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Aulicino A, Antanaviciute A, Frost J, Sousa Geros A, Mellado E, Attar M, Jagielowicz M, Hublitz P, Sinz J, Preciado-Llanes L, Napolitani G, Bowden R, Koohy H, Drakesmith H, Simmons A. Dual RNA sequencing reveals dendritic cell reprogramming in response to typhoidal Salmonella invasion. Commun Biol 2022; 5:111. [PMID: 35121793 PMCID: PMC8816929 DOI: 10.1038/s42003-022-03038-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 12/15/2021] [Indexed: 12/19/2022] Open
Abstract
Salmonella enterica represent a major disease burden worldwide. S. enterica serovar Typhi (S. Typhi) is responsible for potentially life-threatening Typhoid fever affecting 10.9 million people annually. While non-typhoidal Salmonella (NTS) serovars usually trigger self-limiting diarrhoea, invasive NTS bacteraemia is a growing public health challenge. Dendritic cells (DCs) are key professional antigen presenting cells of the human immune system. The ability of pathogenic bacteria to subvert DC functions and prevent T cell recognition contributes to their survival and dissemination within the host. Here, we adapted dual RNA-sequencing to define how different Salmonella pathovariants remodel their gene expression in tandem with that of infected DCs. We find DCs harness iron handling pathways to defend against invading Salmonellas, which S. Typhi is able to circumvent by mounting a robust response to nitrosative stress. In parallel, we uncover the alternative strategies invasive NTS employ to impair DC functions. Aulicino, Antanaviciute et al investigate the transcriptional response to invasive Salmonella strains in dendritic cells (DCs). They show that S. Typhi mount a response against nitrosative stress pathways and propose a role of iron uptake and transport in preventing infection, which the pathogen can bypass. In parallel, they find that invasive Salmonella employs several mechanisms targeting more classic aspects of immunity to impair DC function.
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Affiliation(s)
- Anna Aulicino
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.,Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Agne Antanaviciute
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.,Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK.,MRC WIMM Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joe Frost
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana Sousa Geros
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.,Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Esther Mellado
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
| | - Moustafa Attar
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK.,Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, UK
| | - Marta Jagielowicz
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.,Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Philip Hublitz
- MRC Weatherall Institute of Molecular Medicine, Genome Engineering Facility, University of Oxford, Oxford, OX3 9DS, UK
| | - Julia Sinz
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.,Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Lorena Preciado-Llanes
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.,Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Giorgio Napolitani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
| | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.,MRC WIMM Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK. .,Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK.
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2
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Abstract
Iron is an essential element for almost all living organisms, but can be extremely toxic in high concentrations. All organisms must therefore employ homeostatic mechanisms to finely regulate iron uptake, usage and storage in the face of dynamic environmental conditions. The critical step in mammalian systemic iron homeostasis is the fine regulation of dietary iron absorption. However, as the gastrointestinal system is also home to >1014 bacteria, all of which engage in their own programmes of iron homeostasis, the gut represents an anatomical location where the inter-kingdom fight for iron is never-ending. Here, we explore the molecular mechanisms of, and interactions between, host and bacterial iron homeostasis in the gastrointestinal tract. We first detail how mammalian systemic and cellular iron homeostasis influences gastrointestinal iron availability. We then focus on two important human pathogens, Salmonella and Clostridia; despite their differences, they exemplify how a bacterial pathogen must navigate and exploit this web of iron homeostasis interactions to avoid host nutritional immunity and replicate successfully. We then reciprocally explore how iron availability interacts with the gastrointestinal microbiota, and the consequences of this on mammalian physiology and pathogen iron acquisition. Finally, we address how understanding the battle for iron in the gastrointestinal tract might inform clinical practice and inspire new treatments for important diseases.
