Genomics of host-pathogen interactions

Current Opinion in Immunology

Volumn 30, Issue 1, 2014, Pages 32-38

  Rausell, Antonio ^a,b   Telenti, Amalio ^a  

^a LAUSANNE UNIVERSITY HOSPITAL   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA; TRIPARTITE MOTIF PROTEIN 5;

CELL ACTIVATION; CELL DIFFERENTIATION; GENE; GENE MAPPING; GENE MUTATION; GENE REPLICATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMICS; GENOTYPE; HOST PATHOGEN INTERACTION; HUMAN; IMMUNE DEFICIENCY; IMMUNITY GENE; INFECTION SENSITIVITY; INNATE IMMUNITY; LOSS OF FUNCTION MUTATION; MOLECULAR EVOLUTION; NEXT GENERATION SEQUENCING; NONHUMAN; PHENOTYPE; PROTEIN PROCESSING; REVIEW; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; ANIMAL; CHROMOSOME MAP; ADAPTIVE IMMUNITY; EVOLUTIONARY ADAPTATION; GENE FUNCTION; GENE LOCUS; GENE ONTOLOGY; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOTYPE PHENOTYPE CORRELATION; HUMAN IMMUNODEFICIENCY VIRUS 1; VIRUS CAPSID; VIRUS TRANSMISSION;

ANIMALS; CHROMOSOME MAPPING; EVOLUTION, MOLECULAR; GENOMICS; HOST-PATHOGEN INTERACTIONS; HUMANS;

EID: 84902989494     PISSN: 09527915     EISSN: 18790372     Source Type: Journal    
DOI: 10.1016/j.coi.2014.06.001     Document Type: Review

References (36)

