Human Genetics

, Volume 131, Issue 9, pp 1433–1451 | Cite as

Genome-wide genetic associations with IFNγ response to smallpox vaccine

  • Richard B. Kennedy
  • Inna G. Ovsyannikova
  • V. Shane Pankratz
  • Iana H. Haralambieva
  • Robert A. Vierkant
  • Robert M. Jacobson
  • Gregory A. Poland
Original Investigation


Smallpox is a deadly and debilitating disease that killed hundreds of millions of people in the past century alone. The use of Vaccinia virus-based smallpox vaccines led to the eradication of smallpox. These vaccines are remarkably effective, inducing the characteristic pustule or “take” at the vaccine site in >97 % of recipients, and inducing a wide spectrum of long-lasting humoral and cellular immune responses. The mechanisms behind inter-individual vaccine-response variability are likely to involve host genetic variation, but have not been fully characterized. We report here the first smallpox vaccine response genome-wide association study of over 1,000 recent recipients of Dryvax®. The data presented here focus on cellular immune responses as measured by both production of secreted IFNγ and quantitation of IFNγ secreting cells by ELISPOT assay. We identified multiple significant SNP associations in genes (RASA1, ADRA1D, TCF7L1, FAS) that are critical components of signaling pathways that directly control lymphocyte IFNγ production or cytotoxic T cell function. Similarly, we found many associations with SNPs located in genes integral to nerve cell function; findings that, given the complex interplay between the nervous and immune systems, deserve closer examination in follow-up studies.



The authors thank the subjects who participated in this study and the research staff at the NHRC and Mayo Clinic that made this study possible—particularly, Drs. Meg Ryan and Kevin Russell. The authors also wish to recognize Dave Watson and Megan O’Byrne for their statistical programming and analytical support as well as Julie M. Cunningham and the Mayo Advanced Genomic Technology Center for the genotyping efforts. The funding agencies had no role in study design, data collection and analysis, decision to publish, or preparation of this manuscript. This project was funded by federal funds from the National Institute of Allergies and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN266200400065C.

Conflict of interest

The authors have no conflicts of interest.

Ethical standards

All experiments described here followed current, applicable US laws.


