1. Extremely
Rapid
H7N9
Immunogenicity
Analysis
and
Vaccine
Design
April
13
2013
Annie
De
Groot
M.D.
CEO/CSO
www.epvax.com
1
2. Adapted
from
a
Presenta?on
to
NIAID
Universal
Flu
Vaccines:
Now
More
than
Ever
EpiVax
has
a
flu
SBIR
that
was
scored
and
we
are
wai?ng
for
a
decision
about
funding
21
March
2013
Presented
by
Annie
De
Groot
MD
to
Rachelle
Salomon,
NIH,
NIAID,
DMID
EpiVax:
Lenny
Moise,
Frances
Terry,
Bill
MarMn
Mindy
Cote,
Ryan
Tassone,
Howie
LaMmer
Lauren
Levitz,
ChrisMne
Boyle
VGTI:
Ted
Ross
2
5. WHO
Report
Graph
This
picture
shows
the
geographically
wide
distribuMon
of
flu
cases
-‐
suggesMng
widespread
distribuMon
of
the
virus
rather
than
a
point
outbreak.
6. Time
to
consider
T
cell
epitopes?
hRp://www.ncbi.nlm.nih.gov/pmc/arMcles/PMC2936654/
8. 2009
Worry:
CDC
-‐
No
Cross-‐reacMve
Ab
• Preliminary
studies
of
individuals
showed
that
anMbodies
induced
by
seasonal
influenza
vaccinaMon
were
not
cross-‐
reacMve
with
novel
H1N1.
• What
if
the
T
cell
epitopes
were
cross-‐
reacMve?
Would
that
help?
Centers
for
Disease
Control
and
PrevenMon.
Serum
anMbody
response
to
a
novel
influenza
A
(H1N1)
virus
a`er
vaccinaMon
with
seasonal
influenza
vaccine.
MMWR
Morb
Mortal
Wkly
Rep
2009;58(19):521–4.
9. Second
Exposure
Response
if
Exposure
or
Related
or
strain
is
VaccinaMon
Unrelated
Strain
idenMcal.
.
.
Or
if
cross-‐reacMve
.
.
.
if
no
T
cell
epitopes
cross-‐
reacMve
T
cell
response
IniMal
response
to
exposure
or
vaccinaMon
11. Iden?fied
immunogenic
and
conserved
Sequences
–
Predicted
Cross
Protec?on
Immunogenic
Enough
Cross-‐
T cell protecMve
Epitopes
epitopes that
Seasonal
Flu
vaccinaMon
or
exposure
may
protect
Conserved
T-Cell
Epitopes
De Groot et al. Vaccine 2009;27:5740-7
12. Valida?on
that
cross-‐conserved
T
cell
epitopes
are
an?genic
“Immunized”
with
Brisbane
HA
whole
Flu
vaccine
-‐
Response
to
X-‐Conserved
T
cell
epitopes
HA394-411
0.09 0.034
No Ag
Culture Antigen
0.027
1.19 6.44
Brisbane HA
CD154
IFNγ
4.7
hRp://www.ncbi.nlm.nih.gov/pmc/arMcles/PMC3130614/
Schanen et al. Vaccine 2011;29:3299-309
14. New
Case
in
Beijing
H7N9%Cases%and%Deaths%/%WHO%Report%
60# 70%#
50# 60%#
50%#
40#
40%#
30#
30%#
20#
20%#
10# 10%#
0# 0%#
#
#
#
#
#
r#
r#
r#
r#
r#
r#
r#
r#
GE
pr
pr
pr
pr
Ap
Ap
Ap
Ap
Ap
Ap
Ap
Ap
+A
+A
+A
+A
RA
1+
3+
4+
5+
6+
7+
8+
9+
10
11
12
13
E
AV
Total#Cases# Total#Deaths# New#Cases/Day# Mortality#Rate#
New
Case
in
Beijing
15. H7N9
Morbidity
and
Mortality
Quick
numbers...
• Total
confirmed
human
cases
of
influenza
A
virus
H7N9:
49
• Total
deaths
aRributed
to
infecMon
with
influenza
A
virus
H7N9:
11
• Case
Fatality
Rate
(CFR):
22%
• Average
Mme
from
illness
onset
to
first
confirmaMon
of
H7N9
(days):
10
• Average
age
of
the
H7N9-‐confirmed
cases
(including
deaths;
years):
60
• Median
age
of
the
H7N9-‐confirmed
cases
(including
deaths;
years):
65
• Mode
age
of
the
H7N9-‐confirmed
cases
(including
deaths;
years):
74
• Average
age
of
the
deceased
(years):
59
• Males:
70%
of
cases,
82%
of
deaths
hRp://pandemicinformaMonnews.blogspot.com
hRp://www.uq.edu.au/vdu/VDUInfluenza_H7N9.htm
16. What
About
H7N9?
Novel
or
Conserved?
