GD 10 (24 hours postexposure). Functionally, the differentially regulated genes at GD 10 were related to organogenesis and cell migration. CONCLUSIONS These data give a comprehensive view of the changing landscape of the embryonic transcriptome networks in regions of the neural tube that give rise to brain structures impacted by a neurulation-stage alcohol exposure. Identification of gene networks dysregulated by alcohol will help elucidate the pathogenic mechanisms of alcohol's actions.
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Affiliation(s)
- Karen E Boschen
- From the Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Travis S Ptacek
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeremy M Simon
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Scott E Parnell
- From the Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Quesada Dorador A, Fernandez C, Quesada-Ocete B, Sancho-Peluz P, Quesada-Ocete J, Martinez JG, Jimenez-Bello JG, Climent Paya V, Paya R, Bochard B, Palanca V, Vano-Bodi J, Simon JM, Perez-Bosca JL, Belchi J. P1475Impact of automatic screening and parasternal rights positions in the eligibility of patients with hypertrophic cardiomyopathy for subcutaneous automatic cardioverter defibrillator implant. Europace 2020. [DOI: 10.1093/europace/euaa162.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
A high percentage of failures in the detection of QRS and T wave in patients (pts) with hypertrophic cardiomyopathy (HCM) have been reported. This finding would prevent them from being eligible for an implantable subcutaneous automatic defibrillator (S-ICD). However, recently 2 changes in the detection have been proposed, automatic screening and the use of right parasternal position of the lead.
The aim of our work was to study if the elegibility proportion of patients was increased with both 2 advacements.
Methods
We included 31 patients (18 male)with a diagnosis of HCM and at least 1 risk factor for sudden death, in follow-up at the outdoor clinic of of 2 cardiology centers. We performed elegibility screening test in supine position and standing using both the automatic screening (AS) obtained by Boston Scientific Zoom Latitude programmer) and the manual (MS), to simulate the detection of the 3 vectors utilized in S-ICD detection. And both screens were registered with the surface electrodes in parasternal left and right position. A pte was considered eligible if at least one vector was correct in supine position and in standing position, well in parasternal left or right position.
Results
Using MS with left parasternal position, 22 patients (71%) were eligible. Adding the right parasternal lead, the eligibility increased by 10%, reaching 81%. In addition, in automatic screening, eligibility in right shifts (81%) it is 7% more than in the left and, with the addition of the rights to the left, the eligibility reaches up to 84%. Figure shows the three-lead ECG factors influencing screening pass vs failure.
Conclusion
AS, right parasternal lead position and the combination of right and left parasternal lead position, increase the eligibility of sICD candidates with HCM.
Abstract Figure. ECG factors influencing screening pass
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Affiliation(s)
- A Quesada Dorador
- University General Hospital of Valencia, Department of Cardiology, Valencia, Spain
| | - C Fernandez
- University General Hospital of Valencia, Department of Cardiology, Valencia, Spain
| | - B Quesada-Ocete
- Johannes Gutenberg University Mainz (JGU), Cardiology, Mainz, Germany
| | - P Sancho-Peluz
- Catholic University of Valencia "San Vicente Martir", Cardiology, Valencia, Spain
| | - J Quesada-Ocete
- University General Hospital of Valencia, Department of Cardiology, Valencia, Spain
| | - J G Martinez
- General University Hospital of Alicante, Alicante, Spain
| | - J G Jimenez-Bello
- University General Hospital of Valencia, Department of Cardiology, Valencia, Spain
| | - V Climent Paya
- General University Hospital of Alicante, Alicante, Spain
| | - R Paya
- University General Hospital of Valencia, Department of Cardiology, Valencia, Spain
| | - B Bochard
- University General Hospital of Valencia, Department of Cardiology, Valencia, Spain
| | - V Palanca
- University General Hospital of Valencia, Department of Cardiology, Valencia, Spain
| | - J Vano-Bodi
- University General Hospital of Valencia, Department of Cardiology, Valencia, Spain
| | - J M Simon
- University General Hospital of Valencia, Department of Cardiology, Valencia, Spain
