Systems vaccinology: A promise for the young and the poor

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 370, Issue 1671, 2015, Pages

  Amenyogbe, Nelly ^a   Levy, Ofer ^b,c   Kollmann, Tobias R ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b BOSTON CHILDREN S HOSPITAL   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Immune response; Ontogeny; Systems vaccinology; Vaccine response

Indexed keywords

CHILD HEALTH; HEALTH RISK; IMMUNE RESPONSE; INFANT MORTALITY; INFECTIOUS DISEASE; VACCINATION; VULNERABILITY;

VACCINE;

AGING; COMMUNICABLE DISEASE CONTROL; ECONOMICS; HUMAN; IMMUNOLOGY; POVERTY; PROCEDURES; SYSTEM ANALYSIS;

AGING; COMMUNICABLE DISEASE CONTROL; HUMANS; POVERTY; SYSTEMS ANALYSIS; VACCINES;

EID: 84929246691     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2014.0340     Document Type: Article

References (56)

1. Hostetter MK. 2012 What we don’t see. N. Engl. J. Med. 366, 1328–1334. (doi:10.1056/NEJMra1111421)
2. Liu L et al. 2012 Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since 2000. Lancet 379, 2151–2161. (doi:10.1016/S0140-6736(12)60560-1)
3. Bhutta ZA, Black RE. 2013 Global maternal, newborn, and child health: so near and yet so far. N. Engl. J. Med. 369, 2226–2235. (doi:10.1056/NEJMra1111853)
4. Sepulveda J, Murray C. 2014 The state of global health in 2014. Science 345, 1275–1278. (doi:10.1126/science.1257099)
5. Chan M, Lake A. 2012 Towards ending preventable child deaths. Lancet 379, 2119–2120. (doi:10.1016/S0140-6736(12)60908-8)
6. Ghazal P, Dickinson P, Smith CL. 2013 Early life response to infection. Curr. Opin. Infect. Dis 26, 213–218. (doi:10.1097/QCO.0b013e32835fb8bf)
7. Darmstadt GL, Kinney MV, Chopra M, Cousens S, Kak L, Paul VK, Martines J, Bhutta ZA, Lawn JE. 2014 Who has been caring for the baby? Lancet 384, 174–188. (doi:10.1016/S0140-6736(14)60458-X)
8. Lawn JE et al. 2014 Every newborn: progress, priorities, and potential beyond survival. Lancet 384, 189–205. (doi:10.1016/S0140-6736(14)60496-7)
9. Andre FE et al. 2008 Vaccination greatly reduces disease, disability, death and inequity worldwide. Bull. World Health Organ. 86, 140–146. (doi:10.2471/BLT.07.040089)
10. Whitney CG, Zhou F, Singleton J, Schuchat A. 2014 Benefits from immunization during the vaccines for children program era—United States, 1994–2013. MMWR Morb. Mortal. Wkly Rep. 63, 352–355.
11. Roush SW, Murphy TV. 2007 Historical comparisons of morbidity and mortality for vaccine-preventable diseases in the United States. JAMA 298, 2155–2163. (doi:10.1001/jama.298.18.2155)
12. McMorrow M. 2006 Vaccine preventable deaths and the global immunization vision and strategy, 2006–2015. MMWR Morb. Mortal. Wkly Rep. 55, 511–515.
13. Plotkin SA. 2010 Correlates of protection induced by vaccination. Clin. Vaccine Immunol. 17, 1055–1065. (doi:10.1128/CVI.00131-10)
14. Barnighausen T, Bloom DE, Cafiero-Fonseca ET, O’Brien JC. 2014 Valuing vaccination. Proc. Natl Acad. Sci. USA 111, 12313–12319. (doi:10.1073/pnas.1400475111)
15. Anon. 1999 Impact of vaccines universally recommended for children: United States, 1990–1998. MMWR Morb. Mortal. Wkly Rep. 48, 243–248.
16. Pulendran B, Ahmed R. 2011 Immunological mechanisms of vaccination. Nat. Immunol. 12, 509–517. (doi:10.1038/ni.2039)
17. Lernout T, Theeten H, Leuridan E, Van Damme P. 2014 Do vaccines save lives? Yes they do! Acta Med. Portuguesa 27, 160–162.
18. Clemens J, Holmgren J, Kaufmann SH, Mantovani A. 2010 Ten years of the global alliance for vaccines and immunization: challenges and progress. Nat. Immunol. 11, 1069–1072. (doi:10.1038/ni1210-1069)
19. Clemens J, Jodar L. 2005 Introducing new vaccines into developing countries: obstacles, opportunities and complexities. Nat. Med. 11(Suppl. 4), S12–S15. (doi:10.1038/nm1225)
