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Tian X, Li S, Wang C, Zhang Y, Feng X, Yan Q, Guo R, Wu F, Wu C, Wang Y, Huo X, Ma X. Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease. MICROBIOME 2024; 12:130. [PMID: 39026313 PMCID: PMC11256409 DOI: 10.1186/s40168-024-01832-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/08/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.
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Affiliation(s)
- Xiangge Tian
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Chao Wang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Yanyan Zhang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Chunxue Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Yan Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
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2
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Gholamzad A, Khakpour N, Hashemi SMA, Goudarzi Y, Ahmadi P, Gholamzad M, Mohammadi M, Hashemi M. Exploring the virome: An integral part of human health and disease. Pathol Res Pract 2024; 260:155466. [PMID: 39053136 DOI: 10.1016/j.prp.2024.155466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024]
Abstract
The human microbiome is a complex network of microorganisms that includes viruses, bacteria, and fungi. The gut virome is an essential component of the immune system, which is responsible for regulating the growth and responses of the host's immune system. The virome maintains a crucial role in the development of numerous diseases, including inflammatory bowel disease (IBD), Crohn's disease, and neurodegenerative disorders. The human virome has emerged as a promising biomarker and therapeutic target. This comprehensive review summarizes the present understanding of the virome and its implications in matters of health and disease, with a focus on the Human Microbiome Project.
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Affiliation(s)
- Amir Gholamzad
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Ali Hashemi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yalda Goudarzi
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Parisa Ahmadi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehrdad Gholamzad
- Department of Microbiology and Immunology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mahya Mohammadi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology ,Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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3
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Yasmeen F, Pirzada RH, Ahmad B, Choi B, Choi S. Understanding Autoimmunity: Mechanisms, Predisposing Factors, and Cytokine Therapies. Int J Mol Sci 2024; 25:7666. [PMID: 39062908 PMCID: PMC11277571 DOI: 10.3390/ijms25147666] [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: 06/27/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Autoimmunity refers to an organism's immune response against its own healthy cells, tissues, or components, potentially leading to irreversible damage to vital organs. Central and peripheral tolerance mechanisms play crucial roles in preventing autoimmunity by eliminating self-reactive T and B cells. The disruption of immunological tolerance, characterized by the failure of these mechanisms, results in the aberrant activation of autoreactive lymphocytes that target self-tissues, culminating in the pathogenesis of autoimmune disorders. Genetic predispositions, environmental exposures, and immunoregulatory disturbances synergistically contribute to the susceptibility and initiation of autoimmune pathologies. Within the realm of immune therapies for autoimmune diseases, cytokine therapies have emerged as a specialized strategy, targeting cytokine-mediated regulatory pathways to rectify immunological imbalances. Proinflammatory cytokines are key players in inducing and propagating autoimmune inflammation, highlighting the potential of cytokine therapies in managing autoimmune conditions. This review discusses the etiology of autoimmune diseases, current therapeutic approaches, and prospects for future drug design.
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Affiliation(s)
- Farzana Yasmeen
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea; (F.Y.); (B.C.)
- S&K Therapeutics, Ajou University Campus Plaza 418, Worldcup-ro 199, Yeongtong-gu, Suwon 16502, Republic of Korea
| | - Rameez Hassan Pirzada
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea; (F.Y.); (B.C.)
- S&K Therapeutics, Ajou University Campus Plaza 418, Worldcup-ro 199, Yeongtong-gu, Suwon 16502, Republic of Korea
| | - Bilal Ahmad
- S&K Therapeutics, Ajou University Campus Plaza 418, Worldcup-ro 199, Yeongtong-gu, Suwon 16502, Republic of Korea
| | - Bogeum Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea; (F.Y.); (B.C.)
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea; (F.Y.); (B.C.)
- S&K Therapeutics, Ajou University Campus Plaza 418, Worldcup-ro 199, Yeongtong-gu, Suwon 16502, Republic of Korea
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4
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Do WL, Wang L, Forgues M, Liu J, Rabibhadana S, Pupacdi B, Zhao Y, Gholian H, Bhudhisawasdi V, Pairojkul C, Sukeepaisarnjaroen W, Pugkhem A, Luvira V, Lertprasertsuke N, Chotirosniramit A, Auewarakul CU, Ungtrakul T, Sricharunrat T, Sangrajrang S, Phornphutkul K, Budhu A, Harris CC, Mahidol C, Ruchirawat M, Wang XW. Pan-viral serology uncovers distinct virome patterns as risk predictors of hepatocellular carcinoma and intrahepatic cholangiocarcinoma. Cell Rep Med 2023; 4:101328. [PMID: 38118412 PMCID: PMC10772458 DOI: 10.1016/j.xcrm.2023.101328] [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: 03/13/2023] [Revised: 07/31/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
This study evaluates the pan-serological profiles of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) compared to several diseased and non-diseased control populations to identify risk factors and biomarkers of liver cancer. We used phage immunoprecipitation sequencing, an anti-viral antibody screening method using a synthetic-phage-displayed human virome epitope library, to screen patient serum samples for exposure to over 1,280 strains of pathogenic and non-pathogenic viruses. Using machine learning methods to develop an HCC or iCCA viral score, we discovered that both viral scores were positively associated with several liver function markers in two separate at-risk populations independent of viral hepatitis status. The HCC score predicted all-cause mortality over 8 years in patients with chronic liver disease at risk of HCC, while the viral hepatitis status was not predictive of survival. These results suggest that non-hepatitis viral infections may contribute to HCC and iCCA development and could be biomarkers in at-risk populations.
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Affiliation(s)
- Whitney L Do
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Limin Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jinping Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Yongmei Zhao
- Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Heelah Gholian
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | | | | | | | - Vor Luvira
- Khon Kaen University, Khon Kaen, Thailand
| | | | | | | | | | | | | | | | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Mathuros Ruchirawat
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Center of Excellence on Environmental Health and Toxicology, Office of Higher Education Commission, Ministry of Education, Bangkok, Thailand.
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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5
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Scarmozzino F, Pizzi M, Pelizzaro F, Angerilli V, Dei Tos AP, Piazza F, Savarino EV, Zingone F, Fassan M. Refractory celiac disease and its mimickers: a review on pathogenesis, clinical-pathological features and therapeutic challenges. Front Oncol 2023; 13:1273305. [PMID: 38023263 PMCID: PMC10662059 DOI: 10.3389/fonc.2023.1273305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Refractory celiac disease (RCD) and enteropathy-associated T-cell lymphoma (EATL) are rare, yet severe complications of celiac disease (CD). Over the last decades, several studies have addressed the biology and clinical-pathological features of such conditions, highlighting unique disease patterns and recurrent genetic events. Current classification proposals identify two forms of RCD, namely: (i) type 1 RCD (RCD-I), characterized by phenotypically normal intra-epithelial lymphocytes (IELs); and (ii) type 2 RCD (RCD-II), featuring phenotypically aberrant IELs. While RCD-I likely represents a gluten-independent dysimmune reaction against small bowel epithelial cells, RCD-II is better considered an in situ aggressive T-cell lymphoma, with high rates of progression to overt EATL. The diagnosis of RCD and EATL is often challenging, due to misleading clinical-pathological features and to significant overlap with several CD-unrelated gastro-intestinal disorders. Similarly, the treatment of RCD and EATL is an unmet clinical need for both gastroenterologists and hematologists. Moving from such premises, this review aims to provide a comprehensive view of RCD and EATL, specifically considering their pathogenesis and the many still open issues concerning their diagnosis and clinical management.
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Affiliation(s)
- Federico Scarmozzino
- Surgical Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padua School of Medicine, Padua, Italy
| | - Marco Pizzi
- Surgical Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padua School of Medicine, Padua, Italy
| | - Filippo Pelizzaro
- Gastroenterology Unit, Department of Surgical, Gastroenterological and Oncological Sciences -DISCOG, University of Padua School of Medicine, Padua, Italy
| | - Valentina Angerilli
- Surgical Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padua School of Medicine, Padua, Italy
| | - Angelo Paolo Dei Tos
- Surgical Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padua School of Medicine, Padua, Italy
| | - Francesco Piazza
- Hematology & Clinical Immunology Unit, Department of Medicine-DIMED, University of Padua School of Medicine, Padua, Italy
| | - Edoardo Vincenzo Savarino
- Gastroenterology Unit, Department of Surgical, Gastroenterological and Oncological Sciences -DISCOG, University of Padua School of Medicine, Padua, Italy
| | - Fabiana Zingone
- Gastroenterology Unit, Department of Surgical, Gastroenterological and Oncological Sciences -DISCOG, University of Padua School of Medicine, Padua, Italy
| | - Matteo Fassan
- Surgical Pathology and Cytopathology Unit, Department of Medicine-DIMED, University of Padua School of Medicine, Padua, Italy
- Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
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6
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Lane S, Hilliam Y, Bomberger JM. Microbial and Immune Regulation of the Gut-Lung Axis during Viral-Bacterial Coinfection. J Bacteriol 2023; 205:e0029522. [PMID: 36409130 PMCID: PMC9879096 DOI: 10.1128/jb.00295-22] [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] [Indexed: 11/23/2022] Open
Abstract
Viral-bacterial coinfections of the respiratory tract have long been associated with worsened disease outcomes. Clinical and basic research studies demonstrate that these infections are driven via complex interactions between the infecting pathogens, microbiome, and host immune response, although how these interactions contribute to disease progression is still not fully understood. Research over the last decade shows that the gut has a significant role in mediating respiratory outcomes, in a phenomenon known as the "gut-lung axis." Emerging literature demonstrates that acute respiratory viruses can modulate the gut-lung axis, suggesting that dysregulation of gut-lung cross talk may be a contributing factor during respiratory coinfection. This review will summarize the current literature regarding modulation of the gut-lung axis during acute respiratory infection, with a focus on the role of the microbiome, secondary infections, and the host immune response.
