1
|
Ratnasiri K, Zheng H, Toh J, Yao Z, Duran V, Donato M, Roederer M, Kamath M, Todd JPM, Gagne M, Foulds KE, Francica JR, Corbett KS, Douek DC, Seder RA, Einav S, Blish CA, Khatri P. Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans. Cell Rep 2024; 43:113706. [PMID: 38294906 PMCID: PMC10915397 DOI: 10.1016/j.celrep.2024.113706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/02/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Viral pandemics and epidemics pose a significant global threat. While macaque models of viral disease are routinely used, it remains unclear how conserved antiviral responses are between macaques and humans. Therefore, we conducted a cross-species analysis of transcriptomic data from over 6,088 blood samples from macaques and humans infected with one of 31 viruses. Our findings demonstrate that irrespective of primate or viral species, there are conserved antiviral responses that are consistent across infection phase (acute, chronic, or latent) and viral genome type (DNA or RNA viruses). Leveraging longitudinal data from experimental challenges, we identify virus-specific response kinetics such as host responses to Coronaviridae and Orthomyxoviridae infections peaking 1-3 days earlier than responses to Filoviridae and Arenaviridae viral infections. Our results underscore macaque studies as a powerful tool for understanding viral pathogenesis and immune responses that translate to humans, with implications for viral therapeutic development and pandemic preparedness.
Collapse
Affiliation(s)
- Kalani Ratnasiri
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiaying Toh
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhiyuan Yao
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Veronica Duran
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Michele Donato
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megha Kamath
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph R Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirit Einav
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
2
|
Gokemeijer J, Balasubramanian N, Ogasawara K, Grudzinska-Goebel J, Upreti VV, Mody H, Kasar S, Vepachedu VR, Xu W, Gupta S, Tarcsa E, Dodge R, Herr K, Yang TY, Tourdot S, Jawa V. An IQ Consortium Perspective on Best Practices for Bioanalytical and Immunogenicity Assessment Aspects of CAR-T and TCR-T Cellular Therapies Development. Clin Pharmacol Ther 2024; 115:188-200. [PMID: 37983584 DOI: 10.1002/cpt.3111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/05/2023] [Indexed: 11/22/2023]
Abstract
CAR-T therapies have shown remarkable efficacy against hematological malignancies in the clinic over the last decade and new studies indicate that progress is being made to use these novel therapies to target solid tumors as well as treat autoimmune disease. Innovation in the field, including TCR-T, allogeneic or "off the shelf" CAR-T, and autoantigen/armored CAR-Ts are likely to increase the efficacy and applications of these therapies. The unique aspects of these cell-based therapeutics; patient-derived cells, intracellular expression, in vivo expansion, and phenotypic changes provide unique bioanalytical challenges to develop pharmacokinetic and immunogenicity assessments. The International Consortium for Innovation and Quality in Pharmaceutical Development (IQ) Translational and ADME Sciences Leadership Group (TALG) has brought together a group of industry experts to discuss and consider these challenges. In this white paper, we present the IQ consortium perspective on the best practices and considerations for bioanalytical and immunogenicity aspects toward the optimal development of CAR-T and TCR-T cell therapies.
Collapse
Affiliation(s)
- Jochem Gokemeijer
- Discovery Biotherapeutics, Bristol Myers Squibb, Cambridge, Massachusetts, USA
| | - Nanda Balasubramanian
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Ken Ogasawara
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | | | - Vijay V Upreti
- Clinical Pharmacology, Modeling & Simulation, Amgen, Inc., South San Francisco, California, USA
| | - Hardik Mody
- Clinical Pharmacology, Genentech Inc., South San Francisco, California, USA
| | - Siddha Kasar
- Oncology Precision & Translational Medicine, Takeda Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Venkata R Vepachedu
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Weifeng Xu
- Preclinical Development, Bioanalytical, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Swati Gupta
- Development Biological Sciences, Immunology, AbbVie, Irvine, California, USA
| | - Edit Tarcsa
- Abbvie Bioresearch Center, Worcester, Massachusetts, USA
| | - Robert Dodge
- Novartis Institutes for BioMedical Research, One Health Plaza, East Hanover, New Jersey, USA
| | - Kate Herr
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Tong-Yuan Yang
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Sophie Tourdot
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Vibha Jawa
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| |
Collapse
|
3
|
Guito JC, Arnold CE, Schuh AJ, Amman BR, Sealy TK, Spengler JR, Harmon JR, Coleman-McCray JD, Sanchez-Lockhart M, Palacios GF, Towner JS, Prescott JB. Peripheral immune responses to filoviruses in a reservoir versus spillover hosts reveal transcriptional correlates of disease. Front Immunol 2024; 14:1306501. [PMID: 38259437 PMCID: PMC10800976 DOI: 10.3389/fimmu.2023.1306501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/27/2023] [Indexed: 01/24/2024] Open
Abstract
Several filoviruses, including Marburg virus (MARV), cause severe disease in humans and nonhuman primates (NHPs). However, the Egyptian rousette bat (ERB, Rousettus aegyptiacus), the only known MARV reservoir, shows no overt illness upon natural or experimental infection, which, like other bat hosts of zoonoses, is due to well-adapted, likely species-specific immune features. Despite advances in understanding reservoir immune responses to filoviruses, ERB peripheral blood responses to MARV and how they compare to those of diseased filovirus-infected spillover hosts remain ill-defined. We thus conducted a longitudinal analysis of ERB blood gene responses during acute MARV infection. These data were then contrasted with a compilation of published primate blood response studies to elucidate gene correlates of filovirus protection versus disease. Our work expands on previous findings in MARV-infected ERBs by supporting both host resistance and disease tolerance mechanisms, offers insight into the peripheral immunocellular repertoire during infection, and provides the most direct known cross-examination between reservoir and spillover hosts of the most prevalently-regulated response genes, pathways and activities associated with differences in filovirus pathogenesis and pathogenicity.
Collapse
Affiliation(s)
- Jonathan C. Guito
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Catherine E. Arnold
- Biological Defense Research Directorate, Naval Medical Research Center, Frederick, MD, United States
- RD-CBR, Research and Development Directorate, Chemical and Biological Technologies Directorate, Research Center of Excellence, Defense Threat Reduction Agency, Fort Belvoir, VA, United States
| | - Amy J. Schuh
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Brian R. Amman
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Tara K. Sealy
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jessica R. Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jessica R. Harmon
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Joann D. Coleman-McCray
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, Molecular Biology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Gustavo F. Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jonathan S. Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Joseph B. Prescott
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, United States
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| |
Collapse
|
4
|
Speranza E. Understanding virus-host interactions in tissues. Nat Microbiol 2023; 8:1397-1407. [PMID: 37488255 DOI: 10.1038/s41564-023-01434-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Although virus-host interactions are usually studied in a single cell type using in vitro assays in immortalized cell lines or isolated cell populations, it is important to remember that what is happening inside one infected cell does not translate to understanding how an infected cell behaves in a tissue, organ or whole organism. Infections occur in complex tissue environments, which contain a host of factors that can alter the course of the infection, including immune cells, non-immune cells and extracellular-matrix components. These factors affect how the host responds to the virus and form the basis of the protective response. To understand virus infection, tools are needed that can profile the tissue environment. This Review highlights methods to study virus-host interactions in the infection microenvironment.
