Vaccine Development in the Context of Synthetic …sites.nationalacademies.org/cs/groups/pgasite/documents/...Vaccine Development in the Context of Synthetic Biology Principles Opportunities

Vaccine Development in the Context of Synthetic Biology Principles

Opportunities and Challenges in the Emerging Field of Synthetic Biology

Washington, DC July 9th 2009Frank Notka, GENEARTRalf Wagner, GENEART, University of Regensburg

Overview

How to build a novel system?

Construction Cycle

Specification of parts, devices, systems…

Design circuits

Modeling in silico

Implementationin vivo / chassis

Testing „-omics“

Knowledge based

2

constitutive nc export

syn-gag

CRM1ran

REV

RRE

degradation

wt - gag

cis activerepressor sequenzes

UTR

SDREV

RRE

splicingmachinery

?

2

3

1

wt-gag

- - - - + + + +Rev

syng

ag-R

REUT

R-wtg

ag-R

RE

wtgag

-RRE

UTR-

wtgag

-RRE

gag

C C C CN N NN

actin

Northern

Knowledge: Understanding Regulation of ExpressionLentiviral Gene Expression: HIV-GAG

Knowledge

Specification

Design

testing

Modeling

Implementation

Graf et al., 1998

Specification: Integrated Vaccine Strategies

immunogen designmolecular virology

basic immunology / micepreclinic / rhesus macaques

clinic / phase 1/2

• envelope proteins: Env• structural proteins: Gag, Pol• regulatory proteins: Tat, Rev, Nef• accessory proteins: Vpr

Targets of immune response

+ +

Peptides DNA Viral Vectors

Bacterial Vectors

Pseudovirions

Novel Adjuvants (CpG, PEI, MF59)Proteins

Delivery / Combination of Multivalent HIV/AIDS Vaccine Strategies

?

rAd, NYVAC

Bojak, et al., 2002

• neutralizing AB • mucosal immunity• CD4+ T cell response• CD8+ CTLs• broad, cross clade, • high quality, polyfunctional• long term memory

Immune response

• A (Africa) • B (Europe, N & S-America)• C (Asia, Africa …)• E (Asia)• F (Africa)• G (South America, Africa)

HIV Clades

Knowledge

Specification

Design

testing

Modeling

Implementation

Design: Function – Safety - Efficacy

Sequence analysis of C (CN54)

Su et al., 2000

LTRLTR

gagpol

vif

vpr

vpuenv

rev

tat

tev

nef

gag (myr)

5' pol (RT)

3’nef

5’nef

3' pol (IN)

RT as

Harari et al., 2008

Rational Antigen Design

Knowledge

Specification

Design

testing

Modeling

Implementation

Modeling: Gene Analysis & Optimization

In silico multi-parameter sequence analysis and optimization

Sliding window approach (Gene Optimizer™)

Knowledge

Specification

Design

testing

Modeling

Implementation

Clade Delivery Developer / Manufacturer

GagPolNef C (CN54) DNA-C UREG / CobraEnv C (CN54) DNA-C UREG CobraGagPolNef / Env C (CN54) NYVAC-C Sanofi PasteurGagPolNef / Env C (CN54) MVA-C Esteban GagPolNef / Env C (CN54) vTT-C Y. Shao / S-CDCGagPolNef / Env B NYVAC-B Sanofi PasteurGagPolNef / Env B MVA-B Esteban

Implementation: Gene Synthesis & Vector Production

Oligo/Fragment

DesignGene SynthesisFragment Construction

QC Gen Assembly

Oligosynthesis

Laboratory Information Management System

Gene synthesis process

“Chassis” Production

Knowledge

Specification

Design

testing

Modeling

Implementation

Testing: Clinical trial EV02

Higher percentage of responders in DNA-C prime / NYVAC-C boost group (>90%)compared to NYVAC-C group (<40%)

Durability DNA-C / NYVAC-C >> NYVAC-C

A. Harrari, G.Pantaleo et al.

0

20

40

60

80

100

Perc

enta

ge o

f res

pond

er

NYVAC CAlone

DNA C + NYVAC C

P = 0.003

Percentage of Responders (gIFN+ T cells) Study design: 2 x 20 HIV negative volunteersLondon and Lausanne

0

20

40

60

80

100

W0 W5 W20 W24 W26 W28 W48

Perc

enta

ge o

f res

pond

ers DNA C + NYVAC C

NYVAC C alone

P < 0.001P = 0.019

P = 0.001P < 0.001

DNA-C NYVAC-C

NYVAC NYVACDNA DNAKnowledge

Specification

Design

testing

Modeling

Implementation

Implications

What is new?

Construction Cycle

Specification of parts, devices, systems…

Design

Modeling in silico

Implementationin vivo / chassis

Testing „-omics“

Knowledge based

0

20

40

60

80

100