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Affiliation(s)
- Ana Sousa Gerós
- MRC Human Immunology UnitWeatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
- Translational Gastroenterology UnitJohn Radcliffe HospitalOxfordUK
| | - Alison Simmons
- MRC Human Immunology UnitWeatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
- Translational Gastroenterology UnitJohn Radcliffe HospitalOxfordUK
| | - Hal Drakesmith
- MRC Human Immunology UnitWeatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Anna Aulicino
- MRC Human Immunology UnitWeatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
- Translational Gastroenterology UnitJohn Radcliffe HospitalOxfordUK
| | - Joe N. Frost
- MRC Human Immunology UnitWeatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
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3
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Corridoni D, Antanaviciute A, Gupta T, Fawkner-Corbett D, Aulicino A, Jagielowicz M, Parikh K, Repapi E, Taylor S, Ishikawa D, Hatano R, Yamada T, Xin W, Slawinski H, Bowden R, Napolitani G, Brain O, Morimoto C, Koohy H, Simmons A. Single-cell atlas of colonic CD8 + T cells in ulcerative colitis. Nat Med 2020; 26:1480-1490. [PMID: 32747828 DOI: 10.1038/s41591-020-1003-4] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [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: 07/31/2019] [Accepted: 06/04/2020] [Indexed: 12/17/2022]
Abstract
Colonic antigen-experienced lymphocytes such as tissue-resident memory CD8+ T cells can respond rapidly to repeated antigen exposure. However, their cellular phenotypes and the mechanisms by which they drive immune regulation and inflammation remain unclear. Here we compiled an unbiased atlas of human colonic CD8+ T cells in health and ulcerative colitis (UC) using single-cell transcriptomics with T-cell receptor repertoire analysis and mass cytometry. We reveal extensive heterogeneity in CD8+ T-cell composition, including expanded effector and post-effector terminally differentiated CD8+ T cells. While UC-associated CD8+ effector T cells can trigger tissue destruction and produce tumor necrosis factor (TNF)-α, post-effector cells acquire innate signatures to adopt regulatory functions that may mitigate excessive inflammation. Thus, we identify colonic CD8+ T-cell phenotypes in health and UC, define their clonal relationships and characterize terminally differentiated dysfunctional UC CD8+ T cells expressing IL-26, which attenuate acute colitis in a humanized IL-26 transgenic mouse model.
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Affiliation(s)
- Daniele Corridoni
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Agne Antanaviciute
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre For Computational Biology, MRC WIMM, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Tarun Gupta
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - David Fawkner-Corbett
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Anna Aulicino
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Marta Jagielowicz
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Kaushal Parikh
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Emmanouela Repapi
- Computational Biology Research Group, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Steve Taylor
- Computational Biology Research Group, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Dai Ishikawa
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo, Japan
| | - Ryo Hatano
- Department of Therapy Development and Innovation for Immune Disorders and Cancers, Juntendo University, Tokyo, Japan
| | - Taketo Yamada
- Department of Pathology, Saitama Medical University, Saitama, Japan
| | - Wei Xin
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Hubert Slawinski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Giorgio Napolitani
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Oliver Brain
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Chikao Morimoto
- Department of Therapy Development and Innovation for Immune Disorders and Cancers, Juntendo University, Tokyo, Japan
| | - Hashem Koohy
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK.
- MRC WIMM Centre For Computational Biology, MRC WIMM, John Radcliffe Hospital, University of Oxford, Oxford, UK.
| | - Alison Simmons
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK.
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4
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Chapman TP, Corridoni D, Shiraishi S, Pandey S, Aulicino A, Wigfield S, do Carmo Costa M, Thézénas ML, Paulson H, Fischer R, Kessler BM, Simmons A. Ataxin-3 Links NOD2 and TLR2 Mediated Innate Immune Sensing and Metabolism in Myeloid Cells. Front Immunol 2019; 10:1495. [PMID: 31379806 PMCID: PMC6659470 DOI: 10.3389/fimmu.2019.01495] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/14/2019] [Indexed: 12/15/2022] Open
Abstract
The interplay between NOD2 and TLR2 following recognition of components of the bacterial cell wall peptidoglycan is well-established, however their role in redirecting metabolic pathways in myeloid cells to degrade pathogens and mount antigen presentation remains unclear. We show NOD2 and TLR2 mediate phosphorylation of the deubiquitinase ataxin-3 via RIPK2 and TBK1. In myeloid cells ataxin-3 associates with the mitochondrial cristae protein MIC60, and is required for oxidative phosphorylation. Depletion of ataxin-3 leads to impaired induction of mitochondrial reactive oxygen species (mROS) and defective bacterial killing. A mass spectrometry analysis of NOD2/TLR2 triggered ataxin-3 deubiquitination targets revealed immunometabolic regulators, including HIF-1α and LAMTOR1 that may contribute to these effects. Thus, we define how ataxin-3 plays an essential role in NOD2 and TLR2 sensing and effector functions in myeloid cells.