Collapse
Affiliation(s)
- Emily Speranza
- Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL, USA.
| |
Collapse
|
5
|
de Koning W, Feenstra FF, Calkoen FGJ, van der Lugt J, Kester LA, Mustafa DAM. Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA sequencing. Cancer Immunol Immunother 2023; 72:2659-2670. [PMID: 37072536 PMCID: PMC10361846 DOI: 10.1007/s00262-023-03450-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/07/2023] [Indexed: 04/20/2023]
Abstract
BACKGROUND Defining the tumor immune microenvironment (TIME) of patients using transcriptome analysis is gaining more popularity. Here, we examined and discussed the pros and cons of using RNA sequencing for fresh frozen samples and targeted gene expression immune profiles (NanoString) for formalin-fixed, paraffin-embedded (FFPE) samples to characterize the TIME of ependymoma samples. RESULTS Our results showed a stable expression of the 40 housekeeping genes throughout all samples. The Pearson correlation of the endogenous genes was high. To define the TIME, we first checked the expression of the PTPRC gene, known as CD45, and found it was above the detection limit in all samples by both techniques. T cells were identified consistently using the two types of data. In addition, both techniques showed that the immune landscape was heterogeneous in the 6 ependymoma samples used for this study. CONCLUSIONS The low-abundant genes were detected in higher quantities using the NanoString technique, even when FFPE samples were used. RNA sequencing is better suited for biomarker discovery, fusion gene detection, and getting a broader overview of the TIME. The technique that was used to measure the samples had a considerable effect on the type of immune cells that were identified. The limited number of tumor-infiltrating immune cells compared to the high density of tumor cells in ependymoma can limit the sensitivity of RNA expression techniques regarding the identification of the infiltrating immune cells.
Collapse
Affiliation(s)
- W. de Koning
- Tumor Immuno-Pathology Laboratory, Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, The Netherlands
- Clinical Bioinformatics Unit, Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - F. F. Feenstra
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - F. G. J. Calkoen
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - J. van der Lugt
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - L. A. Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - D. A. M. Mustafa
- Tumor Immuno-Pathology Laboratory, Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| |
Collapse
|
6
|
Maier AD. Malignant meningioma. APMIS 2022; 130 Suppl 145:1-58. [DOI: 10.1111/apm.13276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Andrea Daniela Maier
- Department of Neurosurgery, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
- Department of Pathology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
| |
Collapse
|
7
|
Kaipilyawar V, Zhao Y, Wang X, Joseph NM, Knudsen S, Prakash Babu S, Muthaiah M, Hochberg NS, Sarkar S, Horsburgh CR, Ellner JJ, Johnson WE, Salgame P. Development and Validation of a Parsimonious Tuberculosis Gene Signature Using the digital NanoString nCounter Platform. Clin Infect Dis 2022; 75:1022-1030. [PMID: 35015839 PMCID: PMC9522394 DOI: 10.1093/cid/ciac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Blood-based biomarkers for diagnosing active tuberculosis (TB), monitoring treatment response, and predicting risk of progression to TB disease have been reported. However, validation of the biomarkers across multiple independent cohorts is scarce. A robust platform to validate TB biomarkers in different populations with clinical end points is essential to the development of a point-of-care clinical test. NanoString nCounter technology is an amplification-free digital detection platform that directly measures mRNA transcripts with high specificity. Here, we determined whether NanoString could serve as a platform for extensive validation of candidate TB biomarkers. METHODS The NanoString platform was used for performance evaluation of existing TB gene signatures in a cohort in which signatures were previously evaluated on an RNA-seq dataset. A NanoString codeset that probes 107 genes comprising 12 TB signatures and 6 housekeeping genes (NS-TB107) was developed and applied to total RNA derived from whole blood samples of TB patients and individuals with latent TB infection (LTBI) from South India. The TBSignatureProfiler tool was used to score samples for each signature. An ensemble of machine learning algorithms was used to derive a parsimonious biomarker. RESULTS Gene signatures present in NS-TB107 had statistically significant discriminative power for segregating TB from LTBI. Further analysis of the data yielded a NanoString 6-gene set (NANO6) that when tested on 10 published datasets was highly diagnostic for active TB. CONCLUSIONS The NanoString nCounter system provides a robust platform for validating existing TB biomarkers and deriving a parsimonious gene signature with enhanced diagnostic performance.
Collapse
Affiliation(s)
- Vaishnavi Kaipilyawar
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Yue Zhao
- Department of Medicine, Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Xutao Wang
- Department of Medicine, Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Noyal M Joseph
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | | | - Senbagavalli Prakash Babu
- Department of Preventive and Social Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Muthuraj Muthaiah
- Department of Microbiology, State TB Training and Demonstration Center, Government Hospital for Chest Disease, Gorimedu, Puducherry, India
| | - Natasha S Hochberg
- Boston Medical Center, Boston, Massachusetts, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Sonali Sarkar
- Department of Preventive and Social Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Charles R Horsburgh
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Jerrold J Ellner
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - W Evan Johnson
- Department of Medicine, Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Padmini Salgame
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| |
Collapse
|
8
|
Avatar Mice Underscore the Role of the T Cell-Dendritic Cell Crosstalk in Ebola Virus Disease and Reveal Mechanisms of Protection in Survivors. J Virol 2022; 96:e0057422. [PMID: 36073921 PMCID: PMC9517696 DOI: 10.1128/jvi.00574-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ebola virus disease (EVD) is a complex infectious disease characterized by high inflammation, multiorgan failure, the dysregulation of innate and adaptive immune responses, and coagulation abnormalities. Evidence accumulated over the last 2 decades indicates that, during fatal EVD, the infection of antigen-presenting cells (APC) and the dysregulation of T cell immunity preclude a successful transition between innate and adaptive immunity, which constitutes a key disease checkpoint. In order to better understand the contribution of the APC-T cell crosstalk to EVD pathophysiology, we have developed avatar mice transplanted with human, donor-specific APCs and T cells. Here, we show that the transplantation of T cells and APCs from Ebola virus (EBOV)-naive individuals into avatar mice results in severe disease and death and that this phenotype is dependent on T cell receptor (TCR)-major histocompatibility complex (MCH) recognition. Conversely, avatar mice were rescued from death induced by EBOV infection after the transplantation of both T cells and plasma from EVD survivors. These results strongly suggest that protection from EBOV reinfection requires both cellular and humoral immune memory responses. IMPORTANCE The crosstalk between dendritic cells and T cells marks the transition between innate and adaptive immune responses, and it constitutes an important checkpoint in EVD. In this study, we present a mouse avatar model in which T cell and dendritic cell interactions from a specific donor can be studied during EVD. Our findings indicate that T cell receptor-major histocompatibility complex-mediated T cell-dendritic cell interactions are associated with disease severity, which mimics the main features of severe EVD in these mice. Resistance to an EBOV challenge in the model was achieved via the transplantation of both survivor T cells and plasma.
