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2010 Mining Human Antibody Repertoires
2010 Mining Human Antibody Repertoires
†
Current Address: Intercell AG; Wagistrasse 25; CH-8952 Schlieren, Switzerland
Key words: human monoclonal antibodies, B cells, hybridoma technology, display technologies, antibody libraries,
antibody engineering
Abbreviations: Ig, immunoglobulin; mAbs, monoclonal antibodies; HAMA, human anti-mouse antibody; HARA, human anti-rat
antibody; HACA, human anti-chimeric antibody; HAHA, human anti-human antibody; FDA, Food and Drug Administration;
EMA, European Medicines Agency; GC, germinal centers; EBV, Epstein-Barr virus; AID, activation-induced deaminase;
PCR, polymerase chain reaction; RT, reverse transcriptase; CDR, complementarity-determining region; FACS,
fluorescence-activated cell sorting; GMP; good manufacturing practice; pAbs, polyclonal antibodies
Human monoclonal antibodies (mAbs) have become drugs of domains. Human mAbs (also referred to as fully human mAbs)
choice for the management of an increasing number of human are defined as having variable domains that are entirely derived
diseases. Human antibody repertoires provide a rich source for from human antibody repertoires, whereas chimeric and human-
human mAbs. Here we review the characteristics of natural and ized mAbs feature variable domains that originate from non-
non-natural human antibody repertoires and their mining with human antibody repertoires. A key feature of human mAbs is
non-combinatorial and combinatorial strategies. In particular, their ability to fully blend in with the human immune system.
we discuss the selection of human mAbs from naïve, immune, Being indistinguishable from endogenous human antibodies,
transgenic and synthetic human antibody repertoires using human mAbs are generally anticipated to have superior pharma-
methods based on hybridoma technology, clonal expansion cokinetic and pharmacodynamic properties compared to mAbs
of peripheral B cells, single-cell PCR, phage display, yeast
from nonhuman antibody repertoires. Ideally, human mAbs
display and mammalian cell display. Our reliance on different
strategies is shifting as we gain experience and refine methods
are not recognized as foreign by the human immune system,
to the efficient generation of human mAbs with superior i.e., are not immunogenic. Human and humanized mAbs have
pharmacokinetic and pharmacodynamic properties. been found to be less immunogenic than nonhuman and chi-
meric mAbs, the latter of which trigger human anti-mouse anti-
body (HAMA), human anti-rat antibody (HARA) and human
anti-chimeric antibody (HACA) responses.1 It is expected, but
Introduction remains to be substantiated, that human mAbs are generally less
immunogenic than humanized mAbs.2,3 Human anti-human
Human antibody repertoires are collections of human immuno- antibody (HAHA) responses are mainly due to idiotypic, allo-
globulin (Ig) genes that encode human heavy and light chains. typic and glycosylation differences between human mAbs and
These include V H, D, JH and CH gene segments of the heavy endogenous human antibodies. Although potentially beneficial
chain locus on chromosome 14; Vk, Jk and C k gene segments of for certain therapeutic applications,4 it is likely that fine tuning
the kappa light chain locus on chromosome 2; and Vl, Jl and Cl of human mAb engineering and manufacturing will reduce the
gene segments of the lambda light chain locus on chromosome remaining immunogenicity of human mAbs.
22 in the human genome. In addition, transgenic animals with Hybridoma technology 5 has been extremely successful in the
complete or partial human antibody repertoires have been gener- generation of mouse and rat mAbs; however, the initial failure
ated. Human antibody repertoires can be mined in vivo and in to robustly apply this method to the generation of human mAbs
vitro for human monoclonal antibodies (mAbs). paired with the prospect of lucrative intellectual property accel-
Chimeric, humanized and human mAbs, which collectively erated the development of a variety of alternative methods over
are the prevailing formats of therapeutic mAbs, share human the past three decades.2,6-8 The medical and commercial success
constant domains but are discerned by the origin of their variable of mAbs in the management of human disease drove this growth
and diversification.9,10 Although only six out of 28 mAbs that were
Correspondence to: Roger R. Beerli and Christoph Rader; approved by the US Food and Drug Administration (FDA) and/
Email: rbeerli@intercell.com and raderc@mail.nih.gov or the European Medicines Agency (EMA) are human mAbs
Submitted: 03/26/10; Accepted: 04/27/10 (Table 1), four of these antibodies were approved as recently
Previously published online: as 2009, and their proportion is likely to increase, owing to an
www.landesbioscience.com/journals/mabs/article/12187
unremitting pipeline of human mAbs in Phase 3 clinical trials.11
Here we review the generation of human mAbs from naïve, mAbs, first with non-combinatorial and later with combina-
immune, transgenic and synthetic human antibody repertoires. torial strategies. By contrast, combinatorial strategies have
Strictly speaking, only human mAbs from naïve and immune dominated access to human mAbs from the naïve repertoire
repertoires, which we summarize as natural repertoires in the (Table 2).
next section, as well as human mAbs from transgenic reper- The bone marrow is a primary lymphoid tissue of interest
toires, which nonetheless are products of artificial immune sys- for mining natural human antibody repertoires. The principle
tems, meet the above stated criterion of having variable domains site of differentiation of hematopoietic stem cells into immature
that are entirely derived from human antibody repertoires and B cells,12 the bone marrow generates pro-B cells and pre-B cells
are therefore indistinguishable from endogenous human anti- with partially rearranged heavy and light chain genes. While
bodies. By contrast, human mAbs from synthetic repertoires these partially developed human antibody repertoires are gener-
generally contain artificial sequences that are not encoded in ally not suitable for mining human mAbs, surrobody libraries
the human genome and cannot be generated by natural pro- that pair rearranged heavy chains with surrogate light chains of
cesses such as V HDJH, VkJk and VlJl rearrangements and pre-B cells have been described recently.13 The ultimate products
somatic hypermutation. Transgenic and synthetic repertoires of B-cell development in the bone marrow are immature B cells
are summarized as non-natural repertoires in a subsequent sec- that express cell surface IgM. Upon exiting the bone marrow and
tion. Furthermore, we distinguish between non-combinatorial entering the circulation, immature B cells mature to naïve B cells,
and combinatorial strategies for mining human antibody rep- the latter of which express cell surface IgD in addition to IgM.
