The viral microbiome
Assoc. Prof. Dr. Christoph Steininger Klinik für Innere Medizin I Medizinische Universität Wien Viruses
. Size 1/100 of bacteria . Replication only in living cells . High genetic variability (no conserved regions like 16S rRNA) . Genome: RNA & DNA, single- & double-stranded
Course of infection . Acute (Rhinovirus, Influenza) . Persistent (Lymphocytic choriomeningitis virus) . Latent, reactivating (Herpesviruses) . Slow virus infection (HIV, Measles SSPE) Discovery of transmissible tumors
Francis Peyton Rous
1911: Cancer has to be caused by a virus 1961: Identification of Rous Sarcoma Virus as ssRNA virus
Rous Sarcoma Virus 1966: Nobel prize in Physiology/Medicine Cancer associated with human papillomaviruses
High-grade cervical lesions in Australian women aged <18 yrs
Margaret Stanley, Nature 2012
Brotherton et al. Lancet 2011 Merkel cell carcinoma
• Rare, aggressive skin cancer • Merkel cell polyomavirus (MCPyV) DNA detectable in 80% of MCC tumors • Seroprevalence of polyomavirus infections in general population: . BK virus 92% . JC virus 45% . WU polyomavirus 98% . KI polyomavirus 90% . MCPyV 59% Carter et al. J Natl Cancer Inst 2009; Pastrana et al. PlosPathogens 2009 Cancer caused by infectious pathogens (Status 2014)
EBV; 5% KSHV; Other; 1% 2%
Helicobacter; HBV & HCV; 32,5% 30%
HPV; 30%
De Martel et al. Lancet Oncology 2012 . 12,7 Mio new cases of cancer in 2008 . 16% of cancer cases attributable to infections . Relevance of infections in carcinogenesis higher in developing countries Estimated burden of chronic viral infections in humans
. ~8–12 chronic viral infections per individuum
Virgin et al. Cell 2009 Diseases of unknown etiology with suspected viral cause
Wylie et al. Curr Opin Microbiol 2013
Virus-host equilibrium in chronic viral infections
Chronic infection - Continuous/intermittent Ag presentation - Tissue damage & aberrant repair - Altered homeostasis - Genotoxicity - Proliferative responses
Cancer
Viral strategies Immune response - Latency - Dampen responses - Immune evasion - Chronic activation - Mutation - Immunopathology - Immunoprivilege - Repertoire contraction Detection of novel oncogenic viruses
Method Issues Cell culture • Selection of cells for permissivity • Identification of viral replication Microscopy • Insensitive • Size of viral particles • Differentiation of viruses PCR • Genomes highly variable Serology • Cross-reactivity
Adenovirus
Virus attachment Virus culture Electron microscope Metagenomics
Breitbart et al. Res. Microbiol. (2008); Allander et al. Proc. Natl. Acad. Sci. USA (2005); Breitbart et al. J. Bacteriol. (2003); Breitbart et al. Biotechniques (2005); Bibby et al. Trends in Biotechnology 2013 The human microbiome
. Bacteria . Fungi . Parasites & Ova Meiofauna (Eukaryote) . Protozoa . Viruses (109 virus particles/gram feces) 1. Eukaryotic Viruses 2. Prokaryotic Viruses (Bakteriophages) 3. Plantviruses 4. Human endogeneous retroviruses (HERV) ScienceNews
Popgeorgiev et al. Journal of Infectious Diseases 2013; Ogilvie et al. Nat Comm 2013 Plasma DNA Source: 1. Eukaryotic intestinal viruses
. Rotavirus Documented outbreaks of gastroenteritis in the US . Norovirus Caliciviruses . Sapovirus . Enteric Adenoviruses . Astrovirus . Aichivirus
Source: CDC 2014 Discovery of novel eukaryotic viruses
Virus Replication Disease Reservoir Ref. Cyclovirus-Vietnam Feces & CSF Encephalitis Pigs, poultry Van Tan et al. Mbio 2013 Burkina Faso Feces Diarrhea ??? Phan et al. J Clin Astrovirus Virol 2014 Virginia Astrovirus Feces Diarrhea Mammals Finkbeiner et al. J Virol 2009 Torque Teno Serum (HIV- ??? ??? Farsani et al. Virology Journal Mimi Virus 13 positiv) 2013 Humanes Respiratory Bronchilitis Bats, civet cat Van der Hoek et Coronavirus NL63 secretions al. Nat Med 2004 Lujovirus Serum & Tissue Hemorrhagic ??? Briese et al. PlosPathogens fever 2009 Picobirnavirus Feces Diarrhea ??? Leeuwen et al. J Clin Microbiol 2011 Human Plasma Fever African Green Scuda et al. J polyomavirus 9 Monkey Virol 2011 (HPyV9). Discovery of novel human viruses