Collapse
|
9
|
Mintz R, Wang M, Xu S, Colditz GA, Markovic C, Toriola AT. Hormone and receptor activator of NF-κB (RANK) pathway gene expression in plasma and mammographic breast density in postmenopausal women. Breast Cancer Res 2022; 24:28. [PMID: 35422057 PMCID: PMC9008951 DOI: 10.1186/s13058-022-01522-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/27/2022] [Indexed: 12/22/2022] Open
Abstract
Background Hormones impact breast tissue proliferation. Studies investigating the associations of circulating hormone levels with mammographic breast density have reported conflicting results. Due to the limited number of studies, we investigated the associations of hormone gene expression as well as their downstream mediators within the plasma with mammographic breast density in postmenopausal women. Methods We recruited postmenopausal women at their annual screening mammogram at Washington University School of Medicine, St. Louis. We used the NanoString nCounter platform to quantify gene expression of hormones (prolactin, progesterone receptor (PGR), estrogen receptor 1 (ESR1), signal transducer and activator of transcription (STAT1 and STAT5), and receptor activator of nuclear factor-kB (RANK) pathway markers (RANK, RANKL, osteoprotegerin, TNFRSF18, and TNFRSF13B) in plasma. We used Volpara to measure volumetric percent density, dense volume, and non-dense volume. Linear regression models, adjusted for confounders, were used to evaluate associations between gene expression (linear fold change) and mammographic breast density. Results One unit increase in ESR1, RANK, and TNFRSF18 gene expression was associated with 8% (95% CI 0–15%, p value = 0.05), 10% (95% CI 0–20%, p value = 0.04) and % (95% CI 0–9%, p value = 0.04) higher volumetric percent density, respectively. There were no associations between gene expression of other markers and volumetric percent density. One unit increase in osteoprotegerin and PGR gene expression was associated with 12% (95% CI 4–19%, p value = 0.003) and 7% (95% CI 0–13%, p value = 0.04) lower non-dense volume, respectively. Conclusion These findings provide new insight on the associations of plasma hormonal and RANK pathway gene expression with mammographic breast density in postmenopausal women and require confirmation in other studies. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-022-01522-2.
Collapse
Affiliation(s)
- Rachel Mintz
- Biomedical Engineering Department, Washington University, St. Louis, MO, 63110, USA
| | - Mei Wang
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, Campus Box 8100, 660 South Euclid Ave, St. Louis, MO, 63110, USA
| | - Shuai Xu
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, Campus Box 8100, 660 South Euclid Ave, St. Louis, MO, 63110, USA
| | - Graham A Colditz
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, Campus Box 8100, 660 South Euclid Ave, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA
| | - Chris Markovic
- McDonnell Genome Institute at Washington University, St. Louis, MO, 63018, USA
| | - Adetunji T Toriola
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, Campus Box 8100, 660 South Euclid Ave, St. Louis, MO, 63110, USA. .,Siteman Cancer Center, Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
10
|
Host response transcriptomic analysis of Crimean-Congo hemorrhagic fever pathogenesis in the cynomolgus macaque model. Sci Rep 2021; 11:19807. [PMID: 34615921 PMCID: PMC8494817 DOI: 10.1038/s41598-021-99130-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022] Open
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a highly pathogenic tick-borne RNA virus prevalent in Asia, Europe, and Africa, and can cause a hemorrhagic disease (CCHF) in humans with mortality rates as high as 60%. A general lack of both effective medical countermeasures and a comprehensive understanding of disease pathogenesis is partly driven by an historical lack of viable CCHF animal models. Recently, a cynomolgous macaque model of CCHF disease was developed. Here, we document the targeted transcriptomic response of non-human primates (NHP) to two different CCHFV strains; Afghan09-2990 and Kosova Hoti that both yielded a mild CCHF disease state. We utilized a targeted gene panel to elucidate the transcriptomic changes occurring in NHP whole blood during CCHFV infection; a first for any primate species. We show numerous upregulated genes starting at 1 day post-challenge through 14 days post-challenge. Early gene changes fell predominantly in the interferon stimulated gene family with later gene changes coinciding with an adaptive immune response to the virus. There are subtle differences between viral strains, namely duration of the differentially expressed gene response and biological pathways enriched. After recovery, NHPs showed no lasting transcriptomic changes at the end of sample collection.
Collapse
|
11
|
Paparisto E, Hunt NR, Labach DS, Coleman MD, Di Gravio EJ, Dodge MJ, Friesen NJ, Côté M, Müller A, Hoenen T, Barr SD. Interferon-Induced HERC5 Inhibits Ebola Virus Particle Production and Is Antagonized by Ebola Glycoprotein. Cells 2021; 10:cells10092399. [PMID: 34572049 PMCID: PMC8472148 DOI: 10.3390/cells10092399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/11/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
Survival following Ebola virus (EBOV) infection correlates with the ability to mount an early and robust interferon (IFN) response. The host IFN-induced proteins that contribute to controlling EBOV replication are not fully known. Among the top genes with the strongest early increases in expression after infection in vivo is IFN-induced HERC5. Using a transcription- and replication-competent VLP system, we showed that HERC5 inhibits EBOV virus-like particle (VLP) replication by depleting EBOV mRNAs. The HERC5 RCC1-like domain was necessary and sufficient for this inhibition and did not require zinc finger antiviral protein (ZAP). Moreover, we showed that EBOV (Zaire) glycoprotein (GP) but not Marburg virus GP antagonized HERC5 early during infection. Our data identify a novel ‘protagonist–antagonistic’ relationship between HERC5 and GP in the early stages of EBOV infection that could be exploited for the development of novel antiviral therapeutics.
Collapse
Affiliation(s)
- Ermela Paparisto
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Nina R. Hunt
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Daniel S. Labach
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Macon D. Coleman
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Eric J. Di Gravio
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Mackenzie J. Dodge
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Nicole J. Friesen
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Marceline Côté
- Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Roger-Guindon Hall Room 4214, Ottawa, ON K1H 8M5 , Canada;
| | - Andreas Müller
- Friedrich-Loeffler-Institut, Institute of Molecular Virology and Cell Biology, Südufer 10, 17493 Greifswald—Insel Riems, Germany; (A.M.); (T.H.)
| | - Thomas Hoenen
- Friedrich-Loeffler-Institut, Institute of Molecular Virology and Cell Biology, Südufer 10, 17493 Greifswald—Insel Riems, Germany; (A.M.); (T.H.)
| | - Stephen D. Barr
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
- Correspondence:
| |
Collapse
|
12
|
Bundibugyo ebolavirus Survival Is Associated with Early Activation of Adaptive Immunity and Reduced Myeloid-Derived Suppressor Cell Signaling. mBio 2021; 12:e0151721. [PMID: 34372693 PMCID: PMC8406165 DOI: 10.1128/mbio.01517-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ebolaviruses Bundibugyo virus (BDBV) and Ebola virus (EBOV) cause fatal hemorrhagic disease in humans and nonhuman primates. While the host response to EBOV is well characterized, less is known about BDBV infection. Moreover, immune signatures that mediate natural protection against all ebolaviruses remain poorly defined. To explore these knowledge gaps, we transcriptionally profiled BDBV-infected rhesus macaques, a disease model that results in incomplete lethality. This approach enabled us to identify prognostic indicators. As expected, survival (∼60%) correlated with reduced clinical pathology and circulating infectious virus, although peak viral RNA loads were not significantly different between surviving and nonsurviving macaques. Survivors had higher anti-BDBV antibody titers and transcriptionally derived cytotoxic T cell-, memory B cell-, and plasma cell-type quantities, demonstrating activation of adaptive immunity. Conversely, a poor prognosis was associated with lack of an appropriate adaptive response, sustained innate immune signaling, and higher expression of myeloid-derived suppressor cell (MDSC)-related transcripts (S100A8, S100A9, CEBPB, PTGS2, CXCR1, and LILRA3). MDSCs are potent immunosuppressors of cellular and humoral immunity, and therefore, they represent a potential therapeutic target. Circulating plasminogen activator inhibitor 1 (PAI-1) and tissue plasminogen activator (tPA) levels were also elevated in nonsurvivors and in survivors exhibiting severe illness, emphasizing the importance of maintaining coagulation homeostasis to control disease progression.
