New technologies for vaccine development

Vaccines offer protection against infectious diseases, but the successes from the years of development have been mixed. Some diseases have been effectively controlled or eradicated through vaccination, whereas treatments for a number of diseases, especially the reemerging diseases, currently do not exist. Improved understanding of pathogen variability as well as of the diversity of the human immune system, plus technological advances in genetic and molecular biology provide better insights in the host–pathogen interaction and new avenues for vaccine development. In this article we discuss the latest trends in vaccine research with focus on epitope‐based DNA vaccines and trafficking components for efficient vaccine delivery. These approaches are promising in dealing with host and pathogen diversity as well as with diversity within human populations. Drug Dev. Res. 62:383–392, 2004. © 2004 Wiley‐Liss, Inc.

[1]  Vladimir Brusic,et al.  Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens , 2004, ISMB/ECCB.

[2]  L. B. de Arruda,et al.  DNA vaccine encoding human immunodeficiency virus‐1 Gag, targeted to the major histocompatibility complex II compartment by lysosomal‐associated membrane protein, elicits enhanced long‐term memory response , 2004, Immunology.

[3]  S. Brunak,et al.  SARS CTL vaccine candidates; HLA supertype‐, genome‐wide scanning and biochemical validation , 2004, Tissue antigens.

[4]  D. Flower,et al.  Identifiying Human MHC Supertypes Using Bioinformatic Methods , 2004, The Journal of Immunology.

[5]  O. Lund,et al.  Definition of supertypes for HLA molecules using clustering of specificity matrices , 2004, Immunogenetics.

[6]  C. Leclerc,et al.  New tools for antigen delivery to the MHC class I pathway. , 2004, Trends in immunology.

[7]  D. Venter,et al.  Chips with everything: DNA microarrays in infectious diseases. , 2004, The Lancet. Infectious diseases.

[8]  Mark Peakman,et al.  Autoreactive T cell responses show proinflammatory polarization in diabetes but a regulatory phenotype in health. , 2004, The Journal of clinical investigation.

[9]  Vladimir Brusic,et al.  Bioinformatics tools for identifying T-cell epitopes , 2004 .

[10]  Channa K. Hattotuwagama,et al.  Quantitative online prediction of peptide binding to the major histocompatibility complex. , 2004, Journal of molecular graphics & modelling.

[11]  Jeannette Adu-Bobie,et al.  The genome revolution in vaccine research. , 2004, Current issues in molecular biology.

[12]  G. Dietrich.  DNA microarrays in vaccine research. , 2003, Current opinion in molecular therapeutics (Print).

[13]  Darren R Flower,et al.  Towards in silico prediction of immunogenic epitopes. , 2003, Trends in immunology.

[14]  Genhong Cheng,et al.  The Art of War: Innate and adaptive immune responses , 2003, Cellular and Molecular Life Sciences CMLS.

[15]  Yingdong Zhao,et al.  Application of support vector machines for T-cell epitopes prediction , 2003, Bioinform..

[16]  I. C. Leão,et al.  HIV-1 p55Gag Encoded in the Lysosome-associated Membrane Protein-1 as a DNA Plasmid Vaccine Chimera Is Highly Expressed, Traffics to the Major Histocompatibility Class II Compartment, and Elicits Enhanced Immune Responses* , 2003, Journal of Biological Chemistry.

[17]  K. Brown,et al.  Genetic Vaccines and Therapy , 2003 .

[18]  K. Schulten,et al.  Molecular biomimetics: nanotechnology through biology , 2003, Nature materials.

[19]  W. Heath,et al.  The role of dendritic cell subsets in immunity to viruses. , 2003, Current opinion in immunology.

[20]  C. Franco-Paredes,et al.  Infectious Diseases, Non–Zero‐Sum Thinking, and the Developing World , 2003, The American journal of the medical sciences.

[21]  T. Ben-Yedidia,et al.  Old and new vaccine approaches. , 2003, International immunopharmacology.

[22]  G. Ada.  Progress towards achieving new vaccine and vaccination goals , 2003, Internal medicine journal.

[23]  Pingping Guan,et al.  MHCPred: a server for quantitative prediction of peptide-MHC binding , 2003, Nucleic Acids Res..

[24]  S. Brunak,et al.  Predicting proteasomal cleavage sites: a comparison of available methods. , 2003, International immunology.

[25]  R. Zagursky,et al.  Bioinformatics: how it is being used to identify bacterial vaccine candidates , 2003, Expert review of vaccines.

