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Stribling D, Xia Y, Amer MK, Graim KS, Mulligan CJ, Renne R. The model student: GPT-4 performance on graduate biomedical science exams. Sci Rep 2024; 14:5670. [PMID: 38453979 PMCID: PMC10920673 DOI: 10.1038/s41598-024-55568-7] [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: 09/28/2023] [Accepted: 02/25/2024] [Indexed: 03/09/2024] Open
Abstract
The GPT-4 large language model (LLM) and ChatGPT chatbot have emerged as accessible and capable tools for generating English-language text in a variety of formats. GPT-4 has previously performed well when applied to questions from multiple standardized examinations. However, further evaluation of trustworthiness and accuracy of GPT-4 responses across various knowledge domains is essential before its use as a reference resource. Here, we assess GPT-4 performance on nine graduate-level examinations in the biomedical sciences (seven blinded), finding that GPT-4 scores exceed the student average in seven of nine cases and exceed all student scores for four exams. GPT-4 performed very well on fill-in-the-blank, short-answer, and essay questions, and correctly answered several questions on figures sourced from published manuscripts. Conversely, GPT-4 performed poorly on questions with figures containing simulated data and those requiring a hand-drawn answer. Two GPT-4 answer-sets were flagged as plagiarism based on answer similarity and some model responses included detailed hallucinations. In addition to assessing GPT-4 performance, we discuss patterns and limitations in GPT-4 capabilities with the goal of informing design of future academic examinations in the chatbot era.
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Affiliation(s)
- Daniel Stribling
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, 32610, USA.
- UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.
| | - Yuxing Xia
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
- Department of Neurology, UCLA, Los Angeles, CA, 90095, USA
| | - Maha K Amer
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, 32610, USA
| | - Kiley S Graim
- Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, 32610, USA
| | - Connie J Mulligan
- UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Department of Anthropology, University of Florida, Gainesville, FL, 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, 32610, USA.
- UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.
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2
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Chekka LMS, Tantawy M, Langaee T, Wang D, Renne R, Chapman AB, Gums JG, Boerwinkle E, Cooper-DeHoff RM, Johnson JA. Circulating microRNA Biomarkers of Thiazide Response in Hypertension. J Am Heart Assoc 2024; 13:e032433. [PMID: 38353215 PMCID: PMC11010084 DOI: 10.1161/jaha.123.032433] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024]
Abstract
BACKGROUND Thiazide diuretics are the second most frequently prescribed class of antihypertensives, but up to 50% of patients with hypertension have minimal antihypertensive response to thiazides. We explored circulating microRNAs (miRNAs) in search of predictive biomarkers of thiazide response. METHODS AND RESULTS We profiled 754 miRNAs in baseline plasma samples of 36 hypertensive European American adults treated with hydrochlorothiazide, categorized into responders (n=18) and nonresponders (n=18) on the basis of diastolic blood pressure response to hydrochlorothiazide. miRNAs with ≥2.5-fold differential expression between responders and nonresponders were considered for validation in 3 cohorts (n=50 each): hydrochlorothiazide-treated European Americans, chlorthalidone-treated European Americans, and hydrochlorothiazide-treated Black individuals. Different blood pressure phenotypes including categorical (responder versus nonresponder) and continuous diastolic blood pressure and systolic blood pressure were tested for association with the candidate miRNA expression using multivariate regression analyses adjusting for age, sex, and baseline blood pressure. After quality control, 74 miRNAs were available for screening, 19 of which were considered for validation. In the validation cohort, miR-193b-3p and 30d-5p showed significant associations with continuous SBP or diastolic blood pressure response or both, to hydrochlorothiazide in European Americans at Benjamini-Hochberg adjusted P<0.05. In the combined analysis of validation cohorts, let-7g (odds ratio, 0.6 [95% CI, 0.4-0.8]), miR-142-3p (odds ratio, 1.1 [95% CI, 1.0, 1.2]), and miR-423-5p (odds ratio, 0.7 [95% CI, 0.5-0.9]) associated with categorical diastolic blood pressure response at Benjamini-Hochberg adjusted P<0.05. Predicted target genes of the 5 miRNAs were mapped to key hypertension pathways: lysine degradation, fatty acid biosynthesis, and metabolism. CONCLUSIONS The above identified circulating miRNAs may have a potential for clinical use as biomarkers for thiazide diuretic selection in hypertension. REGISTRATION URL: ClinicalTrials.gov. Unique identifiers: NCT00246519, NCT01203852, NCT00005520.
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Affiliation(s)
- Lakshmi Manasa S Chekka
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine University of Florida Gainesville FL
| | - Marwa Tantawy
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine University of Florida Gainesville FL
| | - Taimour Langaee
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine University of Florida Gainesville FL
| | - Danxin Wang
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine University of Florida Gainesville FL
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, College of Medicine University of Florida Gainesville FL
| | | | - John G Gums
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine University of Florida Gainesville FL
| | - Eric Boerwinkle
- University of Texas at Houston Center for Human Genetics Houston TX
| | - Rhonda M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine University of Florida Gainesville FL
- Division of Cardiovascular Medicine, Department of Medicine University of Florida Gainesville FL
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine University of Florida Gainesville FL
- Division of Cardiovascular Medicine, Department of Medicine University of Florida Gainesville FL
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Staras SAS, Wollney EN, Emerson LE, Silver N, Dziegielewski PT, Hansen MD, Sanchez G, D'Ingeo D, Johnson‐Mallard V, Renne R, Fredenburg K, Gutter M, Zamojski K, Vandeweerd C, Bylund CL. Identifying locally actionable strategies to increase participant acceptability and feasibility to participate in Phase I cancer clinical trials. Health Expect 2023; 27:e13920. [PMID: 38041447 PMCID: PMC10726272 DOI: 10.1111/hex.13920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/16/2023] [Accepted: 11/09/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Recruitment of cancer clinical trial (CCT) participants, especially participants representing the diversity of the US population, is necessary to create successful medications and a continual challenge. These challenges are amplified in Phase I cancer trials that focus on evaluating the safety of new treatments and are the gateway to treatment development. In preparation for recruitment to a Phase I recurrent head and neck cancer (HNC) trial, we assessed perceived barriers to participation or referral and suggestions for recruitment among people with HNC and community physicians (oncologist, otolaryngologist or surgeon). METHODS Between December 2020 and February 2022, we conducted a qualitative needs assessment via semistructured interviews with a race and ethnicity-stratified sample of people with HNC (n = 30: 12 non-Hispanic White, 9 non-Hispanic African American, 8 Hispanic and 1 non-Hispanic Pacific Islander) and community physicians (n = 16) within the University of Florida Health Cancer Center catchment area. Interviews were analyzed using a qualitative content analysis approach to describe perspectives and identify relevant themes. RESULTS People with HNC reported thematic barriers included: concerns about side effects, safety and efficacy; lack of knowledge and systemic and environmental obstacles. Physicians identified thematic barriers of limited physician knowledge; clinic and physician barriers and structural barriers. People with HNC and physicians recommended themes included: improved patient education, dissemination of trial information and interpersonal communication between community physicians and CCT staff. CONCLUSIONS The themes identified by people with HNC and community physicians are consistent with research efforts and recommendations on how to increase the participation of people from minoritized populations in CCTs. This community needs assessment provides direction on the selection of strategies to increase CCT participation and referral. PATIENT OR PUBLIC CONTRIBUTION This study focused on people with HNC and community physicians' lived experience and their interpretations of how they would consider a future Phase I clinical trial. In addition to our qualitative data reflecting community voices, a community member reviewed the draft interview guide before data collection and both people with HNC and physicians aided interpretation of the findings.
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Affiliation(s)
- Stephanie A. S. Staras
- Department of Health Outcomes and Biomedical InformaticsUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Easton N. Wollney
- Department of Health Outcomes and Biomedical InformaticsUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Lisa E. Emerson
- Department of Microbiology and Cell Science, Institute of Food and Agricultural SciencesUniversity of FloridaGainesvilleFloridaUSA
| | | | - Peter T. Dziegielewski
- Department of OtolaryngologyUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Marta D. Hansen
- Department of Health Outcomes and Biomedical InformaticsUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Gabriela Sanchez
- Department of Health Outcomes and Biomedical InformaticsUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Dalila D'Ingeo
- Department of Health Outcomes and Biomedical InformaticsUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | | | - Rolf Renne
- Department of Molecular Genetics and MicrobiologyUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Kristianna Fredenburg
- Department of PathologyUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Michael Gutter
- Department of Family, Youth and Community Sciences, Institute of Food and Agricultural SciencesUniversity of FloridaGainesvilleFloridaUSA
| | - Kendra Zamojski
- Department of Family, Youth and Community Sciences, Institute of Food and Agricultural SciencesUniversity of FloridaGainesvilleFloridaUSA
| | - Carla Vandeweerd
- Department of Health Outcomes and Biomedical InformaticsUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Carma L. Bylund
- Department of Health Outcomes and Biomedical InformaticsUniversity of Florida College of MedicineGainesvilleFloridaUSA
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4
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Stribling D, Gay LA, Renne R. Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods. Bioinformatics 2023; 39:btad721. [PMID: 38006335 PMCID: PMC10701094 DOI: 10.1093/bioinformatics/btad721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 11/27/2023] Open
Abstract
SUMMARY Experimental methods using microRNA/target ligation have recently provided significant insights into microRNA functioning through generation of chimeric (hybrid) RNA sequences. Here, we introduce Hybkit, a Python3 API, and command-line toolkit for analysis of hybrid sequence data in the "hyb" file format to enable customizable evaluation and annotation of hybrid characteristics. The Hybkit API includes a suite of python objects for developing custom analyses of hybrid data as well as miRNA-specific analysis methods, built-in plotting of analysis results, and incorporation of predicted miRNA/target interactions in Vienna format. AVAILABILITY AND IMPLEMENTATION Hybkit is provided free and open source under the GNU GPL license at github.com/RenneLab/hybkit and archived on Zenodo (doi.org/10.5281/zenodo.7834299). Hybkit distributions are also provided via PyPI (pypi.org/project/hybkit), Conda (bioconda.github.io/recipes/hybkit/README.html), and Docker (quay.io/repository/biocontainers/hybkit).
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Affiliation(s)
- Daniel Stribling
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, United States
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, United States
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, United States
| | - Lauren A Gay
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, United States
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, United States
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, United States
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, United States
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5
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Nanni AV, Martinez N, Graze R, Morse A, Newman JRB, Jain V, Vlaho S, Signor S, Nuzhdin SV, Renne R, McIntyre LM. Sex-Biased Expression Is Associated With Chromatin State in Drosophila melanogaster and Drosophila simulans. Mol Biol Evol 2023; 40:msad078. [PMID: 37116218 PMCID: PMC10162771 DOI: 10.1093/molbev/msad078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 02/24/2023] [Accepted: 03/13/2023] [Indexed: 04/30/2023] Open
Abstract
In Drosophila melanogaster and D. simulans head tissue, 60% of orthologous genes show evidence of sex-biased expression in at least one species. Of these, ∼39% (2,192) are conserved in direction. We hypothesize enrichment of open chromatin in the sex where we see expression bias and closed chromatin in the opposite sex. Male-biased orthologs are significantly enriched for H3K4me3 marks in males of both species (∼89% of male-biased orthologs vs. ∼76% of unbiased orthologs). Similarly, female-biased orthologs are significantly enriched for H3K4me3 marks in females of both species (∼90% of female-biased orthologs vs. ∼73% of unbiased orthologs). The sex-bias ratio in female-biased orthologs was similar in magnitude between the two species, regardless of the closed chromatin (H3K27me2me3) marks in males. However, in male-biased orthologs, the presence of H3K27me2me3 in both species significantly reduced the correlation between D. melanogaster sex-bias ratio and the D. simulans sex-bias ratio. Male-biased orthologs are enriched for evidence of positive selection in the D. melanogaster group. There are more male-biased genes than female-biased genes in both species. For orthologs with gains/losses of sex-bias between the two species, there is an excess of male-bias compared to female-bias, but there is no consistent pattern in the relationship between H3K4me3 or H3K27me2me3 chromatin marks and expression. These data suggest chromatin state is a component of the maintenance of sex-biased expression and divergence of sex-bias between species is reflected in the complexity of the chromatin status.
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Affiliation(s)
- Adalena V Nanni
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL
| | - Natalie Martinez
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Rita Graze
- Department of Biological Sciences, Auburn University, Auburn, AL
| | - Alison Morse
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL
| | - Jeremy R B Newman
- University of Florida Genetics Institute, University of Florida, Gainesville, FL
| | - Vaibhav Jain
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Srna Vlaho
- Department of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Sarah Signor
- Department of Biological Sciences, North Dakota State University, Fargo, ND
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL
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6
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Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. Virology under the Microscope-a Call for Rational Discourse. mSphere 2023; 8:e0003423. [PMID: 36700653 PMCID: PMC10117089 DOI: 10.1128/msphere.00034-23] [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: 01/27/2023] Open
Abstract
Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.