Cumulative number of viruses discovered
Arboviruses and non-arboviruses discovered annually
Woolhouse et al. Proc Biol Sci. 2008; Rosenberg et al. PNAS 2013 Transspecies transfer of viruses
Graham et al. Nat Rev Microbiol 2013
. >80 Mio pet cats worldwide . Feline Co-infections common (40% of cats shed >5 viruses in feces) . Novel viruses in asymptomatic cats (Sakobuvirus, Bocavirus, Astroviren, Picobirnavirus)
Ng et al. Veterinary Microbiol 2013; Benedictis et al. Infection, Genetics, Evolution 2011 The „silent“ human virome
Group Family Species dsDNA Adenoviridae Enteric adenovirus 40, 41 Iridoviridae Lymphocystis disease virus Myoviridae phiBCD7, Bacillus phage G, phiP-SSM4 Podoviridae Enterobacteria phage P22, phage T3 Siphoviridae Listeria phage A118, phiE125 Lactococcus phage bIL285, phiCP39-O, Clostridium Phages Halophage eHP-10 Papillomaviridae Human papillomavirus 6, 18, 66 Polyomaviridae BK virus, JC virus, SV40 virus, Human polyomavirus 9, 12, Merkel cell polyomavirus Herpesviridae Epstein-Barr virus, Human cytomegalovirus ssDNA Anelloviridae TTV Circoviridae Chicken anemia virus, TN9, PK5034, PK5222, NG12 Microviridae Chlamydia phage 1,3,4, Bdellovibrio phage phiMH2K, Chlamydia phage CPG1, Spiroplasma phage 4, Chlamydia phage CPAR39 dsRNA Picobirnaviridae Human picobirnavirus Reoviridae Human rotavirus (+) ssRNA Caliciviridae Norwalk virus Astroviridae Human astrovirus Virgaviridae Pepper mild mottle virus, Tobacco mosaic virus Picornaviridae Cosavirus, Klassevirus/salivirus, Aichi virus, Enterovirus, Parechovirus, Saffold cardiovirus, Echovirus, Coxsackievirus, Poliovirus Popgeorgiev et al. Intervirology 2013; Wylie et al. BMC Biology 2014; Foulongne et al. PlosOne 2012 The human megavirome
. Mimi-, Mega-, Pandoravirus – infect Acanthamoeba . Human, intestinale Megaviridae . Iridoviridae Acanthamoeba Pithovirus polyphaga sibericum . Poxvirus-related genomic sequences Mimivirus . Senegalvirus . Marseillevirus . Human, Plasma-Megaviridae Poxvirus . Giant Blood Marseillevirus (infects T-cells) E. coli Sputnik Virophage . Discovery of Virophages Parvovirus Myovirus Bacteriophage Mimi- Legendre et al. PNAS 2013; virus Popgeorgiev et al. Intervirology 2013; Popgeorgiev et al. J Infect Dis 2013 Raoult, The Scientist 2014 2. Intestinal Bacteriophages
. ~10x more viral particles than bacteria in feces
. High level of genetic diversity . Source of transfer of genes between bacteria
. Bactericidal due to lytic replication Norman et al. Gastroenterology 2014; Barr et al. PNAS 2013 Phages protect from pathogenic bacteria
Barr et al. PNAS 2013 crAssphage
. 6x more abundant in feces than all other known phages together . 90% of all reads in virus-like particle (VLP)-derived metagenomes . 22% of total community metagenomes . 1.68% of all human fecal metagenomic sequencing reads in the public databases
. Year of discovery: 2014 . Majority of crAssphage-encoded proteins match no known sequences in the database discarded as data junk
Dutilh et al. Nat Comm 2014 3. Intestinal plant viruses
Pepper mild mottle virus
Zhang et al. Plos Biology 2006; Colson Plos ONE 2010 4. Human endogenous retroviruses (HERV)
. 8%–9% of the human genome EBV infects T-cells . HERVs are mostly replication defective (no virus generated) . Defective HERVs may still IFN-α↑ . express viral proteins . regulate cellular gene expression Activation of silent . modulate host immune response HERV-K18 element . participate in mutagenic events
Env overexpressed (superantigen activity)
Inflammatory cascade Feschotte & Gilbert, Nat Rev Genetics 2012 initiated Role of HERV-W env (syncytin-1) in human cancer
. Overexpressed in 76% of urothelial cell carcinoma tissues (controls, 6%) . Overexpression increases proliferation and viability of immortalized human uroepithelial cells . Involved in mediating cancer-endothelial cell fusions in vitro
. Syncytin-1 expression = positive Urogenital cancer tissue prognostic factor in breast cancer . Syncytin-1 expression in 38% of all breast cancer samples . Upregulated in endometrial carcinoma
