NEWS AND VIEWS
Putting immunoinformatics to the test
Leonard Moise & Anne S De Groot
A consensus epitope prediction approach identifies the epitopes responsible for 95% of the murine T-cell response
to vaccinia virus.
© 2006 Nature Publishing Group http://www.nature.com/naturebiotechnology
Although invasive pathogens may express
thousands of proteins containing millions
of potential epitopes, only a small subset of
these sequences actually stimulates immunity.
Indeed, accurate prediction of epitopes is akin
to finding a needle in a haystack. In this issue,
Moutaftsi et al.1 convincingly demonstrate that
epitope-mapping tools accelerate the discovery
of viral sequences that account for an over-
whelmingly large proportion of the response
to vaccinia virus infection in a mouse model.
In addition to revealing the power of immuno-
informatics, this study shows that when a host
mounts an anti-viral attack, it may sample and
respond to a broader array of antigens than was
previously thought.
Epitope-mapping algorithms, of which
several are available, are relevant not only
to vaccine design but also for characteriz-
ing and modifying immune responses in the
context of autoimmunity2, endocrinology3,
allergy4, transplantation5,6, diagnostics7 and
the engineering of therapeutic proteins8. But
controversy has centered around whether
bioinformatics can identify all of the epit-
opes responsible for protective immunity.
Previous studies demonstrated that a sub-
stantial percentage of predicted epitopes
indeed function as such and that a substantial
fraction of known epitopes can be predicted.
However, the fraction of the total immuno-
logical response that can be attributed to the
predicted epitopes of a complex virus has yet
to be estimated.
Exposure to foreign antigens induces the
adaptive immune system to eliminate infection
and develop protective immunity. Central to
this process are T lymphocytes, which activate
the growth and differentiation of B lymphocytes
and trigger cell-mediated immunity. T cells
perform these roles in response to peptide
fragments of pathogen proteins that are
displayed by major histocompatibility complex
(MHC) proteins at the surface of antigen-
Leonard Moise and Anne S. De Groot are
associated with Brown Medical School, 70 Ship
Street, Providence, Rhode Island 02903, USA
and EpiVax, Inc., 146 Clifford Street, Providence,
Rhode Island 02903, USA.
e-mail: annied@brown.edu or
Leonard_Moise@brown.edu
NATURE BIOTECHNOLOGY VOLUME 24 NUMBER 7 JULY 2006
Vaccinia ‘peptidome’
175,716 potential
MHC I epitopes
Informatics: top-ranking
1% of peptides from
2,256 predicted
consensus epitope
epitopes
prediction approach,
pooled and screened
49 confirmed
epitopes
Epitopes from ORFs Epitopes from ORFs
representing proteins representing structural
involved in viral genome proteins
regulation
Epitopes from ORFs
Bob Crimi
representing virulence
factors
Figure 1 The traditional approach to epitope mapping the vaccinia genome would involve synthesizing
almost 176,000 overlapping 8-mer, 9-mer and 10-mer peptides (gray). A computational approach
reduces that figure more than 85-fold, accelerating the discovery of 49 epitopes (yellow/orange) that
account for ~95% of the immunome in a mouse model of vaccinia infection. Although additional epitopes
might have been discovered had the peptidome been synthesized, informatics reveals the overwhelming
majority of total vaccinia T-cell responses. The distribution of epitopes derived from open reading frames
(ORFs) encoding the three main functional classes of viral protein does not differ from the incidence
of these categories in the vaccinia proteome. This suggests that proteins from all functional classes are
equally likely to carry epitopes.
presenting cells. Peptides that are presented to algorithms have given immunologists a head
T helper cells are presented by MHC class II start at vaccine design without requiring prior
molecules; peptides that trigger cytotoxic knowledge of a protein’s structure and func-
T cell responses are presented by MHC class I tion. Computational strategies are far faster
molecules. than experimental approaches for identifica-
As the strength of peptide binding to MHC tion of MHC-binding peptides. However, not
molecules is a critical determinant of immuno- all methods are equivalent and no ‘gold stan-
genicity9, algorithms that accurately model the dard’ means of comparing or standardizing
MHC-peptide interface are central to a priori these tools exists. Complicating matters fur-
strategies for the prediction of T-cell epitopes. ther, researchers often combine several tools, as
With the availability of complete genome was done in this study, resulting in predictions
sequences for numerous pathogens, these that may be difficult to replicate.
791
 NEWS AND VIEWS
Moutaftsi et al. set out to computationally
predict and experimentally validate vaccinia
T-cell epitopes in a mouse model by com-
bining four matrix-based epitope prediction
algorithms. Using cytokine and cell-marker
measurement techniques, the authors deter-
mined the proportion of CD8 T cells arising
from vaccinia challenge that can be attributed
to predicted epitopes. These computations nar-
© 2006 Nature Publishing Group http://www.nature.com/naturebiotechnology
rowed down the vaccinia proteome from nearly
176,000 possible 8-mer, 9-mer and 10-mer
peptides to merely ~2,200 (Fig. 1). Certainly,
testing more than 2,000 peptides for MHC
binding and immunogenicity is not trivial.
However, it is a far less daunting task—and
carries a tremendously lower price tag—than
testing almost 176,000 peptides of 8–10 amino
acids in length, or even 12,000 longer, overlap-
ping peptides, which would still require addi-
tional experimentation to identify the minimal
epitope repertoire of the virus.