  1. Artenstein AW, Grabenstein JD (2008) Smallpox vaccines for biodefense: need and feasibility. Expert Rev Vaccines 7:1225–1237PubMedCrossRefGoogle Scholar
  2. Bechmann I, Mor G, Nilsen J, Eliza M, Nitsch R, Naftolin F (1999) FasL (CD95L, Apo1L) is expressed in the normal rat and human brain: evidence for the existence of an immunological brain barrier. Glia 27:62–74PubMedCrossRefGoogle Scholar
  3. Behrens P, Brinkmann U, Wellmann A (2003) CSE1L/CAS: its role in proliferation and apoptosis. Apoptosis 8:39–44PubMedCrossRefGoogle Scholar
  4. Bond C, LaForge KS, Tian M, Melia D, Zhang S, Borg L, Gong J, Schluger J, Strong JA, Leal SM, Tischfield JA, Kreek MJ, Yu L (1998) Single-nucleotide polymorphism in the human mu opioid receptor gene alters beta-endorphin binding and activity: possible implications for opiate addiction. Proc Natl Acad Sci USA 95:9608–9613PubMedCrossRefGoogle Scholar
  5. Brown SL, Van Epps DE (1986) Opioid peptides modulate production of interferon gamma by human mononuclear cells. Cell Immunol 103:19–26PubMedCrossRefGoogle Scholar
  6. Bruno JF, Whittaker J, Song JF, Berelowitz M (1991) Molecular cloning and sequencing of a cDNA encoding a human alpha 1A adrenergic receptor. Biochem Biophys Res Commun 179:1485–1490PubMedCrossRefGoogle Scholar
  7. Burton EA, Tinsley JM, Holzfeind PJ, Rodrigues NR, Davies KE (1999) A second promoter provides an alternative target for therapeutic up-regulation of utrophin in Duchenne muscular dystrophy. Proc Natl Acad Sci USA 96:14025–14030PubMedCrossRefGoogle Scholar
  8. Chatterjee TK, Eapen A, Kanis AB, Fisher RA (1997) Genomic organization, 5′-flanking region, and chromosomal localization of the human RGS3 gene. Genomics 45:429–433PubMedCrossRefGoogle Scholar
  9. Chen L, Hodges RR, Funaki C, Zoukhri D, Gaivin RJ, Perez DM, Dartt DA (2006) Effects of alpha1D-adrenergic receptors on shedding of biologically active EGF in freshly isolated lacrimal gland epithelial cells. Am J Physiol Cell Physiol 291:C946–C956PubMedCrossRefGoogle Scholar
  10. Chuang TK, Killam KF Jr, Chuang LF, Kung HF, Sheng WS, Chao CC, Yu L, Chuang RY (1995) Mu opioid receptor gene expression in immune cells. Biochem Biophys Res Commun 216:922–930PubMedCrossRefGoogle Scholar
  11. Chumakov I, Blumenfeld M, Guerassimenko O, Cavarec L, Palicio M, Abderrahim H, Bougueleret L, Barry C, Tanaka H, La Rosa P, Puech A, Tahri N, Cohen-Akenine A, Delabrosse S, Lissarrague S, Picard FP, Maurice K, Essioux L, Millasseau P, Grel P, Debailleul V, Simon AM, Caterina D, Dufaure I, Malekzadeh K, Belova M, Luan JJ, Bouillot M, Sambucy JL, Primas G, Saumier M, Boubkiri N, Martin-Saumier S, Nasroune M, Peixoto H, Delaye A, Pinchot V, Bastucci M, Guillou S, Chevillon M, Sainz-Fuertes R, Meguenni S, Aurich-Costa J, Cherif D, Gimalac A, Van Duijn C, Gauvreau D, Ouellette G, Fortier I, Raelson J, Sherbatich T, Riazanskaia N, Rogaev E, Raeymaekers P, Aerssens J, Konings F, Luyten W, Macciardi F, Sham PC, Straub RE, Weinberger DR, Cohen N, Cohen D (2002) Genetic and physiological data implicating the new human gene G72 and the gene for d-amino acid oxidase in schizophrenia. Proc Natl Acad Sci USA 99:13675–13680PubMedCrossRefGoogle Scholar
  12. Cohen-Barak O, Hagiwara N, Arlt MF, Horton JP, Brilliant MH (2001) Cloning, characterization and chromosome mapping of the human SOX6 gene. Gene 265:157–164PubMedCrossRefGoogle Scholar
  13. Combadiere B, Boissonnas A, Carcelain G, Lefranc E, Samri A, Bricaire F, Debre P, Autran B (2004) Distinct time effects of vaccination on long-term proliferative and IFN-gamma-producing T cell memory to smallpox in humans. J Exp Med 199:1585–1593PubMedCrossRefGoogle Scholar