Yu et al. Oncogene 2014; Blesa et al. Cancer Therapy 2008; Larsson et al. Placenta 2002 Physiologic functions of syncytins
. Inserted in human-prehominoids chromosome 7q21, 40-45 millions years ago . Absolute requirement for placenta development and embryo survival
. Positive selective Syncytin gene advantage – switch from capture events egg to uterus . Induction of maternal immune tolerance to fetus? . Cellular resistance against infection by retroviruses of family spleen necrosis virus
Lavialle et al. Phil. Trans. R. Soc. B 2013; Blesa et al. Cancer Therapy 2008 Endogenous viral elements (EVE)
Family or Taxa Number per haploid . Chromosomal genus genome integration of viral Baculovirus Insects Unknown Herpesviridae Humans 1 DNA (or DNA Nudivirus Parasitic wasps Several Phycodnaviridae Brown algae 1 copies of viral RNA) Circoviridae Mammals 1 to 2 in the host germ Geminiviridae Tomentosae 5 to 120 Parvoviridae Mammals; shrimp 1 to 3 cells Partitiviridae Plants; arthropods; Protozoa 1 to 4 Reovirus Aedes spp. mosquitoes 1 . All major types of Totiviridae Fungi; plants; ticks 1 to 6 Dicistroviridae Honeybees 1 eukaryotic viruses Flaviviridae Medaka fish; mosquitoes 1 to 4 can give rise to Potyviridae Grapes Several Bornaviridae Vertebrates 1 to 17 EVEs Bunyaviridae Ticks 14 Filoviridae Mammals 1 to 13 Nyavirus Zebrafish 6 Orthomyxoviridae Ticks 1 Rhabdoviridae Insects (ticks and mosquitoes) 1 to 28 Retroviridae Vertebrates Several hundreds to several hundreds of Feschotte & Gilbert, Nat thousands Rev Genetics 2012 Hepadnavirus Passerine birds 15 Pararetrovirus Plants A dozen to a thousand Immune response to the „silent“ virome
Pepper mild mottled virus- specific IgG
Vanura, Steininger et al. PlosOne 2013
Colson et al. PlosOne 2010 Restrained T-cell proliferation in chronic viral infections γ - 2 Viral pathogen IL - CTL TNF IFN potential Apoptosis Proliferative
Cytomegalovirus +++ ++ ++/- +/- ++ - Epstein-Barr virus ++ + + - + - HIV, HCV, HBV +/- +/- +/- - +/- +/-
Murali-Krishna et Chronic LCMV +/- - - - - ++ al. Immunity 1998; Miller et al. Apoptotic T cell +++ Immunity 2008; Virgin et al. Cell 2009 Transkingdom interactions
Opportunistic infections in AIDS patients
CMV Retinitis
Tuberculosis Toxoplasmosis
PML
Kaposi Pneumocystis sarcoma pneumonia Expansion of the intestinal virome during HIV replication
Bacterial microbiom not affected by SIV- infection
Handley et al. Cell 2012; McKenna et al. PLoS Pathogens 2008; Duerkop & Hooper, Nat Rev Immunol 2013; Salzman et al. Nat. Immunol 2010; Fukuda et al. Nature 2011; Scott et al. Cell 2012 Protection of mice from Yersinia pestis and Listeria monocytogenes infection by latent herpesvirus infection
Y. pestis L. monocytogenes
Barton et al. Nature 2007 The parasites of the parasites of the …
Susceptibility to Cervical Vaginal Trichomonas other STI (HIV & & dysbiosis infection HPV) prostate cancer . Metronidazole Treatment: . Parasite clearance . Prognosis for pregnancy and fertility unchanged . Protozoa carry endosymbiotic dsRNA viruses (Trichomonas, Leishmania, Giardia, Plasmodium, Entamoeba, Naegleria, Eimeria, Cryptosporidum, Babesia) . 50% of Trichomonas isolate carry Trichomonasvirus . Nonpathogenic to protozoan host . Contribute to adaptation to and pathogenicity in human host . Metronidazole releases virus from protozoan host proinflammatory cascade Fichorova et al. PlosOne 2012 Conclusions
Viral pathogens have been linked to multiple human malignancies
Underestimated role of viral infection in evolution of human malignancy suspected:
Kingdom of viruses extensive
„Silent“ viral infections may be associated with significant inflammatory response
Extensive interactions between host, virus and other microbes
Metagenomic studies will very likely open whole new avenues better understanding and targeted therapies in cancer research Antiviral drugs and vaccines are developed at rapidly increasing pace Targeted therapies may become available soon Thanks for your attention