20. Kollmann TR. 2013 Variation between populations in the innate immune response to vaccine adjuvants. Front. Immunol. 4, 81. (doi:10.3389/fimmu.2013.00081)
21. WHO. 2013 Correlates of vaccine-induced protection: methods and implications. Geneva: Initiative for Vaccine Research (IVR), of the Department of Immunization, Vaccines and Biologicals. See http://www.who.int/vaccines-documents/.
22. Mangtani P et al. 2014 Protection by BCG vaccine against tuberculosis: a systematic review of randomized controlled trials. Clin. Infect. Dis. 58, 470–480. (doi:10.1093/cid/cit790)
23. Kagina BM et al. 2010 Specific T cell frequency and cytokine expression profile do not correlate with protection against tuberculosis after bacillus Calmette–Guerin vaccination of newborns. Am. J. Respir. Crit. Care Med. 182, 1073–1079. (doi:10.1164/rccm.201003-0334OC)
24. Netea MG, van Crevel R. 2014 BCG-induced protection: effects on innate immune memory. Semin. Immunol. 26, 512–517. (doi:10.1016/j.smim.2014.09.006)
25. Pulendran B. 2014 Systems vaccinology: probing humanity’s diverse immune systems with vaccines. Proc. Natl Acad. Sci. USA 111, 12300–12306. (doi:10.1073/pnas.1400476111)
26. Poland GA, Kennedy RB, McKinney BA, Ovsyannikova IG, Lambert ND, Jacobson RM, Oberg AL. 2013 Vaccinomics, adversomics, and the immune response network theory: individualized vaccinology in the 21st century. Semin. Immunol. 25, 89–103. (doi:10.1016/j.smim.2013.04.007)
27. Zhang W, Li F, Nie L. 2010 Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies. Microbiology 156, 287–301. (doi:10.1099/mic.0.034793-0)
28. Obermoser G et al. 2013 Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines. Immunity 38, 831–844. (doi:10.1016/j.immuni.2012.12.008)
29. Oh JZ et al. 2014 TLR5-mediated sensing of gut microbiota is necessary for antibody responses to seasonal influenza vaccination. Immunity 41, 478–492. (doi:10.1016/j.immuni.2014.08.009)
30. Mooney M, McWeeney S, Canderan G, Sekaly RP. 2013 A systems framework for vaccine design. Curr. Opin. Immunol. 25, 551–555. (doi:10.1016/j.coi.2013.09.014)
31. Haining WN, Pulendran B. 2012 Identifying Gnostic predictors of the vaccine response. Curr. Opin. Immunol. 24, 332–336. (doi:10.1016/j.coi.2012.03.010)
32. Hegde PS, White IR, Debouck C. 2003 Interplay of transcriptomics and proteomics. Curr. Opin. Biotechnol. 14, 647–651. (doi:10.1016/j.copbio.2003.10.006)
33. Mootha VK et al. 2003 Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115, 629–640. (doi:10.1016/S0092-8674(03)00926-7)
34. Alter O, Golub GH. 2004 Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription. Proc. Natl Acad. Sci. USA 101, 16577–16582. (doi:10.1073/pnas.0406767101)
35. Xia J, Fjell CD, Mayer ML, Pena OM, Wishart DS, Hancock RE. 2013 INMEX: a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res. 41, W63–W70. (doi:10.1093/nar/gkt338)
36. Le Cao KA, Gonzalez I, Dejean S. 2009 IntegrOmics: an R package to unravel relationships between two omics datasets. Bioinformatics 25, 2855–2856. (doi:10.1093/bioinformatics/btp515)
37. Day RS et al. 2011 Identifier mapping performance for integrating transcriptomics and proteomics experimental results. BMC Bioinformatics 12, 213. (doi:10.1186/1471-2105-12-213)
38. Gunther OP, Shin H, Ng RT, McMaster WR, McManus BM, Keown PA, Tebbutt SJ, Le Cao KA. 2014 Novel multivariate methods for integration of genomics and proteomics data: applications in a kidney transplant rejection study. OMICS 18, 682–695. (doi:10.1089/omi.2014.0062)
39. Maecker HT, McCoy JP, Nussenblatt R. 2012 Standardizing immunophenotyping for the Human Immunology Project. Nat. Rev. 12, 191–200. (doi:10.1038/nri3158)