  14. Crotty S, Felgner P, Davies H, Glidewell J, Villarreal L, Ahmed R (2003) Cutting edge: long-term B cell memory in humans after smallpox vaccination. J Immunol 171:4969–4973PubMedGoogle Scholar
  15. Crowe JE Jr (2007) Genetic predisposition for adverse events after vaccination. J Infect Dis 196:176–177PubMedCrossRefGoogle Scholar
  16. Demkowicz WE Jr, Littaua RA, Wang J, Ennis FA (1996) Human cytotoxic T-cell memory: long-lived responses to Vaccinia virus. J Virol 70:2627–2631PubMedGoogle Scholar
  17. Earl PL, Moss B, Wyatt LS, Carroll MW (2001) Generation of recombinant Vaccinia viruses. Curr Protoc Protein Sci Chapter 5:Unit5.13Google Scholar
  18. Eerola I, Boon LM, Mulliken JB, Burrows PE, Dompmartin A, Watanabe S, Vanwijck R, Vikkula M (2003) Capillary malformation-arteriovenous malformation, a new clinical and genetic disorder caused by RASA1 mutations. Am J Hum Genet 73:1240–1249PubMedCrossRefGoogle Scholar
  19. Ehrhardt A, Ehrhardt GR, Guo X, Schrader JW (2002) Ras and relatives—job sharing and networking keep an old family together. Exp Hematol 30:1089–1106PubMedCrossRefGoogle Scholar
  20. Elenkov IJ, Wilder RL, Chrousos GP, Vizi ES (2000) The sympathetic nerve—an integrative interface between two supersystems: the brain and the immune system. Pharmacol Rev 52:595–638PubMedGoogle Scholar
  21. Finley MJ, Happel CM, Kaminsky DE, Rogers TJ (2008) Opioid and nociceptin receptors regulate cytokine and cytokine receptor expression. Cell Immunol 252:146–154PubMedCrossRefGoogle Scholar
  22. Florio SK, Prusti RK, Beavo JA (1996) Solubilization of membrane-bound rod phosphodiesterase by the rod phosphodiesterase recombinant delta subunit. J Biol Chem 271:24036–24047PubMedCrossRefGoogle Scholar
  23. Frey SE, Newman FK, Cruz J, Shelton WB, Tennant JM, Polach T, Rothman AL, Kennedy JS, Wolff M, Belshe RB, Ennis FA (2002) Dose-related effects of smallpox vaccine. N Engl J Med 346:1275–1280PubMedCrossRefGoogle Scholar
  24. Friedman E, Gejman PV, Martin GA, McCormick F (1993) Nonsense mutations in the C-terminal SH2 region of the GTPase activating protein (GAP) gene in human tumours. Nat Genet 5:242–247PubMedCrossRefGoogle Scholar
  25. Fulginiti VA (2003) Risks of smallpox vaccination. JAMA 290:1452 (author reply 1452)Google Scholar
  26. Fulginiti VA, Papier A, Lane JM, Neff JM, Henderson DA (2003) Smallpox vaccination: a review, part II. Adverse events. Clin Infect Dis 37:251–271PubMedCrossRefGoogle Scholar
  27. Goldrath AW, Bogatzki LY, Bevan MJ (2000) Naive T cells transiently acquire a memory-like phenotype during homeostasis-driven proliferation. J Exp Med 192:557–564PubMedCrossRefGoogle Scholar
  28. Gronostajski RM (2000) Roles of the NFI/CTF gene family in transcription and development. Gene 249:31–45PubMedCrossRefGoogle Scholar
  29. Grunder A, Qian F, Ebel TT, Mincheva A, Lichter P, Kruse U, Sippel AE (2003) Genomic organization, splice products and mouse chromosomal localization of genes for transcription factor Nuclear Factor One. Gene 304:171–181PubMedCrossRefGoogle Scholar
  30. Hammarlund E, Lewis MW, Hansen SG, Strelow LI, Nelson JA, Sexton GJ, Hanifin JM, Slifka MK (2003) Duration of antiviral immunity after smallpox vaccination. Nat Med 9:1131–1137PubMedCrossRefGoogle Scholar
  31. Hanai N, Nagata K, Kawajiri A, Shiromizu T, Saitoh N, Hasegawa Y, Murakami S, Inagaki M (2004) Biochemical and cell biological characterization of a mammalian septin, Sept11. FEBS Lett 568:83–88PubMedCrossRefGoogle Scholar