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Affiliation(s)
- Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Seema Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - James Alwine
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael J Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daphne Avgousti
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | | | - David Bloom
- University of Florida, Gainesville, Florida, USA
| | - Adrianus Boon
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Curtis Brandt
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | | | - Craig Cameron
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | - Gary Chan
- SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anna Cliffe
- University of Virginia, Charlottesville, Virginia, USA
| | - John Coffin
- Tufts University, Boston, Massachusetts, USA
| | | | - Blossom Damania
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Kari Debbink
- Johns Hopkins University, Baltimore, Maryland, USA
| | | | | | | | | | | | - W Paul Duprex
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Nels Elde
- University of Utah, Salt Lake City, Utah, USA
| | - Michael Emerman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lynn Enquist
- Princeton University, Princeton, New Jersey, USA
| | | | | | | | | | | | - Klaus Frueh
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Michaela Gack
- Florida Research and Innovation Center, Port Saint Lucie, Florida, USA
| | - Marta Gaglia
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Denise Galloway
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Adam Geballe
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Meaghan Hancock
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Eva Harris
- University of California, Berkeley, Berkeley, California, USA
| | | | - Mark Heise
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | | | | | - Jeremy Kamil
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | - David Knipe
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Ryan Langlois
- University of Minnesota, Minneapolis, Minnesota, USA
| | - Adam Lauring
- University of Michigan, Ann Arbor, Michigan, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Leib
- Dartmouth College, Lebanon, New Hampshire, USA
| | - Shan-Lu Liu
- The Ohio State University, Columbus, Ohio, USA
| | | | | | | | - Jennifer Lund
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Andrew Mehle
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Ian Mohr
- New York University, New York, New York, USA
| | - Cary Moody
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | - Karl Münger
- Tufts University, Boston, Massachusetts, USA
| | - Eain Murphy
- SUNY Upstate Medical University, Syracuse, New York, USA
| | | | - Jay Nelson
- Oregon Health and Science University, Beaverton, Oregon, USA
| | | | | | | | - Akira Ono
- University of Michigan, Ann Arbor, Michigan, USA
| | | | - David Ornelles
- Wake Forest University, Winston-Salem, North Carolina, USA
| | - Jing-Hsiung Ou
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | | | | | | | - John Purdy
- University of Arizona, Tucson, Arizona, USA
| | - Dohun Pyeon
- Michigan State University, East Lansing, Michigan, USA
| | | | - Rolf Renne
- University of Florida, Gainesville, Florida, USA
| | - Charles Rice
- The Rockefeller University, New York, New York, USA
| | | | | | - Charles Russell
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Martin Sapp
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | | | - Bert Semler
- University of California, Irvine, Irvine, California, USA
| | - Thomas Shenk
- Princeton University, Princeton, New Jersey, USA
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Jason Smith
- University of Washington, Seattle, Washington, USA
| | | | | | - Kanta Subbarao
- The Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Troy Sutton
- The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew Tai
- University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Zsolt Toth
- University of Florida, Gainesville, Florida, USA
| | | | | | | | - Derek Walsh
- Northwestern University, Chicago, Illinois, USA
| | | | | | | | - Sandra Weller
- University of Connecticut, Farmington, Connecticut, USA
| | - Sean Whelan
- Washington University, St. Louis, Missouri, USA
| | | | | | | | - Scott Wong
- Oregon Health and Science University, Beaverton, Oregon, USA
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7
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Gobin C, Inkabi S, Lattimore CC, Gu T, Menefee JN, Rodriguez M, Kates H, Fields C, Bian T, Silver N, Xing C, Yates C, Renne R, Xie M, Fredenburg KM. Investigating miR-9 as a mediator in laryngeal cancer health disparities. Front Oncol 2023; 13:1096882. [PMID: 37081981 PMCID: PMC10112398 DOI: 10.3389/fonc.2023.1096882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Background For several decades, Black patients have carried a higher burden of laryngeal cancer among all races. Even when accounting for sociodemographics, a disparity remains. Differentially expressed microRNAs have been linked to racially disparate clinical outcomes in breast and prostate cancers, yet an association in laryngeal cancer has not been addressed. In this study, we present our computational analysis of differentially expressed miRNAs in Black compared with White laryngeal cancer and further validate microRNA-9-5p (miR-9-5p) as a potential mediator of cancer phenotype and chemoresistance. Methods Bioinformatic analysis of 111 (92 Whites, 19 Black) laryngeal squamous cell carcinoma (LSCC) specimens from the TCGA revealed miRNAs were significantly differentially expressed in Black compared with White LSCC. We focused on miR-9-5 p which had a significant 4-fold lower expression in Black compared with White LSCC (p<0.05). After transient transfection with either miR-9 mimic or inhibitor in cell lines derived from Black (UM-SCC-12) or White LSCC patients (UM-SCC-10A), cellular migration and cell proliferation was assessed. Alterations in cisplatin sensitivity was evaluated in transient transfected cells via IC50 analysis. qPCR was performed on transfected cells to evaluate miR-9 targets and chemoresistance predictors, ABCC1 and MAP1B. Results Northern blot analysis revealed mature miR-9-5p was inherently lower in cell line UM-SCC-12 compared with UM-SCC-10A. UM -SCC-12 had baseline increase in cellular migration (p < 0.01), proliferation (p < 0.0001) and chemosensitivity (p < 0.01) compared to UM-SCC-10A. Increasing miR-9 in UM-SCC-12 cells resulted in decreased cellular migration (p < 0.05), decreased proliferation (p < 0.0001) and increased sensitivity to cisplatin (p < 0.001). Reducing miR-9 in UM-SCC-10A cells resulted in increased cellular migration (p < 0.05), increased proliferation (p < 0.05) and decreased sensitivity to cisplatin (p < 0.01). A significant inverse relationship in ABCC1 and MAP1B gene expression was observed when miR-9 levels were transiently elevated or reduced in either UM-SCC-12 or UM-SCC-10A cell lines, respectively, suggesting modulation by miR-9. Conclusion Collectively, these studies introduce differential miRNA expression in LSCC cancer health disparities and propose a role for low miR-9-5p as a mediator in LSCC tumorigenesis and chemoresistance.
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Affiliation(s)
- Christina Gobin
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Samuel Inkabi
- College of Graduate Health Studies, A.T. Still University, Kirksville, MO, United States
| | - Chayil C. Lattimore
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Tongjun Gu
- Interdisciplinary Center for Biotechnology Research Bioinformatics Core Facility, University of Florida, Gainesville, FL, United States
| | - James N. Menefee
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Mayrangela Rodriguez
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Heather Kates
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Christopher Fields
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Tengfei Bian
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, United States
| | - Natalie Silver
- Head and Neck Institute/Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Chengguo Xing
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, United States
| | - Clayton Yates
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, United States
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States
| | - Kristianna M. Fredenburg
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
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8
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Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. Virology under the Microscope-a Call for Rational Discourse. mBio 2023; 14:e0018823. [PMID: 36700642 PMCID: PMC9973315 DOI: 10.1128/mbio.00188-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.
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Affiliation(s)
- Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Seema Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - James Alwine
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael J. Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daphne Avgousti
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | | | - David Bloom
- University of Florida, Gainesville, Florida, USA
| | - Adrianus Boon
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Curtis Brandt
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | | | - Craig Cameron
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | - Gary Chan
- SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anna Cliffe
- University of Virginia, Charlottesville, Virginia, USA
| | - John Coffin
- Tufts University, Boston, Massachusetts, USA
| | | | - Blossom Damania
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Kari Debbink
- Johns Hopkins University, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | - Nels Elde
- University of Utah, Salt Lake City, Utah, USA
| | - Michael Emerman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lynn Enquist
- Princeton University, Princeton, New Jersey, USA
| | | | | | | | | | | | - Klaus Frueh
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Michaela Gack
- Florida Research and Innovation Center, Port Saint Lucie, Florida, USA
| | - Marta Gaglia
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Denise Galloway
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Adam Geballe
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Meaghan Hancock
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Eva Harris
- University of California, Berkeley, Berkeley, California, USA
| | | | - Mark Heise
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | | | | | - Jeremy Kamil
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | - David Knipe
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Ryan Langlois
- University of Minnesota, Minneapolis, Minnesota, USA
| | - Adam Lauring
- University of Michigan, Ann Arbor, Michigan, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Leib
- Dartmouth College, Lebanon, New Hampshire, USA
| | - Shan-Lu Liu
- The Ohio State University, Columbus, Ohio, USA
| | | | | | | | - Jennifer Lund
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Andrew Mehle
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Ian Mohr
- New York University, New York, New York, USA
| | - Cary Moody
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | - Karl Münger
- Tufts University, Boston, Massachusetts, USA
| | - Eain Murphy
- SUNY Upstate Medical University, Syracuse, New York, USA
| | | | - Jay Nelson
- Oregon Health and Science University, Beaverton, Oregon, USA
| | | | | | | | - Akira Ono
- University of Michigan, Ann Arbor, Michigan, USA
| | | | - David Ornelles
- Wake Forest University, Winston-Salem, North Carolina, USA
| | - Jing-hsiung Ou
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | | | | | | | - John Purdy
- University of Arizona, Tucson, Arizona, USA
| | - Dohun Pyeon
- Michigan State University, East Lansing, Michigan, USA
| | | | - Rolf Renne
- University of Florida, Gainesville, Florida, USA
| | - Charles Rice
- The Rockefeller University, New York, New York, USA
| | | | | | - Charles Russell
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Martin Sapp
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | | | - Bert Semler
- University of California, Irvine, Irvine, California, USA
| | - Thomas Shenk
- Princeton University, Princeton, New Jersey, USA
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Jason Smith
- University of Washington, Seattle, Washington, USA
| | | | | | - Kanta Subbarao
- The Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Troy Sutton
- The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew Tai
- University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Zsolt Toth
- University of Florida, Gainesville, Florida, USA
| | | | | | | | - Derek Walsh
- Northwestern University, Chicago, Illinois, USA
| | | | | | | | - Sandra Weller
- University of Connecticut, Farmington, Connecticut, USA
| | - Sean Whelan
- Washington University, St. Louis, Missouri, USA
| | | | | | | | - Scott Wong
- Oregon Health and Science University, Beaverton, Oregon, USA
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9
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Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. Virology under the Microscope-a Call for Rational Discourse. J Virol 2023; 97:e0008923. [PMID: 36700640 PMCID: PMC9972907 DOI: 10.1128/jvi.00089-23] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.
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Affiliation(s)
- Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Seema Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - James Alwine
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael J. Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daphne Avgousti
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | | | - David Bloom
- University of Florida, Gainesville, Florida, USA
| | - Adrianus Boon
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Curtis Brandt
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | | | - Craig Cameron
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | - Gary Chan
- SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anna Cliffe
- University of Virginia, Charlottesville, Virginia, USA
| | - John Coffin
- Tufts University, Boston, Massachusetts, USA
| | | | - Blossom Damania
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Kari Debbink
- Johns Hopkins University, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | - Nels Elde
- University of Utah, Salt Lake City, Utah, USA
| | - Michael Emerman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lynn Enquist
- Princeton University, Princeton, New Jersey, USA
| | | | | | | | | | | | - Klaus Frueh
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Michaela Gack
- Florida Research and Innovation Center, Port Saint Lucie, Florida, USA
| | - Marta Gaglia
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Denise Galloway
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Adam Geballe
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Meaghan Hancock
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Eva Harris
- University of California, Berkeley, Berkeley, California, USA
| | | | - Mark Heise
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | | | | | - Jeremy Kamil
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | - David Knipe
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Ryan Langlois
- University of Minnesota, Minneapolis, Minnesota, USA
| | - Adam Lauring
- University of Michigan, Ann Arbor, Michigan, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Leib
- Dartmouth College, Lebanon, New Hampshire, USA
| | - Shan-Lu Liu
- The Ohio State University, Columbus, Ohio, USA
| | | | | | | | - Jennifer Lund
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Andrew Mehle
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Ian Mohr
- New York University, New York, New York, USA
| | - Cary Moody
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | - Karl Münger
- Tufts University, Boston, Massachusetts, USA
| | - Eain Murphy
- SUNY Upstate Medical University, Syracuse, New York, USA
| | | | - Jay Nelson
- Oregon Health and Science University, Beaverton, Oregon, USA
| | | | | | | | - Akira Ono
- University of Michigan, Ann Arbor, Michigan, USA
| | | | - David Ornelles
- Wake Forest University, Winston-Salem, North Carolina, USA
| | - Jing-hsiung Ou
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | | | | | | | - John Purdy
- University of Arizona, Tucson, Arizona, USA
| | - Dohun Pyeon
- Michigan State University, East Lansing, Michigan, USA
| | | | - Rolf Renne
- University of Florida, Gainesville, Florida, USA
| | - Charles Rice
- The Rockefeller University, New York, New York, USA
| | | | | | - Charles Russell
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Martin Sapp
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | | | - Bert Semler
- University of California, Irvine, Irvine, California, USA
| | - Thomas Shenk
- Princeton University, Princeton, New Jersey, USA
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Jason Smith
- University of Washington, Seattle, Washington, USA
| | | | | | - Kanta Subbarao
- The Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Troy Sutton
- The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew Tai
- University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Zsolt Toth
- University of Florida, Gainesville, Florida, USA
| | | | | | | | - Derek Walsh
- Northwestern University, Chicago, Illinois, USA
| | | | | | | | - Sandra Weller
- University of Connecticut, Farmington, Connecticut, USA
| | - Sean Whelan
- Washington University, St. Louis, Missouri, USA
| | | | | | | | - Scott Wong
- Oregon Health and Science University, Beaverton, Oregon, USA
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10
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Nanni AV, Martinez N, Graze R, Morse A, Newman JRB, Jain V, Vlaho S, Signor S, Nuzhdin SV, Renne R, McIntyre LM. Sex-biased expression is associated with chromatin state in D. melanogaster and D. simulans. bioRxiv 2023:2023.01.13.523946. [PMID: 36711631 PMCID: PMC9882225 DOI: 10.1101/2023.01.13.523946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We propose a new model for the association of chromatin state and sex-bias in expression. We hypothesize enrichment of open chromatin in the sex where we see expression bias (OS) and closed chromatin in the opposite sex (CO). In this study of D. melanogaster and D. simulans head tissue, sex-bias in expression is associated with H3K4me3 (open mark) in males for male-biased genes and in females for female-biased genes in both species. Sex-bias in expression is also largely conserved in direction and magnitude between the two species on the X and autosomes. In male-biased orthologs, the sex-bias ratio is more divergent between species if both species have H3K27me2me3 marks in females compared to when either or neither species has H3K27me2me3 in females. H3K27me2me3 marks in females are associated with male-bias in expression on the autosomes in both species, but on the X only in D. melanogaster . In female-biased orthologs the relationship between the species for the sex-bias ratio is similar regardless of the H3K27me2me3 marks in males. Female-biased orthologs are more similar in the ratio of sex-bias than male-biased orthologs and there is an excess of male-bias in expression in orthologs that gain/lose sex-bias. There is an excess of male-bias in sex-limited expression in both species suggesting excess male-bias is due to rapid evolution between the species. The X chromosome has an enrichment in male-limited H3K4me3 in both species and an enrichment of sex-bias in expression compared to the autosomes.
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Affiliation(s)
- Adalena V Nanni
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Natalie Martinez
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Rita Graze
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Alison Morse
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Jeremy R B Newman
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Vaibhav Jain
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Srna Vlaho
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Sarah Signor
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
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11
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Mahar R, Ragavan M, Chang MC, Hardiman S, Moussatche N, Behar A, Renne R, Merritt ME. Metabolic signatures associated with oncolytic myxoma viral infections. Sci Rep 2022; 12:12599. [PMID: 35871072 PMCID: PMC9308783 DOI: 10.1038/s41598-022-15562-3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/27/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractOncolytic viral therapy is a recent advance in cancer treatment, demonstrating promise as a primary treatment option. To date, the secondary metabolic effects of viral infection in cancer cells has not been extensively studied. In this work, we have analyzed early-stage metabolic changes in cancer cells associated with oncolytic myxoma virus infection. Using GC–MS based metabolomics, we characterized the myxoma virus infection induced metabolic changes in three cancer cell lines—small cell (H446) and non-small cell (A549) lung cancers, and glioblastoma (SFxL). We show that even at an early stage (6 and 12 h) myxoma infection causes profound changes in cancer cell metabolism spanning several important pathways such as the citric acid cycle, fatty acid metabolism, and amino acid metabolism. In general, the metabolic effects of viral infection across cell lines are not conserved. However, we have identified several candidate metabolites that can potentially serve as biomarkers for monitoring oncolytic viral action in general.