Collapse
|
13
|
Transcriptomic Analysis Reveals Host miRNAs Correlated with Immune Gene Dysregulation during Fatal Disease Progression in the Ebola Virus Cynomolgus Macaque Disease Model. Microorganisms 2021; 9:microorganisms9030665. [PMID: 33806942 PMCID: PMC8005181 DOI: 10.3390/microorganisms9030665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022] Open
Abstract
Ebola virus is a continuing threat to human populations, causing a virulent hemorrhagic fever disease characterized by dysregulation of both the innate and adaptive host immune responses. Severe cases are distinguished by an early, elevated pro-inflammatory response followed by a pronounced lymphopenia with B and T cells unable to mount an effective anti-viral response. The precise mechanisms underlying the dysregulation of the host immune system are poorly understood. In recent years, focus on host-derived miRNAs showed these molecules to play an important role in the host gene regulation arsenal. Here, we describe an investigation of RNA biomarkers in the fatal Ebola virus disease (EVD) cynomolgus macaque model. We monitored both host mRNA and miRNA responses in whole blood longitudinally over the disease course in these non-human primates (NHPs). Analysis of the interactions between these classes of RNAs revealed several miRNA markers significantly correlated with downregulation of genes; specifically, the analysis revealed those involved in dysregulated immune pathways associated with EVD. In particular, we noted strong interactions between the miRNAs hsa-miR-122-5p and hsa-miR-125b-5p with immunological genes regulating both B and T-cell activation. This promising set of biomarkers will be useful in future studies of severe EVD pathogenesis in both NHPs and humans and may serve as potential prognostic targets.
Collapse
|
14
|
Popeda M, Markiewicz A, Stokowy T, Szade J, Niemira M, Kretowski A, Bednarz-Knoll N, Zaczek AJ. Reduced expression of innate immunity-related genes in lymph node metastases of luminal breast cancer patients. Sci Rep 2021; 11:5097. [PMID: 33658651 PMCID: PMC7930267 DOI: 10.1038/s41598-021-84568-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/18/2021] [Indexed: 01/31/2023] Open
Abstract
Immune system plays a dual role in cancer by either targeting or supporting neoplastic cells at various stages of disease, including metastasis. Yet, the exact immune-related transcriptome profiles of primary tumours (PT) and lymph node metastases (LNM) and their evolution during luminal breast cancer (BCa) dissemination remain undiscovered. In order to identify the immune-related transcriptome changes that accompany lymphatic spread, we analysed PT-LNM pairs of luminal BCa using NanoString technology. Decrease in complement C3-one of the top-downregulated genes, in LNM was validated at the protein level using immunohistochemistry. Thirty-three of 360 analysed genes were downregulated (9%), whereas only 3 (0.8%) upregulated in LNM when compared to the corresponding PT. In LNM, reduced expression was observed in genes related to innate immunity, particularly to the complement system (C1QB, C1S, C1R, C4B, CFB, C3, SERPING1 and C3AR1). In validation cohort, complement C3 protein was less frequently expressed in LNM than in PT and it was associated with worse prognosis. To conclude, local expression of the complement system components declines during lymphatic spread of non-metastatic luminal BCa, whilst further reduction of tumoral complement C3 in LNM is indicative for poor survival. This points to context-dependent role of complement C3 in BCa dissemination.
Collapse
Affiliation(s)
- Marta Popeda
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdansk, 80-211, Gdansk, Poland
| | - Aleksandra Markiewicz
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdansk, 80-211, Gdansk, Poland
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Jolanta Szade
- Department of Pathomorphology, Medical University of Gdansk, 80-211, Gdansk, Poland
| | - Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, 15-276, Bialystok, Poland
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, 15-276, Bialystok, Poland
| | - Natalia Bednarz-Knoll
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdansk, 80-211, Gdansk, Poland
| | - Anna J Zaczek
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdansk, 80-211, Gdansk, Poland.
| |
Collapse
|
15
|
Prasad AN, Woolsey C, Geisbert JB, Agans KN, Borisevich V, Deer DJ, Mire CE, Cross RW, Fenton KA, Broder CC, Geisbert TW. Resistance of Cynomolgus Monkeys to Nipah and Hendra Virus Disease Is Associated With Cell-Mediated and Humoral Immunity. J Infect Dis 2021; 221:S436-S447. [PMID: 32022850 DOI: 10.1093/infdis/jiz613] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The henipaviruses, Hendra virus (HeV) and Nipah virus (NiV), are capable of causing severe and often lethal respiratory and/or neurologic disease in animals and humans. Given the sporadic nature of henipavirus outbreaks, licensure of vaccines and therapeutics for human use will likely require demonstration of efficacy in animal models that faithfully reproduce the human condition. Currently, the African green monkey (AGM) best mimics human henipavirus-induced disease. METHODS The pathogenic potential of HeV and both strains of NiV (Malaysia, Bangladesh) was assessed in cynomolgus monkeys and compared with henipavirus-infected historical control AGMs. Multiplex gene and protein expression assays were used to compare host responses. RESULTS In contrast to AGMs, in which henipaviruses cause severe and usually lethal disease, HeV and NiVs caused only mild or asymptomatic infections in macaques. All henipaviruses replicated in macaques with similar kinetics as in AGMs. Infection in macaques was associated with activation and predicted recruitment of cytotoxic CD8+ T cells, Th1 cells, IgM+ B cells, and plasma cells. Conversely, fatal outcome in AGMs was associated with aberrant innate immune signaling, complement dysregulation, Th2 skewing, and increased secretion of MCP-1. CONCLUSION The restriction factors identified in macaques can be harnessed for development of effective countermeasures against henipavirus disease.
Collapse
Affiliation(s)
- Abhishek N Prasad
- Galveston National Laboratory, University of Texas Medical Branch, Galveston.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Courtney Woolsey
- Galveston National Laboratory, University of Texas Medical Branch, Galveston.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Joan B Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, Galveston.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Krystle N Agans
- Galveston National Laboratory, University of Texas Medical Branch, Galveston.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Viktoriya Borisevich
- Galveston National Laboratory, University of Texas Medical Branch, Galveston.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Daniel J Deer
- Galveston National Laboratory, University of Texas Medical Branch, Galveston.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Chad E Mire
- Galveston National Laboratory, University of Texas Medical Branch, Galveston.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch, Galveston.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Karla A Fenton
- Galveston National Laboratory, University of Texas Medical Branch, Galveston.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland
| | - Thomas W Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, Galveston.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| |
Collapse
|
16
|
Chen Z, Wu A. Progress and challenge for computational quantification of tissue immune cells. Brief Bioinform 2021; 22:6065002. [PMID: 33401306 DOI: 10.1093/bib/bbaa358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/23/2020] [Accepted: 11/07/2020] [Indexed: 12/28/2022] Open
Abstract
Tissue immune cells have long been recognized as important regulators for the maintenance of balance in the body system. Quantification of the abundance of different immune cells will provide enhanced understanding of the correlation between immune cells and normal or abnormal situations. Currently, computational methods to predict tissue immune cell compositions from bulk transcriptomes have been largely developed. Therefore, summarizing the advantages and disadvantages is appropriate. In addition, an examination of the challenges and possible solutions for these computational models will assist the development of this field. The common hypothesis of these models is that the expression of signature genes for immune cell types might represent the proportion of immune cells that contribute to the tissue transcriptome. In general, we grouped all reported tools into three groups, including reference-free, reference-based scoring and reference-based deconvolution methods. In this review, a summary of all the currently reported computational immune cell quantification tools and their applications, limitations, and perspectives are presented. Furthermore, some critical problems are found that have limited the performance and application of these models, including inadequate immune cell type, the collinearity problem, the impact of the tissue environment on the immune cell expression level, and the deficiency of standard datasets for model validation. To address these issues, tissue specific training datasets that include all known immune cells, a hierarchical computational framework, and benchmark datasets including both tissue expression profiles and the abundances of all the immune cells are proposed to further promote the development of this field.
