Conserved Epitope Regions

Transcription

1 Conserved Epitope Regions R. Burke Squires Influenza Research Database ASV 2011, Minneapolis, MN

2 Influenza Research Database (IRD) NIAID BioinformaLcs Resource Center (BRC) Free, public resource Support development of Vaccines DiagnosLcs TherapeuLcs

3 MoLvaLon Influenza viruses evolve through compelng forces: Immune pressure Select for altered protein regions recognized by immune system Protein funclonal constraints Retain essenlal funclonality for effeclve virus replicalon and transmission. Ideal immunogen Protein regions that are both strong immune epitopes and funclonally constrained.

4 Data and Methods Data Influenza sequence data Imported into IRD from GenBank Experimentally determined epitopes Immune Epitope Database (IEDB) T cell, B Cell Polymorphism scores Pre- computed in IRD using in- house curalon pipeline Crooks, G.E., Hon, G., Chandonia, J.- M. & Brenner, S.E. WebLogo: a sequence logo generator. Genome Res. 14, (2004).

5 Data and Methods, cont. Workflow for Polymorphism Analysis in IRD Download pre- computed polymorphism scores for Human, H1N1 from IRD 0 2 / 5 = A B C A B C A B C AAC A B C A B C A B C A B C A B C A B A B C A B C A B C A B C A B C A B CCBBA B C A B C A B A B C A B C A B C A CCA B C A B C A BBA B C A B C A B Averaged polymorphism scores using a 5 amino acids window

6 Materials and Methods, cont. Workflow for Epitope PosiLon QuanLtaLon Download immune epitope metadata from IRD Compute epitope coverage score for each posilon 3 Influenza HA protein T cell epitope Graph polymorphism versus epitope coverage

7 Polymorphism Score Vs. Epitope Coverage!" #!" $!" %!" &!" '!!" '#!"!" #" $" %" &" '!" '#" '" '!" '(" #&" )*" $%" ++" %$" *)" &#" ('" '!!" '!(" ''&" '#*" ')%" '$+" '+$" '%)" '*#" '&'" '(!" '((" #!&" #'*" ##%" #)+" #$$" #+)" #%#" #*'" #&!" #&(" #(&" )!*" )'%" )#+" ))$" )$)" )+#" )%'" )*!" )*(" )&&" )(*" $!%" $'+" $#$" $))" $$#" $+'" $%!" $%("!"#$%"&'()*%+,-"&.+ /')0"'.+1"2.& !" #!" $!" %!" &!" '!!" '#!"!" #" $" %" &" '!" '#" '$" '%" '&" '" '#" #(" ($" $)" )%" %*" *&" &+" '!!" '''" '##" '((" '$$" '))" '%%" '**" '&&" '++" #'!" ##'" #(#" #$(" #)$" #%)" #*%" #&*" #+&" (!+" (#!" (('" ($#" ()(" (%$" (*)" (&%" (+*" $!&" $'+" $(!" $$'" $)#" $%(" $*$" $&)" $+%" )!*" )'&" )#+" )$!" ))'" )%#"!"#$%"&'()*%+,-"&.+ /')0"'.+1"2.& Polymorphism score - T cell epitope coverage - B cell epitope coverage

8 Scenarios Low Epitope Coverage High Epitope Coverage Conserved Epitope Regions Low Polymorphism (Func. Constained)) Immunodominance High Polymorphism Polymorphism (Avg.) T cell B cell

9 Conserved Epitope Regions Protein Regions HA (HA- CER1); (HA- CER2); (HA- CER3); (HA- CER4); (HA- CER5) NA (NA- CER1); (NA- CER2); (NA- CER3) M (M1- CER1) NS (NS1- CER1); (NS1- CER2); (NS1- CER3) PA (PA- CER1)

10 Conserved Epitope Regions!" #!" $!" %!" &!" '!!" '#!"!" #" $" %" &" '!" '#" '$" '%" '&" '" '#" #(" ($" $)" )%" %*" *&" &+" '!!" '''" '##" '((" '$$" '))" '%%" '**" '&&" '++" #'!" ##'" #(#" #$(" #)$" #%)" #*%" #&*" #+&" (!+" (#!" (('" ($#" ()(" (%$" (*)" (&%" (+*" $!&" $'+" $(!" $$'" $)#" $%(" $*$" $&)" $+%" )!*" )'&" )#+" )$!" ))'" )%#"!"#$%"&'()*%+,-"&.+ /')0"'.+1"2.& HemaggluLnin PDB ID: 1RUZ

11 ValidaLon Reference Region LocaJon H0 coord. CER coverage Eikert et al Broadly neutralizing anlbody (CR6261) Region 1 Broadly neutralizing anlbody (CR6261) Region 2 HA1 Val40 47 HA- CER1 HA1 Leu42 49 HA- CER1 HA1 Leu ? none HA2 Thr none HA2 Val HA- CER4 HA2 Ile HA- CER4 HA1 His18 25 HA- CER1 HA1 His38 45 HA- CER1 HA2 Trp HA- CER3 HA2 Thr none HA2 Ile none Wang et al D1 HA HA- CER5 Ekiert, D., et al., An#body recogni#on of a highly conserved influenza virus epitope. Science, (5924): p Wang, T., et al., Broadly protec#ve monoclonal an#bodies against H3 influenza viruses following sequen#al immuniza#on with different hemagglu#nins. PLoS Pathog, : p. e

12 Summary Conserved Epitope Regions (CERs) ULlizing the data from resources within the IRD Amino acids appear to be highly conserved in spite of immune recognilon Ideal vaccine would focus the immune response to protein regions that are both strong immune epitopes and funclonally constrained

13 Acknowledgments U.T. Southwestern Richard Scheuermann Jyothi Noronha Victoria Hunt Yun Zhang Brei Pickei Eva Rab MSSM Adolfo Garcia- Sastre Eric Bortz Gina Conenello Peter Palese Vecna Chris Larsen Al Ramsey LANL Catherine Macken Northrop Grumman Ed Klem Mike Atassi Jon Dietrich Wei Jen Sanjeev Kumar Xiaomei Li Jason Lucas Huarong Lu Jianjun Wang Liwei Zhou U.C. Davis Nicole Baumgarth USDA David Suarez CEIRS Centers NIAID N01AI40041 IRD SWG Gillian Air, OMRF Carol Cardona, Univ. Minnesota Adolfo Garcia- Sastre, Mt Sinai Elodie Ghedin, Univ. Piisburgh Martha Nelson, Fogarty Daniel Perez, Univ. Maryland Gavin Smith, Duke Singapore David Spiro, JCVI Dave Stallknecht, Univ. Georgia David Topham, Rochester Richard Webby, St Jude 13

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