1. Karlsson E.K., Kwiatkowski D.P., Sabeti P.C. Natural selection and infectious disease in human populations. Nat Rev Genet 2014, 15:379-393.
2. Patel M.R., Emerman M., Malik H.S. Paleovirology-ghosts and gifts of viruses past. Curr Opin Virol 2011, 1:304-309.
3. Keinan A., Clark A.G. Recent explosive human population growth has resulted in an excess of rare genetic variants. Science 2012, 336:740-743.
4. Duggal N.K., Emerman M. Evolutionary conflicts between viruses and restriction factors shape immunity. Nat Rev Immunol 2012, 12:687-695.
5. Rausell A., McLaren P., Telenti A. HIV and innate immunity-a genomics perspective. F1000 Prime Rep 2013, 5:29.
6. Quintana-Murci L., Clark A.G. Population genetic tools for dissecting innate immunity in humans. Nat Rev Immunol 2013, 13:280-293.
7. Fagny M., Patin E., Enard D., Barreiro L.B., Quintana-Murci L., Laval G. Exploring the occurrence of classic selective sweeps in humans using whole-genome sequencing datasets. Mol Biol Evol 2014, first published online April 1, 2014. 10.1093/molbev/msu118.
8. Daugherty M.D., Malik H.S. Rules of engagement: molecular insights from host-virus arms races. Annu Rev Genet 2012, 46:677-700.
9. Sanz-Ramos M., Stoye J.P. Capsid-binding retrovirus restriction factors: discovery, restriction specificity and implications for the development of novel therapeutics. J Gen Virol 2013, 94(Pt 12):2587-2598.
10. Rahm N., Yap M., Snoeck J., Zoete V., Munoz M., Radespiel U., et al. Unique spectrum of activity of prosimian TRIM5alpha against exogenous and endogenous retroviruses. J Virol 2011, 85:4173-4183.
11. Rahm N., Gfeller D., Snoeck J., Martinez R., McLaren P.J., Ortiz M., et al. Susceptibility and adaptation to human TRIM5alpha alleles at positive selected sites in HIV-1 capsid. Virology 2013, 441:162-170.
12. Laguette N., Rahm N., Sobhian B., Chable-Bessia C., Munch J., Snoeck J., et al. Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. Cell Host Microbe 2012, 11:205-217.
13. Fregoso O.I., Ahn J., Wang C., Mehrens J., Skowronski J., Emerman M. Evolutionary toggling of Vpx/Vpr specificity results in divergent recognition of the restriction factor SAMHD1. PLoS Pathog 2013, 9:e1003496.
14. Lim E.S., Fregoso O.I., McCoy C.O., Matsen F.A., Malik H.S., Emerman M. The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx. Cell Host Microbe 2012, 11:194-204.
15. Fenton-May A.E., Dibben O., Emmerich T., Ding H., Pfafferott K., Aasa-Chapman M.M., et al. Relative resistance of HIV-1 founder viruses to control by interferon-alpha. Retrovirology 2013, 10:146.
16. Serre S.B., Krarup H.B., Bukh J., Gottwein J.M. Identification of alpha interferon-induced envelope mutations of hepatitis C virus in vitro associated with increased viral fitness and interferon resistance. J Virol 2013, 87:12776-12793.
17. Patel M.R., Loo Y.M., Horner S.M., Gale M., Malik H.S. Convergent evolution of escape from hepaciviral antagonism in primates. PLoS Biol 2012, 10:e1001282.
18. Wang B., Xi X., Lei X., Zhang X., Cui S., Wang J., et al. Enterovirus 71 protease 2Apro targets MAVS to inhibit anti-viral type I interferon responses. PLoS Pathog 2013, 9:e1003231.
19. Faure M., Rabourdin-Combe C. Innate immunity modulation in virus entry. Curr Opin Virol 2011, 1:6-12.
20. Mitchell P.S., Patzina C., Emerman M., Haller O., Malik H.S., Kochs G. Evolution-guided identification of antiviral specificity determinants in the broadly acting interferon-induced innate immunity factor MxA. Cell Host Microbe 2012, 12:598-604.
21. Mitchell P.S., Emerman M., Malik H.S. An evolutionary perspective on the broad antiviral specificity of MxA. Curr Opin Microbiol 2013, 16:493-499.
22. Gack M.U. Mechanisms of RIG-I-like receptor activation and manipulation by viral pathogens. J Virol 2014, 88:5213-5216.
23. Elde N.C., Child S.J., Eickbush M.T., Kitzman J.O., Rogers K.S., Shendure J., et al. Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses. Cell 2012, 150:831-841.
24. de Bakker P.I., Telenti A. Infectious diseases not immune to genome-wide association. Nat Genet 2010, 42:731-732.
25. Jostins L., Ripke S., Weersma R.K., Duerr R.H., McGovern D.P., Hui K.Y., et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012, 491:119-124.
26. Raj T., Kuchroo M., Replogle J.M., Raychaudhuri S., Stranger B.E., De Jager P.L. Common risk alleles for inflammatory diseases are targets of recent positive selection. Am J Human Genet 2013, 92:517-529.
27. MacArthur D.G., Balasubramanian S., Frankish A., Huang N., Morris J., Walter K., et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012, 335:823-828.
28. Rausell A., Mohammadi P., McLaren P., Xenarios I., Fellay J., Telenti A. Analysis of stop-gain and frameshift variants in human innate immunity genes. BioRxiv 2014, http://biorxiv.org/content/early/2014/03/17/003376.
29. Bartha I., Carlson J.M., Brumme C.J., McLaren P.J., Brumme Z.L., John M., et al. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. eLife 2013, 2:e01123.
30. Depledge D.P., Kundu S., Jensen N.J., Gray E.R., Jones M., Steinberg S., et al. Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of varicella zoster virus and its vaccine in humans. Mol Biol Evol 2014, 31:397-409.
31. Depledge D.P., Palser A.L., Watson S.J., Lai I.Y., Gray E.R., Grant P., et al. Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS One 2011, 6:e27805.
32. Wagner A. Distributed robustness versus redundancy as causes of mutational robustness. BioEssays 2005, 27:176-188.
33. Barreiro L.B., Tailleux L., Pai A.A., Gicquel B., Marioni J.C., Gilad Y. Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection. Proc Natl Acad Sci U S A 2012, 109:1204-1209.
34. Lee M.N., Ye C., Villani A.C., Raj T., Li W., Eisenhaure T.M., et al. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science 2014, 343:1246980.
35. Fairfax B.P., Humburg P., Makino S., Naranbhai V., Wong D., Lau E., et al. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science 2014, 343:1246949.
36. Jojic V., Shay T., Sylvia K., Zuk O., Sun X., Kang J., et al. Identification of transcriptional regulators in the mouse immune system. Nat Immunol 2013, 14:633-643.