| | - J L Perez-Bosca
- University General Hospital of Valencia, Department of Cardiology, Valencia, Spain
| | - J Belchi
- University General Hospital of Valencia, Department of Cardiology, Valencia, Spain
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Dugyala S, Ptacek TS, Simon JM, Li Y, Fröhlich F. Putative modulation of the gut microbiome by probiotics enhances preference for novelty in a preliminary double-blind placebo-controlled study in ferrets. Anim Microbiome 2020; 2. [PMID: 32490353 PMCID: PMC7266289 DOI: 10.1186/s42523-020-00030-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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] [Indexed: 12/14/2022] Open
Abstract
Background Increasing evidence suggests a causal relationship between the gut microbiome and psychiatric illnesses. In particular, autism spectrum disorder is associated with gastrointestinal symptoms and alterations in the gut microbiome. Administration of probiotics is a commonly used strategy by caregivers of people with neurodevelopmental illness. However, evidence for successful improvement in gut microbiome and (behavioral) symptoms has been lacking. Results Here, we use a novel ferret model of maternal immune activation to show that high-dose probiotic administration in a placebo-controlled study design causes changes in the gut microbiome in the form of a transient increase in the administered bacterial species. In contrast, we found no differences in baseline microbiome composition or changes induced by probiotic administration between animals exposed in utero to maternal immune activation and control animals. However, the relative presence of several bacterial species correlated with an increased preference for novelty (object and conspecific). Intriguingly, several of the hits in this screen are species that have previously emerged in the literature as being associated with autism and anxiety. Conclusions Together, our results suggest that high-dose probiotic interventions may be beneficial for the adjunct treatment of psychiatric illnesses. Placebo-controlled clinical trials in humans are urgently needed.
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Affiliation(s)
- Supritha Dugyala
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Travis S Ptacek
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Yuhui Li
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Flavio Fröhlich
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.,Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Carolina Center for Neurostimulation, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, 115 Mason Farm Rd. NRB 4109F, Chapel Hill, NC 27599, USA
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40
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Fragola G, Mabb AM, Taylor-Blake B, Niehaus JK, Chronister WD, Mao H, Simon JM, Yuan H, Li Z, McConnell MJ, Zylka MJ. Deletion of Topoisomerase 1 in excitatory neurons causes genomic instability and early onset neurodegeneration. Nat Commun 2020; 11:1962. [PMID: 32327659 PMCID: PMC7181881 DOI: 10.1038/s41467-020-15794-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 03/28/2020] [Indexed: 12/14/2022] Open
Abstract
Topoisomerase 1 (TOP1) relieves torsional stress in DNA during transcription and facilitates the expression of long (>100 kb) genes, many of which are important for neuronal functions. To evaluate how loss of Top1 affected neurons in vivo, we conditionally deleted (cKO) Top1 in postmitotic excitatory neurons in the mouse cerebral cortex and hippocampus. Top1 cKO neurons develop properly, but then show biased transcriptional downregulation of long genes, signs of DNA damage, neuroinflammation, increased poly(ADP-ribose) polymerase-1 (PARP1) activity, single-cell somatic mutations, and ultimately degeneration. Supplementation of nicotinamide adenine dinucleotide (NAD+) with nicotinamide riboside partially blocked neurodegeneration, and increased the lifespan of Top1 cKO mice by 30%. A reduction of p53 also partially rescued cortical neuron loss. While neurodegeneration was partially rescued, behavioral decline was not prevented. These data indicate that reducing neuronal loss is not sufficient to limit behavioral decline when TOP1 function is disrupted. Topoisomerase 1 (TOP1) relieves DNA torsional stress during transcription and facilitates the expression of long neuronal genes. Here we show that deletion of Top1 in excitatory neurons leads to early onset neurodegeneration that is partially dependent on p53/PARP1 activation and NAD+ depletion.