Collapse
Affiliation(s)
- Ziyi Chen
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu, Suzhou, China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu, Suzhou, China
| |
Collapse
|
17
|
Ykema BLM, Hoefnagel SJM, Rigter LS, Kodach LL, Meijer GA, van Leeuwen FE, Khan HN, Snaebjornsson P, Aleman BMP, Broeks A, Meijer SL, Wang KK, Carvalho B, Krishnadath KK, van Leerdam ME. Gene expression profiles of esophageal squamous cell cancers in Hodgkin lymphoma survivors versus sporadic cases. PLoS One 2020; 15:e0243178. [PMID: 33347497 PMCID: PMC7751872 DOI: 10.1371/journal.pone.0243178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022] Open
Abstract
Hodgkin lymphoma (HL) survivors are at increased risk of developing second primary esophageal squamous cell cancer (ESCC). We aimed to gain insight in the driving events of ESCC in HL survivors (hESCC) by using RNA sequencing and NanoString profiling. Objectives were to investigate differences in RNA signaling between hESCC and sporadic ESCC (sESCC), and to look for early malignant changes in non-neoplastic esophageal tissue of HL survivors (hNN-tissue). We analyzed material of 26 hESCC cases, identified via the Dutch pathology registry (PALGA) and 17 sESCC cases from one academic institute and RNA sequencing data of 44 sESCC cases from TCGA. Gene expression profiles for the NanoString panel PanCancer IO 360 were obtained from 16/26 hESCC and four hNN-tissue, while non-neoplastic squamous tissue of four sporadic cases (sNN-tissue) served as reference profile. Hierarchical clustering, differential expression and pathway analyses were performed. Overall, the molecular profiles of hESCC and sESCC were similar. There was increased immune, HMGB1 and ILK signaling compared to sNN-tissue. The profiles of hNN-tissue were distinct from sNN-tissue, indicating early field effects in the esophagus of HL survivors. The BRCA1 pathway was upregulated in hESCC tissue, compared to hNN tissue. Analysis of expression profiles reveals overlap between hESCC and sESCC, and differences between hESCC and its surrounding hNN-tissue. Further research is required to validate our results and to investigate whether the changes observed in hNN-tissue are already detectable before development of hESCC. In the future, our findings could be used to improve hESCC patient management.
Collapse
Affiliation(s)
- Berbel L M Ykema
- Department of Gastroenterology and Hepatology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sanne J M Hoefnagel
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Amsterdam, The Netherlands.,Center for Experimental and Molecular Medicine, Amsterdam UMC, Amsterdam, The Netherlands
| | - Lisanne S Rigter
- Department of Gastroenterology and Hepatology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Liudmila L Kodach
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Flora E van Leeuwen
- Department of Epidemiology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hina N Khan
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Amsterdam, The Netherlands
| | - Petur Snaebjornsson
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Berthe M P Aleman
- Department of Radiation Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology and Biobanking, Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sybren L Meijer
- Department of Pathology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Kenneth K Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kausilia K Krishnadath
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Amsterdam, The Netherlands.,Center for Experimental and Molecular Medicine, Amsterdam UMC, Amsterdam, The Netherlands
| | - Monique E van Leerdam
- Department of Gastroenterology and Hepatology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | | |
Collapse
|
18
|
Guito JC, Prescott JB, Arnold CE, Amman BR, Schuh AJ, Spengler JR, Sealy TK, Harmon JR, Coleman-McCray JD, Kulcsar KA, Nagle ER, Kumar R, Palacios GF, Sanchez-Lockhart M, Towner JS. Asymptomatic Infection of Marburg Virus Reservoir Bats Is Explained by a Strategy of Immunoprotective Disease Tolerance. Curr Biol 2020; 31:257-270.e5. [PMID: 33157026 DOI: 10.1016/j.cub.2020.10.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/28/2020] [Accepted: 10/07/2020] [Indexed: 12/25/2022]
Abstract
Marburg virus (MARV) is among the most virulent pathogens of primates, including humans. Contributors to severe MARV disease include immune response suppression and inflammatory gene dysregulation ("cytokine storm"), leading to systemic damage and often death. Conversely, MARV causes little to no clinical disease in its reservoir host, the Egyptian rousette bat (ERB). Previous genomic and in vitro data suggest that a tolerant ERB immune response may underlie MARV avirulence, but no significant examination of this response in vivo yet exists. Here, using colony-bred ERBs inoculated with a bat isolate of MARV, we use species-specific antibodies and an immune gene probe array (NanoString) to temporally characterize the transcriptional host response at sites of MARV replication relevant to primate pathogenesis and immunity, including CD14+ monocytes/macrophages, critical immune response mediators, primary MARV targets, and skin at the inoculation site, where highest viral loads and initial engagement of antiviral defenses are expected. Our analysis shows that ERBs upregulate canonical antiviral genes typical of mammalian systems, such as ISG15, IFIT1, and OAS3, yet demonstrate a remarkable lack of significant induction of proinflammatory genes classically implicated in primate filoviral pathogenesis, including CCL8, FAS, and IL6. Together, these findings offer the first in vivo functional evidence for disease tolerance as an immunological mechanism by which the bat reservoir asymptomatically hosts MARV. More broadly, these data highlight factors determining disparate outcomes between reservoir and spillover hosts and defensive strategies likely utilized by bat hosts of other emerging pathogens, knowledge that may guide development of effective antiviral therapies.
Collapse
Affiliation(s)
- Jonathan C Guito
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joseph B Prescott
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Catherine E Arnold
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD 21702, USA
| | - Brian R Amman
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Amy J Schuh
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Tara K Sealy
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jessica R Harmon
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - JoAnn D Coleman-McCray
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Kirsten A Kulcsar
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Elyse R Nagle
- Center for Genome Sciences, USAMRIID, Fort Detrick, MD 21702, USA
| | - Raina Kumar
- Center for Genome Sciences, USAMRIID, Fort Detrick, MD 21702, USA
| | | | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, USAMRIID, Fort Detrick, MD 21702, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| |
Collapse
|
19
|
Greenberg A, Huber BR, Liu DX, Logue JP, Hischak AMW, Hart RJ, Abbott M, Isic N, Hisada YM, Mackman N, Bennett RS, Hensley LE, Connor JH, Crossland NA. Quantification of Viral and Host Biomarkers in the Liver of Rhesus Macaques: A Longitudinal Study of Zaire Ebolavirus Strain Kikwit (EBOV/Kik). THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1449-1460. [PMID: 32275904 PMCID: PMC7322367 DOI: 10.1016/j.ajpath.2020.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 12/21/2022]
Abstract
Zaire ebolavirus (EBOV) causes Ebola virus disease (EVD), which carries a fatality rate between 25% and 90% in humans. Liver pathology is a hallmark of terminal EVD; however, little is known about temporal disease progression. We used multiplexed fluorescent immunohistochemistry and in situ hybridization in combination with whole slide imaging and image analysis (IA) to quantitatively characterize temporospatial signatures of viral and host factors as related to EBOV pathogenesis. Eighteen rhesus monkeys euthanized between 3 and 8 days post-infection, and 3 uninfected controls were enrolled in this study. Compared with semiquantitative histomorphologic ordinal scoring, quantitative IA detected subtle and progressive features of early and terminal EVD that was not feasible with routine approaches. Sinusoidal macrophages were the earliest cells to respond to infection, expressing proinflammatory cytokine interleukin 6 (IL6) mRNA, which was subsequently also observed in fibrovascular compartments. The mRNA of interferon-stimulated gene-15 (ISG-15), also known as ISG15 ubiquitin like modifier (ISG15), was observed early, with a progressive and ubiquitous hybridization signature involving mesenchymal and epithelial compartments. ISG-15 mRNA was prominent near infected cells, but not in infected cells, supporting the hypothesis that bystander cells produce a robust interferon gene response. This study contributes to our current understanding of early EVD progression and illustrates the value that digital pathology and quantitative IA serve in infectious disease research.