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12
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Serfecz JC, Hong Y, Gay LA, Shekhar R, Turner PC, Renne R. DExD/H Box Helicases DDX24 and DDX49 Inhibit Reactivation of Kaposi’s Sarcoma Associated Herpesvirus by Interacting with Viral mRNAs. Viruses 2022; 14:v14102083. [PMID: 36298642 PMCID: PMC9609691 DOI: 10.3390/v14102083] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/12/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is an oncogenic gammaherpesvirus that is the causative agent of primary effusion lymphoma and Kaposi’s sarcoma. In healthy carriers, KSHV remains latent, but a compromised immune system can lead to lytic viral replication that increases the probability of tumorigenesis. RIG-I-like receptors (RLRs) are members of the DExD/H box helicase family of RNA binding proteins that recognize KSHV to stimulate the immune system and prevent reactivation from latency. To determine if other DExD/H box helicases can affect KSHV lytic reactivation, we performed a knock-down screen that revealed DHX29-dependent activities appear to support viral replication but, in contrast, DDX24 and DDX49 have antiviral activity. When DDX24 or DDX49 are overexpressed in BCBL-1 cells, transcription of all lytic viral genes and genome replication were significantly reduced. RNA immunoprecipitation of tagged DDX24 and DDX49 followed by next-generation sequencing revealed that the helicases bind to mostly immediate-early and early KSHV mRNAs. Transfection of expression plasmids of candidate KSHV transcripts, identified from RNA pull-down, demonstrated that KSHV mRNAs stimulate type I interferon (alpha/beta) production and affect the expression of multiple interferon-stimulated genes. Our findings reveal that host DExD/H box helicases DDX24 and DDX49 recognize gammaherpesvirus transcripts and convey an antiviral effect in the context of lytic reactivation.
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Affiliation(s)
- Jacquelyn C. Serfecz
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Yuan Hong
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lauren A. Gay
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ritu Shekhar
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Peter C. Turner
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
- Correspondence: ; Tel.: +1-(352)-273-8214
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13
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Fields CJ, Li L, Hiers NM, Li T, Sheng P, Huda T, Shan J, Gay L, Gu T, Bian J, Kilberg MS, Renne R, Xie M. Sequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a. PLoS Genet 2021; 17:e1009934. [PMID: 34914716 PMCID: PMC8675727 DOI: 10.1371/journal.pgen.1009934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNA) are short non-coding RNAs widely implicated in gene regulation. Most metazoan miRNAs utilize the RNase III enzymes Drosha and Dicer for biogenesis. One notable exception is the RNA polymerase II transcription start sites (TSS) miRNAs whose biogenesis does not require Drosha. The functional importance of the TSS-miRNA biogenesis is uncertain. To better understand the function of TSS-miRNAs, we applied a modified Crosslinking, Ligation, and Sequencing of Hybrids on Argonaute (AGO-qCLASH) to identify the targets for TSS-miRNAs in HCT116 colorectal cancer cells with or without DROSHA knockout. We observed that miR-320a hybrids dominate in TSS-miRNA hybrids identified by AGO-qCLASH. Targets for miR-320a are enriched for the eIF2 signaling pathway, a downstream component of the unfolded protein response. Consistently, in miR-320a mimic- and antagomir- transfected cells, differentially expressed gene products are associated with eIF2 signaling. Within the AGO-qCLASH data, we identified the endoplasmic reticulum (ER) chaperone calnexin as a direct miR-320a down-regulated target, thus connecting miR-320a to the unfolded protein response. During ER stress, but not amino acid deprivation, miR-320a up-regulates ATF4, a critical transcription factor for resolving ER stress. In summary, our study investigates the targetome of the TSS-miRNAs in colorectal cancer cells and establishes miR-320a as a regulator of unfolded protein response.
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Affiliation(s)
- Christopher J. Fields
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Nicholas M. Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Taha Huda
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Jixiu Shan
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lauren Gay
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Tongjun Gu
- Bioinformatics, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America
| | - Jiang Bian
- Department of Health Outcomes and Biomedical Informatics, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Michael S. Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Rolf Renne
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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14
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Abstract
This protocol was designed to identify microRNA (miRNA) targetomes from smaller‐input samples by performing a simplified workflow of the Cross‐Linking and Sequencing of Hybrids (CLASH) technique developed in the Tollervey group. In this ribonomics‐based technique, Cross‐Linking and Immunoprecipitation (CLIP) of Argonaute (Ago) is combined with an RNA ligase reaction that yields covalently bound “hybrids” between miRNAs and their target RNAs. While this iteration of CLIP identifies “high‐confidence” or “unambiguous” miRNA targets, the added ligation step is highly inefficient and therefore requires large numbers of cultured cells. To make this powerful approach applicable to smaller cell numbers, we created qCLASH, incorporating a workflow that performs all enzymatic reactions on bead‐bound complexes and omits gel purification of immunoprecipitated Ago complexes associated with major loss of RNA. At a sequencing depth of 100 million reads per library, which is highly feasible with rapidly decreasing sequencing costs, qCLASH, when used with three biological replicates, results in thousands of high‐confidence miRNA targets. qCLASH was first developed to identify viral miRNA targetomes of endothelial cells infected with Kaposi's sarcoma−associated herpesvirus. Since then, qCLASH has been applied to Epstein‐Barr virus− and MHV68‐infected cells, and more recently to metastatic melanoma and breast cancer cells. Currently, protocols are under development to apply qCLASH to human solid tumor specimens. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Quick Cross‐Linking and Sequencing of Hybrids (qCLASH) Support Protocol: Optimization of Ago immunoprecipitation
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Affiliation(s)
- Lauren A Gay
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida
| | - Peter C Turner
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida.,UF Health Cancer Center, University of Florida, Gainesville, Florida.,UF Genetics Institute, University of Florida, Gainesville, Florida
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15
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Stribling D, Lei Y, Guardia CM, Li L, Fields CJ, Nowialis P, Opavsky R, Renne R, Xie M. A noncanonical microRNA derived from the snaR-A noncoding RNA targets a metastasis inhibitor. RNA 2021; 27:694-709. [PMID: 33795480 PMCID: PMC8127991 DOI: 10.1261/rna.078694.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 01/26/2021] [Accepted: 03/24/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that function as critical posttranscriptional regulators in various biological processes. While most miRNAs are generated from processing of long primary transcripts via sequential Drosha and Dicer cleavage, some miRNAs that bypass Drosha cleavage can be transcribed as part of another small noncoding RNA. Here, we develop the target-oriented miRNA discovery (TOMiD) bioinformatic analysis method to identify Drosha-independent miRNAs from Argonaute crosslinking and sequencing of hybrids (Ago-CLASH) data sets. Using this technique, we discovered a novel miRNA derived from a primate specific noncoding RNA, the small NF90 associated RNA A (snaR-A). The miRNA derived from snaR-A (miR-snaR) arises independently of Drosha processing but requires Exportin-5 and Dicer for biogenesis. We identify that miR-snaR is concurrently up-regulated with the full snaR-A transcript in cancer cells. Functionally, miR-snaR associates with Ago proteins and targets NME1, a key metastasis inhibitor, contributing to snaR-A's role in promoting cancer cell migration. Our findings suggest a functional link between a novel miRNA and its precursor noncoding RNA.
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Affiliation(s)
- Daniel Stribling
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
- UF Informatics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Yi Lei
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Casey M Guardia
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Christopher J Fields
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Pawel Nowialis
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32610, USA
| | - Rene Opavsky
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
- UF Informatics Institute, University of Florida, Gainesville, Florida 32611, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Mingyi Xie
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
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16
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Ungerleider N, Bullard W, Kara M, Wang X, Roberts C, Renne R, Tibbetts S, Flemington EK. EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape. PLoS Pathog 2021; 17:e1009217. [PMID: 33956915 PMCID: PMC8130916 DOI: 10.1371/journal.ppat.1009217] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 12/16/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
The Epstein Barr virus (EBV) contributes to the tumor phenotype through a limited set of primarily non-coding viral RNAs, including 31 mature miRNAs. Here we investigated the impact of EBV miRNAs on remodeling the tumor cell transcriptome. Strikingly, EBV miRNAs displayed exceptionally abundant expression in primary EBV-associated Burkitt’s Lymphomas (BLs) and Gastric Carcinomas (GCs). To investigate viral miRNA targeting, we used the high-resolution approach, CLASH in GC and BL cell models. Affinity constant calculations of targeting efficacies for CLASH hits showed that viral miRNAs bind their targets more effectively than their host counterparts, as did Kaposi’s sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68) miRNAs. Using public BL and GC RNA-seq datasets, we found that high EBV miRNA targeting efficacies translates to enhanced reduction of target expression. Pathway analysis of high efficacy EBV miRNA targets showed enrichment for innate and adaptive immune responses. Inhibition of the immune response by EBV miRNAs was functionally validated in vivo through the finding of inverse correlations between EBV miRNAs and immune cell infiltration and T-cell diversity in BL and GC datasets. Together, this study demonstrates that EBV miRNAs are potent effectors of the tumor transcriptome that play a role in suppressing host immune response. Burkitt’s Lymphoma and gastric cancer are both associated with EBV, a prolific DNA tumor virus that latently resides in nearly all human beings. Despite mostly restricting viral gene expression to noncoding RNAs, EBV has important influences on the fitness of infected tumor cells. Here, we show that the miRNA class of viral noncoding RNAs are a major viral contributor to remodeling the tumor cell regulatory machinery in patient tumor samples. First, an assessment of miRNA expression in clinical tumor samples showed that EBV miRNAs are expressed at unexpectedly high levels relative to cell miRNAs. Using a highly specific miRNA target identification approach, CLASH, we comprehensively identified both viral and cellular miRNA targets and the relative abundance of each miRNA-mRNA interaction. We also show that viral miRNAs bind to and alter the expression of their mRNA targets more effectively than their cellular miRNA counterparts. Pathway analysis of the most effectively targeted mRNAs revealed enrichment of immune signaling pathways and we show a corresponding inverse correlation between EBV miRNA expression and infiltrating immune cells in EBV positive primary tumors. Altogether, this study shows that EBV miRNAs are key regulators of the tumor cell phenotype and the immune cell microenvironment.
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Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Whitney Bullard
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Mehmet Kara
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Scott Tibbetts
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (ST); (EKF)
| | - Erik K. Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
- * E-mail: (ST); (EKF)
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17
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Ungerleider N, Bullard W, Kara M, Wang X, Roberts C, Renne R, Tibbetts S, Flemington EK. EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape. PLoS Pathog 2021; 17:e1009217. [PMID: 33956915 DOI: 10.1101/2020.12.21.423766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 05/21/2023] Open
Abstract
The Epstein Barr virus (EBV) contributes to the tumor phenotype through a limited set of primarily non-coding viral RNAs, including 31 mature miRNAs. Here we investigated the impact of EBV miRNAs on remodeling the tumor cell transcriptome. Strikingly, EBV miRNAs displayed exceptionally abundant expression in primary EBV-associated Burkitt's Lymphomas (BLs) and Gastric Carcinomas (GCs). To investigate viral miRNA targeting, we used the high-resolution approach, CLASH in GC and BL cell models. Affinity constant calculations of targeting efficacies for CLASH hits showed that viral miRNAs bind their targets more effectively than their host counterparts, as did Kaposi's sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68) miRNAs. Using public BL and GC RNA-seq datasets, we found that high EBV miRNA targeting efficacies translates to enhanced reduction of target expression. Pathway analysis of high efficacy EBV miRNA targets showed enrichment for innate and adaptive immune responses. Inhibition of the immune response by EBV miRNAs was functionally validated in vivo through the finding of inverse correlations between EBV miRNAs and immune cell infiltration and T-cell diversity in BL and GC datasets. Together, this study demonstrates that EBV miRNAs are potent effectors of the tumor transcriptome that play a role in suppressing host immune response.
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Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Whitney Bullard
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Mehmet Kara
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Scott Tibbetts
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
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18
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Kozar I, Philippidou D, Margue C, Gay LA, Renne R, Kreis S. Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells. Cancers (Basel) 2021; 13:cancers13051096. [PMID: 33806450 PMCID: PMC7961530 DOI: 10.3390/cancers13051096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/18/2021] [Accepted: 02/26/2021] [Indexed: 01/13/2023] Open
Abstract
MicroRNAs are key post-transcriptional gene regulators often displaying aberrant expression patterns in cancer. As microRNAs are promising disease-associated biomarkers and modulators of responsiveness to anti-cancer therapies, a solid understanding of their targetome is crucial. Despite enormous research efforts, the success rates of available tools to reliably predict microRNAs (miRNA)-target interactions remains limited. To investigate the disease-associated miRNA targetome, we have applied modified cross-linking ligation and sequencing of hybrids (qCLASH) to BRAF-mutant melanoma cells. The resulting RNA-RNA hybrid molecules provide a comprehensive and unbiased snapshot of direct miRNA-target interactions. The regulatory effects on selected miRNA target genes in predicted vs. non-predicted binding regions was validated by miRNA mimic experiments. Most miRNA-target interactions deviate from the central dogma of miRNA targeting up to 60% interactions occur via non-canonical seed pairing with a strong contribution of the 3' miRNA sequence, and over 50% display a clear bias towards the coding sequence of mRNAs. miRNAs targeting the coding sequence can directly reduce gene expression (miR-34a/CD68), while the majority of non-canonical miRNA interactions appear to have roles beyond target gene suppression (miR-100/AXL). Additionally, non-mRNA targets of miRNAs (lncRNAs) whose interactions mainly occur via non-canonical binding were identified in melanoma. This first application of CLASH sequencing to cancer cells identified over 8 K distinct miRNA-target interactions in melanoma cells. Our data highlight the importance non-canonical interactions, revealing further layers of complexity of post-transcriptional gene regulation in melanoma, thus expanding the pool of miRNA-target interactions, which have so far been omitted in the cancer field.
