Vaccines 2

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Vaccines 2 Immunomics Virus Pathogen Vaccines
J. Thomas August Department of Pharmacology and
Molecular Sciences The Johns Hopkins School of
Medicine Emailtaugust_at_jhmi.edu
The Johns Hopkins School of Medicine
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Immunomics - Virus epitope discovery -
Epitope-based vaccines

• Harvard Medical School
• Vladimir Brusic, Harvard Medical School,
  Director of Bioinformatics, Dana-Farber
• National University of Singapore Immunomics
• Tin Wee Tan, Assoc. Prof, Dept. Biochemistry
• Olivo Miotto, Program Director (Research),
  ?Institute Systems Science
• Asif Khan, pre-doctoral student, dengue and
  flaviviruses
• A.H. Heiny, pre-doctoral student, influenza and
  rabies
• Hu Yongli, pre-doctoral student, Hantavirus,
  HIV-1
• Koo Qiying, undergraduate, West Nile virus
• George Au-Yeung, undergraduate, Japanese
  encephalitis virus
• Johns Hopkins University School of Medicine,
  Molecular biology and vaccine development
• Ernesto Marques, Asst. Prof., Director of
  Recife, Brazil, human cohort program
• Greg Simon, post-doctoral fellow, influenza
• Vladimir Perovic, post-doctoral fellow, rabies
• Paul Tan, post-doctoral fellow, influenza and
  HAV
• Keun-Ok Jeng, post-doctoral fellow, West Nile
  and SARS CoV
• Eduardo Nasciamento, post-doctoral fellow,
  dengue
• Brunda Ganneru, post-doctoral fellow
• NIAID funded

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Platform Technologies for Genetic Vaccine
Development

• Database mining for all pathogen gene
  sequences.
• Entropy analysis of pathogen protein
  variability.
• Consensus sequence selection of conserved
  sequences.
• - Highly conserved sequences lacking epitope
  variants
• - Epitope hot spots
• DNA vaccine constructs encoding relevant
  proteins
• HLA transgenic mice immunization for HLA
  epitope validation
• Animal model vaccination and challenge.
• Synthesis of advanced DNA plasmid vector
  vaccine
• - Sequences for targeting of antigen to MHCII
  compartment.
• - Sequences for pathogen RNA elements as
  adjuvants.
• IND clinical trials.

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Virus systems under study

• Dengue viruses 1 - 4
• Influenza viruses, avian and human
• HIV-1
• West Nile virus
• Japanese encephalitis virus
• Yellow fever virus
• Hepatitis A virus
• Rabies virus
• Hanta virus

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Dengue virus 1-4
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DENV 1-4 protein sequences (NCBI Entrez DB)
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Nonamer entropy analysis of viral variability
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Variant analysis possibility of altered-ligand
effect
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Protein representation of pan-DENV sequences
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Functional correlations of conserved sequences
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• Pan-dengue predicted supertype epitopes

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• Pan-dengue predicted HLA supertype epitopes

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ELISpot dengue envelope DR2 epitopes
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ELISpot Dengue envelope DR3 epitopes
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Dengue NS3 DR3 epitopes
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Dengue NS3 DR4 epitopes
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Influenza A viruses, avian human
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Plan for pan-influenza A virus conserved sequence
analysis
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Human isolates avian group A influenza viruses
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Avian group A influenza virus isolates
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Avian influenza virus proteome nonamer entropy of
all recorded avian genotypic variants
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Entropy of human influenza A virus subtypes
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Correspondence of entropy and percent conservation
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Conserved sequences human influenza virus
subtypes issue of variant sequences
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Pan-influenza A conserved sequences
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• Pan-influenza virus conserved sequences

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Predicted pan-influenza A supertype epitopes
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Identified human epitopes of conserved sequences
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West Nile virus
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Number of WNV sequences retrieved from databasesa
a Collected from the NCBI Entrez database, as of
Feb. 2007 b Approximate size indicated in amino
acids.
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Peptide entropy of WNV nonamer sequences
Nonamer entropy
Proteins
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WNV conserved sequences (100 )
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Predictions of HLA binding sequences WNV 100
conserved sequences
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WNV HLA DRB1 ELISpot positive peptides
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WNV HLA DRB1 ELISpot positive conserved sequences
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WNV-JEV conserved sequences (HLA epitopes
experimental predictions)
a) Net CTL b) TEPITOPE
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WNV HLA DRB1 Hot spots
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• IEDB virus T cell epitope database

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Future directions

• Immunomics and vaccines
• Innate response system and activation
• B-cell immunity
• Refined class I and II predictions
• - Correlation with ELISpot as well as MHC
  binding data
• Epitope analysis
• - Protein structural relationships to epitope
  selection
• - Hierarchy of variant epitopes to immune
  responses
• T-cell activation
• Vaccines
• Human IND clinical trials
• Questions or comments taugust_at_jhmi.edu

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SARS-N peptide-specific HLA transgenic mice
ELISpot assay
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LAMP-targeted, Epitope-based DNA Vaccine Timeline

• Late-stage preclinical
• HIV-1 therapeutic - IND
• Pan-influenza A, avian and human - animal
  model, IND
• West Nile - animal model, IND
• Japanese encephalitis virus - animal model, IND
• Yellow fever virus - animal model, IND
• Developmental
• Rabies, hepatitis A, dengue, pan-flavivirus,
  Hanta viruses
• Allergy
• Cancer telomerase, HPV, melanoma

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WNV protein sequence conservation and HLA
epitopes (Keun-OK Jung and Asif Kahn)

• Nonamer entropy analysis of sequences
  variability
• Variants of WNV NS4b protein
• WNV conserved sequences
• Predictions of HLA binding sequences of
  conserved sequences
• WNV HLA DR-2, -3, -4 ELISpot positive peptides
• WNV HLA DR-2, -3,-4 ELISpot positive conserved
  sequences
• WNV-JEV conserved sequences
• WNV HLA DR-2, -3, -4 clusters (hot spots)

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WNV HLA DRB1 ELISpot positive peptides
(continued)
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WNV HLA DRB1 ELISpot positive peptides
(continued)
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WNV HLA DRB1 ELISpot positive peptides
(continued)
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WNV-JEV conserved sequences (continued) (HLA
epitopes experimental predictions)
a) Net CTL b) TEPITOPE
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Hantavirus Entropy Plot
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continued