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Affiliation(s)
- Thomas P. Chapman
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Daniele Corridoni
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Seiji Shiraishi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Sumeet Pandey
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Anna Aulicino
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Simon Wigfield
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | | | - Marie-Laëtitia Thézénas
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Henry Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Benedikt M. Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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5
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Xu J, Preciado-Llanes L, Aulicino A, Decker CM, Depke M, Gesell Salazar M, Schmidt F, Simmons A, Huang WE. Single-Cell and Time-Resolved Profiling of Intracellular Salmonella Metabolism in Primary Human Cells. Anal Chem 2019; 91:7729-7737. [PMID: 31117406 PMCID: PMC7006958 DOI: 10.1021/acs.analchem.9b01010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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] [Indexed: 12/22/2022]
Abstract
![]()
The
intracellular pathogen Salmonella enterica has evolved
an array of traits for propagation and invasion of the
intestinal layers. It remains largely elusive how Salmonella adjusts its metabolic states to survive inside immune host cells.
In this study, single-cell Raman biotechnology combined with deuterium
isotope probing (Raman-DIP) have been applied to reveal metabolic
changes of the typhoidal Salmonella Typhi Ty2, the
nontyphoidal Salmonella Typhimurium LT2, and a clinical
isolate Typhimurium D23580. By initially labeling the Salmonella strains with deuterium, we employed reverse labeling to track their
metabolic changes in the time-course infection of THP-1 cell line,
human monocyte-derived dendritic cells (MoDCs) and macrophages (Mf).
We found that, in comparison with a noninvasive serovar, the invasive Salmonella strains Ty2 and D23580 have downregulated metabolic
activity inside human macrophages and dendritic cells and used lipids
as alternative carbon source, perhaps a strategy to escape from the
host immune response. Proteomic analysis using high sensitivity mass
spectrometry validated the findings of Raman-DIP analysis.
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Affiliation(s)
- Jiabao Xu
- Department of Engineering Science , University of Oxford , Parks Road , Oxford OX1 3PJ , United Kingdom
| | - Lorena Preciado-Llanes
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine , University of Oxford , Oxford OX3 9DS , United Kingdom.,Translational Gastroenterology Unit, John Radcliffe Hospital , Headington, Oxford OX3 9DU , United Kingdom
| | - Anna Aulicino
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine , University of Oxford , Oxford OX3 9DS , United Kingdom.,Translational Gastroenterology Unit, John Radcliffe Hospital , Headington, Oxford OX3 9DU , United Kingdom
| | - Christoph Martin Decker
- Interfaculty Institute for Genetics and Functional Genomics , University Medicine Greifswald , Felix-Hausdorff-Str. 8 , 17475 Greifswald , Germany
| | - Maren Depke
- Interfaculty Institute for Genetics and Functional Genomics , University Medicine Greifswald , Felix-Hausdorff-Str. 8 , 17475 Greifswald , Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics , University Medicine Greifswald , Felix-Hausdorff-Str. 8 , 17475 Greifswald , Germany
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics , University Medicine Greifswald , Felix-Hausdorff-Str. 8 , 17475 Greifswald , Germany.,Proteomics Core, Weill Cornel Medicine-Qatar , Education City , PO 24144 Doha , Qatar
| | - Alison Simmons
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine , University of Oxford , Oxford OX3 9DS , United Kingdom.,Translational Gastroenterology Unit, John Radcliffe Hospital , Headington, Oxford OX3 9DU , United Kingdom
| | - Wei E Huang
- Department of Engineering Science , University of Oxford , Parks Road , Oxford OX1 3PJ , United Kingdom
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6
