U.S. patent application number 11/766624 was filed with the patent office on 2007-10-11 for fc variants having decreased affinity for fcyrllla.
This patent application is currently assigned to Xencor, Inc.. Invention is credited to Wei Dang, John R. Desjarlais, Robert Hayes, Sher Bahadur Karki, Gregory Alan Lazar, Omid Vafa.
Application Number | 20070237767 11/766624 |
Document ID | / |
Family ID | 46328045 |
Filed Date | 2007-10-11 |
United States Patent
Application |
20070237767 |
Kind Code |
A1 |
Lazar; Gregory Alan ; et
al. |
October 11, 2007 |
Fc Variants Having Decreased Affinity for FcyRllla
Abstract
The present invention relates to Fc variants having decreased
affinity for Fc.gamma.RIIIa, methods for their generation, Fc
polypeptides comprising optimized Fc variants, and methods for
using optimized Fc variants.
Inventors: |
Lazar; Gregory Alan; (Los
Angeles, CA) ; Dang; Wei; (Pasadena, CA) ;
Desjarlais; John R.; (Pasadena, CA) ; Karki; Sher
Bahadur; (Pasadena, CA) ; Vafa; Omid;
(Monrovia, CA) ; Hayes; Robert; (Paoli,
PA) |
Correspondence
Address: |
MORGAN, LEWIS & BOCKIUS, LLP
ONE MARKET SPEAR STREET TOWER
SAN FRANCISCO
CA
94105
US
|
Assignee: |
Xencor, Inc.
Monrovia
CA
|
Family ID: |
46328045 |
Appl. No.: |
11/766624 |
Filed: |
June 21, 2007 |
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11124620 |
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11766624 |
Jun 21, 2007 |
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10822231 |
Mar 26, 2004 |
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11766624 |
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10672280 |
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10822231 |
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10372392 |
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60627026 |
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Current U.S.
Class: |
424/133.1 ;
530/387.3 |
Current CPC
Class: |
C07K 2317/77 20130101;
C07K 2317/41 20130101; C07K 16/2887 20130101; C07K 16/18 20130101;
C07K 16/32 20130101; C07K 2317/34 20130101; C07K 16/2863 20130101;
C07K 2317/72 20130101; A61K 2039/505 20130101; C07K 2317/52
20130101; C07K 2317/71 20130101; C07K 2317/24 20130101; C07K
16/2893 20130101; C07K 2317/732 20130101; C07K 2317/734
20130101 |
Class at
Publication: |
424/133.1 ;
530/387.3 |
International
Class: |
A61K 39/395 20060101
A61K039/395; C07K 16/44 20060101 C07K016/44 |
Claims
1. A polypeptide comprising an Fc variant comprising at least one
amino acid substitution in the Fc region of a parent polypeptide,
wherein said Fc variant comprises at least one substitution at at
least one position selected from the group consisting of: 227, 228,
230, 231, 232, 237, 241, 244, 247, 264, 266, 271, 281, 282, 291,
299, 300, 304, 317, 325, 328, 332, and 336, wherein numbering is
according to the EU index and wherein said Fc variant has decreased
binding affinity to Fc.gamma.RIIIa relative to said parent
polypeptide.
2. The polypeptide of claim 1 wherein the Fc variant comprises at
least one substitution at at least one position selected from the
group consisting of: 227, 228, 231, 232, 244, 247, 282, 291, and
336.
3. The polypeptide of claim 1 wherein said Fc variant comprises at
least one substitution selected from the group consisting of: 227Y,
228Y, 228G, 230Y, 230G, 231K, 231P, 232K, 232Y, 232G, 237D, 237E,
237K, 237R, 237S, 237T, 237H, 237V, 237L, 237I, 237F, 237M, 237Y,
241W, 241D, 241E, 244H, 247V, 247G, 264D, 264E, 264N, 264Q, 264K,
264S, 264H, 264W, 264G, 266T, 271E, 271N, 271Q, 271K, 271R, 271S,
271T, 271H, 271V, 271L, 271F, 271M, 271Y, 271W, 281K, 281Y, 282E,
282K, 282G, 291D, 291E, 291Q, 291T, 291I, 291G, 299I, 299A, 299V,
299H, 299D, 299E, 299N, 299Q, 299K, 299L, 299F, 299M, 299Y, 299W,
299P, 299G, 300E, 300N, 300K, 300R, 300A, 300V, 300P, 300G, 304D,
304H, 317E, 325L, 325I, 325D, 325E, 325A, 325V, 325S, 325F, 325Y,
325W, 325P, 325G, 328E, 328F, 328N, 328H, 328D, 328Q, 328K, 328R,
328S, 328T, 328Y, 328W, 328G, 332Q, 332K, 332R, 336E, 336K, and
336Y.
4. The polypeptide of claim 1 wherein the Fc variant comprises at
least one combination of substitutions selected from the group
consisting of: 230A/233D, 235D/239D/297D/332E, 239N/332N,
239N/332Q, 239Q/332N, 239Q/332Q, 239D/297D/332E, 239E/297D/332E,
239D/278T/332E, 239D/265V/297D/332E, 239D/265I/297D/332E,
239D/265L/297D/332E, 239D/265F/297D/332E, 239D/265Y/297D/332E,
239D/265H/297D/332E, 239D/265T/297D/332E, 239D/297D/330Y/332E,
239D/297D/326E/332E, 239D/241S/243H/262T/264T/297D/330Y/332E,
241W/243W, 241L/262I, 241L/243L/262I/264I, 241W/243W/262A/264A,
241Y/243Y/262T/264T, 241E/243R/262E/264R, 241E/243Q/262T/264E,
241R/243Q/262T/264R, 241E/243Y/262T/264R, 241E/243R/262E/264R/332E,
241E/243Y/262T/264R/332E, 241Y/243Y/262T/264T/297D/332E,
243L/262I/264W, 244H/245A/247V, 264E/297D/332E, 265Y/297D/332E,
296E/297D/332E, 296N/297D/332E, 296Q/297D/332E, 296H/297D/332E,
296T/297D/332E, 297S/332E, 297D/332E, 297E/332E, 297D/299V/332E,
297D/299I/332E, 297D/299L/332E, 297D/299F/332E, 297D/299H/332E,
297D/299E/332E, 297D/330Y/332E, 297D/298A/330Y/332E, 328E/332E, and
328Q/332E.
5. The polypeptide of claim 1 wherein said parent polypeptide is an
antibody.
6. The polypeptide of claim 1 wherein said parent polypeptide is an
Fc fusion protein.
7. The polypeptide of claim 1 wherein said polypeptide further
comprises an engineered glycoform.
8. The polypeptide of claim 7 wherein said engineered glycoform
comprises an altered level of fucosylation or bisecting
oligosaccharides as compared to said parent polypeptide.
9. A pharmaceutical composition comprising the polypeptide of claim
1 and a pharmaceutically acceptable carrier.
10. A method of treating a mammal in need of said treatment
comprising administering the polypeptide of claim 1.
11. The polypeptide of claim 1 wherein said polypeptide is a full
length antibody.
12. The polypeptide of claim 1 wherein said polypeptide is a human
antibody.
13. The polypeptide of claim 1 wherein said polypeptide is an
antibody fragment.
Description
[0001] This application is a continuation of U.S. application Ser.
No. 11/124,620, filed May 5, 2005, which claims benefit under 35
U.S.C. .sctn. 119(e) to U.S. Ser. Nos. 60/568,440, filed May 5,
2004; 60/589,906 filed Jul. 20, 2004; 60/627,026 filed Nov. 9,
2004; 60/626,991 filed Nov. 10, 2004; 60/627,774 filed Nov. 12,
2004, 60/531,752, filed Dec. 22, 2003; and, 60/531,891, filed Dec.
22, 2003; and which is continuation-in-part of U.S. Ser. No.
10/822,231, filed Mar. 26, 2004; which is continuation-in-part of
Ser. No. 10/672,280, filed Sep. 26, 2003; which is a
continuation-in-part of Ser. No. 10/379,392, filed Mar. 3, 2003,
all of which are incorporated by reference in their entirety.
FIELD OF THE INVENTION
[0002] The present invention relates to novel optimized Fc
variants, engineering methods for their generation, and their
application, particularly for therapeutic purposes.
BACKGROUND OF THE INVENTION
[0003] Antibodies are immunological proteins that bind a specific
antigen. In most mammals, including humans and mice, antibodies are
constructed from paired heavy and light polypeptide chains. Each
chain is made up of individual immunoglobulin (Ig) domains, and
thus the generic term immunoglobulin is used for such proteins.
Each chain is made up of two distinct regions, referred to as the
variable and constant regions. The light and heavy chain variable
regions show significant sequence diversity between antibodies, and
are responsible for binding the target antigen. The constant
regions show less sequence diversity, and are responsible for
binding a number of natural proteins to elicit important
biochemical events. In humans there are five different classes of
antibodies including IgA (which includes subclasses IgA1 and IgA2),
IgD, IgE, IgG (which includes subclasses IgG1, IgG2, IgG3, and
IgG4), and IgM. The distinguishing features between these antibody
classes are their constant regions, although subtler differences
may exist in the variable region. FIG. 1 shows an IgG1 antibody,
used here as an example to describe the general structural features
of immunoglobulins. IgG antibodies are tetrameric proteins composed
of two heavy chains and two light chains. The IgG heavy chain is
composed of four immunoglobulin domains linked from N- to
C-terminus in the order V.sub.H-C.sub.H1-C.sub.H2-C.sub.H3,
referring to the variable heavy domain, constant heavy domain 1,
constant heavy domain 2, and constant heavy domain 3. The IgG
C.sub.H1, C.sub.H2, and C.sub.H3 domains are also referred to as
constant gamma 1 domain (C.gamma.1), constant gamma 2 domain
(C.gamma.2), and constant gamma 3 domain (C.gamma.3) respectively.
The IgG light chain is composed of two immunoglobulin domains
linked from N- to C-terminus in the order V.sub.L-C.sub.L,
referring to the light chain variable domain and the light chain
constant domain respectively.
[0004] The variable region of an antibody contains the antigen
binding determinants of the molecule, and thus determines the
specificity of an antibody for its target antigen. The variable
region is so named because it is the most distinct in sequence from
other antibodies within the same class. The majority of sequence
variability occurs in the complementarity determining regions
(CDRs). There are 6 CDRs total, three each per heavy and light
chain, designated V.sub.H CDR1, V.sub.H CDR2, V.sub.H CDR3, V.sub.L
CDR1, V.sub.L CDR2, and V.sub.L CDR3. The variable region outside
of the CDRs is referred to as the framework (FR) region. Although
not as diverse as the CDRs, sequence variability does occur in the
FR region between different antibodies. Overall, this
characteristic architecture of antibodies provides a stable
scaffold (the FR region) upon which substantial antigen binding
diversity (the CDRs) can be explored by the immune system to obtain
specificity for a broad array of antigens. A number of
high-resolution structures are available for a variety of variable
region fragments from different organisms, some unbound and some in
complex with antigen. The sequence and structural features of
antibody variable regions are well characterized (Morea et al.,
1997, Biophys Chem 68:9-16; Morea et al., 2000, Methods 20:267-279,
incorporated by reference), and the conserved features of
antibodies have enabled the development of a wealth of antibody
engineering techniques (Maynard et al., 2000, Annu Rev Biomed Eng
2:339-376, incorporated by reference). For example, it is possible
to graft the CDRs from one antibody, for example a murine antibody,
onto the framework region of another antibody, for example a human
antibody. This process, referred to in the art as "humanization",
enables generation of less immunogenic antibody therapeutics from
nonhuman antibodies. Fragments comprising the variable region can
exist in the absence of other regions of the antibody, including
for example the antigen binding fragment (Fab) comprising
V.sub.H-C.gamma.1 and V.sub.H-C.sub.L, the variable fragment (Fv)
comprising V.sub.H and V.sub.L, the single chain variable fragment
(scFv) comprising V.sub.H and V.sub.L linked together in the same
chain, as well as a variety of other variable region fragments
(Little et al., 2000, Immunol Today 21:364-370, incorporated by
reference).
[0005] The Fc region of an antibody interacts with a number of Fc
receptors and ligands, imparting an array of important functional
capabilities referred to as effector functions. For IgG the Fc
region, as shown in FIG. 1, comprises Ig domains C.gamma.2 and
C.gamma.3 and the N-terminal hinge leading into C.gamma.2. An
important family of Fc receptors for the IgG class are the Fc gamma
receptors (Fc.gamma.Rs). These receptors mediate communication
between antibodies and the cellular arm of the immune system
(Raghavan et al., 1996, Annu Rev Cell Dev Biol 12:181-220; Ravetch
et al., 2001, Annu Rev immunol 19:275-290). In humans this protein
family includes Fc.gamma.RI (CD64), including isoforms
Fc.gamma.RIa, Fc.gamma.RIb, and Fc.gamma.RIc; Fc.gamma.RII (CD32),
including isoforms Fc.gamma.RIIa (including allotypes H131 and
R131), Fc.gamma.RIIb (including Fc.gamma.RIIb-1 and
Fc.gamma.RIIb-2), and Fc.gamma.RIIc; and Fc.gamma.RII (CD16),
including isoforms Fc.gamma.RIIIa (including allotypes V158 and
F158) and Fc.gamma.RIIIb (including allotypes Fc.gamma.RIIIb-NA1
and Fc.gamma.RIIIb-NA2) (Jefferis et al., 2002, Immunol Lett
82:57-65, incorporated by reference). These receptors typically
have an extracellular domain that mediates binding to Fc, a
membrane spanning region, and an intracellular domain that may
mediate some signaling event within the cell. These receptors are
expressed in a variety of immune cells including monocytes,
macrophages, neutrophils, dendritic cells, eosinophils, mast cells,
platelets, B cells, large granular lymphocytes, Langerhans' cells,
natural killer (NK) cells, and .gamma..delta. T cells. Formation of
the Fc/Fc.gamma.R complex recruits these effector cells to sites of
bound antigen, typically resulting in signaling events within the
cells and important subsequent immune responses such as release of
inflammation mediators, B cell activation, endocytosis,
phagocytosis, and cytotoxic attack. The ability to mediate
cytotoxic and phagocytic effector functions is a potential
mechanism by which antibodies destroy targeted cells. The
cell-mediated reaction wherein nonspecific cytotoxic cells that
express Fc.gamma.Rs recognize bound antibody on a target cell and
subsequently cause lysis of the target cell is referred to as
antibody dependent cell-mediated cytotoxicity (ADCC) (Raghavan et
al., 1996, Annu Rev Cell Dev Biol 12:181-220; Ghetie et al., 2000,
Annu Rev Immunol 18:739-766; Ravetch et al., 2001, Annu Rev Immunol
19:275-290, incorporated by reference). The cell-mediated reaction
wherein nonspecific cytotoxic cells that express Fc.gamma.Rs
recognize bound antibody on a target cell and subsequently cause
phagocytosis of the target cell is referred to as antibody
dependent cell-mediated phagocytosis (ADCP). A number of structures
have been solved of the extracellular domains of human Fc.gamma.Rs,
including Fc.gamma.RIIa (pdb accession code 1H9V) (Sondermann et
al., 2001, J Mol Biol 309:737-749) (pdb accession code 1FCG)
(Maxwell et al., 1999, Nat Struct Biol 6:437-442), Fc.gamma.RIIb
(pdb accession code 2FCB) (Sondermann et al., 1999, Embo J
18:1095-1103); and Fc.gamma.RIIIb (pdb accession code 1E4J)
(Sondermann et al., 2000, Nature 406:267-273, incorporated by
reference). All Fc.gamma.Rs bind the same region on Fc, at the
N-terminal end of the C.gamma.2 domain and the preceding hinge,
shown in FIG. 2. This interaction is well characterized
structurally (Sondermann et al., 2001, J Mol Biol 309:737-749
incorporated by reference), and several structures of the human Fc
bound to the extracellular domain of human Fc.gamma.RIIIb have been
solved (pdb accession code 1 E4K)(Sondermann et al., 2000, Nature
406:267-273) (pdb accession codes 1IIS and 1IIX) (Radaev et al.,
2001, J Biol Chem 276:16469-16477, incorporated by reference), as
well as has the structure of the human IgE Fc/Fc.epsilon.RI.alpha.
complex (pdb accession code 1F6A) (Garman et al., 2000, Nature
406:259-266, incorporated by reference).
[0006] The different IgG subclasses have different affinities for
the Fc.gamma.Rs, with IgG1 and IgG3 typically binding substantially
better to the receptors than IgG2 and IgG4. All Fc.gamma.Rs bind
the same region on IgG Fc, yet with different affinities: the high
affinity binder Fc.gamma.RI has a Kd for IgG1 of 10.sup.-8
M.sup.-1, whereas the low affinity receptors Fc.gamma.RII and
Fc.gamma.RIII generally bind at 10.sup.-6 and 10.sup.-5
respectively. The extracellular domains of Fc.gamma.RIIIa and
Fc.gamma.RIIIb are 96% identical, however Fc.gamma.RIIIb does not
have a intracellular signaling domain. Furthermore, whereas
Fc.gamma.RI, Fc.gamma.RIIa/c, and Fc.gamma.RIIIa are positive
regulators of immune complex-triggered activation, characterized by
having an intracellular domain that has an immunoreceptor
tyrosine-based activation motif (ITAM), Fc.gamma.RIIb has an
immunoreceptor tyrosine-based inhibition motif (ITIM) and is
therefore inhibitory. Thus the former are referred to as activation
receptors, and Fc.gamma.RIIb is referred to as an inhibitory
receptor. The receptors also differ in expression pattern and
levels on different immune cells. Yet another level of complexity
is the existence of a number of Fc.gamma.R polymorphisms in the
human proteome. A particularly relevant polymorphism with clinical
significance is V158/F158 Fc.gamma.RIIIa. Human IgG1 binds with
greater affinity to the V158 allotype than to the F158 allotype.
This difference in affinity, and presumably its effect on ADCC
and/or ADCP, has been shown to be a significant determinant of the
efficacy of the anti-CD20 antibody rituximab (Rituxan.RTM., a
registered trademark of IDEC Pharmaceuticals Corporation). Patients
with the V158 allotype respond favorably to rituximab treatment;
however, patients with the lower affinity F158 allotype respond
poorly (Cartron et al., 2002, Blood 99:754-758, incorporated by
reference). Approximately 10-20% of humans are V158/V158
homozygous, 45% are V158/F158 heterozygous, and 35-45% of humans
are F158/F158 homozygous (Lehrnbecher et al., 1999, Blood
94:4220-4232; Cartron et al., 2002, Blood 99:754-758, incorporated
by reference). Thus 80-90% of humans are poor responders, that is
they have at least one allele of the F158 Fc.gamma.RIIIa.
[0007] An overlapping but separate site on Fc, shown in FIG. 1,
serves as the interface for the complement protein C1q. In the same
way that Fc/Fc.gamma.R binding mediates ADCC, Fc/C1q binding
mediates complement dependent cytotoxicity (CDC). C1q forms a
complex with the serine proteases C1r and C1s to form the C1
complex. C1q is capable of binding six antibodies, although binding
to two IgGs is sufficient to activate the complement cascade.
Similar to Fc interaction with Fc.gamma.Rs, different IgG
subclasses have different affinity for C1q, with IgG1 and IgG3
typically binding substantially better to the Fc.gamma.Rs than IgG2
and IgG4. There is currently no structure available for the Fc/C1q
complex; however, mutagenesis studies have mapped the binding site
on human IgG for C1q to a region involving residues D270, K322,
K326, P329, and P331, and E333 (Idusogie et al., 2000, J Immunol
164:4178-4184; Idusogie et al., 2001, J Immunol 166:2571-2575,
incorporated by reference).
[0008] A site on Fc between the C.gamma.2 and C.gamma.3 domains,
shown in FIG. 1, mediates interaction with the neonatal receptor
FcRn, the binding of which recycles endocytosed antibody from the
endosome back to the bloodstream (Raghavan et al., 1996, Annu Rev
Cell Dev Biol 12:181-220; Ghetie et al., 2000, Annu Rev Immunol
18:739-766, incorporated by reference). This process, coupled with
preclusion of kidney filtration due to the large size of the full
length molecule, results in favorable antibody serum half-lives
ranging from one to three weeks. Binding of Fc to FcRn also plays a
key role in antibody transport. The binding site for FcRn on Fc is
also the site at which the bacterial proteins A and G bind. The
tight binding by these proteins is typically exploited as a means
to purify antibodies by employing protein A or protein G affinity
chromatography during protein purification. Thus the fidelity of
this region on Fc is important for both the clinical properties of
antibodies and their purification. Available structures of the rat
Fc/FcRn complex (Martin et al., 2001, Mol Cell 7:867-877,
incorporated by reference), and of the complexes of Fc with
proteins A and G (Deisenhofer, 1981, Biochemistry 20:2361-2370;
Sauer-Eriksson et al., 1995, Structure 3:265-278; Tashiro et al.,
1995, Curr Opin Struct Biol 5:471-481, incorporated by reference)
provide insight into the interaction of Fc with these proteins.
[0009] A key feature of the Fc region is the conserved N-linked
glycosylation that occurs at N297, shown in FIG. 1. This
carbohydrate, or oligosaccharide as it is sometimes referred, plays
a critical structural and functional role for the antibody, and is
one of the principle reasons that antibodies must be produced using
mammalian expression systems. While not wanting to be limited to
one theory, it is believed that the structural purpose of this
carbohydrate may be to stabilize or solubilize Fc, determine a
specific angle or level of flexibility between the C.gamma.3 and
C.gamma.2 domains, keep the two C.gamma.2 domains from aggregating
with one another across the central axis, or a combination of
these. Efficient Fc binding to Fc.gamma.R and C1q requires this
modification, and alterations in the composition of the N297
carbohydrate or its elimination affect binding to these proteins
(Umana et al., 1999, Nat Biotechnol 17:176-180; Davies et at.,
2001, Biotechnol Bioeng 74:288-294; Mimura et al., 2001, J Biol
Chem 276:45539-45547.; Radaev et al., 2001, J Biol Chem
276:16478-16483; Shields et al., 2001, J Biol Chem 276:6591-6604;
Shields et al., 2002, J Biol Chem 277:26733-26740; Simmons et al.,
2002, J Immunol Methods 263:133-147, incorporated by reference).
Yet the carbohydrate makes little if any specific contact with
Fc.gamma.Rs (Radaev et al., 2001, J Biol Chem 276:16469-16477,
incorporated by reference), indicating that the functional role of
the N297 carbohydrate in mediating Fc/Fc.gamma.R binding may be via
the structural role it plays in determining the Fc conformation.
This is supported by a collection of crystal structures of four
different Fc glycoforms, which show that the composition of the
oligosaccharide impacts the conformation of C.gamma.2 and as a
result the Fc/Fc.gamma.R interface (Krapp et al., 2003, J Mol Biol
325:979-989, incorporated by reference).
[0010] The features of antibodies discussed above--specificity for
target, ability to mediate immune effector mechanisms, and long
half-life in serum--make antibodies powerful therapeutics.
Monoclonal antibodies are used therapeutically for the treatment of
a variety of conditions including cancer, inflammation, and
cardiovascular disease. There are currently over ten antibody
products on the market and hundreds in development. In addition to
antibodies, an antibody-like protein that is finding an expanding
role in research and therapy is the Fc fusion (Chamow et al., 1996,
Trends Biotechnol 14:52-60; Ashkenazi et al., 1997, Curr Opin
Immunol 9:195-200, incorporated by reference). An Fc fusion is a
protein wherein one or more polypeptides is operably linked to Fc.
An Fc fusion combines the Fc region of an antibody, and thus its
favorable effector functions and pharmacokinetics, with the
target-binding region of a receptor, ligand, or some other protein
or protein domain. The role of the latter is to mediate target
recognition, and thus it is functionally analogous to the antibody
variable region. Because of the structural and functional overlap
of Fc fusions with antibodies, the discussion on antibodies in the
present invention extends directly to Fc fusions.
[0011] There are a number of possible mechanisms by which
antibodies destroy tumor cells, including anti-proliferation via
blockage of needed growth pathways, intracellular signaling leading
to apoptosis, enhanced down regulation and/or turnover of
receptors, CDC, ADCC, ADCP, and promotion of an adaptive immune
response (Cragg et al., 1999, Curr Opin Immunol 11:541-547; Glennie
et al., 2000, Immunol Today 21:403-410. incorporated by reference).
Anti-tumor efficacy may be due to a combination of these
mechanisms, and their relative importance in clinical therapy
appears to be cancer dependent. Despite this arsenal of anti-tumor
weapons, the potency of antibodies as anti-cancer agents is
unsatisfactory, particularly given their high cost. Patient tumor
response data show that monoclonal antibodies provide only a small
improvement in therapeutic success over normal single-agent
cytotoxic chemotherapeutics. For example, just half of all relapsed
low-grade non-Hodgkin's lymphoma patients respond to the anti-CD20
antibody rituximab (McLaughlin et al., 1998, J Clin Oncol
16:2825-2833. incorporated by reference). Of 166 clinical patients,
6% showed a complete response and 42% showed a partial response,
with median response duration of approximately 12 months.
Trastuzumab (Herceptin.RTM., a registered trademark of Genentech),
an anti-HER2/neu antibody for treatment of metastatic breast
cancer, has less efficacy. The overall response rate using
trastuzumab for the 222 patients tested was only 15%, with 8
complete and 26 partial responses and a median response duration
and survival of 9 to 13 months (Cobleigh et al., 1999, J Clin Oncol
17:2639-2648, incorporated by reference). Currently for anticancer
therapy, any small improvement in mortality rate defines success.
Thus there is a significant need to enhance the capacity of
antibodies to destroy targeted cancer cells.
[0012] The role of Fc.gamma.R-mediated effector functions in the
anti-cancer activity of antibodies has been demonstrated in mice
(Clynes et al., 1998, Proc Natl Acad Sci USA 95:652-656; Clynes et
al., 2000, Nat Med 6:443-446, incorporated by reference), and the
affinity of interaction between Fc and certain Fc.gamma.Rs
correlates with targeted cytotoxicity in cell-based assays (Shields
et al., 2001, J Biol Chem 276:6591-6604; Presta et al., 2002,
Biochem Soc Trans 30:487-490; Shields et al., 2002, J Biol Chem
277:26733-26740, incorporated by reference). Additionally, a
correlation has been observed between clinical efficacy in humans
and their allotype of high (V158) or low (F158) affinity
polymorphic forms of Fc.gamma.RIIIa (Cartron et al., 2002, Blood
99:754-758, incorporated by reference).
[0013] Mutagenesis studies have been carried out on Fc towards
various goals, with substitutions typically made to alanine
(referred to as alanine scanning) or guided by sequence homology
substitutions (Duncan et al., 1988, Nature 332:563-564; Lund et
al., 1991, J Immunol 147:2657-2662; Lund et al., 1992, Mol Immunol
29:53-59; Jefferis et al., 1995, Immunol Lett 44:111-117; Lund et
al., 1995, Faseb J 9:115-119; Jefferis et al., 1996, Immunol Lett
54:101-104; Lund et al., 1996, J Immunol 157:4963-4969; Armour et
al., 1999, Eur J Immunol 29:2613-2624; Shields et al., 2001, J Biol
Chem 276:6591-6604) (U.S. Pat. No. 5,624,821; U.S. Pat. No.
5,885,573; PCT WO 00/42072; PCT WO 99/58572), all incorporated by
reference. The majority of substitutions reduce or ablate binding
with Fc.gamma.Rs. However some success has been achieved at
obtaining Fc variants with higher Fc.gamma.R affinity. (See for
example U.S. Pat. No. 5,624,821 and PCT WO 00/42072). For example,
Winter and colleagues substituted the human amino acid at position
235 of mouse IgG2b antibody (a glutamic acid to leucine mutation)
that increased binding of the mouse antibody to human Fc.gamma.RI
by 100-fold (Duncan et al., 1988, Nature 332:563-564) (U.S. Pat.
No. 5,624,821). Shields et al. used alanine scanning mutagenesis to
map Fc residues important to Fc.gamma.R binding, followed by
substitution of select residues with non-alanine mutations (Shields
et al., 2001, J Biol Chem 276:6591-6604; Presta et al., 2002,
Biochem Soc Trans 30:487-490) (PCT WO 00/42072), incorporated by
reference.
[0014] Enhanced affinity of Fc for Fc.gamma.R has also been
achieved using engineered glycoforms generated by expression of
antibodies in engineered or variant cell lines (Umana et al., 1999,
Nat Biotechnol 17:176-180; Davies et al., 2001, Biotechnol Bioeng
74:288-294; Shields et al., 2002, J Biol Chem 277:26733-26740;
Shinkawa et al., 2003, J Biol Chem 278:3466-3473, incorporated by
reference). This approach has generated enhancement of the capacity
of antibodies to bind Fc.gamma.RIIIa and to mediate ADCC.
[0015] Another major shortcoming of antibodies is their demanding
production requirements (Garber, 2001, Nat Biotechnol 19:184-185;
Dove, 2002, Nat Biotechnol 20:777-779, incorporated by reference).
Antibodies must be expressed in mammalian cells, and the currently
marketed antibodies together with other high-demand biotherapeutics
consume essentially all of the available manufacturing capacity.
With hundreds of biologics in development, the majority of which
are antibodies, there is an urgent need for more efficient and
cheaper methods of production. The downstream effects of
insufficient antibody manufacturing capacity are three-fold. First,
it dramatically raises the cost of goods to the producer, a cost
that is passed on to the patient. Second, it hinders industrial
production of approved antibody products, limiting availability of
high demand therapeutics to patients. Finally, because clinical
trials require large amounts of a protein that is not yet
profitable, the insufficient supply impedes progress of the growing
antibody pipeline to market.
[0016] Alternative production methods have been explored in
attempts at alleviating this problem. Transgenic plants and animals
are being pursued as potentially cheaper and higher capacity
production systems (Chadd et al., 2001, Curr Opin Biotechnol
12:188-194, incorporated by reference). Such expression systems,
however, can generate glycosylation patterns significantly
different from human glycoproteins. This may result in reduced or
even lack of effector function because, as discussed above, the
carbohydrate structure can significantly impact Fc.gamma.R and
complement binding. A potentially greater problem with nonhuman
glycoforms may be immunogenicity; carbohydrates are a key source of
antigenicity for the immune system, and the presence of nonhuman
glycoforms has a significant chance of eliciting antibodies that
neutralize the therapeutic, or worse cause adverse immune
reactions. Thus the efficacy and safety of antibodies produced by
transgenic plants and animals remains uncertain. Bacterial
expression is another attractive solution to the antibody
production problem. Expression in bacteria, for example E. coli,
provides a cost-effective and high capacity method for producing
proteins. For complex proteins such as antibodies there are a
number of obstacles to bacterial expression, including folding and
assembly of these complex molecules, proper disulfide formation,
and solubility, stability, and functionality in the absence of
glycosylation because proteins expressed in bacteria are not
glycosylated. Full length unglycosylated antibodies that bind
antigen have been successfully expressed in E. coli (Simmons et
al., 2002, J Immunol Methods 263:133-147, incorporated by
reference), and thus, folding, assembly, and proper disulfide
formation of bacterially expressed antibodies are possible in the
absence of the eukaryotic chaperone machinery. However the ultimate
utility of bacterially expressed antibodies as therapeutics remains
hindered by the lack of glycosylation, which results in lack
effector function and may result in poor stability and solubility.
This will likely be more problematic for formulation at the high
concentrations for the prolonged periods demanded by clinical
use.
[0017] In summary, there is a need for antibodies with enhanced
therapeutic properties.
SUMMARY OF THE INVENTION
[0018] The present invention provides Fc variants that are
optimized for a number of therapeutically relevant properties.
These Fc variants are generally contained within a variant protein,
that preferably comprises an antibody or a Fc fusion protein.
[0019] It is an object of the present invention to provide novel Fc
positions at which amino acid modifications may be made to generate
optimized Fc variants. Said Fc positions include 230, 240, 244,
245, 247, 262, 263, 266, 273, 275, 299, 302, 313, 323, 325, 328,
and 332, wherein the numbering of the residues in the Fc region is
that of the EU index as in Kabat. The present invention describes
any amino acid modification at any of said novel Fc positions in
order to generate an optimized Fc variant.
[0020] It is a further object of the present invention to provide
Fc variants that have been characterized herein. In one embodiment,
said Fc variants comprise at least one amino acid substitution at a
position selected from the group consisting of 221, 222, 223, 224,
225, 227, 228, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239,
240, 241, 243, 244, 245, 246, 247, 249, 255, 258, 260, 262, 263,
264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276,
278, 280, 281, 282, 283, 284, 285, 286, 288, 290, 291, 292, 293,
294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 313,
317, 318, 320, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331,
332, 333, 334, 335, 336, and 337, wherein the numbering of the
residues in the Fc region is that of the EU index as in Kabat. In a
preferred embodiment, said Fc variants comprise at least one
substitution selected from the group consisting of D221K, D221Y,
K222E, K222Y, T223E, T223K, H224E, H224Y, T225E, T225K, T225W,
P227E, P227G, P227K, P227Y, P228E, P228G, P228K, P228Y, P230A,
P230E, P230G, P230Y, A231E, A231G, A231K, A231P, A231Y, P232E,
P232G, P232K, P232Y, E233A, E233D, E233F, E233G, E233H, E233I,
E233K, E233L, E233M, E233N, E233Q, E233R, E233S, E233T, E233V,
E233W, E233Y, L234A, L234D, L234E, L234F, L234G, L234H, L234I,
L234K, L234M, L234N, L234P, L234Q, L234R, L234S, L234T, L234V,
L234W, L234Y, L235A, L235D, L235E, L235F, L235G, L235H, L235I,
L235K, L235M, L235N, L235P, L235Q, L235R, L235S, L235T, L235V,
L235W, L235Y, G236A, G236D, G236E, G236F, G236H, G236I, G236K,
G236L, G236M, G236N, G236P, G236Q, G236R, G236S, G236T, G236V,
G236W, G236Y, G237D, G237E, G237F, G237H, G237I, G237K, G237L,
G237M, G237N, G237P, G237Q, G237R, G237S, G237T, G237V, G237W,
G237Y, P238D, P238E, P238F, P238G, P238H, P238I, P238K, P238L,
P238M, P238N, P238Q, P238R, P238S, P238T, P238V, P238W, P238Y,
S239D, S239E, S239F, S239G, S239H, S239I, S239K, S239L, S239M,
S239N, S239P, S239Q, S239R, S239T, S239V, S239W, S239Y, V240A,
V240I, V240M, V240T, F241D, F241E, F241L, F241R, F241S, F241W,
F241Y, F243E, F243H, F243L, F243Q, F243R, F243W, F243Y, P244H,
P245A, K246D, K246E, K246H, K246Y, P247G, P247V, D249H, D249Q,
D249Y, R255E, R255Y, E258H, E258S, E258Y, T260D, T260E, T260H,
T260Y, V262A, V262E, V262F, V262I, V262T, V263A, V263I, V263M,
V263T, V264A, V264D, V264E, V264F, V264G, V264H, V264I, V264K,
V264L, V264M, V264N, V264P, V264Q, V264R, V264S, V264T, V264W,
V264Y, D265F, D265G, D265H, D265I, D265K, D265L, D265M, D265N,
D265P, D265Q, D265R, D265S, D265T, D265V, D265W, D265Y, V266A,
V266I, V266M, V266T, S267D, S267E, S267F, S267H, S267I, S267K,
S267L, S267M, S267N, S267P, S267Q, S267R, S267T, S267V, S267W,
S267Y, H268D, H268E, H268F, H268G, H268I, H268K, H268L, H268M,
H268P, H268Q, H268R, H268T, H268V, H268W, E269F, E269G, E269H,
E269I, E269K, E269L, E269M, E269N, E269P, E269R, E269S, E269T,
E269V, E269W, E269Y, D270F, D270G, D270H, D270I, D270L, D270M,
D270P, D270Q, D270R, D270S, D270T, D270W, D270Y, P271A, P271D,
P271E, P271F, P271G, P271H, P271I, P271K, P271L, P271M, P271N,
P271Q, P271R, P271S, P271T, P271V, P271W, P271Y, E272D, E272F,
E272G, E272H, E272I, E272K, E272L, E272M, E272P, E272R, E272S,
E272T, E272V, E272W, E272Y, V273I, K274D, K274E, K274F, K274G,
K274H, K274I, K274L, K274M, K274N, K274P, K274R, K274T, K274V,
K274W, K274Y, F275L, F275W, N276D, N276E, N276F, N276G, N276H,
N276I, N276L, N276M, N276P, N276R, N276S, N276T, N276V, N276W,
N276Y, Y278D, Y278E, Y278G, Y278H, Y278I, Y278K, Y278L, Y278M,
Y278N, Y278P, Y278Q, Y278R, Y278S, Y278T, Y278V, Y278W, D280G,
D280K, D280L, D280P, D280W, G281D, G281E, G281K, G281N, G281P,
G281Q, G281Y, V282E, V282G, V282K, V282P, V282Y, E283G, E283H,
E283K, E283L, E283P, E283R, E283Y, V284D, V284E, V284L, V284N,
V284Q, V284T, V284Y, H285D, H285E, H285K, H285Q, H285W, H285Y,
N286E, N286G, N286P, N286Y, K288D, K288E, K288Y, K290D, K290H,
K290L, K290N, K290W, P291D, P291E, P291G, P291H, P291I, P291Q,
P291T, R292D, R292E, R292T, R292Y, E293F, E293G, E293H, E293I,
E293L, E293M, E293N, E293P, E293R, E293S, E293T, E293V, E293W,
E293Y, E294F, E294G, E294H, E294I, E294K, E294L, E294M, E294P,
E294R, E294S, E294T, E294V, E294W, E294Y, Q295D, Q295E, Q295F,
Q295G, Q295H, Q295I, Q295M, Q295N, Q295P, Q295R, Q295S, Q295T,
Q295V, Q295W, Q295Y, Y296A, Y296D, Y296E, Y296G, Y296H, Y296I,
Y296K, Y296L, Y296M, Y296N, Y296Q, Y296R, Y296S, Y296T, Y296V,
N297D, N297E, N297F, N297G, N297H, N297I, N297K, N297L, N297M,
N297P, N297Q, N297R, N297S, N297T, N297V, N297W, N297Y, S298D,
S298E, S298F, S298H, S298I, S298K, S298M, S298N, S298Q, S298R,
S298T, S298W, S298Y, T299A, T299D, T299E, T299F, T299G, T299H,
T299I, T299K, T299L, T299M, T299N, T299P, T299Q, T299R, T299S,
T299V, T299W, T299Y, Y300A, Y300D, Y300E, Y300G, Y300H, Y300K,
Y300M, Y300N, Y300P, Y300Q, Y300R, Y300S, Y300T, Y300V, Y300W,
R301D, R301E, R301H, R301Y, V302I, V303D, V303E, V303Y, S304D,
S304H, S304L, S304N, S304T, V305E, V305T, V305Y, W313F, K317E,
K317Q, E318H, E318L, E318Q, E318R, E318Y, K320D, K320F, K320G,
K320H, K320I, K320L, K320N, K320P, K320S, K320T, K320V, K320W,
K320Y, K322D, K322F, K322G, K322H, K322I, K322P, K322S, K322T,
K322V, K322W, K322Y, V323I, S324D, S324F, S324G, S324H, S324I,
S324L, S324M, S324P, S324R, S324T, S324V, S324W, S324Y, N325A,
N325D, N325E, N325F, N325G, N325H, N325I, N325K, N325L, N325M,
N325P, N325Q, N325R, N325S, N325T, N325V, N325W, N325Y, K326I,
K326L, K326P, K326T, A327D, A327E, A327F, A327H, A327I, A327K,
A327L, A327M, A327N, A327P, A327R, A327S, A327T, A327V, A327W,
A327Y, L328A, L328D, L328E, L328F, L328G, L328H, L328I, L328K,
L328M, L328N, L328P, L328Q, L328R, L328S, L328T, L328V, L328W,
L328Y, P329D, P329E, P329F, P329G, P329H, P329I, P329K, P329L,
P329M, P329N, P329Q, P329R, P329S, P329T, P329V, P329W, P329Y,
A330E, A330F, A330G, A330H, A330I, A330L, A330M, A330N, A330P,
A330R, A330S, A330T, A330V, A330W, A330Y, P331D, P331F, P331H,
P331I, P331L, P331M, P331Q, P331R, P331T, P331V, P331W, P331Y,
I332A, I332D, I332E, I332F, I332H, I332K, I332L, I332M, I332N,
I332P, I332Q, I332R, I332S, I332T, I332V, I332W, I332Y, E333F,
E333H, E333I, E333L, E333M, E333P, E333T, E333Y, K334F, K334I,
K334L, K334P, K334T, T335D, T335F, T335G, T335H, T335I, T335L,
T335M, T335N, T335P, T335R, T335S, T335V, T335W, T335Y, I336E,
I336K, I336Y, S337E, S337H, and S337N, wherein the numbering of the
residues in the Fc region is that of the EU index as in Kabat. This
set of variants is sometimes referenced to as "the single variant
set" of the invention.
[0021] It is an additional aspect of the invention to provide Fc
variants (and proteins containing these variants) that have at
least 1, 2, 3, 4, 5, 6, 7, 8, 9 and 10 or more amino acid
substitutions as compared to the parent Fc polypeptide, for example
the Fc region SEQ ID NO:1. In some embodiments, 1, 2, 3 and 4
substitutions find particular use.
[0022] It is a further aspect of the invention to provide Fc
variants (and proteins containing these variants) that exhibit
altered Fc ligand binding as compared to the parent Fc polypeptide,
for example the Fc region of SEQ ID NO:1, and that are encoded by
nucleic acids that hybridize under high stringency conditions to a
gene that encodes a human Fc polypeptide. High stringency
conditions are known in the art; see for example U.S. Pat. No.
6,875,846, hereby incorporated by reference, particularly for high
stringency conditions. Genes that encode human Fc polypeptides are
usually fragments of larger genes, and are also known in the art,
as well as genes that due to the degeneracy of the genetic code
will encode a naturally occurring Fc polypeptide even if not
naturally occurring themselves.
[0023] It is an additional aspect of the invention to provide Fc
variants (and proteins containing these variants) that have at
least 1, 2, 3, 4, 5, 6, 7, 8, 9 and 10 or more amino acid
substitutions as compared to the parent Fc polypeptide, for example
the Fc region SEQ ID NO:X. In some embodiments, 1, 2, 3 and 4
substitutions find particular use.
[0024] It is a further aspect of the invention to provide Fc
variants (and proteins containing these variants) that exhibit
altered Fc ligand binding as compared to the parent Fc polypeptide,
for example the Fc region of SEQ ID NO:X, and that are encoded by
nucleic acids that hybridize under high stringency conditions to a
gene that encodes a human Fc polypeptide. High stringency
conditions are known in the art; see for example U.S. Pat. No.
6,875,846, hereby incorporated by reference, particularly for high
stringency conditions. Genes that encode human Fc polypeptides are
usually fragments of larger genes, and are also known in the art,
as well as genes that due to the degeneracy of the genetic code
will encode a naturally occurring Fc polypeptide even if not
naturally occurring themselves.
[0025] It is an additional aspect of the invention to provide for
variant Fc polypeptides that exhibit altered ADCC activity,
particularly increased ADCC activity. In some aspects, these
variants comprise an amino acid substitution at position 239,
optionally amino acid substitutions at positions 239 and 332, and
optionally can include any other substitutions outlined in the
single variant set above, to create variants comprising multiple
substitutions.
[0026] It is a further object of the present invention to provide
Fc variants that have been characterized herein, wherein said Fc
variants are selected from the group consisting of D221K, D221Y,
K222E, K222Y, T223E, T223K, H224E, H224Y, T225E, T225K, T225W,
P227E, P227G, P227K, P227Y, P228E, P228G, P228K, P228Y, P230A,
P230A/E233D, P230A/E233D/I332E, P230E, P230G, P230Y, A231E, A231G,
A231K, A231P, A231Y, P232E, P232G, P232K, P232Y, E233A, E233D,
E233F, E233G, E233H, E233I, E233K, E233L, E233M, E233N, E233Q,
E233R, E233S, E233T, E233V, E233W, E233Y, L234A, L234D, L234E,
L234F, L234G, L234H, L234I, L234I/L235D, L234K, L234M, L234N,
L234P, L234Q, L234R, L234S, L234T, L234V, L234W, L234Y, L235A,
L235D, L235D/S239D/A330Y/I332E, L235D/S239D/N297D/I332E, L235E,
L235F, L235G, L235H, L235I, L235K, L235M, L235N, L235P, L235Q,
L235R, L235S, L235T, L235V, L235W, L235Y, G236A, G236D, G236E,
G236F, G236H, G236I, G236K, G236L, G236M, G236N, G236P, G236Q,
G236R, G236S, G236T, G236V, G236W, G236Y, G237D, G237E, G237F,
G237H, G237I, G237K, G237L, G237M, G237N, G237P, G237Q, G237R,
G237S, G237T, G237V, G237W, G237Y, P238D, P238E, P238F, P238G,
P238H, P238I, P238K, P238L, P238M, P238N, P238Q, P238R, P238S,
P238T, P238V, P238W, P238Y, S239D, S239D/A330L/I332E,
S239D/A330Y/I332E/L234I, S239D/A330Y/I332E/V266I,
S239D/D265F/N297D/I332E, S239D/D265H/N297D/I332E,
S239D/D265I/N297D/I332E, S239D/D265L/N297D/I332E,
S239D/D265T/N297D/I332E, S239D/D265Y/N297D/I332E,
S239D/E272I/A330L/I332E, S239D/E272I/I332E,
S239D/E272K/A330L/I332E, S239D/E272K/I332E,
S239D/E272S/A330L/I332E, S239D/E272S/I332E,
S239D/E272Y/A330L/I332E, S239D/E272Y/I332E,
S239D/F241S/F243H/V262T/V264T/N297D/A330Y/I332E, S239D/H268D,
S239D/H268E, S239D/I332D, S239D/I332E, S239D/I332E/A327D,
S239D/I332E/A330I, S239D/I332E/A330Y, S239D/I332E/E272H,
S239D/I332E/E272R, S239D/I332E/E283H, S239D/I332E/E283L,
S239D/I332E/G236A, S239D/I332E/G236S, S239D/I332E/H268D,
S239D/I332E/H268E, S239D/I332E/K246H, S239D/I332E/R255Y,
S239D/I332E/S267E, S239D/I332E/V264I, S239D/I332E/V264I/A330L,
S239D/I332E/V264I/S298A, S239D/I332E/V284D, S239D/I332E/V284E,
S239D/I332E/V284E, S239D/I332N, S239D/I332Q,
S239D/K274E/A330L/I332E, S239D/K274E/I332E,
S239D/K326E/A330L/I332E, S239D/K326E/A330Y/I332E,
S239D/K326E/I332E, S239D/K326T/A330Y/I332E, S239D/K326T/I332E,
S239D/N297D/A330Y/I332E, S239D/N297D/I332E,
S239D/N297D/K326E/I332E, S239D/S267E/A330L/I332E,
S239D/S267E/I332E, S239D/S298A/K326E/I332E,
S239D/S298A/K326T/I332E, S239D/V240I/A330Y/I332E,
S239D/V264T/A330Y/I332E, S239D/Y278T/A330L/I332E,
S239D/Y278T/I332E, S239E, S239E/D265G, S239E/D265N, S239E/D265Q,
S239E/I332D, S239E/I332E, S239E/I332N, S239E/I332Q,
S239E/N297D/I332E, S239E/V264I/A330Y/I332E, S239E/V264I/I332E,
S239E/V264I/S298A/A330Y/I332E, S239F, S239G, S239H, S239I, S239K,
S239L, S239M, S239N, S239N/I332D, S239N/I332E, S239N/I332E/A330L,
S239N/I332E/A330Y, S239N/I332N, S239N/I332Q, S239P, S239Q,
S239Q/I332D, S239Q/I332E, S239Q/I332N, S239Q/I332Q,
S239Q/V264I/I332E, S239R, S239T, S239V, S239W, S239Y, V240A, V240I,
V240I/V266I, V240M, V240T, F241D, F241E,
F241E/F243Q/V262T/V264E/I332E, F241E/F243Q/V262T/V264E,
F241E/F243R/V262E/V264R/I332E, F241E/F243R/V262E/V264R,
F241E/F243Y/V262T/V264R/I332E, F241E/F243Y/V262T/V264R, F241L,
F241L/F243L/V262I/V264I, F241L/V262I,
F241R/F243Q/V262T/V264R/I332E, F241R/F243Q/V262T/V264R, F241W,
F241W/F243W, F241W/F243W/V262A/V264A, F241Y,
F241Y/F243Y/V262T/V264T/N297D/I332E, F241Y/F243Y/V262T/V264T,
F243E, F243L, F243L/V262I/V264W, F243L/V264I, F243W, P244H,
P244H/P245A/P247V, P245A, K246D, K246E, K246H, K246Y, P247G, P247V,
D249H, D249Q, D249Y, R255E, R255Y, E258H, E258S, E258Y, T260D,
T260E, T260H, T260Y, V262E, V262F, V263A, V263I, V263M, V263T,
V264A, V264D, V264E, V264E/N297D/I332E, V264F, V264G, V264H, V264I,
V264I/A330L/I332E, V264I/A330Y/I332E, V264I/I332E, V264K, V264L,
V264M, V264N, V264P, V264Q, V264R, V264S, V264T, V264W, V264Y,
D265F, D265F/N297E/I332E, D265G, D265H, D265I, D265K, D265L, D265M,
D265N, D265P, D265Q, D265R, D265S, D265T, D265V, D265W, D265Y,
D265Y/N297D/I332E, D265Y/N297D/T299L/I332E, V266A, V266I, V266M,
V266T, S267D, S267E, S267E, S267E/A327D, S267E/P331D, S267E/S324I,
S267E/V282G, S267F, S267H, S267I, S267K, S267L, S267L/A327S, S267M,
S267N, S267P, S267Q, S267Q/A327S, S267R, S267T, S267V, S267W,
S267Y, H268D, H268E, H268F, H268G, H268I, H268K, H268L, H268M,
H268P, H268Q, H268R, H268T, H268V, H268W, E269F, E269G, E269H,
E269I, E269K, E269L, E269M, E269N, E269P, E269R, E269S, E269T,
E269V, E269W, E269Y, D270F, D270G, D270H, D270I, D270L, D270M,
D270P, D270Q, D270R, D270S, D270T, D270W, D270Y, P271A, P271D,
P271E, P271F, P271G, P271H, P271I, P271K, P271L, P271M, P271N,
P271Q, P271R, P271S, P271T, P271V, P271W, P271Y, E272D, E272F,
E272G, E272H, E272I, E272K, E272L, E272M, E272P, E272R, E272S,
E272T, E272V, E272W, E272Y, V273I, K274D, K274E, K274F, K274G,
K274H, K274I, K274L, K274M, K274N, K274P, K274R, K274T, K274V,
K274W, K274Y, F275L, F275W, N276D, N276E, N276F, N276G, N276H,
N276I, N276L, N276M, N276P, N276R, N276S, N276T, N276V, N276W,
N276Y, Y278D, Y278E, Y278G, Y278H, Y278I, Y278K, Y278L, Y278M,
Y278N, Y278P, Y278Q, Y278R, Y278S, Y278T, Y278V, Y278W, Y278W,
Y278W/E283R/V302I, Y278W/V302I, D280G, D280K, D280L, D280P, D280W,
G281D, G281D/V282G, G281E, G281K, G281N, G281P, G281Q, G281Y,
V282E, V282G, V282G/P331D, V282K, V282P, V282Y, E283G, E283H,
E283K, E283L, E283P, E283R, E283R/V302I/Y278W/E283R, E283Y, V284D,
V284E, V284L, V284N, V284Q, V284T, V284Y, H285D, H285E, H285K,
H285Q, H285W, H285Y, N286E, N286G, N286P, N286Y, K288D, K288E,
K288Y, K290D, K290H, K290L, K290N, K290W, P291D, P291E, P291G,
P291H, P291I, P291Q, P291T, R292D, R292E, R292T, R292Y, E293F,
E293G, E293H, E293I, E293L, E293M, E293N, E293P, E293R, E293S,
E293T, E293V, E293W, E293Y, E294F, E294G, E294H, E294I, E294K,
E294L, E294M, E294P, E294R, E294S, E294T, E294V, E294W, E294Y,
Q295D, Q295E, Q295F, Q295G, Q295H, Q295I, Q295M, Q295N, Q295P,
Q295R, Q295S, Q295T, Q295V, Q295W, Q295Y, Y296A, Y296D, Y296E,
Y296G, Y296I, Y296K, Y296L, Y296M, Y296N, Y296Q, Y296R, Y296S,
Y296T, Y296V, N297D, N297D/I332E, N297D/I332E/A330Y,
N297D/I332E/S239D/A330L, N297D/I332E/S239D/D265V,
N297D/I332E/S298A/A330Y, N297D/I332E/T299E, N297D/I332E/T299F,
N297D/I332E/T299H, N297D/I332E/T299I, N297D/I332E/T299L,
N297D/I332E/T299V, N297D/I332E/Y296D, N297D/I332E/Y296E,
N297D/I332E/Y296H, N297D/I332E/Y296N, N297D/I332E/Y296Q,
N297D/I332E/Y296T, N297E/I332E, N297F, N297G, N297H, N297I, N297K,
N297L, N297M, N297P, N297Q, N297R, N297S, N297S/I332E, N297T,
N297V, N297W, N297Y, S298A/I332E, S298A/K326E, S298A/K326E/K334L,
S298A/K334L, S298D, S298E, S298F, S298H, S298I, S298K, S298M,
S298N, S298Q, S298R, S298T, S298W, S298Y, T299A, T299D, T299E,
T299F, T299G, T299H, T299I, T299K, T299L, T299M, T299N, T299P,
T299Q, T299R, T299S, T299V, T299W, T299Y, Y300A, Y300D, Y300E,
Y300G, Y300H, Y300K, Y300M, Y300N, Y300P, Y300Q, Y300R, Y300S,
Y300T, Y300V, Y300W, R301D, R301E, R301H, R301Y, V302I, V303D,
V303E, V303Y, S304D, S304H, S304L, S304N, S304T, V305E, V305T,
V305Y, W313F, K317E, K317Q, E318H, E318L, E318Q, E318R, E318Y,
K320D, K320F, K320G, K320H, K320I, K320L, K320N, K320P, K320S,
K320T, K320V, K320W, K320Y, K322D, K322F, K322G, K322H, K322I,
K322P, K322S, K322T, K322V, K322W, K322Y, V323I, S324D, S324F,
S324G, S324H, S324I, S324I/A327D, S324L, S324M, S324P, S324R,
S324T, S324V, S324W, S324Y, N325A, N325D, N325E, N325F, N325G,
N325H, N325I, N325K, N325L, N325M, N325P, N325Q, N325R, N325S,
N325T, N325V, N325W, N325Y, K326I, K326L, K326P, K326T, A327D,
A327E, A327F, A327H, A327I, A327K, A327L, A327M, A327N, A327P,
A327R, A327S, A327T, A327V, A327W, A327Y, L328A, L328D,
L328D/I332E, L328E, L328E/I332E, L328F, L328G, L328H, L328H/I332E,
L328I, L328I/I332E, L328I/I332E, L328K, L328M, L328M/I332E, L328N,
L328N/I332E, L328P, L328Q, L328Q/I332E, L328Q/I332E, L328R, L328S,
L328T, L328T/I332E, L328V, L328V/I332E, L328W, L328Y, P329D, P329E,
P329F, P329G, P329H, P329I, P329K, P329L, P329M, P329N, P329Q,
P329R, P329S, P329T, P329V, P329W, P329Y, A330E, A330F, A330G,
A330H, A330I, A330L, A330L/I332E, A330M, A330N, A330P, A330R,
A330S, A330T, A330V, A330W, A330Y, A330Y/I332E, P331D, P331F,
P331H, P331I, P331L, P331M, P331Q, P331R, P331T, P331V, P331W,
P331Y, I332A, I332D, I332E, I332E/G281D, I332E/H268D, I332E/H268E,
I332E/S239D/S298A, I332E/S239N/S298A, I332E/V264I/S298A,
I332E/V284E, I332F, I332H, I332K, I332L, I332M, I332N, I332P,
I332Q, I332R, I332S, I332T, I332V, I332W, I332Y, E333F, E333H,
E333I, E333L, E333M, E333P, E333T, E333Y, K334F, K334I, K334P,
K334T, T335D, T335F, T335G, T335H, T335I, T335L, T335M, T335N,
T335P, T335R, T335S, T335V, T335W, T335Y, I336E, I336K, I336Y,
S337E, S337H, and S337N, wherein the numbering of the residues in
the Fc region is that of the EU index as in Kabat.