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Affiliation(s)
- Ines Kozar
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
| | - Demetra Philippidou
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
| | - Christiane Margue
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
| | - Lauren A. Gay
- Department of Molecular Genetics and Microbiology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610, USA; (L.A.G.); (R.R.)
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610, USA; (L.A.G.); (R.R.)
| | - Stephanie Kreis
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
- Correspondence:
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19
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Jahn SC, Gay LA, Weaver CJ, Renne R, Langaee TY, Stacpoole PW, James MO. Age-Related Changes in miRNA Expression Influence GSTZ1 and Other Drug Metabolizing Enzymes. Drug Metab Dispos 2020; 48:563-569. [PMID: 32357971 DOI: 10.1124/dmd.120.090639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/07/2020] [Indexed: 11/22/2022] Open
Abstract
Previous work has shown that hepatic levels of human glutathione transferase zeta 1 (GSTZ1) protein, involved in tyrosine catabolism and responsible for metabolism of the investigational drug dichloroacetate, increase in cytosol after birth before reaching a plateau around age 7. However, the mechanism regulating this change of expression is still unknown, and previous studies showed that GSTZ1 mRNA levels did not correlate with GSTZ1 protein expression. In this study, we addressed the hypothesis that microRNAs (miRNAs) could regulate expression of GSTZ1. We obtained liver samples from donors aged less than 1 year or older than 13 years and isolated total RNA for use in a microarray to identify miRNAs that were downregulated in the livers of adults compared with children. From a total of 2578 human miRNAs tested, 63 miRNAs were more than 2-fold down-regulated in adults, of which miR-376c-3p was predicted to bind to the 3' untranslated region of GSTZ1 mRNA. There was an inverse correlation of miR-376c-3p and GSTZ1 protein expression in the liver samples. Using cell culture, we confirmed that miR-376c-3p could downregulate GSTZ1 protein expression. Our findings suggest that miR-376c-3p prevents production of GSTZ1 through inhibition of translation. These experiments further our understanding of GSTZ1 regulation. Furthermore, our array results provide a database resource for future studies on mechanisms regulating human hepatic developmental expression. SIGNIFICANCE STATEMENT: Hepatic glutathione transferase zeta 1 (GSTZ1) is responsible for metabolism of the tyrosine catabolite maleylacetoacetate as well as the investigational drug dichloroacetate. Through examination of microRNA (miRNA) expression in liver from infants and adults and studies in cells, we showed that expression of GSTZ1 is controlled by miRNA. This finding has application to the dosing regimen of the drug dichloroacetate. The miRNA expression profiles are provided and will prove useful for future studies of drug-metabolizing enzymes in infants and adults.
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Affiliation(s)
- Stephan C Jahn
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Lauren A Gay
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Claire J Weaver
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Rolf Renne
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Taimour Y Langaee
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Peter W Stacpoole
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
| | - Margaret O James
- Departments of Medicinal Chemistry (S.C.J., C.J.W., M.O.J.), Pharmacotherapy and Translational Research (T.Y.L.), Medicine (P.W.S.), Biochemistry and Molecular Biology (P.W.S.), and Molecular Genetics and Microbiology (L.A.G., R.R.), University of Florida, Gainesville, Florida
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20
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Abstract
In this issue of Cell Host & Microbe, Hancock et al., 2020 show that latent HCMV infection, and specifically miR-US5-2, induces TGF-β secretion, which inhibits myelopoiesis in uninfected HPCs. They also show that HCMV-infected cells become resistant to TGF-β signaling through targeting of SMAD3 by miR-UL22-A-3p and -5p.
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Affiliation(s)
- Lauren Gay
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA; University of Florida Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; University of Florida Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
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21
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Serfecz J, Bazick H, Al Salihi MO, Turner P, Fields C, Cruz P, Renne R, Notterpek L. Downregulation of the human peripheral myelin protein 22 gene by miR-29a in cellular models of Charcot-Marie-Tooth disease. Gene Ther 2019; 26:455-464. [PMID: 31455873 PMCID: PMC6920087 DOI: 10.1038/s41434-019-0098-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 01/26/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 12/22/2022]
Abstract
The majority of hereditary neuropathies are caused by duplication of the peripheral myelin protein 22 (PMP22) gene. Therefore, mechanisms to suppress the expression of the PMP22 gene have high therapeutic significance. Here we asked whether the human PMP22 gene is a target for regulation by microRNA 29a (miR-29a). Using bioinformatics, we determined that the human PMP22 gene contains the conserved seed sequence of the miR-29a binding site and this regulatory motif is included in the duplicated region in neuropathic patients. Using luciferase reporter assays in HEK293 cells, we demonstrated that transient transfection of a miR-29a mimic is associated with reduction in PMP22 3'UTR reporter activity. Transfecting normal and humanized transgenic neuropathic mouse Schwann cells with a miR-29a expression plasmid effectively lowered both the endogenous mouse and the transgenic human PMP22 transcripts compared with control vector. In dermal fibroblasts derived from neuropathic patients, ectopic expression of miR-29a led to ~50% reduction in PMP22 mRNA, which corresponded to ~20% decrease in PMP22 protein levels. Significantly, miR-29a-mediated reduction in PMP22 mitigated the reduced mitotic capacity of the neuropathic cells. Together, these results support further testing of miR-29a and/or PMP22-targeting siRNAs as therapeutic agents for correcting the aberrant expression of PMP22 in neuropathic patients.
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Affiliation(s)
- Jacquelyn Serfecz
- Department of Molecular Genetics & Microbiology, College of Medicine University of Florida, Gainesville, FL, 32610, USA
| | - Hannah Bazick
- Department of Neuroscience, College of Medicine University of Florida, Gainesville, FL, 32610, USA
| | - Mohammed Omar Al Salihi
- Department of Neuroscience, College of Medicine University of Florida, Gainesville, FL, 32610, USA
| | - Peter Turner
- Department of Molecular Genetics & Microbiology, College of Medicine University of Florida, Gainesville, FL, 32610, USA
| | - Christopher Fields
- Department of Molecular Genetics & Microbiology, College of Medicine University of Florida, Gainesville, FL, 32610, USA
| | - Pedro Cruz
- Department of Neuroscience, College of Medicine University of Florida, Gainesville, FL, 32610, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine University of Florida, Gainesville, FL, 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics & Microbiology, College of Medicine University of Florida, Gainesville, FL, 32610, USA
- UF Health Cancer Center, College of Medicine University of Florida, Gainesville, FL, 32610, USA
| | - Lucia Notterpek
- Department of Neuroscience, College of Medicine University of Florida, Gainesville, FL, 32610, USA.
- Center for Translational Research in Neurodegenerative Disease, College of Medicine University of Florida, Gainesville, FL, 32610, USA.
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22
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Sethuraman S, Thomas M, Gay LA, Renne R. Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs. Nucleic Acids Res 2019; 46:8574-8589. [PMID: 29846699 PMCID: PMC6144796 DOI: 10.1093/nar/gky459] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 01/17/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022] Open
Abstract
Ribonomics experiments involving crosslinking and immuno-precipitation (CLIP) of Ago proteins have expanded the understanding of the miRNA targetome of several organisms. These techniques, collectively referred to as CLIP-seq, have been applied to identifying the mRNA targets of miRNAs expressed by Kaposi’s Sarcoma-associated herpes virus (KSHV) and Epstein–Barr virus (EBV). However, these studies focused on identifying only those RNA targets of KSHV and EBV miRNAs that are known to encode proteins. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are also targeted by miRNAs. In this study, we performed a systematic re-analysis of published datasets from KSHV- and EBV-driven cancers. We used CLIP-seq data from lymphoma cells or EBV-transformed B cells, and a crosslinking, ligation and sequencing of hybrids dataset from KSHV-infected endothelial cells, to identify novel lncRNA targets of viral miRNAs. Here, we catalog the lncRNA targetome of KSHV and EBV miRNAs, and provide a detailed in silico analysis of lncRNA–miRNA binding interactions. Viral miRNAs target several hundred lncRNAs, including a subset previously shown to be aberrantly expressed in human malignancies. In addition, we identified thousands of lncRNAs to be putative targets of human miRNAs, suggesting that miRNA–lncRNA interactions broadly contribute to the regulation of gene expression.
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Affiliation(s)
- Sunantha Sethuraman
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Merin Thomas
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Lauren A Gay
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA.,UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.,UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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23
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Bullard WL, Kara M, Gay LA, Sethuraman S, Wang Y, Nirmalan S, Esemenli A, Feswick A, Hoffman BA, Renne R, Tibbetts SA. Identification of murine gammaherpesvirus 68 miRNA-mRNA hybrids reveals miRNA target conservation among gammaherpesviruses including host translation and protein modification machinery. PLoS Pathog 2019; 15:e1007843. [PMID: 31393953 PMCID: PMC6687095 DOI: 10.1371/journal.ppat.1007843] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/15/2019] [Indexed: 02/07/2023] Open
Abstract
Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), establish lifelong latent infection in B cells and are associated with a variety of tumors. In addition to protein coding genes, these viruses encode numerous microRNAs (miRNAs) within their genomes. While putative host targets of EBV and KSHV miRNAs have been previously identified, the specific functions of these miRNAs during in vivo infection are largely unknown. Murine gammaherpesvirus 68 (MHV68) is a natural pathogen of rodents that is genetically related to both EBV and KSHV, and thus serves as an excellent model for the study of EBV and KSHV genetic elements such as miRNAs in the context of infection and disease. However, the specific targets of MHV68 miRNAs remain completely unknown. Using a technique known as qCLASH (quick crosslinking, ligation, and sequencing of hybrids), we have now identified thousands of Ago-associated, direct miRNA-mRNA interactions during lytic infection, latent infection and reactivation from latency. Validating this approach, detailed molecular analyses of specific interactions demonstrated repression of numerous host mRNA targets of MHV68 miRNAs, including Arid1a, Ctsl, Ifitm3 and Phc3. Notably, of the 1,505 MHV68 miRNA-host mRNA targets identified in B cells, 86% were shared with either EBV or KSHV, and 64% were shared among all three viruses, demonstrating significant conservation of gammaherpesvirus miRNA targeting. Pathway analysis of MHV68 miRNA targets further revealed enrichment of cellular pathways involved in protein synthesis and protein modification, including eIF2 Signaling, mTOR signaling and protein ubiquitination, pathways also enriched for targets of EBV and KSHV miRNAs. These findings provide substantial new information about specific targets of MHV68 miRNAs and shed important light on likely conserved functions of gammaherpesvirus miRNAs. Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), establish lifelong infections and are associated with a variety of tumors. These viruses encode numerous molecules called microRNAs (miRNAs) within their genomes, which target and suppress the products of specific genes within infected host cells. However, the function of these miRNAs during in vivo infection is largely unknown. Murine gammaherpesvirus 68 (MHV68) is a natural pathogen of rodents that is genetically related to both EBV and KSHV, and thus serves as an excellent model for the study of EBV and KSHV. Here, we describe the identification and validation of thousands of new MHV68 miRNA targets. Notably, 86% of the MHV68 miRNA targets identified were shared with either EBV or KSHV, and 64% were shared among all three viruses. Further analyses revealed enrichment of cellular pathways involved in protein synthesis and protein modification, including pathways also enriched for targets of EBV and KSHV miRNAs. These findings provide substantial new information about specific targets of MHV68 miRNAs and shed important light on likely conserved functions of gammaherpesvirus miRNAs.
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Affiliation(s)
- Whitney L. Bullard
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Mehmet Kara
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lauren A. Gay
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Sunantha Sethuraman
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Yiping Wang
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Shreya Nirmalan
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Alim Esemenli
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - April Feswick
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Brett A. Hoffman
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Rolf Renne
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Scott A. Tibbetts
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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24
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Abstract
After an adaptive immune response is mounted, gammaherpesviruses achieve persistence through the utilization of viral noncoding RNAs to craft a suitable host cell environment in an immunologically transparent manner. While gammaherpesvirus long noncoding RNAs (lncRNAs) and microRNAs have been recognized for some time and have been actively investigated, a recent spate of reports have now identified repertoires of the circular RNA (circRNA) class of noncoding RNAs in both the lymphocryptovirus and rhadinovirus genera of gammaherpesviruses. Despite the recent nature of these findings, the detection of circRNAs across viruses and viral gene expression programs, the conservation of some viral circRNAs, and their detection in the clinical setting already raises the spectrum of functional importance in gammaherpesvirus biology and associated malignancies. Here, we provide an overview of currently known gammaherpesvirus circular RNAs and discuss reported physical and contextual properties that may be germane to future functional studies. With the Epstein-Barr virus (EBV) circRNAome being the most extensively studied to date, our discussions will be weighted toward EBV circRNAs while also addressing circRNAs discovered in the rhesus macaque lymphocryptovirus (rLCV), the Kaposi's sarcoma herpesvirus (KSHV), and the murid gammaherpesvirus 68 (MHV68). We hope that this will help set the stage for future investigations into the functions and relevance of this new class of viral noncoding RNAs in infection and disease.