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Napolitani G, Kurupati P, Teng KWW, Gibani MM, Rei M, Aulicino A, Preciado-Llanes L, Wong MT, Becht E, Howson L, de Haas P, Salio M, Blohmke CJ, Olsen LR, Pinto DMS, Scifo L, Jones C, Dobinson H, Campbell D, Juel HB, Thomaides-Brears H, Pickard D, Bumann D, Baker S, Dougan G, Simmons A, Gordon MA, Newell EW, Pollard AJ, Cerundolo V. Publisher Correction: Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses. Nat Immunol 2019; 20:514. [PMID: 30862955 DOI: 10.1038/s41590-019-0357-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article initially published, the first affiliation lacked 'MRC'; the correct name of the institution is 'MRC Weatherall Institute of Molecular Medicine'. Two designations (SP110Y and ST110H) were incorrect in the legend to Fig. 6f,h,i. The correct text is as follows: for panel f, "...loaded with either the CdtB(105-125)SP110Y (DRB4*SP110Y) or the CdtB(105-125)ST110H (DRB4*ST110H) peptide variants..."; for panel h, "...decorated by the DRB4*SP110Y tetramer (lower-right quadrant), the DRB4*ST110H (upper-left quadrant)..."; and for panel i, "...stained ex vivo with DRB4*SP110Y, DRB4*ST110H...". In Fig. 8e, the final six residues (LTEAFF) of the sequence in the far right column of the third row of the table were missing; the correct sequence is 'CASSYRRTPPLTEAFF'. In the legend to Fig. 8d, a designation (HLyE) was incorrect; the correct text is as follows: "(HlyE?)." Portions of the Acknowledgements section were incorrect; the correct text is as follows: "This work was supported by the UK Medical Research Council (MRC) (MR/K021222/1) (G.N., M.A.G., A.S., V.C., A.J.P.),...the Oxford Biomedical Research Centre (A.J.P., V.C.),...and core funding from the Singapore Immunology Network (SIgN) (E.W.N.) and the SIgN immunomonitoring platform (E.W.N.)." Finally, a parenthetical element was phrased incorrectly in the final paragraph of the Methods subsection "T cell cloning and live fluorescence barcoding"; the correct phrasing is as follows: "...(which in all cases included HlyE, CdtB, Ty21a, Quailes, NVGH308, and LT2 strains and in volunteers T5 and T6 included PhoN)...". Also, in Figs. 3c and 4a, the right outlines of the plots were not visible; in the legend to Fig. 3, panel letter 'f' was not bold; and in Fig. 8f, 'ND' should be aligned directly beneath DRB4 in the key and 'ND' should be removed from the diagram at right, and the legend should be revised accordingly as follows: "...colors indicate the HLA class II restriction (gray indicates clones for which restriction was not determined (ND)). Clonotypes are grouped on the basis of pathogen selectivity (continuous line), protein specificity (dashed line) and epitope specificity; for ten HlyE-specific clones (pixilated squares), the epitope specificity was not determined...". The errors have been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Giorgio Napolitani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Prathiba Kurupati
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Karen Wei Weng Teng
- Singapore Immunology Network, Agency of Science, Technology and Research, Singapore, Singapore
| | - Malick M Gibani
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford and NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Margarida Rei
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Anna Aulicino
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Lorena Preciado-Llanes
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Michael Thomas Wong
- Singapore Immunology Network, Agency of Science, Technology and Research, Singapore, Singapore
| | - Etienne Becht
- Singapore Immunology Network, Agency of Science, Technology and Research, Singapore, Singapore
| | - Lauren Howson
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paola de Haas
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mariolina Salio
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Christoph J Blohmke
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford and NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Lars Rønn Olsen
- Department of Bio and Health Informatics, Technical University of Denmark, Copenhagen, Denmark
| | | | - Laura Scifo
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Claire Jones
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford and NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Hazel Dobinson
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford and NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Danielle Campbell
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford and NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Helene B Juel
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford and NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Helena Thomaides-Brears
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford and NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | - Dirk Bumann
- Biozentrum, University of Basel, Basel, Switzerland
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Melita A Gordon