H7N9
CirculaMng
Flu
Very
Poor
Cross-‐ConservaMon
–
Only
within
Internal
Proteins
17. Which
H7N9
Proteins
Ian
Mackey
hRp://www.uq.edu.au/vdu/
VDUInfluenza_H7N9.htm
20. This
is
a
unique
virus
• Low
conservaMon
of
HA,
NA
surface
proteins
is
not
surprising
• Internal
proteins
are
more
conserved
• And
–
HA
is
has
unusually
low
immunogenicity
• May
explain
why
infecMon
is
widespread:
• Difficult
to
make
anMbodies
to
the
HA
21. How
do
we
measure
Immunogenicity?
Vaccine
anMgen
epitope
epitope
epitope
1
+
1
+
1
=
Response
Immune
response
to
a
vaccine
anMgen
can
be
predicted
by
measuring
the
number
of
T
cell
epitopes
contained
in
the
anMgen
with
immunoinformaMcs
tools.
23. New
H7N9
Flu
is
Predicted
to
be
POORLY
IMMUNOGENIC
- 80 -
www.EpiVax.com
- 70 -
- 60 -
- 50 - Hemagglu?nin
- 40 -
A/Brisbane/59/2007(H1N1)
- 30 -
- 20 -
Neuraminidase
A/Perth/16/2009
(H3N2)
- 10 -
Average
Epitope
Content
- 00 - (Random
Expecta?on)
A/Brisbane/59/2007(H1N1)
- -10 - A/Shanghai/1/2013
(H7N9)
- -20 -
A/Perth/16/2009
(H3N2)
- -30 -
A/Shanghai/1/2013
(H7N9)
Immunogenicity
based
on
T
- -40 - helper
epitope
content
per
amino
- -50 - acid.
Performed
by
Ardito,
Terry,
De
Groot
and
MarMn,
April
2013
- -60 -
- -70 -
24. Spread
to
Beijing
on
4/13/13
This
figure
was
published
online
at
hRp://www.epivax.com/blog/h7n9-‐
shanghai-‐2013-‐the-‐new-‐stealth-‐virus/
Hemagglu?nin
Neuraminidase
28. Fully
integrated
From
genome
to
vaccine
• EpiMatrix – maps T cell epitopes
• ClustiMer - Promiscuous / Supertype Epitopes
Seamless
Vaccine
• BlastiMer - Avoiding “self” - autoimmunity
Design
• Conservatrix – Identifies Conserved Segments
Integrated
toolkit
is
• EpiAssembler - Immunogenic Consensus Sequences
unique
to
iVax
• Aggregatrix – Optimizing the coverage of vaccines
• VaxCAD - Processing and Assembly
28
29. A
beier/faster
way
to
make
flu
vaccine?
BeRer
understanding
of
vaccine
MOA
Egg-‐based/Cell
Genome-‐
Whole
(live/ Culture
Based
Derived,
Epitope
killed)
flu
Whole
Ag
(HA)
Driven
(GD-‐ED)
vaccines
vaccines
Vaccines
Improve
vaccine
safety
and
efficacy
Accelerate
Vaccine
Design
Genome-‐derived
Epitope-‐driven
Influenza
Vaccines
(R21
/
NIAID
/
NIH
30. T
cells
=
Immune
System
Body
Armor
T
cell
response
cannot
prevent
InfecMon
but
.
.
.
T
cell
response
can
arm
against
Disease
31. FastVax: Vaccines on demand
Rapid
deployment
when
genome
sequence
is
in
hand
• High throughput computing
Prebuilt
• Immunoinformatics
• Vaccine design algorithms
• Vaccine Production
• Delivery device Pilot
program
Funded
by
DARPA
• Animal safety/tox/immunogenicity/validation
• Deployment by established distribution systems
31
32. 20
hours
-‐
April
05
–
April
06
2013
Extremely
Rapid
H7N9
Vaccine
Design
April
05,
2013:
Obtain
H7N9
Sequences
(4
human-‐sourced;
GISAID)
Obtain
all
available
H7N9
sequences
EpiMatrix
Analysis:
IdenMficaMon
of
H7N9
Class
I
and
Class
II
Epitopes
Compare
with
previous
epitopes
(IEDB)
And
other
H7N9
strains;
create
final
list
20
hours
(Logged).
101
H7N9
ICS*
Class
II
Epitopes
+
586
Class
I
Epitopes
Eliminate
Epitopes
highly
conserved
with
Human
Design
vaccine:
12
hours
(Logged).
April
06,
2013:
H7N9
Vaccine:
Two
Constructs,
Class
I
and
Class
II
33. Predic?ng
Epitopes
that
Drive
Immune
Response
is
our
Exper?se
HLA (Human MHC), are comprised of
MHC II Pocket a limited number of pockets.
EpiMatrix predicts how well a side
chain will bind to a specific pocket.
MHC II Peptide
Epitope 8 class II Archetype matrices which
taken together incorporate 95% of
human populations (and pockets)
Mature worldwide.
APC
Each 9-mer/10-mer is analyzed for
binding potential to each of those 8
allele matrices.
The
EpiMatrix
Score
describes
how
well
.