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Affiliation(s)
- Sidney Lane
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yasmin Hilliam
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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7
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CRISPR FISHer enables high-sensitivity imaging of nonrepetitive DNA in living cells through phase separation-mediated signal amplification. Cell Res 2022; 32:969-981. [PMID: 36104507 PMCID: PMC9652286 DOI: 10.1038/s41422-022-00712-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/31/2022] [Indexed: 02/07/2023] Open
Abstract
The dynamic three-dimensional structures of chromatin and extrachromosomal DNA molecules regulate fundamental cellular processes and beyond. However, the visualization of specific DNA sequences in live cells, especially nonrepetitive sequences accounting for most of the genome, is still vastly challenging. Here, we introduce a robust CRISPR-mediated fluorescence in situ hybridization amplifier (CRISPR FISHer) system, which exploits engineered sgRNA and protein trimerization domain-mediated, phase separation-based exponential assembly of fluorescent proteins in the CRISPR-targeting locus, conferring enhancements in both local brightness and signal-to-background ratio and thus achieving single sgRNA-directed visualization of native nonrepetitive DNA loci in live cells. In one application, by labeling and tracking the broken ends of chromosomal fragments, CRISPR FISHer enables real-time visualization of the entire process of chromosome breakage, separation, and subsequent intra- or inter-chromosomal ends rejoining in a single live cell. Furthermore, CRISPR FISHer allows the movement of small extrachromosomal circular DNAs (eccDNAs) and invading DNAs to be recorded, revealing substantial differences in dynamic behaviors between chromosomal and extrachromosomal loci. With the potential to track any specified self or non-self DNA sequences, CRISPR FISHer dramatically broadens the scope of live-cell imaging in biological events and for biomedical diagnoses.
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8
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Wang L, Candia J, Ma L, Zhao Y, Imberti L, Sottini A, Quiros-Roldan E, Dobbs K, Burbelo PD, Cohen JI, Delmonte OM, Forgues M, Liu H, Matthews HF, Shaw E, Stack MA, Weber SE, Zhang Y, Lisco A, Sereti I, Su HC, Notarangelo LD, Wang XW. Serological responses to human virome define clinical outcomes of Italian patients infected with SARS-CoV-2. Int J Biol Sci 2022; 18:5591-5606. [PMID: 36263161 PMCID: PMC9576512 DOI: 10.7150/ijbs.78002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 08/14/2022] [Indexed: 01/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic respiratory infectious disease COVID-19. However, clinical manifestations and outcomes differ significantly among COVID-19 patients, ranging from asymptomatic to extremely severe, and it remains unclear what drives these disparities. Here, we studied 159 sequentially enrolled hospitalized patients with COVID-19-associated pneumonia from Brescia, Italy using the VirScan phage-display method to characterize circulating antibodies binding to 96,179 viral peptides encoded by 1,276 strains of human viruses. SARS-CoV-2 infection was associated with a marked increase in immune antibody repertoires against many known pathogenic and non-pathogenic human viruses. This antiviral antibody response was linked to longitudinal trajectories of disease severity and was further confirmed in additional 125 COVID-19 patients from the same geographical region in Northern Italy. By applying a machine-learning-based strategy, a viral exposure signature predictive of COVID-19-related disease severity linked to patient survival was developed and validated. These results provide a basis for understanding the role of memory B-cell repertoire to viral epitopes in COVID-19-related symptoms and suggest that a unique anti-viral antibody repertoire signature may be useful to define COVID-19 clinical severity.
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Affiliation(s)
- Limin Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892
- These authors contributed equally
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892
- These authors contributed equally
| | - Lichun Ma
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892
- These authors contributed equally
| | - Yongmei Zhao
- CCR-SF Bioinformatics Group, Advanced Biomedical and Computational Sciences, Frederick National Laboratory for Cancer Research, 8560 Progress Drive, Frederick, Maryland 21701
- These authors contributed equally
| | - Luisa Imberti
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili, Brescia, Italy
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Peter D. Burbelo
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland 20892
| | - Jeffrey I. Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Ottavia M. Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892
| | - Hui Liu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Helen F. Matthews
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Michael A. Stack
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Sarah E. Weber
- Section of Molecular Development of the Immune System, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Irini Sereti
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892
- Lead Contact
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9
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Porto BN. Insights Into the Role of the Lung Virome During Respiratory Viral Infections. Front Immunol 2022; 13:885341. [PMID: 35572506 PMCID: PMC9091589 DOI: 10.3389/fimmu.2022.885341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
The virome constitutes the viral component of the microbiome and it consists of the genomes of all the viruses that inhabit a particular region of the human body, including those that cause acute, persistent or latent infection, and retroviral elements integrated to host chromosomes. The human virome is composed by eukaryotic viruses, bacteriophages and archaeal viruses. The understanding of the virome composition and role on human health has been delayed by the absence of specific tools and techniques to accurately characterize viruses. However, more recently, advanced methods for viral diagnostics, such as deep sequencing and metagenomics, have allowed a better understanding of the diverse viral species present in the human body. Previous studies have shown that the respiratory virome modulates the host immunity and that, since childhood, the human lung is populated by viruses for whom there is no disease association. Whether these viruses are potentially pathogenic and the reason for their persistence remain elusive. Increased respiratory viral load can cause exacerbation of chronic pulmonary diseases, including COPD, cystic fibrosis, and asthma. Moreover, the presence of resident viral populations may contribute to the pathogenesis of community-acquired respiratory virus infections. In this mini review, I will discuss the recent progress on our understanding of the human lung virome and summarize the up-to-date knowledge on the relationships among community-acquired respiratory viruses, the lung virome and the immune response to better understand disease pathophysiology and the factors that may lead to viral persistence.
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Affiliation(s)
- Bárbara N Porto
- Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Biology of Breathing Group, Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
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10
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Monaco DR, Kottapalli SV, Breitwieser FP, Anderson DE, Wijaya L, Tan K, Chia WN, Kammers K, Caturegli P, Waugh K, Roederer M, Petri M, Goldman DW, Rewers M, Wang LF, Larman HB. Deconvoluting virome-wide antibody epitope reactivity profiles. EBioMedicine 2022; 75:103747. [PMID: 34922324 PMCID: PMC8688874 DOI: 10.1016/j.ebiom.2021.103747] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Comprehensive characterization of exposures and immune responses to viral infections is critical to a basic understanding of human health and disease. We previously developed the VirScan system, a programmable phage-display technology for profiling antibody binding to a library of peptides designed to span the human virome. Previous VirScan analytical approaches did not carefully account for antibody cross-reactivity among sequences shared by related viruses or for the disproportionate representation of individual viruses in the library. METHODS Here we present the AntiViral Antibody Response Deconvolution Algorithm (AVARDA), a multi-module software package for analyzing VirScan datasets. AVARDA provides a probabilistic assessment of infection with species-level resolution by considering sequence alignment of all library peptides to each other and to all human viruses. We employed AVARDA to analyze VirScan data from a cohort of encephalitis patients with either known viral infections or undiagnosed etiologies. We further assessed AVARDA's utility in associating viral infection with type 1 diabetes and lupus. FINDINGS By comparing acute and convalescent sera, AVARDA successfully confirmed or detected encephalitis-associated responses to human herpesviruses 1, 3, 4, 5, and 6, improving the rate of diagnosing viral encephalitis in this cohort by 44%. AVARDA analyses of VirScan data from the type 1 diabetes and lupus cohorts implicated enterovirus and herpesvirus infections, respectively. INTERPRETATION AVARDA, in combination with VirScan and other pan-pathogen serological techniques, is likely to find broad utility in the epidemiology and diagnosis of infectious diseases. FUNDING This work was made possible by support from the National Institutes of Health (NIH), the US Army Research Office, the Singapore Infectious Diseases Initiative (SIDI), the Singapore Ministry of Health's National Medical Research Council (NMRC) and the Singapore National Research Foundation (NRF).
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Affiliation(s)
- Daniel R Monaco
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sanjay V Kottapalli
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Florian P Breitwieser
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Limin Wijaya
- Department of Infectious Diseases, Singapore General Hospital, 20 College Road, 169856, Singapore
| | - Kevin Tan
- National Neuroscience Institute, 11 Jalan Tan Tock Seng, 308433, Singapore
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Kai Kammers
- Department of Oncology, Division of Biostatistics and Bioinformatics, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patrizio Caturegli
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michelle Petri
- Department of Medicine, Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel W Goldman
- Department of Medicine, Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - H Benjamin Larman
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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11
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Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome. Viruses 2021; 13:v13122538. [PMID: 34960807 PMCID: PMC8705478 DOI: 10.3390/v13122538] [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: 10/29/2021] [Accepted: 12/13/2021] [Indexed: 12/24/2022] Open
Abstract
A commercial pig farm with no history of porcine circovirus 2 (PCV2) or porcine reproductive and respiratory syndrome virus (PRRSV) repeatedly reported a significant reduction in body weight gain and wasting symptoms in approximately 20–30% of the pigs in the period between three and six weeks after weaning. As standard clinical interventions failed to tackle symptomatology, viral metagenomics were used to describe and monitor the enteric virome at birth, 3 weeks, 4 weeks, 6 weeks, and 9 weeks of age. The latter four sampling points were 7 days, 3 weeks, and 6 weeks post weaning, respectively. Fourteen distinct enteric viruses were identified within the herd, which all have previously been linked to enteric diseases. Here we show that wasting is associated with alterations in the enteric virome of the pigs, characterized by: (1) the presence of enterovirus G at 3 weeks of age, followed by a higher prevalence of the virus in wasting pigs at 6 weeks after weaning; (2) rotaviruses at 3 weeks of age; and (3) porcine sapovirus one week after weaning. However, the data do not provide a causal link between specific viral infections and the postweaning clinical problems on the farm. Together, our results offer evidence that disturbances in the enteric virome at the preweaning stage and early after weaning have a determining role in the development of intestinal barrier dysfunctions and nutrient uptake in the postweaning growth phase. Moreover, we show that the enteric viral load sharply increases in the week after weaning in both healthy and wasting pigs. This study is also the first to report the dynamics and co-infection of porcine rotavirus species and porcine astrovirus genetic lineages during the first 9 weeks of the life of domestic pigs.