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Affiliation(s)
- Giulia Fragola
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Angela M Mabb
- Neuroscience Institute, Georgia State University, Atlanta, GA, 30303, USA
| | - Bonnie Taylor-Blake
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jesse K Niehaus
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - William D Chronister
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hanqian Mao
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Hong Yuan
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Biomedical Imaging Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Zibo Li
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Biomedical Imaging Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, 22908, USA
| | - Mark J Zylka
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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41
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Liu X, Simon JM, Xie H, Hu L, Wang J, Zurlo G, Fan C, Ptacek TS, Herring L, Tan X, Li M, Baldwin AS, Kim WY, Wu T, Kirschner MW, Gong K, Zhang Q. Genome-wide Screening Identifies SFMBT1 as an Oncogenic Driver in Cancer with VHL Loss. Mol Cell 2020; 77:1294-1306.e5. [PMID: 32023483 DOI: 10.1016/j.molcel.2020.01.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 06/11/2019] [Revised: 11/09/2019] [Accepted: 01/01/2020] [Indexed: 11/15/2022]
Abstract
von Hippel-Lindau (VHL) is a critical tumor suppressor in clear cell renal cell carcinomas (ccRCCs). It is important to identify additional therapeutic targets in ccRCC downstream of VHL loss besides hypoxia-inducible factor 2α (HIF2α). By performing a genome-wide screen, we identified Scm-like with four malignant brain tumor domains 1 (SFMBT1) as a candidate pVHL target. SFMBT1 was considered to be a transcriptional repressor but its role in cancer remains unclear. ccRCC patients with VHL loss-of-function mutations displayed elevated SFMBT1 protein levels. SFMBT1 hydroxylation on Proline residue 651 by EglN1 mediated its ubiquitination and degradation governed by pVHL. Depletion of SFMBT1 abolished ccRCC cell proliferation in vitro and inhibited orthotopic tumor growth in vivo. Integrated analyses of ChIP-seq, RNA-seq, and patient prognosis identified sphingosine kinase 1 (SPHK1) as a key SFMBT1 target gene contributing to its oncogenic phenotype. Therefore, the pVHL-SFMBT1-SPHK1 axis serves as a potential therapeutic avenue for ccRCC.
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Affiliation(s)
- Xijuan Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Haibiao Xie
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Lianxin Hu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Giada Zurlo
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Travis S Ptacek
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Laura Herring
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Proteomics Core Facility, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Xianming Tan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Mingjie Li
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Albert S Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Tao Wu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Kan Gong
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Qing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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42
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Keele GR, Quach BC, Israel JW, Chappell GA, Lewis L, Safi A, Simon JM, Cotney P, Crawford GE, Valdar W, Rusyn I, Furey TS. Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. PLoS Genet 2020; 16:e1008537. [PMID: 31961859 PMCID: PMC7010298 DOI: 10.1371/journal.pgen.1008537] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 05/28/2019] [Revised: 02/10/2020] [Accepted: 11/23/2019] [Indexed: 01/08/2023] Open
Abstract
Gene transcription profiles across tissues are largely defined by the activity of regulatory elements, most of which correspond to regions of accessible chromatin. Regulatory element activity is in turn modulated by genetic variation, resulting in variable transcription rates across individuals. The interplay of these factors, however, is poorly understood. Here we characterize expression and chromatin state dynamics across three tissues-liver, lung, and kidney-in 47 strains of the Collaborative Cross (CC) mouse population, examining the regulation of these dynamics by expression quantitative trait loci (eQTL) and chromatin QTL (cQTL). QTL whose allelic effects were consistent across tissues were detected for 1,101 genes and 133 chromatin regions. Also detected were eQTL and cQTL whose allelic effects differed across tissues, including local-eQTL for Pik3c2g detected in all three tissues but with distinct allelic effects. Leveraging overlapping measurements of gene expression and chromatin accessibility on the same mice from multiple tissues, we used mediation analysis to identify chromatin and gene expression intermediates of eQTL effects. Based on QTL and mediation analyses over multiple tissues, we propose a causal model for the distal genetic regulation of Akr1e1, a gene involved in glycogen metabolism, through the zinc finger transcription factor Zfp985 and chromatin intermediates. This analysis demonstrates the complexity of transcriptional and chromatin dynamics and their regulation over multiple tissues, as well as the value of the CC and related genetic resource populations for identifying specific regulatory mechanisms within cells and tissues.