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Affiliation(s)
- Nathan A Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Scott A Tibbetts
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
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25
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Ungerleider NA, Jain V, Wang Y, Maness NJ, Blair RV, Alvarez X, Midkiff C, Kolson D, Bai S, Roberts C, Moss WN, Wang X, Serfecz J, Seddon M, Lehman T, Ma T, Dong Y, Renne R, Tibbetts SA, Flemington EK. Comparative Analysis of Gammaherpesvirus Circular RNA Repertoires: Conserved and Unique Viral Circular RNAs. J Virol 2019; 93:e01952-18. [PMID: 30567979 PMCID: PMC6401440 DOI: 10.1128/jvi.01952-18] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [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: 11/02/2018] [Accepted: 12/11/2018] [Indexed: 01/02/2023] Open
Abstract
Recent studies have identified circular RNAs (circRNAs) expressed from the Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus (KSHV) human DNA tumor viruses. To gain initial insights into the potential relevance of EBV circRNAs in virus biology and disease, we assessed the circRNAome of the interspecies homologue rhesus macaque lymphocryptovirus (rLCV) in a naturally occurring lymphoma from a simian immunodeficiency virus (SIV)-infected rhesus macaque. This analysis revealed rLCV orthologues of the latency-associated EBV circular RNAs circRPMS1_E4_E3a and circEBNA_U. Also identified in two samples displaying unusually high lytic gene expression was a novel rLCV circRNA that contains both conserved and rLCV-specific RPMS1 exons and whose backsplice junctions flank an rLCV lytic origin of replication (OriLyt). Analysis of a lytic infection model for the murid herpesvirus 68 (MHV68) rhadinovirus identified a cluster of circRNAs near an MHV68 lytic origin of replication, with the most abundant of these, circM11_ORF69, spanning the OriLyt. Lastly, analysis of KSHV latency and reactivation models revealed the latency associated circRNA originating from the vIRF4 gene as the predominant viral circRNA. Together, the results of this study broaden our appreciation for circRNA repertoires in the Lymphocryptovirus and Rhadinovirus genera of gammaherpesviruses and provide evolutionary support for viral circRNA functions in latency and viral replication.IMPORTANCE Infection with oncogenic gammaherpesviruses leads to long-term viral persistence through a dynamic interplay between the virus and the host immune system. Critical for remodeling of the host cell environment after the immune responses are viral noncoding RNAs that modulate host signaling pathways without attracting adaptive immune recognition. Despite the importance of noncoding RNAs in persistent infection, the circRNA class of noncoding RNAs has only recently been identified in gammaherpesviruses. Accordingly, their roles in virus infection and associated oncogenesis are unknown. Here we report evolutionary conservation of EBV-encoded circRNAs determined by assessing the circRNAome in rLCV-infected lymphomas from an SIV-infected rhesus macaque, and we report latent and lytic circRNAs from KSHV and MHV68. These experiments demonstrate utilization of the circular RNA class of RNAs across 4 members of the gammaherpesvirus subfamily, and they identify orthologues and potential homoplastic circRNAs, implying conserved circRNA functions in virus biology and associated malignancies.
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Affiliation(s)
- Nathan A Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Vaibhav Jain
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Yiping Wang
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Nicholas J Maness
- Department of Microbiology and Immunology, Tulane Regional Primate Center, Covington, Louisiana, USA
| | - Robert V Blair
- Division of Comparative Pathology, Tulane Regional Primate Center, Covington, Louisiana, USA
| | - Xavier Alvarez
- Division of Comparative Pathology, Tulane Regional Primate Center, Covington, Louisiana, USA
| | - Cecily Midkiff
- Division of Comparative Pathology, Tulane Regional Primate Center, Covington, Louisiana, USA
| | - Dennis Kolson
- Division of Comparative Pathology, Tulane Regional Primate Center, Covington, Louisiana, USA
| | - Shanshan Bai
- Department of Neurology, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Jacqueline Serfecz
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | | | | | - Tianfang Ma
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Yan Dong
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
| | - Rolf Renne
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Scott A Tibbetts
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, USA
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26
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Bullard WL, Flemington EK, Renne R, Tibbetts SA. Connivance, Complicity, or Collusion? The Role of Noncoding RNAs in Promoting Gammaherpesvirus Tumorigenesis. Trends Cancer 2018; 4:729-740. [PMID: 30352676 DOI: 10.1016/j.trecan.2018.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/20/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022]
Abstract
EBV and KSHV are etiologic agents of multiple types of lymphomas and carcinomas. The frequency of EBV+ or KSHV+ malignancies arising in immunocompromised individuals reflects the intricate evolutionary balance established between these viruses and their immunocompetent hosts. However, the specific mechanisms by which these pathogens drive tumorigenesis remain poorly understood. In recent years an enormous array of cellular and viral noncoding RNAs (ncRNAs) have been discovered, and host ncRNAs have been revealed as contributory factors to every single cancer hallmark cellular process. As new evidence emerges that gammaherpesvirus ncRNAs also alter host processes and viral factors dysregulate host ncRNA expression, and as novel viral ncRNAs continue to be discovered, we examine the contribution of small, non-miRNA ncRNAs and long ncRNAs to gammaherpesvirus tumorigenesis.
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Affiliation(s)
- Whitney L Bullard
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Erik K Flemington
- Department of Pathology, Tulane Cancer Center, Tulane University, New Orleans, LA, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Scott A Tibbetts
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
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27
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Ungerleider N, Concha M, Lin Z, Roberts C, Wang X, Cao S, Baddoo M, Moss WN, Yu Y, Seddon M, Lehman T, Tibbetts S, Renne R, Dong Y, Flemington EK. The Epstein Barr virus circRNAome. PLoS Pathog 2018; 14:e1007206. [PMID: 30080890 PMCID: PMC6095625 DOI: 10.1371/journal.ppat.1007206] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [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: 05/23/2018] [Revised: 08/16/2018] [Accepted: 07/11/2018] [Indexed: 11/18/2022] Open
Abstract
Our appreciation for the extent of Epstein Barr virus (EBV) transcriptome complexity continues to grow through findings of EBV encoded microRNAs, new long non-coding RNAs as well as the more recent discovery of over a hundred new polyadenylated lytic transcripts. Here we report an additional layer to the EBV transcriptome through the identification of a repertoire of latent and lytic viral circular RNAs. Utilizing RNase R-sequencing with cell models representing latency types I, II, and III, we identified EBV encoded circular RNAs expressed from the latency Cp promoter involving backsplicing from the W1 and W2 exons to the C1 exon, from the EBNA BamHI U fragment exon, and from the latency long non-coding RPMS1 locus. In addition, we identified circular RNAs expressed during reactivation including backsplicing from exon 8 to exon 2 of the LMP2 gene and a highly expressed circular RNA derived from intra-exonic backsplicing within the BHLF1 gene. While expression of most of these circular RNAs was found to depend on the EBV transcriptional program utilized and the transcription levels of the associated loci, expression of LMP2 exon 8 to exon 2 circular RNA was found to be cell model specific. Altogether we identified over 30 unique EBV circRNAs candidates and we validated and determined the structural features, expression profiles and nuclear/cytoplasmic distributions of several predominant and notable viral circRNAs. Further, we show that two of the EBV circular RNAs derived from the RPMS1 locus are detected in EBV positive clinical stomach cancer specimens. This study increases the known EBV latency and lytic transcriptome repertoires to include viral circular RNAs and it provides an essential foundation and resource for investigations into the functions and roles of this new class of EBV transcripts in EBV biology and diseases. Our understanding of the extent of EBV transcriptome complexity has recently come to light with discoveries of viral microRNAs, snoRNAs, and a diverse set of transcript isoforms expressed during reactivation. While EBV utilizes distinct transcriptional programs during it’s normal infection cycle, the latency programs are critical drivers of EBV associated oncogenesis where they activate oncogenic pathways without killing the cell via lytic viral replication. Further, pathogenic latency programs typically express minimal levels of viral protein coding genes and instead rely on non-coding RNA mechanisms to alter the host cell environment. The utilization of non-coding RNAs in these settings is presumably an effort to minimize infected cell killing by the immune system through adaptive immune responses. Using tissue culture models representing the spectrum of EBV transcriptional states that occur in vivo, we report here that EBV expresses the circular class of predominantly non-coding RNAs. This stands to reveal a previously unknown set of players in EBV associated biology and disease. The findings reported here set a key platform from which future functional and potentially clinical related studies can be carried out to bring the initial findings from discovery to a new understanding of EBV biology and disease.
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Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Monica Concha
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Zhen Lin
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Subing Cao
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Melody Baddoo
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Walter N. Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Yi Yu
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | | | - Terri Lehman
- Reprocell USA, Beltsville, MD, United States of America
| | - Scott Tibbetts
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, United States of America
| | - Yan Dong
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
| | - Erik K. Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, United States of America
- * E-mail:
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28
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Li W, Jia X, Shen C, Zhang M, Xu J, Shang Y, Zhu K, Hu M, Yan Q, Qin D, Lee MS, Zhu J, Lu H, Krueger BJ, Renne R, Gao SJ, Lu C. A KSHV microRNA enhances viral latency and induces angiogenesis by targeting GRK2 to activate the CXCR2/AKT pathway. Oncotarget 2017; 7:32286-305. [PMID: 27058419 PMCID: PMC5078013 DOI: 10.18632/oncotarget.8591] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/28/2016] [Indexed: 12/24/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL) and multicentric Castleman's disease (MCD). Most tumor cells in these malignancies are latently infected by KSHV. Thus, viral latency is critical for the development of tumor and induction of tumor-associated angiogenesis. KSHV encodes more than two dozens of miRNAs but their roles in KSHV-induced angiogenesis remains unknown. We have recently shown that miR-K12-3 (miR-K3) promoted cell migration and invasion by targeting GRK2/CXCR2/AKT signaling (PLoS Pathog, 2015;11(9):e1005171). Here, we further demonstrated a role of miR-K3 and its induced signal pathway in KSHV latency and KSHV-induced angiogenesis. We found that overexpression of miR-K3 not only promoted viral latency by inhibiting viral lytic replication, but also induced angiogenesis. Further, knockdown of GRK2 inhibited KSHV replication and enhanced KSHV-induced angiogenesis by enhancing the CXCR2/AKT signals. As a result, blockage of CXCR2 or AKT increased KSHV replication and decreased angiogenesis induced by PEL cells in vivo. Finally, deletion of miR-K3 from viral genome reduced KSHV-induced angiogenesis and increased KSHV replication. These findings indicate that the miR-K3/GRK2/CXCR2/AKT axis plays an essential role in KSHV-induced angiogenesis and promotes KSHV latency, and thus may be a potential therapeutic target of KSHV-associated malignancies.
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Affiliation(s)
- Wan Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, P. R. China.,Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, P. R. China.,Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Xuemei Jia
- Department of Gynecology and Obstetrics, Nanjing Maternity and Child Health Hospital Affiliated Hospital of Nanjing Medical University, Nanjing, P. R. China
| | - Chenyou Shen
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Mi Zhang
- Department of Gynecology and Obstetrics, Nanjing Maternity and Child Health Hospital Affiliated Hospital of Nanjing Medical University, Nanjing, P. R. China.,The Fourth Clinical Medical College of Nanjing Medical University, Nanjing, P. R. China
| | - Jingyun Xu
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Yuancui Shang
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Kaixiang Zhu
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Minmin Hu
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Qin Yan
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Di Qin
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Myung-Shin Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, Republic of Korea
| | - Jianzhong Zhu
- Cancer Virology Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Hongmei Lu
- Department of Obstetrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - Brian J Krueger
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Shou-Jiang Gao
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chun Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, P. R. China.,Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, P. R. China.,Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
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Sethuraman S, Gay LA, Jain V, Haecker I, Renne R. microRNA dependent and independent deregulation of long non-coding RNAs by an oncogenic herpesvirus. PLoS Pathog 2017; 13:e1006508. [PMID: 28715488 PMCID: PMC5531683 DOI: 10.1371/journal.ppat.1006508] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/27/2017] [Accepted: 07/02/2017] [Indexed: 02/07/2023] Open
Abstract
Kaposi’s sarcoma (KS) is a highly prevalent cancer in AIDS patients, especially in sub-Saharan Africa. Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent of KS and other cancers like Primary Effusion Lymphoma (PEL). In KS and PEL, all tumors harbor latent KSHV episomes and express latency-associated viral proteins and microRNAs (miRNAs). The exact molecular mechanisms by which latent KSHV drives tumorigenesis are not completely understood. Recent developments have highlighted the importance of aberrant long non-coding RNA (lncRNA) expression in cancer. Deregulation of lncRNAs by miRNAs is a newly described phenomenon. We hypothesized that KSHV-encoded miRNAs deregulate human lncRNAs to drive tumorigenesis. We performed lncRNA expression profiling of endothelial cells infected with wt and miRNA-deleted KSHV and identified 126 lncRNAs as putative viral miRNA targets. Here we show that KSHV deregulates host lncRNAs in both a miRNA-dependent fashion by direct interaction and in a miRNA-independent fashion through latency-associated proteins. Several lncRNAs that were previously implicated in cancer, including MEG3, ANRIL and UCA1, are deregulated by KSHV. Our results also demonstrate that KSHV-mediated UCA1 deregulation contributes to increased proliferation and migration of endothelial cells. KS is the most prevalent cancer associated with AIDS in sub-Saharan Africa, and is also common in males not affected by AIDS. KSHV manipulates human cells by targeting protein-coding genes and cell signaling. Here we show that KSHV alters the expression of hundreds of human lncRNAs, a broad class of regulatory molecules involved in a variety of cellular pathways including cell cycle and apoptosis. KSHV uses both latency proteins and miRNAs to target lncRNAs. miRNA-mediated targeting of lncRNAs is a novel regulatory mechanism of gene expression. Given that most herpesviruses encode miRNAs, this mechanism might be a common theme during herpesvirus infections. Understanding lncRNA deregulation by KSHV will help decipher the important molecular mechanisms underlying viral pathogenesis and tumorigenesis.
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Affiliation(s)
- Sunantha Sethuraman
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Lauren Appleby Gay
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Vaibhav Jain
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Irina Haecker
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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30
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Li W, Hu M, Wang C, Lu H, Chen F, Xu J, Shang Y, Wang F, Qin J, Yan Q, Krueger BJ, Renne R, Gao SJ, Lu C. A viral microRNA downregulates metastasis suppressor CD82 and induces cell invasion and angiogenesis by activating the c-Met signaling. Oncogene 2017; 36:5407-5420. [PMID: 28534512 PMCID: PMC5608636 DOI: 10.1038/onc.2017.139] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [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: 12/26/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 02/06/2023]
Abstract
Kaposi’s sarcoma (KS) is the most common AIDS-associated malignancy etiologically caused by Kaposi’s sarcoma-associated herpesvirus (KSHV). KS is a highly disseminated and vascularized tumor comprised of poorly differentiated spindle-shaped endothelial cells. KSHV encodes 12 pre-microRNAs (pre-miRNAs) that yield 25 mature miRNAs, but their roles in KSHV-induced tumor dissemination and angiogenesis remain largely unknown. KSHV-encoded miR-K12-6 (miR-K6) can produce two mature miRNAs, miR-K6-3p and miR-K6-5p. Recently, we have shown that miR-K6-3p promoted cell migration and angiogenesis by directly targeting SH3 domain binding glutamate-rich protein (SH3BGR) (PLoS Pathog. 2016;12(4):e1005605). Here, by using mass spectrometry, bioinformatics analysis and luciferase reporter assay, we showed that miR-K6-5p directly targeted the coding sequence (CDS) of CD82 molecule (CD82), a metastasis suppressor. Ectopic expression of miR-K6-5p specifically inhibited the expression of endogenous CD82 and strongly promoted endothelial cells invasion in vitro and angiogenesis in vivo. Overexpression of CD82 significantly inhibited cell invasion and angiogenesis induced by miR-K6-5p. Mechanistically, CD82 directly interacted with c-Met to inhibit its activation. MiR-K6-5p directly repressed CD82, relieving its inhibition on c-Met activation and inducing cell invasion and angiogenesis. Deletion of miR-K6 from KSHV genome abrogated KSHV suppression of CD82 resulting in compromised KSHV activation of c-Met pathway, and KSHV-induced invasion and angiogenesis. In conclusion, these results show that by inhibiting CD82, KSHV miR-K6-5p promotes cell invasion and angiogenesis by activating the c-Met pathway. Our findings illustrate that KSHV miRNAs may play an essential role in the dissemination and angiogenesis of KSHV-induced malignancies.
