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Hockberger P, Valdes KM, Bosc J, Iadicicco L, Georganopoulou D. Work-life integration survey addresses the needs of women working in life sciences. Nat Biotechnol 2021; 39:523-525. [PMID: 33846650 DOI: 10.1038/s41587-021-00882-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Philip Hockberger
- Northwestern University, Evanston, IL, USA.
- Chicago Biomedical Innovation Alliance (CBIA), Chicago, IL, USA.
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Li K, Rodosthenous RS, Kashanchi F, Gingeras T, Gould SJ, Kuo LS, Kurre P, Lee H, Leonard JN, Liu H, Lombo TB, Momma S, Nolan JP, Ochocinska MJ, Pegtel DM, Sadovsky Y, Sánchez-Madrid F, Valdes KM, Vickers KC, Weaver AM, Witwer KW, Zeng Y, Das S, Raffai RL, Howcroft TK. Advances, challenges, and opportunities in extracellular RNA biology: insights from the NIH exRNA Strategic Workshop. JCI Insight 2018; 3:98942. [PMID: 29618663 DOI: 10.1172/jci.insight.98942] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Extracellular RNA (exRNA) has emerged as an important transducer of intercellular communication. Advancing exRNA research promises to revolutionize biology and transform clinical practice. Recent efforts have led to cutting-edge research and expanded knowledge of this new paradigm in cell-to-cell crosstalk; however, gaps in our understanding of EV heterogeneity and exRNA diversity pose significant challenges for continued development of exRNA diagnostics and therapeutics. To unravel this complexity, the NIH convened expert teams to discuss the current state of the science, define the significant bottlenecks, and brainstorm potential solutions across the entire exRNA research field. The NIH Strategic Workshop on Extracellular RNA Transport helped identify mechanistic and clinical research opportunities for exRNA biology and provided recommendations on high priority areas of research that will advance the exRNA field.
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Affiliation(s)
- Kang Li
- Division of Vascular and Endovascular Surgery, Department of Surgery, University of California, San Francisco, and Veterans Affairs Medical Center, San Francisco, California, USA
| | | | - Fatah Kashanchi
- Laboratory of Molecular Virology, National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, USA
| | - Thomas Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Stephen J Gould
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lillian S Kuo
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Peter Kurre
- Doernbecher Children's Hospital, Department of Pediatrics and Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Huiping Liu
- Departments of Pharmacology and Medicine (Hematology and Oncology), Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tania B Lombo
- NIH, Office of the Director, Environmental Influences on Child Health Outcomes Program, Bethesda, Maryland, USA
| | - Stefan Momma
- Institute of Neurology (Edinger Institute), Frankfurt University Medical School, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Frankfurt, Heidelberg, Germany
| | - John P Nolan
- Scintillon Institute, San Diego, California, USA
| | | | - D Michiel Pegtel
- Department of Pathology, Cancer Center Amsterdam, Vrije Universiteit (VU) University Medical Center, Amsterdam, The Netherlands
| | - Yoel Sadovsky
- Magee-Womens Research Institute, Department of Microbiology and Molecular Genetics, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Francisco Sánchez-Madrid
- Instituto de Investigación Sanitaria Princesa, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Kayla M Valdes
- National Center for Advancing Translational Science, Bethesda, Maryland, USA
| | - Kasey C Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Department of Neurology, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Yong Zeng
- Department of Chemistry, University of Kansas Cancer Center, Lawrence, Kansas, USA
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Robert L Raffai
- Division of Vascular and Endovascular Surgery, Department of Surgery, University of California, San Francisco, and Veterans Affairs Medical Center, San Francisco, California, USA
| | - T Kevin Howcroft
- Cancer Immunology, Hematology, and Etiology Branch, Division of Cancer Biology, National Cancer Institute, Bethesda, Maryland, USA
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Valdes KM, Sundar GS, Belew AT, Islam E, El-Sayed NM, Le Breton Y, McIver KS. Glucose Levels Alter the Mga Virulence Regulon in the Group A Streptococcus. Sci Rep 2018; 8:4971. [PMID: 29563558 PMCID: PMC5862849 DOI: 10.1038/s41598-018-23366-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/06/2018] [Indexed: 12/25/2022] Open
Abstract
Many bacterial pathogens coordinately regulate genes encoding important metabolic pathways during disease progression, including the phosphoenolpyruvate (PEP)-phosphotransferase system (PTS) for uptake of carbohydrates. The Gram-positive Group A Streptococcus (GAS) is a pathogen that infects multiple tissues in the human host. The virulence regulator Mga in GAS can be phosphorylated by the PTS, affecting Mga activity based on carbohydrate availability. Here, we explored the effects of glucose availability on the Mga regulon. RNA-seq was used to identify transcriptomic differences between the Mga regulon grown to late log phase in the presence of glucose (THY) or after glucose has been expended (C media). Our results revealed a correlation between the genes activated in C media with those known to be repressed by CcpA, indicating that C media mimics a non-preferred sugar environment. Interestingly, we found very little overlap in the Mga regulon from GAS grown in THY versus C media beyond the core virulence genes. We also observed an alteration in the phosphorylation status of Mga, indicating that the observed media differences in the Mga regulon may be directly attributed to glucose levels. Thus, these results support an in vivo link between glucose availability and virulence regulation in GAS.