[0027] It is a further object of the present invention to provide
an Fc variant that binds with greater affinity to one or more
Fc.gamma.Rs. In one embodiment, said Fc variants have affinity for
an FC.gamma.R that is more than 1-fold greater than that of the
parent Fc polypeptide. In an alternate embodiment, said Fc variants
have affinity for an Fc.gamma.R that is more than 5-fold greater
than that of the parent Fc polypeptide. In a preferred embodiment,
said Fc variants have affinity for an Fc.gamma.R that is between
about 5-fold and 300-fold greater than that of the parent Fc
polypeptide.
[0028] It is a further object of the present invention to provide
Fc variant that have a Fc.gamma.RIIIa-fold:Fc.gamma.RIIb-fold ratio
greater than 1:1. In one embodiment, said Fc variants have a
Fc.gamma.RIIIa-fold:Fc.gamma.RIIb-fold ratio greater than 11:1. In
a preferred embodiment, said Fc variants have a
Fc.gamma.RIIa-fold:Fc.gamma.RIIb-fold ratio between 11:1 and
86:1.
[0029] It is a further object of the present invention to provide
Fc variants that mediate effector function more effectively in the
presence of effector cells. In one embodiment, said Fc variants
mediate ADCC that is greater than that mediated by the parent Fc
polypeptide. In a preferred embodiment, said Fc variants mediate
ADCC that is more than 5-fold greater than that mediated by the
parent Fc polypeptide. In a mostly preferred embodiment, said Fc
variants mediate ADCC that is between 5-fold and 1000-fold greater
than that mediated by the parent Fc polypeptide.
[0030] It is a further object of the present invention to provide
Fc variants that bind with weaker affinity to one or more
Fc.gamma.Rs. It is a further object of the present invention to
provide Fc variants that mediate ADCC in the presence of effector
cells less effectively.
[0031] It is a further object of the present invention to provide
Fc variants that have improved function and/or solution properties
as compared to the aglycosylated form of the parent Fc polypeptide.
Improved functionality herein includes but is not limited to
binding affinity to an Fc ligand. Improved solution properties
herein includes but is not limited to stability and solubility. In
an one embodiment, said Fc variants bind to an Fc.gamma.R with an
affinity that is within about 0.5-fold of the glycosylated form of
the parent Fc polypeptide. In an alternate embodiment, said
aglycosylated Fc variants bind to an Fc.gamma.R with an affinity
that is comparable to the glycosylated parent Fc polypeptide. In an
alternate embodiment, said Fc variants bind to an Fc.gamma.R with
an affinity that is greater than the glycosylated form of the
parent Fc polypeptide.
[0032] The present invention also provides methods for engineering
optimized Fc variants. It is a further object of the present
invention to provide experimental production and screening methods
for obtaining optimized Fc variants.
[0033] The present invention provides isolated nucleic acids
encoding the Fc variants described herein. The present invention
provides vectors comprising said nucleic acids, optionally,
operably linked to control sequences. The present invention
provides host cells containing the vectors, and methods for
producing and optionally recovering the Fc variants.
[0034] The present invention provides novel Fc polypeptides,
including antibodies, Fc fusions, isolated Fc, and Fc fragments,
that comprise the Fc variants disclosed herein. Said novel Fc
polypeptides may find use in a therapeutic product.
[0035] The present invention provides compositions comprising Fc
polypeptides that comprise the Fc variants described herein, and a
physiologically or pharmaceutically acceptable carrier or
diluent.
[0036] The present invention contemplates therapeutic and
diagnostic uses for Fc polypeptides that comprise the Fc variants
disclosed herein.
BRIEF DESCRIPTION OF THE DRAWINGS
[0037] FIG. 1. Antibody structure and function. Shown is a model of
a full length human IgG1 antibody, modeled using a humanized Fab
structure from pdb accession code 1CE1 (James et al., 1999, J Mol
Biol 289:293-301) and a human IgG1 Fc structure from pdb accession
code 1DN2 (DeLano et al., 2000, Science 287:1279-1283). The
flexible hinge that links the Fab and Fc regions is not shown. IgG1
is a homodimer of heterodimers, made up of two light chains and two
heavy chains. The Ig domains that comprise the antibody are
labeled, and include V.sub.L and C.sub.L for the light chain, and
V.sub.H, Cgammal (C.gamma.1), Cgamma2 (C.gamma.2), and Cgamma3
(C.gamma.3) for the heavy chain. The Fc region is labeled. Binding
sites for relevant proteins are labeled, including the antigen
binding site in the variable region, and the binding sites for
Fc.gamma.Rs, FcRn, C1q, and proteins A and G in the Fc region.
[0038] FIG. 2. The Fc/Fc.gamma.RIIIb complex structure 1IIS. Fc is
shown as a gray ribbon diagram, and Fc.gamma.RIIIb is shown as a
black ribbon. The N297 carbohydrate is shown as black sticks.
[0039] FIGS. 3a-3b. Alignment of the amino acid sequences of the
human IgG immunoglobulins IgG1, IgG2, IgG3, and IgG4. FIG. 3a
provides the sequences of the CH1 (C.gamma.1) and hinge domains,
and FIG. 3b provides the sequences of the CH2 (C.gamma.2) and CH3
(C.gamma.3) domains. Positions are numbered according to the EU
index of the IgG1 sequence, and differences between IgG1 and the
other immunoglobulins IgG2, IgG3, and IgG4 are shown in grey.
Polymorphisms exist at a number of positions (Kim et al., 2001, J.
Mol. Evol. 54:1-9), and thus slight differences between the
presented sequences and sequences in the prior art may exist. The
possible beginnings of the Fc region are labeled, defined herein as
either EU position 226 or 230.
[0040] FIG. 4. Residues at which amino acid modifications were made
in the Fc variants of the present invention, mapped onto the
Fc/Fc.gamma.RIIIb complex structure 1IIS. Fc is shown as a gray
ribbon diagram, and Fc.gamma.RIIIb is shown as a black ribbon.
Experimental library residues are shown in black, the N297
carbohydrate is shown in grey.
[0041] FIG. 5. Expression of Fc variant and wild type (WT) proteins
of alemtuzumab in 293T cells. Plasmids containing alemtuzumab heavy
chain genes (WT or variants) were co-transfected with plasmid
containing the alemtuzumab light chain gene. Media were harvested 5
days after transfection. For each transfected sample, 10 ul medium
was loaded on a SDS-PAGE gel for Western analysis. The probe for
Western was peroxidase-conjugated goat-anti human IgG (Jackson
Immuno-Research, catalog # 109-035-088). WT: wild type alemtuzumab;
1-10: alemtuzumab variants. H and L indicate antibody heavy chain
and light chain, respectively.
[0042] FIG. 6. Purification of alemtuzumab using protein A
chromatography. WT alemtuzumab proteins was expressed in 293T cells
and the media was harvested 5 days after transfection. The media
were diluted 1:1 with PBS and purified with protein A (Pierce,
Catalog # 20334). O: original sample before purification; FT: flow
through; E: elution; C: concentrated final sample. The left picture
shows a Simple Blue-stained SDS-PAGE gel, and the right shows a
western blot labeled using peroxidase-conjugated goat-anti human
IgG.
[0043] FIG. 7. Production of deglycosylated antibodies. Wild type
and variants of alemtuzumab were expressed in 293T cells and
purified with protein A chromatography. Antibodies were incubated
with peptide-N-glycosidase (PNGase F) at 37.degree. C. for 24 h.
For each antibody, a mock treated sample (-PNGase F) was done in
parallel. WT: wild-type alemtuzumab; #15, #16, #17, #18, #22:
alemtuzumab variants F241E/F243R/V262E/V264R,
F241E/F243Q/V262T/V264E, F241R/F243Q/V262T/V264R,
F241E/F243Y/V262T/V264R, and I332E respectively. The faster
migration of the PNGase F treated versus the mock treated samples
represents the deglycosylated heavy chains.
[0044] FIG. 8. Alemtuzumab expressed from 293T cells binds its
antigen. The antigenic CD52 peptide, fused to GST, was expressed in
E. coli BL21 (DE3) under IPTG induction. Both uninduced and induced
samples were run on a SDS-PAGE gel, and transferred to PVDF
membrane. For western analysis, either alemtuzumab from Sotec
(a-CD52, Sotec) (final concentration 2.5 ng/ul) or media of
transfected 293T cells (Campath, Xencor) (final alemtuzumab
concentration approximately 0.1-0.2 ng/ul) were used as primary
antibody, and peroxidase-conjugated goat-anti human IgG was used as
secondary antibody. M: pre-stained marker; U: un-induced sample for
GST-CD52; I: induced sample for GST-CD52.
[0045] FIG. 9. Expression and purification of extracellular region
of human V158 Fc.gamma.RIIIa. Tagged Fc.gamma.RIIIa was transfected
in 293T cells, and media containing secreted Fc.gamma.RIIIa were
harvested 3 days later and purified using affinity chromatography.
1: media; 2: flow through; 3: wash; 4-8: serial elutions. Both
simple blue-stained SDS-PAGE gel and western result are shown. For
the western blot, membrane was probed with anti-GST antibody.
[0046] FIG. 10. Binding to human V158 Fc.gamma.RIIIa by select
alemtuzumab Fc variants from the experimental library as determined
by the AlphaScreen.TM. assay, described in Example 2. In the
presence of competitor antibody (Fc variant or WT alemtuzumab) a
characteristic inhibition curve is observed as a decrease in
luminescence signal. Phosphate buffer saline (PBS) alone was used
as the negative control. The binding data were normalized to the
maximum and minimum luminescence signal for each particular curve,
provided by the baselines at low and high antibody concentrations
respectively. The curves represent the fits of the data to a one
site competition model using nonlinear regression. These fits
provide IC50s for each antibody, illustrated for WT and S239D by
the dotted lines.
[0047] FIGS. 11a and 11b. AlphaScreen assay showing binding of
select alemtuzumab (FIG. 11a) and trastuzumab (FIG. 11b) Fc
variants to human Val158 Fc.gamma.RIIIa. The binding data were
normalized to the upper and lower baselines for each particular
antibody, and the curves represent the fits of the data to a one
site competition model. PBS was used as a negative control.
[0048] FIGS. 12. AlphaScreen assay showing binding of select
alemtuzumab Fc variants to human Fc.gamma.RIIb. The binding data
were normalized to the upper and lower baselines for each
particular antibody, and the curves represent the fits of the data
to a one site competition model. PBS was used as a negative
control.
[0049] FIGS. 13. AlphaScreen assay showing binding of select
alemtuzumab Fc variants to human R131 Fc.gamma.RIIa. The binding
data were normalized to the upper and lower baselines for each
particular antibody, and the curves represent the fits of the data
to a one site competition model.
[0050] FIG. 14. AlphaScreen assay measuring binding of select
alemtuzumab Fc variants to human FcRn, as described in Example 2.
The binding data were normalized to the upper and lower baselines
for each particular antibody, and the curves represent the fits of
the data to a one site competition model. PBS was used as a
negative control.
[0051] FIG. 15. AlphaScreen assay measuring binding of select
alemtuzumab Fc variants to bacterial protein A, as described in
Example 2. The binding data were normalized to the upper and lower
baselines for each particular antibody, and the curves represent
the fits of the data to a one site competition model. PBS was used
as a negative control.
[0052] FIGS. 16a-16b. AlphaScreen assay comparing binding of select
alemtuzumab Fc variants to human V158 Fc.gamma.RIIIa (FIG. 16a) and
human Fc.gamma.RIIb (FIG. 16b). The binding data were normalized to
the upper and lower baselines for each particular antibody, and the
curves represent the fits of the data to a one site competition
model. PBS was used as a negative control.
[0053] FIGS. 17a-17b. AlphaScreen assay measuring binding to human
V158 Fc.gamma.RIIIa (FIGS. 17a and 17b) and human Fc.gamma.RIIb
(FIG. 17c) by select Fc variants in the context of trastuzumab. The
binding data were normalized to the upper and lower baselines for
each particular antibody, and the curves represent the fits of the
data to a one site competition model. PBS was used as a negative
control.
[0054] FIG. 18. AlphaScreen assay measuring binding to human V158
Fc.gamma.RIIIa by select Fc variants in the context of rituximab.
The binding data were normalized to the upper and lower baselines
for each particular antibody, and the curves represent the fits of
the data to a one site competition model. PBS was used as a
negative control.
[0055] FIG. 19. AlphaScreen assay measuring binding to human V158
Fc.gamma.RIIIa by select Fc variants in the context of cetuximab.
The binding data were normalized to the upper and lower baselines
for each particular antibody, and the curves represent the fits of
the data to a one site competition model. PBS was used as a
negative control.
[0056] FIGS. 20a-20b. AlphaScreen assay showing binding of select
alemtuzumab Fc variants to the V158 (FIG. 20a) and F158 (FIG. 20b)
allotypes of human Fc.gamma.RIIIa. The binding data were normalized
to the upper and lower baselines for each particular antibody, and
the curves represent the fits of the data to a one site competition
model. PBS was used as a negative control.
[0057] FIGS. 21a-21d. FIGS. 21a and 21b show the correlation
between SPR Kd's and AlphaScreen IC50's from binding of select
alemtuzumab Fc variants to V158 Fc.gamma.RIIIa (FIG. 21a) and F158
Fc.gamma.RIIIa (FIG. 21b). FIGS. 21c and 21d show the correlation
between SPR and AlphaScreen fold-improvements over WT for binding
of select alemtuzumab Fc variants to V158 Fc.gamma.RIIIa (FIG. 21c)
and F158 Fc.gamma.RIIIa (FIG. 21d). Binding data are presented in
Table 3. The lines through the data represent the linear fits of
the data, and the r.sup.2 values indicate the significance of these
fits.
[0058] FIGS. 22a and 22b. AlphaScreen assay showing binding of
select alemtuzumab Fc variants to human V158 Fc.gamma.RIIIa. The
binding data were normalized to the upper and lower baselines for
each particular antibody, and the curves represent the fits of the
data to a one site competition model. PBS was used as a negative
control.
[0059] FIGS. 23a-23b. Cell-based ADCC assays of select Fc variants
in the context of alemtuzumab. ADCC was measured using the
DELFIA.RTM. EuTDA-based cytotoxicity assay (Perkin Elmer, Mass.),
as described in Example 3, using DoHH-2 lymphoma target cells and
50-fold excess human PBMCs. FIG. 23a is a bar graph showing the raw
fluorescence data for the indicated alemtuzumab antibodies at 10
ng/ml. The PBMC bar indicates basal levels of cytotoxicity in the
absence of antibody. FIG. 23b shows the dose-dependence of ADCC on
antibody concentration for the indicated alemtuzumab antibodies,
normalized to the minimum and maximum fluorescence signal for each
particular curve, provided by the baselines at low and high
antibody concentrations respectively. The curves represent the fits
of the data to a sigmoidal dose-response model using nonlinear
regression.
[0060] FIGS. 24a-24c. Cell-based ADCC assays of select Fc variants
in the context of trastuzumab. ADCC was measured using the
DELFIA.RTM. EuTDA-based cytotoxicity assay, as described in Example
3, using BT474 and Sk-Br-3 breast carcinoma target cells and
50-fold excess human PBMCs. FIG. 24a is a bar graph showing the raw
fluorescence data for the indicated trastuzumab antibodies at 1
ng/ml. The PBMC bar indicates basal levels of cytotoxicity in the
absence of antibody. FIGS. 24b and 24c show the dose-dependence of
ADCC on antibody concentration for the indicated trastuzumab
antibodies, normalized to the minimum and maximum fluorescence
signal for each particular curve, provided by the baselines at low
and high antibody concentrations respectively. The curves represent
the fits of the data to a sigmoidal dose-response model using
nonlinear regression.
[0061] FIGS. 25a-25c. Cell-based ADCC assays of select Fc variants
in the context of rituximab. ADCC was measured using the
DELFIA.RTM. EuTDA-based cytotoxicity assay, as described in Example
3, using WIL2-S lymphoma target cells and 50-fold excess human
PBMCs. FIG. 25a is a bar graph showing the raw fluorescence data
for the indicated rituximab antibodies at 1 ng/ml. The PBMC bar
indicates basal levels of cytotoxicity in the absence of antibody.
FIGS. 25b and 25c show the dose-dependence of ADCC on antibody
concentration for the indicated rituximab antibodies, normalized to
the minimum and maximum fluorescence signal for each particular
curve, provided by the baselines at low and high antibody
concentrations respectively. The curves represent the fits of the
data to a sigmoidal dose-response model using nonlinear
regression.
[0062] FIGS. 26a-26b. Cell-based ADCC assay of select trastuzumab
(FIG. 26a) and rituximab (FIG. 26b) Fc variants showing
enhancements in potency and efficacy. Both assays used homozygous
F158/F158 Fc.gamma.RIIIa PBMCs as effector cells at a 25-fold
excess to target cells, which were Sk-Br-3 for the trastuzumab
assay and WIL2-S for the rituximab assay. Data were normalized
according to the absolute minimal lysis for the assay, provided by
the fluorescence signal of target cells in the presence of PBMCs
alone (no antibody), and the absolute maximal lysis for the assay,
provided by the fluorescence signal of target cells in the presence
of Triton X1000, as described in Example 3.
[0063] FIG. 27. AlphaScreen assay showing binding of select
alemtuzumab Fc variants to human V158 Fc.gamma.RIIIa. The binding
data were normalized to the upper and lower baselines for each
particular antibody, and the curves represent the fits of the data
to a one site competition model. PBS was used as a negative
control.
[0064] FIG. 28. ADCC. Cell-based ADCC assays of select Fc variant
trastuzumab antibodies as compared to WT trastuzumab. Purified
human peripheral blood monocytes (PBMCs) were used as effector
cells, and Sk-Br-3 breast carcinoma cells were used as target
cells. Lysis was monitored by measuring LDH activity using the
Cytotoxicity Detection Kit (LDH, Roche Diagnostic Corporation,
Indianapolis, Ind.). Samples were run in triplicate to provide
error estimates (n=3, +/-S.D.). The figure shows the dose
dependence of ADCC at various antibody concentrations, normalized
to the minimum and maximum levels of lysis for the assay. The
curves represent the fits of the data to a sigmoidal dose-response
model using nonlinear regression.
[0065] FIGS. 29a-29b. Cell-based ADCC assay of select trastuzumab
Fc variants against different cell lines expressing varying levels
of the Her2/neu target antigen. ADCC assays were run as described
in Example 5, with various cell lines expressing amplified to low
levels of Her2/neu receptor, including Sk-Br-3 (1.times.106
copies), SkOV3 (.about.1.times.105), OVCAR3(.about.1.times.104),
and MCF-7 (.about.3.times.103 copies). FIG. 29a provides a western
blot showing the Her2 expression level for each cell line;
equivalent amounts of cell lysate were loaded on an SDS-PAGE gel,
and Her2 was detected using trastuzumab. Human PBMCs allotyped as
homozygous F158/F158 Fc.gamma.RIIIa were used at 25-fold excess to
target cells. The bar graph in FIG. 29b provides ADCC data for WT
and Fc variant against the indicated cell lines, normalized to the
minimum and maximum fluorescence signal provided by minimal lysis
(PBMCs alone) and maximal lysis (Triton X1000).
[0066] FIG. 30. Cell-based ADCC assays of select Fc variants in the
context of trastuzumab using natural killer (NK) cells as effector
cells and measuring LDH release to monitor cell lysis. NK cells,
allotyped as heterozygous F158/F158 Fc.gamma.RIIIa, were at an
4-fold excess to Sk-Br-3 breast carcinoma target cells, and the
level of cytotoxicity was measured using the LDH Cytotoxicity
Detection Kit, according to the manufacturer's protocol (Roche
Diagnostics GmbH, Penzberg, Germany). The graph shows the
dose-dependence of ADCC on antibody concentration for the indicated
trastuzumab antibodies, normalized to the minimum and maximum
fluorescence signal for each particular curve, provided by the
baselines at low and high antibody concentrations respectively. The
curves represent the fits of the data to a sigmoidal dose-response
model using nonlinear regression.
[0067] FIG. 31. Cell-based ADCP assay of select variants. The ADCP
assay was carried out as described in Example 7, using a
co-labeling strategy coupled with flow cytometry. Differentiated
macrophages were used as effector cells, and Sk-Br-3 cells were
used as target cells. Percent phagocytosis represents the number of
co-labeled cells (macrophage+Sk-Br-3) over the total number of
Sk-Br-3 in the population (phagocytosed+non-phagocytosed).
[0068] FIGS. 32a-32c. Capacity of select Fc variants to mediate
binding and activation of complement. FIG. 32a shows an AlphaScreen
assay measuring binding of select alemtuzumab Fc variants to C1q.
The binding data were normalized to the upper and lower baselines
for each particular antibody, and the curves represent the fits of
the data to a one site competition model. FIGS. 32b and 31c show a
cell-based assay measuring capacity of select rituximab Fc variants
to mediate CDC. CDC assays were performed using Alamar Blue to
monitor lysis of Fc variant and WT rituximab-opsonized WIL2-S
lymphoma cells by human serum complement (Quidel, San Diego,
Calif.). The dose-dependence on antibody concentration of
complement-mediated lysis is shown for the indicated rituximab
antibodies, normalized to the minimum and maximum fluorescence
signal for each particular curve, provided by the baselines at low
and high antibody concentrations respectively. The curves represent
the fits of the data to a sigmoidal dose-response model using
nonlinear regression.
[0069] FIGS. 33a-33c. Enhanced B cell depletion by Fc variants in
macaques, as described in Example 9. FIG. 33a shows the percent B
cells remaining in Macaca Fascicularis monkeys during treatment
with anti-CD20 WT and S239D/I332E rituximab antibodies, measured
using markers CD20+ and CD40+. FIG. 33b shows the percent natural
killer (NK) cells remaining in the monkeys during treatment,
measured using markers CD3-/CD16+ and CD3-/CD8+. FIG. 33c shows the
dose response of CD20+ B cell levels to treatment with S239D/I332E
rituximab. Data are presented as the average of 3
monkeys/sample.
[0070] FIGS. 34a and 34b. AlphaScreen assay measuring binding of
select alemtuzumab (FIG. 34a) and trastuzumab (FIG. 34b) Fc
variants to mouse Fc.gamma.RIII, as described in Example 10. The
binding data were normalized to the upper and lower baselines for
each particular antibody, and the curves represent the fits of the
data to a one site competition model. PBS was used as a negative
control.
[0071] FIG. 35. Cell-based ADCC assays of select Fc variants in the
context of trastuzumab using mouse PBMCs as effector cells. ADCC
was measured using the DELFIA.RTM. EuTDA-based cytotoxicity assay
using Sk-Br-3 breast carcinoma target cells and 8-fold excess mouse
PBMCs. The bar graph shows the raw fluorescence data for the
indicated trastuzumab antibodies at 10 ng/ml. The PBMC bar
indicates basal levels of cytotoxicity in the absence of antibody,
and TX indicates complete cell lysis in the presence of Triton
X1000.
[0072] FIG. 36. AlphaScreen assay measuring binding to human V158
Fc.gamma.RIIIa by select trastuzumab Fc variants expressed in 293T
and CHO cells, as described in Example 11. The binding data were
normalized to the upper and lower baselines for each particular
antibody, and the curves represent the fits of the data to a one
site competition model. PBS was used as a negative control.
[0073] FIGS. 37a-37b. Synergy of Fc variants and engineered
glycoforms. FIG. 37a presents an AlphaScreen assay showing V158
Fc.gamma.RIIIa binding by WT and Fc variant (V209,
S239/I332E/A330L) trastuzumab expressed in 293T, CHO, and Lec-13
CHO cells. The data were normalized to the upper and lower
baselines for each antibody, and the curves represent the fits of
the data to a one site competition model. PBS was used as a
negative control. FIG. 37b presents a cell-based ADCC assay showing
the ability of 239T, CHO, and Lec-13 CHO expressed WT and V209
trastuzumab to mediate ADCC. ADCC was measured using the
DELFIA.RTM. EuTDA-based cytotoxicity assay as described previously,
with Sk-Br-3 breast carcinoma target cells. The data show the
dose-dependence of ADCC on antibody concentration for the indicated
trastuzumab antibodies, normalized to the minimum and maximum
fluorescence signal for each particular curve, provided by the
baselines at low and high antibody concentrations respectively. The
curves represent the fits of the data to a sigmoidal dose-response
model using nonlinear regression.
[0074] FIG. 38. AlphaScreen assay showing binding of aglycosylated
alemtuzumab Fc variants to human V158 Fc.gamma.RIIIa. The binding
data were normalized to the upper and lower baselines for each
particular antibody, and the curves represent the fits of the data
to a one site competition model. PBS was used as a negative
control.
[0075] FIG. 39. AlphaScreen assay comparing human V158
Fc.gamma.RIIIa binding by select alemtuzumab Fc variants in
glycosylated (solid symbols, solid lines) and deglycosylated (open
symbols, dotted lines). The binding data were normalized to the
upper and lower baselines for each particular antibody, and the
curves represent the fits of the data to a one site competition
model.
[0076] FIGS. 40a-40c. Sequences showing improved anti-CD20
antibodies. The light and heavy chain sequences of rituximab are
presented in FIG. 40a and FIG. 40b respectively, and are taken from
translated Sequence 3 of U.S. Pat. No. 5,736,137. Relevant
positions in FIG. 40b are bolded, including S239, V240, V264I,
H268, E272, K274, N297, S298, K326, A330, and I332. FIG. 40c shows
the improved anti-CD20 antibody heavy chain sequences, with
variable positions designated in bold as X1, X2, X3, X4, X5, X6,
X7, X8, X9, Z1, and Z2. The table below the sequence provides
possible substitutions for these positions. The improved anti-CD20
antibody sequences comprise at least one non-WT amino acid selected
from the group of possible substitutions for X1, X2, X3, X4, X5,
X6, X7, X8, and X9. These improved anti-CD20 antibody sequences may
also comprise a substitution Z1 and/or Z2. These positions are
numbered according to the EU index as in Kabat, and thus do not
correspond to the sequential order in the sequence.
[0077] FIG. 41 depicts the set of Fc variants that were constructed
and experimentally tested.
[0078] FIG. 42 depicts SEQ ID NO:8; the particular Xaa residues are
as shown in Table 10.
DETAILED DESCRIPTION OF THE INVENTION
[0079] In order that the invention may be more completely
understood, several definitions are set forth below. Such
definitions are meant to encompass grammatical equivalents.
[0080] By "ADCC" or "antibody dependent cell-mediated cytotoxicity"
as used herein is meant the cell-mediated reaction wherein
nonspecific cytotoxic cells that express Fc.gamma.Rs recognize
bound antibody on a target cell and subsequently cause lysis of the
target cell.
[0081] By "ADCP" or antibody dependent cell-mediated phagocytosis
as used herein is meant the cell-mediated reaction wherein
nonspecific cytotoxic cells that express Fc.gamma.Rs recognize
bound antibody on a target cell and subsequently cause phagocytosis
of the target cell.
[0082] By "amino acid modification" herein is meant an amino acid
substitution, insertion, and/or deletion in a polypeptide sequence.
The preferred amino acid modification herein is a substitution. By
"amino acid substitution" or "substitution" herein is meant the
replacement of an amino acid at a particular position in a parent
polypeptide sequence with another amino acid. For example, the
substitution I332E refers to a variant polypeptide, in this case an
Fc variant, in which the isoleucine at position 332 is replaced
with a glutamic acid. In some embodiments, the WT identity need not
be defined. For example, the substitution 332E referes to a variant
polypeptide in which position 332 is mutated to glutamic acid.
[0083] By "antibody" herein is meant a protein consisting of one or
more polypeptides substantially encoded by all or part of the
recognized immunoglobulin genes. The recognized immunoglobulin
genes, for example in humans, include the kappa (.kappa.), lambda
(.lamda.), and heavy chain genetic loci, which together comprise
the myriad variable region genes, and the constant region genes mu
(.mu.), delta (.delta.), gamma (.gamma.), sigma (.sigma.), and
alpha (.alpha.) which encode the IgM, IgD, IgG, IgE, and IgA
isotypes respectively. Antibody herein is meant to include full
length antibodies and antibody fragments, and may refer to a
natural antibody from any organism, an engineered antibody, or an
antibody generated recombinantly for experimental, therapeutic, or
other purposes as further defined below. The term "antibody"
includes antibody fragments, as are known in the art, such as Fab,
Fab', F(ab').sub.2, Fv, scFv, or other antigen-binding subsequences
of antibodies, either produced by the modification of whole
antibodies or those synthesized de novo using recombinant DNA
technologies. Particularly preferred are full length antibodies
that comprise Fc variants as described herein. The term "antibody"
comprises monoclonal and polyclonal antibodies. Antibodies can be
antagonists, agonists, neutralizing, inhibitory, or stimulatory.
The antibodies of the present invention may be nonhuman, chimeric,
humanized, or fully human, as described below in more detail.
[0084] Specifically included within the definition of "antibody"
are aglycosylated antibodies. By "aglycosylated antibody" as used
herein is meant an antibody that lacks carbohydrate attached at
position 297 of the Fc region, wherein numbering is according to
the EU system as in Kabat. The aglycosylated antibody may be a
deglycosylated antibody, that is an antibody for which the Fc
carbohydrate has been removed, for example chemically or
enzymatically. Alternatively, the aglycosylated antibody may be a
nonglycosylated or unglycosylated antibody, that is an antibody
that was expressed without Fc carbohydrate, for example by mutation
of one or residues that encode the glycosylation pattern or by
expression in an organism that does not attach carbohydrates to
proteins, for example bacteria.
[0085] Specifically included within the definition of "antibody"
are full-length antibodies that contain an Fc variant portion. By
"full length antibody" herein is meant the structure that
constitutes the natural biological form of an antibody, including
variable and constant regions. For example, in most mammals,
including humans and mice, the full length antibody of the IgG
class is a tetramer and consists of two identical pairs of two
immunoglobulin chains, each pair having one light and one heavy
chain, each light chain comprising immunoglobulin domains V.sub.L
and C.sub.L, and each heavy chain comprising immunoglobulin domains
V.sub.H, C.gamma.1 (C.sub.H1), C.gamma.2 (C.sub.H2), and C.gamma.3
(C.sub.H3). In some mammals, for example in camels and llamas, IgG
antibodies may consist of only two heavy chains, each heavy chain
comprising a variable domain attached to the Fc region. By "IqG" as
used herein is meant a polypeptide belonging to the class of
antibodies that are substantially encoded by a recognized
immunoglobulin gamma gene. In humans this class comprises IgG1,
IgG2, IgG3, and IgG4. In mice this class comprises IgG1, IgG2a,
IgG2b, IgG3.
[0086] By "amino acid" and "amino acid identity" as used herein is
meant one of the 20 naturally occurring amino acids or any
non-natural analogues that may be present at a specific, defined
position. By "protein" herein is meant at least two covalently
attached amino acids, which includes proteins, polypeptides,
oligopeptides and peptides. The protein may be made up of naturally
occurring amino acids and peptide bonds, or synthetic
peptidomimetic structures, i.e. "analogs", such as peptoids (see
Simon et al., 1992, Proc Natl Acad Sci USA 89(20):9367,
incorporated by reference) particularly when LC peptides are to be
administered to a patient. Thus "amino acid", or "peptide residue",
as used herein means both naturally occurring and synthetic amino
acids. For example, homophenylalanine, citrulline and noreleucine
are considered amino acids for the purposes of the invention.
"Amino acid" also includes imino acid residues such as proline and
hydroxyproline. The side chain may be in either the (R) or the (S)
configuration. In the preferred embodiment, the amino acids are in
the (S) or L-configuration. If non-naturally occurring side chains
are used, non-amino acid substituents may be used, for example to
prevent or retard in vivo degradation.
[0087] By "effector function" as used herein is meant a biochemical
event that results from the interaction of an antibody Fc region
with an Fc receptor or ligand. Effector functions include but are
not limited to ADCC, ADCP, and CDC. By "effector cell" as used
herein is meant a cell of the immune system that expresses one or
more Fc receptors and mediates one or more effector functions.
Effector cells include but are not limited to monocytes,
macrophages, neutrophils, dendritic cells, eosinophils, mast cells,
platelets, B cells, large granular lymphocytes, Langerhans' cells,
natural killer (NK) cells, and .gamma..gamma. T cells, and may be
from any organism including but not limited to humans, mice, rats,
rabbits, and monkeys. By "library" herein is meant a set of Fc
variants in any form, including but not limited to a list of
nucleic acid or amino acid sequences, a list of nucleic acid or
amino acid substitutions at variable positions, a physical library
comprising nucleic acids that encode the library sequences, or a
physical library comprising the Fc variant proteins, either in
purified or unpurified form.
[0088] By "Fc" or "Fc region", as used herein is meant the
polypeptide comprising the constant region of an antibody excluding
the first constant region immunoglobulin domain. Thus Fc refers to
the last two constant region immunoglobulin domains of IgA, IgD,
and IgG, and the last three constant region immunoglobulin domains
of IgE and IgM, and the flexible hinge N-terminal to these domains.
For IgA and IgM, Fc may include the J chain. For IgG, as
illustrated in FIG. 1, Fc comprises immunoglobulin domains Cgamma2
and Cgamma3 (C.gamma.2 and C.gamma.3) and the hinge between Cgammal
(C.gamma.1) and Cgamma2 (C.gamma.2). Although the boundaries of the
Fc region may vary, the human IgG heavy chain Fc region is usually
defined to comprise residues C226 or P230 to its carboxyl-terminus,
wherein the numbering is according to the EU index as in Kabat. Fc
may refer to this region in isolation, or this region in the
context of an Fc polypeptide, as described below. By "Fc
polypeptide" as used herein is meant a polypeptide that comprises
all or part of an Fc region. Fc polypeptides include antibodies, Fc
fusions, isolated Fcs, and Fc fragments.
[0089] By "Fc fusion" as used herein is meant a protein wherein one
or more polypeptides or small molecules is operably linked to an Fc
region or a derivative thereof. Fc fusion is herein meant to be
synonymous with the terms "immunoadhesin", "Ig fusion", "Ig
chimera", and "receptor globulin" (sometimes with dashes) as used
in the prior art (Chamow et al., 1996, Trends Biotechnol 14:52-60;
Ashkenazi et al., 1997, Curr Opin Immunol 9:195-200. incorporated
by reference). An Fc fusion combines the Fc region of an
immunoglobulin with a fusion partner, which in general can be any
protein or small molecule. The role of the non-Fc part of an Fc
fusion, i.e. the fusion partner, may be to mediate target binding,
and thus it is functionally analogous to the variable regions of an
antibody.
[0090] By "Fc gamma receptor" or "Fc.gamma.R" as used herein is
meant any member of the family of proteins that bind the IgG
antibody Fc region and are substantially encoded by the Fc.gamma.R
genes. In humans this family includes but is not limited to
Fc.gamma.RI (CD64), including isoforms Fc.gamma.RIa, Fc.gamma.RIb,
and Fc.gamma.RIc; Fc.gamma.RII (CD32), including isoforms
Fc.gamma.RIIa (including allotypes H131 and R131), Fc.gamma.RIIb
(including Fc.gamma.RIIb-1 and Fc.gamma.RIIb-2), and Fc.gamma.RIIc;
and Fc.gamma.RIII (CD16), including isoforms Fc.gamma.RIIIa
(including allotypes V158 and F158) and Fc.gamma.RIIIb (including
allotypes Fc.gamma.RIIIb-NA1 and Fc.gamma.RIIIb-NA2), as well as
any undiscovered human Fc.gamma.Rs or Fc.gamma.R isoforms or
allotypes. An Fc.gamma.R may be from any organism, including but
not limited to humans, mice, rats, rabbits, and monkeys. Mouse
Fc.gamma.Rs include but are not limited to Fc.gamma.RI (CD64),
Fc.gamma.RII (CD32), Fc.gamma.RIII (CD16), and Fc.gamma.RIII-2
(CD16-2), as well as any undiscovered mouse Fc.gamma.Rs or
Fc.gamma.R isoforms or allotypes.
[0091] By "Fc ligand" or "effector ligand" as used herein is meant
a molecule, preferably a polypeptide, from any organism that binds
to the Fc region of an antibody to form an Fc/Fc ligand complex.
Binding of an Fc ligand to Fc preferably elicits or more effector
functions. Fc ligands include but are not limited to Fc receptors,
Fc.gamma.Rs, Fc.alpha.Rs, Fc.epsilon.ERs, FcRn, C1q, C3, mannan
binding lectin, mannose receptor, staphylococcal protein A,
streptococcal protein G, and viral Fc.gamma.R. Fc ligands also
include Fc receptor homologs (FcRH), which are a family of Fc
receptors that are homologous to the Fc.gamma.Rs (Davis et al.,
2002, Immunological Reviews 190:123-136, incorporated by
reference). Fc ligands may include undiscovered molecules that bind
Fc.
[0092] By "IgG" as used herein is meant a polypeptide belonging to
the class of antibodies that are substantially encoded by a
recognized immunoglobulin gamma gene. In humans this class
comprises IgG1, IgG2, IgG3, and IgG4. In mice this class comprises
IgG1, IgG2a, IgG2b, IgG3. By "immunoglobulin (Ig)" herein is meant
a protein consisting of one or more polypeptides substantially
encoded by immunoglobulin genes. Immunoglobulins include but are
not limited to antibodies. Immunoglobulins may have a number of
structural forms, including but not limited to full length
antibodies, antibody fragments, and individual immunoglobulin
domains. By "immunoglobulin (Ig) domain" herein is meant a region
of an immunoglobulin that exists as a distinct structural entity as
ascertained by one skilled in the art of protein structure. Ig
domains typically have a characteristic .beta.-sandwich folding
topology. The known Ig domains in the IgG class of antibodies are
V.sub.H, C.gamma.1, C.gamma.2, C.gamma.3, V.sub.L, and C.sub.L.
[0093] By "parent polypeptide" or "precursor polypeptide"
(including Fc parent or precursors) as used herein is meant a
polypeptide that is subsequently modified to generate a variant.
Said parent polypeptide may be a naturally occurring polypeptide,
or a variant or engineered version of a naturally occurring
polypeptide. Parent polypeptide may refer to the polypeptide
itself, compositions that comprise the parent polypeptide, or the
amino acid sequence that encodes it. Accordingly, by "parent Fc
polvpeptide" as used herein is meant a Fc polypeptide that is
modified to generate a variant, and by "parent antibody" as used
herein is meant an antibody that is modified to generate a variant
antibody.
[0094] As outlined above, certain positions of the Fc molecule can
be altered. By "Position" as used herein is meant a location in the
sequence of a protein. Positions may be numbered sequentially, or
according to an established format, for example the EU index as in
Kabat. For example, position 297 is a position in the human
antibody IgG1. Corresponding positions are determined as outlined
above, generally through alignment with other parent sequences.
[0095] By "residue" as used herein is meant a position in a protein
and its associated amino acid identity. For example, Asparagine 297
(also referred to as Asn297, also referred to as N297) is a residue
in the human antibody IgG1.
[0096] By "target antigen" as used herein is meant the molecule
that is bound specifically by the variable region of a given
antibody. A target antigen may be a protein, carbohydrate, lipid,
or other chemical compound.
[0097] By "target cell" as used herein is meant a cell that
expresses a target antigen.
[0098] By "variable region" as used herein is meant the region of
an immunoglobulin that comprises one or more Ig domains
substantially encoded by any of the V.kappa., V.lamda., and/or
V.sub.H genes that make up the kappa, lambda, and heavy chain
immunoglobulin genetic loci respectively.
[0099] By "variant polype tide" as used herein is meant a
polypeptide sequence that differs from that of a parent polypeptide
sequence by virtue of at least one amino acid modification. The
parent polypeptide may be a naturally occurring or wild-type (WT)
polypeptide, or may be a modified version of a WT polypeptide.
Variant polypeptide may refer to the polypeptide itself, a
composition comprising the polypeptide, or the amino sequence that
encodes it. Preferably, the variant polypeptide has at least one
amino acid modification compared to the parent polypeptide, e.g.
from about one to about ten amino acid modifications, and
preferably from about one to about five amino acid modifications
compared to the parent. The variant polypeptide sequence herein
will preferably possess at least about 80% homology with a parent
polypeptide sequence, and most preferably at least about 90%
homology, more preferably at least about 95% homology. Accordingly,
by "Fc variant" as used herein is meant an Fc sequence that differs
from that of a parent Fc sequence by virtue of at least one amino
acid modification. An Fc variant may only encompass an Fc region,
or may exist in the context of an antibody, Fc fusion, isolated Fc,
Fc fragment, or other polypeptide that is substantially encoded by
Fc. Fc variant may refer to the Fc polypeptide itself, compositions
comprising the Fc variant polypeptide, or the amino acid sequence
that encodes it.
[0100] The Fc variants of the present invention are defined
according to the amino acid modifications that compose them. Thus,
for example, I332E is an Fc variant with the substitution I332E
relative to the parent Fc polypeptide. Likewise, S239D/A330L/I332E
(also referred to as 239D/330L/332E) defines an Fc variant with the
substitutions S239D, A330L, and I332E (239D, 330L, and 332E)
relative to the parent Fc polypeptide. It is noted that the order
in which substitutions are provided is arbitrary, that is to say
that, for example, S239D/A330L/I332E is the same Fc variant as
S239D/I332E/A330L, and so on. For all positions discussed in the
present invention, numbering is according to the EU index or EU
numbering scheme (Kabat et al., 1991, Sequences of Proteins of
Immunological Interest, 5th Ed., United States Public Health
Service, National Institutes of Health, Bethesda, incorporated by
reference). The EU index or EU index as in Kabat refers to the
numbering of the EU antibody (Edelman et al., 1969, Proc Natl Acad
Sci USA 63:78-85, incorporated by reference).
[0101] The present invention is directed to optimized Fc variants
useful in a variety of contexts. As outlined above, current
antibody therapies suffer from a variety of problems. The present
invention provides a promising means for enhancing the anti-tumor
potency of antibodies is via enhancement of their ability to
mediate cytotoxic effector functions such as ADCC, ADCP, and CDC.
The present invention shows that antibodies with an Fc region
optimized for binding to certain Fc.gamma.Rs may better mediate
effector functions and thereby destroy cancer cells more
effectively in patients. The balance between activating and
inhibiting receptors is an important consideration, and optimal
effector function may result from an Fc with enhanced affinity for
activation receptors, for example Fc.gamma.RI, Fc.gamma.RIIa/c, and
Fc.gamma.RIIa, yet reduced affinity for the inhibitory receptor
Fc.gamma.RIIb. Furthermore, because Fc.gamma.Rs can mediate antigen
uptake and processing by antigen presenting cells, enhanced
Fc/Fc.gamma.R affinity may also improve the capacity of antibody
therapeutics to elicit an adaptive immune response. For example,
several mutations disclosed in this application, including S298A,
E333A, and K334A, show enhanced binding to the activating receptor
Fc.gamma.RIIIa and reduced binding to the inhibitory receptor
Fc.gamma.RIIb. These mutations maybe combined to obtain double and
triple mutation variants that show additive improvements in
binding. A particular variant is a S298A/E333A/K334A triple mutant
with approximately a 1.7-fold increase in binding to F158
Fc.gamma.RIIIa, a 5-fold decrease in binding to Fc.gamma.RIIb, and
a 2.1 -fold enhancement in ADCC.