  32. Haralambieva IH, Ovsyannikova IG, Dhiman N, Kennedy RB, O’Byrne M, Pankratz VS, Jacobson RM, Poland GA (2011) Common SNPs/haplotypes in IL18R1 and IL18 genes are associated with variations in humoral immunity to smallpox vaccination in Caucasians and African Americans. J Infect Dis 204:433–441PubMedCrossRefGoogle Scholar
  33. Hattori E, Liu C, Badner JA, Bonner TI, Christian SL, Maheshwari M, Detera-Wadleigh SD, Gibbs RA, Gershon ES (2003) Polymorphisms at the G72/G30 gene locus, on 13q33, are associated with bipolar disorder in two independent pedigree series. Am J Hum Genet 72:1131–1140PubMedCrossRefGoogle Scholar
  34. Hu X, Stern HM, Ge L, O’Brien C, Haydu L, Honchell CD, Haverty PM, Peters BA, Wu TD, Amler LC, Chant J, Stokoe D, Lackner MR, Cavet G (2009) Genetic alterations and oncogenic pathways associated with breast cancer subtypes. Mol Cancer Res 7:511–522PubMedCrossRefGoogle Scholar
  35. Itoh N, Yonehara S, Ishii A, Yonehara M, Mizushima S, Sameshima M, Hase A, Seto Y, Nagata S (1991) The polypeptide encoded by the cDNA for human cell surface antigen Fas can mediate apoptosis. Cell 66:233–243PubMedCrossRefGoogle Scholar
  36. Jeannet G, Boudousquie C, Gardiol N, Kang J, Huelsken J, Held W (2010) Essential role of the Wnt pathway effector Tcf-1 for the establishment of functional CD8 T cell memory. Proc Natl Acad Sci USA 107:9777–9782PubMedCrossRefGoogle Scholar
  37. Kennedy R, Pankratz VS, Swanson E, Watson D, Golding H, Poland GA (2009a) Statistical approach to estimate Vaccinia-specific neutralizing antibody titers using a high throughput assay. Clin Vaccine Immunol 16(8):1105–1112PubMedCrossRefGoogle Scholar
  38. Kennedy RB, Ovsyannikova IG, Jacobson RM, Poland GA (2009b) The immunology of smallpox vaccines. Curr Opin Immunol 21:314–320PubMedCrossRefGoogle Scholar
  39. Kennedy RB, Ovsyannikova IG, Pankratz VS, Vierkant RA, Jacobson RM, Ryan MA, Poland GA (2009c) Gender effects on humoral immune responses to smallpox vaccine. Vaccine 27(25–26):3319–3323PubMedCrossRefGoogle Scholar
  40. Li L, Yee C, Beavo JA (1999) CD3- and CD28-dependent induction of PDE7 required for T cell activation. Science 283:848–851PubMedCrossRefGoogle Scholar
  41. Lin CS, Park T, Chen ZP, Leavitt J (1993) Human plastin genes. Comparative gene structure, chromosome location, and differential expression in normal and neoplastic cells. J Biol Chem 268:2781–2792PubMedGoogle Scholar
  42. Lorenz B, Migliaccio C, Lichtner P, Meyer C, Strom TM, D’Urso M, Becker J, Ciccodicola A, Meitinger T (1998) Cloning and gene structure of the rod cGMP phosphodiesterase delta subunit gene (PDED) in man and mouse. Eur J Hum Genet 6:283–290PubMedCrossRefGoogle Scholar
  43. Lowin B, Hahne M, Mattmann C, Tschopp J (1994) Cytolytic T-cell cytotoxicity is mediated through perforin and Fas lytic pathways. Nature 370:650–652. doi:10.1038/370650a0 PubMedCrossRefGoogle Scholar
  44. Lysle DT, Coussons ME, Watts VJ, Bennett EH, Dykstra LA (1993) Morphine-induced alterations of immune status: dose dependency, compartment specificity and antagonism by naltrexone. J Pharmacol Exp Ther 265:1071–1078PubMedGoogle Scholar
  45. Malnic B, Godfrey PA, Buck LB (2004) The human olfactory receptor gene family. Proc Natl Acad Sci USA 101:2584–2589PubMedCrossRefGoogle Scholar
  46. McKenzie E, Tyson K, Stamps A, Smith P, Turner P, Barry R, Hircock M, Patel S, Barry E, Stubberfield C, Terrett J, Page M (2000) Cloning and expression profiling of Hpa2, a novel mammalian heparanase family member. Biochem Biophys Res Commun 276:1170–1177PubMedCrossRefGoogle Scholar