ertoires. Non-combinatorial strategies retrieve human mAbs Immature and naïve B cells collectively provide a fully developed
from single B-cells with the original heavy and light chain human antibody repertoire that has not been shaped, at least not
pairs (Fig. 1). Combinatorial strategies involve human anti- extensively, by antigen encounter and is therefore termed primary
body libraries with randomly combined heavy and light chains repertoire or naïve repertoire.
(Fig. 2). Hybridoma technology and phage display technology When naïve B cells encounter new antigens that bind to
exemplify non-combinatorial and combinatorial mining tools, their surface Ig they become activated B cells, proliferate and go
respectively. Both approaches have led to FDA- and EMA- through differentiation processes that typically involve somatic
approved human mAbs (Table 1). hypermutation and class switch recombination from the earliest
expressed IgM isotype to IgG, IgE and IgA isotypes. These pro-
Natural Repertoires cesses are T-cell-dependent and take place in germinal centers
(GC) of secondary lymphoid tissues such as lymph nodes, spleen
Each B cell encodes a single antibody with defined specificity. and tonsils. Post-GC B cells with affinity and isotype matured
The clonal diversity of the natural human antibody repertoire antibodies differentiate further into antibody secreting cells and
is defined by the number of B cells that encode antibodies with memory B cells.14 Antibody secreting cells can be divided into
unique specificities, i.e., the number of independent clones. In proliferating plasma blasts and fully differentiated plasma cells
an individual, this number is estimated to be at least 108. B that no longer proliferate. Plasma cells exit secondary lymphoid
cells from primary and secondary lymphoid tissues along with tissues, enter the circulation, and migrate to the bone marrow
B cells in circulation, i.e., in peripheral blood, constitute the where they may survive for weeks, months, or even years in spe-
natural human antibody repertoire. The natural repertoire cialized niches. Antibody titers in circulation are maintained by
can be divided into naïve and immune repertoires depending plasma cells residing in the bone marrow.15 In contrast to anti-
on whether or not it has been shaped by antigen encounter. body secreting cells, memory B cells do not secrete antibodies but
The immune repertoire has been extensively mined for human express cell surface Ig. Memory B cells are found in secondary
lymphoid tissues, in circulation and in the bone marrow. Upon Human immune repertoires are highly attractive because
recall antigen encounters, memory B cells rapidly differentiate they contain antibodies of high affinity with minimal immu-
into antibody secreting cells. Both memory B cells and plasma nogenicity and off-target reactivity. Unlike nonhuman immune
cells can be long-lived, maintaining immunological memory for repertoires that have been mined extensively for mAbs, the
a lifetime.16 human immune repertoire lacks both availability and accessi-
The secondary repertoire, or immune repertoire, is largely bility. First of all, humans cannot be exposed to antigens at
defined by the pool of post-GC B cells, plasma blasts, plasma will, limiting available immune repertoires to those induced
cells and memory B cells. Expression of CD27 distinguishes by infections, vaccinations, autoimmunity and alloimmunity.
this B-cell pool from other B cells. Antibody-secreting cells Furthermore, secondary lymphoid tissues such as the spleen,
and memory B cells can also arise from T-cell-independent which is a preferred source of mouse, rat and rabbit immune
processes that play a role in both adaptive and innate immunity. repertoires for mAb mining, are difficult to access in humans.
Adaptive immunity to T-cell-independent antigens such as Although tonsillectomy provides access to tonsils, it generally
carbohydrates and lipids contributes to the immune repertoire. does not coincide with an immune response of interest. Access
By contrast, cells expressing natural antibodies, which play a to the human immune repertoire is therefore generally limited
key role in innate immunity,17 can be considered to belong to to peripheral blood and, to a lesser extent, bone marrow. As dis-
the naïve repertoire. These two types are difficult to distinguish cussed above, these compartments also contain the naïve rep-
and typically share IgM isotype, low affinity and polyreactivity. ertoire. Combinatorial strategies allow the retrieval of human
They illustrate that immune and naïve repertoires often mAbs from the naïve repertoire. Typically, these mAbs need
overlap without clear anatomical localizations or functional to be improved by affinity maturation in vitro to compensate
distinctions. for their lack of efficient selection by antigens in vivo. The next
two sections discuss various features of naïve and immune rep- available and can be produced in almost unlimited quantities due
ertoires that are exploited in non-combinatorial and combinato- to this robust underlying technology.5 Unfortunately, the therapeu-
rial strategies for mining human mAbs. tic use of rodent mAbs in humans is limited by their propensity to
induce strong HAMA and HARA responses that quickly neutral-
Non-Combinatorial Mining ize the rodent mAb. Given this, the mining of human antibody
repertoires using hybridoma technology was investigated exten-
Hybridoma technology. The advent of hybridoma technology had sively. Despite significant efforts, the adaptation of hybridoma
a tremendous impact on biomedical research, yielding mAbs that technology to the generation of human mAbs has been a slow and
have become an indispensable part of everyday laboratory work. difficult process due to the limited number of B cells stimulated
Today rodent mAbs against a plethora of antigens are widely with an antigen of interest and a lack of suitable drug-resistant