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Affiliation(s)
- Gregory R. Keele
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Bryan C. Quach
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Center for Omics Discovery and Epidemiology, Research Triangle Institute (RTI) International, Research Triangle Park, North Carolina, United States of America
| | - Jennifer W. Israel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Grace A. Chappell
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Lauren Lewis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Alexias Safi
- Department of Pediatrics, Duke University, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Jeremy M. Simon
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paul Cotney
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gregory E. Crawford
- Department of Pediatrics, Duke University, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Terrence S. Furey
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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43
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Ocasio J, Babcock B, Malawsky D, Weir SJ, Loo L, Simon JM, Zylka MJ, Hwang D, Dismuke T, Sokolsky M, Rosen EP, Vibhakar R, Zhang J, Saulnier O, Vladoiu M, El-Hamamy I, Stein LD, Taylor MD, Smith KS, Northcott PA, Colaneri A, Wilhelmsen K, Gershon TR. scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy. Nat Commun 2019; 10:5829. [PMID: 31863004 PMCID: PMC6925218 DOI: 10.1038/s41467-019-13657-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [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: 04/05/2019] [Accepted: 11/14/2019] [Indexed: 01/23/2023] Open
Abstract
Targeting oncogenic pathways holds promise for brain tumor treatment, but inhibition of Sonic Hedgehog (SHH) signaling has failed in SHH-driven medulloblastoma. Cellular diversity within tumors and reduced lineage commitment can undermine targeted therapy by increasing the probability of treatment-resistant populations. Using single-cell RNA-seq and lineage tracing, we analyzed cellular diversity in medulloblastomas in transgenic, medulloblastoma-prone mice, and responses to the SHH-pathway inhibitor vismodegib. In untreated tumors, we find expected stromal cells and tumor-derived cells showing either a spectrum of neural progenitor-differentiation states or glial and stem cell markers. Vismodegib reduces the proliferative population and increases differentiation. However, specific cell types in vismodegib-treated tumors remain proliferative, showing either persistent SHH-pathway activation or stem cell characteristics. Our data show that even in tumors with a single pathway-activating mutation, diverse mechanisms drive tumor growth. This diversity confers early resistance to targeted inhibitor therapy, demonstrating the need to target multiple pathways simultaneously. Although the hedgehog (HH) pathway is known to be deregulated in medulloblastoma, inhibitors of the pathway have shown disappointing clinical benefit. Using single-cell sequencing in a mouse model of the disease, the authors show that the response to the HH pathway inhibitor vismodegib is cell-type specific.
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Affiliation(s)
- Jennifer Ocasio
- Department of Neurology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Benjamin Babcock
- Department of Neurology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Daniel Malawsky
- Department of Neurology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Seth J Weir
- Department of Neurology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Lipin Loo
- UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Mark J Zylka
- UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Duhyeong Hwang
- UNC Eshelman School of Pharmacy, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Taylor Dismuke
- Department of Neurology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Marina Sokolsky
- UNC Eshelman School of Pharmacy, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Elias P Rosen
- UNC Eshelman School of Pharmacy, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Jiao Zhang
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Olivier Saulnier
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Maria Vladoiu
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Ibrahim El-Hamamy
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 0A4, Canada.,Program in Computational Biology, Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada
| | - Lincoln D Stein
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 0A4, Canada.,Program in Computational Biology, Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada
| | - Michael D Taylor
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, M5S 3E1, Canada
| | - Kyle S Smith
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alejandro Colaneri
- Department of Neurology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Kirk Wilhelmsen
- Department of Neurology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA. .,Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA. .,Renaissance Computing Institute at UNC (RENCI), Chapel Hill, NC, 27517, USA.
| | - Timothy R Gershon
- Department of Neurology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA. .,UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA. .,Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA. .,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.
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44
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Zurlo G, Liu X, Takada M, Fan C, Simon JM, Ptacek TS, Rodriguez J, von Kriegsheim A, Liu J, Locasale JW, Robinson A, Zhang J, Holler JM, Kim B, Zikánová M, Bierau J, Xie L, Chen X, Li M, Perou CM, Zhang Q. Prolyl hydroxylase substrate adenylosuccinate lyase is an oncogenic driver in triple negative breast cancer. Nat Commun 2019; 10:5177. [PMID: 31729379 PMCID: PMC6858455 DOI: 10.1038/s41467-019-13168-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 02/07/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Protein hydroxylation affects protein stability, activity, and interactome, therefore contributing to various diseases including cancers. However, the transiency of the hydroxylation reaction hinders the identification of hydroxylase substrates. By developing an enzyme-substrate trapping strategy coupled with TAP-TAG or orthogonal GST- purification followed by mass spectrometry, we identify adenylosuccinate lyase (ADSL) as an EglN2 hydroxylase substrate in triple negative breast cancer (TNBC). ADSL expression is higher in TNBC than other breast cancer subtypes or normal breast tissues. ADSL knockout impairs TNBC cell proliferation and invasiveness in vitro and in vivo. An integrated transcriptomics and metabolomics analysis reveals that ADSL activates the oncogenic cMYC pathway by regulating cMYC protein level via a mechanism requiring ADSL proline 24 hydroxylation. Hydroxylation-proficient ADSL, by affecting adenosine levels, represses the expression of the long non-coding RNA MIR22HG, thus upregulating cMYC protein level. Our findings highlight the role of ADSL hydroxylation in controlling cMYC and TNBC tumorigenesis.