[0102] Although there is a need for greater effector function, for
some antibody therapeutics reduced or eliminated effector function
may be desired. This is often the case for therapeutic antibodies
whose mechanism of action involves blocking or antagonism but not
killing of the cells bearing target antigen. In these cases
depletion of target cells is undesirable and can be considered a
side effect. For example, the ability of anti-CD4 antibodies to
block CD4 receptors on T cells makes them effective
anti-inflammatories, yet their ability to recruit Fc.gamma.R
receptors also directs immune attack against the target cells,
resulting in T cell depletion (Reddy et al., 2000, J Immunol
164:1925-1933, incorporated by reference). Effector function can
also be a problem for radiolabeled antibodies, referred to as
radioconjugates, and antibodies conjugated to toxins, referred to
as immunotoxins. These drugs can be used to destroy cancer cells,
but the recruitment of immune cells via Fc interaction with
Fc.gamma.Rs brings healthy immune cells in proximity to the deadly
payload (radiation or toxin), resulting in depletion of normal
lymphoid tissue along with targeted cancer cells (Hutchins et al.,
1995, Proc Natl Acad Sci USA 92:11980-11984; White et al., 2001,
Annu Rev Med 52:125-145, incorporated by reference). This problem
can potentially be circumvented by using IgG isotypes that poorly
recruit complement or effector cells, for example IgG2 and IgG4. An
alternate solution is to develop Fc variants that reduce or ablate
binding (Alegre et al., 1994, Transplantation 57:1537-1543;
Hutchins et al., 1995, Proc Natl Acad Sci USA 92:11980-11984;
Armour et al., 1999, Eur J Immunol 29:2613-2624; Reddy et al.,
2000, J Immunol 164:1925-1933; Xu et al., 2000, Cell Immunol
200:16-26; Shields et al., 2001, J Biol Chem 276:6591-6604) (U.S.
Pat. No. 6,194,551; U.S. Pat. No. 5,885,573; PCT WO 99/58572), all
incorporated by reference. A critical consideration for the
reduction or elimination of effector function is that other
important antibody properties not be perturbed. Fc variants should
be engineered that not only ablate binding to Fc.gamma.Rs and/or
C1q, but also maintain antibody stability, solubility, and
structural integrity, as well as ability to interact with other
important Fc ligands such as FcRn and proteins A and G.
[0103] In addition, the invention utilizes engineered glycoforms
that can enhance Fc/Fc.gamma.R affinity and effector function. An
aglycosylated Fc with favorable solution properties and the
capacity to mediate effector functions would be significantly
enabling for the alternate production methods described above. By
overcoming the structural and functional shortcomings of
aglycosylated Fc, antibodies can be produced in bacteria and
transgenic plants and animals with reduced risk of immunogenicity,
and with effector function for clinical applications in which
cytotoxicity is desired such as cancer. The present invention
describes the utilization of protein engineering methods to develop
stable, soluble Fc variants with effector function. Currently, such
Fc variants do not exist in the art.
Fc Variants of the Present Invention
[0104] The Fc variants of the present invention may find use in a
variety of Fc polypeptides. An Fc polypeptide that comprises an Fc
variant of the present invention is herein referred to as an "Fc
polypeptide of the present invention". Fc polypeptides of the
present invention include polypeptides that comprise the Fc
variants of the present invention in the context of a larger
polypeptide, such as an antibody or Fc fusion. That is, Fc
polypeptides of the present invention include antibodies and Fc
fusions that comprise Fc variants of the present invention. By
"antibody of the present invention" as used herein is meant an
antibody that comprises an Fc variant of the present invention. By
"Fc fusion of the Present invention" as used herein refers to an Fc
fusion that comprises an Fc variant of the present invention. Fc
polypeptides of the present invention also include polypeptides
that comprise little or no additional polypeptide sequence other
than the Fc region, referred to as an isolated Fc. By "isolated Fc
of the present invention" used herein is meant an Fc polypeptide
that comprises an Fc variant of the present invention, and
comprises little or no additional polypeptide sequence other than
the Fc region. Fc polypeptides of the present invention also
include fragments of the Fc region. By "Fc fragment of the present
invention" as used herein is meant an Fc fragment that comprises an
Fc variant of the present invention. As described below, any of the
aforementioned Fc polypeptides of the present invention may be
fused to one or more fusion partners or conjugate partners to
provide desired functional properties.
[0105] Fc variants may be constructed in a parent Fc polypeptide
irrespective of its context. That is to say that, the sole criteria
for a parent Fc polypeptide is that it comprise an Fc region. The
parent Fc polypeptides described herein may be derived from a wide
range of sources, and may be substantially encoded by one or more
Fc genes from any organism, including but not limited to humans,
rodents including but not limited to mice and rats, lagomorpha such
as rabbits and hares, camelidae such as camels, llamas, and
dromedaries, and non-human primates, including but not limited to
Prosimians, Platyrrhini (New World monkeys), Cercopithecoidea (Old
World monkeys), and Hominoidea include the Gibbons, Lesser and
Great Apes, with humans most preferred. The parent Fc polypeptides
of the present invention may be substantially encoded by
immunoglobulin genes belonging to any of the antibody classes,
including but not limited to sequences belonging to the IgG
(including human subclasses IgG1, IgG2, IgG3, or IgG4), IgA
(including human subclasses IgA1 and IgA2), IgD, IgE, IgG, or IgM
classes of antibodies. Most preferably the parent Fc polypeptides
of the present invention comprise sequences belonging to the human
IgG class of antibodies. For example, the parent Fc polypeptide may
be a parent antibody, for example a human IgG1 antibody, a human
IgA antibody, or a mouse IgG2a or IgG2b antibody. Said parent
antibody may be nonhuman, chimeric, humanized, or fully human as
described in detail below. The parent Fc polypeptide may be
modified or engineered in some way, for example a parent antibody
may be affinity matured, or may possess engineered glycoforms, all
as described more fully below. Alternatively, the parent Fc
polypeptide may be an Fc fusion, for example an Fc fusion wherein
the fusion partner targets a cell surface receptor. Alternatively,
the parent Fc polypeptide may be an isolated Fc region, comprising
little or no other polypeptide sequence outside the Fc region. The
parent Fc polypeptide may be a naturally existing Fc region, or may
be an existing engineered variant of an Fc polypeptide. What is
important is that the parent Fc polypeptide comprise an Fc region,
which can then be mutated to generate an Fc variant.
[0106] The Fc variants of the present invention may be an antibody,
referred to herein as an "antibody of the present invention".
Antibodies of the present invention may comprise immunoglobulin
sequences that are substantially encoded by immunoglobulin genes
belonging to any of the antibody classes, including but not limited
to IgG (including human subclasses IgG1, IgG2, IgG3, or IgG4), IgA
(including human subclasses IgA1 and IgA2), IgD, IgE, IgG, and IgM
classes of antibodies. Most preferably the antibodies of the
present invention comprise sequences belonging to the human IgG
class of antibodies. Antibodies of the present invention may be
nonhuman, chimeric, humanized, or fully human. As will be
appreciated by one skilled in the art, these different types of
antibodies reflect the degree of "humanness" or potential level of
immunogenicity in a human. For a description of these concepts, see
Clark et al., 2000 and references cited therein (Clark, 2000,
Immunol Today 21:397-402, incorporated by reference). Chimeric
antibodies comprise the variable region of a nonhuman antibody, for
example V.sub.H and V.sub.L domains of mouse or rat origin,
operably linked to the constant region of a human antibody (see for
example U.S. Pat. No. 4,816,567, incorporated by reference). Said
nonhuman variable region may be derived from any organism as
described above, preferably mammals and most preferably rodents or
primates. In one embodiment, the antibody of the present invention
comprises monkey variable domains, for example as described in
Newman et al., 1992, Biotechnology 10:1455-1460, U.S. Pat. No.
5,658,570, and U.S. Pat. No. 5,750,105, incorporated by reference.
In a preferred embodiment, the variable region is derived from a
nonhuman source, but its immunogenicity has been reduced using
protein engineering. In a preferred embodiment, the antibodies of
the present invention are humanized (Tsurushita & Vasquez,
2004, Humanization of Monoclonal Antibodies, Molecular Biology of B
Cells, 533-545, Elsevier Science (USA), incorporated by reference).
By "humanized" antibody as used herein is meant an antibody
comprising a human framework region (FR) and one or more
complementarity determining regions (CDR's) from a non-human
(usually mouse or rat) antibody. The non-human antibody providing
the CDR's is called the "donor" and the human immunoglobulin
providing the framework is called the "acceptor". Humanization
relies principally on the grafting of donor CDRs onto acceptor
(human) V.sub.L and V.sub.H frameworks (Winter U.S. Pat. No.
5,225,539, incorporated by reference). This strategy is referred to
as "CDR grafting". "Backmutation" of selected acceptor framework
residues to the corresponding donor residues is often required to
regain affinity that is lost in the initial grafted construct (U.S.
Pat. No. 5,530,101; U.S. Pat. No. 5,585,089; U.S. Pat. No.
5,693,761; U.S. Pat. No. 5,693,762; U.S. Pat. No. 6,180,370; U.S.
Pat. No. 5,859,205; U.S. Pat. No. 5,821,337; U.S. Pat. No.
6,054,297; U.S. Pat. No. 6,407,213, incorporated by reference). A
large number of other methods for humanization are known in the art
(Tsurushita & Vasquez, 2004, Humanization of Monoclonal
Antibodies, Molecular Biology of B Cells, 533-545, Elsevier Science
(USA), incorporated by reference), and any of such methods may find
use in the present invention for modifying Fc variants for reduced
immunogenicity. The humanized antibody optimally also will comprise
at least a portion of an immunoglobulin constant region, typically
that of a human immunoglobulin, and thus will typically comprise a
human Fc region. In a most preferred embodiment, the immunogenicity
of an Fc variant of the present invention is reduced using a method
described in U.S. Ser. No. 11/004,590, filed Dec. 3, 2004, entitled
"Methods of Generating Variant Proteins with Increased Host String
Content and Compositions Thereof," incorporated by reference. In an
alternate embodiment, the antibodies of the present invention may
be fully human, that is the sequences of the antibodies are
completely or substantially human. A number of methods are known in
the art for generating fully human antibodies, including the use of
transgenic mice (Bruggemann et al., 1997, Curr Opin Biotechnol
8:455-458, incorporated by reference) or human antibody libraries
coupled with selection methods (Griffiths et al., 1998, Curr Opin
Biotechnol 9:102-108, incorporated by reference).
[0107] The Fc variants of the present invention may be an Fc
fusion, referred to herein as an "Fc fusion of the present
invention". Fc fusions of the present invention comprise an Fc
polypeptide operably linked to one or more fusion partners. The
role of the fusion partner typically, but not always, is to mediate
binding of the Fc fusion to a target antigen. (Chamow et al., 1996,
Trends Biotechnol 14:52-60; Ashkenazi et al., 1997, Curr Opin
Immunol 9:195-200, incorporated by reference). For example, the
approved drug alefacept (marketed as AMEVIVE.RTM.) is an
immunosuppressive Fc fusion that consists of the extracellular
CD2-binding portion of the human leukocyte function antigen-3
(LFA-3) linked to the Fc region of human IgG1. The approved drug
etanercept (marketed as ENBREL.RTM.) is an Fc fusion comprising the
extracellular ligand-binding portion of human tumor necrosis factor
receptor (TNFR) linked to human IgG1 Fc. Virtually any protein,
polypeptide, peptide, or small molecule may be linked to Fc to
generate an Fc fusion. Fusion partners include but are not limited
to receptors and extracellular receptor domains, adhesion
molecules, ligands, enzymes, cytokines, chemokines, or some other
protein or protein domain. The fusion partner may also play a role
as a chemoattractant. Undiscovered ligands or receptors may serve
as fusion partners for the Fc variants of the present invention.
Small molecules may serve as fusion partners, and may include any
therapeutic agent that directs the Fc fusion to a therapeutic
target. Such targets may be any molecule, preferrably an
extracellular receptor, that is implicated in disease. Two families
of surface receptors that are targets of a number of approved small
molecule drugs are G-Protein Coupled Receptors (GPCRs), and ion
channels, including K+, Na+, Ca+ channels. Nearly 70% of all drugs
currently marketed worldwide target GPCRs. Thus the Fc variants of
the present invention may be fused to a small molecule that
targets, for example, one or more GABA receptors, purinergic
receptors, adrenergic receptors, histaminergic receptors, opiod
receptors, chemokine receptors, glutamate receptors, nicotinic
receptors, the 5HT (serotonin) receptor, and estrogen receptors. A
fusion partner may be a small-molecule mimetic of a protein that
targets a therapeutically useful target. Specific examples of
particular drugs that may serve as Fc fusion partners can be found
in L. S. Goodman et al., Eds., Goodman and Gilman's The
Pharmacological Basis of Therapeutics (McGraw-Hill, New York, ed.
9, 1996, incorporated by reference). Fusion partners include not
only small molecules and proteins that bind known targets for
existing drugs, but orphan receptors that do not yet exist as drug
targets. The completion of the genome and proteome projects are
proving to be a driving force in drug discovery, and these projects
have yielded a trove of orphan receptors. There is enormous
potential to validate these new molecules as drug targets, and
develop protein and small molecule therapeutics that target them.
Such protein and small molecule therapeutics are contemplated as Fc
fusion partners that employ the Fc variants of the present
invention. Fc fusions of the invention may comprise immunoglobulin
sequences that are substantially encoded by immunoglobulin genes
belonging to any of the antibody classes, including but not limited
to IgG (including human subclasses IgG1, IgG2, IgG3, or IgG4), IgA
(including human subclasses IgA1 and IgA2), IgD, IgE, IgG, and IgM
classes of antibodies. Most preferably the Fc fusions of the
present invention comprise sequences belonging to the human IgG
class of antibodies. A variety of linkers, defined and described
below, may be used to covalently link Fc to a fusion partner to
generate an Fc fusion.
[0108] The Fc variants of the present invention may find use in an
isolated Fc, that is an Fc polypeptide that comprises little or no
additional polypeptide sequence other than the Fc region and that
comprises an Fc variant of the present invention. Isolated Fc of
the present invention are meant as molecules wherein the desired
function of the molecule, for example the desired therapeutic
function, resides solely in the Fc region. Thus the therapeutic
target of an isolated Fc of the present invention is likely to
involve one or more Fc ligands. An isolated Fc that comprises the
Fc variant may require no additional covalent polypeptide sequence
to achieve its desired outcome. In a preferred embodiment, said
isolated Fc comprises from 90-100% of the Fc region, with little or
no "extra" sequence. Thus, for example, an isolated Fc of the
present invention may comprise residues C226 or P230 to the
carboxyl-terminus of human IgG1, wherein the numbering is according
to the EU index as in Kabat. In one embodiment, the isolated Fc of
the present invention may contain no extra sequence outside the Fc
region. However it is also contemplated that isolated Fc's may not
also comprise additional polypeptide sequences. For example, an
isolated Fc may, in addition to comprising an Fc variant Fc region,
comprise additional polypeptide sequence tags that enable
expression, purification, and the like.
[0109] The Fc variants of the present invention may find use in a
fragment of the Fc region, that is an Fc polypeptide that comprises
an Fc fragment that comprises an Fc variant of the present
invention. Clearly a requirement of an Fc fragment of the present
invention is that it contains the position(s) at which the amino
acid modifications of the Fc variant are made. An Fc fragment of
the present invention may comprise from 1-90% of the Fc region,
with 10-90% being preferred, and 30-90% being most preferred. Thus
for example, an Fc fragment of the present invention may comprise
an Fc variant IgG1 C.gamma.2 domain, an Fc variant IgG1 C.gamma.2
domain and hinge region, an Fc variant IgG1 C.gamma.3 domain, and
so forth. In one embodiment, an Fc fragment of the present
invention additionally comprises a fusion partner, effectively
making it an Fc fragment fusion. As with isolated Fcs, Fc fragments
may or may not contian extra polypeptide sequence.
[0110] Fc variants of the present invention may be substantially
encoded by genes from any organism, preferably mammals, including
but not limited to humans, rodents including but not limited to
mice and rats, lagomorpha including but not limited to rabbits and
hares, camelidae including but not limited to camels, llamas, and
dromedaries, and non-human primates, including but not limited to
Prosimians, Platyrrhini (New World monkeys), Cercopithecoidea (Old
World monkeys), and Hominoidea including the Gibbons and Lesser and
Great Apes. In a most preferred embodiment, the Fc variants of the
present invention are substantially human. The Fc variants of the
present invention may be substantially encoded by immunoglobulin
genes belonging to any of the antibody classes. In a most preferred
embodiment, the Fc variants of the present invention comprise
sequences belonging to the IgG class of antibodies, including human
subclasses IgG1, IgG2, IgG3, and IgG4. In an alternate embodiment,
the Fc variants of the present invention comprise sequences
belonging to the IgA (including human subclasses IgA1 and IgA2),
IgD, IgE, IgG, or IgM classes of antibodies. The Fc variants of the
present invention may comprise more than one protein chain. That
is, the present invention may find use in an Fc variant that is a
monomer or an oligomer, including a homo- or hetero-oligomer.
[0111] In the most preferred embodiment, the Fc polypeptides of the
invention are based on human IgG sequences, and thus human IgG
sequences are used as the "base" sequences against which other
sequences are compared, including but not limited to sequences from
other organisms, for example rodent and primate sequences, as well
as sequences from other immunoglobulin classes such as IgA, IgE,
IgGD, IgGM, and the like. It is contemplated that, although the Fc
variants of the present invention are engineered in the context of
one parent Fc variant, the variants may be engineered in or
"transferred" to the context of another, second parent Fc variant.
This is done by determining the "equivalent" or "corresponding"
residues and substitutions between the first and second Fc
variants, typically based on sequence or structural homology
between the sequences of the two Fc variants. In order to establish
homology, the amino acid sequence of a first Fc variant outlined
herein is directly compared to the sequence of a second Fc variant.
After aligning the sequences, using one or more of the homology
alignment programs known in the art (for example using conserved
residues as between species), allowing for necessary insertions and
deletions in order to maintain alignment (i.e., avoiding the
elimination of conserved residues through arbitrary deletion and
insertion), the residues equivalent to particular amino acids in
the primary sequence of the first Fc variant are defined. Alignment
of conserved residues preferably should conserve 100% of such
residues. However, alignment of greater than 75% or as little as
50% of conserved residues is also adequate to define equivalent
residues. Equivalent residues may also be defined by determining
structural homology between a first and second Fc variant that is
at the level of tertiary structure for Fc variants whose structures
have been determined. In this case, equivalent residues are defined
as those for which the atomic coordinates of two or more of the
main chain atoms of a particular amino acid residue of the parent
or precursor (N on N, CA on CA, C on C and O on O) are within 0.13
nm and preferably 0.1 nm after alignment. Alignment is achieved
after the best model has been oriented and positioned to give the
maximum overlap of atomic coordinates of non-hydrogen protein atoms
of the proteins. Regardless of how equivalent or corresponding
residues are determined, and regardless of the identity of the
parent Fc variant in which the Fc variants are made, what is meant
to be conveyed is that the Fc variants discovered by the present
invention may be engineered into any second parent Fc variant that
has significant sequence or structural homology with said Fc
variant. Thus for example, if a variant antibody is generated
wherein the parent antibody is human IgG1, by using the methods
described above or other methods for determining equivalent
residues, said variant antibody may be engineered in a human IgG2
parent antibody, a human IgA parent antibody, a mouse IgG2a or
IgG2b parent antibody, and the like. Again, as described above, the
context of the parent Fc variant does not affect the ability to
transfer the Fc variants of the present invention to other parent
Fc variants. For example, the variant antibodies that are
engineered in a human IgG1 antibody that targets one epitope may be
transferred into a human IgG2 antibody that targets a different
epitope, into an Fc fusion that comprises a human IgG1 Fc region
that targets yet a different epitope, and so forth.
[0112] The Fc variants of the present invention may find use in a
wide range of products. In one embodiment the Fc variant of the
invention is a therapeutic, a diagnostic, or a research reagent,
preferably a therapeutic. Alternatively, the Fc variant of the
present invention may be used for agricultural or industrial uses.
An antibody of the present invention may find use in an antibody
composition that is monoclonal or polyclonal. The Fc variants of
the present invention may be agonists, antagonists, neutralizing,
inhibitory, or stimulatory. In a preferred embodiment, the Fc
variants of the present invention are used to kill target cells
that bear the target antigen, for example cancer cells. In an
alternate embodiment, the Fc variants of the present invention are
used to block, antagonize, or agonize the target antigen. In an
alternately preferred embodiment, the Fc variants of the present
invention are used to block, antagonize, or agonize the target
antigen and kill the target cells that bear the target antigen.
Targets
[0113] Virtually any antigen may be targeted by the Fc variants of
the present invention, including but not limited to proteins,
subunits, domains, motifs, and/or epitopes belonging to the
following list of targets: 17-IA, 4-1BB, 4Dc, 6-keto-PGF1a,
8-iso-PGF2a, 8-oxo-dG, A1 Adenosine Receptor, A33, ACE, ACE-2,
Activin, Activin A, Activin AB, Activin B, Activin C, Activin RIA,
Activin RIA ALK-2, Activin RIB ALK-4, Activin RIIA, Activin RIIB,
ADAM, ADAM10, ADAM12, ADAM15, ADAM17/TACE, ADAM8, ADAM9, ADAMTS,
ADAMTS4, ADAMTS5, Addressins, aFGF, ALCAM, ALK, ALK-1, ALK-7,
alpha-1-antitrypsin, alpha-V/beta-1 antagonist, ANG, Ang, APAF-1,
APE, APJ, APP, APRIL, AR, ARC, ART, Artemin, anti-Id, ASPARTIC,
Atrial natriuretic factor, av/b3 integrin, Axl, b2M, B7-1, B7-2,
B7-H, B-lymphocyte Stimulator (BlyS), BACE, BACE-1, Bad, BAFF,
BAFF-R, Bag-1, BAK, Bax, BCA-1, BCAM, Bcl, BCMA, BDNF, b-ECGF,
bFGF, BID, Bik, BIM, BLC, BL-CAM, BLK, BMP, BMP-2 BMP-2a, BMP-3
Osteogenin, BMP-4 BMP-2b, BMP-5, BMP-6 Vgr-1, BMP-7 (OP-1), BMP-8
(BMP-8a, OP-2), BMPR, BMPR-IA (ALK-3), BMPR-IB (ALK-6), BRK-2,
RPK-1, BMPR-II (BRK-3), BMPs, b-NGF, BOK, Bombesin, Bone-derived
neurotrophic factor, BPDE, BPDE-DNA, BTC, complement factor 3 (C3),
C3a, C4, C5, C5a, C10, CA125, CAD-8, Calcitonin, cAMP,
carcinoembryonic antigen (CEA), carcinoma-associated antigen,
Cathepsin A, Cathepsin B, Cathepsin C/DPPI, Cathepsin D, Cathepsin
E, Cathepsin H, Cathepsin L, Cathepsin O, Cathepsin S, Cathepsin V,
Cathepsin X/Z/P, CBL, CCI, CCK2, CCL, CCL1, CCL11, CCL12, CCL13,
CCL14, CCL15, CCL16, CCL17, CCL18, CCL19, CCL2, CCL20, CCL21,
CCL22, CCL23, CCL24, CCL25, CCL26, CCL27, CCL28, CCL3, CCL4, CCL5,
CCL6, CCL7, CCL8, CCL9/10, CCR, CCR1, CCR10, CCR10, CCR2, CCR3,
CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CD1, CD2, CD3, CD3E, CD4, CD5,
CD6, CD7, CD8, CD10, CD11a, CD11b, CD11c, CD13, CD14, CD15, CD16,
CD18, CD19, CD20, CD21, CD22, CD23, CD25, CD27L, CD28, CD29, CD30,
CD30L, CD32, CD33 (p67 proteins), CD34, CD38, CD40, CD40L, CD44,
CD45, CD46, CD49a, CD52, CD54, CD55, CD56, CD61, CD64, CD66e, CD74,
CD80 (B7-1), CD89, CD95, CD123, CD137, CD138, CD140a, CD146, CD147,
CD148, CD152, CD164, CEACAM5, CFTR, cGMP, CINC, Clostridium
botulinum toxin, Clostridium perfringens toxin, CKb8-1, CLC, CMV,
CMV UL, CNTF, CNTN-1, COX, C-Ret, CRG-2, CT-1, CTACK, CTGF, CTLA-4,
CX3CL1, CX3CR1, CXCL, CXCL1, CXCL2, CXCL3, CXCL4, CXCL5, CXCL6,
CXCL7, CXCL8, CXCL9, CXCL10, CXCL11, CXCL12, CXCL13, CXCL14,
CXCL15, CXCL16, CXCR, CXCR1, CXCR2, CXCR3, CXCR4, CXCR5, CXCR6,
cytokeratin tumor-associated antigen, DAN, DCC, DcR3, DC-SIGN,
Decay accelerating factor, des(1-3)-IGF-I (brain IGF-1), Dhh,
digoxin, DNAM-1, Dnase, Dpp, DPPIV/CD26, Dtk, ECAD, EDA, EDA-A1,
EDA-A2, EDAR, EGF, EGFR (ErbB-1), EMA, EMMPRIN, E/VA, endothelin
receptor, Enkephalinase, eNOS, Eot, eotaxin1, EpCAM, Ephrin
B2/EphB4, EPO, ERCC, E-selectin, ET-1, Factor IIa, Factor VII,
Factor VIIIc, Factor IX, fibroblast activation protein (FAP), Fas,
FcR1, FEN-1, Ferritin, FGF, FGF-19, FGF-2, FGF3, FGF-8, FGFR,
FGFR-3, Fibrin, FL, FLIP, Flt-3, Flt-4, Follicle stimulating
hormone, Fractalkine, FZD1, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7,
FZD8, FZD9, FZD10, G250, Gas 6, GCP-2, GCSF, GD2, GD3, GDF, GDF-1,
GDF-3 (Vgr-2), GDF-5 (BMP-14, CDMP-1), GDF-6 (BMP-13, CDMP-2),
GDF-7 (BMP-12, CDMP-3), GDF-8 (Myostatin), GDF-9, GDF-15 (MIC-1),
GDNF, GDNF, GFAP, GFRa-1, GFR-alpha1, GFR-alpha2, GFR-alpha3, GITR,
Glucagon, Glut 4, glycoprotein IIb/IIIa (GP IIb/IIIa), GM-CSF,
gp130, gp72, GRO, Growth hormone releasing factor, Hapten (NP-cap
or NIP-cap), HB-EGF, HCC, HCMV gB envelope glycoprotein, HCMV) gH
envelope glycoprotein, HCMV UL, Hemopoietic growth factor (HGF),
Hep B gp120, heparanase, Her2, Her2/neu (ErbB-2), Her3 (ErbB-3),
Her4 (ErbB-4), herpes simplex virus (HSV) gB glycoprotein, HSV gD
glycoprotein, HGFA, High molecular weight melanoma-associated
antigen (HMW-MAA), HIV gp120, HIV IIIB gp 120 V3 loop, HLA, HLA-DR,
HM1.24, HMFG PEM, HRG, Hrk, human cardiac myosin, human
cytomegalovirus (HCMV), human growth hormone (HGH), HVEM, 1-309,
IAP, ICAM, ICAM-1, ICAM-3, ICE, ICOS, IFNg, Ig, IgA receptor, IgE,
IGF, IGF binding proteins, IGF-1R, IGFBP, IGF-I, IGF-II, IL, IL-1,
IL-1R, IL-2, IL-2R, IL-4, IL-4R, IL-5, IL-5R, IL-6, IL-6R, IL-8,
IL-9, IL-10, IL-12, IL-13, IL-15, IL-18, IL-18R, IL-23, interferon
(INF)-alpha, INF-beta, INF-gamma, Inhibin, iNOS, Insulin A-chain,
Insulin B-chain, Insulin-like growth factor 1, integrin alpha2,
integrin alpha3, integrin alpha4, integrin alpha4/beta1, integrin
alpha4/beta7, integrin alpha5 (alphaV), integrin alpha5/beta1,
integrin alpha5/beta3, integrin alpha6, integrin betal, integrin
beta2, interferon gamma, IP-10, I-TAC, JE, Kallikrein 2, Kallikrein
5, Kallikrein 6,, Kallikrein 11, Kallikrein 12, Kallikrein 14,
Kallikrein 15, Kallikrein L1, Kallikrein L2, Kallikrein L3,
Kallikrein L4, KC, KDR, Keratinocyte Growth Factor (KGF), laminin
5, LAMP, LAP, LAP (TGF-1), Latent TGF-1, Latent TGF-1 bp1, LBP,
LDGF, LECT2, Lefty, Lewis-Y antigen, Lewis-Y related antigen,
LFA-1, LFA-3, Lfo, LIF, LIGHT, lipoproteins, LIX, LKN, Lptn,
L-Selectin, LT-a, LT-b, LTB4, LTBP-1, Lung surfactant, Luteinizing
hormone, Lymphotoxin Beta Receptor, Mac-1, MAdCAM, MAG, MAP2, MARC,
MCAM, MCAM, MCK-2, MCP, M-CSF, MDC, Mer, METALLOPROTEASES, MGDF
receptor, MGMT, MHC (HLA-DR), MIF, MIG, MIP, MIP-1-alpha, MK,
MMAC1, MMP, MMP-1, MMP-10, MMP-11, MMP-12, MMP-13, MMP-14, MMP-15,
MMP-2, MMP-24, MMP-3, MMP-7, MMP-8, MMP-9, MPIF, Mpo, MSK, MSP,
mucin (Muc1), MUC18, Muellerian-inhibitin substance, Mug, MuSK,
NAIP, NAP, NCAD, N-Cadherin, NCA 90, NCAM, NCAM, Neprilysin,
Neurotrophin-3, -4, or -6, Neurturin, Neuronal growth factor (NGF),
NGFR, NGF-beta, nNOS, NO, NOS, Npn, NRG-3, NT, NTN, OB, OGG1, OPG,
OPN, OSM, OX40L, OX40R, p150, p95, PADPr, Parathyroid hormone,
PARC, PARP, PBR, PBSF, PCAD, P-Cadherin, PCNA, PDGF, PDGF, PDK-1,
PECAM, PEM, PF4, PGE, PGF, PG12, PGJ2, PIN, PLA2, placental
alkaline phosphatase (PLAP), PIGF, PLP, PP14, Proinsulin,
Prorelaxin, Protein C, PS, PSA, PSCA, prostate specific membrane
antigen (PSMA), PTN, PTHrp, Ptk, PTN, R51, RANK, RANKL, RANTES,
RANTES, Relaxin A-chain, Relaxin B-chain, renin, respiratory
syncytial virus (RSV) F, RSV Fgp, Ret, Rheumatoid factors, RLIP76,
RPA2, RSK, S100, SCF/KL, SDF-1, SERINE, Serum albumin, sFRP-3, Shh,
SIGIRR, SK-1, SLAM, SLPI, SMAC, SMDF, SMOH, SOD, SPARC, Stat,
STEAP, STEAP-II, TACE, TACI, TAG-72 (tumor-associated
glycoprotein-72), TARC, TCA-3, T-cell receptors (e.g., T-cell
receptor alpha/beta), TdT, TECK, TEM1, TEM5, TEM7, TEM8, TERT,
testicular PLAP-like alkaline phosphatase, TfR, TGF, TGF-alpha,
TGF-beta, TGF-beta Pan Specific, TGF-beta RI (ALK-5), TGF-beta RII,
TGF-beta RIIb, TGF-beta RIII, TGF-beta1, TGF-beta2, TGF-beta3,
TGF-beta4, TGF-beta5, Thrombin, Thymus Ck-1, Thyroid stimulating
hormone, Tie, TIMP, TIQ, Tissue Factor, TMEFF2, Tmpo, TMPRSS2, TNF,
TNF-alpha, TNF-alpha beta, TNF-beta2, TNFc, TNF-RI, TNF-RII,
TNFRSF10A (TRAIL R1 Apo-2, DR4), TNFRSF10B (TRAIL R2 DR5, KILLER,
TRICK-2A, TRICK-B), TNFRSF10C (TRAIL R3 DcR1, LIT, TRID), TNFRSF10D
(TRAIL R4 DcR2, TRUNDD), TNFRSF11A (RANK ODF R, TRANCE R),
TNFRSF11B (OPG OCIF, TR1), TNFRSF12 (TWEAK R FN14), TNFRSF13B
(TACI), TNFRSF13C (BAFF R), TNFRSF14 (HVEM ATAR, HveA, LIGHT R,
TR2), TNFRSF16 (NGFR p75NTR), TNFRSF17 (BCMA), TNFRSF18 (GITR
AITR), TNFRSF19 (TROY TAJ, TRADE), TNFRSF19L (RELT), TNFRSF1A (TNF
RI CD120a, p55-60), TNFRSF1B (TNF RII CD120b, p75-80), TNFRSF26
(TNFRH3), TNFRSF3 (LTbR TNF RIII, TNFC R), TNFRSF4 (OX40 ACT35,
TXGP1 R), TNFRSF5 (CD40 p50), TNFRSF6 (Fas Apo-1, APT1, CD95),
TNFRSF6B (DcR3 M68, TR6), TNFRSF7 (CD27), TNFRSF8 (CD30), TNFRSF9
(4-1BB CD137, ILA), TNFRSF21 (DR6), TNFRSF22 (DCTRAIL R2 TNFRH2),
TNFRST23 (DCTRAIL R1 TNFRH1), TNFRSF25 (DR3 Apo-3, LARD, TR-3,
TRAMP, WSL-1), TNFSF10 (TRAIL Apo-2 Ligand, TL2), TNFSF11
(TRANCE/RANK Ligand ODF, OPG Ligand), TNFSF12 (TWEAK Apo-3 Ligand,
DR3 Ligand), TNFSF13 (APRIL TALL2), TNFSF13B (BAFF BLYS, TALL1,
THANK, TNFSF20), TNFSF14 (LIGHT HVEM Ligand, LTg), TNFSF15
(TL1A/VEGI), TNFSF18 (GITR Ligand AITR Ligand, TL6), TNFSF1A (TNF-a
Conectin, DIF, TNFSF2), TNFSF1B (TNF-b LTa, TNFSF1), TNFSF3 (LTb
TNFC, p33), TNFSF4 (OX40 Ligand gp34, TXGP1), TNFSF5 (CD40 Ligand
CD154, gp39, HIGM1, IMD3, TRAP), TNFSF6 (Fas Ligand Apo-1 Ligand,
APT1 Ligand), TNFSF7 (CD27 Ligand CD70), TNFSF8 (CD30 Ligand
CD153), TNFSF9 (4-1BB Ligand CD137 Ligand), TP-1, t-PA, Tpo, TRAIL,
TRAIL R, TRAIL-R1, TRAIL-R2, TRANCE, transferring receptor, TRF,
Trk, TROP-2, TSG, TSLP, tumor-associated antigen CA 125,
tumor-associated antigen expressing Lewis Y related carbohydrate,
TWEAK, TXB2, Ung, UPAR, uPAR-1, Urokinase, VCAM, VCAM-1, VECAD,
VE-Cadherin, VE-cadherin-2, VEFGR-1 (flt-1), VEGF, VEGFR, VEGFR-3
(flt-4), VEGI, VIM, Viral antigens, VLA, VLA-1, VLA-4, VNR
integrin, von Willebrands factor, WIF-1, WNT1, WNT2, WNT2B/13,
WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B,
WNT9A, WNT9A, WNT9B, WNT10A, WNT10B, WNT11, WNT16, XCL1, XCL2,
XCR1, XCR1, XEDAR, XIAP, XPD, and receptors for hormones and growth
factors.
[0114] One skilled in the art will appreciate that the
aforementioned list of targets refers not only to specific proteins
and biomolecules, but the biochemical pathway or pathways that
comprise them. For example, reference to CTLA-4 as a target antigen
implies that the ligands and receptors that make up the T cell
co-stimulatory pathway, including CTLA-4, B7-1, B7-2, CD28, and any
other undiscovered ligands or receptors that bind these proteins,
are also targets. Thus target as used herein refers not only to a
specific biomolecule, but the set of proteins that interact with
said target and the members of the biochemical pathway to which
said target belongs. One skilled in the art will further appreciate
that any of the aforementioned target antigens, the ligands or
receptors that bind them, or other members of their corresponding
biochemical pathway, may be operably linked to the Fc variants of
the present invention in order to generate an Fc fusion. Thus for
example, an Fc fusion that targets EGFR could be constructed by
operably linking an Fc variant to EGF, TGF-.beta., or any other
ligand, discovered or undiscovered, that binds EGFR. Accordingly,
an Fc variant of the present invention could be operably linked to
EGFR in order to generate an Fc fusion that binds EGF, TGF-.beta.,
or any other ligand, discovered or undiscovered, that binds EGFR.
Thus virtually any polypeptide, whether a ligand, receptor, or some
other protein or protein domain, including but not limited to the
aforementioned targets and the proteins that compose their
corresponding biochemical pathways, may be operably linked to the
Fc variants of the present invention to develop an Fc fusion.
[0115] Choosing the right target antigen for antibody therapy is a
complex process and encompasses many variables. For anti-cancer
treatment it is desirable to have a target whose expression is
restricted to the cancerous cells. Some targets that have proven
especially amenable to antibody therapy are those with signaling
functions. Other therapeutic antibodies exert their effects by
blocking signaling of the receptor by inhibiting the binding
between a receptor and it's cognate ligand. Another mechanism of
action of therapeutic antibodies is to cause receptor down
regulation. Although many therapeutically effective antibodies work
in part by signaling through their target antigen, this is not
always the case. For example, some target classes such as cell
surface glycoforms do not generate any biological signal. However,
altered glycoforms are often associated with disease states such as
cancer. Another significant target type are those that internalize
either as a normal function or in response to antibody binding. In
the case of targets that are soluble rather than cell surface bound
the recruitment of effector functions would not result in any cell
death.
[0116] Some targets that have proven especially amenable to
antibody therapy are those with signalling functions. For example,
antibody cross-linking of the Her2/neu antigen may generate an
apoptotic signal that results in cancer cell death. In some cases
such as the CD30 antigen, this clustering with free antibody may be
insufficient to cause apoptosis in vitro. For in vitro assays
sufficient clustering can be mediated by crosslinking the antibody
or by immobilizing it at high density to a surface such as the well
of a microtiter plate. However, in vivo this effect may be mediated
by binding of the antibody to the Fc ligands, for example
Fc.gamma.Rs expressed on a nearby cell. Antibody Fc variants that
bind more tightly to Fc ligands may thus more effectively cluster
the signaling target and lead to enhanced induction of apoptosis.
Such a mechanism could be tested experimentally by adding antibody
with and without enhanced Fc ligand binding to cells expressing the
desired target that signals, and/or adding an Fc receptor and a
corresponding antibody that will cluster the Fc receptor.
Alternative means for clustering Fc receptor include immobilization
on beads, and over-expression in a non-effector cell line. After
allowing apoptosis to occur, measurement of the relative apoptosis
of target expressing cells would enable a quantitiative
determination of the effect.
[0117] Antibodies that cause cell death through their interaction
with targets may have an additional benefit. The signals released
by such dying cells attract macrophages and other cells of the
immune system. These cells can then takeup the dead or dying cells
in an antibody mediated manner. This has been shown to result in
cross-presentation of antigen and the potential for a host immune
response against the target cells. Such auto-antibodies in response
to antibody therapy have been reported for the antigen targets Her2
and CD20. For this reason it may be advantageous to have Fc
variants with altered receptor specificities to specifically
stimulate cross-presentation and an immune response rather than the
undesired effect of tolerance induction.
[0118] Other therapeutic antibodies exert their effects by
inhibiting interaction between a receptor and it's cognate ligand,
ultimately blocking signaling of the receptor. Such antibodies are
used to treat many disease states. In this case it may be
advantageous to utilize antibodies that do not recruit any host
immune functions. A secondary effect of such an antibody may be
actually inducing signalling itself through receptor clustering. In
this case the desired therapeutic effect of blocking signaling
would be abrogated by antibody mediated signaling. As discussed
above, this clustering may be enhanced by antibody interaction with
cells containing an Fc receptor. In this case, use of an Fc variant
that binds less tightly or not at all to the Fc receptor would be
preferable. Such an antibody would not mediate signaling, and its
mechanism of action would thereby be restricted to blockage of
receptor/ligand interactions. Signaling receptors for which this
would be most appropriate would likely be monomeric receptors which
can only be dimerized but not substantially clustered by a primary
antibody. Mulitimeric receptors may be significantly clustered by
the primary antibody and may not require additional clustering by
Fc receptor binding.
[0119] Another potential mechanism of action of therapeutic
antibodies is receptor downregulation. Such may be the case, for
example, with the insulin-like growth factor receptor. Cell growth
depends on continued signaling through the receptor, whereas in its
absence cells cease to grow. One effect of antibodies directed
against this receptor is to downregulate its expression and thereby
ablate signaling. Cell recovery from cytotoxic therapy requires
stimulation of this receptor. Downregulation of this receptor
prevents these cells from recovery and renders the cytotoxic
therapy substantially more effective. For antibodies for which this
is the primary mechanism of action, decreased Fc receptor binding
may prevent the sequestration of antibody by nontarget binding to
Fc receptors.
[0120] Although many therapeutically effective antibodies work in
part by signaling through their target antigen, this is not always
the case. For example, some target classes such as cell surface
glycoforms do not generate any biological signal. However, altered
glycoforms are often associated with disease states such as cancer.
In other cases, interaction of antibodies with different epitopes
of the same target antigen may confer different signaling effects.
In such cases where this is little or no elicited signaling by
binding of antibody or Fc fusion to target antigen, Fc polypeptides
of the present invention may find utility in providing novel
mechanisms of efficacy for otherwise non-efficacious molecules.
[0121] One approach that has been taken in generating therapeutic
antibodies to such nonsignaling targets is to couple the antibody
to a cytotoxic agent such as a radio-isotope, toxin, or an enzyme
that will process a substrate to produce a cytotoxic agent in the
vicinity of the tumor. As an alternative to a cytotoxic moiety, Fc
variants of the present invention may provide increased recruitment
of immune functions that are inherently less toxic to the host
while still effective at destroying target cancer cells. Such Fc
variants may, for example, be more efficient at recruiting NK cells
or at activating phagocytosis or initiating CDC. Alternatively, if
a cytotoxic agent is utilized, it may be advantageous to use an Fc
variant that provides reduced or altered Fc ligand binding. This
may reduce or ablate the cytotoxic effects of the agent on immune
cells that express Fc receptors, thereby reducing toxicity to the
patient. Furthermore, reduction of Fc ligand binding may help to
minimize the generation of an immune response to the toxic agent or
enzyme. As mentioned above, cell death may result in recruitment of
host immune cells; antibody mediated cross-presentation in such a
case may be increased with immune response rather than immune
tolerance if in addition to a cytotoxic moiety the therapeutic
antibody has increased Fc receptor binding affinity or altered
receptor specificity.
[0122] Another significant target type are those targets that
internalize, either as a normal part of their biological function
or in response to antibody binding. For such targets, many efforts
have been made to couple cytotoxic agents such as RNase, ricin and
calicheamicin, which can only exert their effect after
internalization. For such reagents, Fc ligand binding may reduce
efficacy due to nonproductive sequestration of the therapeutic by
Fc ligands. In this case it may be advantageous to utilize Fc
variants that provide decreased Fc ligand affinity. Conversely,
antibody pre-association with Fc ligands prior to their binding to
target antigen presented on cells may serve to inhibit
internalization of the target. In this case, increased Fc ligand
affinity may serve to improve pre-association and thereby
recruitment of effector cells and the host immune response.
[0123] In the case of targets that are soluble rather than cell
surface bound, recruitment of effector functions would not result
directly in cell death. However, there may be utility in
stimulating the generation of host antibodies to the target. For
some disease states, successful treatment may require
administration of the therapeutic antibody for extremely long
periods of time. Such therapy may be prohibitively costly or
cumbersome. In these cases, stimulation of the host immune response
and the generation of antibodies may result in improved efficacy of
the therapeutic. This may be applicable as an adjuvant to vaccine
therapy. Antibody Fc variants that mediate such an effect may have
increased affinity for Fc ligands or altered Fc ligand
specificity.
[0124] A number of antibodies and Fc fusions that are approved for
use, in clinical trials, or in development may benefit from the Fc
variants of the present invention. These antibodies and Fc fusions
are herein referred to as "clinical products and candidates". Thus
in a preferred embodiment, the Fc polypeptides of the present
invention may find use in a range of clinical products and
candidates. For example, a number of antibodies that target CD20
may benefit from the Fc polypeptides of the present invention. For
example the Fc polypeptides of the present invention may find use
in an antibody that is substantially similar to rituximab
(Rituxan.RTM.), IDEC/Genentech/Roche) (see for example U.S. Pat.
No. 5,736,137), a chimeric anti-CD20 antibody approved to treat
Non-Hodgkin's lymphoma; HuMax-CD20, an anti-CD20 currently being
developed by Genmab, an anti-CD20 antibody described in U.S. Pat.
No. 5,500,362, AME-133 (Applied Molecular Evolution), hA20
(Immunomedics, Inc.), HumaLYM (Intracel), and PRO70769
(PCT/US2003/040426, entitled "Immunoglobulin Variants and Uses
Thereof"). A number of antibodies that target members of the family
of epidermal growth factor receptors, including EGFR (ErbB-1),
Her2/neu (ErbB-2), Her3 (ErbB-3), Her4 (ErbB-4), may benefit from
the Fc polypeptides of the present invention. For example the Fc
polypeptides of the present invention may find use in an antibody
that is substantially similar to trastuzumab (Herceptin.RTM.),
Genentech) (see for example U.S. Pat. No. 5,677,171), a humanized
anti-Her2/neu antibody approved to treat breast cancer; pertuzumab
(rhuMab-2C4, Omnitarg.TM.), currently being developed by Genentech;
an anti-Her2 antibody described in U.S. Pat. No. 4,753,894;
cetuximab (Erbitux.RTM., Imclone) (U.S. Pat. No. 4,943,533; PCT WO
96/40210), a chimeric anti-EGFR antibody in clinical trials for a
variety of cancers; ABX-EGF (U.S. Pat. No. 6,235,883), currently
being developed by Abgenix-Immunex-Amgen; HuMax-EGFr (U.S. Ser. No.
10/172,317), currently being developed by Genmab; 425, EMD55900,
EMD62000, and EMD72000 (Merck KGaA) (U.S. Pat. No. 5,558,864;
Murthy et al. 1987, Arch Biochem Biophys. 252(2):549-60; Rodeck et
al., 1987, J Cell Biochem. 35(4):315-20; Kettleborough et al.,
1991, Protein Eng. 4(7):773-83); ICR62 (Institute of Cancer
Research) (PCT WO 95/20045; Modjtahedi et al., 1993, J. Cell
Biophys. 1993, 22(1-3):129-46; Modjtahedi et al., 1993, Br J
Cancer. 1993, 67(2):247-53; Modjtahedi et al, 1996, Br J Cancer,
73(2):228-35; Modjtahedi et al, 2003, Int J Cancer, 105(2):273-80);
TheraCIM hR3 (YM Biosciences, Canada and Centro de Immunologia
Molecular, Cuba (U.S. Pat. No. 5,891,996; U.S. Pat. No. 6,506,883;
Mateo et al, 1997, Immunotechnology, 3(1):71-81); mAb-806 (Ludwig
Institue for Cancer Research, Memorial Sloan-Kettering) (Jungbluth
et al. 2003, Proc Natl Acad Sci USA. 100(2):639-44); KSB-102 (KS
Biomedix); MR1-1 (IVAX, National Cancer Institute) (PCT WO
0162931A2); and SC100 (Scancell) (PCT WO 01/88138). In another
preferred embodiment, the Fc polypeptides of the present invention
may find use in alemtuzumab (Campath.RTM., Millenium), a humanized
monoclonal antibody currently approved for treatment of B-cell
chronic lymphocytic leukemia. The Fc polypeptides of the present
invention may find use in a variety of antibodies or Fc fusions
that are substantially similar to other clinical products and
candidates, including but not limited to muromonab-CD3 (Orthoclone
OKT3.RTM.), an anti-CD3 antibody developed by Ortho Biotech/Johnson
& Johnson, ibritumomab tiuxetan (Zevalin.RTM.), an anti-CD20
antibody developed by IDEC/Schering AG, gemtuzumab ozogamicin
(Mylotarg.RTM.), an anti-CD33 (p67 protein) antibody developed by
Celltech/Wyeth, alefacept (Amevive.RTM.), an anti-LFA-3 Fc fusion
developed by Biogen), abciximab (ReoPro.RTM.), developed by
Centocor/Lilly, basiliximab (Simulect.RTM.), developed by Novartis,
palivizumab (Synagis.RTM.), developed by Medlmmune, infliximab
(Remicade.RTM.), an anti-TNFalpha antibody developed by Centocor,
adalimumab (Humira.RTM.), an anti-TNFalpha antibody developed by
Abbott, Humicade.TM., an anti-TNFalpha antibody developed by
Celltech, etanercept (Enbrel.RTM.), an anti-TNFalpha Fc fusion
developed by Immunex/Amgen, ABX-CBL, an anti-CD147 antibody being
developed by Abgenix, ABX-IL8, an anti-IL8 antibody being developed
by Abgenix, ABX-MA1, an anti-MUC18 antibody being developed by
Abgenix, Pemtumomab (R1549, .sup.90Y-muHMFG1), an anti-MUC1 In
development by Antisoma, Therex (R1550), an anti-MUC1 antibody
being developed by Antisoma, AngioMab (AS1405), being developed by
Antisoma, HuBC-1, being developed by Antisoma, Thioplatin (AS1407)
being developed by Antisoma, Antegren.RTM. (natalizumab), an
anti-alpha-4-beta-1 (VLA-4) and alpha-4-beta-7 antibody being
developed by Biogen, VLA-1 mAb, an anti-VLA-1 integrin antibody
being developed by Biogen, LTBR mAb, an anti-lymphotoxin beta
receptor (LTBR) antibody being developed by Biogen, CAT-152, an
anti-TGF-.beta.2 antibody being developed by Cambridge Antibody
Technology, J695, an anti-IL-12 antibody being developed by
Cambridge Antibody Technology and Abbott, CAT-192, an
anti-TGF.beta.1 antibody being developed by Cambridge Antibody
Technology and Genzyme, CAT-213, an anti-Eotaxin1 antibody being
developed by Cambridge Antibody Technology, LymphoStat-B.TM. an
anti-Blys antibody being developed by Cambridge Antibody Technology
and Human Genome Sciences Inc., TRAIL-R1mAb, an anti-TRAIL-R1
antibody being developed by Cambridge Antibody Technology and Human
Genome Sciences, Inc., Avastin.TM. (bevacizumab, rhuMAb-VEGF), an
anti-VEGF antibody being developed by Genentech, an anti-HER
receptor family antibody being developed by Genentech, Anti-Tissue
Factor (ATF), an anti-Tissue Factor antibody being developed by
Genentech, Xolair.TM. (Omalizumab), an anti-IgE antibody being
developed by Genentech, Raptiva.TM. (Efalizumab), an anti-CD11a
antibody being developed by Genentech and Xoma, MLN-02 Antibody
(formerly LDP-02), being developed by Genentech and Millenium
Pharmaceuticals, HuMax CD4, an anti-CD4 antibody being developed by
Genmab, HuMax-IL15, an anti-IL15 antibody being developed by Genmab
and Amgen, HuMax-Inflam, being developed by Genmab and Medarex,
HuMax-Cancer, an anti-Heparanase I antibody being developed by
Genmab and Medarex and Oxford GcoSciences, HuMax-Lymphoma, being
developed by Genmab and Amgen, HuMax-TAC, being developed by
Genmab, IDEC-131, and anti-CD40L antibody being developed by IDEC
Pharmaceuticals, IDEC-151 (Clenoliximab), an anti-CD4 antibody
being developed by IDEC Pharmaceuticals, IDEC-114, an anti-CD80
antibody being developed by IDEC Pharmaceuticals, IDEC-152, an
anti-CD23 being developed by IDEC Pharmaceuticals, anti-macrophage
migration factor (MIF) antibodies being developed by IDEC
Pharmaceuticals, BEC2, an anti-idiotypic antibody being developed
by Imclone, IMC-1C11, an anti-KDR antibody being developed by
lmclone, DC101, an anti-flk-1 antibody being developed by Imclone,
anti-VE cadherin antibodies being developed by Imclone,
CEA-Cide.TM. (Iabetuzumab), an anti-carcinoembryonic antigen (CEA)
antibody being developed by Immunomedics, LymphoCide.TM.