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12
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Hong T, Parameswaran S, Donmez OA, Miller D, Forney C, Lape M, Saint Just Ribeiro M, Liang J, Edsall LE, Magnusen AF, Miller W, Chepelev I, Harley JB, Zhao B, Kottyan LC, Weirauch MT. Epstein-Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci. Genome Res 2021; 31:2185-2198. [PMID: 34799401 PMCID: PMC8647835 DOI: 10.1101/gr.264705.120] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
The interplay between environmental and genetic factors plays a key role in the development of many autoimmune diseases. In particular, the Epstein-Barr virus (EBV) is an established contributor to multiple sclerosis, lupus, and other disorders. Previously, we showed that the EBV nuclear antigen 2 (EBNA2) transactivating protein occupies up to half of the risk loci for a set of seven autoimmune disorders. To further examine the mechanistic roles played by EBNA2 at these loci on a genome-wide scale, we globally examined gene expression, chromatin accessibility, chromatin looping, and EBNA2 binding in a B cell line that was (1) uninfected, (2) infected with a strain of EBV lacking EBNA2, or (3) infected with a strain that expresses EBNA2. We identified more than 400 EBNA2-dependent differentially expressed human genes and more than 5000 EBNA2 binding events in the human genome. ATAC-seq analysis revealed more than 2000 regions in the human genome with EBNA2-dependent chromatin accessibility, and HiChIP data revealed more than 1700 regions where EBNA2 altered chromatin looping interactions. Autoimmune genetic risk loci were highly enriched at the sites of these EBNA2-dependent chromatin-altering events. We present examples of autoimmune risk genotype-dependent EBNA2 events, nominating genetic risk mechanisms for autoimmune risk loci such as ZMIZ1 Taken together, our results reveal important interactions between host genetic variation and EBNA2-driven disease mechanisms. Further, our study highlights a critical role for EBNA2 in rewiring human gene regulatory programs through rearrangement of the chromatin landscape and nominates these interactions as components of genetic mechanisms that influence the risk of multiple autoimmune diseases.
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Affiliation(s)
- Ted Hong
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pharmacology and Systems Physiology, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Omer A Donmez
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Daniel Miller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Carmy Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Michael Lape
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Mariana Saint Just Ribeiro
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Jun Liang
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Lee E Edsall
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Albert F Magnusen
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - William Miller
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45267, USA
| | - Iouri Chepelev
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio 45229, USA
| | - Bo Zhao
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
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13
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Cheemarla NR, Watkins TA, Mihaylova VT, Wang B, Zhao D, Wang G, Landry ML, Foxman EF. Dynamic innate immune response determines susceptibility to SARS-CoV-2 infection and early replication kinetics. J Exp Med 2021; 218:e20210583. [PMID: 34128960 PMCID: PMC8210587 DOI: 10.1084/jem.20210583] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/21/2021] [Accepted: 06/01/2021] [Indexed: 12/25/2022] Open
Abstract
Initial replication of SARS-CoV-2 in the upper respiratory tract is required to establish infection, and the replication level correlates with the likelihood of viral transmission. Here, we examined the role of host innate immune defenses in restricting early SARS-CoV-2 infection using transcriptomics and biomarker-based tracking in serial patient nasopharyngeal samples and experiments with airway epithelial organoids. SARS-CoV-2 initially replicated exponentially, with a doubling time of ∼6 h, and induced interferon-stimulated genes (ISGs) in the upper respiratory tract, which rose with viral replication and peaked just as viral load began to decline. Rhinovirus infection before SARS-CoV-2 exposure accelerated ISG responses and prevented SARS-CoV-2 replication. Conversely, blocking ISG induction during SARS-CoV-2 infection enhanced viral replication from a low infectious dose. These results show that the activity of ISG-mediated defenses at the time of SARS-CoV-2 exposure impacts infection progression and that the heterologous antiviral response induced by a different virus can protect against SARS-CoV-2.
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Affiliation(s)
- Nagarjuna R. Cheemarla
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Timothy A. Watkins
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Valia T. Mihaylova
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Bao Wang
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Dejian Zhao
- Department of Genetics, Yale School of Medicine, New Haven, CT
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven, CT
| | - Guilin Wang
- Department of Genetics, Yale School of Medicine, New Haven, CT
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven, CT
| | - Marie L. Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Ellen F. Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
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14
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The Role of Coronavirus RNA-Processing Enzymes in Innate Immune Evasion. Life (Basel) 2021; 11:life11060571. [PMID: 34204549 PMCID: PMC8235370 DOI: 10.3390/life11060571] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 01/21/2023] Open
Abstract
Viral RNA sensing triggers innate antiviral responses in humans by stimulating signaling pathways that include crucial antiviral genes such as interferon. RNA viruses have evolved strategies to inhibit or escape these mechanisms. Coronaviruses use multiple enzymes to synthesize, modify, and process their genomic RNA and sub-genomic RNAs. These include Nsp15 and Nsp16, whose respective roles in RNA capping and dsRNA degradation play a crucial role in coronavirus escape from immune surveillance. Evolutionary studies on coronaviruses demonstrate that genome expansion in Nidoviruses was promoted by the emergence of Nsp14-ExoN activity and led to the acquisition of Nsp15- and Nsp16-RNA-processing activities. In this review, we discuss the main RNA-sensing mechanisms in humans as well as recent structural, functional, and evolutionary insights into coronavirus Nsp15 and Nsp16 with a view to potential antiviral strategies.
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15
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Avery EG, Bartolomaeus H, Maifeld A, Marko L, Wiig H, Wilck N, Rosshart SP, Forslund SK, Müller DN. The Gut Microbiome in Hypertension: Recent Advances and Future Perspectives. Circ Res 2021; 128:934-950. [PMID: 33793332 DOI: 10.1161/circresaha.121.318065] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The pathogenesis of hypertension is known to involve a diverse range of contributing factors including genetic, environmental, hormonal, hemodynamic and inflammatory forces, to name a few. There is mounting evidence to suggest that the gut microbiome plays an important role in the development and pathogenesis of hypertension. The gastrointestinal tract, which houses the largest compartment of immune cells in the body, represents the intersection of the environment and the host. Accordingly, lifestyle factors shape and are modulated by the microbiome, modifying the risk for hypertensive disease. One well-studied example is the consumption of dietary fibers, which leads to the production of short-chain fatty acids and can contribute to the expansion of anti-inflammatory immune cells, consequently protecting against the progression of hypertension. Dietary interventions such as fasting have also been shown to impact hypertension via the microbiome. Studying the microbiome in hypertensive disease presents a variety of unique challenges to the use of traditional model systems. Integrating microbiome considerations into preclinical research is crucial, and novel strategies to account for reciprocal host-microbiome interactions, such as the wildling mouse model, may provide new opportunities for translation. The intricacies of the role of the microbiome in hypertensive disease is a matter of ongoing research, and there are several technical considerations which should be accounted for moving forward. In this review we provide insights into the host-microbiome interaction and summarize the evidence of its importance in the regulation of blood pressure. Additionally, we provide recommendations for ongoing and future research, such that important insights from the microbiome field at large can be readily integrated in the context of hypertension.
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Affiliation(s)
- Ellen G Avery
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,For Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.G.A.,H.B., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Berlin, Germany (E.G.A.)
| | - Hendrik Bartolomaeus
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,For Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.G.A.,H.B., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.)
| | - Andras Maifeld
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.)
| | - Lajos Marko
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.)
| | - Helge Wiig
- Department of Biomedicine, University of Bergen, Norway (H.W.)
| | - Nicola Wilck
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,For Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.G.A.,H.B., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,For Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany (N.W.)
| | - Stephan P Rosshart
- Medical Center-University of Freiburg, Department of Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, Freiburg, Germany (S.P.R.)
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,For Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.G.A.,H.B., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.)
| | - Dominik N Müller
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,For Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.G.A.,H.B., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.)
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16
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Porto BN, Moraes TJ. The triad: respiratory microbiome - virus - immune response in the pathophysiology of pulmonary viral infections. Expert Rev Respir Med 2021; 15:635-648. [PMID: 33605840 DOI: 10.1080/17476348.2021.1893168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The longstanding dogma that the healthy lung is sterile has been refuted by recent advances in culture-independent analyses of airway samples. The respiratory microbiome comprises all airway and lung tissue-associated microbes. These micro-organisms occur throughout the upper and lower respiratory tracts, with different populations and distinct burdens at specific sites and can be classified as pathogenic or commensal. AREAS COVERED The majority of studies investigating the respiratory microbiome have focused on bacteria; however, emerging evidence has revealed the composition of the lung virome, the global viral communities present in the lung tissue. In this review, we searched PubMed and used keywords such as airway microbiome. We restricted outputs to English language and did not limit by any dates. We summarize the up-to-date knowledge on how the microbiome interacts with the host immune system and influences the pathogenesis of pulmonary viral infections. EXPERT OPINION The relationship between colonizing microbes and the host is complex and various factors need to be considered in order to appreciate its pathophysiological consequences. Understanding these intricate mechanisms of interaction among the respiratory microbiome, viruses and the immune response may lead to the development of better therapies to treat or prevent respiratory viral infections.
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Affiliation(s)
- Bárbara N Porto
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Theo J Moraes
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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17
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Ruohtula T, Kondrashova A, Lehtonen J, Oikarinen S, Hämäläinen AM, Niemelä O, Peet A, Tillmann V, Nieminen JK, Ilonen J, Knip M, Vaarala O, Hyöty H. Immunomodulatory Effects of Rhinovirus and Enterovirus Infections During the First Year of Life. Front Immunol 2021; 11:567046. [PMID: 33643278 PMCID: PMC7905218 DOI: 10.3389/fimmu.2020.567046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/29/2020] [Indexed: 11/13/2022] Open
Abstract
Early childhood infections have been implicated in the development of immune-mediated diseases, such as allergies, asthma, and type 1 diabetes. We set out to investigate the immunomodulatory effects of early viral infections experienced before the age of one year on the peripheral regulatory T cell population (Treg) and circulating cytokines in a birth-cohort study of Estonian and Finnish infants. We show here a temporal association of virus infection with the expression of FOXP3 in regulatory T cells. Infants with rhinovirus infection during the preceding 30 days had a higher FOXP3 expression in Treg cells and decreased levels of several cytokines related to Th1 and Th2 responses in comparison to the children without infections. In contrast, FOXP3 expression was significantly decreased in highly activated (CD4+CD127-/loCD25+FOXP3high) regulatory T cells (TregFOXP3high) in the infants who had enterovirus infection during the preceding 30 or 60 days. After enterovirus infections, the cytokine profile showed an upregulation of Th1- and Th17-related cytokines and a decreased activation of CCL22, which is a chemokine derived from dendritic cells and associated with Th2 deviation. Our results reveal that immunoregulatory mechanisms are up-regulated after rhinovirus infections, while enterovirus infections are associated with activation of proinflammatory pathways and decreased immune regulation.