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Evan William Newell
- Singapore Immunology Network, Agency of Science, Technology and Research, Singapore, Singapore
| | - Andrew J Pollard
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford and NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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7
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Aulicino A, Rue-Albrecht KC, Preciado-Llanes L, Napolitani G, Ashley N, Cribbs A, Koth J, Lagerholm BC, Ambrose T, Gordon MA, Sims D, Simmons A. Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets. Nat Commun 2018; 9:4883. [PMID: 30451854 PMCID: PMC6242960 DOI: 10.1038/s41467-018-07329-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 04/25/2018] [Accepted: 10/25/2018] [Indexed: 01/06/2023] Open
Abstract
Non-typhoidal Salmonella (NTS) are highly prevalent food-borne pathogens. Recently, a highly invasive, multi-drug resistant S. Typhimurium, ST313, emerged as a major cause of bacteraemia in children and immunosuppressed adults, however the pathogenic mechanisms remain unclear. Here, we utilize invasive and non-invasive Salmonella strains combined with single-cell RNA-sequencing to study the transcriptome of individual infected and bystander monocyte-derived dendritic cells (MoDCs) implicated in disseminating invasive ST313. Compared with non-invasive Salmonella, ST313 directs a highly heterogeneous innate immune response. Bystander MoDCs exhibit a hyper-activated profile potentially diverting adaptive immunity away from infected cells. MoDCs harbouring invasive Salmonella display higher expression of IL10 and MARCH1 concomitant with lower expression of CD83 to evade adaptive immune detection. Finally, we demonstrate how these mechanisms conjointly restrain MoDC-mediated activation of Salmonella-specific CD4+ T cell clones. Here, we show how invasive ST313 exploits discrete evasion strategies within infected and bystander MoDCs to mediate its dissemination in vivo.
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Affiliation(s)
- Anna Aulicino
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Kevin C Rue-Albrecht
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Headington, Oxford, OX3 7FY, UK
| | - Lorena Preciado-Llanes
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Giorgio Napolitani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Neil Ashley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, OX3 9DS, UK
| | - Adam Cribbs
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jana Koth
- MRC Human Immunology Unit and Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - B Christoffer Lagerholm
- MRC Human Immunology Unit and Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Tim Ambrose
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Melita A Gordon
- Institute of Infection and Global Health, University of Liverpool, 8 W Derby St, Liverpool, L7 3EA, UK
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - David Sims
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK.
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8
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Zinecker H, Ouaret D, Ebner D, Gaidt MM, Taylor S, Aulicino A, Jagielowicz M, Hornung V, Simmons A. ICG-001 affects DRP1 activity and ER stress correlative with its anti-proliferative effect. Oncotarget 2017; 8:106764-106777. [PMID: 29290987 PMCID: PMC5739772 DOI: 10.18632/oncotarget.22264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 02/08/2017] [Accepted: 10/17/2017] [Indexed: 11/25/2022] Open
Abstract
Mitochondria form a highly dynamic network driven by opposing scission and fusion events. DRP1 is an essential modulator of mitochondrial fission and dynamics within mammalian cells. Its fission activity is regulated by posttranslational modifications such as activating phosphorylation at serine 616. DRP1 activity has recently been implicated as being dysregulated in numerous human disorders such as cancer and neurodegenerative diseases. Here we describe the development of a cell-based screening assay to detect DRP1 activation. We utilized this to undertake focused compound library screening and identified potent modulators that affected DRP1 activity including ICG-001, which is described as WNT/β-catenin signaling inhibitor. Our findings elucidate novel details about ICG-001’s mechanism of action (MOA) in mediating anti-proliferative activity. We show ICG-001 both inhibits mitochondrial fission and activates an early endoplasmic reticulum (ER) stress response to induce cell death in susceptible colorectal cancer cell lines.