  47. Mitra-Kaushik S, Cruz J, Stern LJ, Ennis FA, Terajima M (2007) Human cytotoxic CD4+ T cells recognize HLA-DR1-restricted epitopes on Vaccinia virus proteins A24R and D1R conserved among poxviruses. J Immunol 179:1303–1312PubMedGoogle Scholar
  48. Nemoto F, Okazaki T, Mizushima H, Muller WE, Kuchino Y (1991) Nucleotide sequence of the human tRNA(UUGGln) gene. Nucleic Acids Res 19:2779PubMedCrossRefGoogle Scholar
  49. Omori K, Kotera J (2007) Overview of PDEs and their regulation. Circ Res 100:309–327PubMedCrossRefGoogle Scholar
  50. Ovsyannikova IG, Jacobson RM, Ryan JE, Vierkant RA, Pankratz VS, Jacobsen SJ, Poland GA (2005) HLA class II alleles and measles virus-specific cytokine immune response following two doses of measles vaccine. Immunogenetics 56:798–807PubMedCrossRefGoogle Scholar
  51. Ovsyannikova IG, Vierkant RA, Pankratz VS, Jacobson RM, Poland GA (2011) Human leukocyte antigen genotypes in the genetic control of adaptive immune responses to smallpox vaccine. J Infect Dis 203:1546–1555PubMedCrossRefGoogle Scholar
  52. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904–909PubMedCrossRefGoogle Scholar
  53. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  54. Puissant-Lubrano B, Bossi P, Gay F, Crance JM, Bonduelle O, Garin D, Bricaire F, Autran B, Combadiere B (2010) Control of Vaccinia virus skin lesions by long-term-maintained IFN-gamma+ TNF-alpha+ effector/memory CD4+ lymphocytes in humans. J Clin Invest 120:1636–1644PubMedCrossRefGoogle Scholar
  55. Reif DM, McKinney BA, Motsinger AA, Chanock SJ, Edwards KM, Rock MT, Moore JH, Crowe JE (2008) Genetic basis for adverse events after smallpox vaccination. J Infect Dis 198:16–22PubMedCrossRefGoogle Scholar
  56. Rincon M, Enslen H, Raingeaud J, Recht M, Zapton T, Su MS, Penix LA, Davis RJ, Flavell RA (1998) Interferon-gamma expression by Th1 effector T cells mediated by the p38 MAP kinase signaling pathway. EMBO J 17:2817–2829PubMedCrossRefGoogle Scholar
  57. Ryan JE, Ovsyannikova IG, Dhiman N, Pinsky NA, Vierkant RA, Jacobson RM, Poland GA (2005) Inter-operator variation in ELISPOT analysis of measles virus-specific IFN-gamma-secreting T cells. Scand J Clin Lab Invest 65:681–689PubMedCrossRefGoogle Scholar
  58. Ryan JE, Dhiman N, Ovsyannikova IG, Vierkant RA, Pankratz VS, Poland GA (2009) Response surface methodology to determine optimal cytokine responses in human peripheral blood mononuclear cells after smallpox vaccination. J Immunol Methods 341:97–105PubMedCrossRefGoogle Scholar
  59. Sagara N, Katoh M (2000) Mitomycin C resistance induced by TCF-3 overexpression in gastric cancer cell line MKN28 is associated with DT-diaphorase down-regulation. Cancer Res 60:5959–5962PubMedGoogle Scholar
  60. Schaid DJ, Batzler AJ, Jenkins GD, Hildebrandt MA (2006) Exact tests of Hardy–Weinberg equilibrium and homogeneity of disequilibrium across strata. Am J Hum Genet 79:1071–1080PubMedCrossRefGoogle Scholar
  61. Schuberth C, Buchberger A (2008) UBX domain proteins: major regulators of the AAA ATPase Cdc48/p97. Cell Mol Life Sci 65:2360–2371PubMedCrossRefGoogle Scholar
  62. Sheeter D, Du P, Rought S, Richman D, Corbeil J (2003) Surface CD4 expression modulated by a cellular factor induced by HIV type 1 infection. AIDS Res Hum Retroviruses 19:117–123PubMedCrossRefGoogle Scholar
  63. Stanley SL Jr, Frey SE, Taillon-Miller P, Guo J, Miller RD, Koboldt DC, Elashoff M, Christensen R, Saccone NL, Belshe RB (2007) The immunogenetics of smallpox vaccination. J Infect Dis 196:212–219PubMedCrossRefGoogle Scholar