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Affiliation(s)
- Kayla M Valdes
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA
| | - Ganesh S Sundar
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA
| | - Ashton T Belew
- Center for Bioinformatics and Computation Biology, UMCP, College Park, MD, USA
| | - Emrul Islam
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA
| | - Najib M El-Sayed
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA.,Center for Bioinformatics and Computation Biology, UMCP, College Park, MD, USA
| | - Yoann Le Breton
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA.
| | - Kevin S McIver
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA.
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Vega LA, Valdes KM, Sundar GS, Belew AT, Islam E, Berge J, Curry P, Chen S, El-Sayed NM, Le Breton Y, McIver KS. The Transcriptional Regulator CpsY Is Important for Innate Immune Evasion in Streptococcus pyogenes. Infect Immun 2017; 85:e00925-16. [PMID: 27993974 PMCID: PMC5328483 DOI: 10.1128/iai.00925-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 11/07/2016] [Accepted: 12/13/2016] [Indexed: 01/01/2023] Open
Abstract
As an exclusively human pathogen, Streptococcus pyogenes (the group A streptococcus [GAS]) has specifically adapted to evade host innate immunity and survive in multiple tissue niches, including blood. GAS can overcome the metabolic constraints of the blood environment and expresses various immunomodulatory factors necessary for survival and immune cell resistance. Here we present our investigation of one such factor, the predicted LysR family transcriptional regulator CpsY. The encoding gene, cpsY, was initially identified as being required for GAS survival in a transposon-site hybridization (TraSH) screen in whole human blood. CpsY is homologous with transcriptional regulators of Streptococcus mutans (MetR), Streptococcus iniae (CpsY), and Streptococcus agalactiae (MtaR) that regulate methionine transport, amino acid metabolism, resistance to neutrophil-mediated killing, and survival in vivo Our investigation indicated that CpsY is involved in GAS resistance to innate immune cells of its human host. However, GAS CpsY does not manifest the in vitro phenotypes of its homologs in other streptococcal species. GAS CpsY appears to regulate a small set of genes that is markedly different from the regulons of its homologs. The differential expression of these genes depends on the growth medium, and CpsY modestly influences their expression. The GAS CpsY regulon includes known virulence factors (mntE, speB, spd, nga [spn], prtS [SpyCEP], and sse) and cell surface-associated factors of GAS (emm1, mur1.2, sibA [cdhA], and M5005_Spy0500). Intriguingly, the loss of CpsY in GAS does not result in virulence defects in murine models of infection, suggesting that CpsY function in immune evasion is specific to the human host.