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Affiliation(s)
- W Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, China.,Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - M Hu
- Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, China
| | - C Wang
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - H Lu
- Department of Obstetrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - F Chen
- Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - J Xu
- Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Y Shang
- Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - F Wang
- Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - J Qin
- Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Q Yan
- Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - B J Krueger
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - R Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - S-J Gao
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - C Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, China.,Department of Microbiology, Nanjing Medical University, Nanjing, China
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31
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Dai L, Qiao J, Nguyen D, Struckhoff AP, Doyle L, Bonstaff K, Del Valle L, Parsons C, Toole BP, Renne R, Qin Z. Role of heme oxygenase-1 in the pathogenesis and tumorigenicity of Kaposi's sarcoma-associated herpesvirus. Oncotarget 2016; 7:10459-71. [PMID: 26859574 PMCID: PMC4891132 DOI: 10.18632/oncotarget.7227] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 12/20/2015] [Accepted: 01/27/2016] [Indexed: 01/01/2023] Open
Abstract
Kaposi's Sarcoma-associated Herpesvirus (KSHV) is the etiologic agent of several malignancies, including Kaposi's Sarcoma (KS), which preferentially arise in immunocompromised patients such as HIV+ subpopulation and lack effective therapeutic options. Heme oxygenase-1 (HO-1) has been reported as an important regulator of endothelial cell cycle control, proliferation and angiogenesis. HO-1 has also been found to be highly expressed in KSHV-infected endothelial cells and oral AIDS-KS lesions. We previously demonstrate that the multifunctional glycoprotein CD147 is required for KSHV/LANA-induced endothelial cell invasiveness. During the identification of CD147 controlled downstream genes by microarray analysis, we found that the expression of HO-1 is significantly elevated in both CD147-overexpressing and KSHV-infected HUVEC cells when compared to control cells. In the current study, we further identify the regulation of HO-1 expression and mediated cellular functions by both CD147 and KSHV-encoded LANA proteins. Targeting HO-1 by either RNAi or the chemical inhibitor, SnPP, effectively induces cell death of KSHV-infected endothelial cells (the major cellular components of KS) through DNA damage and necrosis process. By using a KS-like nude mouse model, we found that SnPP treatment significantly suppressed KSHV-induced tumorigenesis in vivo. Taken together, our data demonstrate the important role of HO-1 in the pathogenesis and tumorigenesis of KSHV-infected endothelial cells, the underlying regulatory mechanisms for HO-1 expression and targeting HO-1 may represent a promising therapeutic strategy against KSHV-related malignancies.
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Affiliation(s)
- Lu Dai
- Research Center for Translational Medicine and Key Laboratory of Arrhythmias, East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Medicine, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, LA, USA
| | - Jing Qiao
- Department of Pediatrics, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - David Nguyen
- William Carey University College of Osteopathic Medicine, Hattiesburg, MS, USA
| | - Amanda P Struckhoff
- Department of Pathology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, LA, USA
| | - Lisa Doyle
- Department of Medicine, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, LA, USA
| | - Karlie Bonstaff
- Department of Medicine, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, LA, USA
| | - Luis Del Valle
- Department of Pathology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, LA, USA
| | - Chris Parsons
- Department of Medicine, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, LA, USA
| | - Bryan P Toole
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina and Hollings Cancer Center, Charleston, SC, USA
| | - Rolf Renne
- Department of Molecular Genetics Microbiology, University of Florida, Gainesville, FL, USA
| | - Zhiqiang Qin
- Research Center for Translational Medicine and Key Laboratory of Arrhythmias, East Hospital, Tongji University School of Medicine, Shanghai, China.,Departments of Microbiology/Immunology/Parasitology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, LA, USA
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32
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Li W, Yan Q, Ding X, Shen C, Hu M, Zhu Y, Qin D, Lu H, Krueger BJ, Renne R, Gao SJ, Lu C. The SH3BGR/STAT3 Pathway Regulates Cell Migration and Angiogenesis Induced by a Gammaherpesvirus MicroRNA. PLoS Pathog 2016; 12:e1005605. [PMID: 27128969 PMCID: PMC4851422 DOI: 10.1371/journal.ppat.1005605] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 12/29/2015] [Accepted: 04/08/2016] [Indexed: 12/27/2022] Open
Abstract
Kaposi’s sarcoma (KS)-associated herpesvirus (KSHV) is a gammaherpesvirus etiologically associated with KS, a highly disseminated angiogenic tumor of hyperproliferative spindle endothelial cells. KSHV encodes 25 mature microRNAs but their roles in KSHV-induced tumor dissemination and angiogenesis remain unknown. Here, we investigated KSHV-encoded miR-K12-6-3p (miR-K6-3p) promotion of endothelial cell migration and angiogenesis, which are the underlying mechanisms of tumor dissemination and angiogenesis. We found that ectopic expression of miR-K6-3p promoted endothelial cell migration and angiogenesis. Mass spectrometry, bioinformatics and luciferase reporter analyses revealed that miR-K6-3p directly targeted sequence in the 3’ untranslated region (UTR) of SH3 domain binding glutamate-rich protein (SH3BGR). Overexpression of SH3BGR reversed miR-K6-3p induction of cell migration and angiogenesis. Mechanistically, miR-K6-3p downregulated SH3BGR, hence relieved STAT3 from SH3BGR direct binding and inhibition, which was required for miR-K6-3p maximum activation of STAT3 and induction of cell migration and angiogenesis. Finally, deletion of miR-K6 from the KSHV genome abrogated its effect on the SH3BGR/STAT3 pathway, and KSHV-induced migration and angiogenesis. Our results illustrated that, by inhibiting SH3BGR, miR-K6-3p enhances cell migration and angiogenesis by activating the STAT3 pathway, and thus contributes to the dissemination and angiogenesis of KSHV-induced malignancies. Kaposi’s Sarcoma (KS), caused by infection of Kaposi’s sarcoma (KS)-associated herpesvirus (KSHV), is a tumor of endothelial cells characterized by angiogenesis and invasiveness. In vitro, KSHV-infected endothelial cells display an increased invasiveness and angiogenicity. KSHV encodes twelve precursor miRNAs (pre-miRNAs), which are processed into at least 25 mature miRNAs. However, the roles of these miRNAs in KSHV-induced tumor dissemination and angiogenesis remain unknown. Here, we investigated KSHV-encoded miR-K12-6-3p (miR-K6-3p) promotion of endothelial cell migration and angiogenesis, which are the underlying mechanisms of tumor dissemination and angiogenesis. We demonstrated that miR-K6-3p promoted cell migration and angiogenesis by directly targeting SH3 domain binding glutamate-rich protein (SH3BGR). Furthermore, we found that STAT3, which was negatively regulated by SH3BGR mediated miR-K6-3p-induced cell migration and angiogenesis. MiR-K6-3p downregulation of SH3BGR, hence relieved SH3BGR direct inhibition of STAT3 resulting in the activation of STAT3 and induction of cell migration and angiogenesis. These results identify miR-K6-3p and its the downstream pathway as potential therapeutic targets for the treatment of KSHV-associated malignancies.
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Affiliation(s)
- Wan Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, People's Republic of China.,Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, People's Republic of China.,Department of Microbiology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Qin Yan
- Department of Microbiology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Xiangya Ding
- Department of Microbiology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Chenyou Shen
- Department of Microbiology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Minmin Hu
- Department of Microbiology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Ying Zhu
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Di Qin
- Department of Microbiology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hongmei Lu
- Department of Obstetrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Brian J Krueger
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Shou-Jiang Gao
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Chun Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, People's Republic of China.,Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, People's Republic of China.,Department of Microbiology, Nanjing Medical University, Nanjing, People's Republic of China
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33
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Gao R, Cao C, Zhang M, Lopez MC, Yan Y, Chen Z, Mitani Y, Zhang L, Zajac-Kaye M, Liu B, Wu L, Renne R, Baker HV, El-Naggar A, Kaye FJ. A unifying gene signature for adenoid cystic cancer identifies parallel MYB-dependent and MYB-independent therapeutic targets. Oncotarget 2015; 5:12528-42. [PMID: 25587024 PMCID: PMC4350357 DOI: 10.18632/oncotarget.2985] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [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: 10/02/2014] [Accepted: 12/09/2014] [Indexed: 12/12/2022] Open
Abstract
MYB activation is proposed to underlie development of adenoid cystic cancer (ACC), an aggressive salivary gland tumor with no effective systemic treatments. To discover druggable targets for ACC, we performed global mRNA/miRNA analyses of 12 ACC with matched normal tissues, and compared these data with 14 mucoepidermoid carcinomas (MEC) and 11 salivary adenocarcinomas (ADC). We detected a unique ACC gene signature of 1160 mRNAs and 22 miRNAs. MYB was the top-scoring gene (18-fold induction), however we observed the same signature in ACC without detectable MYB gene rearrangements. We also found 4 ACC tumors (1 among our 12 cases and 3 from public databases) with negligible MYB expression that retained the same ACC mRNA signature including over-expression of extracellular matrix (ECM) genes. Integration of this signature with somatic mutational analyses suggests that NOTCH1 and RUNX1 participate with MYB to activate ECM elements including the VCAN/HAPLN1 complex. We observed that forced MYB-NFIB expression in human salivary gland cells alters cell morphology and cell adhesion in vitro and depletion of VCAN blocked tumor cell growth of a short-term ACC tumor culture. In summary, we identified a unique ACC signature with parallel MYB-dependent and independent biomarkers and identified VCAN/HAPLN1 complexes as a potential target.
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Affiliation(s)
- Ruli Gao
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, University of Florida, Gainesville, FL, USA. Genetics & Genomics Graduate Program, Genetics Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Chunxia Cao
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Min Zhang
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Maria-Cecilia Lopez
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Yuanqing Yan
- Genetics & Genomics Graduate Program, Genetics Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Zirong Chen
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Yoshitsugu Mitani
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhang
- Department of Computational Biology and Bioinformatics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Zajac-Kaye
- Department of Anatomy & Cell Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Bin Liu
- Department of Molecular Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lizi Wu
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Henry V Baker
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Adel El-Naggar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Frederic J Kaye
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, University of Florida, Gainesville, FL, USA. Genetics & Genomics Graduate Program, Genetics Institute, College of Medicine, University of Florida, Gainesville, FL, USA
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Choi HS, Jain V, Krueger B, Marshall V, Kim CH, Shisler JL, Whitby D, Renne R. Kaposi's Sarcoma-Associated Herpesvirus (KSHV) Induces the Oncogenic miR-17-92 Cluster and Down-Regulates TGF-β Signaling. PLoS Pathog 2015; 11:e1005255. [PMID: 26545119 PMCID: PMC4636184 DOI: 10.1371/journal.ppat.1005255] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [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: 07/08/2015] [Accepted: 10/08/2015] [Indexed: 12/19/2022] Open
Abstract
KSHV is a DNA tumor virus that causes Kaposi's sarcoma. Upon KSHV infection, only a limited number of latent genes are expressed. We know that KSHV infection regulates host gene expression, and hypothesized that latent genes also modulate the expression of host miRNAs. Aberrant miRNA expression contributes to the development of many types of cancer. Array-based miRNA profiling revealed that all six miRNAs of the oncogenic miR-17-92 cluster are up-regulated in KSHV infected endothelial cells. Among candidate KSHV latent genes, we found that vFLIP and vCyclin were shown to activate the miR-17-92 promoter, using luciferase assay and western blot analysis. The miR-17-92 cluster was previously shown to target TGF-β signaling. We demonstrate that vFLIP and vCyclin induce the expression of the miR-17-92 cluster to strongly inhibit the TGF-β signaling pathway by down-regulating SMAD2. Moreover, TGF-β activity and SMAD2 expression were fully restored when antagomirs (inhibitors) of miR-17-92 cluster were transfected into cells expressing either vFLIP or vCyclin. In addition, we utilized viral genetics to produce vFLIP or vCyclin knock-out viruses, and studied the effects in infected TIVE cells. Infection with wildtype KSHV abolished expression of SMAD2 protein in these endothelial cells. While single-knockout mutants still showed a marked reduction in SMAD2 expression, TIVE cells infected by a double-knockout mutant virus were fully restored for SMAD2 expression, compared to non-infected TIVE cells. Expression of either vFLIP or vCycIin was sufficient to downregulate SMAD2. In summary, our data demonstrate that vFLIP and vCyclin induce the oncogenic miR-17-92 cluster in endothelial cells and thereby interfere with the TGF-β signaling pathway. Manipulation of the TGF-β pathway via host miRNAs represents a novel mechanism that may be important for KSHV tumorigenesis and angiogenesis, a hallmark of KS.