Collapse
Affiliation(s)
- Alexandra Greenberg
- Graduate Medical Sciences, Boston University School of Medicine, Boston, Massachusetts
| | - Bertrand R Huber
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | - David X Liu
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - James P Logue
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Amanda M W Hischak
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Randy J Hart
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Maureen Abbott
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Nejra Isic
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Yohei M Hisada
- Division of Hematology and Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nigel Mackman
- Division of Hematology and Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Richard S Bennett
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - Lisa E Hensley
- Integrated Research Facility, National Institute for Allergy and Infectious Diseases (NIAID), Frederick, Maryland
| | - John H Connor
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Nicholas A Crossland
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts.
| |
Collapse
|
20
|
Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection. mBio 2020; 11:mBio.01157-20. [PMID: 32546624 PMCID: PMC7298714 DOI: 10.1128/mbio.01157-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Current molecular tests that identify infection with high-consequence viruses such as Ebola virus and Marburg virus are based on the detection of virus material in the blood. These viruses do not undergo significant early replication in the blood and, instead, replicate in organs such as the liver and spleen. Thus, virus begins to accumulate in the blood only after significant replication has already occurred in those organs, making viremia an indicator of infection only after initial stages have become established. Here, we show that a multianalyte assay can correctly identify the infectious agent in nonhuman primates (NHPs) prior to viremia through tracking host infection response transcripts. This illustrates that a single-tube, sample-to-answer format assay could be used to advance the time at which the type of infection can be determined and thereby improve outcomes. Outbreaks of filoviruses, such as those caused by the Ebola (EBOV) and Marburg (MARV) virus, are difficult to detect and control. The initial clinical symptoms of these diseases are nonspecific and can mimic other endemic pathogens. This makes confident diagnosis based on clinical symptoms alone impossible. Molecular diagnostics for these diseases that rely on the detection of viral RNA in the blood are only effective after significant disease progression. As an approach to identify these infections earlier in the disease course, we tested the effectiveness of viral RNA detection combined with an assessment of sentinel host mRNAs that are upregulated following filovirus infection. RNAseq analysis of EBOV-infected nonhuman primates identified host RNAs that are upregulated at early stages of infection. NanoString probes that recognized these host-response RNAs were combined with probes that recognized viral RNA and were used to classify viral infection both prior to viremia and postviremia. This approach was highly successful at identifying samples from nonhuman primate subjects and correctly distinguished the causative agent in a previremic stage in 10 EBOV and 5 MARV samples. This work suggests that unified host response/viral fingerprint assays can enable diagnosis of disease earlier than testing for viral nucleic acid alone, which could decrease transmission events and increase therapeutic effectiveness.
Collapse
|
21
|
Lee MY, Wang HZ, White TW, Brooks T, Pittman A, Halai H, Petrova A, Xu D, Hart SL, Kinsler VA, Di WL. Allele-Specific Small Interfering RNA Corrects Aberrant Cellular Phenotype in Keratitis-Ichthyosis-Deafness Syndrome Keratinocytes. J Invest Dermatol 2019; 140:1035-1044.e7. [PMID: 31705875 DOI: 10.1016/j.jid.2019.09.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/16/2019] [Accepted: 09/17/2019] [Indexed: 11/29/2022]
Abstract
Keratitis-ichthyosis-deafness (KID) syndrome is a severe, untreatable condition characterized by ocular, auditory, and cutaneous abnormalities, with major complications of infection and skin cancer. Most cases of KID syndrome (86%) are caused by a heterozygous missense mutation (c.148G>A, p.D50N) in the GJB2 gene, encoding gap junction protein Cx26, which alters gating properties of Cx26 channels in a dominant manner. We hypothesized that a mutant allele-specific small interfering RNA could rescue the cellular phenotype in patient keratinocytes (KCs). A KID syndrome cell line (KID-KC) was established from primary patient KCs with a heterozygous p.D50N mutation. This cell line displayed impaired gap junction communication and hyperactive hemichannels, confirmed by dye transfer, patch clamp, and neurobiotin uptake assays. A human-murine chimeric skin graft model constructed with KID-KCs mimicked patient skin in vivo, further confirming the validity of these cells as a model. In vitro treatment with allele-specific small interfering RNA led to robust inhibition of the mutant GJB2 allele without altering expression of the wild-type allele. This corrected both gap junction and hemichannel activity. Notably, allele-specific small interfering RNA treatment caused only low-level off-target effects in KID-KCs, as detected by genome-wide RNA sequencing. Our data provide an important proof-of-concept and model system for the potential use of allele-specific small interfering RNA in treating KID syndrome and other dominant genetic conditions.
Collapse
Affiliation(s)
- Ming Yang Lee
- Infection, Immunity and Inflammation Programme/Immunobiology Section, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Hong-Zhan Wang
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York
| | - Thomas W White
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York
| | - Tony Brooks
- UCL Genomics, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Alan Pittman
- Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom; Genetics Research Centre, St George's, University of London, London, United Kingdom
| | - Heerni Halai
- Infection, Immunity and Inflammation Programme/Immunobiology Section, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Anastasia Petrova
- Infection, Immunity and Inflammation Programme/Immunobiology Section, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Diane Xu
- Infection, Immunity and Inflammation Programme/Immunobiology Section, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Stephen L Hart
- Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Veronica A Kinsler
- Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Wei-Li Di
- Infection, Immunity and Inflammation Programme/Immunobiology Section, UCL Great Ormond Street Institute of Child Health, London, United Kingdom.
| |
Collapse
|
22
|
Evers TMJ, Hochane M, Tans SJ, Heeren RMA, Semrau S, Nemes P, Mashaghi A. Deciphering Metabolic Heterogeneity by Single-Cell Analysis. Anal Chem 2019; 91:13314-13323. [PMID: 31549807 PMCID: PMC6922888 DOI: 10.1021/acs.analchem.9b02410] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Single-cell analysis provides insights into cellular heterogeneity and dynamics of individual cells. This Feature highlights recent developments in key analytical techniques suited for single-cell metabolic analysis with a special focus on mass spectrometry-based analytical platforms and RNA-seq as well as imaging techniques that reveal stochasticity in metabolism.
Collapse
Affiliation(s)
- Tom MJ Evers
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Mazène Hochane
- Leiden Institute of Physics, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sander J Tans
- AMOLF Institute, Science Park 104 1098 XG Amsterdam, The Netherlands
| | - Ron MA Heeren
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Stefan Semrau
- Leiden Institute of Physics, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Alireza Mashaghi
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| |
Collapse
|
23
|
Speranza E, Ruibal P, Port JR, Feng F, Burkhardt L, Grundhoff A, Günther S, Oestereich L, Hiscox JA, Connor JH, Muñoz-Fontela C. T-Cell Receptor Diversity and the Control of T-Cell Homeostasis Mark Ebola Virus Disease Survival in Humans. J Infect Dis 2019; 218:S508-S518. [PMID: 29986035 DOI: 10.1093/infdis/jiy352] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Differences in T-cell phenotype, particularly the expression of markers of T-cell homeostasis, have been observed in fatal and nonfatal Ebola virus disease (EVD). However, the relationship between these markers with T-cell function and virus clearance during EVD is poorly understood. To gain biological insight into the role of T cells during EVD, combined transcriptomics and T-cell receptor sequencing was used to profile blood samples from fatal and nonfatal EVD patients from the recent West African EVD epidemic. Fatal EVD was characterized by strong T-cell activation and increased abundance of T-cell inhibitory molecules. However, the early T-cell response was oligoclonal and did not result in viral clearance. In contrast, survivors mounted highly diverse T-cell responses, maintained low levels of T-cell inhibitors, and cleared Ebola virus. Our findings highlight the importance of T-cell immunity in surviving EVD and strengthen the foundation for further research on targeting of the dendritic cell-T cell interface for postexposure immunotherapy.