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Affiliation(s)
- Heidi Zinecker
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom
| | - Djamila Ouaret
- Department of Oncology, Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom
| | - Daniel Ebner
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, United Kingdom
| | - Moritz M Gaidt
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, 81377, Germany
| | - Steve Taylor
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom
| | - Anna Aulicino
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom
| | - Marta Jagielowicz
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, 81377, Germany
| | - Alison Simmons
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom
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9
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Aulicino A, Dinan AM, Miranda-CasoLuengo AA, Browne JA, Rue-Albrecht K, MacHugh DE, Loftus BJ. High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants. BMC Genomics 2015; 16:1046. [PMID: 26654095 PMCID: PMC4674915 DOI: 10.1186/s12864-015-2246-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 10/30/2015] [Accepted: 11/25/2015] [Indexed: 12/28/2022] Open
Abstract
Background Mycobacterium abscessus (MAB) is an emerging pathogen causing pulmonary infections in those with inflammatory lung disorders, such as Cystic Fibrosis (CF), and is associated with the highest fatality rate among rapidly growing mycobacteria (RGM). Phenotypically, MAB manifests as either a Smooth (MAB-S) or a Rough (MAB-R) morphotype, which differ in their levels of cell wall glycopeptidolipids (GPLs) and in their pathogenicity in vivo. As one of the primary immune cells encountered by MAB, we sought to examine the early transcriptional events within macrophages, following infection with both MAB-S or MAB-R. Results We sampled the transcriptomes (mRNA and miRNA) of THP-1-derived macrophages infected with both MAB-R and MAB-S at 1, 4 and 24 h post-infection (hpi) using RNA-seq. A core set of 606 genes showed consistent expression profiles in response to both morphotypes, corresponding to the early transcriptional response to MAB. The core response is type I Interferon (IFN)-driven, involving the NF-κB and MAPK signaling pathways with concomitant pro-inflammatory cytokine production, and network analysis identified STAT1, EGR1, and SRC as key hub and bottleneck genes. MAB-S elicited a more robust transcriptional response at both the mRNA and miRNA levels, which was reflected in higher cytokine levels in culture supernatants. The transcriptional profiles of macrophages infected with both morphotypes were highly correlated, however, and a direct comparison identified few genes to distinguish them. Most of the induced miRNAs have previously been associated with mycobacterial infection and overall miRNA expression patterns were similarly highly correlated between the morphotypes. Conclusions The report here details the first whole transcriptome analysis of the early macrophage response to MAB infection. The overall picture at the early stages of macrophage infection is similar to that of other mycobacteria, reflected in a core type I IFN and pro-inflammatory cytokine response. Large-scale transcriptional differences in the host response to the different MAB morphotypes are not evident in the early stages of infection, however the subset of genes with distinct expression profiles suggest potentially interesting differences in internal trafficking of MAB within macrophages. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2246-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Aulicino
- School of Medicine & Medical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Adam M Dinan
- School of Medicine & Medical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Aleksandra A Miranda-CasoLuengo
- School of Medicine & Medical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Kévin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Dublin, Ireland.
| | - Brendan J Loftus
- School of Medicine & Medical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Dublin, Ireland.