Southwood et al. J. Immunology 1998 the
pepMde
“fits”
into
the
pockets
Sturniolo et al. Nature Biotechnology, 1999
EpiVax
34. Published
Benchmark
2009
De
Groot
and
MarMn.
Reducing
risk,
improving
outcomes:
Bioengineering
less
immunogenic
protein
therapeuMcs.
Clinical
Immunology
2009.
131,
189-‐201.
35. Epitope
Clusters
=
Immunogenic
• A Key Discovery – Epitopes are Clustered in Protein Sequences
DRB1*0101
DRB1*0301
DRB1*0401
DRB1*0701
DRB1*0801
DRB1*1101
DRB1*1301
DRB1*1501
• T-cell epitope clusters make excellent vaccine candidates:
– compact; relatively easy to deliver as peptides; highly reactive in-vivo
35
36. Building
ICSs
EpiAssembler
–
Final
Immunogenic
Consensus
Sequence
STRAIN 01 Q X S W P K V E Q F W A K H X W N X I S X I Q Y L
STRAIN 02 Q A S W P K V E X F W A K H M W N F I S G I Q Y L
STRAIN 03 Q X S W P K X E Q F W A K H M W N F I S G I Q Y X
STRAIN 04 Q A S W X K V E Q F W A K H M W N F X S X I Q Y L
STRAIN 05 Q X S W P K V E Q F W A K H M W N F I S G I Q Y L
STRAIN 06 Q A S W P K X E Q F W A X H M W N F I S G I Q Y X
STRAIN 07 Q X S W P K V E Q F W A K H M X N F I S G I Q Y L
STRAIN 08 Q A S W X K V E Q F W A K H M W N F I S G I Q Y L
STRAIN 09 Q X S W P K X E Q F W A K H M W N F X S X I X Y X
STRAIN 10 Q A S W P x
R V E Q F W A K H M W N F I X G I Q Y L
STRAIN 11 Q A S W P K V E Q F W A K H M W N F I S G I Q Y L
STRAIN 12 Q A S W X K V E Q F W A X H M W N F I S G I Q Y X
STRAIN 13 Q A S W P K V E Q F W A K H M W N F I S G I Q Y L
STRAIN 14 Q A S W X K X E Q F W A K H M W N F I S X I Q Y L
STRAIN 15 Q A S W P K V E X F W X K H M W N F I S G I Q Y L
STRAIN 16 Q X S W P K V E Q F W A K H M W N F I X G I Q Y L
STRAIN 17 X A S W X K V E Q F W A K H M W N F I S G I Q Y X
STRAIN 18 Q X S W P K X E Q F W A K H M W N X I S G I Q Y L
STRAIN 19 Q A S W X K V E Q F W A K H M W N F I S X I Q Y L
STRAIN 20 Q A S W P K V E Q F W A X H M W N F I S G I Q Y L
F W A K H M W N F
W P K V E Q F W A M W N F I S G I Q
Q A S W P K V E Q N F I S G I Q Y L
Q A S W P K V E Q F W A K H M W N F I S G I Q Y L
37. Building
ICSs
EpiAssembler
–
Final
Immunogenic
Consensus
Sequence
Balance
Score+Conserva?on:
Highest
conserved
epitopes
Selec?on
for
score
Best
Op?on
are
poorly
immunogenic
41. GD-‐IDV
FormulaMons
(plaqorm
independent)
DNA
–
chain
of
epitopes,
or
ICS-‐opMmized
whole
proteins
ICS-‐opMmized
proteins
in
VLP
pepMde
in
liposomes
42. EpiVax
is
eager
to
help
• Seasoned
Research
Team
• Validated
Vaccine
Design
Tools
• H7N9
Analysis/Vaccine
design
complete
• Constructs
sent
for
producMon
• Other
services:
– Analyze
exisMng
H7
vaccines
for
conservaMon
– Advise
on
vaccine
design
EpiVax
Contacts:
Anthony
Marcello,
BDA,
amarcello@epivax.com
Anne
S.
De
Groot
CEO/CSO
annied@epivax.com
43. Ac?ve
Collaborators
/
Vaccines
Alan
Rothman
Bill
MarMn
Carey
Medin
Ted
Ross
Lenny
Moise
Andres
GuiMerrez
Frances
Terry
Danielle
Aguirre
Leslie
Cousens
Joe
Desrosiers
Ryan
Tassone
Thomas
Mather
Don
Drake,
Brian
Schanen
Howie
LaMmer
Wendy
Coy
David
Weiner
Mindy
Cote
Loren
Fast
Lauren
Levitz
ChrisMne
Boyle
Hardy
Kornfeld
Connie
Schmaljohn
Jinhee
Lee
Lesley
C.
Dupuy
Mark
Poznansky
Sharon
Frey
Tim
Brauns
Liisa
Selin
Mark
Buller
Pierre
LeBlanc
Jill
Schreiwer
44. EpiVax:
Four
Core
Strengths
Media
Contact:
Anthony
Marcello,
BDA,
amarcello@epivax.com
44
ConfidenMal