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Affiliation(s)
- Hong Seok Choi
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Vaibhav Jain
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Brian Krueger
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Vickie Marshall
- AIDS and Cancer Virus Program, Leidos Biomedical, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Chang Hee Kim
- AIDS and Cancer Virus Program, Leidos Biomedical, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Joanna L. Shisler
- Department of Microbiology, College of Medicine, University of Illinois, Urbana, Illinois, United States of America
| | - Denise Whitby
- AIDS and Cancer Virus Program, Leidos Biomedical, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- UF Institute of Genetics, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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35
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Hu M, Wang C, Li W, Lu W, Bai Z, Qin D, Yan Q, Zhu J, Krueger BJ, Renne R, Gao SJ, Lu C. A KSHV microRNA Directly Targets G Protein-Coupled Receptor Kinase 2 to Promote the Migration and Invasion of Endothelial Cells by Inducing CXCR2 and Activating AKT Signaling. PLoS Pathog 2015; 11:e1005171. [PMID: 26402907 PMCID: PMC4581863 DOI: 10.1371/journal.ppat.1005171] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [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: 04/25/2015] [Accepted: 08/27/2015] [Indexed: 02/06/2023] Open
Abstract
Kaposi's sarcoma (KS) is a highly disseminated angiogenic tumor of endothelial cells linked to infection by Kaposi's sarcoma-associated herpesvirus (KSHV). KSHV encodes more than two dozens of miRNAs but their roles in KSHV-induced tumor dissemination and metastasis remain unknown. Here, we found that ectopic expression of miR-K12-3 (miR-K3) promoted endothelial cell migration and invasion. Bioinformatics and luciferase reporter analyses showed that miR-K3 directly targeted G protein-coupled receptor (GPCR) kinase 2 (GRK2, official gene symbol ADRBK1). Importantly, overexpression of GRK2 reversed miR-K3 induction of cell migration and invasion. Furthermore, the chemokine receptor CXCR2, which was negatively regulated by GRK2, was upregulated in miR-K3-transduced endothelial cells. Knock down of CXCR2 abolished miR-K3-induced cell migration and invasion. Moreover, miR-K3 downregulation of GRK2 relieved its direct inhibitory effect on AKT. Both CXCR2 induction and the release of AKT from GRK2 were required for miR-K3 maximum activation of AKT and induction of cell migration and invasion. Finally, deletion of miR-K3 from the KSHV genome abrogated its effect on the GRK2/CXCR2/AKT pathway and KSHV-induced migration and invasion. Our data provide the first-line evidence that, by repressing GRK2, miR-K3 facilitates cell migration and invasion via activation of CXCR2/AKT signaling, which likely contribute to the dissemination of KSHV-induced tumors. Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma (KS). KS is a highly disseminated tumor often involved with visceral organs. Experimentally, KSHV infection induces the invasiveness of endothelial cells. KSHV encodes twelve precursor miRNAs (pre-miRNAs), which are processed into at least 25 mature miRNAs. However, the roles of these miRNAs in KSHV-induced tumor dissemination remain unknown. Here, we investigated KSHV-encoded miR-K12-3 (miR-K3) promotion of endothelial cell migration and invasion, which are the underlying mechanisms of tumor dissemination. We demonstrated that miR-K3 promoted cell migration and invasion by directly targeting G protein-coupled receptor (GPCR) kinase 2 (GRK2). Furthermore, we found that the chemokine receptor CXCR2, which was negatively regulated by GRK2, and its downstream AKT signaling positively mediated miR-K3-induced cell migration and invasion. miR-K3 downregulation of GRK2 relieved its direct inhibitory effect on AKT, and both CXCR2 induction and the release of AKT from GRK2 were required for miR-K3 maximum activation of AKT and induction of cell migration and invasion. These results show that miR-K3 and its the downstream pathway may be potential therapeutic targets for the treatment of KSHV-associated malignancies.
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MESH Headings
- Cell Movement
- Cells, Cultured
- Endothelium, Vascular/immunology
- Endothelium, Vascular/metabolism
- Endothelium, Vascular/pathology
- Endothelium, Vascular/virology
- Enzyme Repression
- G-Protein-Coupled Receptor Kinase 2/antagonists & inhibitors
- G-Protein-Coupled Receptor Kinase 2/genetics
- G-Protein-Coupled Receptor Kinase 2/metabolism
- Gene Deletion
- Herpesvirus 8, Human/immunology
- Herpesvirus 8, Human/physiology
- Host-Pathogen Interactions
- Human Umbilical Vein Endothelial Cells/immunology
- Human Umbilical Vein Endothelial Cells/metabolism
- Human Umbilical Vein Endothelial Cells/pathology
- Human Umbilical Vein Endothelial Cells/virology
- Humans
- MicroRNAs/metabolism
- Mutation
- Neoplasm Invasiveness
- Proto-Oncogene Proteins c-akt/agonists
- Proto-Oncogene Proteins c-akt/genetics
- Proto-Oncogene Proteins c-akt/metabolism
- RNA/metabolism
- RNA Interference
- RNA, Viral/metabolism
- Receptors, Interleukin-8B/agonists
- Receptors, Interleukin-8B/genetics
- Receptors, Interleukin-8B/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- Sarcoma, Kaposi/immunology
- Sarcoma, Kaposi/metabolism
- Sarcoma, Kaposi/pathology
- Sarcoma, Kaposi/virology
- Signal Transduction
- Virus Internalization
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Affiliation(s)
- Minmin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, P. R. China
- Key Laboratory Of Pathogen Biology Of Jiangsu Province, Nanjing Medical University, Nanjing, P. R. China
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Cong Wang
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, P. R. China
| | - Wan Li
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Weiping Lu
- Department of Endocrinology and Metabolism, Huai’an First People’s Hospital, Nanjing Medical University, 6 Beijing Road West, Huai’an, Jiangsu, P. R. China
| | - Zhiqiang Bai
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Di Qin
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
| | - Qin Yan
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
- * E-mail: (QY); (CL)
| | - Jianzhong Zhu
- Cancer Virology Program, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
| | - Brian J. Krueger
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Shou-Jiang Gao
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Chun Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, P. R. China
- Key Laboratory Of Pathogen Biology Of Jiangsu Province, Nanjing Medical University, Nanjing, P. R. China
- Department of Microbiology, Nanjing Medical University, Nanjing, P. R. China
- * E-mail: (QY); (CL)
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Abstract
MiRNAs regulate gene expression by binding predominantly to the 3' untranslated region (UTR) of target transcripts to prevent their translation and/or induce target degradation. In addition to the more than 1200 human miRNAs, human DNA tumor viruses such as Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) encode miRNAs. Target predictions indicate that each miRNA targets hundreds of transcripts, many of which are regulated by multiple miRNAs. Thus, target identification is a big challenge for the field. Most methods used currently investigate single miRNA-target interactions and are not able to analyze complex miRNA-target networks. To overcome these challenges, cross-linking and immunoprecipitation (CLIP), a recently developed method to study direct RNA-protein interactions in living cells, has been successfully applied to miRNA target analysis. It utilizes Argonaute (Ago)-immunoprecipitation to isolate native Ago-miRNA-mRNA complexes. In four recent publications, two variants of the CLIP method (HITS-CLIP and PAR-CLIP) were utilized to determine the targetomes of human and viral miRNAs in cells infected with the gamma-herpesviruses KSHV and EBV, which are associated with a number of human cancers. Here, we briefly introduce herpesvirus-encoded miRNAs and then focus on how CLIP technology has largely impacted our understanding of viral miRNAs in viral biology and pathogenesis.
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Affiliation(s)
- Irina Haecker
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, Shands Cancer Center, Genetics Institute, University of Florida, Gainesville, FL, USA
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Yang Y, Boss IW, McIntyre LM, Renne R. A systems biology approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells. BMC Genomics 2014; 15:668. [PMID: 25106478 PMCID: PMC4147158 DOI: 10.1186/1471-2164-15-668] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 04/24/2014] [Accepted: 08/01/2014] [Indexed: 01/01/2023] Open
Abstract
Background Kaposi’s sarcoma associated herpes virus (KSHV) is associated with tumors of endothelial and lymphoid origin. During latent infection, KSHV expresses miR-K12-11, an ortholog of the human tumor gene hsa-miR-155. Both gene products are microRNAs (miRNAs), which are important post-transcriptional regulators that contribute to tissue specific gene expression. Advances in target identification technologies and molecular interaction databases have allowed a systems biology approach to unravel the gene regulatory networks (GRNs) triggered by miR-K12-11 in endothelial and lymphoid cells. Understanding the tissue specific function of miR-K12-11 will help to elucidate underlying mechanisms of KSHV pathogenesis. Results Ectopic expression of miR-K12-11 differentially affected gene expression in BJAB cells of lymphoid origin and TIVE cells of endothelial origin. Direct miRNA targeting accounted for a small fraction of the observed transcriptome changes: only 29 genes were identified as putative direct targets of miR-K12-11 in both cell types. However, a number of commonly affected biological pathways, such as carbohydrate metabolism and interferon response related signaling, were revealed by gene ontology analysis. Integration of transcriptome profiling, bioinformatic algorithms, and databases of protein-protein interactome from the ENCODE project identified different nodes of GRNs utilized by miR-K12-11 in a tissue-specific fashion. These effector genes, including cancer associated transcription factors and signaling proteins, amplified the regulatory potential of a single miRNA, from a small set of putative direct targets to a larger set of genes. Conclusions This is the first comparative analysis of miRNA-K12-11’s effects in endothelial and B cells, from tissues infected with KSHV in vivo. MiR-K12-11 was able to broadly modulate gene expression in both cell types. Using a systems biology approach, we inferred that miR-K12-11 establishes its GRN by both repressing master TFs and influencing signaling pathways, to counter the host anti-viral response and to promote proliferation and survival of infected cells. The targeted GRNs are more reproducible and informative than target gene identification, and our approach can be applied to other regulatory factors of interest. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-668) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, 2033 Mowry Road, Gainesville, FL 32610, USA.
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Hu J, Yang Y, Turner PC, Jain V, McIntyre LM, Renne R. LANA binds to multiple active viral and cellular promoters and associates with the H3K4methyltransferase hSET1 complex. PLoS Pathog 2014; 10:e1004240. [PMID: 25033463 PMCID: PMC4102568 DOI: 10.1371/journal.ppat.1004240] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [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: 11/21/2013] [Accepted: 05/27/2014] [Indexed: 02/07/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a γ-herpesvirus associated with KS and two lymphoproliferative diseases. Recent studies characterized epigenetic modification of KSHV episomes during latency and determined that latency-associated genes are associated with H3K4me3 while most lytic genes are associated with the silencing mark H3K27me3. Since the latency-associated nuclear antigen (LANA) (i) is expressed very early after de novo infection, (ii) interacts with transcriptional regulators and chromatin remodelers, and (iii) regulates the LANA and RTA promoters, we hypothesized that LANA may contribute to the establishment of latency through epigenetic control. We performed a detailed ChIP-seq analysis in cells of lymphoid and endothelial origin and compared H3K4me3, H3K27me3, polII, and LANA occupancy. On viral episomes LANA binding was detected at numerous lytic and latent promoters, which were transactivated by LANA using reporter assays. LANA binding was highly enriched at H3K4me3 peaks and this co-occupancy was also detected on many host gene promoters. Bioinformatic analysis of enriched LANA binding sites in combination with biochemical binding studies revealed three distinct binding patterns. A small subset of LANA binding sites showed sequence homology to the characterized LBS1/2 sequence in the viral terminal repeat. A large number of sites contained a novel LANA binding motif (TCCAT)3 which was confirmed by gel shift analysis. Third, some viral and cellular promoters did not contain LANA binding sites and are likely enriched through protein/protein interaction. LANA was associated with H3K4me3 marks and in PEL cells 86% of all LANA bound promoters were transcriptionally active, leading to the hypothesis that LANA interacts with the machinery that methylates H3K4. Co-immunoprecipitation demonstrated LANA association with endogenous hSET1 complexes in both lymphoid and endothelial cells suggesting that LANA may contribute to the epigenetic profile of KSHV episomes. KSHV is a DNA tumor virus which is associated with Kaposi's sarcoma and some lymphoproliferative diseases. During latent infection, the viral genome persists as circular extrachromosomal DNA in the nucleus and expresses a very limited number of viral proteins, including LANA, a multi-functional protein. KSHV viral episomes, like host genomic DNA, are subject to chromatin formation and histone modifications which contribute to tightly controlled gene expression during latency. We determined where LANA binds on the KSHV and human genomes, and mapped activating and repressing histone marks and RNA polymerase II binding. We found that LANA bound near transcription start sites, and binding correlated with the transcription active mark H3K4me3, but not silencing mark H3K27me3. Binding sites for transcription factors including znf143, CTCF, and Stat1 are enriched at regions where LANA is bound. We identified some LANA binding sites near human gene promoters that resembled KSHV sequences known to bind LANA. We also found a novel motif that occurs frequently in the human genome and that binds LANA directly despite being different from known LANA-binding sequences. Furthermore, we demonstrate that LANA associates with the H3K4 methyltransferase hSET1 which creates activating histone marks.
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Affiliation(s)
- Jianhong Hu
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Yajie Yang
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Peter C. Turner
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Vaibhav Jain
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Lauren M. McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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Reese TA, Wakeman BS, Choi HS, Hufford MM, Huang SC, Zhang X, Buck MD, Jezewski A, Kambal A, Liu CY, Goel G, Murray PJ, Xavier RJ, Kaplan MH, Renne R, Speck SH, Artyomov MN, Pearce EJ, Virgin HW. Helminth infection reactivates latent γ-herpesvirus via cytokine competition at a viral promoter. Science 2014; 345:573-7. [PMID: 24968940 DOI: 10.1126/science.1254517] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mammals are coinfected by multiple pathogens that interact through unknown mechanisms. We found that helminth infection, characterized by the induction of the cytokine interleukin-4 (IL-4) and the activation of the transcription factor Stat6, reactivated murine γ-herpesvirus infection in vivo. IL-4 promoted viral replication and blocked the antiviral effects of interferon-γ (IFNγ) by inducing Stat6 binding to the promoter for an important viral transcriptional transactivator. IL-4 also reactivated human Kaposi's sarcoma-associated herpesvirus from latency in cultured cells. Exogenous IL-4 plus blockade of IFNγ reactivated latent murine γ-herpesvirus infection in vivo, suggesting a "two-signal" model for viral reactivation. Thus, chronic herpesvirus infection, a component of the mammalian virome, is regulated by the counterpoised actions of multiple cytokines on viral promoters that have evolved to sense host immune status.
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Affiliation(s)
- T A Reese
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - B S Wakeman
- Emory University Vaccine Center, Atlanta, GA 30322, USA
| | - H S Choi
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - M M Hufford
- Departments of Pediatrics and Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - S C Huang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - X Zhang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - M D Buck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - A Jezewski
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - A Kambal
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - C Y Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - G Goel
- Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - P J Murray
- Departments of Infectious Diseases and Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - R J Xavier
- Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - M H Kaplan
- Departments of Pediatrics and Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - R Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - S H Speck
- Emory University Vaccine Center, Atlanta, GA 30322, USA
| | - M N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - E J Pearce
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - H W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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40
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Fan AX, Papadopoulos GL, Hossain MA, Lin IJ, Hu J, Tang TM, Kilberg MS, Renne R, Strouboulis J, Bungert J. Genomic and proteomic analysis of transcription factor TFII-I reveals insight into the response to cellular stress. Nucleic Acids Res 2014; 42:7625-41. [PMID: 24875474 PMCID: PMC4081084 DOI: 10.1093/nar/gku467] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ubiquitously expressed transcription factor TFII-I exerts both positive and negative effects on transcription. Using biotinylation tagging technology and high-throughput sequencing, we determined sites of chromatin interactions for TFII-I in the human erythroleukemia cell line K562. This analysis revealed that TFII-I binds upstream of the transcription start site of expressed genes, both upstream and downstream of the transcription start site of repressed genes, and downstream of RNA polymerase II peaks at the ATF3 and other stress responsive genes. At the ATF3 gene, TFII-I binds immediately downstream of a Pol II peak located 5 kb upstream of exon 1. Induction of ATF3 expression increases transcription throughout the ATF3 gene locus which requires TFII-I and correlates with increased association of Pol II and Elongin A. Pull-down assays demonstrated that TFII-I interacts with Elongin A. Partial depletion of TFII-I expression caused a reduction in the association of Elongin A with and transcription of the DNMT1 and EFR3A genes without a decrease in Pol II recruitment. The data reveal different interaction patterns of TFII-I at active, repressed, or inducible genes, identify novel TFII-I interacting proteins, implicate TFII-I in the regulation of transcription elongation and provide insight into the role of TFII-I during the response to cellular stress.