(Epratuzumab), an anti-CD22 antibody being developed by
Immunomedics, AFP-Cide, being developed by Immunomedics,
MyelomaCide, being developed by Immunomedics, LkoCide, being
developed by Immunomedics, ProstaCide, being developed by
Immunomedics, MDX-010, an anti-CTLA4 antibody being developed by
Medarex, MDX-060, an anti-CD30 antibody being developed by Medarex,
MDX-070 being developed by Medarex, MDX-018 being developed by
Medarex, Osidem.TM. (IDM-1), and anti-Her2 antibody being developed
by Medarex and Immuno-Designed Molecules, HuMax.TM.-CD4, an
anti-CD4 antibody being developed by Medarex and Genmab,
HuMax-IL15, an anti-IL15 antibody being developed by Medarex and
Genmab, CNTO 148, an anti-TNF.alpha. antibody being developed by
Medarex and Centocor/J&J, CNTO 1275, an anti-cytokine antibody
being developed by Centocor/J&J, MOR101 and MOR102,
anti-intercellular adhesion molecule-1 (ICAM-1) (CD54) antibodies
being developed by MorphoSys, MOR201, an anti-fibroblast growth
factor receptor 3 (FGFR-3) antibody being developed by MorphoSys,
Nuvion.RTM. (visilizumab), an anti-CD3 antibody being developed by
Protein Design Labs, HuZAF.TM., an anti-gamma interferon antibody
being developed by Protein Design Labs, Anti-.alpha.5.beta.1
Integrin, being developed by Protein Design Labs, anti-IL-12, being
developed by Protein Design Labs, ING-1, an anti-Ep-CAM antibody
being developed by Xoma, and MLN01, an anti-Beta2 integrin antibody
being developed by Xoma, all references incorporated by
reference.
[0125] Application of the Fc polypeptides to the aforementioned
antibody and Fc fusion clinical products and candidates is not
meant to be constrained to their precise composition. The Fc
polypeptides of the present invention may be incorporated into the
aforementioned clinical candidates and products, or into antibodies
and Fc fusions that are substantially similar to them. The Fc
polypeptides of the present invention may be incorporated into
versions of the aforementioned clinical candidates and products
that are humanized, affinity matured, engineered, or modified in
some other way. Furthermore, the entire polypeptide of the
aforementioned clinical products and candidates need not be used to
construct a new antibody or Fc fusion that incorporates the Fc
polypeptides of the present invention; for example only the
variable region of a clinical product or candidate antibody, a
substantially similar variable region, or a humanized, affinity
matured, engineered, or modified version of the variable region may
be used. In another embodiment, the Fc polypeptides of the present
invention may find use in an antibody or Fc fusion that binds to
the same epitope, antigen, ligand, or receptor as one of the
aforementioned clinical products and candidates.
[0126] In one embodiment, the Fc polypeptides of the present
invention are used for the treatment of autoimmune, inflammatory,
or transplant indications. Target antigens and clinical products
and candidates that are relevant for such diseases include but are
not limited to anti-.alpha.4.beta.7 integrin antibodies such as
LDP-02, anti-beta2 integrin antibodies such as LDP-01,
anti-complement (C5) antibodies such as 5G1.1, anti-CD2 antibodies
such as BTI-322, MEDI-507, anti-CD3 antibodies such as OKT3, SMART
anti-CD3, anti-CD4 antibodies such as IDEC-151, MDX-CD4, OKT4A,
anti-CD11a antibodies, anti-CD14 antibodies such as IC14, anti-CD18
antibodies, anti-CD23 antibodies such as IDEC 152, anti-CD25
antibodies such as Zenapax, anti-CD40L antibodies such as 5c8,
Antova, IDEC-131, anti-CD64 antibodies such as MDX-33, anti-CD80
antibodies such as IDEC-114, anti-CD147 antibodies such as ABX-CBL,
anti-E-selectin antibodies such as CDP850, anti-gpIIb/IIIa
antibodies such as ReoPro/Abcixima, anti-ICAM-3 antibodies such as
ICM3, anti-ICE antibodies such as VX-740, anti-FcR1 antibodies such
as MDX-33, anti-IgE antibodies such as rhuMab-E25, anti-IL-4
antibodies such as SB-240683, anti-IL-5 antibodies such as
SB-240563, SCH55700, anti-IL-8 antibodies such as ABX-IL8,
anti-interferon gamma antibodies, anti-TNF (TNF, TNF.alpha., TNFa,
TNF-alpha) antibodies such as CDP571, CDP870, D2E7, Infliximab,
MAK-195F, and anti-VLA-4 antibodies such as Antegren.
[0127] Fc variants of the present invention may be utilized in TNF
inhibitor molecules to provide enhanced properties. It has been
shown that the effector function associated with Fc.gamma.RIIIa may
negatively impact the effectiveness of certain TNF inhibitor
molecules used in the treatment of rheumatoid arthritis or
psoriatic arthritis patients that have a high-affinity polymorphism
(158 F:V discussed herein elsewhere) and vice-versa (Z. Tutuncu et
al., 2004, "FcR Polymorphisms and Treatment Outcomes in Patients
with Inflammatory Arthritis Treated with TNF Blocking Agents", oral
presentation on Oct. 18, 2004 at the 2004 ACR Meeting, San Antonio,
Tex.; abstract published in Arthritis & Rheumatism, September
2004, incorporated by reference). In general for autoimmune
conditions such as rheumatoid arthritis or psoriatic arthritis,
combining a TNF inhibitor with an Fc variant that provides reduced
binding to one or more Fc.gamma.Rs as compared to the parent
enhances the effectiveness of therapy. Ideally, reduced or even
ablated binding to one or more Fc.gamma.Rs, for example
Fc.gamma.RIIIa, with a TNF inhibitor molecule would produce the
best results.
[0128] Useful TNF inhibitor molecules include any molecule that
inhibits the action of TNF-alpha in a mammal. Suitable examples
include the Fc fusion Enbrel.RTM. (etanercept) and the antibodies
Humira.RTM. (adalimumab) and Remicade.RTM. (infliximab). Monoclonal
antibodies (such as Remicade and Humira) engineered using the Fc
variants of the present invention to reduce Fc binding, may
translate to better efficacy. Effector function of Humira,
Remicade, and Enbrel was not considered in the development of these
drugs, let alone modulation of effector function. By using an Fc
variant of the present invention that reduces binding to one or
more Fc.gamma.Rs in the context of an antibody or Fc fusion that
acts on autoimmune conditions, efficacy may be enhanced as compared
to the currently commercialized products. Useful TNF inhibitor
molecules preferably include Dominant Negative TNF molecules (as
defined in U.S. Ser. No. 09/798,789, filed Mar. 2, 2000; Ser. No.
09/981,289, filed Oct. 15, 2001; Ser. No. 10/262,630, filed Sep.
30, 2002; and Ser. No. 10/963,994, filed Oct. 12, 2004, all
incorporated by reference). The Dominant Negative TNF molecules
(DN-TNF) have no intrinsic effector activity, and act to "save"
transmembrane TNF (tmTNF) (i.e., if the killing of cells that
contain tmTNF has a negative effect on disease outcome for
rheumatoid or psoriatic arthritis). A DN-TNF molecule associated
with an Fc variant that reduces or ablates Fc.gamma.R binding to
the receptor is preferred.
[0129] In one embodiment, the Fc polypeptides of the present
invention function therapeutically, in whole or in part, through
ADCC activity. Target antigens and clinical products and candidates
that are relevant for such application may include but are not
limited to: anti-CD20 antibodies such as Bexocar, Rituxan.RTM.,
Zevalin.RTM., and PRO70769, anti-CD33 antibodies such as Smart
M195, anti-CD22 antibodies such as Lymphocide.TM., anti-CD30
antibodies such as AC-10 and SGN-30, anti-EGFR antibodies such as
ABX-EGF, Cetuximab, IMC-C225, Merck Mab 425, anti-EpCAM antibodies
such as Crucell's anti-EpCAM, anti-HER2 antibodies such as
Herceptin and MDX-210, and anti-CEA antibodies such as cantumab and
Pentacea.
[0130] In one embodiment, the Fc polypeptides of the present
invention function therapeutically, in whole or in part, through
CDC activity. Target antigens and clinical products and candidates
that are relevant for such application may include but are not
limited to: anti-CEA antibodies such as cantumab and Pentacea,
anti-CD20 antibodies such as Bexocar, Rituxan.RTM., Zevalin.RTM.,
and PRO70769, anti-EpCAM antibodies such as Crucell's anti-EpCAM
and Edrecolomab, and anti-CD52 antibodies such as Campath.RTM.
(alemtuzumab).
[0131] In one embodiment, the the Fc polypeptides of the present
invention are directed against antigens expressed in the
hematological lineage. Target antigens and clinical products and
candidates that are relevant for such application may include but
are not limited to: anti-CD33 antibodies such as Smart M195,
anti-CD40L antibodies such as Antova.TM., IDEC-131, anti-CD44
antibodies such as Blvatuzumab, anti-CD52 antibodies such as
Campath.RTM. (alemtuzumab), anti-CD80 antibodies such as IDEC-114,
anti-CTLA-4 antibodies such as MDX-101, anti-CD20 antibodies such
as Bexocar, Rituxan.RTM., Zevalin.RTM., and PRO70769, anti-CD22
antibodies such as Lymphocide.TM., anti-CD23 antibodies such as
IDEC-152, anti-CD25 antibodies such as Zenapax.RTM. (daclizumab),
and anti-MHC (HLA-DR) antibodies such as apolizumab.
[0132] In one embodiment, the Fc polypeptides of the present
invention are directed against antigens expressed in solid tumors.
Target antigens and clinical products and candidates that are
relevant for such application may include but are not limited to:
anti-EpCAM antibodies such as Crucell's anti-EpCAM and Edrecolomab,
anti-CEA antibodies such as cantumab and Pentacea, anti-EGFR
antibodies such as ABX-EGF, Cetuximab, IMC-C225, Merck Mab 425,
anti-Muc1 antibodies such as BravaRex, TriAb, anti-Her2 antibodies
such as Herceptin.RTM., MDX-210, anti-GD-2 ganglioside antibodies
such as 3F8 and TriGem, anti-GD-3 ganglioside antibodies such as
mitumomab, anti-PSMA antibodies such as MDX-070, anti-CA125
antibodies such as oregovomab, anti-TAG-72 antibdies such as
MDX-220, and anti-MUC-1 antibodies such as cantuzumab.
[0133] In a preferred embodiment, the target of the Fc variants of
the present invention is itself one or more Fc ligands. Fc
polypeptides of the invention can be utilized to modulate the
activity of the immune system, and in some cases to mimic the
effects of IVIg therapy in a more controlled, specific, and
efficient manner. IVIg is effectively a high dose of
immunoglobulins delivered intravenously. In general, IVIg has been
used to downregulate autoimmune conditions. It has been
hypothesized that the therapeutic mechanism of action of IVIg
involves ligation of Fc receptors at high frequency (J. Bayry et
al., 2003, Transfusion Clinique et Biologique 10: 165-169; Binstadt
et al., 2003, J Allergy Clin. Immunol, 697-704). Indeed animal
models of Ithrombocytopenia purpura (ITP) show that the isolated Fc
are the active portion of IVIg (Samuelsson et al, 2001, Pediatric
Research 50(5), 551). For use in therapy, iimmunoglobulins are
harvested from thousands of donors, with all of the concomitant
problems associated with non-recombinant biotherapeutics collected
from humans. An Fc variant of the present invention should serve
all of the roles of IVIg while being manufactured as a recombinant
protein rather than harvested from donors.
[0134] The immunomodulatory effects of IVIg may be dependent on
productive interaction with one or more Fc ligands, including but
not limited to Fc.gamma.Rs, complement proteins, and FcRn. In some
embodiments, Fc variants of the invention with enhanced affinity
for Fc.gamma.RIIb can be used to promote anti-inflammatory activity
(Samuelsson et al., 2001, Science 291: 484-486) and or to reduce
autoimmunity (Hogarth, 2002, Current Opinion in Immunology,
14:798-802). In other embodiments, Fc polypeptides of the invention
with enhanced affinity for one or more Fc.gamma.Rs can be utilized
by themselves or in combination with additional modifications to
reduce autoimmunity (Hogarth, 2002, Current Opinion in Immunology,
14:798-802). In alternative embodiments, Fc variants of the
invention with enhanced affinity for Fc.gamma.RIIIa but reduced
capacity for intracellular signaling can be used to reduce immune
system activation by competitively interfering with Fc.gamma.RIIIa
binding. The context of the Fc variant drammatically impacts the
desired specificity. For example, Fc variants that provide enhanced
binding to one or more activating Fc.gamma.Rs may provide optimal
immunomodulatory effects in the context of an antibody, Fc fusion,
isolated Fc, or Fc fragment by acting as an Fc.gamma.R antagonist
(van Mirre et al., 2004, J. Immunol. 173:332-339). However, fusion
or conjugation of two or more Fc variants may provide different
effects, and for such an Fc polypeptide it may be optimal to
utilize Fc variants that provide enhanced affinity for an
inhibitory receptor.
[0135] The Fc variants of the present invention may be used as
immunomodulatory therapeutics. Binding to or blocking Fc receptors
on immune system cells may be used to influence immune response in
immunological conditions including but not limited to idiopathic
thrombocytopenia purpura (ITP) and rheumatoid arthritis (RA) among
others. By use of the affinity enhanced Fc variants of the present
invention, the dosages required in typical IVIg applications may be
reduced while obtaining a substantially similar therapeutic effect.
The Fc variants may provide enhanced binding to an Fc.gamma.R,
including but not limited to Fc.gamma.RIIa, Fc.gamma.RIIb,
Fc.gamma.RIIIa, Fc.gamma.RIIIb, and/or Fc.gamma.RI. In particular,
binding enhanements to Fc.gamma.RIIb would increase expression or
inhibitory activity, as needed, of that receptor and improve
efficacy. Alternatively, blocking binding to activation receptors
such as Fc.gamma.RIIIb or Fc.gamma.RI may improve efficacy. In
addition, modulated affinity of the Fc variants for FcRn and/or
also complement may also provide benefits.
[0136] In one embodiment, Fc variants that provide enhanced binding
to the inhibitory receptor Fc.gamma.RIIb provide an enhancement to
the IVIg therapeutic approach. In particular, the Fc variants of
the present invention that bind with greater affinity to the
Fc.gamma.RIIb receptor than parent Fc polypeptide may be used. Such
Fc variants would thus function as Fc.gamma.RIIb agonists, and
would be expected to enhance the beneficial effects of IVIg as an
autoimmune disease therapeutic and also as a modulator of B-cell
proliferation. In addition, such Fc.gamma.RIIb-enhanced Fc variants
may also be further modified to have the same or limited binding to
other receptors. In additional embodiments, the Fc variants with
enhanced Fc.gamma.RIIb affinity may be combined with mutations that
reduce or ablate to other receptors, thereby potentially further
minimizing side effects during therapeutic use.
[0137] Such immunomodulatory applications of the Fc variants of the
present invention may also be utilized in the treatment of
oncological indications, especially those for which antibody
therapy involves antibody-dependant cytotoxic mechanisms. For
example, an Fc variant that enhances affinity to Fc.gamma.RIIb may
be used to antagonize this inhibitory receptor, for example by
binding to the Fc/Fc.gamma.RIIb binding site but failing to
trigger, or reducing cell signaling, potentially enhancing the
effect of antibody-based anti-cancer therapy. Such Fc variants,
functioning as Fc.gamma.RIIb antagonists, may either block the
inhibitory properties of Fc.gamma.RIIb, or induce its inhibitory
function as in the case of IVIg. An Fc.gamma.RIIb antagonist may be
used as co-therapy in combination with any other therapeutic,
including but not limited to antibodies, acting on the basis of
ADCC related cytotoxicity. Fc.gamma.RIIb antagonistic Fc variants
of this type are preferably isolated Fc or Fc fragments, although
in alternate embodiments antibodies and Fc fusions may be used.
Optimized Properties
[0138] The present invention provides Fc variants that are
optimized for a number of therapeutically relevant properties. An
Fc variant comprises one or more amino acid modifications relative
to a parent Fc polypeptide, wherein said amino acid modification(s)
provide one or more optimized properties. An Fc variant of the
present invention differs in amino acid sequence from its parent Fc
polypeptide by virtue of at least one amino acid modification. Thus
Fc variants of the present invention have at least one amino acid
modification compared to the parent. Alternatively, the Fc variants
of the present invention may have more than one amino acid
modification as compared to the parent, for example from about one
to fifty amino acid modifications, preferrably from about one to
ten amino acid modifications, and most preferably from about one to
about five amino acid modifications compared to the parent. Thus
the sequences of the Fc variants and those of the parent Fc
polypeptide are substantially homologous. For example, the variant
Fc variant sequences herein will possess about 80% homology with
the parent Fc variant sequence, preferably at least about 90%
homology, and most preferably at least about 95% homology.
[0139] The Fc variants of the present invention may be optimized
for a variety of properties. An Fc variant that is engineered or
predicted to display one or more optimized properties is herein
referred to as an "optimized Fc variant". Properties that may be
optimized include but are not limited to enhanced or reduced
affinity for an Fc.gamma.R. In a preferred embodiment, the Fc
variants of the present invention are optimized to possess enhanced
affinity for a human activating Fc.gamma.R, preferably Fc.gamma.RI,
Fc.gamma.RIIa, Fc.gamma.RIIc, Fc.gamma.RIIIa, and Fc.gamma.RIIIb,
most preferably Fc.gamma.RIIIa. In an alternately preferred
embodiment, the Fc variants are optimized to possess reduced
affinity for the human inhibitory receptor Fc.gamma.RIIb. These
preferred embodiments are anticipated to provide Fc polypeptides
with enhanced therapeutic properties in humans, for example
enhanced effector function and greater anti-cancer potency. In an
alternate embodiment, the Fc variants of the present invention are
optimized to have reduced or ablated affinity for a human
Fc.gamma.R, including but not limited to Fc.gamma.RI,
Fc.gamma.RIIa, Fc.gamma.RIIb, Fc.gamma.RIIc, Fc.gamma.RIIIa, and
Fc.gamma.RIIIb. These embodiments are anticipated to provide Fc
polypeptides with enhanced therapeutic properties in humans, for
example reduced effector function and reduced toxicity. In other
embodiments, Fc variants of the present invention provide enhanced
affinity for one or more Fc.gamma.Rs, yet reduced affinity for one
or more other Fc.gamma.Rs. For example, an Fc variant of the
present invention may have enhanced binding to Fc.gamma.RIIIa, yet
reduced binding to Fc.gamma.RIIb. Alternately, an Fc variant of the
present invention may have enhanced binding to Fc.gamma.RIIa and
Fc.gamma.RI, yet reduced binding to Fc.gamma.RIIb. In yet another
embodiment, an Fc variant of the present invention may have
enhanced affinity for Fc.gamma.RIIb, yet reduced affinity to one or
more activating Fc.gamma.Rs.
[0140] Preferred embodiments comprise optimization of Fc binding to
a human Fc.gamma.R, however in alternate embodiments the Fc
variants of the present invention possess enhanced or reduced
affinity for Fc.gamma.Rs from nonhuman organisms, including but not
limited to rodents and non-human primates. Fc variants that are
optimized for binding to a nonhuman Fc.gamma.R may find use in
experimentation. For example, mouse models are available for a
variety of diseases that enable testing of properties such as
efficacy, toxicity, and pharmacokinetics for a given drug
candidate. As is known in the art, cancer cells can be grafted or
injected into mice to mimic a human cancer, a process referred to
as xenografting. Testing of Fc variants that comprise Fc variants
that are optimized for one or more mouse Fc.gamma.Rs, may provide
valuable information with regard to the efficacy of the protein,
its mechanism of action, and the like. The Fc variants of the
present invention may also be optimized for enhanced functionality
and/or solution properties in aglycosylated form. In a preferred
embodiment, the aglycosylated Fc variants of the present invention
bind an Fc ligand with greater affinity than the aglycosylated form
of the parent Fc variant. Said Fc ligands include but are not
limited to Fc.gamma.Rs, C1q, FcRn, and proteins A and G, and may be
from any source including but not limited to human, mouse, rat,
rabbit, or monkey, preferably human. In an alternately preferred
embodiment, the Fc variants are optimized to be more stable and/or
more soluble than the aglycosylated form of the parent Fc
variant.
[0141] Fc variants of the invention may comprise modifications that
modulate interaction with Fc ligands other than Fc.gamma.Rs,
including but not limited to complement proteins, FcRn, and Fc
receptor homologs (FcRHs). FcRHs include but are not limited to
FcRH1, FcRH2, FcRH3, FcRH4, FcRH5, and FcRH6 (Davis et al., 2002,
Immunol. Reviews 190:123-136).
[0142] Preferably, the Fc ligand specificity of the Fc variant of
the present invention will determine its therapeutic utility. The
utility of a given Fc variant for therapeutic purposes will depend
on the epitope or form of the Target antigen and the disease or
indication being treated. For some targets and indications,
enhanced Fc.gamma.R-mediated effector functions may be preferable.
This may be particularly favorable for anti-cancer Fc variants.
Thus Fc variants may be used that comprise Fc variants that provide
enhanced affinity for activating Fc.gamma.Rs and/or reduced
affinity for inhibitory Fc.gamma.Rs. For some targets and
indications, it may be further beneficial to utilize Fc variants
that provide differential selectivity for different activating
Fc.gamma.Rs; for example, in some cases enhanced binding to
Fc.gamma.RIIa and Fc.gamma.RIIIa may be desired, but not
Fc.gamma.RI, whereas in other cases, enhanced binding only to
Fc.gamma.RIIa may be preferred. For certain targets and
indications, it may be preferable to utilize Fc variants that
enhance both Fc.gamma.R-mediated and complement-mediated effector
functions, whereas for other cases it may be advantageous to
utilize Fc variants that enhance either Fc.gamma.R-mediated or
complement-mediated effector functions. For some Targets or cancer
indications, it may be advantageous to reduce or ablate one or more
effector functions, for example by knocking out binding to C1q, one
or more Fc.gamma.R's, FcRn, or one or more other Fc ligands. For
other targets and indications, it may be preferable to utilize Fc
variants that provide enhanced binding to the inhibitory
Fc.gamma.RIIb, yet WT level, reduced, or ablated binding to
activating Fc.gamma.Rs. This may be particularly useful, for
example, when the goal of an Fc variant is to inhibit inflammation
or auto-immune disease, or modulate the immune system in some
way.
[0143] Clearly an important parameter that determines the most
beneficial selectivity of a given Fc variant to treat a given
disease is the context of the Fc variant, that is what type of Fc
variant is being used. Thus the Fc ligand selectivity or specifity
of a given Fc variant will provide different properties depending
on whether it composes an antibody, Fc fusion, or an Fc variants
with a coupled fusion or conjugate partner. For example, toxin,
radionucleotide, or other conjugates may be less toxic to normal
cells if the Fc variant that comprises them has reduced or ablated
binding to one or more Fc ligands. As another example, in order to
inhibit inflammation or auto-immune disease, it may be preferable
to utilize an Fc variant with enhanced affinity for activating
Fc.gamma.Rs, such as to bind these Fc.gamma.Rs and prevent their
activation. Conversely, an Fc variant that comprises two or more Fc
regions with enhanced Fc.gamma.RIIb affinity may co-engage this
receptor on the surface of immune cells, thereby inhibiting
proliferation of these cells. Whereas in some cases an Fc variants
may engage its target antigen on one cell type yet engage
Fc.gamma.Rs on separate cells from the target antigen, in other
cases it may be advantageous to engage Fc.gamma.Rs on the surface
of the same cells as the target antigen. For example, if an
antibody targets an antigen on a cell that also expresses one or
more Fc.gamma.Rs, it may be beneficial to utilize an Fc variant
that enhances or reduces binding to the Fc.gamma.Rs on the surface
of that cell. This may be the case, for example when the Fc variant
is being used as an anti-cancer agent, and co-engagement of target
antigen and Fc.gamma.R on the surface of the same cell promote
signaling events within the cell that result in growth inhibition,
apoptosis, or other anti-proliferative effect. Alternatively,
antigen and Fc.gamma.R co-engagement on the same cell may be
advantageous when the Fc variant is being used to modulate the
immune system in some way, wherein co-engagement of target antigen
and Fc.gamma.R provides some proliferative or anti-proliferative
effect. Likewise, Fc variants that comprise two or more Fc regions
may benefit from Fc variants that modulate Fc.gamma.R selectivity
or specifity to co-engage Fc.gamma.Rs on the surface of the same
cell.
[0144] The Fc ligand specificity of the Fc variants of the present
invention can be modulated to create different effector function
profiles that may be suited for particular target antigens,
indications, or patient populations. Table 1 describes several
preferred embodiments of receptor binding profiles that include
improvements to, reductions to or no effect to the binding to
various receptors, where such changes may be beneficial in certain
contexts. The receptor binding profiles in the table could be
varied by degree of increase or decrease to the specified
receptors. Additionally, the binding changes specified could be in
the context of additional binding changes to other receptors such
as C1q or FcRn, for example by combining with ablation of binding
to C1q to shut off complement activation, or by combining with
enhanced binding to C1q to increase complement activiation. Other
embodiments with other receptor binding profiles are possible, the
listed receptor binding profiles are exemplary. TABLE-US-00001
TABLE 1 Affinity Affinity Enhancement Reduction Cell Activity
Therapeutic Activity Fc.gamma.RI only -- Enhanced dendritic cell
activity Enhanced cell-based and uptake, and subsequent immune
response against presentation of antigens target Enhanced monocyte
and macrophage response to antibody Fc.gamma.RIIIa -- Enhanced ADCC
and Increased target cell lysis phagocytosis of broad range of cell
types Fc.gamma.RIIIa Fc.gamma.RIIb Enhanced ADCC and Increased
target cell lysis phagocytosis of broad range of cell types
Fc.gamma.RIIb -- Reduced activity of all Fc.gamma.R Enhancement of
target cell Fc.gamma.RIIc bearing cell types except NK lysis
selective for NK cell cells accessible target cells Possible
activation of NK cells via Fc.gamma.RIIc receptor signaling
Fc.gamma.RIIb -- Possible NK cell specific Enhanced target cell
lysis Fc.gamma.RIIIa activation and enhancement of selective for NK
cell NK cell mediated ADCC accessible target cells Fc.gamma.RIIIb
-- Neutrophil mediated Enhanced target cell phagocytosis
enhancement destruction for neutrophil accessible cells Fc.alpha.R
-- Neutrophil mediated Enhanced target cell phagocytosis
enhancement destruction for neutrophil accessible cells Fc.gamma.RI
Fc.gamma.RIIb Enhanced dendritic cell activity Enhanced cell-based
Fc.gamma.RIIa and uptake, and subsequent immune response against
Fc.gamma.RIIIa presentation of antigens to T target cells Enhanced
monocyte and macrophage response to antibody Fc.gamma.RIIb
Fc.gamma.RI Reduced activity of monocytes, Eliminated or reduced
cell- Fc.gamma.RIIa macrophages, neutrophils, NK, mediated
cytotoxicity Fc.gamma.RIIIa dendritic and other gamma against
target bearing cells receptor bearing cells
[0145] The presence of different polymorphic forms of Fc.gamma.Rs
provides yet another parameter that impacts the therapeutic utility
of the Fc variants of the present invention. Whereas the
specificity and selectivity of a given Fc variant for the different
classes of Fc.gamma.Rs signficantly affects the capacity of an Fc
variant to target a given antigen for treatment of a given disease,
the specificity or selectivity of an Fc variant for different
polymorphic forms of these receptors may in part determine which
research or pre-clinical experiments may be appropriate for
testing, and ultimately which patient populations may or may not
respond to treatment. Thus the specificity or selecitivty of Fc
variants of the present invention to Fc ligand polymorphisms,
including but not limited to Fc.gamma.R, C1q, FcRn, and FcRH
polymorphisms, may be used to guide the selection of valid research
and pre-clinical experiments, clinical trial design, patient
selection, dosing dependence, and/or other aspects concerning
clinical trials.
Additional Modifications
[0146] In addition to comprising an Fc variant of the present
invention, the Fc polypeptides of the present invention may
comprise one or more additional modifications. Said modifications
may be amino acid modifications, or may modifications that are not
amino acid modifications such as modifications that are made
enzymatically or chemically. Combinations of additional amino acid
modifications and modifications that are not amino acid
modifications are contemplated. Such additional modification(s)
likely provide some improvement in the Fc polypeptide, for example
an enhancement in its stability, solubility, function, or clinical
use. The present invention contemplates a variety of improvements
that made be made by coupling the Fc variants of the present
invention with additional modifications.
[0147] The Fc variants of the present invention may be combined
with other amino acid modifications in the Fc region that provide
altered or optimized interaction with one or more Fc ligands,
including but not limited to Fc.gamma.Rs, C1q or other complement
proteins, FcRn, FcR homologues (FcRHs), and/or as yet undiscovered
Fc ligands. It is noted that Fc polypeptides of the present
invention may themselves have as yet unknown useful interaction
properties with one or more Fc ligands, for example FcRHs.
Additional modifications may provide altered or optimized affinity
and/or specificity to the Fc ligands. Additional modifications may
provide altered or optimized effector functions, including but not
limited to ADCC, ADCP, CDC, and/or serum half-life. Such
combination may provide additive, synergistic, or novel properties.
In one embodiment, the Fc variants of the present invention may be
combined with known Fc variants (Duncan et al., 1988, Nature
332:563-564; Lund et al., 1991, J Immunol 147:2657-2662; Lund et
al., 1992, Mol Immunol 29:53-59; Alegre et al., 1994,
Transplantation 57:1537-1543; Hutchins et al., 1995, Proc Natl Acad
Sci USA 92:11980-11984; Jefferis et al., 1995, Immunol Lett
44:111-117; Lund et al., 1995, Faseb J 9:115-119; Jefferis et al.,
1996, Immunol Lett 54:101-104; Lund et al., 1996, J Immunol
157:4963-4969; Armour et al., 1999, Eur J Immunol 29:2613-2624;
Idusogie et al., 2000, J Immunol 164:4178-4184; Reddy et al., 2000,
J Immunol 164:1925-1933; Xu et al., 2000, Cell Immunol 200:16-26;
Idusogie et al., 2001, J Immunol 166:2571-2575; Shields et al.,
2001, J Biol Chem 276:6591-6604; Jefferis et al., 2002, Immunol
Lett 82:57-65; Presta et al., 2002, Biochem Soc Trans 30:487-490;
Hinton et al., 2004, J Biol Chem 279:6213-6216) (U.S. Pat. No.
5,624,821; U.S. Pat. No. 5,885,573; U.S. Pat. No. 6,194,551; PCT WO
00/42072; PCT WO 99/58572; US 2004/0002587 A1), U.S. Pat. No.
6,737,056, PCT US2004/000643, U.S. Ser. No. 10/370,749, and
PCT/US2004/005112), all incorporated by reference. For example, as
described in U.S. Pat. No. 6,737,056, PCT US2004/000643, U.S. Ser.
No. 10/370,749, and PCT/US2004/005112, the substitutions S298A,
S298D, K326E, K326D, E333A, K334A, and P396L provide optimized
Fc.gamma.R binding and/or enhanced ADCC. Furthermore, as disclosed
in Idusogie et al., 2001, J. Immunology 166:2571-2572, incorporated
by reference, substitutions K326W, K326Y, and E333S provide
enhanced binding to the complement protein C1q and enhanced CDC.
Finally, as described in Hinton et al., 2004, J. Biol. Chem.
279(8): 6213-6216, incorporated by reference, substitutions T250Q,
T250E, M428L, and M428F provide enhanced binding to FcRn and
improved pharmacokinetics.
[0148] Because the binding sites for Fc.gamma.Rs, C1q, and FcRn
reside in the Fc region, the differences between the IgGs in the Fc
region are likely to contribute to differences in Fc.gamma.R- and
C1q-mediated effector functions. It is also possible that the
modifications can be made in other non-Fc regions of an Fc variant,
including for example the Fab and hinge regions of an antibody, or
the Fc fusion partner of an Fc fusion. For example, as disclosed in
U.S. Ser. No. 11/090,981, hereby incorporated by reference, the Fab
and hinge regions of an antibody may impact effector functions such
as antibody dependent cell-mediated cytotoxicity (ADCC), antibody
dependent cell-mediated phagocytosis (ADCP), and complement
dependent cytotoxicity (CDC). Thus modifications outside the Fc
region of an Fc variant of the present invention are contemplated.
For example, antibodies of the present invention may comprise one
or more amino acid modifications in the V.sub.L, C.sub.L, V.sub.H,
C.sub.H1, and/or hinge regions of an antibody.
[0149] Other modifications may provide additional or novel binding
determinants into an Fc variant, for example additional or novel Fc
receptor binding sites, for example as described in U.S. Ser. No.
60/531,752, filed Dec. 22, 2003, entitled "Fc variants with novel
Fc receptor binding sites". In one embodiment, an Fc variant of one
antibody isotype may be engineered such that it binds to an Fc
receptor of a different isotype. This may be particularly
applicable when the Fc binding sites for the respective Fc
receptors do not significantly overlap. For example, the structural
determinants of IgA binding to Fc.gamma.RI may be engineered into
an IgG Fc variant.
[0150] The Fc variants of the present invention may comprise
modifications that modulate the in vivo pharmacokinetic properties
of an Fc variant. These include, but are not limited to,
modifications that enhance affinity for the neonatal Fc receptor
FcRn (U.S. Ser. No. 10/020,354; WO2001US0048432; EP2001000997063;
U.S. Pat. No. 6,277,375; U.S. Ser. No. 09/933,497; WO1997US0003321;
U.S. Pat. No. 6,737,056; WO2000US0000973; Shields et al., 2001, J
Biol Chem 276(9): 6591-6604; Zhou et al., 2003, J Mol Biol., 332:
901-913). These further include modifications that modify FcRn
affinity in a pH-specific manner. In some embodiments, where
enhanced in vivo half-life is desired, modifications that
specifically enhance FcRn affinity at lower pH (5.5-6) relative to
higher pH (7-8) are preferred (Hinton et al., 2004, J Biol Chem
279(8): 6213-6216; Dall' Acqua et al., 2002 J Immuno 169:
5171-5180; Ghetie et al., 1997, Nat Biotechnol 15(7): 637-640;
WO2003US0033037; WO2004US0011213). For example, as described in
Hinton et al., 2004, "Engineered Human IgG Antibodies with Longer
Serum Half-lives in Primates" J Biol Chem 279(8): 6213-6216,
substitutions T250Q, T250E, M428L, and M428F provide enhanced
binding to FcRn and improved pharmacokinetics. Additionally
preferred modifications are those that maintain the wild-type Fc's
improved binding at lower pH relative to the higher pH. In
alternative embodiments, where rapid in vivo clearance is desired,
modifications that reduce affinity for FcRn are preferred. (U.S.
Pat. No. 6,165,745; WO1993US0003895; EP1993000910800;
WO1997US0021437; Medesan et al., 1997, J Immunol 158(5): 2211-2217;
Ghetie & Ward, 2000, Annu Rev Immunol 18: 739-766; Martin et
al. 2001, Molecular Cell 7: 867-877; Kim et al. 1999, Eur J Immunol
29: 2819-2825). Preferred variants that enhance FcRn are described
in U.S. Ser. No. 60/627,763, filed Nov. 12, 2004; 60/642,886, filed
Jan. 11, 2005; 60/649,508, filed Feb. 2, 2005; 60/662,468, filed
Mar. 15, 2005, and 60/669,311 filed Apr. 6, 2005, entitled "Fc
Variants with Altered Binding to FcRn", all hereby incorporated by
reference.
[0151] Additional modifications may comprise amino acid
modifications wherein residues in an Fc polypeptide are modified to
the corresponding residue in a homologous Fc polypeptide. Effector
functions such as ADCC, ADCP, CDC, and serum half-life differ
significantly between the different classes of antibodies,
including for example human IgG1, IgG2, IgG3, IgG4, IgA1, IgA2,
IgD, IgE, IgG, and IgM (references--Michaelsen et al., 1992,
Molecular Immunology 29(3): 319-326). Human IgG1 is the most
commonly used antibody for therapeutic purposes, and engineering
studies wherein variants have been constructed that show enhanced
effector function have been carried out predominantly in this
context. As described above, it is possible to determine
corresponding or equivalent residues in Fc polypeptides that have
significant sequence or structural homology with each other. By the
same token, it is possible to use such methods to engineer
additional amino acid modifications in an Fc polypeptide to provide
additional optimized properties, for example as described in U.S.
Ser. No. 60/621,387, filed Oct. 21, 2004. In one embodiment, amino
acid modifications can be made that replace one or more residues in
an Fc polypeptide of the present invention with one or more
residues in another homologous Fc polypeptide. In an alternate
embodiment, hybrid Fc polypeptides are constructed, such that one
or more regions of an Fc polypeptide of the present invention are
replace with the corresponding regions of a homolous Fc
polypeptide. For example, some studies have explored IgG1, IgG2,
IgG3, and IgG4 variants in order to investigate the determinants of
the effector function differences between them. See for example
Canfield & Morrison, 1991, J Exp Med 173: 1483-1491; Chappel et
al., 1991, Proc Natl Acad Sci USA 88(20): 9036-9040; Chappel et
al., 1993, J Biol Chem 268: 25124-25131; Tao, Canfield, and
Morrison, 1991, J Exp Med 173: 1025-1028; Tao et al., 1993, J Exp
Med 178: 661-667; Redpath et al., 1998, Human Immunology, 59,
720-727.
[0152] In one embodiment, the Fc variants of the present invention
comprise one or more engineered glycoforms. By "engineered
glycoform" as used herein is meant a carbohydrate composition that
is covalently attached to an Fc variant, wherein said carbohydrate
composition differs chemically from that of a parent Fc variant.
Engineered glycoforms may be useful for a variety of purposes,
including but not limited to enhancing or reducing effector
function. Engineered glycoforms may be generated by a variety of
methods known in the art (Umana et al., 1999, Nat Biotechnol
17:176-180; Davies et al., 2001, Biotechnol Bioeng 74:288-294;
Shields et al., 2002, J Biol Chem 277:26733-26740; Shinkawa et al.,
2003, J Biol Chem 278:3466-3473); (U.S. Pat. No. 6,602,684; U.S.
Ser. No. 10/277,370; U.S. Ser. No. 10/113,929; PCT WO 00/61739A1;
PCT WO 01/29246A1; PCT WO 02/31140A1; PCT WO 02/30954A1);
(Potelligent.TM. technology [Biowa, Inc., Princeton, N.J.];
GlycoMAb.TM. glycosylation engineering technology [GLYCART
biotechnology AG, Zurich, Switzerland]). Many of these techniques
are based on controlling the level of fucosylated and/or bisecting
oligosaccharides that are covalently attached to the Fc region, for
example by expressing an Fc variant in various organisms or cell
lines, engineered or otherwise (for example Lec-13 CHO cells or rat
hybridoma YB2/0 cells), by regulating enzymes involved in the
glycosylation pathway (for example FUT8
[.alpha.1,6-fucosyltranserase] and/or
.beta.1-4-N-acetylglucosaminyltransferase III [GnTIII]), or by
modifying carbohydrate(s) after the Fc variant has been expressed.
Engineered glycoform typically refers to the different carbohydrate
or oligosaccharide; thus an Fc variant, for example an antibody or
Fc fusion, may comprise an engineered glycoform. Alternatively,
engineered glycoform may refer to the Fc variant that comprises the
different carbohydrate or oligosaccharide.
[0153] Fc variants of the present invention may comprise one or
more modifications that provide optimized properties that are not
specifically related to effector function per se. Said
modifications may be amino acid modifications, or may be
modifications that are made enzymatically or chemically. Such
modification(s) likely provide some improvement in the Fc variant,
for example an enhancement in its stability, solubility, function,
or clinical use. The present invention contemplates a variety of
improvements that made be made by coupling the Fc variants of the
present invention with additional modifications.
[0154] In a preferred embodiment, the Fc variants of the present
invention may comprise modifications to reduce immunogenicity in
humans. In a most preferred embodiment, the immunogenicity of an Fc
variant of the present invention is reduced using a method
described in U.S. Ser. No. 11/004,590, filed Dec. 3, 2004, entitled
"Methods of Generating Variant Proteins with Increased Host String
Content and Compositions Thereof". In alternate embodiments, the
antibodies of the present invention are humanized (Clark, 2000,
Immunol Today 21:397-402). By "humanized" antibody as used herein
is meant an antibody comprising a human framework region (FR) and
one or more complementarity determining regions (CDR's) from a
non-human (usually mouse or rat) antibody. The non-human antibody
providing the CDR's is called the "donor" and the human
immunoglobulin providing the framework is called the "acceptor".
Humanization relies principally on the grafting of donor CDRs onto
acceptor (human) V.sub.L and V.sub.H frameworks (Winter U.S. Pat.
No. 5,225,539). This strategy is referred to as "CDR grafting".
"Backmutation" of selected acceptor framework residues to the
corresponding donor residues is often required to regain affinity
that is lost in the initial grafted construct (U.S. Pat. No.
5,530,101; U.S. Pat. No. 5,585,089; U.S. Pat. No. 5,693,761; U.S.
Pat. No. 5,693,762; U.S. Pat. No. 6,180,370; U.S. Pat. No.
5,859,205; U.S. Pat. No. 5,821,337; U.S. Pat. No. 6,054,297; U.S.
Pat. No. 6,407,213). The humanized antibody optimally also will
comprise at least a portion of an immunoglobulin constant region,
typically that of a human immunoglobulin, and thus will typically
comprise a human Fc region. A variety of techniques and methods for
humanizing and reshaping non-human antibodies are well known in the
art (See Tsurushita & Vasquez, 2004, Humanization of Monoclonal
Antibodies, Molecular Biology of B Cells, 533-545, Elsevier Science
(USA), and references cited therein). Humanization methods include
but are not limited to methods described in Jones et al., 1986,
Nature 321:522-525; Riechmann et al., 1988; Nature 332:323-329;
Verhoeyen et al., 1988, Science, 239:1534-1536; Queen et al., 1989,
Proc Natl Acad Sci, USA 86:10029-33; He et al., 1998, J Immunol
160: 1029-1035; Carter et al., 1992, Proc Natl Acad Sci USA
89:4285-9, Presta et al., 1997, Cancer Res 57(20):4593-9; Gorman et
al., 1991, Proc Natl Acad Sci USA 88:4181-4185; O'Connor et al.,
1998, Protein Eng 11:321-8. Humanization or other methods of
reducing the immunogenicity of nonhuman antibody variable regions
may include resurfacing methods, as described for example in
Roguska et al., 1994, Proc Natl Acad Sci USA 91:969-973. In one
embodiment, selection based methods may be employed to humanize
and/or affinity mature antibody variable regions, including but not
limited to methods described in Wu et al., 1999, J. Mol. Biol.
294:151-162; Baca et al., 1997, J. Biol. Chem. 272(16):10678-10684;
Rosok et al., 1996, J. Biol. Chem. 271(37): 22611-22618; Rader et
al., 1998, Proc. Natl. Acad. Sci. USA 95: 8910-8915; Krauss et al.,
2003, Protein Engineering 16(10):753-759. Other humanization
methods may involve the grafting of only parts of the CDRs,
including but not limited to methods described in U.S. Ser. No.
09/810,502; Tan et al., 2002, J. Immunol. 169:1119-1125; De
Pascalis et al., 2002, J. Immunol. 169:3076-3084. Structure-based
methods may be employed for humanization and affinity maturation,
for example as described in U.S. Ser. No. 10/153,159 and related
applications.
[0155] Modifications to reduce immunogenicity may include
modifications that reduce binding of processed peptides derived
from the parent sequence to MHC proteins. For example, amino acid
modifications would be engineered such that there are no or a
minimal number of immune epitopes that are predicted to bind, with
high affinity, to any prevalent MHC alleles. Several methods of
identifying MHC-binding epitopes in protein sequences are known in
the art and may be used to score epitopes in an Fc variant of the
present invention. See for example WO 98/52976; WO 02/079232; WO
00/3317; U.S. Ser. No. 09/903,378; U.S. Ser. No. 10/039,170; U.S.
Ser. No. 60/222,697; U.S. Ser. No. 10/339,788; PCT WO 01/21823; and
PCT WO 02/00165; Mallios, 1999, Bioinformatics 15: 432-439;
Mallios, 2001, Bioinformatics 17: 942-948; Sturniolo et al., 1999,
Nature Biotech. 17: 555-561; WO 98/59244; WO 02/069232; WO
02/77187; Marshall et al., 1995, J. Immunol. 154: 5927-5933; and
Hammer et al., 1994, J. Exp. Med. 180: 2353-2358. Sequence-based
information can be used to determine a binding score for a given
peptide--MHC interaction (see for example Mallios, 1999,
Bioinformatics 15: 432-439; Mallios, 2001, Bioinformatics 17:
p942-948; Sturniolo et. al., 1999, Nature Biotech. 17: 555-561). It
is possible to use structure-based methods in which a given peptide
is computationally placed in the peptide-binding groove of a given
MHC molecule and the interaction energy is determined (for example,
see WO 98/59244 and WO 02/069232). Such methods may be referred to
as "threading" methods. Alternatively, purely experimental methods
can be used; for example a set of overlapping peptides derived from
the protein of interest can be experimentally tested for the
ability to induce T-cell activation and/or other aspects of an
immune response. (see for example WO 02/77187). In a preferred
embodiment, MHC-binding propensity scores are calculated for each
9-residue frame along the protein sequence using a matrix method
(see Sturniolo et. al., supra; Marshall et. al., 1995, J. Immunol.
154: 5927-5933, and Hammer et. al., 1994, J. Exp. Med. 180:
2353-2358). It is also possible to consider scores for only a
subset of these residues, or to consider also the identities of the
peptide residues before and after the 9-residue frame of interest.
The matrix comprises binding scores for specific amino acids
interacting with the peptide binding pockets in different human
class II MHC molecule. In the most preferred embodiment, the scores
in the matrix are obtained from experimental peptide binding
studies. In an alternate preferred embodiment, scores for a given
amino acid binding to a given pocket are extrapolated from
experimentally characterized alleles to additional alleles with
identical or similar residues lining that pocket. Matrices that are
produced by extrapolation are referred to as "virtual matrices". In
an alternate embodiment, additional amino acid modifications may be
engineered to reduce the propensity of the intact molecule to
interact with B cell receptors and circulating antibodies.
[0156] Antibodies and Fc fusions of the present invention may
comprise amino acid modifications in one or more regions outside
the Fc region, for example the antibody Fab region or the Fc fusion
partner, that provide optimal properties. In one embodiment, the
variable region of an antibody of the present invention may be
affinity matured, that is to say that amino acid modifications have
been made in the V.sub.H and/or V.sub.L domains of the antibody to
enhance binding of the antibody to its target antigen. Likewise,
modifications may be made in the Fc fusion partner to enhance
affinity of the Fc fusion for its target antigen. Such types of
modifications may improve the association and/or the dissociation
kinetics for binding to the target antigen. Other modifications
include those that improve selectivity for target antigen vs.
alternative targets. These include modifications that improve
selectivity for antigen expressed on target vs. non-target cells.
Other improvements to the target recognition properties may be
provided by additional modifications. Such properties may include,
but are not limited to, specific kinetic properties (i.e.
association and dissociation kinetics), selectivity for the
particular target versus alternative targets, and selectivity for a
specific form of target versus alternative forms. Examples include
full-length versus splice variants, aberrant forms of antigens that
are expressed only on certain cell types such as tumor cells,
cell-surface vs. soluble forms, selectivity for various polymorphic
variants, or selectivity for specific conformational forms of the
target.
[0157] Fc variants of the invention may comprise one or more
modifications that provide reduced or enhanced internalization of
an Fc variant. In one embodiment, Fc variants of the present
invention can be utilized or combined with additional modifications
in order to reduce the cellular internalization of an Fc variant
that occurs via interaction with one or more Fc ligands. This
property might be expected to enhance effector function, and
potentially reduce immunogenicity of the Fc variants of the
invention. Alternatively, Fc variants of the present Fc variants of
the present invention can be utilized directly or combined with
additional modifications in order to enhance the cellular
internalization of an Fc variant that occurs via interaction with
one or more Fc ligands. For example, in a prefered embodiment, an
Fc variant is used that provides enhanced binding to Fc.gamma.RI,
which is expressed on dendritic cells and active early in immune
response. This strategy could be further enhanced by combination
with additional modifications, either within the Fc variant or in
an attached fusion or conjugate partner, that promote recognition
and presentation of Fc peptide fragments by MHC molecules. These
strategies are expected to enhance target antigen processing and
thereby improve antigenicity of the target antigen (Bonnerot and
Amigorena, 1999, Immunol Rev. 172:279-84), promoting an adaptive
immune response and greater target cell killing by the human immune
system. These strategies may be particularly advantageous when the
targeted antigen is shed from the cellular surface. An additional
application of these concepts arises with idiotype vaccine
immunotherapies, in which clone-specific antibodies produced by a
patient's lymphoma cells are used to vaccinate the patient.