Collapse
Affiliation(s)
- Emily Speranza
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Bioinformatics Program, Boston University, Boston MA.,Department of National Emerging Infectious Diseases Laboratories, Boston University, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - Paula Ruibal
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Julia R Port
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Feng Feng
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - Lia Burkhardt
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Lisa Oestereich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Julian A Hiscox
- Institute for Infection and Global Health, University of Liverpool, United Kingdom.,Singapore Immunology Network, A*STAR, Singapore
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Bioinformatics Program, Boston University, Boston MA.,Department of National Emerging Infectious Diseases Laboratories, Boston University, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| |
Collapse
|
24
|
Curini V, Marcacci M, Tonelli A, Di Teodoro G, Di Domenico M, D'Alterio N, Portanti O, Ancora M, Savini G, Panfili M, Camma' C, Lorusso A. Molecular typing of Bluetongue virus using the nCounter ® analysis system platform. J Virol Methods 2019; 269:64-69. [PMID: 30951789 DOI: 10.1016/j.jviromet.2019.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/31/2019] [Accepted: 04/01/2019] [Indexed: 11/28/2022]
Abstract
Bluetongue virus (BTV) is a segmented double-stranded RNA virus, existing in multiple serotypes, belonging to the genus Orbivirus of the family Reoviridae. BTV causes Bluetongue (BT), a major OIE-listed disease of ruminants. Identification of BTV serotype is accomplished using multiple typing assays and tends to be executed based on the known epidemiological situation within a given country. Samples containing multiple serotypes, particularly those containing novel introductions, may therefore be missed. The aim of this work was to optimize the nCounter® Analysis System Microarray platform (NanoString technologies), that would simultaneously identify all BTV serotypes and co-infections in analyzed samples. Probes were designed according to all Seg-2 sequences, coding for VP2 proteins which determine serotype specificity, available on line. A specific BTV CodeSet of probes was optimized. Experiments were performed with 30 BTV isolates and with 46 field samples previously shown to be infected with BTV by classical molecular assays. All BTV isolates were correctly identified and the expected BTV serotype was recognized in 35 field samples with CT values between 22.0-33.0. In turn, it was unable to identify 11 samples with CT values between 29.0-38.0. Although specificity of the assay needs to be further investigated against a larger panel of BTVs collected worldwide, RNA loads, which are normally detected in blood samples during the acute phase of infection, are within the range of CT values detectable by the BTV CodeSet. We propose the NanoString RNA microarray as a first-line molecular diagnostic tool for identification and typing of BTV. Once identification of the index cases is performed, diagnosis of the following samples may be performed by specific, more sensitive and cheaper PCR-based tools.
Collapse
Affiliation(s)
- Valentina Curini
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy; National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | - Maurilia Marcacci
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy; National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | - Alfreda Tonelli
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy; National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | - Giovanni Di Teodoro
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy; National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | - Marco Di Domenico
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy; National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | - Nicola D'Alterio
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy; National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | - Ottavio Portanti
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy; National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | - Massimo Ancora
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy; National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | - Giovanni Savini
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy; National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | | | - Cesare Camma'
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy; National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | - Alessio Lorusso
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy; National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy.
| |
Collapse
|
25
|
Colón-López DD, Stefan CP, Koehler JW. Emerging viral infections. GENOMIC AND PRECISION MEDICINE 2019. [PMCID: PMC7150306 DOI: 10.1016/b978-0-12-801496-7.00010-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
26
|
Sharma PP, MacLean AL, Meinecke L, Clouthier DE, Nie Q, Schilling TF. Transcriptomics reveals complex kinetics of dorsal-ventral patterning gene expression in the mandibular arch. Genesis 2018; 57:e23275. [PMID: 30561090 DOI: 10.1002/dvg.23275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 11/06/2022]
Abstract
The mandibular or first pharyngeal arch forms the upper and lower jaws in all gnathostomes. A gene regulatory network that defines ventral, intermediate, and dorsal domains along the dorsal-ventral (D-V) axis of the arch has emerged from studies in zebrafish and mice, but the temporal dynamics of this process remain unclear. To define cell fate trajectories in the arches we have performed quantitative gene expression analyses of D-V patterning genes in pharyngeal arch primordia in zebrafish and mice. Using NanoString technology to measure transcript numbers per cell directly we show that, in many cases, genes expressed in similar D-V domains and induced by similar signals vary dramatically in their temporal profiles. This suggests that cellular responses to D-V patterning signals are likely shaped by the baseline kinetics of target gene expression. Furthermore, similarities in the temporal dynamics of genes that occupy distinct pathways suggest novel shared modes of regulation. Incorporating these gene expression kinetics into our computational models for the mandibular arch improves the accuracy of patterning, and facilitates temporal comparisons between species. These data suggest that the magnitude and timing of target gene expression help diversify responses to patterning signals during craniofacial development.
Collapse
Affiliation(s)
- Praveer P Sharma
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California
| | - Adam L MacLean
- Department of Mathematics, University of California, Irvine, Irvine, California
| | - Lina Meinecke
- Department of Mathematics, University of California, Irvine, Irvine, California
| | - David E Clouthier
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California.,Department of Mathematics, University of California, Irvine, Irvine, California
| | - Thomas F Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California
| |
Collapse
|
27
|
Cross RW, Speranza E, Borisevich V, Widen SG, Wood TG, Shim RS, Adams RD, Gerhardt DM, Bennett RS, Honko AN, Johnson JC, Hensley LE, Geisbert TW, Connor JH. Comparative Transcriptomics in Ebola Makona-Infected Ferrets, Nonhuman Primates, and Humans. J Infect Dis 2018; 218:S486-S495. [PMID: 30476250 PMCID: PMC6249602 DOI: 10.1093/infdis/jiy455] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The domestic ferret is a uniformly lethal model of infection for 3 species of Ebolavirus known to be pathogenic in humans. Reagents to systematically analyze the ferret host response to infection are lacking; however, the recent publication of a draft ferret genome has opened the potential for transcriptional analysis of ferret models of disease. In this work, we present comparative analysis of longitudinally sampled blood taken from ferrets and nonhuman primates infected with lethal doses of the Makona variant of Zaire ebolavirus. Strong induction of proinflammatory and prothrombotic signaling programs were present in both ferrets and nonhuman primates, and both transcriptomes were similar to previously published datasets of fatal cases of human Ebola virus infection.