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10
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Esin S, Counoupas C, Aulicino A, Brancatisano FL, Maisetta G, Bottai D, Di Luca M, Florio W, Campa M, Batoni G. Interaction ofMycobacterium tuberculosisCell Wall Components with the Human Natural Killer Cell Receptors NKp44 and Toll-Like Receptor 2. Scand J Immunol 2013; 77:460-9. [DOI: 10.1111/sji.12052] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/29/2013] [Indexed: 12/30/2022]
Affiliation(s)
- S. Esin
- Department of Translational Research and New Technologies in Medicine and Surgery; University of Pisa; Pisa; Italy
| | - C. Counoupas
- Department of Translational Research and New Technologies in Medicine and Surgery; University of Pisa; Pisa; Italy
| | - A. Aulicino
- Department of Translational Research and New Technologies in Medicine and Surgery; University of Pisa; Pisa; Italy
| | - F. L. Brancatisano
- Department of Translational Research and New Technologies in Medicine and Surgery; University of Pisa; Pisa; Italy
| | - G. Maisetta
- Department of Translational Research and New Technologies in Medicine and Surgery; University of Pisa; Pisa; Italy
| | - D. Bottai
- Department of Translational Research and New Technologies in Medicine and Surgery; University of Pisa; Pisa; Italy
| | - M. Di Luca
- Department of Translational Research and New Technologies in Medicine and Surgery; University of Pisa; Pisa; Italy
| | - W. Florio
- Department of Translational Research and New Technologies in Medicine and Surgery; University of Pisa; Pisa; Italy
| | - M. Campa
- Department of Translational Research and New Technologies in Medicine and Surgery; University of Pisa; Pisa; Italy
| | - G. Batoni
- Department of Translational Research and New Technologies in Medicine and Surgery; University of Pisa; Pisa; Italy
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11
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Calogero RA, Aulicino A. Purification of Recombinant Proteins with High Isoelectric Points. Molecular Diagnosis of Infectious Diseases 2004; 94:225-38. [PMID: 14959833 DOI: 10.1385/1-59259-679-7:225] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The use of recombinant antigens is essential for the construction of robust and sensitive diagnostic assays. A critical step in the preparation of recombinant antigens is protein purification. Purification problems may be very different for related structural proteins expressed in the same host or for the same protein expressed in different hosts, because the biochemical characteristics of a recombinant protein, expressed in a heterologous system, are unique. In this chapter we make a brief introduction to protein purification procedures and we present a quick purification process suitable for the isolation of recombinant protein having high isoelectric points encoding non-conformational epitopes.
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12
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Lener D, Antico G, Andre A, Aulicino A, Bucci E, Darlix JL, Calogero RA. In vitro characterization of peptides interfering with the hiv-1 nucleocapsid protein (ncp7) functions. Protein Pept Lett 1997. [DOI: 10.2174/092986650405221017150752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Abstract:
In HIV-I, the nucleocapsid protein (NCp7) play essential roles in several steps of HIV-I replication. Since NCp7 is required for virion formation and proviral DNA synthesis and is highly conserved, identification of compounds able to inhibit NCp7 activities and functions may lead to the discovery of new anti-HIV drugs. Here we present data showing that peptides derived from the first and second NCp7 zinc finger interfere, in vitro, with NCp7 functions during the early stage of HIV- I reverse transcription.
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Affiliation(s)
- Daniela Lener
- LaboRetro Unite de Virologie Humaine, Ecole Normale Superieure-Institut National de la Sante et de Ia Recherche Medicate U412, 69364 Lyon Cedex 07, France
| | - Giovanni Antico
- Dipartimento di Genetica, Biologia Generate e Molecolare, via Mezzocannone 8; 80134 Napoli, Italy
| | - Alessandra Andre
- Dipartimento di Genetica, Biologia Generate e Molecolare, via Mezzocannone 8; 80134 Napoli, Italy
| | - Anna Aulicino
- Dipartimento di Genetica, Biologia Generate e Molecolare, via Mezzocannone 8; 80134 Napoli, Italy
| | - Enrico Bucci
- Dipartimento di Chimica, via Mezzocannone 4, 80134 Napoli, Italy
| | - Jean-Luc Darlix
- LaboRetro Unite de Virologie Humaine, Ecole Normale Superieure-Institut National de la Sante et de Ia Recherche Medicate U412, 69364 Lyon Cedex 07, France
| | - Raffaele A. Calogero
- Dipartimento di Genetica, Biologia Generate e Molecolare, via Mezzocannone 8; 80134 Napoli, Italy
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