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Affiliation(s)
- Giada Zurlo
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Xijuan Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Mamoru Takada
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Department of Genetics, Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA.,UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Travis S Ptacek
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Javier Rodriguez
- Cancer Research UK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Adam Robinson
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jessica M Holler
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Marie Zikánová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | - Jörgen Bierau
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Ling Xie
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Mingjie Li
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Qing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA. .,Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA. .,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, 27599, USA. .,Department of Pathology, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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45
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Simon JM, Paranjape SR, Wolter JM, Salazar G, Zylka MJ. High-throughput screening and classification of chemicals and their effects on neuronal gene expression using RASL-seq. Sci Rep 2019; 9:4529. [PMID: 30872602 PMCID: PMC6418307 DOI: 10.1038/s41598-019-39016-5] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/11/2019] [Indexed: 12/31/2022] Open
Abstract
We previously used RNA-seq to identify chemicals whose effects on neuronal gene expression mimicked transcriptional signatures of autism, aging, and neurodegeneration. However, this approach was costly and time consuming, which limited our study to testing a single chemical concentration on mixed sex cortical neuron cultures. Here, we adapted a targeted transcriptomic method (RASL-seq, similar to TempO-seq) to interrogate changes in expression of a set of 56 signature genes in response to a library of 350 chemicals and chemical mixtures at four concentrations in male and female mouse neuronal cultures. This enabled us to replicate and expand our previous classifications, and show that transcriptional responses were largely equivalent between sexes. Overall, we found that RASL-seq can be used to accelerate the pace at which chemicals and mixtures that transcriptionally mimic autism and other neuropsychiatric diseases can be identified, and provides a cost-effective way to quantify gene expression with a panel of marker genes.
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Affiliation(s)
- Jeremy M Simon
- Department of Cell Biology and Physiology, UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Smita R Paranjape
- Department of Cell Biology and Physiology, UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Justin M Wolter
- Department of Cell Biology and Physiology, UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gabriela Salazar
- Department of Cell Biology and Physiology, UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Mark J Zylka
- Department of Cell Biology and Physiology, UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Vitucci M, Irvin DM, McNeill RS, Schmid RS, Simon JM, Dhruv HD, Siegel MB, Werneke AM, Bash RE, Kim S, Berens ME, Miller CR. Genomic profiles of low-grade murine gliomas evolve during progression to glioblastoma. Neuro Oncol 2018; 19:1237-1247. [PMID: 28398584 DOI: 10.1093/neuonc/nox050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background Gliomas are diverse neoplasms with multiple molecular subtypes. How tumor-initiating mutations relate to molecular subtypes as these tumors evolve during malignant progression remains unclear. Methods We used genetically engineered mouse models, histopathology, genetic lineage tracing, expression profiling, and copy number analyses to examine how genomic tumor diversity evolves during the course of malignant progression from low- to high-grade disease. Results Knockout of all 3 retinoblastoma (Rb) family proteins was required to initiate low-grade tumors in adult mouse astrocytes. Mutations activating mitogen-activated protein kinase signaling, specifically KrasG12D, potentiated Rb-mediated tumorigenesis. Low-grade tumors showed mutant Kras-specific transcriptome profiles but lacked copy number mutations. These tumors stochastically progressed to high-grade, in part through acquisition of copy number mutations. High-grade tumor transcriptomes were heterogeneous and consisted of 3 subtypes that mimicked human mesenchymal, proneural, and neural glioblastomas. Subtypes were confirmed in validation sets of high-grade mouse tumors initiated by different driver mutations as well as human patient-derived xenograft models and glioblastoma tumors. Conclusion These results suggest that oncogenic driver mutations influence the genomic profiles of low-grade tumors and that these, as well as progression-acquired mutations, contribute strongly to the genomic heterogeneity across high-grade tumors.
