IMMUNOGENICITY OF THERAPEUTIC FUSION PROTEINS: CONTRIBUTORY FACTORS AND CLINICAL EXPERIENCE - Fusion Protein Technologies for Biopharmaceuticals: Applications and Challenges - page 76

FIGURE 5.1 Protein immunogenicity scale. Protein “X” is mapped onto the protein immunoge-
nicity scale according to its EpiMatrix score. Proteins scoring above þ 20 are considered to be
potentially immunogenic. On the left of the scale are included some well-known proteins for
comparison representing a range of immunogenicities, arranged by EpiMatrix score, from highest
(black) to lowest (white).

immunogenicity can be identified, and cluster scores cal-
culated and compiled, a process that has been well estab-
lished by the team of De Groot and Martin [9]. The
frequency and density of these T-cell epitope clusters
canthenbecomparedtoasetofrandomlygenerated
pseudoprotein sequences of similar sizes. Proteins contain-
ing many, or concentrated clusters of, T-cell epitopes are
predicted to be highly immunogenic, while those contain-
ing a few sparse epitopes are more likely to be less
immunogenic. The relationship between the density of
epitope clusters and protein immunogenicity has been
validated extensively in vitro and in vivo. Moreover, these
characteristics can be factored into the estimate of a whole
protein's overall “immunogenicity score,” a useful tool for
consideration in the bioengineering of protein therapeutics.
The ability to assign this standardized measure of immu-
nogenicity to a protein facilitates informed decisions about
the likelihood that a protein will provoke an immune
response [43].
To aid in the direct comparison of immunogenicity
predictions between proteins, an “immunogenicity scale”
that maps immunogenicity predictions of analyzed proteins

onto a scale of known proteins likewise analyzed and
validated for immunogenicity can be developed (Figure
5.1). Using this approach, the De Groot and Martin group
has correctly predicted the clinical immunogenicity of a
novel “peptibody,” a bioengineered autologous protein, and
antibodies in clinical use [9,51,52] among others. Conse-
quently, a number of biotech companies have integrated this
approach to immunogenicity screening into their drug devel-
opment pipeline. Beyond its use in evaluating a single
therapeutic candidate, future applications of the immunoge-
nicity scale might include its utility in the early development
process by aiding in the selection of a lead low-immuno-
genicity candidate from among a panel of protein variants
with a range of predicted immunogenicities.

5.3.2 In Vitro Analysis Tools

For many years, in vitro assays have been used in transplan-
tation research to predict the responsiveness of T cells to a
target tissue based on HLA haplotype matching. Likewise,
given the inherent risks posed by unwanted immunogenicity
elicited by therapeutic proteins, there is an urgent need to