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Affiliation(s)
| | - Anita Kondrashova
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jussi Lehtonen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anu-Maaria Hämäläinen
- Department of Pediatrics, Jorvi Hospital, Helsinki University Hospital, Espoo, Finland
| | - Onni Niemelä
- Department of Laboratory Medicine and Medical Research Unit, Seinäjoki Central Hospital and University of Tampere, Seinäjoki, Finland
| | - Aleksandr Peet
- Department of Pediatrics, University of Tartu and Tartu University Hospital, Tartu, Estonia
| | - Vallo Tillmann
- Department of Pediatrics, University of Tartu and Tartu University Hospital, Tartu, Estonia
| | - Janne K Nieminen
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku, Turku, Finland
| | - Mikael Knip
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Outi Vaarala
- Clinicum, University of Helsinki, Helsinki, Finland
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
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18
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Cheemarla NR, Watkins TA, Mihaylova VT, Wang B, Zhao D, Wang G, Landry ML, Foxman EF. Magnitude and timing of the antiviral response determine SARS-CoV-2 replication early in infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.22.21249812. [PMID: 33532783 PMCID: PMC7852233 DOI: 10.1101/2021.01.22.21249812] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The interferon response is a potent antiviral defense mechanism, but its effectiveness depends on its timing relative to viral replication. Here, we report viral replication and host response kinetics in patients at the start of SARS-CoV-2 infection and explore the impact of these kinetics experimentally. In both longitudinal patient nasopharyngeal samples and airway epithelial organoids, we found that SARS-CoV-2 initially replicated exponentially with a doubling time of ~6hr, and induced interferon stimulated genes (ISGs) with delayed timing relative to viral replication. Prior exposure to rhinovirus increased ISG levels and blocked SARS-CoV-2 replication. Conversely, inhibiting ISG induction abrogated interference by rhinovirus and enhanced SARS-CoV-2 replication rate. These results demonstrate the importance of initial interferon-mediated defenses in determining the extent to which SARS-CoV-2 can replicate at the start of infection and indicate that biological variables that alter the airway interferon response, including heterologous induction of innate immunity by other viruses, could profoundly impact SARS-CoV-2 susceptibility and transmission.
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Affiliation(s)
| | - Timothy A. Watkins
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Immunobiology, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Valia T. Mihaylova
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Bao Wang
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Immunobiology, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Dejian Zhao
- Department of Genetics, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Guilin Wang
- Department of Genetics, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Marie L. Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Internal Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Ellen F. Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Immunobiology, Yale School of Medicine, New Haven CT, U.S.A. 06520
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Wu A, Mihaylova VT, Landry ML, Foxman EF. Interference between rhinovirus and influenza A virus: a clinical data analysis and experimental infection study. THE LANCET. MICROBE 2020; 1:e254-e262. [PMID: 33103132 PMCID: PMC7580833 DOI: 10.1016/s2666-5247(20)30114-2] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND During the 2009 pandemic of an emerging influenza A virus (IAV; H1N1pdm09), data from several European countries indicated that the spread of the virus might have been interrupted by the annual autumn rhinovirus epidemic. We aimed to investigate viral interference between rhinovirus and IAV with use of clinical data and an experimental model. METHODS We did a clinical data analysis and experimental infection study to investigate the co-occurrence of rhinovirus and IAV in respiratory specimens from adults (≥21 years) tested with a multiplex PCR panel at Yale-New Haven Hospital (CT, USA) over three consecutive winter seasons (Nov 1 to March 1, 2016-17, 2017-18, and 2018-19). We compared observed versus expected co-detections using data extracted from the Epic Systems electronic medical record system. To assess how rhinovirus infection affects subsequent IAV infection, we inoculated differentiated primary human airway epithelial cultures with rhinovirus (HRV-01A; multiplicity of infection [MOI] 0·1) or did mock infection. On day 3 post-infection, we inoculated the same cultures with IAV (H1N1 green fluorescent protein [GFP] reporter virus or H1N1pdm09; MOI 0·1). We used reverse transcription quantitative PCR or microscopy to quantify host cell mRNAs for interferon-stimulated genes (ISGs) on day 3 after rhinovirus or mock infection and IAV RNA on days 4, 5, or 6 after rhinovirus or mock infection. We also did sequential infection studies in the presence of BX795 (6 μM), to inhibit the interferon response. We compared ISG expression and IAV RNA and expression of GFP by IAV reporter virus. FINDINGS Between July 1, 2016, and June 30, 2019, examination of 8284 respiratory samples positive for either rhinovirus (n=3821) or IAV (n=4463) by any test method was used to establish Nov 1 to March 1 as the period of peak virus co-circulation. After filtering for samples within this time frame meeting the inclusion criteria (n=13 707), there were 989 (7·2%) rhinovirus and 922 (6·7%) IAV detections, with a significantly lower than expected odds of co-detection (odds ratio 0·16, 95% CI 0·09-0·28). Rhinovirus infection of cell cultures induced ISG expression and protected against IAV infection 3 days later, resulting in an approximate 50 000-fold decrease in IAV H1N1pdm09 viral RNA on day 5 post-rhinovirus inoculation. Blocking the interferon response restored IAV replication following rhinovirus infection. INTERPRETATION These findings show that one respiratory virus can block infection with another through stimulation of antiviral defences in the airway mucosa, supporting the idea that interference from rhinovirus disrupted the 2009 IAV pandemic in Europe. These results indicate that viral interference can potentially affect the course of an epidemic, and this possibility should be considered when designing interventions for seasonal influenza epidemics and the ongoing COVID-19 pandemic. FUNDING National Institutes of Health, National Institute of General Medical Sciences, and the Yale Department of Laboratory Medicine.
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Affiliation(s)
- Anchi Wu
- Department of Laboratory Medicine (A Wu BSE, V T Mihaylova PhD, Prof M L Landry MD, Prof E F Foxman MD), Department of Internal Medicine (Prof M L Landry), and Department of Immunobiology (A Wu, Prof E F Foxman), Yale University School of Medicine, New Haven, CT, USA
| | - Valia T Mihaylova
- Department of Laboratory Medicine (A Wu BSE, V T Mihaylova PhD, Prof M L Landry MD, Prof E F Foxman MD), Department of Internal Medicine (Prof M L Landry), and Department of Immunobiology (A Wu, Prof E F Foxman), Yale University School of Medicine, New Haven, CT, USA
| | - Marie L Landry
- Department of Laboratory Medicine (A Wu BSE, V T Mihaylova PhD, Prof M L Landry MD, Prof E F Foxman MD), Department of Internal Medicine (Prof M L Landry), and Department of Immunobiology (A Wu, Prof E F Foxman), Yale University School of Medicine, New Haven, CT, USA
| | - Ellen F Foxman
- Department of Laboratory Medicine (A Wu BSE, V T Mihaylova PhD, Prof M L Landry MD, Prof E F Foxman MD), Department of Internal Medicine (Prof M L Landry), and Department of Immunobiology (A Wu, Prof E F Foxman), Yale University School of Medicine, New Haven, CT, USA
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20
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Wang L, Candia J, Ma L, Zhao Y, Imberti L, Sottini A, Dobbs K, Lisco A, Sereti I, Su HC, Notarangelo LD, Wang XW. Serological Responses to Human Virome Define Clinical Outcomes of Italian Patients Infected with SARS-CoV-2. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.09.04.20187088. [PMID: 32908997 PMCID: PMC7480049 DOI: 10.1101/2020.09.04.20187088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic respiratory infectious disease COVID-19. However, clinical manifestations and outcomes differ significantly among COVID-19 patients, ranging from asymptomatic to extremely severe, and it remains unclear what drives these disparities. Here, we studied 159 hospitalized Italian patients with pneumonia from the NIAID-NCI COVID-19 Consortium using a phage-display method to characterize circulating antibodies binding to 93,904 viral peptides encoded by 1,276 strains of human viruses. SARS-CoV-2 infection was associated with a marked increase in individual's immune memory antibody repertoires linked to trajectories of disease severity from the longitudinal analysis also including anti-spike protein antibodies. By applying a machine-learning-based strategy, we developed a viral exposure signature predictive of COVID-19-related disease severity linked to patient survival. These results provide a basis for understanding the roles of memory B-cell repertoires in COVID-19-related symptoms as well as a predictive tool for monitoring its clinical severity.
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Affiliation(s)
- Limin Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
- These authors contributed equally
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
- These authors contributed equally
| | - Lichun Ma
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
- These authors contributed equally
| | - Yongmei Zhao
- CCR-SF Bioinformatics Group, Advanced Biomedical and Computational Sciences, Frederick National Laboratory for Cancer Research, 8560 Progress Drive, Frederick, Maryland 21701
- These authors contributed equally
| | - Luisa Imberti
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892
| | | | - Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892
| | - Irini Sereti
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
- Lead Contact
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21
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Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients. Clin Microbiol Rev 2020; 33:33/4/e00027-20. [PMID: 32847820 DOI: 10.1128/cmr.00027-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.
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22
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Liu J, Tang W, Budhu A, Forgues M, Hernandez MO, Candia J, Kim Y, Bowman ED, Ambs S, Zhao Y, Tran B, Wu X, Koh C, Surana P, Liang TJ, Guarnera M, Mann D, Rajaure M, Greten TF, Wang Z, Yu H, Wang XW. A Viral Exposure Signature Defines Early Onset of Hepatocellular Carcinoma. Cell 2020; 182:317-328.e10. [PMID: 32526205 PMCID: PMC8315306 DOI: 10.1016/j.cell.2020.05.038] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/20/2020] [Accepted: 05/20/2020] [Indexed: 12/25/2022]
Abstract
Hepatocellular carcinoma (HCC) is an aggressive malignancy with its global incidence and mortality rate continuing to rise, although early detection and surveillance are suboptimal. We performed serological profiling of the viral infection history in 899 individuals from an NCI-UMD case-control study using a synthetic human virome, VirScan. We developed a viral exposure signature and validated the results in a longitudinal cohort with 173 at-risk patients who had long-term follow-up for HCC development. Our viral exposure signature significantly associated with HCC status among at-risk individuals in the validation cohort (area under the curve: 0.91 [95% CI 0.87-0.96] at baseline and 0.98 [95% CI 0.97-1] at diagnosis). The signature identified cancer patients prior to a clinical diagnosis and was superior to alpha-fetoprotein. In summary, we established a viral exposure signature that can predict HCC among at-risk patients prior to a clinical diagnosis, which may be useful in HCC surveillance.