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Affiliation(s)
- Mark Vitucci
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - David M Irvin
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Robert S McNeill
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Ralf S Schmid
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Jeremy M Simon
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Harshil D Dhruv
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Marni B Siegel
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Andrea M Werneke
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Ryan E Bash
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Seungchan Kim
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Michael E Berens
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - C Ryan Miller
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
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47
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McNeill RS, Canoutas DA, Stuhlmiller TJ, Dhruv HD, Irvin DM, Bash RE, Angus SP, Herring LE, Simon JM, Skinner KR, Limas JC, Chen X, Schmid RS, Siegel MB, Van Swearingen AED, Hadler MJ, Sulman EP, Sarkaria JN, Anders CK, Graves LM, Berens ME, Johnson GL, Miller CR. Combination therapy with potent PI3K and MAPK inhibitors overcomes adaptive kinome resistance to single agents in preclinical models of glioblastoma. Neuro Oncol 2018; 19:1469-1480. [PMID: 28379424 DOI: 10.1093/neuonc/nox044] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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: 12/21/2022] Open
Abstract
Background Glioblastoma (GBM) is the most common and aggressive primary brain tumor. Prognosis remains poor despite multimodal therapy. Developing alternative treatments is essential. Drugs targeting kinases within the phosphoinositide 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) effectors of receptor tyrosine kinase (RTK) signaling represent promising candidates. Methods We previously developed a non-germline genetically engineered mouse model of GBM in which PI3K and MAPK are activated via Pten deletion and KrasG12D in immortalized astrocytes. Using this model, we examined the influence of drug potency on target inhibition, alternate pathway activation, efficacy, and synergism of single agent and combination therapy with inhibitors of these 2 pathways. Efficacy was then examined in GBM patient-derived xenografts (PDX) in vitro and in vivo. Results PI3K and mitogen-activated protein kinase kinase (MEK) inhibitor potency was directly associated with target inhibition, alternate RTK effector activation, and efficacy in mutant murine astrocytes in vitro. The kinomes of GBM PDX and tumor samples were heterogeneous, with a subset of the latter harboring MAPK hyperactivation. Dual PI3K/MEK inhibitor treatment overcame alternate effector activation, was synergistic in vitro, and was more effective than single agent therapy in subcutaneous murine allografts. However, efficacy in orthotopic allografts was minimal. This was likely due to dose-limiting toxicity and incomplete target inhibition. Conclusion Drug potency influences PI3K/MEK inhibitor-induced target inhibition, adaptive kinome reprogramming, efficacy, and synergy. Our findings suggest that combination therapies with highly potent, brain-penetrant kinase inhibitors will be required to improve patient outcomes.
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Affiliation(s)
- Robert S McNeill
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Demitra A Canoutas
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Timothy J Stuhlmiller
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Harshil D Dhruv
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - David M Irvin
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Ryan E Bash
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Steven P Angus
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Laura E Herring
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Jeremy M Simon
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Kasey R Skinner
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Juanita C Limas
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Xin Chen
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Ralf S Schmid
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Marni B Siegel
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Amanda E D Van Swearingen
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Michael J Hadler
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Erik P Sulman
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Jann N Sarkaria
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Carey K Anders
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Lee M Graves
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Michael E Berens
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Gary L Johnson
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - C Ryan Miller
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
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Israel JW, Chappell GA, Simon JM, Pott S, Safi A, Lewis L, Cotney P, Boulos HS, Bodnar W, Lieb JD, Crawford GE, Furey TS, Rusyn I. Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription. Mamm Genome 2018; 29:153-167. [PMID: 29429127 PMCID: PMC6095468 DOI: 10.1007/s00335-018-9739-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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] [Received: 12/27/2017] [Accepted: 02/03/2018] [Indexed: 12/27/2022]