[0158] In a preferred embodiment, modifications are made to improve
biophysical properties of the Fc variants of the present invention,
including but not limited to stability, solubility, and oligomeric
state. Modifications can include, for example, substitutions that
provide more favorable intramolecular interactions in the Fc
variant such as to provide greater stability, or substitution of
exposed nonpolar amino acids with polar amino acids for higher
solubility. A number of optimization goals and methods are
described in U.S. Ser. No. 10/379,392 that may find use for
engineering additional modifications to further optimize the Fc
variants of the present invention. The Fc variants of the present
invention can also be combined with additional modifications that
reduce oligomeric state or size, such that tumor penetration is
enhanced, or in vivo clearance rates are increased as desired.
[0159] Other modifications to the Fc variants of the present
invention include those that enable the specific formation or
homodimeric or homomultimeric molecules. Such modifications include
but are not limited to engineered disulfides, as well as chemical
modifications or aggregation methods which may provide a mechanism
for generating covalent homodimeric or homomultimers. For example,
methods of engineering and compositions of such molecules are
described in Kan et al, 2001, J. Immunol., 2001, 166: 1320-1326;
Stevenson etal., 2002, Recent Results Cancer Res. 159: 104-12; U.S.
Pat. No. 5,681,566; Caron et al., 1992, J Exp Med 176:1191-1195,
and Shopes, 1992, J Immunol 148(9):2918-22. Additional
modifications to the variants of the present invention include
those that enable the specific formation or heterodimeric,
heteromultimeric, bifunctional, and/or multifunctional molecules.
Such modifications include, but are not limited to, one or more
amino acid substitutions in the C.sub.H3 domain, in which the
substitutions reduce homodimer formation and increase heterodimer
formation. For example, methods of engineering and compositions of
such molecules are described in Atwell et al., 1997, J Mol Biol
270(1):26-35, and Carter et al., 2001, J Immunol Methods 248:7-15.
Additional modifications include modifications in the hinge and CH3
domains, in which the modifications reduce the propensity to form
dimers.
[0160] In further embodiments, the Fc variants of the present
invention comprise modifications that remove proteolytic
degradation sites. These may include, for example, protease sites
that reduce production yields, as well as protease sites that
degrade the administered protein in vivo. In a preferred
embodiment, additional modifications are made to remove covalent
degradation sites such as deamidation (i.e. deamidation of
glutaminyl and asparaginyl residues to the corresponding glutamyl
and aspartyl residues), oxidation, and proteolytic degradation
sites. Deamidation sites that are particular useful to remove are
those that have enhance propensity for deamidation, including, but
not limited to asparaginyl and gltuamyl residues followed by
glycines (NG and QG motifs, respectively). In such cases,
substitution of either residue can significantly reduce the
tendancy for deamidation. Common oxidation sites include methionine
and cysteine residues. Other covalent modifications, that can
either be introduced or removed, include hydroxylation of proline
and lysine, phosphorylation of hydroxyl groups of seryl or threonyl
residues, methylation of the "-amino groups of lysine, arginine,
and histidine side chains [T. E. Creighton, Proteins: Structure and
Molecular Properties, W.H. Freeman & Co., San Francisco, pp.
79-86 (1983)], acetylation of the N-terminal amine, and amidation
of any C-terminal carboxyl group. Additional modifications also may
include but are not limited to posttranslational modifications such
as N-linked or O-linked glycosylation and phosphorylation.
[0161] Modifications may include those that improve expression
and/or purification yields from hosts or host cells commonly used
for production of biologics. These include, but are not limited to
various mammalian cell lines (e.g. CHO), yeast cell lines,
bacterial cell lines, and plants. Additional modifications include
modifications that remove or reduce the ability of heavy chains to
form inter-chain disulfide linkages. Additional modifications
include modifications that remove or reduce the ability of heavy
chains to form intra-chain disulfide linkages.
[0162] The Fc variants of the present invention may comprise
modifications that include the use of unnatural amino acids
incorporated using, for example, the technologies developed by
Schultz and colleagues, including but not limited to methods
described by Cropp & Shultz, 2004, Trends Genet. 20(12):625-30,
Anderson et al., 2004, Proc Natl Acad Sci USA 101(2):7566-71, Zhang
et al., 2003, 303(5656):371-3, and Chin et al., 2003, Science
301(5635):964-7. In some embodiments, these modifications enable
manipulation of various functional, biophysical, immunological, or
manufacturing properties discussed above. In additional
embodiments, these modifications enable additional chemical
modification for other purposes. Other modifications are
contemplated herein. For example, the Fc variant may be linked to
one of a variety of nonproteinaceous polymers, e.g., polyethylene
glycol (PEG), polypropylene glycol, polyoxyalkylenes, or copolymers
of polyethylene glycol and polypropylene glycol. Additional amino
acid modifications may be made to enable specific or non-specific
chemical or posttranslational modification of the Fc variants. Such
modifications, include, but are not limited to PEGylation and
glycosylation. Specific substitutions that can be utilized to
enable PEGylation include, but are not limited to, introduction of
novel cysteine residues or unnatural amino acids such that
efficient and specific coupling chemistries can be used to attach a
PEG or otherwise polymeric moiety. Introduction of specific
glycosylation sites can be achieved by introducing novel N-X-T/S
sequences into the Fc variants of the present invention.
[0163] The Fc variants of the present invention may be fused or
conjugated to one or more other molecules or polypeptides.
Conjugate and fusion partners may be any molecule, including small
molecule chemical compounds and polypeptides. For example, a
variety of antibody conjugates and methods are described in Trail
et al., 1999, Curr. Opin. Immunol. 11:584-588. Possible conjugate
partners include but are not limited to cytokines, cytotoxic
agents, toxins, radioisotopes, chemotherapeutic agent,
anti-angiogenic agents, a tyrosine kinase inhibitors, and other
therapeutically active agents. In some embodiments, conjugate
partners may be thought of more as payloads, that is to say that
the goal of a conjugate is targeted delivery of the conjugate
partner to a targeted cell, for example a cancer cell or immune
cell, by the Fc variant. Thus, for example, the conjugation of a
toxin to an antibody or Fc fusion targets the delivery of said
toxin to cells expressing the target antigen.
[0164] In one embodiment, the Fc variants of the present invention
are fused or conjugated to a cytokine. By "cytokine" as used herein
is meant a generic term for proteins released by one cell
population that act on another cell as intercellular mediators. For
example, as described in Penichet et al., 2001, J Immunol Methods
248:91-101, cytokines may be fused to antibody to provide an array
of desirable properties. Examples of such cytokines are
lymphokines, monokines, and traditional polypeptide hormones.
Included among the cytokines are growth hormone such as human
growth hormone, N-methionyl human growth hormone, and bovine growth
hormone; parathyroid hormone; thyroxine; insulin; proinsulin;
relaxin; prorelaxin; glycoprotein hormones such as follicle
stimulating hormone (FSH), thyroid stimulating hormone (TSH), and
luteinizing hormone (LH); hepatic growth factor; fibroblast growth
factor; prolactin; placental lactogen; tumor necrosis factor-alpha
and -beta; mullerian-inhibiting substance; mouse
gonadotropin-associated peptide; inhibin; activin; vascular
endothelial growth factor; integrin; thrombopoietin (TPO); nerve
growth factors such as NGF-beta; platelet-growth factor;
transforming growth factors (TGFS) such as TGF-alpha and TGF-beta;
insulin-like growth factor-I and -II; erythropoietin (EPO);
osteoinductive factors; interferons such as interferon-alpha, beta,
and -gamma; colony stimulating factors (CSFs) such as
macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); and
granulocyte-CSF (G-CSF); interleukins (ILs) such as IL-1,
IL-1alpha, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10,
IL-11, IL-12; IL-15, a tumor necrosis factor such as TNF-alpha or
TNF-beta; C5a; and other polypeptide factors including LIF and kit
ligand (KL). As used herein, the term cytokine includes proteins
from natural sources or from recombinant cell culture, and
biologically active equivalents of the native sequence
cytokines.
[0165] In an alternate embodiment, the Fc polypeptides of the
present invention are fused, conjugated, or operably linked to a
toxin, including but not limited to small molecule toxins and
enzymatically active toxins of bacterial, fungal, plant or animal
origin, including fragments and/or variants thereof. For example, a
variety of immunotoxins and immunotoxin methods are described in
Thrush et al., 1996, Ann. Rev. Immunol. 14:49-71. Small molecule
toxins include but are not limited to calicheamicin, maytansine
(U.S. Pat. No. 5,208,020), trichothene, and CC1065. In one
embodiment of the invention, the Fc polypeptide is conjugated to
one or more maytansine molecules (e.g. about 1 to about 10
maytansine molecules per antibody molecule). Maytansine may, for
example, be converted to May-SS-Me which may be reduced to May-SH3
and reacted with modified Fc polypeptide (Chari et al., 1992,
Cancer Research 52: 127-131) to generate a maytansinoid-antibody or
maytansinoid-Fc fusion conjugate. Another conjugate of interest
comprises an Fc polypeptide, for example an antibody or Fc fusion,
conjugated to one or more calicheamicin molecules. The
calicheamicin family of antibiotics are capable of producing
double-stranded DNA breaks at sub-picomolar concentrations.
Structural analogues of calicheamicin that may be used include but
are not limited to .gamma..sub.1.sup.1, .alpha..sub.2.sup.1,
.alpha..sub.3, N-acetyl-.gamma..sub.1.sup.1, PSAG, and
.crclbar..sup.1.sub.1, (Hinman et al., 1993, Cancer Research
53:3336-3342; Lode et al., 1998, Cancer Research 58:2925-2928)
(U.S. Pat. No. 5,714,586; U.S. Pat. No. 5,712,374; U.S. Pat. No.
5,264,586; U.S. Pat. No. 5,773,001). Dolastatin 10 analogs such as
auristatin E (AE) and monomethylauristatin E (MMAE) may find use as
conjugates for the Fc variants of the present invention (Doronina
et al., 2003, Nat Biotechnol 21(7):778-84; Francisco et al., 2003
Blood 102(4):1458-65). Useful enyzmatically active toxins include
but are not limited to diphtheria A chain, nonbinding active
fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas
aeruginosa), ricin A chain, abrin A chain, modeccin A chain,
alpha-sarcin, Aleurites fordii proteins, dianthin proteins,
Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica
charantia inhibitor, curcin, crotin, sapaonaria officinalis
inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin
and the tricothecenes. See, for example, PCT WO 93/21232, hereby
incorporated by reference. The present invention further
contemplates a conjugate between an Fc variant of the present
invention and a compound with nucleolytic activity, for example a
ribonuclease or DNA endonuclease such as a deoxyribonuclease
(Dnase).
[0166] In an alternate embodiment, an Fc variant of the present
invention may be fused, conjugated, or operably linked to a
radioisotope to form a radioconjugate. A variety of radioactive
isotopes are available for the production of radioconjugate
antibodies and Fc fusions. Examples include, but are not limited
to, At211, I131, I125, Y90, Re186, Re188, Sm153, Bi212, P32, and
radioactive isotopes of Lu. See for example, reference.
[0167] In yet another embodiment, an Fc variant of the present
invention may be conjugated to a "receptor" (e.g., streptavidin)
for utilization in tumor pretargeting wherein the Fc
variant-receptor conjugate is administered to the patient, followed
by removal of unbound conjugate from the circulation using a
clearing agent and then administration of a "ligand" (e.g. avidin)
which is conjugated to a cytotoxic agent (e.g. a radionucleotide).
In an alternate embodiment, the Fc variant is conjugated or
operably linked to an enzyme in order to employ Antibody Dependent
Enzyme Mediated Prodrug Therapy (ADEPT). ADEPT may be used by
conjugating or operably linking the Fc variant to a
prodrug-activating enzyme that converts a prodrug (e.g. a peptidyl
chemotherapeutic agent, see PCT WO 81/01145) to an active
anti-cancer drug. See, for example, PCT WO 88/07378 and U.S. Pat.
No. 4,975,278. The enzyme component of the immunoconjugate useful
for ADEPT includes any enzyme capable of acting on a prodrug in
such a way so as to covert it into its more active, cytotoxic form.
Enzymes that are useful in the method of this invention include but
are not limited to alkaline phosphatase useful for converting
phosphate-containing prodrugs into free drugs; arylsulfatase useful
for converting sulfate-containing prodrugs into free drugs;
cytosine deaminase useful for converting non-toxic 5-fluorocytosine
into the anti-cancer drug, 5-fluorouracil; proteases, such as
serratia protease, thermolysin, subtilisin, carboxypeptidases and
cathepsins (such as cathepsins B and L), that are useful for
converting peptide-containing prodrugs into free drugs;
D-alanylcarboxypeptidases, useful for converting prodrugs that
contain D-amino acid substituents; carbohydrate-cleaving enzymes
such as .beta.-galactosidase and neuramimidase useful for
converting glycosylated prodrugs into free drugs; beta-lactamase
useful for converting drugs derivatized with .alpha.-lactams into
free drugs; and penicillin amidases, such as penicillin V amidase
or penicillin G amidase, useful for converting drugs derivatized at
their amine nitrogens with phenoxyacetyl or phenylacetyl groups,
respectively, into free drugs. Alternatively, antibodies with
enzymatic activity, also known in the art as "abzymes", can be used
to convert the prodrugs of the invention into free active drugs
(see, for example, Massey, 1987, Nature 328: 457-458). Fc
variant-abzyme conjugates can be prepared for delivery of the
abzyme to a tumor cell population. A variety of additional
conjugates are contemplated for the Fc variants of the present
invention. A variety of chemotherapeutic agents, anti-angiogenic
agents, tyrosine kinase inhibitors, and other therapeutic agents
are described below, which may find use as Fc variant
conjugates.
[0168] Also contemplated as fusion and conjugate partners are Fc
polypeptides. Thus an Fc variant may be a multimeric Fc
polypeptide, comprising two or more Fc regions. The advantage of
such a molecule is that it provides multiple binding sites for Fc
receptors with a single protein molecule. In one embodiment, Fc
regions may be linked using a chemical engineering approach. For
example, Fab's and Fc's may be linked by thioether bonds
originating at cysteine residues in the hinges, generating
molecules such as FabFc.sub.2 (Kan et al., 2001, J. Immunol., 2001,
166: 1320-1326; Stevenson et al., 2002, Recent Results Cancer Res.
159: 104-12; U.S. Pat. No. 5,681,566). Fc regions may be linked
using disulfide engineering and/or chemical cross-linking, for
example as described in Caron et al., 1992, J. Exp. Med.
176:1191-1195, and Shopes, 1992, J. Immunol. 148(9):2918-22. In a
preferred embodiment, Fc regions may be linked genetically. For
example multiple C.gamma.2 domains have been fused between the Fab
and Fc regions of an antibody (White et al., 2001, Protein
Expression and Purification 21: 446-455). In a preferred
embodiment, Fc regions in an Fc variant are linked genetically to
generated tandemly linked Fc regions as described in U.S. Ser. No.
60/531,752, filed Dec. 22, 2003, entitled "Fc polypeptides with
novel Fc receptor binding sites". Tandemly linked Fc polypeptides
may comprise two or more Fc regions, preferably one to three, most
preferably two Fc regions. It may be advantageous to explore a
number of engineering constructs in order to obtain homo- or
hetero-tandemly linked Fc variants with the most favorable
structural and functional properties. Tandemly linked Fc variants
may be homo-tandemly linked Fc variants, that is an Fc variant of
one isotype is fused genetically to another Fc variant of the same
isotype. It is anticipated that because there are multiple
Fc.gamma.R, C1q, and/or FcRn binding sites on tandemly linked Fc
polypeptides, effector functions and/or pharmacokinetics may be
enhanced. In an alternate embodiment, Fc variants from different
isotypes may be tandemly linked, referred to as hetero-tandemly
linked Fc variants. For example, because of the capacity to target
Fc.gamma.R and Fc.alpha.RI receptors, an Fc variant that binds both
Fc.gamma.Rs and Fc.alpha.RI may provide a significant clinical
improvement.
[0169] As will be appreciated by one skilled in the art, in reality
the concepts and defintions of fusion and conjugate are
overlapping. The designation of an Fc variant as a fusion or
conjugate is not meant to constrain it to any particular embodiment
of the present invention. Rather, these terms are used loosely to
convey the broad concept that any Fc variant of the present
invention may be linked genetically, chemically, or otherwise, to
one or more polypeptides or molecules to provide some desireable
property.
[0170] Fusion and conjugate partners may be linked to any region of
an Fc variant of the present invention, including at the N- or
C-termini, or at some residue in-between the termini. In a
preferred embodiment, a fusion or conjugate partner is linked at
the N- or C-terminus of the Fc variant, most preferably the
N-terminus. A variety of linkers may find use in the present
invention to covalently link Fc variants to a fusion or conjugate
partner or generate an Fc fusion. By "linker", "linker sequence",
"spacer", "tetherinq sequence" or grammatical equivalents thereof,
herein is meant a molecule or group of molecules (such as a monomer
or polymer) that connects two molecules and often serves to place
the two molecules in a preferred configuration. A number of
strategies may be used to covalently link molecules together. These
include, but are not limited to polypeptide linkages between N- and
C-termini of proteins or protein domains, linkage via disulfide
bonds, and linkage via chemical cross-linking reagents. In one
aspect of this embodiment, the linker is a peptide bond, generated
by recombinant techniques or peptide synthesis. Choosing a suitable
linker for a specific case where two polypeptide chains are to be
connected depends on various parameters, including but not limited
to the nature of the two polypeptide chains (e.g., whether they
naturally oligomerize), the distance between the N- and the
C-termini to be connected if known, and/or the stability of the
linker towards proteolysis and oxidation. Furthermore, the linker
may contain amino acid residues that provide flexibility. Thus, the
linker peptide may predominantly include the following amino acid
residues: Gly, Ser, Ala, or Thr. The linker peptide should have a
length that is adequate to link two molecules in such a way that
they assume the correct conformation relative to one another so
that they retain the desired activity. Suitable lengths for this
purpose include at least one and not more than 50 amino acid
residues. Preferably, the linker is from about 1 to 30 amino acids
in length, with linkers of 1 to 20 amino acids in length being most
preferred. In addition, the amino acid residues selected for
inclusion in the linker peptide should exhibit properties that do
not interfere significantly with the activity of the polypeptide.
Thus, the linker peptide on the whole should not exhibit a charge
that would be inconsistent with the activity of the polypeptide, or
interfere with internal folding, or form bonds or other
interactions with amino acid residues in one or more of the
monomers that would seriously impede the binding of receptor
monomer domains. Useful linkers include glycine-serine polymers
(including, for example, (GS)n, (GSGGS)n SEQ ID NO:9, (GGGGS)n SEQ
ID NO:10, and (GGGS)n SEQ ID NO:11, where n is an integer of at
least one), glycine-alanine polymers, alanine-serine polymers, and
other flexible linkers such as the tether for the shaker potassium
channel, and a large variety of other flexible linkers, as will be
appreciated by those in the art. Glycine-serine polymers are
preferred since both of these amino acids are relatively
unstructured, and therefore may be able to serve as a neutral
tether between components. Secondly, serine is hydrophilic and
therefore able to solubilize what could be a globular glycine
chain. Third, similar chains have been shown to be effective in
joining subunits of recombinant proteins such as single chain
antibodies. Suitable linkers may also be identified by screening
databases of known three-dimensional structures for naturally
occurring motifs that can bridge the gap between two polypeptide
chains. In a preferred embodiment, the linker is not immunogenic
when administered in a human patient. Thus linkers may be chosen
such that they have low immunogenicity or are thought to have low
immunogenicity. For example, a linker may be chosen that exists
naturally in a human. In a most preferred embodiment, the linker
has the sequence of the hinge region of an antibody, that is the
sequence that links the antibody Fab and Fc regions; alternatively
the linker has a sequence that comprises part of the hinge region,
or a sequence that is substantially similar to the hinge region of
an antibody. Another way of obtaining a suitable linker is by
optimizing a simple linker, e.g., (Gly4Ser)n SEQ ID NO:10, through
random mutagenesis. Alternatively, once a suitable polypeptide
linker is defined, additional linker polypeptides can be created to
select amino acids that more optimally interact with the domains
being linked. Other types of linkers that may be used in the
present invention include artificial polypeptide linkers and
inteins. In another embodiment, disulfide bonds are designed to
link the two molecules. In another embodiment, linkers are chemical
cross-linking agents. For example, a variety of bifunctional
protein coupling agents may be used, including but not limited to
N-succinimidyl-3-(2-pyridyldithiol)propionate (SPDP),
succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate,
iminothiolane (IT), bifunctional derivatives of imidoesters (such
as dimethyl adipimidate HCL), active esters (such as disuccinimidyl
suberate), aldehydes (such as glutareldehyde), bis-azido compounds
(such as bis(p-azidobenzoyl)hexanediamine), bis-diazonium
derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine),
diisocyanates (such as tolyene 2,6-diisocyanate), and bis-active
fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). For
example, a ricin immunotoxin can be prepared as described in
Vitetta et al., 1971, Science 238:1098. Chemical linkers may enable
chelation of an isotope. For example, Carbon-14-labeled
1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid
(MX-DTPA) is an exemplary chelating agent for conjugation of
radionucleotide to the antibody (see PCT WO 94/11026). The linker
may be cleavable, facilitating release of the cytotoxic drug in the
cell. For example, an acid-labile linker, peptidase-sensitive
linker, dimethyl linker or disulfide-containing linker (Chari et
al., 1992, Cancer Research 52: 127-131) may be used. Alternatively,
a variety of nonproteinaceous polymers, including but not limited
to polyethylene glycol (PEG), polypropylene glycol,
polyoxyalkylenes, or copolymers of polyethylene glycol and
polypropylene glycol, may find use as linkers, that is may find use
to link the Fc variants of the present invention to a fusion or
conjugate partner to generate an Fc fusion, or to link the Fc
variants of the present invention to a conjugate.
Engineering Methods
[0171] Design strategies, computational screening methods, and
library generation methods are described in U.S. Ser. No.
10/672,280 and U.S. Ser. No. 10/822,231, entitled "Optimized Fc
Variants and Methods for their Generation", herein expressly
incorporated by reference. These strategies, approaches,
techniques, and methods may be applied individually or in various
combinations to generate optimized Fc variants.
Experimental Production of Fc Variants
[0172] The present invention provides methods for producing and
experimentally testing Fc variants. The described methods are not
meant to constrain the present invention to any particular
application or theory of operation. Rather, the provided methods
are meant to illustrate generally that one or more Fc variants may
be produced and experimentally tested to obtain variant Fc
variants. General methods for antibody molecular biology,
expression, purification, and screening are described in Antibody
Engineering, edited by Duebel & Kontermann, Springer-Verlag,
Heidelberg, 2001; and Hayhurst & Georgiou, 2001, Curr Opin Chem
Biol 5:683-689; Maynard & Georgiou, 2000, Annu Rev Biomed Eng
2:339-76; Antibodies: A Laboratory Manual by Harlow & Lane, New
York: Cold Spring Harbor Laboratory Press, 1988.
[0173] In one embodiment of the present invention, nucleic acids
are created that encode the Fc variants, and that may then be
cloned into host cells, expressed and assayed, if desired. Thus,
nucleic acids, and particularly DNA, may be made that encode each
protein sequence. These practices are carried out using well-known
procedures. For example, a variety of methods that may find use in
the present invention are described in Molecular Cloning--A
Laboratory Manual, 3.sup.rd Ed. (Maniatis, Cold Spring Harbor
Laboratory Press, New York, 2001), and Current Protocols in
Molecular Biology (John Wiley & Sons). As will be appreciated
by those skilled in the art, the generation of exact sequences for
a library comprising a large number of sequences is potentially
expensive and time consuming. Accordingly, there are a variety of
techniques that may be used to efficiently generate libraries of
the present invention. Such methods that may find use in the
present invention are described or referenced in U.S. Pat. No.
6,403,312; U.S. Ser. No. 09/782,004; U.S. Ser. No. 09/927,790; U.S.
Ser. No. 10/218,102; PCT WO 01/40091; and PCT WO 02/25588. Such
methods include but are not limited to gene assembly methods,
PCR-based method and methods which use variations of PCR, ligase
chain reaction-based methods, pooled oligo methods such as those
used in synthetic shuffling, error-prone amplification methods and
methods which use oligos with random mutations, classical
site-directed mutagenesis methods, cassette mutagenesis, and other
amplification and gene synthesis methods. As is known in the art,
there are a variety of commercially available kits and methods for
gene assembly, mutagenesis, vector subcloning, and the like, and
such commercial products find use in the present invention for
generating nucleic acids that encode Fc variants.
[0174] The Fc variants of the present invention may be produced by
culturing a host cell transformed with nucleic acid, preferably an
expression vector, containing nucleic acid encoding the Fc
variants, under the appropriate conditions to induce or cause
expression of the protein. The conditions appropriate for
expression will vary with the choice of the expression vector and
the host cell, and will be easily ascertained by one skilled in the
art through routine experimentation. A wide variety of appropriate
host cells may be used, including but not limited to mammalian
cells, bacteria, insect cells, and yeast. For example, a variety of
cell lines that may find use in the present invention are described
in the ATCC.RTM. cell line catalog, available from the American
Type Culture Collection.
[0175] In a preferred embodiment, the Fc variants are expressed in
mammalian expression systems, including systems in which the
expression constructs are introduced into the mammalian cells using
virus such as retrovirus or adenovirus. Any mammalian cells may be
used, with human, mouse, rat, hamster, and primate cells being
particularly preferred. Suitable cells also include known research
cells, including but not limited to Jurkat T cells, NIH3T3, CHO,
BHK, COS, HEK293, PER C.6, HeLa, Sp2/0, NSO cells and variants
thereof. In an alternately preferred embodiment, library proteins
are expressed in bacterial cells. Bacterial expression systems are
well known in the art, and include Escherichia coli (E. coli),
Bacillus subtilis, Streptococcus cremoris, and Streptococcus
lividans. In alternate embodiments, Fc variants are produced in
insect cells (e.g. Sf21/Sf9, Trichoplusia ni Bti-Tn5b1-4) or yeast
cells (e.g. S. cerevisiae, Pichia, etc). In an alternate
embodiment, Fc variants are expressed in vitro using cell free
translation systems. In vitro translation systems derived from both
prokaryotic (e.g. E. coli) and eukaryotic (e.g. wheat germ, rabbit
reticulocytes) cells are available and may be chosen based on the
expression levels and functional properties of the protein of
interest. For example, as appreciated by those skilled in the art,
in vitro translation is required for some display technologies, for
example ribosome display. In addition, the Fc variants may be
produced by chemical synthesis methods. Also transgenic expression
systems both animal (e.g. cow, sheep or goat milk, embryonated
hen's eggs, whole insect larvae, etc.) and plant (e.g. corn,
tobacco, duckweed, etc.)
[0176] The nucleic acids that encode the Fc variants of the present
invention may be incorporated into an expression vector in order to
express the protein. A variety of expression vectors may be
utilized for protein expression. Expression vectors may comprise
self-replicating extra-chromosomal vectors or vectors which
integrate into a host genome. Expression vectors are constructed to
be compatible with the host cell type. Thus expression vectors
which find use in the present invention include but are not limited
to those which enable protein expression in mammalian cells,
bacteria, insect cells, yeast, and in in vitro systems. As is known
in the art, a variety of expression vectors are available,
commercially or otherwise, that may find use in the present
invention for expressing Fc variants.
[0177] Expression vectors typically comprise a protein operably
linked with control or regulatory sequences, selectable markers,
any fusion partners, and/or additional elements. By "operably
linked" herein is meant that the nucleic acid is placed into a
functional relationship with another nucleic acid sequence.
Generally, these expression vectors include transcriptional and
translational regulatory nucleic acid operably linked to the
nucleic acid encoding the Fc variant, and are typically appropriate
to the host cell used to express the protein. In general, the
transcriptional and translational regulatory sequences may include
promoter sequences, ribosomal binding sites, transcriptional start
and stop sequences, translational start and stop sequences, and
enhancer or activator sequences. As is also known in the art,
expression vectors typically contain a selection gene or marker to
allow the selection of transformed host cells containing the
expression vector. Selection genes are well known in the art and
will vary with the host cell used.
[0178] Fc variants may be operably linked to a fusion partner to
enable targeting of the expressed protein, purification, screening,
display, and the like. Fusion partners may be linked to the Fc
variant sequence via a linker sequences. The linker sequence will
generally comprise a small number of amino acids, typically less
than ten, although longer linkers may also be used. Typically,
linker sequences are selected to be flexible and resistant to
degradation. As will be appreciated by those skilled in the art,
any of a wide variety of sequences may be used as linkers. For
example, a common linker sequence comprises the amino acid sequence
GGGGS SEQ ID NO. 10. A fusion partner may be a targeting or signal
sequence that directs Fc variant and any associated fusion partners
to a desired cellular location or to the extracellular media. As is
known in the art, certain signaling sequences may target a protein
to be either secreted into the growth media, or into the
periplasmic space, located between the inner and outer membrane of
the cell. A fusion partner may also be a sequence that encodes a
peptide or protein that enables purification and/or screening. Such
fusion partners include but are not limited to polyhistidine tags
(His-tags) (for example H.sub.6 and H.sub.10 or other tags for use
with Immobilized Metal Affinity Chromatography (IMAC) systems (e.g.
Ni.sup.+2 affinity columns)), GST fusions, MBP fusions, Strep-tag,
the BSP biotinylation target sequence of the bacterial enzyme BirA,
and epitope tags which are targeted by antibodies (for example
c-myc tags, flag-tags, and the like). As will be appreciated by
those skilled in the art, such tags may be useful for purification,
for screening, or both. For example, an Fc variant may be purified
using a His-tag by immobilizing it to a Ni.sup.+2 affinity column,
and then after purification the same His-tag may be used to
immobilize the antibody to a Ni.sup.+2 coated plate to perform an
ELISA or other binding assay (as described below). A fusion partner
may enable the use of a selection method to screen Fc variants (see
below). Fusion partners that enable a variety of selection methods
are well-known in the art, and all of these find use in the present
invention. For example, by fusing the members of an Fc variant
library to the gene III protein, phage display can be employed (Kay
et al., Phage display of peptides and proteins: a laboratory
manual, Academic Press, San Diego, Calif., 1996; Lowman et al.,
1991, Biochemistry 30:10832-10838; Smith, 1985, Science
228:1315-1317). Fusion partners may enable Fc variants to be
labeled. Alternatively, a fusion partner may bind to a specific
sequence on the expression vector, enabling the fusion partner and
associated Fc variant to be linked covalently or noncovalently with
the nucleic acid that encodes them. For example, U.S. Ser. No.
09/642,574; U.S. Ser. No. 10/080,376; U.S. Ser. No. 09/792,630;
U.S. Ser. No. 10/023,208; U.S. Ser. No. 09/792,626; U.S. Ser. No.
10/082,671; U.S. Ser. No. 09/953,351; U.S. Ser. No. 10/097,100;
U.S. Ser. No. 60/366,658; PCT WO 00/22906; PCT WO 01/49058; PCT WO
02/04852; PCT WO 02/04853; PCT WO 02/08023; PCT WO 01/28702; and
PCT WO 02/07466 describe such a fusion partner and technique that
may find use in the present invention.
[0179] The methods of introducing exogenous nucleic acid into host
cells are well known in the art, and will vary with the host cell
used. Techniques include but are not limited to dextran-mediated
transfection, calcium phosphate precipitation, calcium chloride
treatment, polybrene mediated transfection, protoplast fusion,
electroporation, viral or phage infection, encapsulation of the
polynucleotide(s) in liposomes, and direct microinjection of the
DNA into nuclei. In the case of mammalian cells, transfection may
be either transient or stable.
[0180] In a preferred embodiment, Fc variants are purified or
isolated after expression. Proteins may be isolated or purified in
a variety of ways known to those skilled in the art. Standard
purification methods include chromatographic techniques, including
ion exchange, hydrophobic interaction, affinity, sizing or gel
filtration, and reversed-phase, carried out at atmospheric pressure
or at high pressure using systems such as FPLC and HPLC.
Purification methods also include electrophoretic, immunological,
precipitation, dialysis, and chromatofocusing techniques.
Ultrafiltration and diafiltration techniques, in conjunction with
protein concentration, are also useful. As is well known in the
art, a variety of natural proteins bind Fc and antibodies, and
these proteins can find use in the present invention for
purification of Fc variants. For example, the bacterial proteins A
and G bind to the Fc region. Likewise, the bacterial protein L
binds to the Fab region of some antibodies, as of course does the
antibody's target antigen. Purification can often be enabled by a
particular fusion partner. For example, Fc variants may be purified
using glutathione resin if a GST fusion is employed, Ni.sup.+2
affinity chromatography if a His-tag is employed, or immobilized
anti-flag antibody if a flag-tag is used. For general guidance in
suitable purification techniques, see Protein Purification:
Principles and Practice, 3.sup.rd Ed., Scopes, Springer-Verlag,
N.Y., 1994. The degree of purification necessary will vary
depending on the screen or use of the Fc variants. In some
instances no purification is necessary. For example in one
embodiment, if the Fc variants are secreted, screening may take
place directly from the media. As is well known in the art, some
methods of selection do not involve purification of proteins. Thus,
for example, if a library of Fc variants is made into a phage
display library, protein purification may not be performed.
Experimental Assays
[0181] Fc variants may be screened using a variety of methods,
including but not limited to those that use in vitro assays, in
vivo and cell-based assays, and selection technologies. Automation
and high-throughput screening technologies may be utilized in the
screening procedures. Screening may employ the use of a fusion
partner or label. The use of fusion partners has been discussed
above. By "labeled" herein is meant that the Fc variants of the
invention have one or more elements, isotopes, or chemical
compounds attached to enable the detection in a screen. In general,
labels fall into three classes: a) immune labels, which may be an
epitope incorporated as a fusion partner that is recognized by an
antibody, b) isotopic labels, which may be radioactive or heavy
isotopes, and c) small molecule labels, which may include
fluorescent and calorimetric dyes, or molecules such as biotin that
enable other labeling methods. Labels may be incorporated into the
compound at any position and may be incorporated in vitro or in
vivo during protein expression.
[0182] In a preferred embodiment, the functional and/or biophysical
properties of Fc variants are screened in an in vitro assay. In
vitro assays may allow a broad dynamic range for screening
properties of interest. Properties of Fc variants that may be
screened include but are not limited to stability, solubility, and
affinity for Fc ligands, for example Fc.gamma.Rs. Multiple
properties may be screened simultaneously or individually. Proteins
may be purified or unpurified, depending on the requirements of the
assay. In one embodiment, the screen is a qualitative or
quantitative binding assay for binding of Fc variants to a protein
or nonprotein molecule that is known or thought to bind the Fc
variant. In a preferred embodiment, the screen is a binding assay
for measuring binding to the Target antigen. In an alternately
preferred embodiment, the screen is an assay for binding of Fc
variants to an Fc ligand, including but are not limited to the
family of Fc.gamma.Rs, the neonatal receptor FcRn, the complement
protein C1q, and the bacterial proteins A and G. Said Fc ligands
may be from any organism, with humans, mice, rats, rabbits, and
monkeys preferred. Binding assays can be carried out using a
variety of methods known in the art, including but not limited to
FRET (Fluorescence Resonance Energy Transfer) and BRET
(Bioluminescence Resonance Energy Transfer)-based assays,
AlphaScreen.TM. (Amplified Luminescent Proximity Homogeneous
Assay), Scintillation Proximity Assay, ELISA (Enzyme-Linked
Immunosorbent Assay), SPR (Surface Plasmon Resonance, also known as
BIACORE.RTM.), isothermal titration calorimetry, differential
scanning calorimetry, gel electrophoresis, and chromatography
including gel filtration. These and other methods may take
advantage of some fusion partner or label of the Fc variant. Assays
may employ a variety of detection methods including but not limited
to chromogenic, fluorescent, luminescent, or isotopic labels.
[0183] The biophysical properties of Fc variants, for example
stability and solubility, may be screened using a variety of
methods known in the art. Protein stability may be determined by
measuring the thermodynamic equilibrium between folded and unfolded
states. For example, Fc variants of the present invention may be
unfolded using chemical denaturant, heat, or pH, and this
transition may be monitored using methods including but not limited
to circular dichroism spectroscopy, fluorescence spectroscopy,
absorbance spectroscopy, NMR spectroscopy, calorimetry, and
proteolysis. As will be appreciated by those skilled in the art,
the kinetic parameters of the folding and unfolding transitions may
also be monitored using these and other techniques. The solubility
and overall structural integrity of an Fc variant may be
quantitatively or qualitatively determined using a wide range of
methods that are known in the art. Methods which may find use in
the present invention for characterizing the biophysical properties
of Fc variants include gel electrophoresis, isoelectric focusing,
capillary electrophoresis, chromatography such as size exclusion
chromatography, ion-exchange chromatography, and reversed-phase
high performance liquid chromatography, peptide mapping,
oligosaccharide mapping, mass spectrometry, ultraviolet absorbance
spectroscopy, fluorescence spectroscopy, circular dichroism
spectroscopy, isothermal titration calorimetry, differential
scanning calorimetry, analytical ultra-centrifugation, dynamic
light scattering, proteolysis, and cross-linking, turbidity
measurement, filter retardation assays, immunological assays,
fluorescent dye binding assays, protein-staining assays,
microscopy, and detection of aggregates via ELISA or other binding
assay. Structural analysis employing X-ray crystallographic
techniques and NMR spectroscopy may also find use. In one
embodiment, stability and/or solubility may be measured by
determining the amount of protein solution after some defined
period of time. In this assay, the protein may or may not be
exposed to some extreme condition, for example elevated
temperature, low pH, or the presence of denaturant. Because
function typically requires a stable, soluble, and/or
well-folded/structured protein, the aforementioned functional and
binding assays also provide ways to perform such a measurement. For
example, a solution comprising an Fc variant could be assayed for
its ability to bind target antigen, then exposed to elevated
temperature for one or more defined periods of time, then assayed
for antigen binding again. Because unfolded and aggregated protein
is not expected to be capable of binding antigen, the amount of
activity remaining provides a measure of the Fc variant's stability
and solubility.
[0184] In a preferred embodiment, the library is screened using one
or more cell-based or in vitro assays. For such assays, Fc
variants, purified or unpurified, are typically added exogenously
such that cells are exposed to individual variants or groups of
variants belonging to a library. These assays are typically, but
not always, based on the biology of the ability of the antibody or
Fc fusion to bind to the target antigen and mediate some
biochemical event, for example effector functions like cellular
lysis, phagocytosis, ligand/receptor binding inhibition, inhibition
of growth and/or proliferation, apoptosisand the like. Such assays
often involve monitoring the response of cells to Fc variant, for
example cell survival, cell death, cellular phagocytosis, cell
lysis, change in cellular morphology, or transcriptional activation
such as cellular expression of a natural gene or reporter gene. For
example, such assays may measure the ability of Fc variants to
elicit ADCC, ADCP, or CDC. For some assays additional cells or
components, that is in addition to the target cells, may need to be
added, for example example serum complement, or effector cells such
as peripheral blood monocytes (PBMCs), NK cells, macrophages, and
the like. Such additional cells may be from any organism,
preferably humans, mice, rat, rabbit, and monkey. Crosslinked or
monomeric antibodies and Fc fusions may cause apoptosis of certain
cell lines expressing the antibody's target antigen, or they may
mediate attack on target cells by immune cells which have been
added to the assay. Methods for monitoring cell death or viability
are known in the art, and include the use of dyes, fluorophores,
immunochemical, cytochemical, and radioactive reagents. For
example, caspase assays or annexin-flourconjugates may enable
apoptosis to be measured, and uptake or release of radioactive
substrates (e.g. Chromium-51 release assays) or the metabolic
reduction of fluorescent dyes such as alamar blue may enable cell
growth, proliferationor activation to be monitored. In a preferred
embodiment, the DELFIA.RTM. EuTDA-based cytotoxicity assay (Perkin
Elmer, Mass.) is used. Alternatively, dead or damaged target cells
may be monitoried by measuring the release of one or more natural
intracellular proteins, for example lactate dehydrogenase.
Transcriptional activation may also serve as a method for assaying
function in cell-based assays. In this case, response may be
monitored by assaying for natural genes or proteins which may be
upregulated or down-regulated, for example the release of certain
interleukins may be measured, or alternatively readout may be via a
luciferase or GFP-reporter construct. Cell-based assays may also
involve the measure of morphological changes of cells as a response
to the presence of an Fc variant. Cell types for such assays may be
prokaryotic or eukaryotic, and a variety of cell lines that are
known in the art may be employed. Alternatively, cell-based screens
are performed using cells that have been transformed or transfected
with nucleic acids encoding the Fc variants.
[0185] In vitro assays include but are not limited to binding
assays, ADCC, CDC, cytotoxicity, proliferation, peroxide/ozone
release, chemotaxis of effector cells, inhibition of such assays by
reduced effector function antibodies; ranges of activities such as
>100.times. improvement or >100.times. reduction, blends of
receptor activation and the assay outcomes that are expected from
such receptor profiles.
Pre-Clinical Experiments and Animal Models
[0186] The biological properties of the Fc variants of the present
invention may be characterized in cell, tissue, and whole organism
experiments. As is know in the art, drugs are often tested in
animals, including but not limited to mice, rats, rabbits, dogs,
cats, pigs, and monkeys, in order to measure a drug's efficacy for
treatment against a disease or disease model, or to measure a
drug's pharmacokinetics, toxicity, and other properties. Said
animals may be referred to as disease models. With respect to the
Fc variants of the present invention, a particular challenge arises
when using animal models to evaluate the potential for in-human
efficacy of candidate polypeptides--this is due, at least in part,
to the fact that Fc variants that have a specific effect on the
affinity for a human Fc receptor may not have a similar affinity
effect with the orthologous animal receptor. These problems can be
further exacerbated by the inevitable ambiguities associated with
correct assignment of true orthologues (Mechetina et al.,
Immunogenetics, 2002 54:463-468), and the fact that some
orthologues simply do not exist in the animal (for example, humans
possess an Fc.gamma.RIIa whereas mice do not). Therapeutics are
often tested in mice, including but not limited to nude mice, SCID
mice, xenograft mice, and transgenic mice (including knockins and
knockouts). For example, an antibody or Fc fusion of the present
invention that is intended as an anti-cancer therapeutic may be
tested in a mouse cancer model, for example a xenograft mouse. In
this method, a tumor or tumor cell line is grafted onto or injected
into a mouse, and subsequently the mouse is treated with the
therapeutic to determine the ability of the antibody or Fc fusion
to reduce or inhibit cancer growth and metastasis. An alterantive
approach is the use of a SCID murine model in which
immune-deficient mice are injected with human PBLs, conferring a
semi-functional and human immune system--with an appropriate array
of human Fc.gamma.Rs--to the mice that have subsequently been
injected with antibodies or Fc polypeptides that target injected
human tumor cells. In such a model, the Fc polypeptides that target
the desired antigen (such as her2/neu on SkOV3 ovarian cancer
cells) interact with human PBLs within the mice to engage
tumoricidal effector functions. Such experimentation may provide
meaningful data for determination of the potential of said Fc
variant to be used as a therapeutic. Any organism, preferably
mammals, may be used for testing. For example because of their
genetic similarity to humans, monkeys can be suitable therapeutic
models, and thus may be used to test the efficacy, toxicity,
pharmacokinetics, or other property of the Fc polypeptides of the
present invention. Tests of the Fc variants of the present
invention in humans are ultimately required for approval as drugs,
and thus of course these experiments are contemplated. Thus the Fc
variants of the present invention may be tested in humans to
determine their therapeutic efficacy, toxicity, pharmacokinetics,
and/or other clinical properties.
[0187] The Fc variants of the present invention may confer superior
performance on Fc polypeptides therapeutics in animal models or in
humans. The receptor binding profiles of such Fc variants, as
described in this specification, may, for example, be selected to
increase the potency of cytotoxic drugs or to target specific
effector functions or effector cells to improve the selectivity of
the drug's action. Further, receptor binding profiles can be
selected that may reduce some or all effector functions thereby
reducing the side-effects or toxicity of such Fc polypeptide drugs.
For example, an Fc variant with reduced binding to Fc.gamma.RIIa,
Fc.gamma.RI and Fc.gamma.RIIa can be selected to eliminate most
cell-mediated effector function, or an Fc variant with reduced
binding to C1q may be selected to limit complement-mediated
effector functions. In some contexts, such effector functions are
known to have potential toxic effects, therefore eliminating them
may increase the safety of the Fc polypeptide drug, and such
improved safety may be characterized in animal models. In some
contexts, such effector functions are known to mediate the
desirable therapeutic activity, therefore enhancing them may
increase the activity or potency of the Fc polypeptide drug and
such improved activity or potency may be characterized in animal
models.
[0188] Optimized Fc variants can be tested in a variety of
orthotopic tumor models. These clinically relevant animal models
are important in the study of pathophysiology and therapy of
aggressive cancers like pancreatic, prostate and breast cancer.
Immune deprived mice including, but not limited to athymic nude or
SCID mice are frequently used in scoring of local and systemic
tumor spread from the site of intraorgan (e.g. pancreas, prostate
or mammary gland) injection of human tumor cells or fragments of
donor patients.
[0189] In preferred embodiments, Fc variants of the present
invention may be assessed for efficacy in clinically relevant
animal models of various human diseases. In many cases, relevant
models include various transgenic animals for specific tumor
antigens. Relevant transgenic models such as those that express
human Fc receptors (e.g., Fc.gamma.RIIIa including the gamma chain,
Fc.gamma.RI, Fc.gamma.RIIa, Fc.gamma.RIIb, and others) could be
used to evaluate and test the efficacy of Fc polypeptides of the
present invention. Evaluation of Fc variants by the introduction of
human genes which directly or indirectly mediate effector function
in mice or other rodents, may enable physiological studies of
efficacy in tumor toxicity or other diseases such as autoimmune
disorders and RA. Human Fc receptors such as Fc.gamma.RIIIa may
possess polymorphisms, such as that at position 158 (V or F as
described) which would further enable the introduction of specific
and combinations of human polymorphisms into rodents. The various
studies involving polymorphism-specific Fc.gamma.Rs is not limited
to this section, however, and encompasses all discussions and
applications of Fc.gamma.Rs in general as specficied in throughout
this application. Fc variants of the present invention may confer
superior activity on Fc polypeptides in such transgenic models. In
particular, variants with binding profiles optimized for human
Fc.gamma.RIIIa mediated activity may show superior activity in
transgenic CD16 (Fc.gamma.RIII) mice. Similar improvements in
efficacy in mice transgenic for the other human Fc receptors, e.g.
Fc.gamma.RIIa, Fc.gamma.RI, etc., may be observed for Fc variants
with binding profiles optimized for the respective receptors. Mice
transgenic for multiple human receptors would show improved
activity for Fc variants with binding profiles optimized for the
corresponding multiple receptors, for example as outlined in Table
1.
[0190] The introduction of target tumor antigens such as human CD20
into rodent B-cells in the form of a transgenic animal model can be
used to provide a more relevant evaluation of efficacy. As such,
the target antigen need not be limited to a fully human construct
but could be a fusion protein containing the relevant human epitope
of the target antigen. In a preferred embodiment, the testing of Fc
polypeptides may include transgenic model systems, which include
the combination of but not limited to both human target antigen and
human Fc receptors (e.g. CD16 and other related receptors mediating
effector functions) to evaluate efficacy and tumoricidal
activity.
[0191] In a preferred embodiment, Fc polypeptides of the present
invention that target the Her2 antigen (e.g. Fc variants of mu4D5
or its humanized analogues) may be assessed for efficacy in a
clinically relevant mouse model of breast cancer. Examples of
relevant models include, but are not limited to: 1) the HER2/neu
(neu-N)-transgenic mice, which are derived from the parental FVB/N
mouse strain and are transgenic for the rat form of the
proto-oncogene HER2/neu (neu); and 2) transgenic mice that
overexpress human HER2 under the murine mammary tumor virus
promoter (Finkle et al., 2004, Clin Cancer Res.10 (7):2499-511). Fc
polypeptides of the present invention that show superior efficacy
in these models represent likely candidates for further
development.
[0192] Because of the difficulties and ambiguities associated with
using animal models to characterize the potential efficacy of
candidate therapeutic antibodies in a human patient, some variant
polypeptides of the present invention may find utility as proxies
for assessing potential in-human efficacy. Such proxy molecules
would preferably mimic, in the animal system, the Fc.gamma.R and/or
complement biology of a corresponding candidate human Fc variant.
This mimicry is most likely to be manifested by relative
association affinities between specific Fc variants and animal vs.
human receptors. For example, if one were using a mouse model to
assess the potential in-human efficacy of an Fc variant that has
enhanced affinity for human Fc.gamma.RIIIa, an appropriate proxy
variant would have enhanced affinity for mouse Fc.gamma.RIII-2
(mouse CD16-2). Alternatively if one were using a mouse model to
assess the potential in-human efficacy of an Fc variant that has
reduced affinity for the human inhibitory receptor Fc.gamma.RIIb,
an appropriate proxy variant would have reduced affinity for mouse
Fc.gamma.RII. It should also be noted that the proxy Fc variants
could be created in the context of a human Fc variant, an animal Fc
variant, or both.
[0193] In a preferred embodiment, the testing of Fc variants may
include study of efficacy in primates (e.g. cynomolgus monkey
model) to facilitate the evaluation of depletion of specific target
cells harboring target antigen. Additional primate models include
but not limited to that of the rhesus monkey and Fc polypetides in
therapeutic studies of autoimmune, transplantation and cancer.
[0194] Toxicity studies are performed to determine the Fc
polypeptide related effects that cannot be evaluated in standard
pharmacology profile or occur only after repeated administration of
the agent. Most toxicity tests are performed in two species--a
rodent and a non-rodent--to ensure that any unexpected adverse
effects are not overlooked before new therapeutic entities are
introduced into humans. In general, these models may measure a
variety of toxicities including genotoxicity, chronic toxicity,
immunogenicity, reproductive/developmental toxicity and
carcinogenicity. Included within the aforementioned parameters are
standard measurement of food consumption, bodyweight, antibody
formation, clinical chemistry, and macro- and microscopic
examination of standard organs/tissues (e.g. cardiotoxicity).