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Affiliation(s)
- Jinping Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wei Tang
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Maria O Hernandez
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yujin Kim
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stefan Ambs
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yongmei Zhao
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Bao Tran
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Xiaolin Wu
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Christopher Koh
- Liver Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD 20892, USA
| | - Pallavi Surana
- Liver Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD 20892, USA
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD 20892, USA
| | - Maria Guarnera
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Dean Mann
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Manoj Rajaure
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tim F Greten
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Zhanwei Wang
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Herbert Yu
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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23
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Ansari MH, Ebrahimi M, Fattahi MR, Gardner MG, Safarpour AR, Faghihi MA, Lankarani KB. Viral metagenomic analysis of fecal samples reveals an enteric virome signature in irritable bowel syndrome. BMC Microbiol 2020; 20:123. [PMID: 32429898 PMCID: PMC7236503 DOI: 10.1186/s12866-020-01817-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 05/10/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Changes in the enteric microbiota have been suggested to contribute to gastrointestinal diseases, including irritable bowel syndrome. Most of the published work is on bacterial dysbiosis with meager data on the role of the virome in irritable bowel syndrome and other gastrointestinal diseases. In the current study, we therefore aimed to investigate the viral community composition of the gut and test for potential dysbiosis linked to irritable bowel syndrome. RESULTS A metagenomics analysis on fecal samples of 50 individuals - 30 of whom met the Rome IV criteria for IBS and 20 healthy controls- was conducted. There was a noticeable alteration in viral taxa observed in association with irritable bowel syndrome when compared to healthy individuals - where some eukaryotic viral taxa noticeably prevail over others. We observed a significant decrease in the diversity and abundance of enteric virome particularly in eukaryotic viruses of Megavirales in patients with irritable bowel syndrome. CONCLUSIONS These findings shed light on a new hypothesis that the alteration of the viral taxa contributes to the pathogenesis of irritable bowel syndrome and related symptoms, and therefore, pave the way for developing a new diagnostic biomarker or anti-viral drugs for the treatment of irritable bowel syndrome.
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Affiliation(s)
- Mina Hojat Ansari
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehregan Ebrahimi
- Department of Biology, Shiraz University, Shiraz, Fars Province, Iran
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Mohammad Reza Fattahi
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Michael G Gardner
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia
| | - Ali Reza Safarpour
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Ali Faghihi
- Persian Bayan Gene Research and Training Center, Dr. Faghihi's Medical Genetics Center, Shiraz, Iran
- Center for Therapeutic Innovation, Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kamran Bagheri Lankarani
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
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24
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Affiliation(s)
- Gordan Lauc
- University of Zagreb Faculty of Pharmacy and Biochemistry & Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Alemka Markotić
- Clinics for Infective Diseases, Dr. Fran Mihaljević, Zagreb, Croatia
| | - Ivan Gornik
- Department of Emergency Medicine, Clinical Hospital Zagreb, Zagreb, Croatia
| | - Dragan Primorac
- St Catharine Hospital, Zagreb, Croatia.,Medical School REGIOMED, Coburg, Germany
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25
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Abstract
The seasonal cycle of respiratory viral diseases has been widely recognized for thousands of years, as annual epidemics of the common cold and influenza disease hit the human population like clockwork in the winter season in temperate regions. Moreover, epidemics caused by viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) and the newly emerging SARS-CoV-2 occur during the winter months. The mechanisms underlying the seasonal nature of respiratory viral infections have been examined and debated for many years. The two major contributing factors are the changes in environmental parameters and human behavior. Studies have revealed the effect of temperature and humidity on respiratory virus stability and transmission rates. More recent research highlights the importance of the environmental factors, especially temperature and humidity, in modulating host intrinsic, innate, and adaptive immune responses to viral infections in the respiratory tract. Here we review evidence of how outdoor and indoor climates are linked to the seasonality of viral respiratory infections. We further discuss determinants of host response in the seasonality of respiratory viruses by highlighting recent studies in the field.
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Affiliation(s)
- Miyu Moriyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA;
| | - Walter J Hugentobler
- Institute of Primary Care, University of Zurich and University Hospital, Zurich, Switzerland CH-8091
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA; .,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06512, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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26
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Abstract
The etiology and pathogenesis of MS is likely to involve multiple factors interacting with each other, and the role of infectious and viral agents is still under debate, however a consistent amount of studies suggests that some viruses are associated with the disease. The strongest documentation has come from the detection of viral nucleic acid or antigen or of an anti-viral antibody response in MS patients. A further step for the study of the mechanism viruses might be involved in can be made using in vitro and in vivo models. While in vitro models, based on glial and neural cell lines from various sources are widely used, in vivo animal models present challenges. Indeed neurotropic animal viruses are currently used to study demyelination in well-established models, but animal models of demyelination by human virus infection have only recently been developed, using animal gammaherpesviruses closely related to Epstein Barr virus (EBV), or using marmosets expressing the specific viral receptor for Human Herpesvirus 6 (HHV-6). The present review will illustrate the main potential mechanisms of MS pathogenesis possibly associated with viral infections and viruses currently used to study demyelination in animal models. Then the viruses most strongly linked with MS will be discussed, in the perspective that more than one virus might have a role, with varying degrees of interaction, contributing to MS heterogeneity.
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Affiliation(s)
- Donatella Donati
- Neurologia e Neurofisiologia Clinica, Azienda Ospedaliera Universitaria Senese I 53100 Siena, Italy
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27
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Secor PR, Burgener EB, Kinnersley M, Jennings LK, Roman-Cruz V, Popescu M, Van Belleghem JD, Haddock N, Copeland C, Michaels LA, de Vries CR, Chen Q, Pourtois J, Wheeler TJ, Milla CE, Bollyky PL. Pf Bacteriophage and Their Impact on Pseudomonas Virulence, Mammalian Immunity, and Chronic Infections. Front Immunol 2020; 11:244. [PMID: 32153575 PMCID: PMC7047154 DOI: 10.3389/fimmu.2020.00244] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022] Open
Abstract
Pf bacteriophage are temperate phages that infect the bacterium Pseudomonas aeruginosa, a major cause of chronic lung infections in cystic fibrosis (CF) and other settings. Pf and other temperate phages have evolved complex, mutualistic relationships with their bacterial hosts that impact both bacterial phenotypes and chronic infection. We and others have reported that Pf phages are a virulence factor that promote the pathogenesis of P. aeruginosa infections in animal models and are associated with worse skin and lung infections in humans. Here we review the biology of Pf phage and what is known about its contributions to pathogenesis and clinical disease. First, we review the structure, genetics, and epidemiology of Pf phage. Next, we address the diverse and surprising ways that Pf phages contribute to P. aeruginosa phenotypes including effects on biofilm formation, antibiotic resistance, and motility. Then, we cover data indicating that Pf phages suppress mammalian immunity at sites of bacterial infection. Finally, we discuss recent literature implicating Pf in chronic P. aeruginosa infections in CF and other settings. Together, these reports suggest that Pf bacteriophage have direct effects on P. aeruginosa infections and that temperate phages are an exciting frontier in microbiology, immunology, and human health.
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Affiliation(s)
- Patrick R. Secor
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
- Center for Translational Medicine, University of Montana, Missoula, MT, United States
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, United States
| | - Elizabeth B. Burgener
- Department of Pediatrics, Center for Excellence in Pulmonary Biology, Stanford University, Stanford, CA, United States
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - M. Kinnersley
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Laura K. Jennings
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
- Center for Translational Medicine, University of Montana, Missoula, MT, United States
| | - Valery Roman-Cruz
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
- Center for Translational Medicine, University of Montana, Missoula, MT, United States
| | - Medeea Popescu
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Jonas D. Van Belleghem
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Naomi Haddock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Conner Copeland
- Department of Computer Science, University of Montana, Missoula, MT, United States
| | - Lia A. Michaels
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Christiaan R. de Vries
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Julie Pourtois
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Travis J. Wheeler
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, United States
- Department of Computer Science, University of Montana, Missoula, MT, United States
| | - Carlos E. Milla
- Department of Pediatrics, Center for Excellence in Pulmonary Biology, Stanford University, Stanford, CA, United States
| | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
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28
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Talwar P, Gupta R, Kushwaha S, Agarwal R, Saso L, Kukreti S, Kukreti R. Viral Induced Oxidative and Inflammatory Response in Alzheimer's Disease Pathogenesis with Identification of Potential Drug Candidates: A Systematic Review using Systems Biology Approach. Curr Neuropharmacol 2019; 17:352-365. [PMID: 29676229 PMCID: PMC6482477 DOI: 10.2174/1570159x16666180419124508] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/19/2018] [Accepted: 04/10/2018] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is genetically complex with multifactorial etiology. Here, we aim to identify the potential viral pathogens leading to aberrant inflammatory and oxidative stress response in AD along with potential drug candidates using systems biology approach. We retrieved protein interactions of amyloid precursor protein (APP) and tau protein (MAPT) from NCBI and genes for oxidative stress from NetAge, for inflammation from NetAge and InnateDB databases. Genes implicated in aging were retrieved from GenAge database and two GEO expression datasets. These genes were individually used to create protein-protein interaction network using STRING database (score≥0.7). The interactions of candidate genes with known viruses were mapped using virhostnet v2.0 database. Drug molecules targeting candidate genes were retrieved using the Drug- Gene Interaction Database (DGIdb). Data mining resulted in 2095 APP, 116 MAPT, 214 oxidative stress, 1269 inflammatory genes. After STRING PPIN analysis, 404 APP, 109 MAPT, 204 oxidative stress and 1014 inflammation related high confidence proteins were identified. The overlap among all datasets yielded eight common markers (AKT1, GSK3B, APP, APOE, EGFR, PIN1, CASP8 and SNCA). These genes showed association with hepatitis C virus (HCV), Epstein- Barr virus (EBV), human herpes virus 8 and Human papillomavirus (HPV). Further, screening of drugs targeting candidate genes, and possessing anti-inflammatory property, antiviral activity along with a suggested role in AD pathophysiology yielded 12 potential drug candidates. Our study demonstrated the role of viral etiology in AD pathogenesis by elucidating interaction of oxidative stress and inflammation causing candidate genes with common viruses along with the identification of potential AD drug candidates.