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Affiliation(s)
- Luis A Vega
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Kayla M Valdes
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Ganesh S Sundar
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Ashton T Belew
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Emrul Islam
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Jacob Berge
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Patrick Curry
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Steven Chen
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Najib M El-Sayed
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Yoann Le Breton
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Kevin S McIver
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
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Le Breton Y, Belew AT, Valdes KM, Islam E, Curry P, Tettelin H, Shirtliff ME, El-Sayed NM, McIver KS. Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes. Sci Rep 2015; 5:9838. [PMID: 25996237 PMCID: PMC4440532 DOI: 10.1038/srep09838] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [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: 01/30/2015] [Accepted: 03/23/2015] [Indexed: 02/01/2023] Open
Abstract
Streptococcus pyogenes (Group A Streptococcus, GAS) remains a major public health burden worldwide, infecting over 750 million people leading to over 500,000 deaths annually. GAS pathogenesis is complex, involving genetically distinct GAS strains and multiple infection sites. To overcome fastidious genetic manipulations and accelerate pathogenesis investigations in GAS, we developed a mariner-based system (Krmit) for en masse monitoring of complex mutant pools by transposon sequencing (Tn-seq). Highly saturated transposant libraries (Krmit insertions in ca. every 25 nucleotides) were generated in two distinct GAS clinical isolates, a serotype M1T1 invasive strain 5448 and a nephritogenic serotype M49 strain NZ131, and analyzed using a Bayesian statistical model to predict GAS essential genes, identifying sets of 227 and 241 of those genes in 5448 and NZ131, respectively. A large proportion of GAS essential genes corresponded to key cellular processes and metabolic pathways, and 177 were found conserved within the GAS core genome established from 20 available GAS genomes. Selected essential genes were validated using conditional-expression mutants. Finally, comparison to previous essentiality analyses in S. sanguinis and S. pneumoniae revealed significant overlaps, providing valuable insights for the development of new antimicrobials to treat infections by GAS and other pathogenic streptococci.
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Affiliation(s)
- Yoann Le Breton
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, MD USA
| | - Ashton T. Belew
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, MD USA
| | - Kayla M. Valdes
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, MD USA
| | - Emrul Islam
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, MD USA
| | - Patrick Curry
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, MD USA
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Mark E. Shirtliff
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD USA
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland School of Medicine, Baltimore, MD USA
| | - Najib M. El-Sayed
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, MD USA
- Center for Bioinformatics and Computation Biology, University of Maryland, College Park, MD USA
| | - Kevin S. McIver
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, MD USA
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Le Breton Y, Mistry P, Valdes KM, Quigley J, Kumar N, Tettelin H, McIver KS. Genome-wide identification of genes required for fitness of group A Streptococcus in human blood. Infect Immun 2013; 81:862-75. [PMID: 23297387 PMCID: PMC3584890 DOI: 10.1128/iai.00837-12] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 12/15/2012] [Indexed: 12/27/2022] Open
Abstract
The group A streptococcus (GAS) is a strict human pathogen responsible for a wide spectrum of diseases. Although GAS genome sequences are available, functional genomic analyses have been limited. We developed a mariner-based transposon, osKaR, designed to perform Transposon-Site Hybridization (TraSH) in GAS and successfully tested its use in several invasive serotypes. A complex osKaR mutant library in M1T1 GAS strain 5448 was subjected to negative selection in human blood to identify genes important for GAS fitness in this clinically relevant environment. Mutants underrepresented after growth in blood (output pool) compared to growth in rich media (input pool) were identified using DNA microarray hybridization of transposon-specific tags en masse. Using blood from three different donors, we identified 81 genes that met our criteria for reduced fitness in blood from at least two individuals. Genes known to play a role in survival of GAS in blood were found, including those encoding the virulence regulator Mga (mga), the peroxide response regulator PerR (perR), and the RofA-like regulator Ralp-3 (ralp3). We also identified genes previously reported for their contribution to sepsis in other pathogens, such as de novo nucleotide synthesis (purD, purA, pyrB, carA, carB, guaB), sugar metabolism (scrB, fruA), zinc uptake (adcC), and transcriptional regulation (cpsY). To validate our findings, independent mutants with mutations in 10 different genes identified in our screen were confirmed to be defective for survival in blood bactericidal assays. Overall, this work represents the first use of TraSH in GAS to identify potential virulence genes.
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Affiliation(s)
- Yoann Le Breton
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Pragnesh Mistry
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Kayla M. Valdes
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Jeffrey Quigley
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Nikhil Kumar
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Hervé Tettelin
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kevin S. McIver
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
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