  64. Sugiura T, Noguchi Y, Sakurai K, Hattori C (2008) Protein phosphatase 1H, overexpressed in colon adenocarcinoma, is associated with CSE1L. Cancer Biol Ther 7:285–292PubMedCrossRefGoogle Scholar
  65. Sullivan KA, Liao YC, Alborzi A, Beiderman B, Chang FH, Masters SB, Levinson AD, Bourne HR (1986) Inhibitory and stimulatory G proteins of adenylate cyclase: cDNA and amino acid sequences of the alpha chains. Proc Natl Acad Sci USA 83:6687–6691PubMedCrossRefGoogle Scholar
  66. Team RDC (2008) R: a language and environment for statistical computingGoogle Scholar
  67. Trahey M, Wong G, Halenbeck R, Rubinfeld B, Martin GA, Ladner M, Long CM, Crosier WJ, Watt K, Koths K et al (1988) Molecular cloning of two types of GAP complementary DNA from human placenta. Science 242:1697–1700PubMedCrossRefGoogle Scholar
  68. Tybulewicz VL, Henderson RB (2009) Rho family GTPases and their regulators in lymphocytes. Nat Rev Immunol 9:630–644PubMedCrossRefGoogle Scholar
  69. Wang Q, Curran ME, Splawski I, Burn TC, Millholland JM, VanRaay TJ, Shen J, Timothy KW, Vincent GM, de Jager T, Schwartz PJ, Toubin JA, Moss AJ, Atkinson DL, Landes GM, Connors TD, Keating MT (1996) Positional cloning of a novel potassium channel gene: KVLQT1 mutations cause cardiac arrhythmias. Nat Genet 12:17–23PubMedCrossRefGoogle Scholar
  70. Wang J, Charboneau R, Balasubramanian S, Barke RA, Loh HH, Roy S (2001) Morphine modulates lymph node-derived T lymphocyte function: role of caspase-3, -8, and nitric oxide. J Leukoc Biol 70:527–536PubMedGoogle Scholar
  71. Witherden DA, Verdino P, Rieder SE, Garijo O, Mills RE, Teyton L, Fischer WH, Wilson IA, Havran WL (2010) The junctional adhesion molecule JAML is a costimulatory receptor for epithelial gammadelta T cell activation. Science 329:1205–1210PubMedCrossRefGoogle Scholar
  72. Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, Bar-Even A, Horn-Saban S, Safran M, Domany E, Lancet D, Shmueli O (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21:650–659PubMedCrossRefGoogle Scholar
  73. Yokoyama C, Miyata A, Ihara H, Ullrich V, Tanabe T (1991) Molecular cloning of human platelet thromboxane A synthase. Biochem Biophys Res Commun 178:1479–1484PubMedCrossRefGoogle Scholar
  74. Zhao DM, Yu S, Zhou X, Haring JS, Held W, Badovinac VP, Harty JT, Xue HH (2010) Constitutive activation of Wnt signaling favors generation of memory CD8 T cells. J Immunol 184:1191–1199PubMedCrossRefGoogle Scholar
  75. Zhou X, Yu S, Zhao DM, Harty JT, Badovinac VP, Xue HH (2010) Differentiation and persistence of memory CD8(+) T cells depend on T cell factor 1. Immunity 33:229–240PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Richard B. Kennedy
    • 2
    • 5
  • Inna G. Ovsyannikova
    • 2
    • 6
  • V. Shane Pankratz
    • 3
  • Iana H. Haralambieva
    • 2
    • 7
  • Robert A. Vierkant
    • 3
  • Robert M. Jacobson
    • 4
    • 8
  • Gregory A. Poland
    • 1
    • 2
    • 4
  1. 1.Mayo Vaccine Research GroupMayo ClinicRochesterUSA
  2. 2.Program in Translational Immunovirology and BiodefenseMayo ClinicRochesterUSA
  3. 3.Division of Biomedical Statistics and InformaticsMayo ClinicRochesterUSA
  4. 4.Department of Pediatric and Adolescent MedicineMayo ClinicRochesterUSA
  5. 5.Mayo Vaccine Research GroupMayo ClinicRochesterUSA
  6. 6.Mayo Vaccine Research GroupMayo ClinicRochesterUSA
  7. 7.Mayo Vaccine Research GroupMayo ClinicRochesterUSA
  8. 8.Mayo Vaccine Research GroupMayo ClinicRochesterUSA

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