Additional parameters of measurement are injection site trauma and
the measurement of neutralizing antibodies, if any. Traditionally,
monoclonal antibody therepeutics, naked or conjugated are evaluated
for cross-reactivity with normal tissues, immunogenicity/antibody
production, conjugate or linker toxicity and "bystander" toxicity
of radiolabeled species. Nonetheless, such studies may have to be
individualized to address specific concerns and following the
guidance set by ICH S6 (Safety studies for biotechnological
products also noted above). As such, the general principles are
that the products are sufficiently well characterized and for which
impurities/contaminants have been removed, that the test material
is comparable throughout development, and GLP compliance.
[0195] The pharmacokinetics (PK) of the Fc variants of the
invention can be studied in a variety of animal systems, with the
most relevant being non-human primates such as the cynomolgus,
rhesus monkeys. Single or repeated i.v./s.c. administrations over a
dose range of 6000-fold (0.05-300 mg/kg) can be evaluated for the
half-life (days to weeks) using plasma concentration and clearance
as well as volume of distribution at a steady state and level of
systemic absorbance can be measured. Examples of such parameters of
measurement generally include maximum observed plasma concentration
(Cmax), the time to reach Cmax (Tmax), the area under the plasma
concentration-time curve from time 0 to infinity [AUC(0-inf] and
apparent elimination half-life (T1/2). Additional measured
prameters could include compartmental analysis of
concentration-time data obtained following i.v. adminsturation and
bioavailability. Examples of pharmacological/toxicological studies
using cynomolgus have been established for Rituxan and Zevalin in
which monoclonal antibodies to CD20 are cross-reactive.
Biodistribution, dosimetry (for radiolabled antibodies or Fc
fusions), and PK studies can also be done in rodent models. Such
studies would evaluate tolerance at all doses administered,
toxicity to local tissues, preferential localization to rodent
xenograft animal models, depletion of target cells (e.g. CD20
positive cells).
[0196] The Fc variants of the present invention may confer superior
pharmacokinetics on Fc polypeptide therapeutics in animal systems
or in humans. For example, increased binding to FcRn may increase
the half-life and exposure of the Fc polypeptide. Alternatively,
decreased binding to FcRn may decrease the half-life and exposure
of the Fc polypeptide in cases where reduced exposure is favorable,
such as when such drug has side-effects.
[0197] It is known in the art that the array of Fc receptors is
differentially expressed on various immune cell types, as well as
in different tissues. Differential tissue distribution of Fc
receptors may ultimately have an impact on the pharmacodynamic (PD)
and pharmacokinetic (PK) properties of Fc variants of the present
invention. Because Fc variants of the presentation have varying
affinities for the array of Fc receptors, further screening of the
polypeptides for PD and/or PK properties may be extremely useful
for definining the optimal balance of PD, PK, and therapeutic
efficacy conferred by each candidate polypeptide.
[0198] Pharmacodynamic studies may include, but are not limited to,
targeting specific tumor cells or blocking signaling mechanisms,
measuring depletion of target antigen expressing cells or signals,
etc. The Fc variants of the present invention may target particular
effector cell populations and thereby direct Fc polypeptides to
recruit certain activities to improve potency or to increase
penetration into a particularly favorable physiological
compartment. For example, neutrophil activity and localization can
be targeted by an Fc variant that preferentially targets
Fc.gamma.RIIIb. Such pharmacodynamic effects may be demonstrated in
animal models or in humans.
Therapeutic Use of Fc Variants
[0199] The Fc variants of the present invention may be used for
various therapeutic purposes. As will be appreciated by those in
the art, the Fc variants of the present invention may be used for
any therapeutic purpose for which antibodies, Fc fusions, and the
like may be used. In a preferred embodiment, the Fc variants are
administered to a patient to treat disorders including but not
limited to autoimmune and inflammatory diseases, infectious
diseases, and cancer.
[0200] A "patient" for the purposes of the present invention
includes both humans and other animals, preferably mammals and most
preferably humans. Thus the Fc variants of the present invention
have both human therapy and veterinary applications. The term
"treatment" in the present invention is meant to include
therapeutic treatment, as well as prophylactic, or suppressive
measures for a disease or disorder. Thus, for example, successful
administration of an Fc variant prior to onset of the disease
results in treatment of the disease. As another example, successful
administration of an optimized Fc variant after clinical
manifestation of the disease to combat the symptoms of the disease
comprises treatment of the disease. "Treatment" also encompasses
administration of an optimized Fc variant after the appearance of
the disease in order to eradicate the disease. Successful
administration of an agent after onset and after clinical symptoms
have developed, with possible abatement of clinical symptoms and
perhaps amelioration of the disease, comprises treatment of the
disease. Those "in need of treatment" include mammals already
having the disease or disorder, as well as those prone to having
the disease or disorder, including those in which the disease or
disorder is to be prevented.
[0201] In one embodiment, an Fc variant of the present invention is
administered to a patient having a disease involving inappropriate
expression of a protein or other molecule. Within the scope of the
present invention this is meant to include diseases and disorders
characterized by aberrant proteins, due for example to alterations
in the amount of a protein present, protein localization,
posttranslational modification, conformational state, the presence
of a mutant or pathogen protein, etc. Similarly, the disease or
disorder may be characterized by alterations molecules including
but not limited to polysaccharides and gangliosides. An
overabundance may be due to any cause, including but not limited to
overexpression at the molecular level, prolonged or accumulated
appearance at the site of action, or increased activity of a
protein relative to normal. Included within this definition are
diseases and disorders characterized by a reduction of a protein.
This reduction may be due to any cause, including but not limited
to reduced expression at the molecular level, shortened or reduced
appearance at the site of action, mutant forms of a protein, or
decreased activity of a protein relative to normal. Such an
overabundance or reduction of a protein can be measured relative to
normal expression, appearance, or activity of a protein, and said
measurement may play an important role in the development and/or
clinical testing of the Fc variants of the present invention.
[0202] "Cancer" and "cancerous" herein refer to or describe the
physiological condition in mammals that is typically characterized
by unregulated cell growth. Examples of cancer include but are not
limited to carcinoma, lymphoma, blastoma, sarcoma (including
liposarcoma), neuroendocrine tumors, mesothelioma, schwanoma,
meningioma, adenocarcinoma, melanoma, and leukemia or lymphoid
malignancies.
[0203] More particular examples of such cancers include hematologic
malignancies, such as Hodgkin's lymphoma; non-Hodgkin's lymphomas
(Burkitt's lymphoma, small lymphocytic lymphoma/chronic lymphocytic
leukemia, mycosis fungoides, mantle cell lymphoma, follicular
lymphoma, diffuse large B-cell lymphoma, marginal zone lymphoma,
hairy cell leukemia and lymphoplasmacytic leukemia), tumors of
lymphocyte precursor cells, including B-cell acute lymphoblastic
leukemia/lymphoma, and T-cell acute lymphoblastic
leukemia/lymphoma, thymoma, tumors of the mature T and NK cells,
including peripheral T-cell leukemias, adult T-cell leukemia/T-cell
lymphomas and large granular lymphocytic leukemia, Langerhans cell
histocytosis, myeloid neoplasias such as acute myelogenous
leukemias, including AML with maturation, AML without
differentiation, acute promyelocytic leukemia, acute myelomonocytic
leukemia, and acute monocytic leukemias, myelodysplastic syndromes,
and chronic myeloproliferative disorders, including chronic
myelogenous leukemia; tumors of the central nervous system such as
glioma, glioblastoma, neuroblastoma, astrocytoma, medulloblastoma,
ependymoma, and retinoblastoma; solid tumors of the head and neck
(eg. nasopharyngeal cancer, salivary gland carcinoma, and
esophagael cancer), lung (eg. small-cell lung cancer, non-small
cell lung cancer, adenocarcinoma of the lung and squamous carcinoma
of the lung), digestive system (eg. gastric or stomach cancer
including gastrointestinal cancer, cancer of the bile duct or
biliary tract, colon cancer, rectal cancer, colorectal cancer, and
anal carcinoma), reproductive system (eg. testicular, penile, or
prostate cancer, uterine, vaginal, vulval, cervical, ovarian, and
endometrial cancer), skin (eg. melanoma, basal cell carcinoma,
squamous cell cancer, actinic keratosis), liver (eg. liver cancer,
hepatic carcinoma, hepatocellular cancer, and hepatoma), bone (eg.
osteoclastoma, and osteolytic bone cancers) additional tissues and
organs (eg. pancreatic cancer, bladder cancer, kidney or renal
cancer, thyroid cancer, breast cancer, cancer of the peritoneum,
and Kaposi's sarcoma), and tumors of the vascular system (eg.
angiosarcoma and hemagiopericytoma).
[0204] "Autoimmune diseases" herein include allogenic islet graft
rejection, alopecia areata, ankylosing spondylitis,
antiphospholipid syndrome, autoimmune Addison's disease,
antineutrophil cytoplasmic autoantibodies (ANCA), autoimmune
diseases of the adrenal gland, autoimmune hemolytic anemia,
autoimmune hepatitis, autoimmune myocarditis, autoimmune
neutropenia, autoimmune oophoritis and orchitis, autoimmune
thrombocytopenia, autoimmune urticaria, Behcet's disease, bullous
pemphigoid, cardiomyopathy, Castleman's syndrome, celiac
spruce-dermatitis, chronic fatigue immune disfunction syndrome,
chronic inflammatory demyelinating polyneuropathy, Churg-Strauss
syndrome, cicatrical pemphigoid, CREST syndrome, cold agglutinin
disease, Crohn's disease, dermatomyositis, discoid lupus, essential
mixed cryoglobulinemia, factor VIII deficiency,
fibromyalgia-fibromyositis, glomerulonephritis, Grave's disease,
Guillain-Barre, Goodpasture's syndrome, graft-versus-host disease
(GVHD), Hashimoto's thyroiditis, hemophilia A, idiopathic pulmonary
fibrosis, idiopathic thrombocytopenia purpura (ITP), IgA
neuropathy, IgM polyneuropathies, immune mediated thrombocytopenia,
juvenile arthritis, Kawasaki's disease, lichen plantus, lupus
erthematosis, Meniere's disease, mixed connective tissue disease,
multiple sclerosis, type 1 diabetes mellitus, myasthenia gravis,
pemphigus vulgaris, pernicious anemia, polyarteritis nodosa,
polychrondritis, polyglandular syndromes, polymyalgia rheumatica,
polymyositis and dermatomyositis, primary agammaglobinulinemia,
primary biliary cirrhosis, psoriasis, psoriatic arthritis,
Reynauld's phenomenon, Reiter's syndrome, rheumatoid arthritis,
sarcoidosis, scleroderma, Sjorgen's syndrome, solid organ
transplant rejection, stiff-man syndrome, systemic lupus
erythematosus, takayasu arteritis, temporal arteristis/giant cell
arteritis, thrombotic thrombocytopenia purpura, ulcerative colitis,
uveitis, vasculitides such as dermatitis herpetiformis vasculitis,
vitiligo, and Wegner's granulomatosis.
[0205] "Inflammatory disorders" herein include acute respiratory
distress syndrome (ARDS), acute septic arthritis, allergic
encephalomyelitis, allergic rhinitis, allergic vasculitis, allergy,
asthma, atherosclerosis, chronic inflammation due to chronic
bacterial or viral infectionis, chronic obstructive pulmonary
disease (COPD), coronary artery disease, encephalitis, inflammatory
bowel disease, inflammatory osteolysis, inflammation associated
with acute and delayed hypersensitivity reactions, inflammation
associated with tumors, peripheral nerve injury or demyelinating
diseases, inflammation associated with tissue trauma such as burns
and ischemia, inflammation due to meningitis, multiple organ injury
syndrome, pulmonary fibrosis, sepsis and septic shock,
Stevens-Johnson syndrome, undifferentiated arthropy, and
undifferentiated spondyloarthropathy.
[0206] "Infectious diseases" herein include diseases caused by
pathogens such as viruses, bacteria, fungi, protozoa, and
parasites. Infectious diseases may be caused by viruses including
adenovirus, cytomegalovirus, dengue, Epstein-Barr, hanta, hepatitis
A, hepatitis B, hepatitis C, herpes simplex type I, herpes simplex
type II, human immunodeficiency virus, (HIV), human papilloma virus
(HPV), influenza, measles, mumps, papova virus, polio, respiratory
syncytial virus, rinderpest, rhinovirus, rotavirus, rubella, SARS
virus, smallpox, viral meningitis, and the like. Infections
diseases may also be caused by bacteria including Bacillus
antracis, Borrelia burgdorferi, Campylobacter jejuni, Chlamydia
trachomatis, Clostridium botulinum, Clostridium tetani, Diptheria,
E. coli, Legionella, Helicobacter pylori, Mycobacterium rickettsia,
Mycoplasma nesisseria, Pertussis, Pseudomonas aeruginosa, S.
pneumonia, Streptococcus, Staphylococcus, Vibria cholerae, Yersinia
pestis, and the like. Infectious diseases may also be caused by
fungi such as Aspergillus fumigatus, Blastomyces dermatitidis,
Candida albicans, Coccidioides immitis, Cryptococcus neoformans,
Histoplasma capsulatum, Penicillium marneffei, and the like.
Infectious diseases may also be caused by protozoa and parasites
such as chlamydia, kokzidioa, leishmania, malaria, rickettsia,
trypanosoma, and the like.
[0207] Furthermore, Fc variants of the present invention may be
used to prevent or treat additional conditions including but not
limited to heart conditions such as congestive heart failure (CHF),
myocarditis and other conditions of the myocardium; skin conditions
such as rosecea, acne, and eczema; bone and tooth conditions such
as bone loss, osteoporosis, Paget's disease, Langerhans' cell
histiocytosis, periodontal disease, disuse osteopenia,
osteomalacia, monostotic fibrous dysplasia, polyostotic fibrous
dysplasia, bone metastasis, bone pain management, humoral malignant
hypercalcemia, periodontal reconstruction, spinal cord injury, and
bone fractures; metabolic conditions such as Gaucher's disease;
endocrine conditions such as Cushing's syndrome; and neurological
conditions.
Formulation, Administration, and Dosing
[0208] Pharmaceutical compositions are contemplated wherein an Fc
variant of the present invention and one or more therapeutically
active agents are formulated. Formulations of the Fc variants of
the present invention are prepared for storage by mixing said Fc
variant having the desired degree of purity with optional
pharmaceutically acceptable carriers, excipients or stabilizers
(Remington's Pharmaceutical Sciences 16th edition, Osol, A.
Ed.,1980), in the form of lyophilized formulations or aqueous
solutions. Acceptable carriers, excipients, or stabilizers are
nontoxic to recipients at the dosages and concentrations employed,
and include buffers such as phosphate, citrate, acetate, and other
organic acids; antioxidants including ascorbic acid and methionine;
preservatives (such as octadecyldimethylbenzyl ammonium chloride;
hexamethonium chloride; benzalkonium chloride, benzethonium
chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as
methyl or propyl paraben; catechol; resorcinol; cyclohexanol;
3-pentanol; and m-cresol); low molecular weight (less than about 10
residues) polypeptides; proteins, such as serum albumin, gelatin,
or immunoglobulins; hydrophilic polymers such as
polyvinylpyrrolidone; amino acids such as glycine, glutamine,
asparagine, histidine, arginine, or lysine; monosaccharides,
disaccharides, and other carbohydrates including glucose, mannose,
or dextrins; chelating agents such as EDTA; sugars such as sucrose,
mannitol, trehalose or sorbitol; sweeteners and other flavoring
agents; fillers such as microcrystalline cellulose, lactose, corn
and other starches; binding agents; additives; coloring agents;
salt-forming counter-ions such as sodium; metal complexes (e.g.
Zn-protein complexes); and/or non-ionic surfactants such as
TWEEM.TM., PLURONICS.TM. or polyethylene glycol (PEG). In a
preferred embodiment, the pharmaceutical composition that comprises
the Fc variant of the present invention may be in a water-soluble
form, such as being present as pharmaceutically acceptable salts,
which is meant to include both acid and base addition salts.
"Pharmaceutically acceptable acid addition salt" refers to those
salts that retain the biological effectiveness of the free bases
and that are not biologically or otherwise undesirable, formed with
inorganic acids such as hydrochloric acid, hydrobromic acid,
sulfuric acid, nitric acid, phosphoric acid and the like, and
organic acids such as acetic acid, propionic acid, glycolic acid,
pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic
acid, fumaric acid, tartaric acid, citric acid, benzoic acid,
cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic
acid, p-toluenesulfonic acid, salicylic acid and the like.
"Pharmaceutically acceptable base addition salts" include those
derived from inorganic bases such as sodium, potassium, lithium,
ammonium, calcium, magnesium, iron, zinc, copper, manganese,
aluminum salts and the like. Particularly preferred are the
ammonium, potassium, sodium, calcium, and magnesium salts. Salts
derived from pharmaceutically acceptable organic non-toxic bases
include salts of primary, secondary, and tertiary amines,
substituted amines including naturally occurring substituted
amines, cyclic amines and basic ion exchange resins, such as
isopropylamine, trimethylamine, diethylamine, triethylamine,
tripropylamine, and ethanolamine. The formulations to be used for
in vivo administration are preferrably sterile. This is readily
accomplished by filtration through sterile filtration membranes or
other methods.
[0209] The Fc variants disclosed herein may also be formulated as
immunoliposomes. A liposome is a small vesicle comprising various
types of lipids, phospholipids and/or surfactant that is useful for
delivery of a therapeutic agent to a mammal. Liposomes containing
the Fc variant are prepared by methods known in the art, such as
described in Epstein et al., 1985, Proc Natl Acad Sci USA, 82:3688;
Hwang et al., 1980, Proc Nat Acad Sci USA, 77:4030; U.S. Pat. No.
4,485,045; U.S. Pat. No. 4,544,545; and PCT WO 97/38731. Liposomes
with enhanced circulation time are disclosed in U.S. Pat. No.
5,013,556. The components of the liposome are commonly arranged in
a bilayer formation, similar to the lipid arrangement of biological
membranes. Particularly useful liposomes can be generated by the
reverse phase evaporation method with a lipid composition
comprising phosphatidylcholine, cholesterol and PEG-derivatized
phosphatidylethanolamine (PEG-PE). Liposomes are extruded through
filters of defined pore size to yield liposomes with the desired
diameter. A chemotherapeutic agent or other therapeutically active
agent is optionally contained within the liposome (Gabizon et al.,
1989, J National Cancer Inst 81:1484).
[0210] The Fc variant and other therapeutically active agents may
also be entrapped in microcapsules prepared by methods including
but not limited to coacervation techniques, interfacial
polymerization (for example using hydroxymethylcellulose or
gelatin-microcapsules, or poly-(methylmethacylate) microcapsules),
colloidal drug delivery systems (for example, liposomes, albumin
microspheres, microemulsions, nano-particles and nanocapsules), and
macroemulsions. Such techniques are disclosed in Remington's
Pharmaceutical Sciences 16th edition, Osol, A. Ed., 1980.
Sustained-release preparations may be prepared. Suitable examples
of sustained-release preparations include semipermeable matrices of
solid hydrophobic polymer, which matrices are in the form of shaped
articles, e.g. films, or microcapsules. Examples of
sustained-release matrices include polyesters, hydrogels (for
example poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)),
polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic
acid and gamma ethyl-L-glutamate, non-degradable ethylene-vinyl
acetate, degradable lactic acid-glycolic acid copolymers such as
the LUPRON DEPOT.RTM. (which are injectable microspheres composed
of lactic acid-glycolic acid copolymer and leuprolide acetate),
poly-D-(-)-3-hydroxybutyric acid, and ProLease.RTM. (commercially
available from Alkermes), which is a microsphere-based delivery
system composed of the desired bioactive molecule incorporated into
a matrix of poly-DL-lactide-co-glycolide (PLG).
[0211] Administration of the pharmaceutical composition comprising
an Fc variant of the present invention, preferably in the form of a
sterile aqueous solution, may be done in a variety of ways,
including, but not limited to orally, subcutaneously,
intravenously, intranasally, intraotically, transdermally,
topically (e.g., gels, salves, lotions, creams, etc.),
intraperitoneally, intramuscularly, intrapulmonary, vaginally,
parenterally, rectally, or intraocularly. In some instances, for
example for the treatment of wounds, inflammation, etc., the Fc
variant may be directly applied as a solution or spray. As is known
in the art, the pharmaceutical composition may be formulated
accordingly depending upon the manner of introduction.
[0212] Subcutaneous administration may be preferable in some
circumstances because the patient may self-administer the
pharmaceutical composition. Many protein therapeutics are not
sufficiently potent to allow for formulation of a therapeutically
effective dose in the maximum acceptable volume for subcutaneous
administration. This problem may be addressed in part by the use of
protein formulations comprising arginine-HCl, histidine, and
polysorbate (see WO 04091658). Fc polypeptides of the present
invention may be more amenable to subcutaneous administration due
to, for example, increased potency, improved serum half-life, or
enhanced solubility.
[0213] As is known in the art, protein therapeutics are often
delivered by IV infusion or bolus. The Fc variants of the present
invention may also be delivered using such methods. For example,
administration may venious be by intravenous infusion with 0.9%
sodium chloride as an infusion vehicle.
[0214] Pulmonary delivery may be accomplished using an inhaler or
nebulizer and a formulation comprising an aerosolizing agent. For
example, AERX.RTM. inhalable technology commercially available from
Aradigm, or Inhance.TM. pulmonary delivery system commercially
available from Nektar Therapeutics may be used. Fc variants of the
present invention may be more amenable to intrapulmonary delivery.
FcRn is present in the lung, and may promote transport from the
lung to the bloodstream (e.g. Syntonix WO 04004798, Bitonti et. al.
(2004) Proc. Nat. Acad. Sci. 101:9763-8). Accordingly, antibodes or
Fc fusions that bind FcRn more effectively in the lung or that are
released more efficiently in the bloodstream may have improved
bioavailability following intrapulmonary administration. Fc
variants of the present invention may also be more amenable to
intrapulmonary administration due to, for example, improved
solubility or altered isoelectric point.
[0215] Furthermore, Fc polypeptides of the present invention may be
more amenable to oral delivery due to, for example, improved
stability at gastric pH and increased resistance to proteolysis.
Furthermore, FcRn appears to be expressed in the intestinal
epithelia of adults (Dickinson et al., 1999, J Clin Invest
104:903-11), so Fc polypeptides of the present invention, for
example antibodies or Fc fusions, with improved FcRn interaction
profiles may show enhanced bioavailability following oral
administration. FcRn mediated transport of Fc variants may also
occur at other mucus membranes such as those in the
gastrointestinal, respiratory, and genital tracts (Yoshida et al.,
2004, Immunity 20:769-83).
[0216] In addition, any of a number of delivery systems are known
in the art and may be used to administer the Fc variants of the
present invention. Examples include, but are not limited to,
encapsulation in liposomes, microparticles, microspheres (eg.
PLA/PGA microspheres), and the like. Alternatively, an implant of a
porous, non-porous, or gelatinous material, including membranes or
fibers, may be used. Sustained release systems may comprise a
polymeric material or matrix such as polyesters, hydrogels,
poly(vinylalcohol), polylactides, copolymers of L-glutamic acid and
ethyl-L-gutamate, ethylene-vinyl acetate, lactic acid-glycolic acid
copolymers such as the LUPRON DEPOT.RTM., and
poly-D-(-)-3-hydroxyburyric acid. It is also possible to administer
a nucleic acid encoding the Fc variant of the current invention,
for example by retroviral infection, direct injection, or coating
with lipids, cell surface receptors, or other transfection agents.
In all cases, controlled release systems may be used to release the
Fc variant at or close to the desired location of action.
[0217] The dosing amounts and frequencies of administration are, in
a preferred embodiment, selected to be therapeutically or
prophylactically effective. As is known in the art, adjustments for
protein degradation, systemic versus localized delivery, and rate
of new protease synthesis, as well as the age, body weight, general
health, sex, diet, time of administration, drug interaction and the
severity of the condition may be necessary, and will be
ascertainable with routine experimentation by those skilled in the
art.
[0218] The concentration of the therapeutically active Fc variant
in the formulation may vary from about 0.1 to 100 weight %. In a
preferred embodiment, the concentration of the Fc variant is in the
range of 0.003 to 1.0 molar. In order to treat a patient, a
therapeutically effective dose of the Fc variant of the present
invention may be administered. By "therapeutically effective dose"
herein is meant a dose that produces the effects for which it is
administered. The exact dose will depend on the purpose of the
treatment, and will be ascertainable by one skilled in the art
using known techniques. Dosages may range from 0.0001 to 100 mg/kg
of body weight or greater, for example 0.1, 1, 10, or 50 mg/kg of
body weight, with 1 to 10 mg/kg being preferred.
[0219] In some embodiments, only a single dose of the Fc variant is
used. In other embodiments, multiple doses of the Fc variant are
administered. The elapsed time between administrations may be less
than 1 hour, about 1 hour, about 1-2 hours, about 2-3 hours, about
3-4 hours, about 6 hours, about 12 hours, about 24 hours, about 48
hours, about 2-4 days, about 4-6 days, about 1 week, about 2 weeks,
or more than 2 weeks.
[0220] In other embodiments the Fc variants of the present
invention are administered in metronomic dosing regimes, either by
continuous infusion or frequent administration without extended
rest periods. Such metronomic administration may involve dosing at
constant intervals without rest periods. Typically such regimens
encompass chronic low-dose or continuous infusion for an extended
period of time, for example 1-2 days, 1-2 weeks, 1-2 months, or up
to 6 months or more. The use of lower doses may minimize side
effects and the need for rest periods.
[0221] In certain embodiments the Fc variant of the present
invention and one or more other prophylactic or therapeutic agents
are cyclically administered to the patient. Cycling therapy
involves administration of a first agent at one time, a second
agent at a second time, optionally additional agents at additional
times, optionally a rest period, and then repeating this sequence
of administration one or more times. The number of cycles is
typically from 2-10. Cycling therapy may reduce the development of
resistance to one or more agents, may minimize side effects, or may
improve treatment efficacy.
Combination- and Co-Therapies
[0222] The Fc variants of the present invention may be administered
concomitantly with one or more other therapeutic regimens or
agents. The additional therapeutic regimes or agents may be used to
improve the efficacy or safety of the Fc variant. Also, the
additional therapeutic regimes or agents may be used to treat the
same disease or a comorbidity rather than to alter the action of
the Fc variant. For example, an Fc variant of the present invention
may be administered to the patient along with chemotherapy,
radiation therapy, or both chemotherapy and radiation therapy. The
Fc variant of the present invention may be administered in
combination with one or more other prophylactic or therapeutic
agents, including but not limited to cytotoxic agents,
chemotherapeutic agents, cytokines, growth inhibitory agents,
anti-hormonal agents, kinase inhibitors, anti-angiogenic agents,
cardioprotectants, immunostimulatory agents, immunosuppressive
agents, agents that promote proliferation of hematological cells,
angiogenesis inhibitors, protein tyrosine kinase (PTK) inhibitors,
additional Fc variants, Fc.gamma.RIIb or other Fc receptor
inhibitors, or other therapeutic agents.
[0223] The terms "in combination with" and "co-administration" are
not limited to the administration of said prophylactic or
therapeutic agents at exactly the same time. Instead, it is meant
that the Fc variant of the present invention and the other agent or
agents are administered in a sequence and within a time interval
such that they may act together to provide a benefit that is
increased versus treatment with only either the Fc variant of the
present invention or the other agent or agents. It is preferred
that the Fc variant and the other agent or agents act additively,
and especially preferred that they act synergistically. Such
molecules are suitably present in combination in amounts that are
effective for the purpose intended. The skilled medical
practitioner can determine empirically, or by considering the
pharmacokinetics and modes of action of the agents, the appropriate
dose or doses of each therapeutic agent, as well as the appropriate
timings and methods of administration.
[0224] In one embodiment, the Fc variants of the present invention
are administered with one or more additional molecules comprising
antibodies or Fc. The Fc variants of the present invention may be
co-administered with one or more other antibodies that have
efficacy in treating the same disease or an additional comorbidity;
for example two antibodies may be administered that recognize two
antigens that are overexpressed in a given type of cancer, or two
antigens that mediate pathogenesis of an autoimmune or infectious
disease.
[0225] Examples of anti-cancer antibodies that may be
co-administered include, but are not limited to, anti 17-IA cell
surface antigen antibodies such as Panorex.TM. (edrecolomab);
anti-4-1BB antibodies; anti-4Dc antibodies; anti-A33 antibodies
such as A33 and CDP-833; anti-.alpha.4.beta.1 integrin antibodies
such as natalizumab; anti-.alpha.4.beta.7 integrin antibodies such
as LDP-02; anti-.alpha.V.beta.1 integrin antibodies such as F-200,
M-200, and SJ-749; anti-.alpha.V.beta.3 integrin antibodies such as
abciximab, CNTO-95, Mab-17E6, and Vitaxin.TM.; anti-complement
factor 5 (C5) antibodies such as 5G1.1; anti-CA125 antibodies such
as OvaRex.RTM. (oregovomab); anti-CD3 antibodies such as
Nuvion.RTM. (visilizumab) and Rexomab; anti-CD4 antibodies such as
IDEC-151, MDX-CD4, OKT4A; anti-CD6 antibodies such as Oncolysin B
and Oncolysin CD6; anti-CD7 antibodies such as HB2; anti-CD19
antibodies such as B43, MT-103, and Oncolysin B; anti-CD20
antibodies such as 2H7, 2H7.v16, 2H7.v114, 2H7.v115, Bexxar.RTM.
(tositumomab), Rituxan.RTM. (rituximab), Zevalin.RTM. (Ibritumomab
tiuxetan), and PRO70769; anti-CD22 antibodies such as
Lymphocide.TM. (epratuzumab); anti-CD23 antibodies such as
IDEC-152; anti-CD25 antibodies such as basiliximab and Zenapax.RTM.
(daclizumab); anti-CD30 antibodies such as AC10, MDX-060, and
SGN-30; anti-CD33 antibodies such as Mylotarg.RTM. (gemtuzumab
ozogamicin), Oncolysin M, and Smart M195; anti-CD38 antibodies;
anti-CD40 antibodies such as SGN-40 and toralizumab; anti-CD40L
antibodies such as 5c8, Antova.TM., and IDEC-131; anti-CD44
antibodies such as bivatuzumab; anti-CD46 antibodies; anti-CD52
antibodies such as Campath.RTM. (alemtuzumab); anti-CD55 antibodies
such as SC-1; anti-CD56 antibodies such as huN901-DM1; anti-CD64
antibodies such as MDX-33; anti-CD66e antibodies such as XR-303;
anti-CD74 antibodies such as IMMU-110; anti-CD80 antibodies such as
galiximab and IDEC-114; anti-CD89 antibodies such as MDX-214;
anti-CD123 antibodies; anti-CD138 antibodies such as B-B4-DM1;
anti-CD146 antibodies such as AA-98; anti-CD148 antibodies;
anti-CEA antibodies such as cT84.66, Labetuzumab, and Pentacea.TM.;
anti-CTLA-4 antibodies such as MDX-101; anti-CXCR4 antibodies;
antibodies such as ABX-EGF, Erbitux.RTM. (cetuximab), IMC-C225, and
Merck Mab 425; anti-EpCAM antibodies such as Crucell's anti-EpCAM,
ING-1, and IS-IL-2; anti-ephrin B2/EphB4 antibodies; anti-Her2
antibodies such as Herceptin.RTM., MDX-210; anti-FAP (fibroblast
activation protein) antibodies such as sibrotuzumab; anti-ferritin
antibodies such as NXT-211; anti-FGF-1 antibodies; anti-FGF-3
antibodies; anti-FGF-8 antibodies; anti-FGFR antibodies,
anti-fibrin antibodies; anti-G250 antibodies such as WX-G250 and
Rencarex.RTM.; anti-GD2 ganglioside antibodies such as EMD-273063
and TriGem; anti-GD3 ganglioside antibodies such as BEC2, KW-2871,
and mitumomab; anti-gpIIb/IIIa antibodies such as ReoPro;
anti-heparinase antibodies; anti-Her2/ErbB2 antibodies such as
Herceptin.RTM. (trastuzumab), MDX-210, and pertuzumab; anti-HLA
antibodies such as Oncolym.RTM., Smart 1D10; anti-HM1.24
antibodies; anti-ICAM antibodies such as ICM3; anti-IgA receptor
antibodies; anti-IGF-1 antibodies such as CP-751871 and EM-164;
anti-IGF-1R antibodies such as IMC-A12; anti-IL-6 antibodies such
as CNTO-328 and elsilimomab; anti-IL-15 antibodies such as
HuMax.TM.-IL15; anti-KDR antibodies; anti-laminin 5 antibodies;
anti-Lewis Y antigen antibodies such as Hu3S193 and IGN-311;
anti-MCAM antibodies; anti-Muc1 antibodies such as BravaRex and
TriAb; anti-NCAM antibodies such as ERIC-1 and ICRT; anti-PEM
antigen antibodies such as Theragyn and Therex; anti-PSA
antibodies; anti-PSCA antibodies such as IG8; anti-Ptk antbodies;
anti-PTN antibodies; anti-RANKL antibodies such as AMG-162;
anti-RLIP76 antibodies; anti-SK-1 antigen antibodies such as
Monopharm C; anti-STEAP antibodies; anti-TAG72 antibodies such as
CC49-SCA and MDX-220; anti-TGF-.beta. antibodies such as CAT-152;
anti-TNF-.alpha. antibodies such as CDP571, CDP870, D2E7,
Humira.RTM. (adalimumab), and Remicade.RTM. (infliximab);
anti-TRAIL-R1 and TRAIL-R2 antibodies; anti-VE-cadherin-2
antibodies; and anti-VLA-4 antibodies such as Antegren.TM..
Furthermore, anti-idiotype antibodies including but not limited to
the GD3 epitope antibody BEC2 and the gp72 epitope antibody 105AD7,
may be used. In addition, bispecific antibodies including but not
limited to the anti-CD3/CD20 antibody Bi20 may be used.
[0226] Examples of antibodies that may be co-administered to treat
autoimmune or inflammatory disease, transplant rejection, GVHD, and
the like include, but are not limited to, anti-.alpha.4.beta.7
integrin antibodies such as LDP-02, anti-beta2 integrin antibodies
such as LDP-01, anti-complement (C5) antibodies such as 5G1.1,
anti-CD2 antibodies such as BTI-322, MEDI-507, anti-CD3 antibodies
such as OKT3, SMART anti-CD3, anti-CD4 antibodies such as IDEC-151,
MDX-CD4, OKT4A, anti-CD11a antibodies, anti-CD14 antibodies such as
IC14, anti-CD18 antibodies, anti-CD23 antibodies such as IDEC 152,
anti-CD25 antibodies such as Zenapax, anti-CD40L antibodies such as
5c8, Antova, IDEC-131, anti-CD64 antibodies such as MDX-33,
anti-CD80 antibodies such as IDEC-114, anti-CD147 antibodies such
as ABX-CBL, anti-E-selectin antibodies such as CDP850,
anti-gpIIb/IIIa antibodies such as ReoPro/Abcixima, anti-ICAM-3
antibodies such as ICM3, anti-ICE antibodies such as VX-740,
anti-FcR1 antibodies such as MDX-33, anti-IgE antibodies such as
rhuMab-E25, anti-IL-4 antibodies such as SB-240683, anti-IL-5
antibodies such as SB-240563, SCH55700, anti-IL-8 antibodies such
as ABX-IL8, anti-interferon gamma antibodies, and anti-TNFa
antibodies such as CDP571, CDP870, D2E7, Infliximab, MAK-195F,
anti-VLA-4 antibodies such as Antegren. Examples of other
Fc-containing molecules that may be co-administered to treat
autoimmune or inflammatory disease, transplant rejection, GVHD, and
the like include, but are not limited to, the p75 TNF receptor/Fc
fusion Enbrel.RTM. (etanercept) and Regeneron's IL-1 trap.
[0227] Examples of antibodies that may be co-administered to treat
infectious diseases include, but are not limited to, anti-anthrax
antibodies such as ABthrax, anti-CMV antibodies such as CytoGam and
sevirumab, anti-cryptosporidium antibodies such as CryptoGAM,
Sporidin-G, anti-helicobacter antibodies such as Pyloran,
anti-hepatitis B antibodies such as HepeX-B, Nabi-HB, anti-HIV
antibodies such as HRG-214, anti-RSV antibodies such as felvizumab,
HNK-20, palivizumab, RespiGam, and anti-staphylococcus antibodies
such as Aurexis, Aurograb, BSYX-A110, and SE-Mab.
[0228] Alternatively, the Fc variants of the present invention may
be co-administered or with one or more other molecules that compete
for binding to one or more Fc receptors. For example,
co-administering inhibitors of the inhibitory receptor
Fc.gamma.RIIb may result in increased effector function. Similarly,
co-administering inhibitors of activating receptors, for example
Fc.gamma.RIIIa, may minimize unwanted effector function. Fc
receptor inhibitors include but are not limited to Fc variants that
are engineered to act as competitive Fc.gamma.R inhibitors, as well
as other immunoglobulins and specifically intravenous
immunoglobulin (IVIg). In one embodiment, the inhibitor is
administered and allowed to act before the Fc variant is
administered. An alternative way of achieving the effect of
sequential dosing would be to provide an immediate release dosage
form of the Fc receptor inhibitor and then a sustained release
formulation of the Fc variant of the invention. The immediate
release and controlled release formulations could be administered
separately or be combined into one unit dosage form. Administration
of an Fc.gamma.RIIb inhibitor may also be used to limit unwanted
immune responses, for example anti-Factor VIII antibody response
following Factor VIII administration to hemophiliacs.
[0229] In one embodiment, the Fc variants of the present invention
are administered with a chemotherapeutic agent. By
"chemotherapeutic agent" as used herein is meant a chemical
compound useful in the treatment of cancer. Examples of
chemotherapeutic agents include but are not limited to alkylating
agents such as thiotepa and cyclosphosphamide (CYTOXAN.TM.); alkyl
sulfonates such as busulfan, improsulfan and piposulfan; androgens
such as calusterone, dromostanolone propionate, epitiostanol,
mepitiostane, testolactone; anti-adrenals such as
aminoglutethimide, mitotane, trilostane; anti-androgens such as
flutamide, nilutamide, bicalutamide, leuprolide, and goserelin;
antibiotics such as aclacinomysins, actinomycin, authramycin,
azaserine, bleomycins, cactinomycin, calicheamicin, carabicin,
caminomycin, carzinophilin, chromomycins, dactinomycin,
daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin,
epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins,
mycophenolic acid, nogalamycin, olivomycins, peplomycin,
potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin,
streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti
estrogens including for example tamoxifen, raloxifene, aromatase
inhibiting 4(5)-imidazoles, 4-hydroxytamoxifen, trioxifene,
keoxifene, LY 117018, onapristone, and toremifene (Fareston);
anti-metabolites such as methotrexate and 5-fluorouracil (5-FU);
folic acid analogues such as denopterin, methotrexate, pteropterin,
trimetrexate; aziridines such as benzodopa, carboquone, meturedopa,
and uredopa; ethylenimines and methylamelamines including
altretamine, triethylenemelamine, trietylenephosphoramide,
triethylenethiophosphaoramide and trimethylolomelamine; folic acid
replenisher such as frolinic acid; nitrogen mustards such as
chlorambucil, chlornaphazine, cholophosphamide, estramustine,
ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride,
melphalan, novembichin, phenesterine, prednimustine, trofosfamide,
uracil mustard; nitrosureas such as carmustine, chlorozotocin,
fotemustine, lomustine, nimustine, ranimustine; platinum analogs
such as cisplatin and carboplatin; vinblastine; platinum; proteins
such as arginine deiminase and asparaginase; purine analogs such as
fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine
analogs such as ancitabine, azacitidine, 6-azauridine, carmofur,
cytarabine, dideoxyuridine, doxifluridine, enocitabine,
floxuridine, 5-FU; taxanes, e.g. paclitaxel (TAXOL.RTM.,
Bristol-Myers Squibb Oncology, Princeton, N.J.) and docetaxel
(TAXOTERE.RTM.), Rhne-Poulenc Rorer, Antony, France); topoisomerase
inhibitor RFS 2000; thymidylate synthase inhibitor (such as
Tomudex); additional chemotherapeutics including aceglatone;
aldophosphamide glycoside; aminolevulinic acid; amsacrine;
bestrabucil; bisantrene; edatraxate; defofamine; demecolcine;
diaziquone; difluoromethylornithine (DMFO); elformithine;
elliptinium acetate; etoglucid; gallium nitrate; hydroxyurea;
lentinan; lonidamine; mitoguazone; mitoxantrone; mopidamol;
nitracrine; pentostatin; phenamet; pirarubicin; podophyllinic acid;
2-ethylhydrazide; procarbazine; PSK.RTM.; razoxane; sizofuran;
spirogermanium; tenuazonic acid; triaziquone;
2,2',2''-trichlorotriethylamine; urethan; vindesine; dacarbazine;
mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine;
arabinoside ("Ara-C"); cyclophosphamide; thiotepa; chlorambucil;
gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; etoposide
(VP-16); ifosfamide; mitomycin C; mitoxantrone; vincristine;
vinorelbine; navelbine; novantrone; teniposide; daunomycin;
aminopterin; xeloda; ibandronate; CPT-11; retinoic acid;
esperamicins; capecitabine. Pharmaceutically acceptable salts,
acids or derivatives of any of the above may also be used.
[0230] A chemotherapeutic or other cytotoxic agent may be
administered as a prodrug. By "prodrug" as used herein is meant a
precursor or derivative form of a pharmaceutically active substance
that is less cytotoxic to tumor cells compared to the parent drug
and is capable of being enzymatically activated or converted into
the more active parent form. See, for example Wilman, 1986,
Biochemical Society Transactions, 615th Meeting Belfast,
14:375-382; and Stella et al., "Prodrugs: A Chemical Approach to
Targeted Drug Delivery," Directed Drug Delivery, Borchardt et al.,
(ed.): 247-267, Humana Press, 1985. The prodrugs that may find use
with the present invention include but are not limited to
phosphate-containing prodrugs, thiophosphate-containing prodrugs,
sulfate-containing prodrugs, peptide-containing prodrugs, D-amino
acid-modified prodrugs, glycosylated prodrugs,
beta-lactam-containing prodrugs, optionally substituted
phenoxyacetamide-containing prodrugs or optionally substituted
phenylacetamide-containing prodrugs, 5-fluorocytosine and other
5-fluorouridine prodrugs which can be converted into the more
active cytotoxic free drug. Examples of cytotoxic drugs that can be
derivatized into a prodrug form for use with the Fc variants of the
present invention include but are not limited to any of the
aforementioned chemotherapeutic agents.
[0231] A variety of other therapeutic agents may find use for
administration with the Fc variants of the present invention. In
one embodiment, the Fc variant is administered with an
anti-angiogenic agent. By "anti-angiogenic agent" as used herein is
meant a compound that blocks, or interferes to some degree, the
development of blood vessels. The anti-angiogenic factor may, for
instance, be a small molecule or a protein, for example an
antibody, Fc fusion, or cytokine, that binds to a growth factor or
growth factor receptor involved in promoting angiogenesis. The
preferred anti-angiogenic factor herein is an antibody that binds
to Vascular Endothelial Growth Factor (VEGF). Other agents that
inhibit signaling through VEGF may also be used, for example
RNA-based therapeutics that reduce levels of VEGF or VEGF-R
expression, VEGF-toxin fusions, Regeneron's VEGF-trap, and
antibodies that bind VEGF-R. In an alternate embodiment, the Fc
variant is administered with a therapeutic agent that induces or
enhances adaptive immune response, for example an antibody that
targets CTLA-4. Additional anti-angiogenesis agents include, but
are not limited to, angiostatin (plasminogen fragment),
antithrombin III, angiozyme, ABT-627, Bay 12-9566, benefin,
bevacizumab, bisphosphonates, BMS-275291, cartilage-derived
inhibitor (CDI), CAI, CD59 complement fragment, CEP-7055, Col 3,
combretastatin A-4, endostatin (collagen XVIII fragment), farnesyl
transferase inhibitors, fibronectin fragment, gro-beta,
halofuginone, heparinases, heparin hexasaccharide fragment, HMV833,
human chorionic gonadotropin (hCG), IM-862, interferon alpha,
interferon beta, interferon gamma, interferon inducible protein 10
(IP-10), interleukin-12, kringle 5 (plasminogen fragment),
marimastat, metalloproteinase inhibitors (eg. TIMPS),
2-methodyestradiol, MMI 270 (CGS 27023A), plasminogen activiator
inhibitor (PAI), platelet factor-4 (PF4), prinomastat, prolactin 16
kDa fragment, proliferin-related protein (PRP), PTK 787/ZK 222594,
retinoids, solimastat, squalamine, SS3304, SU5416, SU6668, SU11248,
tetrahydrocortisol-S, tetrathiomolybdate, thalidomide,
thrombospondin-1 (TSP-1), TNP-470, transforming growth factor beta
(TGF-.beta.), vasculostatin, vasostatin (calreticulin fragment),
ZS6126,and ZD6474.
[0232] In a preferred embodiment, the Fc variant is administered
with a tyrosine kinase inhibitor. By "tyrosine kinase inhibitor" as
used herein is meant a molecule that inhibits to some extent
tyrosine kinase activity of a tyrosine kinase. Examples of such
inhibitors include but are not limited to quinazolines, such as PD
153035, 4-(3-chloroanilino)quinazoline; pyridopyrimidines;
pyrimidopyrimidines; pyrrolopyrimidines, such as CGP 59326, CGP
60261 and CGP 62706; pyrazolopyrimidines,
4-(phenylamino)-7H-pyrrolo(2,3-d)pyrimidines; curcumin (diferuloyl
methane, 4,5-bis(4-fluoroanilino)-phthalimide); tyrphostines
containing nitrothiophene moieties; PD-0183805 (Warner-Lambert);
antisense molecules (e.g. those that bind to ErbB-encoding nucleic
acid); quinoxalines (U.S. Pat. No. 5,804,396); tryphostins (U.S.
Pat. No. 5,804,396); ZD6474 (Astra Zeneca); PTK-787
(Novartis/Schering A G); pan-ErbB inhibitors such as C1-1033
(Pfizer); Affinitac (ISIS 3521; Isis/Lilly); Imatinib mesylate
(STI571,Gleevec.RTM.; Novartis); PKI 166 (Novartis); GW2016 (Glaxo
SmithKline); C1-1033 (Pfizer); EKB-569 (Wyeth); Semaxinib (Sugen);
ZD6474 (AstraZeneca); PTK-787 (Novartis/Schering AG); INC-1C11
(Imclone); or as described in any of the following patent
publications: U.S. Pat. No. 5,804,396; PCT WO 99/09016 (American
Cyanimid); PCT WO 98/43960 (American Cyanamid); PCT WO 97/38983
(Warner-Lambert); PCT WO 99/06378 (Warner-Lambert); PCT WO 99/06396
(Warner-Lambert); PCT WO 96/30347 (Pfizer, Inc); PCT WO 96/33978
(AstraZeneca); PCT WO96/3397 (AstraZeneca); PCT WO 96/33980
(AstraZeneca), gefitinib (IRESSA.TM., ZD1839, AstraZeneca), and
OSI-774 (Tarceva.TM., OSI Pharmaceuticals/Genentech).
[0233] In another embodiment, the Fc variant is administered with
one or more immunomodulatory agents. Such agents may increase or
decrease production of one or more cytokines, up- or down-regulate
self-antigen presentation, mask MHC antigens, or promote the
proliferation, differentiation, migration, or activation state of
one or more types of immune cells. Immunomodulatory agents include
but not limited to: non-steroidal anti-inflammatory drugs (NSAIDs)
such as asprin, ibuprofed, celecoxib, diclofenac, etodolac,
fenoprofen, indomethacin, ketoralac, oxaprozin, nabumentone,
sulindac, tolmentin, rofecoxib, naproxen, ketoprofen, and
nabumetone; steroids (eg. glucocorticoids, dexamethasone,
cortisone, hydroxycortisone, methylprednisolone, prednisone,
prednisolone, trimcinolone, azulfidineicosanoids such as
prostaglandins, thromboxanes, and leukotrienes; as well as topical
steroids such as anthralin, calcipotriene, clobetasol, and
tazarotene); cytokines such as TGFb, IFNa, IFNb, IFNg, IL-2, IL-4,
IL-10; cytokine, chemokine, or receptor antagonists including
antibodies, soluble receptors, and receptor-Fc fusions against
BAFF, B7, CCR2, CCR5, CD2, CD3, CD4, CD6, CD7, CD8, CD11, CD14,
CD15, CD17, CD18, CD20, CD23, CD28, CD40, CD40L, CD44, CD45, CD52,
CD64, CD80, CD86, CD147, CD152, complement factors (C5, D) CTLA4,
eotaxin, Fas, ICAM, ICOS, IFN.alpha., IFN.beta., IFN.gamma., IFNAR,
IgE, IL-1, IL-2, IL-2R, IL-4, IL-5R, IL-6, IL-8, IL-9 IL-12, IL-13,
IL-13R1, IL-15, IL-18R, IL-23, integrins, LFA-1, LFA-3, MHC,
selectins, TGF.beta., TNF.alpha., TNF.beta., TNF-R1, T-cell
receptor, including Enbrel.RTM.) (etanercept), Humira.RTM.
(adalimumab), and Remicade.RTM. (infliximab); heterologous
anti-lymphocyte globulin; other immunomodulatory molecules such as
2-amino-6-aryl-5 substituted pyrimidines, anti-idiotypic antibodies
for MHC binding peptides and MHC fragments, azathioprine,
brequinar, bromocryptine, cyclophosphamide, cyclosporine A,
D-penicillamine, deoxyspergualin, FK506, glutaraldehyde, gold,
hydroxychloroquine, leflunomide, malononitriloamides (eg.
leflunomide), methotrexate, minocycline, mizoribine, mycophenolate
mofetil, rapamycin, and sulfasasazine.
[0234] In an alternate embodiment, Fc variants of the present
invention are administered with a cytokine. By "cytokine" as used
herein is meant a generic term for proteins released by one cell
population that act on another cell as intercellular mediators.