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Affiliation(s)
- Puneet Talwar
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Renu Gupta
- Institute of Human Behaviour & Allied Sciences (IHBAS), Dilshad Garden, Delhi 110 095, India
| | - Suman Kushwaha
- Institute of Human Behaviour & Allied Sciences (IHBAS), Dilshad Garden, Delhi 110 095, India
| | - Rachna Agarwal
- Institute of Human Behaviour & Allied Sciences (IHBAS), Dilshad Garden, Delhi 110 095, India
| | - Luciano Saso
- Department of Physiology and Pharmacology, Sapienza University of Rome, Italy
| | | | - Ritushree Kukreti
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi, India
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29
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Abstract
Refractory celiac disease (RCD) refers to persistence of malnutrition and intestinal villous atrophy for more than 1 to 2 years despite strict gluten-free diet in patients with celiac disease. Diagnosis remains difficult and impacts treatment and follow-up. RCD has been subdivided into 2 subgroups according to the normal (RCDI) or abnormal phenotype of intraepithelial lymphocytes (IELs) (RCDII). RCDII is considered as a low-grade intraepithelial lymphoma and has a poor prognosis due to gastrointestinal and extraintestinal dissemination of the abnormal IELs, and high risk of overt lymphoma.
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Affiliation(s)
- Georgia Malamut
- Paris Descartes University, 15 rue de l'Ecole de Médecine, Paris 75006, France; Gastroenterology Department, Hôpital Européen Georges Pompidou, APHP, 20 rue Leblanc, Paris 75015, France; UMR1163 Institute Imagine, 24 Boulevard du Montparnasse, Paris 75015, France.
| | - Christophe Cellier
- Paris Descartes University, 15 rue de l'Ecole de Médecine, Paris 75006, France; Gastroenterology Department, Hôpital Européen Georges Pompidou, APHP, 20 rue Leblanc, Paris 75015, France; UMR1163 Institute Imagine, 24 Boulevard du Montparnasse, Paris 75015, France
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30
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Sulovari A, Li D. VIpower: Simulation-based tool for estimating power of viral integration detection via high-throughput sequencing. Genomics 2019; 112:207-211. [PMID: 30710609 DOI: 10.1016/j.ygeno.2019.01.015] [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: 08/10/2018] [Revised: 12/31/2018] [Accepted: 01/22/2019] [Indexed: 12/12/2022]
Abstract
Viral sequence integrations in the human genome have been implicated in various human diseases. Viral integrations remain among the most challenging-to-detect structural changes of the human genome. No studies have systematically analyzed how molecular and bioinformatics factors affect the power (sensitivity) to detect viral integrations using high-throughput sequencing (HTS). We selected a wide-range of molecular and bioinformatics factors covering genome sequence characteristics, HTS features, and viral integration detection. We designed a fast simulation-based framework to model the process of detecting variable viral integration events in the human genome. We then examined the associations of selected factors with viral integration detection power. We identified six factors that significantly affected viral integration detection power (P < 2 × 10-16). The strongest factors associated with detection power included proportion of sample cells with clonal viral integrations (Pearson's ρ = 0.64), sequencing depth (ρ = 0.37), length of viral integration (ρ = 0.37), paired-end read insert size (ρ = 0.23), user-defined threshold (number of supporting reads) to claim successful identification of integrations (ρ = -0.19), and read length (when sequence volume was fixed) (ρ = -0.09). As the first tool of its kind, VIpower incorporates all these factors, which can be manipulated in concert with each other to optimize the detection power. This tool may be used to estimate viral integration detection power for various combinations of sequencing or analytic parameters. It may also be used to estimate the parameters required to achieve a specific power when designing new sequencing experiments.
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Affiliation(s)
- Arvis Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; Department of Computer Science, University of Vermont, Burlington, VT 05405, USA; Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, VT 05405, USA.
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Stefanaki C. The Gut Microbiome Beyond the Bacteriome—The Neglected Role of Virome and Mycobiome in Health and Disease. MICROBIOME AND METABOLOME IN DIAGNOSIS, THERAPY, AND OTHER STRATEGIC APPLICATIONS 2019. [DOI: 10.1016/b978-0-12-815249-2.00003-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Van Belleghem JD, Dąbrowska K, Vaneechoutte M, Barr JJ, Bollyky PL. Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System. Viruses 2018; 11:E10. [PMID: 30585199 PMCID: PMC6356784 DOI: 10.3390/v11010010] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 02/07/2023] Open
Abstract
The human body is host to large numbers of bacteriophages (phages)⁻a diverse group of bacterial viruses that infect bacteria. Phage were previously regarded as bystanders that only impacted immunity indirectly via effects on the mammalian microbiome. However, it has become clear that phages also impact immunity directly, in ways that are typically anti-inflammatory. Phages can modulate innate immunity via phagocytosis and cytokine responses, but also impact adaptive immunity via effects on antibody production and effector polarization. Phages may thereby have profound effects on the outcome of bacterial infections by modulating the immune response. In this review we highlight the diverse ways in which phages interact with human cells. We present a computational model for predicting these complex and dynamic interactions. These models predict that the phageome may play important roles in shaping mammalian-bacterial interactions.
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Affiliation(s)
- Jonas D Van Belleghem
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, 9000 Ghent, Belgium.
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Krystyna Dąbrowska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland.
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, 9000 Ghent, Belgium.
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Nakatsu G, Zhou H, Wu WKK, Wong SH, Coker OO, Dai Z, Li X, Szeto CH, Sugimura N, Lam TYT, Yu ACS, Wang X, Chen Z, Wong MCS, Ng SC, Chan MTV, Chan PKS, Chan FKL, Sung JJY, Yu J. Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes. Gastroenterology 2018; 155:529-541.e5. [PMID: 29689266 DOI: 10.1053/j.gastro.2018.04.018] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 03/31/2018] [Accepted: 04/17/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Patients with colorectal cancer (CRC) have a different gut microbiome signature than individuals without CRC. Little is known about the viral component of CRC-associated microbiome. We aimed to identify and validate viral taxonomic markers of CRC that might be used in detection of the disease or predicting outcome. METHODS We performed shotgun metagenomic analyses of viromes of fecal samples from 74 patients with CRC (cases) and 92 individuals without CRC (controls) in Hong Kong (discovery cohort). Viral sequences were classified by taxonomic alignment against an integrated microbial reference genome database. Viral markers associated with CRC were validated using fecal samples from 3 separate cohorts: 111 patients with CRC and 112 controls in Hong Kong, 46 patients with CRC and 63 controls in Austria, and 91 patients with CRC and 66 controls in France and Germany. Using abundance profiles of CRC-associated virome genera, we constructed random survival forest models to identify those associated with patient survival times. RESULTS The diversity of the gut bacteriophage community was significantly increased in patients with CRC compared with controls. Twenty-two viral taxa discriminated cases from controls with an area under the receiver operating characteristic curve of 0.802 in the discovery cohort. The viral markers were validated in 3 cohorts, with area under the receiver operating characteristic curves of 0.763, 0.736, and 0.715, respectively. Clinical subgroup analysis showed that dysbiosis of the gut virome was associated with early- and late-stage CRC. A combination of 4 taxonomic markers associated with reduced survival of patients with CRC (log-rank test, P = 8.1 × 10-6) independently of tumor stage, lymph node metastases, or clinical parameters. We found altered interactions between bacteriophages and oral bacterial commensals in fecal samples from patients with CRC compared with controls. CONCLUSIONS In a metagenomic analysis of fecal samples from patients and controls, we identified virome signatures associated with CRC. These data might be used to develop tools to identify individuals with CRC or predict outcomes.
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Affiliation(s)
- Geicho Nakatsu
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Haokui Zhou
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - William Ka Kei Wu
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China; Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny Hei Wong
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Olabisi Oluwabukola Coker
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhenwei Dai
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiangchun Li
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun-Ho Szeto
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Naoki Sugimura
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Thomas Yuen-Tung Lam
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Allen Chi-Shing Yu
- School of Life Sciences and Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiansong Wang
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China; Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Martin Chi-Sang Wong
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Siew Chien Ng
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew Tak Vai Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul Kay Sheung Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Francis Ka Leung Chan
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Jao-Yiu Sung
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Institute of Digestive Disease and the Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China.
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Freer G, Maggi F, Pifferi M, Di Cicco ME, Peroni DG, Pistello M. The Virome and Its Major Component, Anellovirus, a Convoluted System Molding Human Immune Defenses and Possibly Affecting the Development of Asthma and Respiratory Diseases in Childhood. Front Microbiol 2018; 9:686. [PMID: 29692764 PMCID: PMC5902699 DOI: 10.3389/fmicb.2018.00686] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 03/23/2018] [Indexed: 12/13/2022] Open
Abstract
The microbiome, a thriving and complex microbial community colonizing the human body, has a broad impact on human health. Colonization is a continuous process that starts very early in life and occurs thanks to shrewd strategies microbes have evolved to tackle a convoluted array of anatomical, physiological, and functional barriers of the human body. Cumulative evidence shows that viruses are part of the microbiome. This part, called virome, has a dynamic composition that reflects what we eat, how and where we live, what we do, our genetic background, and other unpredictable variables. Thus, the virome plays a chief role in shaping innate and adaptive host immune defenses. Imbalance of normal microbial flora is thought to trigger or exacerbate many acute and chronic disorders. A compelling example can be found in the respiratory apparatus, where early-life viral infections are major determinants for the development of allergic diseases, like asthma, and other non-transmissible diseases. In this review, we focus on the virome and, particularly, on Anelloviridae, a recently discovered virus family. Anelloviruses are major components of the virome, present in most, if not all, human beings, where they are acquired early in life and replicate persistently without causing apparent disease. We will discuss how modulation of innate and adaptive immune systems by Anelloviruses can influence the development of respiratory diseases in childhood and provide evidence for the use of Anelloviruses as useful and practical molecular markers to monitor inflammatory processes and immune system competence.