[26]  I. C. Leão,et al.  Dengue 2 PreM-E/LAMP chimera targeted to the MHC class II compartment elicits long-lasting neutralizing antibodies. , 2003, Vaccine.

[27]  G. Grandi.  Rational antibacterial vaccine design through genomic technologies. , 2003, International journal for parasitology.

[28]  R. Edelman.  Survey of human-use adjuvants , 2003, Expert review of vaccines.

[29]  C. Pinilla,et al.  Use of combinatorial peptide libraries for T-cell epitope mapping. , 2003, Methods.

[30]  Vladimir Brusic,et al.  MAGE-6 encodes HLA-DRbeta1*0401-presented epitopes recognized by CD4+ T cells from patients with melanoma or renal cell carcinoma. , 2003, Clinical cancer research : an official journal of the American Association for Cancer Research.

[31]  S. Yi,et al.  Tolerability and single dose pharmacokinetics of a new PDE5 inhibitor, DA‐8159 in healthy male subjects , 2003 .

[32]  T. Elliott,et al.  Assembly and export of MHC class I peptide ligands. , 2003, Current opinion in immunology.

[33]  C. Hung,et al.  Improving DNA vaccine potency via modification of professional antigen presenting cells. , 2003, Current opinion in molecular therapeutics.

[34]  G. Nossal.  The double helix and immunology , 2003, Nature.

[35]  M. Britschgi,et al.  Molecular aspects of drug recognition by specific T cells. , 2003, Current drug targets.

[36]  G. Bishop,et al.  Antigen-specific B-lymphocyte activation. , 2003, Critical reviews in immunology.

[37]  D. Munn,et al.  Macrophages and the regulation of self-reactive T cells. , 2003, Current pharmaceutical design.

[38]  K. Lam,et al.  Combinatorial peptide library methods for immunobiology research. , 2003, Experimental hematology.

[39]  Vladimir Brusic,et al.  Bioinformatic strategies for better understanding of immune function , 2003, Silico Biol..

[40]  Jürgen Braun,et al.  Age at disease onset and diagnosis delay in HLA-B27 negative vs. positive patients with ankylosing spondylitis , 2003, Rheumatology International.

[41]  D. Weiner,et al.  T-cell responses induced in normal volunteers immunized with a DNA-based vaccine containing HIV-1 env and rev , 2002, AIDS.

[42]  B. Schweiger,et al.  Antigenic drift and variability of influenza viruses , 2002, Medical Microbiology and Immunology.

[43]  R. Levy,et al.  Immunogenicity of a plasmid DNA vaccine encoding chimeric idiotype in patients with B-cell lymphoma. , 2002, Cancer research.

[44]  F. Weber,et al.  Antigenic drift, antigenic shift and interferon antagonists: how bunyaviruses counteract the immune system. , 2002, Virus research.

[45]  P. van Endert,et al.  Powering the peptide pump: TAP crosstalk with energetic nucleotides. , 2002, Trends in biochemical sciences.

[46]  Hassan M E Azzazy,et al.  Phage display technology: clinical applications and recent innovations. , 2002, Clinical biochemistry.

[47]  E. Gilboa,et al.  Enhanced induction of telomerase-specific CD4(+) T cells using dendritic cells transfected with RNA encoding a chimeric gene product. , 2002, Cancer research.

[48]  Vladimir Brusic,et al.  Prediction of promiscuous peptides that bind HLA class I molecules , 2002, Immunology and cell biology.

[49]  A. Jabri,et al.  HLA and in vitro susceptibility to HIV infection. , 2002 .

[50]  James McCluskey,et al.  Optimization of the MHC class I peptide cargo is dependent on tapasin. , 2002, Immunity.

[51]  Fabio Grassi,et al.  Identification of a Promiscuous T-Cell Epitope in Mycobacterium tuberculosis Mce Proteins , 2002, Infection and Immunity.

[52]  Kun Yu,et al.  Methods for Prediction of Peptide Binding to MHC Molecules: A Comparative Study , 2002, Molecular medicine.

[53]  K. Porter,et al.  Synergistic neutralizing antibody response to a dengue virus type 2 DNA vaccine by incorporation of lysosome-associated membrane protein sequences and use of plasmid expressing GM-CSF. , 2001, Virology.

[54]  S. Stevanović,et al.  Combining computer algorithms with experimental approaches permits the rapid and accurate identification of T cell epitopes from defined antigens. , 2001, Journal of immunological methods.

[55]  E. Celis,et al.  Identification of helper T-cell epitopes that encompass or lie proximal to cytotoxic T-cell epitopes in the gp100 melanoma tumor antigen. , 2001, Cancer research.