Remarkably, the authors found that 49 of the
~2,200 predicted epitopes represent ~95% of
the vaccinia-specific CD8 T-cell repertoire. This
shows that, at least in this instance, noncanoni-
cal epitopes (which don’t fit the parameters
set out by computational tools) do not make
an important contribution to the immune
response. Moreover, the robustness of predic-
tive algorithms is illustrated by the fact that all
49 epitopes scored in the top 1% of sequences
that could potentially bind class I MHC.
At the same time, the study also confirms res-
ervations that experiments validate only a small
fraction of predicted epitopes and that at least
certain epitopes may not be identified by avail-
able algorithms or combinations thereof. Thus
there is still room to enhance the power of pre-
dictive tools. In particular, the greatest challenge
may lie in taking into account extrinsic factors
such as antigen abundance and processing.
Besides the striking success of the consensus
epitope prediction strategy in identifying the
majority of epitopes responsible for the com-
plete T-cell response to vaccinia virus, another
792
noteworthy finding is that vaccinia-exposed
mice recognize a broad range of epitopes
derived from the major groupings of viral anti-
gens in proportion to their proteomic incidence
(Fig. 1). In contrast with other mouse CD8 T-
cell responses to viral infections, no single epi-
tope was overwhelmingly immunodominant.
Preliminary work suggests that the same is true
for vaccinia in humans10. Therefore, computa-
tional tools may lead us to pay less heed to the
concept of immunodominance in favor of a
new view that the immune system can recog-
nize a broad range of epitopes derived from the
proteome of the pathogen, and that proteins of
all types—not just envelope proteins but also
those with regulatory properties—may con-
tribute to a competent immune response.
The relatively small size and democratic rep-
resentation of the epitope repertoire (immu-
nome) defined in this study will encourage
researchers both to define the immunome of
other pathogens to determine whether the set
of peptides responsible for immune response
is similarly limited in size and to attempt to
determine whether immunization with a lim-
ited set of epitopes will replicate a competent
immune response. Using this approach, sci-
entists can begin to measure the breadth and
overlap of pathogen immunomes that give rise
to both favorable and unfavorable aspects of
heterologous immunity.
Several other compelling potential applica-
tions of epitope-mapping tools come to mind.
First, as prior exposure to one pathogen may
modulate immune responses to another, par-
ticularly if both share certain epitopes11, bio-
informatics promises to aid comparisons of
pathogen immunomes. Second, immunoinfor-
matics might facilitate assessment of the impact
of pathogen exposure on autoimmunity. For
example, exposure to epitopes from parasites
such as Schistosoma mansoni may diminish the
chance of developing thyroid disease12. Third,
epitope mapping might predict the effects
of priming on transplantation. For example,
VOLUME 24 NUMBER 7 JULY 2006 NATURE BIOTECHNOLOGY
exposure to heterologous T-cell epitopes from
different pathogens may also prime cross-reac-
tive T cells that impair tolerance to transplanta-
tion5,6. Fourth, epitope-mapping tools might
improve immunogenicity, as the half-life of
class II MHC-peptide complexes appears to be
the primary parameter that dictates the ulti-
mate hierarchy of T-cell responses9. Finally,
algorithms that predict binding to MHC mol-
ecules might open the way for modification
of proteins to eliminate T-cell epitopes. Some
innovators are turning the vaccine paradigm
on its head and using epitope-mapping tools
to identify and eliminate T-cell epitopes in pro-
tein therapeutics8.
Along with sensitive T-cell assay technolo-
gies, these immunoinformatics tools should
enable researchers to identify epitopes with
increasing ease, thereby improving their like-
lihood of success when endeavoring to either
amplify or diminish immune responses. In
the course of this work, researchers will bridge
informatics and immunology while harness-
ing genome data, proteomics and immunology
techniques in a new, interdisciplinary realm of
inquiry.
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(2006).
2. Santori, F.R., Brown, S.M. & Vukmanovic, S. Immunol.
Rev. 190, 146–160 (2002).
3. Inaba, H. et al. J. Clin. Endocrinol. Metab. 91, 2286–
2294 (2006).
4. Westritschnig, K. & Valenta, R. Curr. Opin. Allergy Clin.
Immunol. 3, 495–500 (2003).
5. Ely, L.K. et al. J. Immunol. 174, 5593–5601 (2005).
6. Wu, Z. et al. Nat. Med. 10, 87–92 (2004).
7. Mallone, R. & Nepom, G.T. Clin. Immunol. 110, 232–
242 (2004).
8. De Groot, A.S., Knopf, P.M. & Martin W. De-
immunization of therapeutic proteins by T cell epitope
modification. In State of the Art Analytical Methods
for the Characterization of Biological Products and
Assessment of Comparabilitiy. (ed. Mire Sluis, A.) Vol
122. pp 137–160 (Dev. Biol. Basel, Karger, 2005).
9. Lazarski C.A. et al. Immunity 23, 29–40 (2005).
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(2005).
11. Kim, S.K. et al. J. Exp. Med. 201, 523–533 (2005).
12. Nagayama Y. et al. J. Immunol. 173, 2167–2173
(2004).