Collapse
Affiliation(s)
- Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Emily Speranza
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Disease Laboratories, Boston University, Massachusetts
| | - Viktoriya Borisevich
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - Steven G Widen
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
| | - Thomas G Wood
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
| | - Rebecca S Shim
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Ricky D Adams
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Dawn M Gerhardt
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Richard S Bennett
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Anna N Honko
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Joshua C Johnson
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Lisa E Hensley
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland
| | - Thomas W Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, Galveston
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston
| | - John H Connor
- Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Disease Laboratories, Boston University, Massachusetts
| |
Collapse
|
28
|
Diagnostic accuracy of digital RNA quantification versus real-time PCR for the detection of respiratory syncytial virus in nasopharyngeal aspirates from children with acute respiratory infection. J Clin Virol 2018; 106:34-40. [PMID: 30031351 DOI: 10.1016/j.jcv.2018.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/12/2018] [Accepted: 07/13/2018] [Indexed: 11/21/2022]
Abstract
BACKGROUND Virus-specific molecular assays such as real-time polymerase chain reaction (RT-PCR) are regularly used as the gold standard to diagnose viral respiratory tract infections, but simultaneous detection of multiple different pathogens is often challenging. A multiplex digital method of RNA quantification, nCounter (NanoString Technologies), can overcome this disadvantage and identify, in a single reaction, the presence of different respiratory viruses. OBJECTIVES To evaluate the accuracy of nCounter to identify and quantify RSV-A and RSV-B in nasopharyngeal aspirates (NPA) of children (6-23-months-old) with acute respiratory infection. STUDY DESIGN NPA was collected at enrolment in a prospective cross-sectional study conducted in Salvador, Brazil. A quantitative RT-PCR with a subgroup-specific primer and probeset for RSV-A and RSV-B was performed in parallel with a customized nCounter probeset containing viral targets in NPA. RESULTS Of 559 NPA tested, RSV was detected by RT-PCR in 139 (24.9%), by nCounter in 122 (21.8%) and by any method in 158 (28.3%) cases. Compared to the gold standard of qRT-PCR, sensitivity of nCounter was 74.3% (95%CI:63.3%-82.9% RSV-A) and 77.6% (95%CI:66.3%-85.9% RSV-B); specificity was 98.4% (95%CI:96.8%-99.2% RSV-A) and 97.8% (95%CI:96.0%-98.8% RSV-B); positive predictive value was 87.3% (95%CI:76.9%-93.4% RSV-A) and 82.5% (95%CI:71.4%-90.0% RSV-B) and negative predictive value was 96.1% (95%CI:94.1%-97.5% RSV-A), and 96.9% (95%CI:95.1%-98.2% RSV-B). Accuracy was 95.2% (95%CI:93.1%-96.7%) for RSV-A and 95.3% (95%CI:93.3%-96.9%) for RSV-B, while both methods significantly correlated for RSV-A (r = 0.44, p = 8 × 10-5) and RSV-B (r = 0.73, p = 3 × 10-12) quantification. CONCLUSIONS nCounter is highly accurate in detecting RSV-A/B in NPA. Robustness and high-throughput multiplexing indicate its use in large-scale epidemiological studies.
Collapse
|
29
|
Duy J, Honko AN, Altamura LA, Bixler SL, Wollen-Roberts S, Wauquier N, O'Hearn A, Mucker EM, Johnson JC, Shamblin JD, Zelko J, Botto MA, Bangura J, Coomber M, Pitt ML, Gonzalez JP, Schoepp RJ, Goff AJ, Minogue TD. Virus-encoded miRNAs in Ebola virus disease. Sci Rep 2018; 8:6480. [PMID: 29691416 PMCID: PMC5915558 DOI: 10.1038/s41598-018-23916-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Ebola virus (EBOV) is a negative-strand RNA virus that replicates in the cytoplasm and causes an often-fatal hemorrhagic fever. EBOV, like other viruses, can reportedly encode its own microRNAs (miRNAs) to subvert host immune defenses. miRNAs are short noncoding RNAs that can regulate gene expression by hybridizing to multiple mRNAs, and viral miRNAs can enhance viral replication and infectivity by regulating host or viral genes. To date, only one EBOV miRNA has been examined in human infection. Here, we assayed mouse, rhesus macaque, cynomolgus macaque, and human samples infected with three EBOV variants for twelve computationally predicted viral miRNAs using RT-qPCR. Ten miRNAs aligned to EBOV variants and were detectable in the four species during disease with several viral miRNAs showing presymptomatic amplification in animal models. miRNA abundances in both the mouse and nonhuman primate models mirrored the human cohort, with miR-1-5p, miR-1-3p, and miR-T3-3p consistently at the highest levels. These striking similarities in the most abundant miRNAs during infection with different EBOV variants and hosts indicate that these miRNAs are potential valuable diagnostic markers and key effectors of EBOV pathogenesis.
Collapse
Affiliation(s)
- Janice Duy
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Anna N Honko
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Louis A Altamura
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Sandra L Bixler
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Suzanne Wollen-Roberts
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Nadia Wauquier
- Metabiota, Kenema, Sierra Leone.,MRIGlobal - Global Health Surveillance and Diagnostics, Gaithersburg, MD, USA
| | - Aileen O'Hearn
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Eric M Mucker
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Joshua C Johnson
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Joshua D Shamblin
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Justine Zelko
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Miriam A Botto
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | | | | | - M Louise Pitt
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Jean-Paul Gonzalez
- Metabiota, Washington, DC, USA.,Center of Excellence for Emerging & Zoonotic Animal Disease, Kansas State University, Manhattan, KS, USA
| | - Randal J Schoepp
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Arthur J Goff
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Timothy D Minogue
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA.
| |
Collapse
|
30
|
Speranza E, Bixler SL, Altamura LA, Arnold CE, Pratt WD, Taylor-Howell C, Burrows C, Aguilar W, Rossi F, Shamblin JD, Wollen SE, Zelko JM, Minogue T, Nagle E, Palacios G, Goff AJ, Connor JH. A conserved transcriptional response to intranasal Ebola virus exposure in nonhuman primates prior to onset of fever. Sci Transl Med 2018; 10:10/434/eaaq1016. [PMID: 29593102 PMCID: PMC9986849 DOI: 10.1126/scitranslmed.aaq1016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/13/2018] [Indexed: 12/18/2022]
Abstract
Ebola virus disease (EVD), caused by Ebola virus (EBOV), is a severe illness characterized by case fatality rates of up to 90%. The sporadic nature of outbreaks in resource-limited areas has hindered the ability to characterize the pathogenesis of EVD at all stages of infection but particularly early host responses. Pathogenesis is often studied in nonhuman primate (NHP) models of disease that replicate major aspects of human EVD. Typically, NHP models use a large infectious dose, are carried out through intramuscular or aerosol exposure, and have a fairly uniform disease course. By contrast, we report our analysis of the host response to EBOV after intranasal exposure. Twelve cynomolgus macaques were infected with 100 plaque-forming units of EBOV/Makona through intranasal exposure and presented with varying times to onset of EVD. We used RNA sequencing and a newly developed NanoString CodeSet to monitor the host response via changes in RNA transcripts over time. When individual animal gene expression data were phased based on the onset of sustained fever, the first clinical sign of severe disease, mathematical models indicated that interferon-stimulated genes appeared as early as 4 days before fever onset. This demonstrates that lethal EVD has a uniform and predictable response to infection regardless of time to onset. Furthermore, expression of a subset of genes could predict disease development before other host-based indications of infection such as fever.
Collapse
Affiliation(s)
- Emily Speranza
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Sandra L Bixler
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Louis A Altamura
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Catherine E Arnold
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - William D Pratt
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Cheryl Taylor-Howell
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Christina Burrows
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - William Aguilar
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Franco Rossi
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Joshua D Shamblin
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Suzanne E Wollen
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Justine M Zelko
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Timothy Minogue
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Elyse Nagle
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Arthur J Goff
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - John H Connor
- Department of Microbiology, Bioinformatics Program, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA.
| |
Collapse
|