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Affiliation(s)
- Alex Xiucheng Fan
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
| | - Giorgio L Papadopoulos
- Departmentof Biology, University of Crete, GR1409 Heraklion, Greece Divisionof Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari GR 16672, Greece
| | - Mir A Hossain
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
| | - I-Ju Lin
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
| | - Jianhong Hu
- Departmentof Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida, 32610, USA
| | - Tommy Ming Tang
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
| | - Michael S Kilberg
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
| | - Rolf Renne
- Divisionof Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari GR 16672, Greece
| | - John Strouboulis
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA Departmentof Biology, University of Crete, GR1409 Heraklion, Greece Divisionof Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari GR 16672, Greece Departmentof Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida, 32610, USA
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
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Yang Y, Fear J, Hu J, Haecker I, Zhou L, Renne R, Bloom D, McIntyre LM. Leveraging biological replicates to improve analysis in ChIP-seq experiments. Comput Struct Biotechnol J 2014; 9:e201401002. [PMID: 24688750 PMCID: PMC3962196 DOI: 10.5936/csbj.201401002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [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: 08/30/2013] [Revised: 01/17/2014] [Accepted: 01/17/2014] [Indexed: 12/27/2022] Open
Abstract
ChIP-seq experiments identify genome-wide profiles of DNA-binding molecules including transcription factors, enzymes and epigenetic marks. Biological replicates are critical for reliable site discovery and are required for the deposition of data in the ENCODE and modENCODE projects. While early reports suggested two replicates were sufficient, the widespread application of the technique has led to emerging consensus that the technique is noisy and that increasing replication may be worthwhile. Additional biological replicates also allow for quantitative assessment of differences between conditions. To date it has remained controversial about how to confirm peak identification and to determine signal strength across biological replicates, particularly when the number of replicates is greater than two. Using objective metrics, we evaluate the consistency of biological replicates in ChIP-seq experiments with more than two replicates. We compare several approaches for binding site determination, including two popular but disparate peak callers, CisGenome and MACS2. Here we propose read coverage as a quantitative measurement of signal strength for estimating sample concordance. Determining binding based on genomic features, such as promoters, is also examined. We find that increasing the number of biological replicates increases the reliability of peak identification. Critically, binding sites with strong biological evidence may be missed if researchers rely on only two biological replicates. When more than two replicates are performed, a simple majority rule (>50% of samples identify a peak) identifies peaks more reliably in all biological replicates than the absolute concordance of peak identification between any two replicates, further demonstrating the utility of increasing replicate numbers in ChIP-seq experiments.
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Affiliation(s)
- Yajie Yang
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA ; UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Justin Fear
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA ; UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Irina Haecker
- Department of Applied Entomology, University of Giessen, Giessen, Germany
| | - Lei Zhou
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA ; UF Genetics Institute, University of Florida, Gainesville, Florida, USA ; UF Shands Cancer Center, University of Florida, Gainesville, Florida, USA
| | - David Bloom
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA ; UF Genetics Institute, University of Florida, Gainesville, Florida, USA
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Pantry SN, Medveczky MM, Arbuckle JH, Luka J, Montoya JG, Hu J, Renne R, Peterson D, Pritchett JC, Ablashi DV, Medveczky PG. Persistent human herpesvirus-6 infection in patients with an inherited form of the virus. J Med Virol 2013; 85:1940-6. [PMID: 23893753 DOI: 10.1002/jmv.23685] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2013] [Indexed: 01/26/2023]
Abstract
Human herpesvirus-6 (HHV-6)A and 6B are ubiquitous betaherpesviruses viruses with lymphotropic and neurotropic potential. As reported earlier, these viruses establish latency by integration into the telomeres of host chromosomes. Chromosomally integrated HHV-6 (CIHHV-6) can be transmitted vertically from parent to child. Some CIHHV-6 patients are suffering from neurological symptoms, while others remain asymptomatic. Four patients with CIHHV-6 and CNS dysfunction were treated with valganciclovir or foscarnet. HHV-6 replication was detected by reverse transcriptase polymerase chain reaction amplification of a late envelope glycoprotein. In this study we also compared the inherited and persistent HHV-6 viruses by DNA sequencing. The prevalence of CIHHV-6 in this cohort of adult patients from the USA suffering from a wide range of neurological symptoms including long-term fatigue were found significantly greater than the reported 0.8% in the general population. Long-term antiviral therapy inhibited HHV-6 replication as documented by loss of viral mRNA production. Sequence comparison of the mRNA and the inherited viral genome revealed that the transcript is produced by an exogenous virus. In conclusion, the data presented here document that some individuals with CIHHV-6 are infected persistently with exogenous HHV-6 strains that lead to a wide range of neurological symptoms; the proposed name for this condition is inherited herpesvirus 6 syndrome or IHS.
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Affiliation(s)
- Shara N Pantry
- Department of Molecular Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida 33612, USA
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43
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Abstract
Spontaneous lytic reactivation of Kaposi’s sarcoma–associated herpesvirus (KSHV) occurs at a low rate in latently infected cells in disease and culture. This suggests imperfect epigenetic maintenance of viral transcription programs, perhaps due to variability in chromatin structure at specific loci across the population of KSHV episomal genomes. To characterize this locus-specific chromatin structural diversity, we used MAPit single-molecule footprinting, which simultaneously maps endogenous CG methylation and accessibility to M.CviPI at GC sites. Diverse chromatin structures were detected at the LANA, RTA and vIL6 promoters. At each locus, chromatin ranged from fully closed to fully open across the population. This diversity has not previously been reported in a virus. Phorbol ester and RTA transgene induction were used to identify chromatin conformations associated with reactivation of lytic transcription, which only a fraction of episomes had. Moreover, certain chromatin conformations correlated with CG methylation patterns at the RTA and vIL6 promoters. This indicated that some of the diverse chromatin conformations at these loci were epigenetically distinct. Finally, by comparing chromatin structures from a cell line infected with constitutively latent virus, we identified products of lytic replication. Our findings show that epigenetic drift can restrict viral propagation by chromatin compaction at latent and lytic promoters.
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Affiliation(s)
- Russell P Darst
- Department of Biochemistry and Molecular Biology, 2033 Mowry Road, Box 103633, University of Florida College of Medicine, Gainesville, FL, 32610, USA
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Krueger B, Plaisance K, Sangani R, Lanier C, Jain V, Hu J, Renne R. A core laboratory for the generation of quality-controlled g-herpesvirus bacmids: generation of KSHV microRNA mutants. Infect Agent Cancer 2012. [PMCID: PMC3330030 DOI: 10.1186/1750-9378-7-s1-p27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Haecker I, Gay L, Morse A, McCrory M, Yang Y, Hu J, McIntyre L, Renne R. Comprehensive analysis of the KSHV MiRNA targetome by Ago-HITS-CLIP. Infect Agent Cancer 2012. [PMCID: PMC3330110 DOI: 10.1186/1750-9378-7-s1-o4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Marshall V, Ray A, Han SJ, Uldrick T, Barsov E, Quinones O, Leighty R, Labo N, Wyvill K, Aleman K, Polizzotto MN, Little RF, Ott D, Yarchoan R, Renne R, Whitby D. Genetic variation in KSHV encoded microRNAs affects microRNA expression and is associated with multicentric Castleman’s disease risk. Infect Agent Cancer 2012. [PMCID: PMC3330049 DOI: 10.1186/1750-9378-7-s1-o5] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Vickie Marshall
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, National Cancer Institute (NCI)-Frederick, Frederick, MD, USA
| | - Alex Ray
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, National Cancer Institute (NCI)-Frederick, Frederick, MD, USA
| | - Soo-Jin Han
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | | | - Eugene Barsov
- Retrovirus Assembly Laboratory, AIDS and Cancer Virus Program, SAIC-Frederick, Frederick, MD, USA
| | - Octavio Quinones
- Data Management Services, Inc, NCI-Frederick, Frederick, MD, USA
| | - Robert Leighty
- Data Management Services, Inc, NCI-Frederick, Frederick, MD, USA
| | - Nazzarena Labo
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, National Cancer Institute (NCI)-Frederick, Frederick, MD, USA
| | - Kathy Wyvill
- HIV and AIDS Malignancy Branch, NCI, Bethesda, MD, USA
| | - Karen Aleman
- HIV and AIDS Malignancy Branch, NCI, Bethesda, MD, USA
| | | | | | - David Ott
- Retrovirus Assembly Laboratory, AIDS and Cancer Virus Program, SAIC-Frederick, Frederick, MD, USA
| | | | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, National Cancer Institute (NCI)-Frederick, Frederick, MD, USA
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Marshall V, Han SJ, Barsov E, Quinones O, Ray A, Yarchoan R, Ott D, Renne R, Whitby D. KSHV encoded miRNA single nucleotide polymorphisms identified in clinical samples can affect miRNA processing and level of expression. Infect Agent Cancer 2012. [PMCID: PMC3330105 DOI: 10.1186/1750-9378-7-s1-p40] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Vickie Marshall
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Soo-Jin Han
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Eugene Barsov
- Retrovirus Assembly Section, AIDS and Cancer Virus Program, SAIC-Frederick, Frederick, MD, USA
| | - Octavio Quinones
- Data Management Services, Inc., NCI-Frederick, Frederick, MD, USA
| | - Alex Ray
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Ott
- Retrovirus Assembly Section, AIDS and Cancer Virus Program, SAIC-Frederick, Frederick, MD, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
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Boss IW, Renne R. Viral miRNAs and immune evasion. Biochim Biophys Acta 2011; 1809:708-14. [PMID: 21757042 DOI: 10.1016/j.bbagrm.2011.06.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/27/2011] [Accepted: 06/28/2011] [Indexed: 11/29/2022]
Abstract
Viral miRNAs, ~22nt RNA molecules which post-transcriptionally regulate gene expression, are emerging as important tools in immune evasion. Viral infection is a complex process that requires immune evasion in order to establish persistent life-long infection of the host. During this process viruses express both protein-coding and non-coding genes, which help to modulate the cellular environment making it more favorable for infection. In the last decade, it was uncovered that DNA viruses express a diverse and abundant pool of small non-coding RNA molecules, called microRNAs (miRNAs). These virally encoded miRNAs are non-immunogenic and therefore are important tools used to evade both innate and adaptive immune responses. This review aims to summarize our current knowledge of herpesvirus- and polyomavirus-encoded miRNAs, and how they contribute to immune evasion by targeting viral and/or host cellular genes. This article is part of a Special Issue entitled: MicroRNAs in viral gene regulation.
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Affiliation(s)
- Isaac W Boss
- Department of Molecular Genetics and Microbiology, University of Florida, Gainsville, FL, USA.
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Abstract
Since 2004, more than 200 microRNAs (miRNAs) have been discovered in double-stranded DNA viruses, mainly herpesviruses and polyomaviruses (Nucleic Acids Res 32:D109-D111, 2004). miRNAs are short 22 ± 3 nt RNA molecules that posttranscriptionally regulate gene expression by binding to 3'-untranslated regions (3'UTR) of target mRNAs, thereby inducing translational silencing and/or transcript degradation (Nature 431:350-355, 2004; Cell 116:281-297, 2004). Since miRNAs require only limited complementarity for binding, miRNA targets are difficult to determine (Mol Cell 27:91-105, 2007). To date, targets have only been experimentally verified for relatively few viral miRNAs, which either target viral or host cellular gene expression: For example, SV40 and related polyomaviruses encode miRNAs which target viral large T antigen expression (Nature 435:682-686, 2005; J Virol 79:13094-13104, 2005; Virology 383:183-187, 2009; J Virol 82:9823-9828, 2008) and miRNAs of α-, β-, and γ-herpesviruses have been implicated in regulating the transition from latent to lytic gene expression, a key step in the herpesvirus life cycle. Viral miRNAs have also been shown to target various host cellular genes. Although this field is just beginning to unravel the multiple roles of viral miRNA in biology and pathogenesis, the current data strongly suggest that virally encoded miRNAs are able to regulate fundamental biological processes such as immune recognition, promotion of cell survival, angiogenesis, proliferation, and cell differentiation. This chapter aims to summarize our current knowledge of viral miRNAs, their targets and function, and the challenges lying ahead to decipher their role in viral biology, pathogenesis, and for γ-herepsvirus-encoded miRNAs, potentially tumorigenesis.
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Affiliation(s)
- Karlie Plaisance-Bonstaff
- Department of Molecular Genetics and Microbiology, University of Florida Shands Cancer Center, University of Florida, Gainesville, FL, USA
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Abstract
MicroRNAs (miRNAs) are noncoding RNA molecules approximately 22 nucleotides in length that post-transcriptionally regulate gene expression by complementary binding to target mRNAs. MiRNAs have been identified in a diverse range of both metazoan and plant species. Functionally, miRNAs modulate multiple cellular processes including development, hematopoiesis, immunity, and oncogenesis. More recently, DNA viruses were found to encode and express miRNAs during host infection. Although the functions of most viral miRNAs are not well understood, early analysis of target genes pointed to immune modulation suggesting that viral miRNAs are a component of the immune evasion repertoire, which facilitates viral persistence. In addition to directly targeting immune functions, viral encoded miRNAs contribute to immune evasion by targeting proapoptotic genes, and in the case of herpesviruses, by controlling viral latency. Here we summarize the recently discovered targets of viral miRNAs and discuss the complex nature of this novel emerging regulatory mechanism.
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Affiliation(s)
- Isaac W Boss
- Department of Molecular Genetics and Microbiology and UF Shands Cancer Center, University of Florida, 1376 Mowry Road, Gainesville, FL 32610, USA
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