Abstract
Epigenetic effects of environmental chemicals are under intense investigation to fill existing knowledge gaps between environmental/occupational exposures and adverse health outcomes. Chromatin accessibility is one prominent mechanism of epigenetic control of transcription, and understanding of the chemical effects on both could inform the causal role of epigenetic alterations in disease mechanisms. In this study, we hypothesized that baseline variability in chromatin organization and transcription profiles among various tissues and mouse strains influence the outcome of exposure to the DNA damaging chemical 1,3-butadiene. To test this hypothesis, we evaluated DNA damage along with comprehensive quantification of RNA transcripts (RNA-seq), identification of accessible chromatin (ATAC-seq), and characterization of regions with histone modifications associated with active transcription (ChIP-seq for acetylation at histone 3 lysine 27, H3K27ac). We collected these data in the lung, liver, and kidney of mice from two genetically divergent strains, C57BL/6J and CAST/EiJ, that were exposed to clean air or to 1,3-butadiene (~600 ppm) for 2 weeks. We found that tissue effects dominate differences in both gene expression and chromatin states, followed by strain effects. At baseline, xenobiotic metabolism was consistently more active in CAST/EiJ, while immune system pathways were more active in C57BL/6J across tissues. Surprisingly, even though all three tissues in both strains harbored butadiene-induced DNA damage, little transcriptional effect of butadiene was observed in liver and kidney. Toxicologically relevant effects of butadiene in the lung were on the pathways of xenobiotic metabolism and inflammation. We also found that variability in chromatin accessibility across individuals (i.e., strains) only partially explains the variability in transcription. This study showed that variation in the basal states of epigenome and transcriptome may be useful indicators for individuals or tissues susceptible to genotoxic environmental chemicals.
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Affiliation(s)
- Jennifer W Israel
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Grace A Chappell
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC, USA
| | - Jeremy M Simon
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Sebastian Pott
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Alexias Safi
- Department of Pediatrics, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Lauren Lewis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Paul Cotney
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Hala S Boulos
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Wanda Bodnar
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC, USA
| | - Jason D Lieb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Gregory E Crawford
- Department of Pediatrics, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Terrence S Furey
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.
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49
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Weiser M, Simon JM, Kochar B, Tovar A, Israel JW, Robinson A, Gipson GR, Schaner MS, Herfarth HH, Sartor RB, McGovern DP, Rahbar R, Sadiq TS, Koruda MJ, Furey TS, Sheikh SZ. Molecular classification of Crohn's disease reveals two clinically relevant subtypes. Gut 2018; 67:36-42. [PMID: 27742763 PMCID: PMC5426990 DOI: 10.1136/gutjnl-2016-312518] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/09/2016] [Accepted: 09/18/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The clinical presentation and course of Crohn's disease (CD) is highly variable. We sought to better understand the cellular and molecular mechanisms that guide this heterogeneity, and characterise the cellular processes associated with disease phenotypes. DESIGN We examined both gene expression and gene regulation (chromatin accessibility) in non-inflamed colon tissue from a cohort of adult patients with CD and control patients. To support the generality of our findings, we analysed previously published expression data from a large cohort of treatment-naïve paediatric CD and control ileum. RESULTS We found that adult patients with CD clearly segregated into two classes based on colon tissue gene expression-one that largely resembled the normal colon and one where certain genes showed expression patterns normally specific to the ileum. These classes were supported by changes in gene regulatory profiles observed at the level of chromatin accessibility, reflective of a fundamental shift in underlying molecular phenotypes. Furthermore, gene expression from the ilea of a treatment-naïve cohort of paediatric patients with CD could be similarly subdivided into colon-like and ileum-like classes. Finally, expression patterns within these CD subclasses highlight large-scale differences in the immune response and aspects of cellular metabolism, and were associated with multiple clinical phenotypes describing disease behaviour, including rectal disease and need for colectomy. CONCLUSIONS Our results strongly suggest that these molecular signatures define two clinically relevant forms of CD irrespective of tissue sampling location, patient age or treatment status.