[56]  J Zeleznikow,et al.  Efficient discovery of immune response targets by cyclical refinement of QSAR models of peptide binding. , 2001, Journal of molecular graphics & modelling.

[57]  Michael A. Gonzalez,et al.  From genome to vaccine: in silico predictions, ex vivo verification. , 2001, Vaccine.

[58]  Y. Liu,et al.  Dendritic Cell Subsets and Lineages, and Their Functions in Innate and Adaptive Immunity , 2001, Cell.

[59]  N. Hamasaki,et al.  Expression of lysosome-associated membrane proteins in human colorectal neoplasms and inflammatory diseases. , 2001, The American journal of pathology.

[60]  A. Goldstein,et al.  Effect of peptide-carrier coupling on peptide-specific immune responses. , 2001, Immunobiology.

[61]  Karl-Heinz Wiesmüller,et al.  Peptide Vaccines and Peptide Libraries , 2001, Biological chemistry.

[62]  M. Edidin,et al.  Selective export of MHC class I molecules from the ER after their dissociation from TAP. , 2000, Immunity.

[63]  J. Ulmer,et al.  Antigen presentation and DNA vaccines. , 2000, American journal of respiratory and critical care medicine.

[64]  Mitchell L. Cohen.  Changing patterns of infectious disease , 2000, Nature.

[65]  F. Guarnieri,et al.  Targeting antigen-specific T cells by genetically engineered antigen presenting cells A strategy for specific immunotherapy of autoimmune disease , 2000, Journal of Neuroimmunology.

[66]  R. Doebele,et al.  Accessory molecules for MHC class II peptide loading. , 2000, Current opinion in immunology.

[67]  S. Pierce,et al.  A Role for MHC Class II Antigen Processing in B Cell Development , 2000, International reviews of immunology.

[68]  R. Tampé,et al.  Function of the transport complex TAP in cellular immune recognition. , 1999, Biochimica et biophysica acta.

[69]  J. Sidney,et al.  Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism , 1999, Immunogenetics.

[70]  A. Sidoli,et al.  Cutting edge: identification of novel T cell epitopes in Lol p5a by computational prediction. , 1999, Journal of immunology.

[71]  S. Pierce,et al.  MHC class II antigen processing in B cells: accelerated intracellular targeting of antigens. , 1999, Journal of immunology.

[72]  U. Şahin,et al.  Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices , 1999, Nature Biotechnology.

[73]  S O'Brien,et al.  New class I and II HLA alleles strongly associated with opposite patterns of progression to AIDS. , 1999, Journal of immunology.

[74]  J. Neefjes.  CIIV, MIIC and other compartments for MHC class II loading , 1999, European journal of immunology.

[75]  G Y Ishioka,et al.  Utilization of MHC class I transgenic mice for development of minigene DNA vaccines encoding multiple HLA-restricted CTL epitopes. , 1999, Journal of immunology.

[76]  D. Baltimore,et al.  HIV's evasion of the cellular immune response , 1999, Immunological reviews.

[77]  E. Cunha-Neto.  MHC-restricted antigen presentation and recognition: constraints on gene, recombinant and peptide vaccines in humans. , 1999, Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas.

[78]  Satoru Kuhara,et al.  Use of Bonsai Decision Trees for the Identification of Potential MHC Class I Peptide Epitope Motifs , 1998, Pacific Symposium on Biocomputing.

[79]  H. Davis,et al.  DNA vaccines for viral diseases. , 1999, Microbes and infection.

[80]  C. Watts,et al.  Pathways of antigen processing and presentation. , 1999, Reviews in immunogenetics.

[81]  A. Goldberg,et al.  Degradation of cell proteins and the generation of MHC class I-presented peptides. , 1999, Annual review of immunology.

[82]  R. Alam.  A brief review of the immune system. , 1998, Primary care.

[83]  H Mamitsuka,et al.  Predicting peptides that bind to MHC molecules using supervised learning of hidden markov models , 1998, Proteins.

[84]  V. Brusic,et al.  Neural network-based prediction of candidate T-cell epitopes , 1998, Nature Biotechnology.

[85]  P. Ricciardi-Castagnoli,et al.  MHC Class II Transport from Lysosomal Compartments to the Cell Surface Is Determined by Stable Peptide Binding, But Not by the Cytosolic Domains of the α- and β-Chains , 1998, The Journal of Immunology.

[86]  J. Sidney,et al.  HLA supertypes and supermotifs: a functional perspective on HLA polymorphism. , 1998, Current opinion in immunology.