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Affiliation(s)
- Giulia Freer
- Retrovirus Center, Department of Translational Research, University of Pisa, Pisa, Italy
| | | | - Massimo Pifferi
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy
| | - Maria E Di Cicco
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy
| | - Diego G Peroni
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy
| | - Mauro Pistello
- Retrovirus Center, Department of Translational Research, University of Pisa, Pisa, Italy.,Virology Unit, University Hospital of Pisa, Pisa, Italy
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Rampelli S, Turroni S, Schnorr SL, Soverini M, Quercia S, Barone M, Castagnetti A, Biagi E, Gallinella G, Brigidi P, Candela M. Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin. Environ Microbiol 2017; 19:4728-4735. [DOI: 10.1111/1462-2920.13938] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/17/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Simone Rampelli
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Stephanie L. Schnorr
- Department of Anthropology, Laboratories of Molecular Anthropology and Microbiome Research; University of Oklahoma; Norman OK USA
| | - Matteo Soverini
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Sara Quercia
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Monica Barone
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Andrea Castagnetti
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Elena Biagi
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Giorgio Gallinella
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
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Watanabe T, Shibasaki M, Maruyama F, Sekizaki T, Nakagawa I. Investigation of potential targets of Porphyromonas CRISPRs among the genomes of Porphyromonas species. PLoS One 2017; 12:e0183752. [PMID: 28837670 PMCID: PMC5570325 DOI: 10.1371/journal.pone.0183752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/10/2017] [Indexed: 12/13/2022] Open
Abstract
The oral bacterial species Porphyromonas gingivalis, a periodontal pathogen, has plastic genomes that may be driven by homologous recombination with exogenous deoxyribonucleic acid (DNA) that is incorporated by natural transformation and conjugation. However, bacteriophages and plasmids, both of which are main resources of exogenous DNA, do not exist in the known P. gingivalis genomes. This could be associated with an adaptive immunity system conferred by clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (cas) genes in P. gingivalis as well as innate immune systems such as a restriction-modification system. In a previous study, few immune targets were predicted for P. gingivalis CRISPR/Cas. In this paper, we analyzed 51 P. gingivalis genomes, which were newly sequenced, and publicly available genomes of 13 P. gingivalis and 46 other Porphyromonas species. We detected 6 CRISPR/Cas types (classified by sequence similarity of repeat) in P. gingivalis and 12 other types in the remaining species. The Porphyromonas CRISPR spacers with potential targets in the genus Porphyromonas were approximately 23 times more abundant than those with potential targets in other genus taxa (1,720/6,896 spacers vs. 74/6,896 spacers). Porphyromonas CRISPR/Cas may be involved in genome plasticity by exhibiting selective interference against intra- and interspecies nucleic acids.
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Affiliation(s)
- Takayasu Watanabe
- Laboratory of Food-borne Pathogenic Microbiology, Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
- * E-mail:
| | - Masaki Shibasaki
- Department of Oral Implantology and Regenerative Dental Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Tsutomu Sekizaki
- Laboratory of Food-borne Pathogenic Microbiology, Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
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Chow J, Márka Z, Bartos I, Márka S, Kagan JC. Environmental Stress Causes Lethal Neuro-Trauma during Asymptomatic Viral Infections. Cell Host Microbe 2017; 22:48-60.e5. [PMID: 28704652 PMCID: PMC5560172 DOI: 10.1016/j.chom.2017.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/16/2017] [Accepted: 06/20/2017] [Indexed: 02/07/2023]
Abstract
Asymptomatic infections often proceed undetected, yet can still prime the host to be sensitive to secondary environmental stress. While the mechanisms underlying disease caused by asymptomatic infections are unknown, it is believed that productive pathogen replication is required. We report that the environmental stress of carbon dioxide (CO2) anesthesia converts an asymptomatic rhabdovirus infection in Drosophila to one that is lethal. This lethality results from a pool of infectious virus in glial cells and is regulated by the antiviral RNAi pathway of the host. CO2 sensitivity is caused by the fusogenic activity of the viral glycoprotein, which results in fusion of neurons and glia. Expression of the viral glycoprotein, but not a fusion defective mutant, is sufficient to cause CO2 sensitivity, which can occur even in the absence of productive viral replication. These findings highlight how viral proteins, independent of pathogen replication, may predispose hosts to life-threatening environmental stress.
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Affiliation(s)
- Jonathan Chow
- Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Zsuzsa Márka
- Department of Physics, Columbia University, New York, NY, USA
| | - Imre Bartos
- Department of Physics, Columbia University, New York, NY, USA
| | - Szabolcs Márka
- Department of Physics, Columbia University, New York, NY, USA
| | - Jonathan C Kagan
- Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA.
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38
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Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children. Proc Natl Acad Sci U S A 2017; 114:E6166-E6175. [PMID: 28696303 DOI: 10.1073/pnas.1706359114] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Viruses have long been considered potential triggers of autoimmune diseases. Here we defined the intestinal virome from birth to the development of autoimmunity in children at risk for type 1 diabetes (T1D). A total of 220 virus-enriched preparations from serially collected fecal samples from 11 children (cases) who developed serum autoantibodies associated with T1D (of whom five developed clinical T1D) were compared with samples from controls. Intestinal viromes of case subjects were less diverse than those of controls. Among eukaryotic viruses, we identified significant enrichment of Circoviridae-related sequences in samples from controls in comparison with cases. Enterovirus, kobuvirus, parechovirus, parvovirus, and rotavirus sequences were frequently detected but were not associated with autoimmunity. For bacteriophages, we found higher Shannon diversity and richness in controls compared with cases and observed that changes in the intestinal virome over time differed between cases and controls. Using Random Forests analysis, we identified disease-associated viral bacteriophage contigs after subtraction of age-associated contigs. These disease-associated contigs were statistically linked to specific components of the bacterial microbiome. Thus, changes in the intestinal virome preceded autoimmunity in this cohort. Specific components of the virome were both directly and inversely associated with the development of human autoimmune disease.
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Vu DL, Kaiser L. The concept of commensal viruses almost 20 years later: redefining borders in clinical virology. Clin Microbiol Infect 2017; 23:688-690. [PMID: 28288831 PMCID: PMC7130093 DOI: 10.1016/j.cmi.2017.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/28/2017] [Accepted: 03/04/2017] [Indexed: 01/21/2023]
Affiliation(s)
- D-L Vu
- Geneva University Hospital, Department of Internal Medicine Specialties, Division of Infectious Diseases, Switzerland.
| | - L Kaiser
- Geneva University Hospital, Department of Internal Medicine Specialties, Division of Infectious Diseases, Switzerland
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Abstract
The three common themes that underlie the induction and perpetuation of autoimmunity are genetic predisposition, environmental factors, and immune regulation. Environmental factors have gained much attention for their role in triggering autoimmunity, with increasing evidence of their influence as demonstrated by epidemiological studies, laboratory research, and animal studies. Environmental factors known to trigger and perpetuate autoimmunity include infections, gut microbiota, as well as physical and environmental agents. To address these issues, we will review major potential mechanisms that underlie autoimmunity including molecular mimicry, epitope spreading, bystander activation, polyclonal activation of B and T cells, infections, and autoinflammatory activation of innate immunity. The association of the gut microbiota on autoimmunity will be particularly highlighted by their interaction with pharmaceutical agents that may lead to organ-specific autoimmunity. Nonetheless, and we will emphasize this point, the precise mechanism of environmental influence on disease pathogenesis remains elusive.
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Affiliation(s)
- Annarosa Floreani
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Via Giustiniani, 2, 35128, Padova, Italy.
| | - Patrick S C Leung
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Via Giustiniani, 2, 35128, Padova, Italy
| | - M Eric Gershwin
- Division of Rheumatology, Allergy, and Clinical Immunology, University of California Davis, Davis, CA, USA
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Distribution and characteristics of rodent picornaviruses in China. Sci Rep 2016; 6:34381. [PMID: 27682620 PMCID: PMC5041129 DOI: 10.1038/srep34381] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/12/2016] [Indexed: 01/13/2023] Open
Abstract
Rodents are important reservoir hosts of many important zoonotic viruses. The family Picornaviridae contains clinically important pathogens that infect humans and animals, and increasing numbers of rodent picornaviruses have recently been associated with zoonoses. We collected 574 pharyngeal and anal swab specimens from 287 rodents of 10 different species from eight representative regions of China from October 2013 to July 2015. Seven representative sequences identified from six rodent species were amplified as full genomes and classified into four lineages. Three lineage 1 viruses belonged to a novel genus of picornaviruses and was more closely related to Hepatovirus than to others genera of picornaviruses based on aa homology. Lineage 2, lineage 3, and lineage 4 viruses belonged to the genera Rosavirus, Hunnivirus, and Enterovirus, respectively, representing new species. According to both phylogenetic and identity analyses, Lineage 2 viruses had a close relationship with rosavirus 2 which was recovered from the feces of a child in Gambia and Lineage 3 viruses had a close relationship with domestic animal Hunnivirus. Lineage 4 viruses provide the first evidence of these enteroviruses and their evolution in rodent hosts in China.
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Microbiomic and Posttranslational Modifications as Preludes to Autoimmune Diseases. Trends Mol Med 2016; 22:746-757. [DOI: 10.1016/j.molmed.2016.07.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/08/2023]
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Zou S, Caler L, Colombini-Hatch S, Glynn S, Srinivas P. Research on the human virome: where are we and what is next. MICROBIOME 2016; 4:32. [PMID: 27341799 PMCID: PMC4919837 DOI: 10.1186/s40168-016-0177-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/10/2016] [Indexed: 06/06/2023]
Abstract
The National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health convened a Working Group on the Microbiome in Cardiovascular, Pulmonary and Hematologic Health and Diseases from June 25, 2014, to June 26, 2014. The Working Group's central goal was to define what major microbiome research areas warranted additional study in the context of heart, lung, and blood (HLB) diseases. The Working Group identified studies of the human virome a key priority.