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Affiliation(s)
- Matthew Weiser
- Department of Genetics, University of North Carolina at Chapel Hill,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill
| | - Jeremy M. Simon
- Department of Genetics, University of North Carolina at Chapel Hill
| | - Bharati Kochar
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill,Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - Adelaide Tovar
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill
| | | | - Adam Robinson
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - Gregory R. Gipson
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - Matthew S. Schaner
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - Hans H. Herfarth
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - R. Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Reza Rahbar
- Department of Surgery, University of North Carolina at Chapel Hill
| | - Timothy S. Sadiq
- Department of Surgery, University of North Carolina at Chapel Hill
| | - Mark J. Koruda
- Department of Surgery, University of North Carolina at Chapel Hill
| | - Terrence S. Furey
- Department of Genetics, University of North Carolina at Chapel Hill,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill,Department of Biology, University of North Carolina at Chapel Hill
| | - Shehzad Z. Sheikh
- Department of Genetics, University of North Carolina at Chapel Hill,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill,Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill
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Chappell GA, Israel JW, Simon JM, Pott S, Safi A, Eklund K, Sexton KG, Bodnar W, Lieb JD, Crawford GE, Rusyn I, Furey TS. Variation in DNA-Damage Responses to an Inhalational Carcinogen (1,3-Butadiene) in Relation to Strain-Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice. Environ Health Perspect 2017; 125:107006. [PMID: 29038090 PMCID: PMC5944832 DOI: 10.1289/ehp1937] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The damaging effects of exposure to environmental toxicants differentially affect genetically distinct individuals, but the mechanisms contributing to these differences are poorly understood. Genetic variation affects the establishment of the gene regulatory landscape and thus gene expression, and we hypothesized that this contributes to the observed heterogeneity in individual responses to exogenous cellular insults. OBJECTIVES We performed an in vivo study of how genetic variation and chromatin organization may dictate susceptibility to DNA damage, and influence the cellular response to such damage, caused by an environmental toxicant. MATERIALS AND METHODS We measured DNA damage, messenger RNA (mRNA) and microRNA (miRNA) expression, and genome-wide chromatin accessibility in lung tissue from two genetically divergent inbred mouse strains, C57BL/6J and CAST/EiJ, both in unexposed mice and in mice exposed to a model DNA-damaging chemical, 1,3-butadiene. RESULTS Our results showed that unexposed CAST/EiJ and C57BL/6J mice have very different chromatin organization and transcription profiles in the lung. Importantly, in unexposed CAST/EiJ mice, which acquired relatively less 1,3-butadiene-induced DNA damage, we observed increased transcription and a more accessible chromatin landscape around genes involved in detoxification pathways. Upon chemical exposure, chromatin was significantly remodeled in the lung of C57BL/6J mice, a strain that acquired higher levels of 1,3-butadiene-induced DNA damage, around the same genes, ultimately resembling the molecular profile of CAST/EiJ. CONCLUSIONS These results suggest that strain-specific changes in chromatin and transcription in response to chemical exposure lead to a "compensation" for underlying genetic-driven interindividual differences in the baseline chromatin and transcriptional state. This work represents an example of how chemical and environmental exposures can be evaluated to better understand gene-by-environment interactions, and it demonstrates the important role of chromatin response in transcriptomic changes and, potentially, in deleterious effects of exposure. https://doi.org/10.1289/EHP1937.
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Affiliation(s)
- Grace A Chappell
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station , Texas, USA
- Department of Environmental Sciences and Engineering, University of North Carolina , Chapel Hill, North Carolina, USA
| | - Jennifer W Israel
- Department of Genetics, University of North Carolina , Chapel Hill, North Carolina, USA
| | - Jeremy M Simon
- Department of Genetics, University of North Carolina , Chapel Hill, North Carolina, USA
| | - Sebastian Pott
- Department of Human Genetics, University of Chicago , Chicago, Illinois, USA
| | - Alexias Safi
- Department of Pediatrics, Duke Center for Genomic and Computational Biology, Duke University , Durham, North Carolina, USA
| | - Karl Eklund
- Department of Genetics, University of North Carolina , Chapel Hill, North Carolina, USA
| | - Kenneth G Sexton
- Department of Environmental Sciences and Engineering, University of North Carolina , Chapel Hill, North Carolina, USA
| | - Wanda Bodnar
- Department of Environmental Sciences and Engineering, University of North Carolina , Chapel Hill, North Carolina, USA
| | - Jason D Lieb
- Department of Human Genetics, University of Chicago , Chicago, Illinois, USA
| | - Gregory E Crawford
- Department of Pediatrics, Duke Center for Genomic and Computational Biology, Duke University , Durham, North Carolina, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station , Texas, USA
| | - Terrence S Furey
- Department of Genetics, University of North Carolina , Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina , Chapel Hill, North Carolina, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine , Chapel Hill, North Carolina, USA
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