[87]  V Brusic,et al.  Relationship between peptide selectivities of human transporters associated with antigen processing and HLA class I molecules. , 1998, Journal of immunology.

[88]  Fernando Rodriguez,et al.  DNA Immunization with Minigenes: Low Frequency of Memory Cytotoxic T Lymphocytes and Inefficient Antiviral Protection Are Rectified by Ubiquitination , 1998, Journal of Virology.

[89]  E. Gilboa,et al.  Induction of primary carcinoembryonic antigen (CEA)-specific cytotoxic T lymphocytes in vitro using human dendritic cells transfected with RNA , 1998, Nature Biotechnology.

[90]  M. Dertzbaugh.  Genetically engineered vaccines: an overview. , 1998, Plasmid.

[91]  P. Cresswell,et al.  Mechanisms of MHC class I--restricted antigen processing. , 1998, Annual review of immunology.

[92]  O. Bakke,et al.  Intracellular transport of molecules engaged in the presentation of exogenous antigens. , 1998, Current topics in microbiology and immunology.

[93]  Vladimir Brusic,et al.  A neural network model approach to the study of human TAP transporter , 1998, Silico Biol..

[94]  Vladimir Brusic,et al.  MHCPEP, a database of MHC-binding peptides: update 1996 , 1997, Nucleic Acids Res..

[95]  D. Huston.  The biology of the immune system. , 1997, JAMA.

[96]  J. Manuguerra,et al.  Chimeric peptides: a new approach to enhancing the immunogenicity of peptides with low MHC class I affinity: application in antiviral vaccination. , 1997, Journal of immunology.

[97]  R. Siliciano,et al.  The Enhanced Immune Response to the HIV gp160/LAMP Chimeric Gene Product Targeted to the Lysosome Membrane Protein Trafficking Pathway* , 1997, The Journal of Biological Chemistry.

[98]  E. Thorsby,et al.  Invited anniversary review: HLA associated diseases. , 1997, Human immunology.

[99]  Vladimir Brusic,et al.  MHCPEP, a database of MHC-binding peptides: update 1996 , 1997, Nucleic Acids Res..

[100]  T. Kipps.  Human B cell biology. , 1997, International reviews of immunology.

[101]  H. Rammensee.  Antigen presentation--recent developments. , 1996, International archives of allergy and immunology.

[102]  M. V. Regenmortel,et al.  Mapping Epitope Structure and Activity: From One-Dimensional Prediction to Four-Dimensional Description of Antigenic Specificity , 1996 .

[103]  A Sette,et al.  Practical, biochemical and evolutionary implications of the discovery of HLA class I supermotifs. , 1996, Immunology today.

[104]  K. Rock.  A new foreign policy: MHC class I molecules monitor the outside world. , 1996, Immunology today.

[105]  K. Rock,et al.  Antigen processing and presentation by the class I major histocompatibility complex. , 1996, Annual review of immunology.

[106]  F. Guarnieri,et al.  Treatment of established tumors with a novel vaccine that enhances major histocompatibility class II presentation of tumor antigen. , 1996, Cancer research.

[107]  Kathleen R. Cho,et al.  Engineering an intracellular pathway for major histocompatibility complex class II presentation of antigens. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[108]  J. Shiver,et al.  Preclinical efficacy of a prototype DNA vaccine: Enhanced protection against antigenic drift in influenza virus , 1995, Nature Medicine.

[109]  H. Rammensee,et al.  Chemistry of peptides associated with MHC class I and class II molecules. , 1995, Current opinion in immunology.

[110]  G Hermanson,et al.  Binding of a peptide antigen to multiple HLA alleles allows definition of an A2-like supertype. , 1995, Journal of immunology.

[111]  M. V. Van Regenmortel,et al.  Predicting antigenic determinants in proteins: looking for unidimensional solutions to a three-dimensional problem? , 1994, Peptide research.

[112]  K. Parker,et al.  Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. , 1994, Journal of immunology.

[113]  D. Wiley,et al.  Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1 , 1993, Nature.

[114]  C. D. Myers,et al.  Role of B cell antigen processing and presentation in the humoral immune response , 1991, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[115]  M. A. Saper,et al.  Structure of the human class I histocompatibility antigen, HLA-A2 , 1987, Nature.

[116]  J. August,et al.  Lysosomal membrane glycoproteins: properties of LAMP-1 and LAMP-2. , 1986, Biochemical Society symposium.

[117]  I. Pastan,et al.  Identification of two lysosomal membrane glycoproteins , 1985, The Journal of cell biology.