Examples of such cytokines are lymphokines, monokines, and
traditional polypeptide hormones. Included among the cytokines are
growth hormone such as human growth hormone, N-methionyl human
growth hormone, and bovine growth hormone; parathyroid hormone;
thyroxine; insulin; proinsulin; relaxin; prorelaxin; glycoprotein
hormones such as follicle stimulating hormone (FSH), thyroid
stimulating hormone (TSH), and luteinizing hormone (LH); hepatic
growth factor; fibroblast growth factor; prolactin; placental
lactogen; tumor necrosis factor-alpha and -beta;
mullerian-inhibiting substance; mouse gonadotropin-associated
peptide; inhibin; activin; vascular endothelial growth factor;
integrin; thrombopoietin (TPO); nerve growth factors such as
NGF-beta; platelet-growth factor; transforming growth factors
(TGFs) such as TGF-alpha and TGF-beta; insulin-like growth factor-I
and -II; erythropoietin (EPO); osteoinductive factors; interferons
such as interferon-alpha, beta, and -gamma; colony stimulating
factors (CSFs) such as macrophage-CSF (M-CSF);
granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF);
interleukins (ILs) such as IL-1, IL-lalpha, IL-2, IL-3, IL-4, IL-5,
IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12; IL-15, a tumor
necrosis factor such as TNF-alpha or TNF-beta; and other
polypeptide factors including LIF and kit ligand (KL). As used
herein, the term cytokine includes proteins from natural sources or
from recombinant cell culture, and biologically active equivalents
of the native sequence cytokines.
[0235] In a preferred embodiment, cytokines or other agents that
stimulate cells of the immune system are co-administered with an Fc
variant of the present invention. Such a mode of treatment may
enhance desired effector function. For examle, agents that
stimulate NK cells, including but not limited to IL-2 may be
co-administered. In another embodiment, agents that stimulate
macrophages, including but not limited to C5a, formyl peptides such
as N-formyl-methionyl-leucyl-phenylalanine (Beigier-Bompadre et.
al. (2003) Scand. J. Immunol. 57: 221-8), may be co-administered.
Also, agents that stimulate neutrophils, including but not limited
to G-CSF, GM-CSF, and the like may be administered. Furthermore,
agents that promote migration of such immunostimulatory cytokines
may be used. Also additional agents including but not limited to
interferon gamma, IL-3 and IL-7 may promote one or more effector
functions. In an alternate embodiment, cytokines or other agents
that inhibit effector cell function are co-administered with an Fc
variant of the present invention. Such a mode of treatment may
limit unwanted effector function.
[0236] In an additional embodiment, the Fc variant is administered
with one or more antibiotics, including but not limited to:
aminoglycoside antibiotics (eg. apramycin, arbekacin, bambermycins,
butirosin, dibekacin, gentamicin, kanamycin, neomycin, netilmicin,
paromomycin, ribostamycin, sisomycin, spectrinomycin),
aminocyclitols (eg. sprctinomycin), amphenicol antibiotics (eg.
azidamfenicol, chloramphenicol, florfrnicol, and thiamphemicol),
ansamycin antibiotics (eg. rifamide and rifampin), carbapenems (eg.
imipenem, meropenem, panipenem); cephalosporins (eg. cefaclor,
cefadroxil, cefamandole, cefatrizine, cefazedone, cefozopran,
cefpimizole, cefpiramide, cefpirome, cefprozil, cefuroxine,
cefixime, cephalexin, cephradine), cephamycins (cefbuperazone,
cefoxitin, cefminox, cefmetazole, and cefotetan); lincosamides (eg.
clindamycin, lincomycin); macrolide (eg. azithromycin, brefeldin A,
clarithromycin, erythromycin, roxithromycin, tobramycin),
monobactams (eg. aztreonam, carumonam, and tigernonam); mupirocin;
oxacephems (eg. flomoxef, latamoxef, and moxalactam); penicillins
(eg. amdinocillin, amdinocillin pivoxil, amoxicillin,
bacampicillin, bexzylpenicillinic acid, benzylpenicillin sodium,
epicillin, fenbenicillin, floxacillin, penamecillin, penethamate
hydriodide, penicillin o-benethamine, penicillin O, penicillin V,
penicillin V benzoate, penicillin V hydrabamine, penimepicycline,
and phencihicillin potassium); polypeptides (eg. bacitracin,
colistin, polymixin B, teicoplanin, vancomycin); quinolones
(amifloxacin, cinoxacin, ciprofloxacin, enoxacin, enrofloxacin,
feroxacin, flumequine, gatifloxacin, gemifloxacin, grepafloxacin,
lomefloxacin, moxifloxacin, nalidixic acid, norfloxacin, ofloxacin,
oxolinic acid, pefloxacin, pipemidic acid, rosoxacin, rufloxacin,
sparfloxacin, temafloxacin, tosufloxacin, trovafloxacin); rifampin;
streptogramins (eg. quinupristin, dalfopristin); sulfonamides
(sulfanilamide, sulfamethoxazole); tetracyclenes
(chlortetracycline, demeclocycline hydrochloride,
demethylchlortetracycline, doxycycline, duramycin, minocycline,
neomycin, oxytetracycline, streptomycin, tetracycline,
vancomycin).
[0237] Anti-fungal agents such as amphotericin B, ciclopirox,
clotrimazole, econazole, fluconazole, flucytosine, itraconazole,
ketoconazole, niconazole, nystatin, terbinafine, terconazole, and
tioconazole may also be used.
[0238] Antiviral agents including protease inhibitors, reverse
transcriptase inhibitors, and others, including type I interferons,
viral fusion inhibitors, and neuramidase inhibitors, may also be
used. Examples of antiviral agents include, but are not limited to,
acyclovir, adefovir, amantadine, amprenavir, clevadine,
enfuvirtide, entecavir, foscarnet, gangcyclovir, idoxuridine,
indinavir, lopinavir, pleconaril, ribavirin, rimantadine,
ritonavir, saquinavir, trifluridine, vidarabine, and zidovudine,
may be used.
[0239] The Fc variants of the present invention may be combined
with other therapeutic regimens. For example, in one embodiment,
the patient to be treated with an antibody or Fc fusion of the
present invention may also receive radiation therapy. Radiation
therapy can be administered according to protocols commonly
employed in the art and known to the skilled artisan. Such therapy
includes but is not limited to cesium, iridium, iodine, or cobalt
radiation. The radiation therapy may be whole body irradiation, or
may be directed locally to a specific site or tissue in or on the
body, such as the lung, bladder, or prostate. Typically, radiation
therapy is administered in pulses over a period of time from about
1 to 2 weeks. The radiation therapy may, however, be administered
over longer periods of time. For instance, radiation therapy may be
administered to patients having head and neck cancer for about 6 to
about 7 weeks. Optionally, the radiation therapy may be
administered as a single dose or as multiple, sequential doses. The
skilled medical practitioner can determine empirically the
appropriate dose or doses of radiation therapy useful herein. In
accordance with another embodiment of the invention, the Fc variant
of the present invention and one or more other anti-cancer
therapies are employed to treat cancer cells ex vivo. It is
contemplated that such ex vivo treatment may be useful in bone
marrow transplantation and particularly, autologous bone marrow
transplantation. For instance, treatment of cells or tissue(s)
containing cancer cells with Fc variant and one or more other
anti-cancer therapies, such as described above, can be employed to
deplete or substantially deplete the cancer cells prior to
transplantation in a recipient patient.
[0240] Radiation therapy may also comprise treatment with an
isotopically labeled molecule, such as an antibody. Examples of
radioimmunotherapeutics include but Zevalin.TM. (Y-90 labeled
anti-CD20), LymphoCide.TM. (Y-90 labeled anti-CD22) and Bexxar.TM.
(I-131 labeled anti-CD20)
[0241] It is of course contemplated that the Fc variants of the
invention may employ in combination with still other therapeutic
techniques such as surgery or phototherapy.
Clinical Trial Design and Post-Approval Treatment Strategies
[0242] Pharmacogenomic approaches to clinical trials abd therapy
are embodiments of the present invention. A number of the receptors
that may interact with the Fc variants of the present invention are
polymorphic in the human population. For a given patient or
population of patients, the efficacy of the Fc variants of the
present invention may be affected by the presence or absence of
specific polymorphisms in proteins. For example, Fc.gamma.RIIIs is
polymorphic at position 158, which is commonly either V (high
affinity) or F (low affinity). Patients with the V/V homozygous
genotype are observed to have a better clinical response to
treatment with the anti-CD20 antibody Rituxan.RTM. (rituximab)
(Carton et al., 2002, Blood 99:754-758; Weng et al., 2003, J Clin
Oncol 21:3940-3947; Dall'Ozzo et al., 2004, Cancer Res 64:4664-9).
Additional polymorphisms include but are not limited to
Fc.gamma.RIIa R131 or H131, and such polymorphisms are known to
either increase or decrease Fc binding and subsequent biological
activity, depending on the polymorphism. Fc variants of the present
invention may bind preferentially to a particular polymorphic form
of a receptor, for example F158 Fc.gamma.RIIIa, or to bind with
equivalent affinity to all of the polymorphisms at a particular
position in the receptor, for example both the V158 and F158
polymorphisms of Fc.gamma.RIIIa. In a preferred embodiment, Fc
variants of the present invention that provide equivalent binding
to polymorphisms may be used in an antibody to eliminate the
differential efficacy seen in patients with different
polymorphisms. Such a property may give greater consistency in
therapeutic response and reduce non-responding patient populations.
Such variant Fc with indentical binding to receptor polymorphisms
may have increased biological activity, such as ADCC, CDC or
circulating half-life, or alternatively decreased activity, via
modulation of the binding to the relevant Fc receptors. In a
preferred embodiment, Fc variants of the present invention may bind
with higher or lower affinity to one of the polymorphisms of a
receptor, either accentuating the existing difference in binding or
reversing the difference. Such a property may allow creation of
therapeutics particularly tailored for efficacy with a patient
population possessing such polymorphism. For example, a patient
population possessing an Fc.gamma.RIIb polymorphism that binds with
higher affinity to Fc, could receive a drug containing an Fc
variant with reduced binding to such polymorphic form of the
receptor, creating a more efficacious drug.
[0243] In a preferred embodiment, patients are screened for one or
more polymorphisms in order to predict the efficacy of the Fc
variants of the present invention. This information may be used,
for example, to select patients to include or exclude from clinical
trials or, post-approval, to provide guidance to physicians and
patients regarding appropriate dosages and treatment options. For
example, the anti-CD20 antibody rituximab is minimally effective in
patients that are homozygous or heterozygous for F158
Fc.gamma.RIIIa (Carton et al., 2002, Blood 99:754-758; Weng et al.,
2003, J Clin Oncol 21:3940-3947; Dall'Ozzo et al., 2004, Cancer Res
64:4664-9). Such patients may show an improved clinical response to
antibodies comprising an Fc variant of the present invention. In
one embodiment, patients are selected for inclusion in clinical
trials if their genotype indicates that they are likely to respond
significantly better to an antibody of the present invention as
compared to one or more currently used antibody therapeutics. In
another embodiment, appropriate dosages and treatment regimens are
determined using such genotype information. In another embodiment,
patients are selected for inclusion in a clinical trial or for
receipt of therapy post-approval based on their polymorphism
genotype, where such therapy contains an Fc variant engineered to
be specifically efficacious for such population, or alternatively
where such therapy contains an Fc variant that does not show
differential activity to the different forms of the
polymorphism.
[0244] Included in the present invention are diagnostic tests to
identify patients who are likely to show a favorable clinical
response to an Fc variant of the present invention, or who are
likely to exhibit a significantly better response when treated with
an Fc variant of the present invention versus one or more currently
used antibody therapeutics. Any of a number of methods for
determining Fc.gamma.R polymorphisms in humans known in the art may
be used.
[0245] In a preferred embodiment, patients are screened to predict
the efficacy of the Fc polypeptides of the present invention. This
information may be used, for example, to select patients to include
or exclude from clinical trials or, post-approval, to provide
guidance to physicians and patients regarding appropriate dosages
and treatment options. Screening may involve the determination of
the expression level or distribution of the target antigen. For
example, the level of Her2/neu expression is currently used to
select which patients will most favorably respond to trastuzumab
therapy. Screening may also involve determination of genetic
polymorphisms, for example polymorphisms related to Fc.gamma.Rs or
Fc.alpha.Rs. For example, patients who are homozygous or
heterozygous for the F158 polymorphic form of Fc.gamma.RIIIa may
respond clinically more favorably to the Fc polypeptides of the
present invention. Information obtained from patient screening may
be used to select patients for inclusion in clinical trials, to
determine appropriate dosages and treatment regimens, or for other
clinical applications. Included in the present invention are
diagnostic tests to identify patients who are likely to show a
favorable clinical response to an Fc polypeptide of the present
invention, or who are likely to exhibit a significantly better
response when treated with an Fc polypeptide of the present
invention versus one or more currently used biotherapeutics. Any of
a number of methods for determining antigen expression levels,
antigen distribution, and/or genetic polymorphisms in humans known
in the art may be used.
[0246] Furthermore, the present invention comprises prognostic
tests performed on clinical samples such as blood and tissue
samples. Such tests may assay for effector function activity,
including but not limited to opsonization, ADCC, CDC, ADCP, or for
killing, regardless of mechanism, of cancerous or otherwise
pathogenic cells. In a preferred embodiment, ADCC assays, such as
those described herein, are used to predict, for a specific
patient, the efficacy of a given Fc polypeptide of the present
invention. Such information may be used to identify patients for
inclusion or exclusion in clinical trials, or to inform decisions
regarding appropriate dosages and treatment regemins. Such
information may also be used to select a drug that contains a
particular Fc variant that shows superior activity in such an
assay.
EXAMPLES
[0247] Examples are provided below to illustrate the present
invention. These examples are not meant to constrain the present
invention to any particular application or theory of operation.
[0248] For all positions discussed in the present invention,
numbering is according to the EU index or EU numbering scheme
(Kabat et al, 1991, Sequences of Proteins of Immunological
Interest, 5th Ed., United States Public Health Service, National
Institutes of Health, Bethesda), which refers to the numbering of
the EU antibody (Edelman et al., 1969, Proc Natl Acad Sci USA
63:78-85). Those skilled in the art of antibodies will appreciate
that these conventions consist of nonsequential numbering in
specific regions of an immunoglobulin sequence, enabling a
normalized reference to conserved positions in immunoglobulin
families. Accordingly, the positions of any given immunoglobulin as
defined by EU index will not necessarily correspond to its
sequential sequence. FIG. 3 shows the sequential and EU index
numbering schemes for the antibody alemtuzumab in order to
illustrate this principal more clearly. It should also be noted
that polymorphisms have been observed at a number of Fc positions,
including but not limited to Kabat 270, 272, 312, 315, 356, and
358, and thus slight differences between the presented sequence and
sequences in the scientific literature may exist.
[0249] Fc variants and Fc variant libraries were designed using
computational- and sequence-based methods as described in U.S. Ser.
No. 10/672,280 and U.S. Ser. No. 10/822,231. Experimental libraries
were designed in successive rounds of computational and
experimental screening. Design of subsequent Fc libraries
benefitted from feedback from prior libraries, and thus typically
comprised combinations of Fc variants that showed favorable
properties in the previous screen. FIG. 4 shows residues at which
amino acid modifications were made in the Fc variants of the
present invention, mapped onto the human Fc/Fc.gamma.RIIIb
structure. The entire set of Fc variants that were constructed and
experimentally tested is shown in FIG. 41.
Example 1
Molecular Biology and Protein Expression/Purification
[0250] The majority of experimentation on the Fc variants was
carried out in the context of the anti-cancer antibody alemtuzumab
(Campath.RTM., a registered trademark of IIex Pharmaceuticals LP).
Alemtuzumab binds a short linear epitope within its target antigen
CD52 (Hale et al., 1990, Tissue Antigens 35:118-127; Hale, 1995,
Immunotechnology 1:175-187). Alemtuzumab has been chosen as the
primary engineering template because its efficacy is due in part to
its ability to recruit effector cells (Dyer et al., 1989, Blood
73:1431-1439; Friend et al., 1991, Transplant Proc 23:2253-2254;
Hale et al., 1998, Blood 92:4581-4590; Glennie et al., 2000,
Immunol Today 21:403-410), and because production and use of its
antigen in binding assays are relatively straightforward. In order
to evaluate the optimized Fc variants of the present invention in
the context of other antibodies, select Fc variants were evaluated
in the anti-Her2 antibody trastuzumab (Herceptin.RTM.), a
registered trademark of Genentech), the anti-CD20 antibody
rituximab (Rituxan.RTM., a registered trademark of IDEC
Pharmaceuticals Corporation), the anti-EGFR antibody cetuximab
(Erbitux.RTM., a registered trademark of Imclone), and the
anti-CD20 antibody PRO70769 (PCT/US2003/040426, entitled
"Immunoglobulin Variants and Uses Thereof"). The use of
alemtuzumab, trastuzumab, rituximab, cetuximab, and PRO70769 for
screening purposes is not meant to constrain the present invention
to any particular antibody.
[0251] The IgG1 full length light (V.sub.L-C.sub.L) and heavy
(V.sub.H-C.gamma.1-C.gamma.2-C.gamma.3) chain antibody genes for
alemtuzumab (campath-1H, James et al., 1999, J Mol Biol 289:
293-301), trastuzumab (hu4D5-8; Carter et al., 1992, Proc Natl Acad
Sci USA 89:4285-4289; Gerstner et al., 2002, J. Mol. Biol., 321:
851-862), rituximab (C2B8, U.S. Pat. No. 6,399,061), and cetuximab
(C225, PCT US96/09847) were constructed using recursive PCR with
convenient end restriction sites to facilitate subcloning. The
genes were ligated into the mammalian expression vector pcDNA3.1
Zeo (Invitrogen), comprising the full length light kappa (C.kappa.)
and heavy chain IgG1 constant regions. The
V.sub.H-C.gamma.1-C.gamma.2-C.gamma.3 clone in pcDNA3.1 zeo was
used as a template for mutagenesis of the Fc region. Mutations were
introduced into this clone using PCR-based mutagenesis or
quick-change mutagenesis (Stratagene) techniques. Fc variants were
sequenced to confirm the fidelity of the sequence. Plasmids
containing heavy chain gene (V.sub.H-C.gamma.1-C.gamma.2-C.gamma.3)
(wild-type or variants) were co-transfected with plasmid containing
light chain gene (V.sub.L-C.sub.L) into 293T cells. Media were
harvested 5 days after transfection. Expression of immunoglobulin
was monitored by screening the culture supernatant of transfectomas
by western using peroxidase-conjugated goat-anti human IgG (Jackson
lmmunoResearch, catalog # 109-035-088). FIG. 5 shows expression of
wild-type alemtuzumab and variants 1 through 10 in 293T cells.
Antibodies were purified from the supernatant using protein A
affinity chromatography (Pierce, Catalog # 20334. FIG. 6 shows
results of the protein purification for WT alemtuzumab. Antibody Fc
variants showed similar expression and purification results to WT.
Some Fc variants were deglycosylated in order to determine their
solution and functional properties in the absence of carbohydrate.
To obtain deglycosylated antibodies, purified alemtuzumab
antibodies were incubated with peptide-N-glycosidase (PNGase F) at
37.degree. C. for 24 h. FIG. 7 presents an SDS PAGE gel confirming
deglycosylation for several Fc variants and WT alemtuzumab.
[0252] In order to confirm the functional fidelity of alemtuzumab
produced under these conditions, the antigenic CD52 peptide, fused
to GST, was expressed in E. coli BL21 (DE3) under IPTG induction.
Both un-induced and induced samples were run on a SDS PAGE gel, and
transferred to PVDF membrane. For western analysis, either
alemtuzumab from Sotec (final concentration 2.5 ng/ul) or media of
transfected 293T cells (final alemtuzumab concentration about
0.1-0.2 ng/ul) were used as primary antibody, and
peroxidase-conjugated goat-anti human IgG was used as secondary
antibody. FIG. 8 presents these results. The ability to bind target
antigen confirms the structural and functional fidelity of the
expressed alemtuzumab. Fc variants that have the same variable
region as WT alemtuzumab are anticipated to maintain a comparable
binding affinity for antigen.
[0253] The gene encoding the extracellular region of human V158
Fc.gamma.RIIIa was obtained by PCR from a clone obtained from the
Mammalian Gene Collection (MGC:22630). F158 Fc.gamma.RIIIa was
constructed by mutagenesis of the V158 Fc.gamma.RIIIa gene. The
genes encoding the extracellular regions of human Fc.gamma.RI,
human Fc.gamma.RIIa, human Fc.gamma.RIIb, human Fc.gamma.RIIc,
mouse Fc.gamma.RIII, and human FcRn .alpha. chain and
.beta.-microglobulin chain were constructed using recursive PCR.
Fc.gamma.Rs and FcRn .alpha. chain were fused at the C-terminus
with a 6.times. His-tag and a GST-tag. All genes were subcloned
into the pcDNA3.1 zeo vector. For expression, vectors containing
human Fc.gamma.Rs were transfected into 293T cells, FcRn .alpha.
chain and .beta.-microglobulin chain were co-transfected into 293T
cells, and mouse Fc.gamma.RIII was transfected into NIH3T3 cells.
Media containing secreted receptors were harvested 3 days later and
purified using Nickel affinity chromatography. For western
analysis, membrane was probed with an anti-GST antibody. FIG. 9
presents an SDS PAGE gel that shows the results of expression and
purification of human V158 Fc.gamma.RIIIa. Purified human C1q
protein complex was purchased commercially (Quidel Corp., San
Diego).
Example 2
Fc Ligand Binding Assays
[0254] Binding to the human Fc ligands Fc.gamma.RI, Fc.gamma.RIIa,
Fc.gamma.RIIb, Fc.gamma.RIIc, Fc.gamma.RIIIa, C1q, and FcRn was
measured for the designed Fc variants. Binding affinities were
measured using an AlphaScreen.TM. assay (Amplified Luminescent
Proximity Homogeneous Assay (ALPHA), PerkinElmer, Wellesley,
Mass.), a bead-based luminescent proximity assay. Laser excitation
of a donor bead excites oxygen, which if sufficiently close to the
acceptor bead generates a cascade of chemiluminescent events,
ultimately leading to fluorescence emission at 520-620 nm. WT
alemtuzumab antibody was biotinylated by standard methods for
attachment to streptavidin donor beads, and GST-tagged Fc.gamma.Rs
and FcRn were bound to glutathione chelate acceptor beads. For the
C1q binding assay, untagged C1q protein was conjugated with
Digoxygenin (DIG, Roche) using N-hydrosuccinimide (NHS) chemistry
and bound to DIG acceptor beads. For the protein A binding assay,
protein A acceptor beads were purchased directly from PerkinElmer.
The AlphaScreen assay was applied as a competition assay for
screening Fc variants. In the absence of competing Fc variants, WT
antibody and Fc.gamma.R interact and produce a signal at 520-620
nm. Addition of untagged Fc variant competes with the WT
Fc/Fc.gamma.R interaction, reducing fluorescence quantitatively to
enable determination of relative binding affinities. Fc variants
were screened in the context of either alemtuzumab or trastuzumab,
and select Fc variants were also screened in the context of
rituximab and cetuximab.
[0255] FIG. 10 shows AlphaScreen data for binding to human V158
Fc.gamma.RIIa by select Fc variants. The binding data were
normalized to the maximum and minimum luminescence signal for each
particular curve, provided by the baselines at low and high
antibody concentrations respectively. The data were fit to a one
site competition model using nonlinear regression, and these fits
are represented by the curves in the figure. These fits provide the
inhibitory concentration 50% (IC50) (i.e. the concentration
required for 50% inhibition) for each antibody, illustrated by the
dotted lines in FIG. 10, thus enabling the relative binding
affinities of Fc variants to be quantitatively determined. By
dividing the IC50 for each variant by that of WT alemtuzumab, the
fold-enhancement or reduction relative to WT Herceptin (Fold WT)
are obtained. Here, WT alemtuzumab has an IC50 of
(4.63.times.10.sup.-9).times.(2)=9.2 nM, whereas S239D has an IC50
of (3.98.times.10.sup.-10).times.(2)=0.8 nM. Thus S239D alemtuzumab
binds 9.2 nM/0.8 nM=11.64-fold more tightly than WT alemtuzumab to
human V158 Fc.gamma.RIIIa. FIGS. 11a and 11b provide AlphaScreen
data showing additional Fc variants, with substitutions at
positions 239, 264, 272, 274, and 332, that bind more tightly to
Fc.gamma.RIIIa, and thus are candidates for improving the effector
function of Fc polypeptides.
[0256] Fc variants were also screened in parrallel for other Fc
ligands. As discussed, the inhibitory receptor Fc.gamma.RIIb plays
an important role in effector function. Exemplary data for binding
of select Fc variants of the invention to human Fc.gamma.RIIb, as
measured by the AlphaScreen, are provided in FIG. 12. Fc.gamma.RIIa
is an activating receptor that is highly homologous to
Fc.gamma.RIIb. Exemplary data for binding of select Fc variants to
the R131 polymorphic form of human Fc.gamma.RIIa are provided in
FIG. 13. Another important Fc ligand is the neonatal Fc receptor
FcRn. As discussed, this receptor binds to the Fc region between
the C.gamma.2 and C.gamma.3 domains; because binding mediates
endosomal recycling, affinity of Fc for FcRn is a key determinant
of antibody and Fc fusion pharmacokinetics. Exemplary data showing
binding of select Fc variants to FcRn, as measured by the
AlphaScreen, are provided in FIG. 14. The binding site for FcRn on
Fc, between the C.gamma.2 and C.gamma.3 domains, is overlapping
with the binding site for bacterial proteins A and G. Because
protein A is frequently employed for antibody purification, select
variants were tested for binding to this Fc ligand. FIG. 15
provides these AlphaScreen data. Although protein A was not
included in the parrallel screen for all variants, the ability of
the Fc variants to be purified using protein A chromatography (see
Example 1) implies that for the majority of Fc variants the
capacity to bind protein A, and moreover the integrity of the
C.gamma.2-C.gamma.3 hinge region, are unaffected by the Fc
substitutions.
[0257] The data for binding of Fc variants to Fc.gamma.RI,
Fc.gamma.RIIa, Fc.gamma.RIIb, Fc.gamma.RIIc, Fc.gamma.RIIIa, C1q,
and FcRn were analyzed as described above for FIG. 11. The
fold-enhancement or reduction relative to WT for binding of each
variant to each Fc ligand, as measured by the AlphaScreen, are
provided in FIG. 41. The table presents for each variant the
variant number (Variant), the substitution(s) of the variant, the
antibody context (Context), the fold affinity relative to WT (Fold)
and the confidence (Conf) in the fold affinity for binding to each
Fc ligand, and the IIIa:IIb specificity ratio (IIIa:IIb) (see
below). Multiple data sets were acquired for many of the variants,
and all data for a given variant are grouped together. The context
of the antibody indicates which antibodies have been constructed
with the particular Fc variant; a=alemtuzumab, t=trastuzumab,
r=rituximab, c=cetuximab, and p=PRO70769. The data provided were
acquired in the context of the first antibody listed, typically
alemtuzumab, although in some cases trastuzumab. An asterix (*)
indicates that the data for the given Fc ligand was acquired in the
context of trastuzumab. A fold (Fold) above 1 indicates an
enhancement in binding affinity, and a fold below 1 indicates a
reduction in binding affinity relative to the parent antibody for
the given Fc ligand. Confidence values (Conf) correspond to the log
confidence levels, provided from the fits of the data to a
sigmoidal dose response curve. As is known in the art, a lower Conf
value indicates lower error and greater confidence in the Fold
value. The lack of data for a given variant and Fc ligand indicates
either that the fits to the data did not provide a meaningful
value, or that the variant was not tested for that Fc ligand.
[0258] FIG. 41 shows that a number of Fc variants have been
obtained with enhanced affinities and altered specificities for the
various Fc ligands. Some Fc variants of the present invention
provide selective enhancement in binding affinity to different Fc
ligands, whereas other provide selective reduction in binding
affinity to different Fc ligands. By "selective enhancement" as
used herein is meant an improvement in or a greater improvement in
binding affinity of an Fc variant to one or more Fc ligands
relative to one or more other Fc ligands. For example, for a given
variant, the Fold WT for binding to, say Fc.gamma.RIIa, may be
greater than the Fold WT for binding to, say Fc.gamma.RIIb. By
"selective reduction" as used herein is meant a reduction in or a
greater reduction in binding affinity of an Fc variant to one or
more Fc ligands relative to one or more other Fc ligands. For
example, for a given variant, the Fold WT for binding to, say
Fc.gamma.RI, may be lower than the Fold WT for binding to, say
Fc.gamma.RIIb. As an example of such selectivity, G236S provides a
selective enhancement to Fc.gamma.RII's (IIa, IIb, and IIc)
relative to Fc.gamma.RI and Fc.gamma.RIIIa, with a somewhat greater
enhancement to Fc.gamma.RIIa relative to Fc.gamma.RIIb and
Fc.gamma.RIIc. G236A, however, is highly selectively enhanced for
Fc.gamma.RIIa, not only with respect to Fc.gamma.RI and
Fc.gamma.RIIIa, but also over Fc.gamma.RIIb and Fc.gamma.RIIc.
Selective enhancements and reductions are observed for a number of
Fc variants, including but not limited to variants comprising
substitutions at residues L234, L235, G236, S267, H268, R292, E293,
Q295, Y300, S324, A327, L328, A330, and T335. Overall, the data
provided in FIG. 41 show that it is indeed possible to tune the Fc
region for Fc ligand specificity, often by using very subtle
mutational differences, despite the fact that a number of highly
homologous receptors bind to the same Fc.gamma.R binding site. The
present invention provides a number of Fc variants that may be used
to selectively enhance, as well as selectively reduce, affinity of
an Fc polypeptide for certain Fc ligands relative to others.
Collections of Fc variants such as these will not only enable the
generation of antibodies and Fc fusions that have effector function
tailored for the desired outcome, but they also provide a unique
set of reagents with which to experimentally investigate and
characterize effector function biology.
[0259] As discussed, optimal effector function may result from Fc
variants wherein affinity for activating Fc.gamma.Rs is greater
than affinity for the inhibitory Fc.gamma.RIIb. Indeed a number of
Fc variants have been obtained that show differentially enhanced
binding to Fc.gamma.RIIIa over Fc.gamma.RIIb. AlphaScreen data
directly comparing binding to Fc.gamma.RIIIa and Fc.gamma.RIIb for
two Fc variants with this specificity profile, A330L and A330Y, are
shown in FIGS. 16a and 16b. This concept can be defined
quantitatively as the fold-enhancement or -reduction of the
activating Fc.gamma.RIIa (FIG. 41, column 12) divided by the
fold-enhancement or -reduction of the inhibitory Fc.gamma.RIIb
(FIG. 41, column 8), herein referred to as the
"Fc.gamma.RIIIa-fold:Fc.gamma.RIIb-fold ratio" or "IIIa:IIb ratio".
This value is provided in column 18 of FIG. 41 (as IIIa:IIb).
Combination of A330L and A330Y with other variants, for example
A330L/I332E, A330Y/I332, and S239D/A330L/I332E, provide very
favorable IIIa:IIb ratios. FIG. 41 shows that a number of Fc
variants provide a positive, favorable Fc.gamma.RIIIa to
Fc.gamma.RIIb specificity profile, with a IIIa:IIb ratio as high as
86:1.
[0260] Some of the most promising Fc variants of the present
invention for enhancing effector function have both substantial
increases in affinity for Fc.gamma.RIIIa and favorable
Fc.gamma.RIIIa-fold:Fc.gamma.RIIb-fold ratios. These include, for
example, S239D/I332E (Fc.gamma.RIIIa-fold=56-192,
Fc.gamma.RIIIa-fold:Fc.gamma.RIIb-fold=3), S239D/A330Y/I332E
(Fc.gamma.RIIIa-fold=130), S239D/A330L/I332E
(Fc.gamma.RIIIa-fold=139,
Fc.gamma.RIIIa-fold:Fc.gamma.RIIb-fold=18), and S239D/S298A/I332E
(Fc.gamma.RIIIa-fold=295,
Fc.gamma.RIIIa-fold:Fc.gamma.RIIb-fold=48). FIGS. 17a-17c show
AlphaScreen data monitoring binding of these and other Fc variants
in the context of trastuzumab to human V158 Fc.gamma.RIIIa and
human Fc.gamma.RIIb.
[0261] In addition to alemtuzumab and trastuzumab, select Fc
variants were screened in the context of other antibodies in order
to investigate the breadth of their applicability. AlphaScreen data
measuring binding of select Fc variants to human V158
Fc.gamma.RIIIa in the context of rituximab and cetuximab are shown
in FIG. 18 and FIG. 19 respectively. Together with the data shown
previously for alemtuzumab and trastuzumab, the results indicate
consistent binding enhancements regardless of the antibody context,
and thus that the Fc variants of the present invention are broadly
applicable to antibodies and Fc fusions.
[0262] As discussed above, an important parameter of Fc-mediated
effector function is the affinity of Fc for both V158 and F158
polymorphic forms of Fc.gamma.RIIIa. AlphaScreen data comparing
binding of select variants to the two receptor allotypes are shown
in FIG. 20a (V158 Fc.gamma.RIIIa) and FIG. 20b (F158
Fc.gamma.RIIIa). As can be seen, all variants improve binding to
both Fc.gamma.RIIIa allotypes. These data indicate that those Fc
variants of the present invention with enhanced effector function
will be broadly applicable to the entire patient population, and
that enhancement to clinical efficacy will potentially be greatest
for the low responsive patient population who need it most.
[0263] The Fc.gamma.R binding affinities of these Fc variants were
further investigated using Surface Plasmon Resonance (SPR)
(Biacore, Uppsala, Sweden). SPR is a sensitive and extremely
quantitative method that allows for the measurement of binding
affinities of protein-protein interactions, and has been used to
effectively measure Fc/Fc.gamma.R binding (Radaev et al., 2001, J
Biol Chem 276:16478-16483). SPR thus provides an excellent
complementary binding assay to the AlphaScreen assay. His-tagged
V158 Fc.gamma.RIIIa was immobilized to an SPR chip, and WT and Fc
variant alemtuzumab antibodies were flowed over the chip at a range
of concentrations. Binding constants were obtained from fitting the
data using standard curve-fitting methods. Table 3 presents
dissociation constants (Kd) for binding of select Fc variants to
V158 Fc.gamma.RIIIa and F158 Fc.gamma.RIIIa obtained using SPR, and
compares these with IC50s obtained from the AlphaScreen assay. By
dividing the Kd and IC50 for each variant by that of WT
alemtuzumab, the fold-improvements over WT (Fold WT) are obtained.
TABLE-US-00002 TABLE 3 SPR SPR AlphaScreen AlphaScreen V158 F158
V158 F158 Fc.gamma.RIIIa Fc.gamma.RIIIa Fc.gamma.RIIIa
Fc.gamma.RIIIa Kd Fold Kd Fold IC50 Fold IC50 Fold (nM) WT (nM) WT
(nM) WT (nM) WT WT 68 730 6.4 17.2 V264I 64 1.1 550 1.3 4.5 1.4
11.5 1.5 I332E 31 2.2 72 10.1 1.0 6.4 2.5 6.9 V264I/I332E 17 4.0 52
14.0 0.5 12.8 1.1 15.6 S298A 52 1.3 285 2.6 2.9 2.2 12.0 1.4
S298A/E333A/ 39 1.7 156 4.7 2.5 2.6 7.5 2.3 K334A
[0264] The SPR data corroborate the improvements to Fc.gamma.RIIIa
affinity observed by AlphaScreen assay. Table 3 further indicates
the superiority of V264I/I332E and I332E over S298A and
S298A/E333A/K334A; whereas S298A/E333A/K334A improves Fc binding to
V158 and F158 Fc.gamma.RIIIa by 1.7-fold and 4.7-fold respectively,
I332E shows binding enhancements of 2.2-fold and 10.1-fold
respectively, and V264I/I332E shows binding enhancements of
4.0-fold and 14-fold respectively. Also worth noting is that the
affinity of V264I/I332E for F158 Fc.gamma.RIIIa (52 nM) is better
than that of WT for the V158 allotype (68 nM), suggesting that this
Fc variant, as well as those with even greater improvements in
binding, may enable the clinical efficacy of antibodies for the low
responsive patient population to achieve that currently possible
for high responders. The correlation between the SPR and
AlphaScreen binding measurements are shown in FIGS. 21a-21d. FIGS.
21a and 21b show the Kd-IC50 correlations for binding to V158
Fc.gamma.RIIIa and F158 Fc.gamma.RIIIa respectively, and FIGS. 21c
and 21d show the fold-improvement correlations for binding to V158
Fc.gamma.RIIIa and F158 Fc.gamma.RIIIa respectively. The good fits
of these data to straight lines (r.sup.2=0.9, r.sup.2=0.84,
r.sup.2=0.98, and r.sup.2=0.90) support the accuracy the
AlphaScreen measurements, and validate its use for determining the
relative Fc.gamma.R binding affinities of Fc variants.
[0265] SPR data were also acquired for binding of select
trastuzumab Fc variants to human V158 Fc.gamma.RIIIa, F158
Fc.gamma.RIIIa, and Fc.gamma.RIIb. These data are shown in Table 4.
The Fc variants tested show substantial binding enhancements to the
activating receptor Fc.gamma.RIIIa, with over 100-fold tighter
binding observed for interaction of S239D/I332E/S298A with F158
Fc.gamma.RIIa. Furthermore, for the best Fc.gamma.RIIIa binders,
F158 Fc.gamma.RIIIa/Fc.gamma.RIIb ratios of 3-4 are observed.
TABLE-US-00003 TABLE 4 SPR SPR SPR V158 Fc.gamma.RIIIa F158
Fc.gamma.RIIIa Fc.gamma.RIIb Kd Fold Kd Fold IC50 Fold (nM) WT (nM)
WT (nM) WT WT 363.5 503 769 V264I/I332E 76.9 4.7 252 2.0 756 1.0
V264I/I332E/ 113.0 3.2 88 5.7 353 2.2 A330L S239D/I332E/ 8.2 44.3
8.9 56.5 46 16.7 A330L S239D/I332E/ 8.7 41.8 4.9 102.7 32 24.0
S298A S239D/I332E/ 12.7 28.6 6.3 79.8 35 22.0 V264I/A330L
[0266] As discussed, although there is a need for greater effector
function, for some antibody therapeutics, reduced or eliminated
effector function may be desired. Several Fc variants in FIG. 41
substantially reduce or ablate Fc.gamma.R binding, and thus may
find use in antibodies and Fc fusions wherein effector function is
undesirable. AlphaScreen data measuring binding of some exemplary
Fc variants to human V158 Fc.gamma.RIIa are shown in FIGS. 22a and
22b. These Fc variants, as well as their use in combination, may
find use for eliminating effector function when desired, for
example in antibodies and Fc fusions whose mechanism of action
involves blocking or antagonism but not killing of the cells
bearing target antigen. Based on the data provided in FIG. 41,
preferred positions for reducing Fc ligand binding and/or effector
function, that is positions that may be modified to reduce binding
to one or more Fc ligands and/or reduce effector function, include
but are not limited to positions 232, 234, 235, 236, 237, 239, 264,
265, 267, 269, 270, 299, 325, 328, 329, and 330.
Example 3
ADCC of Fc Variants
[0267] In order to determine the effect on effector function,
cell-based ADCC assays were performed on select Fc variants. ADCC
was measured using the DELFIA.RTM. EuTDA-based cytotoxicity assay
(Perkin Elmer, Mass.) with purified human peripheral blood
monocytes (PBMCs) as effector cells. Target cells were loaded with
BATDA at 1.times.10.sup.6 cells/ml, washed 4 times and seeded into
96-well plate at 10,000 cells/well. The target cells were then
opsonized using Fc variant or WT antibodies at the indicated final
concentration. Human PBMCs, isolated from buffy-coat were added at
the indicated fold-excess of target cells and the plate was
incubated at 37.degree. C. for 4 hrs. The co-cultured cells were
centrifuged at 500.times.g, supernatants were transferred to a
separate plate and incubated with Eu solution, and relative
fluorescence units were measured using a Packard Fusion.TM.
.alpha.-FP HT reader (Packard Biosciences, IL). Samples were run in
triplicate to provide error estimates (n=3, +/-S.D.). PBMCs were
allotyped for the V158 or F158 Fc.gamma.RIIIa allotype using
PCR.
[0268] ADCC assays were run on Fc variant and WT alemtuzumab using
DoHH-2 lymphoma target cells. FIG. 23a is a bar graph showing the
ADCC of these proteins at 10 ng/ml antibody. Results show that
alemtuzumab Fc variants I332E, V2641, and I332E/V264I have
substantially enhanced ADCC compared to WT alemtuzumab, with the
relative ADCC enhancements proportional to their binding
improvements to Fc.gamma.RIIIa as indicated by AlphaScreen assay
and SPR. The dose dependence of ADCC on antibody concentration is
shown in FIG. 23b. The binding data were normalized to the minimum
and maximum fluorescence signal for each particular curve, provided
by the baselines at low and high antibody concentrations
respectively. The data were fit to a sigmoidal dose-response model
using nonlinear regression, represented by the curve in the figure.
The fits enable determination of the effective concentration 50%
(EC50) (i.e. the concentration required for 50% effectiveness),
which provides the relative enhancements to ADCC for each Fc
variant. The EC50s for these binding data are analogous to the
IC50s obtained from the AlphaScreen competition data, and
derivation of these values is thus analogous to that described in
Example 2 and FIG. 11. In FIG. 23b, the log(EC50)s, obtained from
the fits to the data, for WT, V264I/I332E, and S239D/I332E
alemtuzumab are 0.99, 0.60, and 0.49 respectively, and therefore
their respective EC50s are 9.9, 4.0, and 3.0. Thus V264I/I332E and
S239E/I332E provide a 2.5-fold and 3.3-fold enhancement
respectively in ADCC over WT alemtuzumab using PBMCs expressing
heterozygous V158/F158 Fc.gamma.RIIIa. These data are summarized in
Table 5 below. TABLE-US-00004 TABLE 5 log(EC50) EC50 (ng/ml) Fold
WT WT 0.99 9.9 V264I/I332E 0.60 4.0 2.5 S239D/I332E 0.49 3.0
3.3
[0269] In order to determine whether these ADCC enhancements are
broadly applicable to antibodies, select Fc variants were evaluated
in the context of trastuzumab and rituximab. ADCC assays were run
on Fc variant and WT trastuzumab using two breast carcinoma target
cell lines BT474 and Sk-Br-3. FIG. 24a shows a bar graph
illustrating ADCC at 1 ng/ml antibody. Results indicate that V264I
and V264I/I332E trastuzumab provide substantially enhanced ADCC
compared to WT trastuzumab, with the relative ADCC enhancements
proportional to their binding improvements to Fc.gamma.RIIIa as
indicated by AlphaScreen assay and SPR. FIGS. 24b and 24c show the
dose dependence of ADCC on antibody concentration for select Fc
variants. The EC50s obtained from the fits of these data and the
relative fold-improvements in ADCC are provided in Table 6 below.
Significant ADCC improvements are observed for I332E trastuzumab
when combined with A330L and A330Y. Furthermore, S239D/A330L/I332E
provides a substantial ADCC enhancement, greater than 300-fold for
PBMCs expressing homozygous F158/F158 Fc.gamma.RIIIa, relative to
WT trastuzumab and S298A/E333A/K334A, consistent with the
Fc.gamma.R binding data observed by the AlphaScreen assay and SPR.
TABLE-US-00005 TABLE 6 log(EC50) EC50 (ng/ml) Fold WT FIG. 24b WT
1.1 11.5 I332E 0.34 2.2 5.2 A330Y/I332E -0.04 0.9 12.8 A330L/I332E
0.04 1.1 10.5 FIG. 24c WT -0.15 0.71 S298A/E333A/K334A -0.72 0.20
3.6 S239D/A330L/I332E -2.65 0.0022 323
[0270] ADCC assays were run on V264I/I332E, WT, and
S298A/D333A/K334A rituximab using WIL2-S lymphoma target cells.
FIG. 25a presents a bar graph showing the ADCC of these proteins at
1 ng/ml antibody. Results indicate that V264I/I332E rituximab
provides substantially enhanced ADCC relative to WT rituximab, as
well as superior ADCC to S298A/D333A/K334A, consistent with the
Fc.gamma.RIIIa binding improvements observed by AlphaScreen assay
and SPR. FIGS. 25b and 25c show the dose dependence of ADCC on
antibody concentration for select Fc variants. The EC50s obtained
from the fits of these data and the relative fold-improvements in
ADCC are provided in Table 7 below. As can be seen
S239D/I332E/A330L rituximab provides greater than 900-fold
enhancement in EC50 over WT for PBMCs expressing homozygous
F158/F158 Fc.gamma.RIIIa. The differences in ADCC enhancements
observed for alemtuzumab, trastuzumab, and rituximab are likely due
to the use of different PBMCs, different antibodies, and different
target cell lines. TABLE-US-00006 TABLE 7 log(EC50) EC50 (ng/ml)
Fold WT FIG. 25b WT 0.23 1.7 S298A/E333A/K334A -0.44 0.37 4.6
V264I/I332E -0.83 0.15 11.3 FIG. 25c WT 0.77 5.9 S239D/I332E/A330L
-2.20 0.0063 937
[0271] Thus far, ADCC data has been normalized such that the lower
and upper baselines of each Fc polypeptide are set to the minimal
and maximal fluorescence signal for that specific Fc polypeptide,
typically being the fluorescence signal at the lowest and highest
antibody concentrations respectively. Although presenting the data
in this matter enables a straightforward visual comparison of the
relative EC50s of different antibodies (hence the reason for
presenting them in this way), important information regarding the
absolute level of effector function achieved by each Fc polypeptide
is lost. FIGS. 26a and 27b present cell-based ADCC data for
trastuzumab and rituximab respectively that have been normalized
according to the absolute minimal lysis for the assay, provided by
the fluorescence signal of target cells in the presence of PBMCs
alone (no antibody), and the absolute maximal lysis for the assay,
provided by the fluorescence signal of target cells in the presence
of Triton X1000. The graphs show that the antibodies differ not
only in their EC50, reflecting their relative potency, but also in
the maximal level of ADCC attainable by the antibodies at
saturating concentrations, reflecting their relative efficacy. Thus
far these two terms, potency and efficacy, have been used loosely
to refer to desired clinical properties. In the current
experimental context, however, they are denoted as specific
quantities, and therefore are here explicitly defined. By "potency"
as used in the current experimental context is meant the EC50 of an
Fc polypeptide. By "efficacv" as used in the current experimental
context is meant the maximal possible effector function of an Fc
polypeptide at saturating levels. In addition to the substantial
enhancements to potency described thus far, FIGS. 26a and 26b show
that the Fc variants of the present invention provide greater than
100% enhancements in efficacy over WT trastuzumab and
rituximab.
Example 4
Cross-Validation of Fc Variants
[0272] Select Fc variants were validated for their Fc.gamma.R
binding and ADCC improvements in the context of two
antibodies--alemtuzumab and trastuzumab. Binding to human V158
Fc.gamma.RIIIa was measured using both AlphaScreen and SPR as
described above. Exemplary AlphaScreen data measuring
Fc.gamma.RIIIa binding are provided in FIG. 27. ADCC was carried
out in the context of trastuzumab using Sk-Br-3 target cells and
LDH detection as described above. Exemplary ADCC data are provided
in FIG. 28. Table 8 provides a summary of the fold Fc.gamma.RIIIa
binding affinities to relative to WT as determined by AlphaScreen
and SPR, and the fold ADCC relative to WT for a series of Fc
variants in the context of alemtuzumab (alem) and trastuzumab
(trast). TABLE-US-00007 TABLE 8 Variant Variant Fold WT V158
Fc.gamma.RIIIa Substitution Number Context AlphaScreen SPR ADCC
G236S 719 trast 2.78 1.34 0.37 G236S 719 alem 6.22 6.69 S239E 43
trast 29.99 4.17 7.6 S239E 43 alem 2.64 3.28 S239D 86 trast 16.9
3.5 6.1 S239D 86 alem 36.56 16.61 K246H 812 trast 17.91 2.67 2
K246H 812 alem 13.58 22.36 K246Y 813 trast 17.44 2.39 1.36 K246Y
813 alem 4.32 7.07 R255Y 818 trast 21.14 2.75 1.6 R255Y 818 alem
0.92 1.41 E258H 820 trast 1.18 0.77 0.76 E258H 820 alem 2.35 5.5
E258Y 821 trast 2.82 1.69 0.92 E258Y 821 alem 0.64 1.77 T260H 824
trast 35.32 2.82 T260H 824 alem 1 1.86 S267E 338 alem 9.33 2.62
H268D 350 trast 45.27 4.76 4.59 H268D 350 alem 10.55 5.66 E272I 237
trast 5.86 1.63 1.38 E272I 237 trast 3.24 1.99 E272R 634 alem 1.38
E272H 636 trast 1.02 0.65 1.28 E272H 636 alem 187.1 383.88 E272P
642 trast 0.005 0.522 0.39 E272P 642 alem 1.46 1.41 E283H 839 trast
0.99 0.71 1.4 E283H 839 alem 2.31 E283L 840 trast 19.88 3.68 5.2
E283L 840 alem 1.36 2.56 V284E 844 trast 2.82 1.26 0.84 V284E 844
alem 1.51 E293R 555 trast 1.15 0.94 0.47 S298D 364 trast 3.48 1.49
0.58 S304T 879 trast 6.33 1.65 1.02 S304T 879 alem 12.85 S324I 267
trast 5.26 1.46 2.21 S324G 608 trast 3.04 1.76 3.23 S324G 608 alem
13.62 14.17 K326E 103 trast 6.12 2.12 2.87 K326E 103 alem 1.86 3.13
A327D 274 trast 2.44 1.31 1.04 I332E 22 trast I332D 62 trast 19
2.57 5 I332D 62 alem 21.65 11.16 E333Y 284 trast 8.24 1.94 2.23
K334I 285 trast 15.24 7.1 1.2 K334T 286 trast 15.73 6.79 3.14 K334F
287 trast 10.46 5.82 1.92
Example 5
ADCC at Varying Target Antigen Expression Levels
[0273] A critical parameter governing the clinical efficacy of
anti-cancer antibodies is the expression level of target antigen on
the surface of tumor cells. Thus a major clinical advantage of Fc
variants that enhance ADCC may be that it enables the targeting of
tumors that express lower levels of antigen. In order to test this
hypothesis, WT and Fc variant trastuzumab antibodies were tested
for their ability to mediate ADCC against different cell lines
expressing varying levels of the Her2/neu target antigen using the
the DELFIA EuTDA method. Four cell lines cell lines expressing
amplified to low levels of Her2/neu receptor were used, including
Sk-Br-3 (1.times.10.sup.6 copies), SkOV3 (.about.1.times.10.sup.5),
OVCAR3(.about.1.times.10.sup.4), and MCF-7 (.about.3.times.10.sup.3
copies) (FIG. 29a). Target cells were loaded with BATDA in batch
for 25 minutes, washed multiple times with medium and seeded at
10,000 cells per well in 96-well plates. Target cells were
opsonized for 15 minutes with various antibodies and concentrations
(final conc. ranging from 100 ng/ml to 0.0316 ng/ml in 1/2 log
steps, including no treatment control). Human PBMCs, isolated from
buffy-coat and allotyped as homozygous F158/F158 Fc.gamma.RIIIa
were then added to opsonized cells at 25-fold excess and
co-cultured at 37.degree. C. for 4 hrs. Thereafter, plates were
centrifuged, supernatants were removed and treated with Eu3+
solution, and relative fluorescence units (correlating to the level
of cell lysis) were measured using a Packard Fusion.TM. .alpha.-FP
HT reader (PerkinElmer, Boston, Mass.). The experiment was carried
out in triplicates. FIG. 29b shows the ADCC data comparing WT and
Fc variant trastuzumab against the four different Her2/neu.sup.+
cell lines. The S239D/I332E and S239D/I332E/A330L variants provide
substantial ADCC enhancements over WT trastuzumab at high,
moderate, and low expression levels of target antigen. This result
suggests that the Fc variants of the present invention may broaden
the therapeutic window of anti-cancer antibodies.