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Affiliation(s)
- Shimian Zou
- National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 6701, Rockledge Drive, Room 9144, Bethesda, MD 20892-7950 USA
| | - Lis Caler
- National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 6701, Rockledge Drive, Room 9144, Bethesda, MD 20892-7950 USA
| | - Sandra Colombini-Hatch
- National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 6701, Rockledge Drive, Room 9144, Bethesda, MD 20892-7950 USA
| | - Simone Glynn
- National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 6701, Rockledge Drive, Room 9144, Bethesda, MD 20892-7950 USA
| | - Pothur Srinivas
- National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 6701, Rockledge Drive, Room 9144, Bethesda, MD 20892-7950 USA
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Abstract
Recurrent aphthous ulcer (RAU) is the most common oral mucosal disease with complex etiology. Since its pathogenesis is still not completely clear, specific clinical treatment is lacking. With the continuous development of oral micro-ecology, oral microbial population imbalance as an important pathogenesis of RAU is gradually recognized. At present, the research of oral flora imbalance has made some progress, but as the largest member of the oral microbial community, the research of the virome is still under development. In recent years, the rapid development of macro virus genome science and high throughput sequencing technology has led to a breakthrough in oral virome.
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Navaneetharaja N, Griffiths V, Wileman T, Carding SR. A Role for the Intestinal Microbiota and Virome in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)? J Clin Med 2016; 5:E55. [PMID: 27275835 PMCID: PMC4929410 DOI: 10.3390/jcm5060055] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 02/06/2023] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a heterogeneous disorder of significant societal impact that is proposed to involve both host and environmentally derived aetiologies that may be autoimmune in nature. Immune-related symptoms of at least moderate severity persisting for prolonged periods of time are common in ME/CFS patients and B cell depletion therapy is of significant therapeutic benefit. The origin of these symptoms and whether it is infectious or inflammatory in nature is not clear, with seeking evidence of acute or chronic virus infections contributing to the induction of autoimmune processes in ME/CFS being an area of recent interest. This article provides a comprehensive review of the current evidence supporting an infectious aetiology for ME/CFS leading us to propose the novel concept that the intestinal microbiota and in particular members of the virome are a source of the "infectious" trigger of the disease. Such an approach has the potential to identify disease biomarkers and influence therapeutics, providing much-needed approaches in preventing and managing a disease desperately in need of confronting.
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Affiliation(s)
- Navena Navaneetharaja
- The Gut Health and Food Safety Research Programme, The Institute of Food Research, University of East Anglia, Norwich NR4 7UA, UK.
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Verity Griffiths
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Tom Wileman
- The Gut Health and Food Safety Research Programme, The Institute of Food Research, University of East Anglia, Norwich NR4 7UA, UK.
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Simon R Carding
- The Gut Health and Food Safety Research Programme, The Institute of Food Research, University of East Anglia, Norwich NR4 7UA, UK.
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK.
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Reese TA, Bi K, Kambal A, Filali-Mouhim A, Beura LK, Bürger MC, Pulendran B, Sekaly RP, Jameson SC, Masopust D, Haining WN, Virgin HW. Sequential Infection with Common Pathogens Promotes Human-like Immune Gene Expression and Altered Vaccine Response. Cell Host Microbe 2016; 19:713-9. [PMID: 27107939 DOI: 10.1016/j.chom.2016.04.003] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/22/2016] [Accepted: 04/01/2016] [Indexed: 12/16/2022]
Abstract
Immune responses differ between laboratory mice and humans. Chronic infection with viruses and parasites are common in humans, but are absent in laboratory mice, and thus represent potential contributors to inter-species differences in immunity. To test this, we sequentially infected laboratory mice with herpesviruses, influenza, and an intestinal helminth and compared their blood immune signatures to mock-infected mice before and after vaccination against yellow fever virus (YFV-17D). Sequential infection altered pre- and post-vaccination gene expression, cytokines, and antibodies in blood. Sequential pathogen exposure induced gene signatures that recapitulated those seen in blood from pet store-raised versus laboratory mice, and adult versus cord blood in humans. Therefore, basal and vaccine-induced murine immune responses are altered by infection with agents common outside of barrier facilities. This raises the possibility that we can improve mouse models of vaccination and immunity by selective microbial exposure of laboratory animals to mimic that of humans.
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Affiliation(s)
- Tiffany A Reese
- Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Kevin Bi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Pediatric Hematology and Oncology, Children's Hospital, Boston, MA 02115, and the Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Amal Kambal
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ali Filali-Mouhim
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Lalit K Beura
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matheus C Bürger
- Department of Clinical Analyses and Toxicology, School of Pharmaceutical Science at University of São Paulo, São Paulo 05508, Brazil
| | - Bali Pulendran
- Emory Vaccine Center, Yerkes National Primate Research Center and Department of Pathology, Emory University, Atlanta, GA 30329, USA
| | - Rafick-Pierre Sekaly
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Stephen C Jameson
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Masopust
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Pediatric Hematology and Oncology, Children's Hospital, Boston, MA 02115, and the Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Karachaliou M, Waterboer T, Casabonne D, Chalkiadaki G, Roumeliotaki T, Michel A, Stiakaki E, Chatzi L, Pawlita M, Kogevinas M, de Sanjose S. The Natural History of Human Polyomaviruses and Herpesviruses in Early Life--The Rhea Birth Cohort in Greece. Am J Epidemiol 2016; 183:671-9. [PMID: 26968942 DOI: 10.1093/aje/kwv281] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/09/2015] [Indexed: 12/25/2022] Open
Abstract
Sparse data exist on the patterns and determinants of acquisition of polyomaviruses and herpesviruses in childhood. We measured immunoglobulin G seroreactivity against 10 polyomaviruses (BKPyV, JCPyV, KIPyV, WUPyV, MCPyV, HPyV6, HPyV7, TSPyV, HPyV9, HPyV10) and 5 herpesviruses (Epstein Barr virus (EBV), cytomegalovirus (CMV), herpes simplex virus types 1 and 2, human herpesvirus 8) using multiplex serology on blood samples collected at birth (cord blood, n = 626) and at follow-up at 3 years (n = 81) and 4 years (n = 690) of age among the Rhea birth cohort recruited in Greece from pregnant women in 2007-2008. We used Poisson regression with robust variance to identify determinants of seropositivity at age 4. Seroprevalence of polyomaviruses ranged from 38.5% to 99.8% in cord blood and from 20.9% to 82.3% at age 4. Seroprevalence of EBV, CMV, herpes simplex virus types 1 and 2, and human herpesvirus 8 was 99.4%, 74.9%, 26.2%, 8.0%, and 1.6% in cord blood and 52.5%, 25.8%, 3.6%, 1.4%, and 0% at age 4, respectively. Determinants of seropositivity at age 4 were cord seropositivity (JCPyV, HPyV7, HPyV10, CMV), vaginal delivery (HPyV10), breastfeeding (CMV), younger age at day-care entry (BKPyV, KIPyV, WUPyV, TSPyV, HPyV10, HPyV9, EBV, CMV), and swimming pool attendance (BKPyV, KIPyV, WUPyV, HPyV10). Television viewing, parental stress, and hygiene practices were inversely associated with the seroprevalence of polyomaviruses and herpesviruses.
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Columpsi P, Sacchi P, Zuccaro V, Cima S, Sarda C, Mariani M, Gori A, Bruno R. Beyond the gut bacterial microbiota: The gut virome. J Med Virol 2016; 88:1467-72. [PMID: 26919534 PMCID: PMC7166815 DOI: 10.1002/jmv.24508] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2016] [Indexed: 12/23/2022]
Abstract
The gastrointestinal tract is colonized with a highly different population of bacterial, viral, ad fungal species; viruses are reported to be dominant. The composition of gut virome is closely related to dietary habits and surrounding environment. Host and their intestinal microbes live in a dynamic equilibrium and viruses stimulate a low degree of immune responses without causing symptoms (host tolerance). However, intestinal phages could lead to a rupture of eubiosis and may contribute to the shift from health to disease in humans and animals. Viral nucleic acids and other products of lysis of bacteria serve as pathogen‐associated molecular patterns (PAMPs) and could trigger specific inflammatory modulations. At the same time, phages could elicit innate antiviral immune responses. Toll‐like receptors (TLRs) operated as innate antiviral immune sensors and their activation triggers signaling cascades that lead to inflammatory response. J. Med. Virol. 88:1467–1472, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Paola Columpsi
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Paolo Sacchi
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Valentina Zuccaro
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Serena Cima
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Cristina Sarda
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marcello Mariani
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Andrea Gori
- Clinic of Infectious Diseases, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Raffaele Bruno
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Clinical, Surgical, Diagnostic and Pediatric Science, University of Pavia, Pavia, Italy
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Rampelli S, Soverini M, Turroni S, Quercia S, Biagi E, Brigidi P, Candela M. ViromeScan: a new tool for metagenomic viral community profiling. BMC Genomics 2016. [PMID: 26932765 DOI: 10.1186/s12864-016-2446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Bioinformatics tools available for metagenomic sequencing analysis are principally devoted to the identification of microorganisms populating an ecological niche, but they usually do not consider viruses. Only some software have been designed to profile the viral sequences, however they are not efficient in the characterization of viruses in the context of complex communities, like the intestinal microbiota, containing bacteria, archeabacteria, eukaryotic microorganisms and viruses. In any case, a comprehensive description of the host-microbiota interactions can not ignore the profile of eukaryotic viruses within the virome, as viruses are definitely critical for the regulation of the host immunophenotype. RESULTS ViromeScan is an innovative metagenomic analysis tool that characterizes the taxonomy of the virome directly from raw data of next-generation sequencing. The tool uses hierarchical databases for eukaryotic viruses to unambiguously assign reads to viral species more accurately and >1000 fold faster than other existing approaches. We validated ViromeScan on synthetic microbial communities and applied it on metagenomic samples of the Human Microbiome Project, providing a sensitive eukaryotic virome profiling of different human body sites. CONCLUSIONS ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples from reads of other microorganisms. This implies that users can fully characterize the microbiome, including bacteria and viruses, by shotgun metagenomic sequencing followed by different bioinformatic pipelines.
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Affiliation(s)
- Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Matteo Soverini
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Sara Quercia
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Elena Biagi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
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