40. Porichis F et al. 2014 High-throughput detection of miRNAs and gene-specific mRNA at the single-cell level by flow cytometry. Nat. Commun. 5, 5641. (doi:10.1038/ncomms6641)
41. Dvinge H, Ries RE, Ilagan JO, Stirewalt DL, Meshinchi S, Bradley RK. 2014 Sample processing obscures cancer-specific alterations in leukemic transcriptomes. Proc. Natl Acad. Sci. USA 111, 16802–16807. (doi:10.1073/pnas.1413374111)
42. Pinto J, Domingues MR, Galhano E, Pita C, Almeida Mdo C, Carreira IM, Gil AM. 2014 Human plasma stability during handling and storage: impact on NMR metabolomics. Analyst 139, 1168–1177. (doi:10.1039/c3an02188b)
43. Lista S, Faltraco F, Hampel H. 2013 Biological and methodical challenges of blood-based proteomics in the field of neurological research. Prog. Neurobiol. 101–102, 18–34. (doi:10.1016/j.pneurobio.2012.06.006)
44. Bernini P, Bertini I, Luchinat C, Nincheri P, Staderini S, Turano P. 2011 Standard operating procedures for pre-analytical handling of blood and urine for metabolomic studies and biobanks. J. Biomol. NMR 49, 231–243. (doi:10.1007/s10858-011-9489-1)
45. Ostroff R, Foreman T, Keeney TR, Stratford S, Walker JJ, Zichi D. 2010 The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array. J. Proteomics 73, 649–666. (doi:10.1016/j.jprot.2009.09.004)
46. Banks RE, Stanley AJ, Cairns DA, Barrett JH, Clarke P, Thompson D, Selby PJ. 2005 Influences of blood sample processing on low-molecular-weight proteome identified by surface-enhanced laser desorption/ionization mass spectrometry. Clin. Chem. 51, 1637–1649. (doi:10.1373/clinchem.2005.051417)
47. Wang IM, Bett AJ, Cristescu R, Loboda A, ter Meulen J. 2012 Transcriptional profiling of vaccineinduced immune responses in humans and nonhuman primates. Microb. Biotechnol. 5, 177–187. (doi:10.1111/j.1751-7915.2011.00317.x)
48. Cao RG et al. 2014 Differences in antibody responses between trivalent inactivated influenza vaccine and live attenuated influenza vaccine correlate with the kinetics and magnitude of interferon signaling in children. J. Infect. Dis. 210, 224–233. (doi:10.1093/infdis/jiu079)
49. Clark A, Sanderson C. 2009 Timing of children’s vaccinations in 45 low-income and middle-income countries: an analysis of survey data. Lancet 373, 1543–1549. (doi:10.1016/S0140-6736(09)60317-2)
50. Lewis DB, Wilson C. 2011 Developmental immunology and role of host defenses in fetal and neonatal susceptibility to infection. In Infectious diseases of the fetus and newborn infant (eds JS Remington, JOK Christopher, B Wilson, CJ Baker), pp. 80–191, 7 edn. Philadelphia, PA: Elsevier Saunders.
51. Kollmann TR, Levy O, Montgomery RR, Goriely S. 2012 Innate immune function by toll-like receptors: distinct responses in newborns and the elderly. Immunity 37, 771–783. (doi:10.1016/j.immuni.2012.10.014)
52. Dowling DJ, Levy O. 2014 Ontogeny of early life immunity. Trends Immunol. 35, 299–310. (doi:10.1016/j.it.2014.04.007)
53. Tsang JS et al. 2014 Global analyses of human immune variation reveal baseline predictors of postvaccination responses. Cell 157, 499–513. (doi:10.1016/j.cell.2014.03.031)
54. Smith CL et al. 2014 Identification of a human neonatal immune-metabolic network associated with bacterial infection. Nat. Commun. 5, 4649. (doi:10.1038/ncomms5649)
55. Mejias A, Ramilo O. 2014 Transcriptional profiling in infectious diseases: ready for prime time? J. Infect. 68(Suppl. 1), S94–S99. (doi:10.1016/j.jinf.2013.09.018)
56. Guerrant RL. 1997 Why America must care about tropical medicine: threats to global health and security from tropical infectious diseases (ASTHM Presidential address). Deerfield, IL: ASTHM. See http://www.astmh.org/AM/Template.cfm?Section=Who_We_Are&Template=/CM/ContentDisplay.cfm&ContentID=1342