Example 6
ADCC with NK Cells as Effector Cells
[0274] Natural killer (NK) cells are a subpopulation of cells
present in PBMCs that are thought to play a significant role in
ADCC. Select Fc variants were tested in a cell-based ADCC assay in
which natural killer (NK) cells rather than PBMCs were used as
effector cells. In this assay the release of endogenous lactose
dehydrogenase (LDH), rather than EuTDA, was used to monitor cell
lysis. FIG. 30 shows that the Fc variants show substantial ADCC
enhancement when NK cells are used as effector cells. Furthermore,
together with previous assays, the results indicate that the Fc
variants of the present invention show substantial ADCC
enhancements regardless of the type of effector cell or the
detection method used.
Example 7
ADCP of Fc Variants
[0275] Another important Fc.gamma.R-mediated effector function is
ADCP. Phagocytosis of target cancer cells may not only lead to the
immediate destruction of target cells, but because phagocytosis is
a potential mechanism for antigen uptake and processing by antigen
presenting cells, enhanced ADCP may also improve the capacity of
the Fc polypeptide to elicit an adaptive immune response. The
ability of the Fc variants of the present invention to mediate ADCP
was therefore investigated. Monocytes were isolated from
heterozygous V158/F158 Fc.gamma.RIIIa PBMCs using a Percoll
gradient. After one week in culture in the presence of 0.1 ng/ml,
differentiated macrophages were detached with EDTA/PBS--and labeled
with the lipophilic fluorophore, PKH26, according to the
manufacturer's protocol (Sigma, St Louis, Mo.). Sk-Br-3 target
cells were labeled with PKH67 (Sigma, St Louis, Mo.), seeded in a
96-well plate at 20,000 cells per well, and treated with designated
final concentrations of WT or Fc variant trastuzumab. PKH26-labeled
macrophages were then added to the opsonized, labeled Sk-Br-3 cells
at 20,000 cells per well and the cells were co-cultured for 18 hrs
before processing cells for analysis of dual label flow cytometry.
Percent phagocytosis was determined as the number of cells
co-labeled with PKH76 and PKH26 (macrophage+Sk-Br-3) over the total
number of Sk-Br-3 in the population (phagocytosed+non-phagocytosed)
after 10,000 counts. FIG. 31 shows data comparing WT and Fc variant
trastuzumab at various antibody concentrations. The results
indicate that the S239D/I332E/A330L variant provides a significant
enhancement in ADCP over WT trastuzumab.
Example 8
Complement Binding and Activation by Fc Variants
[0276] Complement protein C1q binds to a site on Fc that is
proximal to the Fc.gamma.R binding site, and therefore it was
prudent to determine whether the Fc variants have maintained their
capacity to recruit and activate complement. The AlphaScreen assay
was used to measure binding of select Fc variants to the complement
protein C1q. The assay was carried out with biotinylated WT
alemtuzumab antibody attached to streptavidin donor beads as
described in Example 2, and using C1q coupled directly to acceptor
beads. Binding data of V264I, I332E, S239E, and V264I/I332E
rituximab shown in FIG. 32a indicate that C1q binding is
uncompromised. Cell-based CDC assays were also performed on select
Fc variants to investigate whether Fc variants maintain the
capacity to activate complement. Alamar Blue was used to monitor
lysis of Fc variant and WT rituximab-opsonized WIL2-S lymphoma
cells by human serum complement (Quidel, San Diego, Calif.). The
data in FIG. 32b show that CDC is uncompromised for the Fc variants
S239E, V264I, and V264I/I332E rituximab. In contrast, FIG. 32c
shows that CDC of the Fc variant S239D/I332E/A330L is completely
ablated, whereas the S239D/I332E variant mediates CDC that is
comparable to WT rituximab. These results indicate that protein
engineering can be used to distinguish between different effector
functions. Such control will not only enable the generation of Fc
polypeptides, including antibodies and Fc fusions, with properties
tailored for a desired clinical outcome, but also provide a unique
set of reagents with which to experimentally investigate effector
function biology.
Example 9
Enhanced B Cell Depletion in Macagues
[0277] In order to evaluate the capacity of the Fc variants to
enhance effector function in vivo, a pre-clinical study was carried
out wherein B cell depletion was used to measure antibody
cytotoxicity in cynomogus monkeys (Macaca fascicularis). Three
monkeys per sample were injected intravenously with WT or
S239D/I332E rituximab antibody, with injections given once daily
over days 1-4 in approximate dose ranges of 40 .mu.g/kg (WT
control) or 1, 4, 10, or 40 .mu.g/kg (S239D/I332E and/or WT).
Actual concentrations were determined experimentally. B cell and
natural killer cell levels were monitored from days 5 to 28, and
cell populations were counted using flow cytometry using B cell
markers CD20+ and CD40+, and natural killer cell markers CD3-/CD16+
and CD3-/CD8+.
[0278] FIG. 33a shows the percent of CD20+ B cells remaining in
monkeys dosed with antibodies comprising WT or S239D/I332E
rituximab. The S239D/I332E variant and WT control at the lower
dosage (1.8 and 2.1 ug/kg) show the greatest difference in B cell
counts on day 5. NK cell populations were monitored to evaluate the
impact of the effector function enhancement on this cell type; FIG.
33b shows that the increased CD20+ B cell killing of S239D/I332E
variant does not affect natural kill cell population. The reduction
in B cell level is also dose-dependant, as is shown in FIG. 33c for
day 5.
Example 10
Capacity for Testing Fc Variants in Mice
[0279] Optimization of Fc to nonhuman Fc.gamma.Rs may be useful for
experimentally testing Fc variants in animal models. For example,
when tested in mice (for example nude mice, SCID mice, xenograft
mice, and/or transgenic mice), antibodies and Fc fusions that
comprise Fc variants that are optimized for one or more mouse
Fc.gamma.Rs may provide valuable information with regard to
clinical efficacy, mechanism of action, and the like. In order to
evaluate whether the Fc variants of the present invention may be
useful in such experiments, affinity of select Fc variants for
mouse Fc.gamma.RIII was measured using the AlphaScreen assay. The
AlphaScreen assay was carried out using biotinylated WT alemtuzumab
attached to streptavidin donor beads as described in Example 2, and
GST-tagged mouse Fc.gamma.RIII bound to glutathione chelate
acceptor beads, expressed and purified as described in Example 2.
These binding data are shown in FIG. 34a for Fc variants in the
context of alemtuzumab, and in FIGS. 34b and 34c in the context of
trastuzumab. Results show that some Fc variants that enhance
binding to human Fc.gamma.RIIIa also enhance binding to mouse
Fc.gamma.RIII. The enhancement of mouse effector function by the Fc
variants was investigated by performing the aforementioned
cell-based ADCC assays using mouse rather than human PBMC's. FIG.
35 shows that the S239D/I332E/A330L trastuzumab variant provides
substantial ADCC enhancement over WT in the presence of mouse
immune cells. This result indicates that the Fc variants of the
present invention, or other Fc variants that are optimized for
nonhuman Fc.gamma.Rs, may find use in experiments that use animal
models.
Example 11
Validation of Fc Variants Expressed in CHO Cells
[0280] Whereas the Fc variants of the present invention were
expressed in 293T cells for screening purposes, large scale
production of antibodies is typically carried out by expression in
Chinese Hamster Ovary (CHO) cell lines. In order to evaluate the
properties of CHO-expressed Fc variants, select Fc variants and WT
alemtuzumab were expressed in CHO cells and purified as described
in Example 1. FIG. 36 shows AlphaScreen data comparing binding of
CHO- and 293T-expressed Fc variant and WT alemtuzumab to human V158
Fc.gamma.RIIIa. The results indicate that the Fc variants of the
present invention show comparable Fc.gamma.R binding enhancements
whether expressed in 293T or CHO.
Example 12
Enhancement of Fc Variants in Fucose Minus Strain
[0281] Combinations of the Fc variants of the present invention
with other Fc modifications are contemplated with the goal of
generating novel Fc polypeptides with optimized properties. It may
be beneficial to combine the Fc variants of the present invention
with other Fc modifications, including modifications that alter
effector function or interaction with one or more Fc ligands. Such
combination may provide additive, synergistic, or novel properties
in Fc polypeptides. For example, a number of methods exist for
engineering different glycoforms of Fc that alter effector
function. Engineered glycoforms may be generated by a variety of
methods known in the art, many of these techniques are based on
controlling the level of fucosylated and/or bisecting
oligosaccharides that are covalently attached to the Fc region. One
method for engineering Fc glycoforms is to express the Fc
polypeptide in a cell line that generates altered glycoforms, for
example Lec-13 CHO cells. In order to investigate the properties of
Fc variants combined with engineered glycoforms, WT and V209
(S239D/I332E/A330L) trastuzumab were expressed in Lec-13 CHO cells
and purified as described above. FIG. 37a shows AlphaScreen binding
data comparing the binding to human V158 Fc.gamma.RIIIa by WT and
V209 trastuzumab expressed in 293T, CHO, and Lec-13 cells. The
results show that there is substantial synergy between the
engineered glycoforms produced by this cell line and the Fc
variants of the present invention. The cell-based ADCC assay, shown
in FIG. 37b, supports this result. Together these data indicate
that other Fc modifications, particularly engineered glycoforms,
may be combined with the Fc variants of the present invention to
generate Fc polypeptides, for example antibodies and Fc fusions,
with optimized effector functions.
Example 13
Aglvcosylated Fc Variants
[0282] As discussed, one goal of the current experiments was to
obtain optimized aglycosylated Fc variants. Several Fc variants
provide significant progress towards this goal. Because it is the
site of glycosylation, substitution at N297 results in an
aglycosylated Fc. Whereas all other Fc variants that comprise a
substitution at N297 completely ablate Fc.gamma.R binding,
N297D/I332E has significant binding affinity for Fc.gamma.RIIIa,
shown in FIG. 41 and illustrated in FIG. 38. The exact reason for
this result is uncertain in the absence of a high-resolution
structure for this variant, although the computational screening
predictions suggest that it is potentially due to a combination of
new favorable Fc/Fc.gamma.R interactions and favorable
electrostatic properties. Indeed other electrostatic substitutions
are envisioned for further optimization of aglycosylated Fc. FIG.
41 shows that other aglycosylated Fc variants such as
N297D/A330Y/I332E and S239D/N297D/I332E provide binding
enhancements that bring affinity for Fc.gamma.RIIIa within as much
as 0.4- and 0.8-respectively of glycosylated WT alemtuzumab.
Combinations of these variants with other Fc variants that enhance
Fc.gamma.R binding are contemplated, with the goal of obtaining
aglycosylated Fc variants that bind one or more Fc.gamma.Rs with
affinity that is approximately the same as or even better than
glycosylated parent Fc. Preferred Fc variants for enhancing Fc
ligand binding and/or effector function in an aglycosylated Fc
polypeptide include but are not limited to: N297D, N297D/I332E,
N297D/I332D, S239D/N297D, S239D/N297D/I332E, N297D/A330Y/I332E, and
S239D/N297D/A330Y/I332E. The present invention of course
contemplates combinations of these aglycosylated variants with
other Fc variants described herein which also enhance Fc ligand
binding and/or effector function.
[0283] An additional set of promising Fc variants provide stability
and solubility enhancements in the absence of carbohydrate. Fc
variants that comprise substitutions at positions 241, 243, 262,
and 264, positions that do not mediate Fc.gamma.R binding but do
determine the interface between the carbohydrate and Fc, ablate
Fc.gamma.R binding, presumably because they perturb the
conformation of the carbohydrate. In deglycosylated form, however,
Fc variants F241E/F243R/V262E/V264R, F241E/F243Q/V262T/V264E,
F241R/F243Q/V262T/V264R, and F241E/F243Y/V262T/V264R show stronger
binding to Fc.gamma.RIIIa than in glycosylated form, as shown by
the AlphaScreen data in FIG. 39. This result indicates that these
are key positions for optimization of the structure, stability,
solubility, and function of aglycosylated Fc. Together these
results suggests that protein engineering can be used to restore
the favorable functional and solution properties of antibodies and
Fc fusions in the absence of carbohydrate, and pave the way for
aglycosylated antibodies and Fc fusions with favorable solution
properties and full functionality that comprise substitutions at
these and other Fc positions.
Example 14
Preferred Variants
[0284] Taken together, the data provided in the present invention
indicate that Fc variants that provide optimized Fc.gamma.R binding
properties also provide enhanced effector function. Substitutions
at a number of positions, including but not limited to 236, 239,
246, 246, 249, 255, 258, 260, 264, 267, 268, 272, 274, 281, 283,
304, 324, 326, 327, 330, 332, 333, 334, and 334 provide promising
candidates for improving the effector function and therefore the
clinical properties of Fc polypeptides, including antibodies and Fc
fusions. Because combinations of Fc variants of the present
invention have typically resulted in additive or synergistic
binding improvements, and accordingly additive or synergistic
enhancements in effector function, it is anticipated that as yet
unexplored combinations of the Fc variants provided in FIG. 41 will
also provide favorable results. Preferred Fc variants of the
present invention for enhancing Fc ligand binding and/or effector
function are provided in Table 9. TABLE-US-00008 TABLE 9 G236S
S239D/I332E S239D/K246H/I332E S239D/K246H/T260H/I332E G236A
S239D/G236A S239D/V264I/I332E S239D/K246H/H268D/I332E S239D
S239D/G236S S239D/S267E/I332E S239D/K246H/H268E/I332E S239E
S239D/V264I S239D/H268D/I332E S239D/H268D/S324G/I332E S239N
S239D/H268D S239D/H268E/I332E S239D/H268E/S324G/I332E S239Q
S239D/H268E S239D/S298A/I332E S239D/H268D/K326T/I332E S239T
S239D/S298A S239D/S324G/I332E S239D/H268E/K326T/I332E K246H
S239D/K326E S239D/S324I/I332E S239D/H268D/A330L/I332E K246Y
S239D/A330L S239D/K326T/I332E S239D/H268E/A330L/I332E D249Y
S239D/A330Y S239D/K326E/I332E S239D/H268D/A330Y/I332E R255Y
S239D/A330I S239D/K326D/I332E S239D/H268E/A330Y/I332E E258Y
I332E/V264I S239D/A327D/I332E S239D/S298A/S267E/I332E T260H
I332E/H268D S239D/A330L/I332E S239D/S298A/H268D/I332E V264I
I332E/H268E S239D/A330Y/I332E S239D/S298A/H268E/I332E S267E
I332E/S298A S239D/A330I/I332E S239D/S298A/S324G/I332E H268D
I332E/K326E S239D/K334T/I332E S239D/S298A/S324I/I332E H268E
I332E/A330L S239D/S298A/K326T/I332E E272Y I332E/A330Y
S239D/S298A/K326E/I332E E272I I332E/A330I S239D/S298A/A327D/I332E
E272H I332E/G236A S239D/S298A/A330L/I332E K274E I332E/G236S
S239D/S298A/A330Y/I332E G281D I332D/V264I S239D/K326T/A330Y/I332E
E283L I332D/H268D S239D/K326E/A330Y/I332E E283H I332D/H268E
S239D/K326T/A330L/I332E S304T I332D/S298A S239D/K326E/A330L/I332E
S324G I332D/K326E S324I I332D/A330L K326T I332D/A330Y A327D
I332D/A330I A330Y I332D/G236A A330L I332D/G236S A330I I332D I332E
I332N I332Q E333Y K334T K334F
[0285] This list of preferred Fc variants is not meant to constrain
the present invention. Indeed all combinations of the any of the Fc
variants provided in FIG. 41 are embodiments of the present
invention. Furthermore, combinations of any of the Fc variants of
the present invention with other discovered or undiscovered Fc
variants may also provide favorable properties, and these
combinations are also contemplated as embodiments of the present
invention. Finally, it is anticipated from these results that other
substitutions at positions mutated in present invention may also
provide favorable binding enhancements and specificities, and thus
substitutions at all positions in FIG. 41 are contemplated.
Example 15
Therapeutic Application of Fc Variants
[0286] A number of Fc variants described in the present invention
have significant potential for improving the therapeutic efficacy
of anticancer antibodies. For illustration purposes, a number of Fc
variants of the present invention have been incorporated into the
sequence of the antibody rituximab. The WT rituximab light chain
and heavy chain, described in U.S. Pat. No. 5,736,137, are provided
in FIGS. 40a and 40b. The improved anti-CD20 antibody sequences are
provided in FIG. 40c. The improved anti-CD20 antibody sequences
comprise at least non-WT amino acid selected from the group
consisting of X.sub.1, X.sub.2, X.sub.3, X.sub.4, X.sub.5, X.sub.6,
X.sub.7, X.sub.8, and X.sub.9. These improved anti-CD20 antibody
sequences may also comprise a substitution Z.sub.1 and/or Z.sub.2.
The use of rituximab here is solely an example, and is not meant to
constrain application of the Fc variants to this antibody or any
other particular Fc polypeptide.
[0287] Table 10 depicts the positions of human Fc, the wild type
residue, and the variants that are included in particular
embodiments of the invention. Table 10 is based on IgG1, although
as will be appreciated by those in the art, the same thing can be
done to any Ig, particularly IgG2, IgG3 and IgG4. TABLE-US-00009
TABLE 10 Position Wild Type (Human) Variants including wild type
118-220 FX see FIG. 3a Vb(221) D D, K, Y Vb(222) K K, E, Y Vb(223)
T T, E, K Vb(224) H H, E, Y Vb(225) T T, E, K, W Fx(226) WT C
Vb(227) P P, E, G, K, Y Vb(228) P P, E, G, K, Y Fx(229) (OPEN)(WT)
C Vb(230) P P, A, E, G, Y Vb(231) A A, E, G, K, P, Y Vb(232) P P,
E, G, K, Y Vb(233) E A, D, F, G, H, I, K, L, M, N, Q, R, S, T, V,
W, Y Vb(234) L L, A, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V,
W, Y Vb(235) L L, A, D, E, F, G, H, I, K, M, N, P, Q, R, S, T, V,
W, Y Vb(236) G G, A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V,
W, Y Vb(237) G G, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y
Vb(238) P P, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, Y
Vb(239) S S, D, E, F, G, H, I, K, L, M, N, P, Q, R, T, V, W, Y
Vb(240) V V, A, I, M, T Vb(241) F F, D, E, L, R, S, W, Y Fx(242) WT
L Vb(243) F F, E, H, L, Q, R, W, Y Vb(244) P P, H Vb(245) P P, A
Vb(246) K K, D, E, H, Y Vb(247) P P, G, V Vb(248) WT K Vb(249) D D,
H, Q, Y Fx(250-254) WT -(T-L-M-I-S)- Vb(255) R R, E, Y Fx(256-257)
WT -(T-P)- Vb(258) E E, H, S, Y Fx(259) WT V Vb(260) T T, D, E, H,
Y Fx(261) WT C Vb(262) V V, A, E, F, I, T Vb(263) V V, A, I, M, T
Vb(264) V V, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, W, Y
Vb(265) D D, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y Vb(266)
V V, A, I, M, T Vb(267) S S, D, E, F, H, I, K, L, M, N, P, Q, R, T,
V, W, Y Vb(268) H H, D, E, F, G, I, K, L, M, N, P, Q, R, T, V, W, Y
Vb(269) E E, F, G, H, I, K, L, M, N, P, R, S, T, V, W, Y Vb(270) D
D, F, G, H, I, L, M, P, Q, R, S, T, W, Y Vb(271) A A, D, E, F, G,
H, I, K, L, M, N, Q, R, S, T, V, W, Y Vb(272) E E, D, F, G, H, I,
K, L, M, P, R, S, T, V, W, Y Vb(273) V V, I Vb(274) K K, D, E, F,
G, H, L, M, N, P, R, T, V, W, Y Vb(275) F F, L, W Vb(276) N N, D,
E, F, G, H, I, L, M, P, R, S, T, V, W, Y Fx(277) WT W Vb(278) Y Y,
D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W Fx(279) WT V Vb(280)
D D, G, K, L, P, W Vb(281) G G, D, E, K, N, P, Q, Y Vb(282) V V, E,
G, K, P, Y Vb(283) E E, G, H, K, L, P, R, Y Vb(284) V V, D, E, L,
N, Q, T, Y Vb(285) H H, D, E, K, Q, W, Y Vb(286) N N, E, G, P, Y
Fx(287) WT A Vb(288) K K, D, E, Y Fx(289) WT T Vb(290) K K, D, H,
L, N, W Vb(291) P P, D, E, G, H, I, Q, T Vb(292) R R, D, E, T, Y
Vb(293) E E, F, G, H, I, L, M, N, P, R, S, T, V, W, Y Vb(294) E E,
F, G, H, I, K, L, M, P, R, S, T, V, W, Y Vb(295) Q Q, D, E, F, G,
H, I, M, N, P, R, S, T, V, W, Y Vb(296) Y Y, A, D, E, G, H, I, K,
L, M, N, Q, R, S, T, V Vb(297) N N, D, E, F, G, H, I, K, L, M, P,
Q, R, S, T, V, W, Y Vb(298) S S, D, E, F, H, I, K, M, N, Q, R, T,
W, Y Vb(299) T T, A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, V,
W, Y Vb(300) Y Y, A, D, E, G, H, K, M, N, P, Q, R, S, T, V, W
Vb(301) R R, D, E, H, Y Vb(302) V V, I Vb(303) V V, D, E, Y Vb(304)
S S, D, H, L, N, T Vb(305) V V, E, T, Y Fx(306-312) WT
-(L-T-V-L-H-Q-D)-* Vb(313) W W, F Fx(314-316) WT -(L-N-G)- Vb(317)
K K, E, Q Vb(318) E E, H, L, Q, R, Y Fx(319) WT Y Vb(320) K K, D,
F, G, H, I, L, N, P, S, T, V, W, Y Fx(321) WT C Vb(322) K K, D, F,
G, H, I, P, S, T, V, W, Y Vb(323) V V, I Vb(324) S S, D, F, G, H,
I, L, M, P, R, T, V, W, Y Vb(325) N N, A, D, E, F, G, H, I, K, L,
M, P, Q, R, S, T, V, W, Y Vb(326) K K, I, L, P, T Vb(327) A A, D,
E, F, H, I, K, L, M, N, P, R, S, T, V, W, Y Vb(328) L L, A, D, E,
F, G, H, I, K, M, N, P, Q, R, S, T, V, W, Y Vb(329) P P, D, E, F,
G, H, I, K, L, M, N, Q, R, S, T, V, W, Y Vb(330) A A, E, F, G, H,
I, L, M, N, P, R, S, T, V, W, Y Vb(331) P P, D, F, H, I, L, M, Q,
R, T, V, W, Y Vb(332) I I, A, D, E, F, H, K, L, M, N, P, Q, R, S,
T, V, W, Y Vb(333) E E, F, H, I, L, M, N, P, T, Y Vb(334) K K, F,
I, L, P, T Vb(335) T T, D, F, G, H, I, L, M, N, P, R, S, V, W, Y
Vb(336) I I, E, K, Y Vb(337) S S, E, H, N
[0288] All references are herein expressly incorporated by
reference.
[0289] Whereas particular embodiments of the invention have been
described above for purposes of illustration, it will be
appreciated by those skilled in the art that numerous variations of
the details may be made without departing from the invention as
described in the appended claims.
Sequence CWU 1
1
15 1 330 PRT Homo sapiens 1 Ala Ser Thr Lys Gly Pro Ser Val Phe Pro
Leu Ala Pro Ser Ser Lys 1 5 10 15 Ser Thr Ser Gly Gly Thr Ala Ala
Leu Gly Cys Leu Val Lys Asp Tyr 20 25 30 Phe Pro Glu Pro Val Thr
Val Ser Trp Asn Ser Gly Ala Leu Thr Ser 35 40 45 Gly Val His Thr
Phe Pro Ala Val Leu Gln Ser Ser Gly Leu Tyr Ser 50 55 60 Leu Ser
Ser Val Val Thr Val Pro Ser Ser Ser Leu Gly Thr Gln Thr 65 70 75 80
Tyr Ile Cys Asn Val Asn His Lys Pro Ser Asn Thr Lys Val Asp Lys 85
90 95 Lys Val Glu Pro Lys Ser Cys Asp Lys Thr His Thr Cys Pro Pro
Cys 100 105 110 Pro Ala Pro Glu Leu Leu Gly Gly Pro Ser Val Phe Leu
Phe Pro Pro 115 120 125 Lys Pro Lys Asp Thr Leu Met Ile Ser Arg Thr
Pro Glu Val Thr Cys 130 135 140 Val Val Val Asp Val Ser His Glu Asp
Pro Glu Val Lys Phe Asn Trp 145 150 155 160 Tyr Val Asp Gly Val Glu
Val His Asn Ala Lys Thr Lys Pro Arg Glu 165 170 175 Glu Gln Tyr Asn
Ser Thr Tyr Arg Val Val Ser Val Leu Thr Val Leu 180 185 190 His Gln
Asp Trp Leu Asn Gly Lys Glu Tyr Lys Cys Lys Val Ser Asn 195 200 205
Lys Ala Leu Pro Ala Pro Ile Glu Lys Thr Ile Ser Lys Ala Lys Gly 210
215 220 Gln Pro Arg Glu Pro Gln Val Tyr Thr Leu Pro Pro Ser Arg Asp
Glu 225 230 235 240 Leu Thr Lys Asn Gln Val Ser Leu Thr Cys Leu Val
Lys Gly Phe Tyr 245 250 255 Pro Ser Asp Ile Ala Val Glu Trp Glu Ser
Asn Gly Gln Pro Glu Asn 260 265 270 Asn Tyr Lys Thr Thr Pro Pro Val
Leu Asp Ser Asp Gly Ser Phe Phe 275 280 285 Leu Tyr Ser Lys Leu Thr
Val Asp Lys Ser Arg Trp Gln Gln Gly Asn 290 295 300 Val Phe Ser Cys
Ser Val Met His Glu Ala Leu His Asn His Tyr Thr 305 310 315 320 Gln
Lys Ser Leu Ser Leu Ser Pro Gly Lys 325 330 2 326 PRT Homo sapiens
2 Ala Ser Thr Lys Gly Pro Ser Val Phe Pro Leu Ala Pro Cys Ser Arg 1
5 10 15 Ser Thr Ser Glu Ser Thr Ala Ala Leu Gly Cys Leu Val Lys Asp
Tyr 20 25 30 Phe Pro Glu Pro Val Thr Val Ser Trp Asn Ser Gly Ala
Leu Thr Ser 35 40 45 Gly Val His Thr Phe Pro Ala Val Leu Gln Ser
Ser Gly Leu Tyr Ser 50 55 60 Leu Ser Ser Val Val Thr Val Pro Ser
Ser Asn Phe Gly Thr Gln Thr 65 70 75 80 Tyr Thr Cys Asn Val Asp His
Lys Pro Ser Asn Thr Lys Val Asp Lys 85 90 95 Thr Val Glu Arg Lys
Cys Cys Val Glu Cys Pro Pro Cys Pro Ala Pro 100 105 110 Pro Val Ala
Gly Pro Ser Val Phe Leu Phe Pro Pro Lys Pro Lys Asp 115 120 125 Thr
Leu Met Ile Ser Arg Thr Pro Glu Val Thr Cys Val Val Val Asp 130 135
140 Val Ser His Glu Asp Pro Glu Val Gln Phe Asn Trp Tyr Val Asp Gly
145 150 155 160 Val Glu Val His Asn Ala Lys Thr Lys Pro Arg Glu Glu
Gln Phe Asn 165 170 175 Ser Thr Phe Arg Val Val Ser Val Leu Thr Val
Val His Gln Asp Trp 180 185 190 Leu Asn Gly Lys Glu Tyr Lys Cys Lys
Val Ser Asn Lys Gly Leu Pro 195 200 205 Ala Pro Ile Glu Lys Thr Ile
Ser Lys Thr Lys Gly Gln Pro Arg Glu 210 215 220 Pro Gln Val Tyr Thr
Leu Pro Pro Ser Arg Glu Glu Met Thr Lys Asn 225 230 235 240 Gln Val
Ser Leu Thr Cys Leu Val Lys Gly Phe Tyr Pro Ser Asp Ile 245 250 255
Ala Val Glu Trp Glu Ser Asn Gly Gln Pro Glu Asn Asn Tyr Lys Thr 260
265 270 Thr Pro Pro Met Leu Asp Ser Asp Gly Ser Phe Phe Leu Tyr Ser
Lys 275 280 285 Leu Thr Val Asp Lys Ser Arg Trp Gln Gln Gly Asn Val
Phe Ser Cys 290 295 300 Ser Val Met His Glu Ala Leu His Asn His Tyr
Thr Gln Lys Ser Leu 305 310 315 320 Ser Leu Ser Pro Gly Lys 325 3
377 PRT Homo sapiens 3 Ala Ser Thr Lys Gly Pro Ser Val Phe Pro Leu
Ala Pro Cys Ser Arg 1 5 10 15 Ser Thr Ser Gly Gly Thr Ala Ala Leu
Gly Cys Leu Val Lys Asp Tyr 20 25 30 Phe Pro Glu Pro Val Thr Val
Ser Trp Asn Ser Gly Ala Leu Thr Ser 35 40 45 Gly Val His Thr Phe
Pro Ala Val Leu Gln Ser Ser Gly Leu Tyr Ser 50 55 60 Leu Ser Ser
Val Val Thr Val Pro Ser Ser Ser Leu Gly Thr Gln Thr 65 70 75 80 Tyr
Thr Cys Asn Val Asn His Lys Pro Ser Asn Thr Lys Val Asp Lys 85 90
95 Arg Val Glu Leu Lys Thr Pro Leu Gly Asp Thr Thr His Thr Cys Pro
100 105 110 Arg Cys Pro Glu Pro Lys Ser Cys Asp Thr Pro Pro Pro Cys
Pro Arg 115 120 125 Cys Pro Glu Pro Lys Ser Cys Asp Thr Pro Pro Pro
Cys Pro Arg Cys 130 135 140 Pro Glu Pro Lys Ser Cys Asp Thr Pro Pro
Pro Cys Pro Arg Cys Pro 145 150 155 160 Ala Pro Glu Leu Leu Gly Gly
Pro Ser Val Phe Leu Phe Pro Pro Lys 165 170 175 Pro Lys Asp Thr Leu
Met Ile Ser Arg Thr Pro Glu Val Thr Cys Val 180 185 190 Val Val Asp
Val Ser His Glu Asp Pro Glu Val Gln Phe Lys Trp Tyr 195 200 205 Val
Asp Gly Val Glu Val His Asn Ala Lys Thr Lys Pro Arg Glu Glu 210 215
220 Gln Tyr Asn Ser Thr Phe Arg Val Val Ser Val Leu Thr Val Leu His
225 230 235 240 Gln Asp Trp Leu Asn Gly Lys Glu Tyr Lys Cys Lys Val
Ser Asn Lys 245 250 255 Ala Leu Pro Ala Pro Ile Glu Lys Thr Ile Ser
Lys Thr Lys Gly Gln 260 265 270 Pro Arg Glu Pro Gln Val Tyr Thr Leu
Pro Pro Ser Arg Glu Glu Met 275 280 285 Thr Lys Asn Gln Val Ser Leu
Thr Cys Leu Val Lys Gly Phe Tyr Pro 290 295 300 Ser Asp Ile Ala Val
Glu Trp Glu Ser Ser Gly Gln Pro Glu Asn Asn 305 310 315 320 Tyr Asn
Thr Thr Pro Pro Met Leu Asp Ser Asp Gly Ser Phe Phe Leu 325 330 335
Tyr Ser Lys Leu Thr Val Asp Lys Ser Arg Trp Gln Gln Gly Asn Ile 340
345 350 Phe Ser Cys Ser Val Met His Glu Ala Leu His Asn Arg Phe Thr
Gln 355 360 365 Lys Ser Leu Ser Leu Ser Pro Gly Lys 370 375 4 327
PRT Homo sapiens 4 Ala Ser Thr Lys Gly Pro Ser Val Phe Pro Leu Ala
Pro Cys Ser Arg 1 5 10 15 Ser Thr Ser Glu Ser Thr Ala Ala Leu Gly
Cys Leu Val Lys Asp Tyr 20 25 30 Phe Pro Glu Pro Val Thr Val Ser
Trp Asn Ser Gly Ala Leu Thr Ser 35 40 45 Gly Val His Thr Phe Pro
Ala Val Leu Gln Ser Ser Gly Leu Tyr Ser 50 55 60 Leu Ser Ser Val
Val Thr Val Pro Ser Ser Ser Leu Gly Thr Lys Thr 65 70 75 80 Tyr Thr
Cys Asn Val Asp His Lys Pro Ser Asn Thr Lys Val Asp Lys 85 90 95
Arg Val Glu Ser Lys Tyr Gly Pro Pro Cys Pro Ser Cys Pro Ala Pro 100
105 110 Glu Phe Leu Gly Gly Pro Ser Val Phe Leu Phe Pro Pro Lys Pro
Lys 115 120 125 Asp Thr Leu Met Ile Ser Arg Thr Pro Glu Val Thr Cys
Val Val Val 130 135 140 Asp Val Ser Gln Glu Asp Pro Glu Val Gln Phe
Asn Trp Tyr Val Asp 145 150 155 160 Gly Val Glu Val His Asn Ala Lys
Thr Lys Pro Arg Glu Glu Gln Phe 165 170 175 Asn Ser Thr Tyr Arg Val
Val Ser Val Leu Thr Val Leu His Gln Asp 180 185 190 Trp Leu Asn Gly
Lys Glu Tyr Lys Cys Lys Val Ser Asn Lys Gly Leu 195 200 205 Pro Ser
Ser Ile Glu Lys Thr Ile Ser Lys Ala Lys Gly Gln Pro Arg 210 215 220
Glu Pro Gln Val Tyr Thr Leu Pro Pro Ser Gln Glu Glu Met Thr Lys 225
230 235 240 Asn Gln Val Ser Leu Thr Cys Leu Val Lys Gly Phe Tyr Pro
Ser Asp 245 250 255 Ile Ala Val Glu Trp Glu Ser Asn Gly Gln Pro Glu
Asn Asn Tyr Lys 260 265 270 Thr Thr Pro Pro Val Leu Asp Ser Asp Gly
Ser Phe Phe Leu Tyr Ser 275 280 285 Arg Leu Thr Val Asp Lys Ser Arg
Trp Gln Glu Gly Asn Val Phe Ser 290 295 300 Cys Ser Val Met His Glu
Ala Leu His Asn His Tyr Thr Gln Lys Ser 305 310 315 320 Leu Ser Leu
Ser Leu Gly Lys 325 5 451 PRT Artificial Synthetic misc_feature
(243)..(243) Xaa can be Serine, Aspartic Acid, Glutamic Acid,
Asparagine, Glutamine or Threonine misc_feature (244)..(244) Xaa
can be Valine, Isoleucine or Methionine misc_feature (268)..(268)
Xaa can be Valine, Isoleucine, Threonine or Tyrosine misc_feature
(272)..(272) Xaa can be Histidine, Aspartic Acid or Glutamic Acid
misc_feature (276)..(276) Xaa can be Glutamic Acid or Tyrosine
misc_feature (278)..(278) Xaa can be Lysine or Glutamic Acid
misc_feature (301)..(301) Xaa can be Asparagine or Aspartic Acid
misc_feature (302)..(302) Xaa can be Serine, Alanine or Aspartic
Acid misc_feature (330)..(330) Xaa can be Lysine, Glutamic Acid or
Threonine misc_feature (334)..(334) Xaa can be Alanine, Tyrosine,
Leucine or Isoleucine misc_feature (336)..(336) Xaa can be
Isoleucine, Aspartic Acid, Glutamic Acid, Asparagine or Glutamine 5
Gln Val Gln Leu Gln Gln Pro Gly Ala Glu Leu Val Lys Pro Gly Ala 1 5
10 15 Ser Val Lys Met Ser Cys Lys Ala Ser Gly Tyr Thr Phe Thr Ser
Tyr 20 25 30 Asn Met His Trp Val Lys Gln Thr Pro Gly Arg Gly Leu
Glu Trp Ile 35 40 45 Gly Ala Ile Tyr Pro Gly Asn Gly Asp Thr Ser
Tyr Asn Gln Lys Phe 50 55 60 Lys Gly Lys Ala Thr Leu Thr Ala Asp
Lys Ser Ser Ser Thr Ala Tyr 65 70 75 80 Met Gln Leu Ser Ser Leu Thr
Ser Glu Asp Ser Ala Val Tyr Tyr Cys 85 90 95 Ala Arg Ser Thr Tyr
Tyr Gly Gly Asp Trp Tyr Phe Asn Val Trp Gly 100 105 110 Ala Gly Thr
Thr Val Thr Val Ser Ala Ala Ser Thr Lys Gly Pro Ser 115 120 125 Val
Phe Pro Leu Ala Pro Ser Ser Lys Ser Thr Ser Gly Gly Thr Ala 130 135
140 Ala Leu Gly Cys Leu Val Lys Asp Tyr Phe Pro Glu Pro Val Thr Val
145 150 155 160 Ser Trp Asn Ser Gly Ala Leu Thr Ser Gly Val His Thr
Phe Pro Ala 165 170 175 Val Leu Gln Ser Ser Gly Leu Tyr Ser Leu Ser
Ser Val Val Thr Val 180 185 190 Pro Ser Ser Ser Leu Gly Thr Gln Thr
Tyr Ile Cys Asn Val Asn His 195 200 205 Lys Pro Ser Asn Thr Lys Val
Asp Lys Lys Ala Glu Pro Lys Ser Cys 210 215 220 Asp Lys Thr His Thr
Cys Pro Pro Cys Pro Ala Pro Glu Leu Leu Gly 225 230 235 240 Gly Pro
Xaa Xaa Phe Leu Phe Pro Pro Lys Pro Lys Asp Thr Leu Met 245 250 255
Ile Ser Arg Thr Pro Glu Val Thr Cys Val Val Xaa Asp Val Ser Xaa 260
265 270 Glu Asp Pro Xaa Val Xaa Phe Asn Trp Tyr Val Asp Gly Val Glu
Val 275 280 285 His Asn Ala Lys Thr Lys Pro Arg Glu Glu Gln Tyr Xaa
Xaa Thr Tyr 290 295 300 Arg Val Val Ser Val Leu Thr Val Leu His Gln
Asp Trp Leu Asn Gly 305 310 315 320 Lys Glu Tyr Lys Cys Lys Val Ser
Asn Xaa Ala Leu Pro Xaa Pro Xaa 325 330 335 Glu Lys Thr Ile Ser Lys
Ala Lys Gly Gln Pro Arg Glu Pro Gln Val 340 345 350 Tyr Thr Leu Pro
Pro Ser Arg Asp Glu Leu Thr Lys Asn Gln Val Ser 355 360 365 Leu Thr
Cys Leu Val Lys Gly Phe Tyr Pro Ser Asp Ile Ala Val Glu 370 375 380
Trp Glu Ser Asn Gly Gln Pro Glu Asn Asn Tyr Lys Thr Thr Pro Pro 385
390 395 400 Val Leu Asp Ser Asp Gly Ser Phe Phe Leu Tyr Ser Lys Leu
Thr Val 405 410 415 Asp Lys Ser Arg Trp Gln Gln Gly Asn Val Phe Ser
Cys Ser Val Met 420 425 430 His Glu Ala Leu His Asn His Tyr Thr Gln
Lys Ser Leu Ser Leu Ser 435 440 445 Pro Gly Lys 450 6 213 PRT Homo
sapiens 6 Gln Ile Val Leu Ser Gln Ser Pro Ala Ile Leu Ser Ala Ser
Pro Gly 1 5 10 15 Glu Lys Val Thr Met Thr Cys Arg Ala Ser Ser Ser
Val Ser Tyr Ile 20 25 30 His Trp Phe Gln Gln Lys Pro Gly Ser Ser
Pro Lys Pro Trp Ile Tyr 35 40 45 Ala Thr Ser Asn Leu Ala Ser Gly
Val Pro Val Arg Phe Ser Gly Ser 50 55 60 Gly Ser Gly Thr Ser Tyr
Ser Leu Thr Ile Ser Arg Val Glu Ala Glu 65 70 75 80 Asp Ala Ala Thr
Tyr Tyr Cys Gln Gln Trp Thr Ser Asn Pro Pro Thr 85 90 95 Phe Gly
Gly Gly Thr Lys Leu Glu Ile Lys Arg Thr Val Ala Ala Pro 100 105 110
Ser Val Phe Ile Phe Pro Pro Ser Asp Glu Gln Leu Lys Ser Gly Thr 115
120 125 Ala Ser Val Val Cys Leu Leu Asn Asn Phe Tyr Pro Arg Glu Ala
Lys 130 135 140 Val Gln Trp Lys Val Asp Asn Ala Leu Gln Ser Gly Asn
Ser Gln Glu 145 150 155 160 Ser Val Thr Glu Gln Asp Ser Lys Asp Ser
Thr Tyr Ser Leu Ser Ser 165 170 175 Thr Leu Thr Leu Ser Lys Ala Asp
Tyr Glu Lys His Lys Val Tyr Ala 180 185 190 Cys Glu Val Thr His Gln
Gly Leu Ser Ser Pro Val Thr Lys Ser Phe 195 200 205 Asn Arg Gly Glu
Cys 210 7 451 PRT Homo sapiens 7 Gln Val Gln Leu Gln Gln Pro Gly
Ala Glu Leu Val Lys Pro Gly Ala 1 5 10 15 Ser Val Lys Met Ser Cys
Lys Ala Ser Gly Tyr Thr Phe Thr Ser Tyr 20 25 30 Asn Met His Trp
Val Lys Gln Thr Pro Gly Arg Gly Leu Glu Trp Ile 35 40 45 Gly Ala
Ile Tyr Pro Gly Asn Gly Asp Thr Ser Tyr Asn Gln Lys Phe 50 55 60
Lys Gly Lys Ala Thr Leu Thr Ala Asp Lys Ser Ser Ser Thr Ala Tyr 65
70 75 80 Met Gln Leu Ser Ser Leu Thr Ser Glu Asp Ser Ala Val Tyr
Tyr Cys 85 90 95 Ala Arg Ser Thr Tyr Tyr Gly Gly Asp Trp Tyr Phe
Asn Val Trp Gly 100 105 110 Ala Gly Thr Thr Val Thr Val Ser Ala Ala
Ser Thr Lys Gly Pro Ser 115 120 125 Val Phe Pro Leu Ala Pro Ser Ser
Lys Ser Thr Ser Gly Gly Thr Ala 130 135 140 Ala Leu Gly Cys Leu Val
Lys Asp Tyr Phe Pro Glu Pro Val Thr Val 145 150 155 160 Ser Trp Asn
Ser Gly Ala Leu Thr Ser Gly Val His Thr Phe Pro Ala 165 170 175 Val
Leu Gln Ser Ser Gly Leu Tyr Ser Leu Ser Ser Val Val Thr Val 180 185
190 Pro Ser Ser Ser Leu Gly Thr Gln Thr Tyr Ile Cys Asn Val Asn His
195 200 205 Lys Pro Ser Asn Thr Lys Val Asp Lys Lys Ala Glu Pro Lys
Ser Cys 210 215 220 Asp Lys Thr His Thr Cys Pro Pro Cys Pro Ala Pro
Glu Leu Leu Gly 225 230 235 240 Gly Pro Ser Val Phe Leu Phe Pro Pro
Lys Pro Lys Asp Thr Leu Met 245 250 255 Ile Ser Arg Thr Pro Glu Val
Thr Cys Val Val Val Asp Val Ser His 260 265 270 Glu Asp Pro Glu Val
Lys Phe Asn Trp Tyr Val Asp Gly Val
Glu Val 275 280 285 His Asn Ala Lys Thr Lys Pro Arg Glu Glu Gln Tyr
Asn Ser Thr Tyr 290 295 300 Arg Val Val Ser Val Leu Thr Val Leu His
Gln Asp Trp Leu Asn Gly 305 310 315 320 Lys Glu Tyr Lys Cys Lys Val
Ser Asn Lys Ala Leu Pro Ala Pro Ile 325 330 335 Glu Lys Thr Ile Ser
Lys Ala Lys Gly Gln Pro Arg Glu Pro Gln Val 340 345 350 Tyr Thr Leu
Pro Pro Ser Arg Asp Glu Leu Thr Lys Asn Gln Val Ser 355 360 365 Leu
Thr Cys Leu Val Lys Gly Phe Tyr Pro Ser Asp Ile Ala Val Glu 370 375
380 Trp Glu Ser Asn Gly Gln Pro Glu Asn Asn Tyr Lys Thr Thr Pro Pro
385 390 395 400 Val Leu Asp Ser Asp Gly Ser Phe Phe Leu Tyr Ser Lys
Leu Thr Val 405 410 415 Asp Lys Ser Arg Trp Gln Gln Gly Asn Val Phe
Ser Cys Ser Val Met 420 425 430 His Glu Ala Leu His Asn His Tyr Thr
Gln Lys Ser Leu Ser Leu Ser 435 440 445 Pro Gly Lys 450 8 117 PRT
Artificial Synthetic misc_feature (1)..(1) Xaa can be Aspartic
Acid, Lysine or Tyrosine misc_feature (2)..(2) Xaa can be Lysine,
Glutamic Acid or Tyrosine misc_feature (3)..(3) Xaa can be
Threonine, Glutamic Acid or Lysine misc_feature (4)..(4) Xaa can be
Histidine, Glutamic Acid or Tyrosine misc_feature (5)..(5) Xaa can
be Threonine, Glutamic Acid, Lysine or Tryptophan misc_feature
(7)..(8) Xaa can be Proline, Glutamic Acid, Glycine, Lysine or
Tyrosine misc_feature (10)..(10) Xaa can be Proline, Alanine,
Glutamic Acid, Glycine or Tyrosine misc_feature (11)..(11) Xaa can
be Alanine, Glutamic Acid, Glycine, Lysine, Proline or Tyrosine
misc_feature (12)..(12) Xaa can be Proline, Glutamic Acid, Glycine,
Lysine or Tyrosine misc_feature (13)..(13) Xaa can be any amino
acid except Cysteine, Lysine and Proline misc_feature (14)..(16)
Xaa can be any amino acid except Cysteine misc_feature (17)..(19)
Xaa can be any amino acid except Alanine and Cysteine misc_feature
(20)..(20) Xaa can be Valine, Alanine, Isoleucine, Methionine or
Threonine misc_feature (21)..(21) Xaa can be Phenylalanine,
Aspartic Acid, Glutamic Acid, Leucine, Arginine, Serine, Tryptophan
or Tyrosine misc_feature (23)..(23) Xaa can be Phenylalanine,
Glutamic Acid, Histidine, Leucine, Glutamine, Arginine, Tryptophan
or Tyrosine misc_feature (24)..(24) Xaa can be Proline or Histidine
misc_feature (25)..(25) Xaa can be Proline or Alanine misc_feature
(26)..(26) Xaa can be Lysine, Aspartic Acid, Glutamic Acid,
Histidine or Tyrosine misc_feature (27)..(27) Xaa can be Proline,
Glycine or Valine misc_feature (29)..(29) Xaa can be Aspartic Acid,
Histidine, Glutamine or Tyrosine misc_feature (35)..(35) Xaa can be
Arginine, Glutamic Acid or Tyrosine misc_feature (38)..(38) Xaa can
be Glutamic Acid, Histidine, Serine or Tyrosine misc_feature
(40)..(40) Xaa can be Threonine, Aspartic Acid, Glutamic Acid,
Histidine or Tyrosine misc_feature (42)..(42) Xaa can be Valine,
Alanine, Glutamic Acid, Phenylalanine, Isoleucine or Threonine
misc_feature (43)..(43) Xaa can be Valine, Alanine, Isoleucine,
Methionine or Threonine misc_feature (44)..(44) Xaa can be any
amino acid except Cysteine misc_feature (45)..(45) Xaa can be any
amino acid except Cysteine, Alanine, and Glutamic Acid misc_feature
(46)..(46) Xaa can be Valine, Alanine, Isoleucine, Methionine or
Threonine misc_feature (47)..(47) Xaa can be any amino acid except
Cysteine, Alanine, and Glycine misc_feature (48)..(48) Xaa can be
any amino acid except Cysteine, Alanine, and Serine misc_feature
(49)..(49) Xaa can be any amino acid except Cysteine, Alanine,
Aspartic Acid and Glutamine misc_feature (50)..(50) Xaa can be any
amino acid except Cysteine, Alanine, Glutamic Acid, Asparagine,
Lysine and Valine misc_feature (51)..(51) Xaa can be any amino acid
except Cysteine and Proline misc_feature (52)..(52) Xaa can be any
amino acid except Cysteine, Alanine, Arginine and Glutamine
misc_feature (53)..(53) Xaa can be Valine or Isoleucine
misc_feature (54)..(54) Xaa can be any amino acid except Alanine,
Cysteine, Glutamine, Isoleucine and Serine misc_feature (55)..(55)
Xaa can be Phenylalanine, Leucine or Tryptophan misc_feature
(56)..(56) Xaa can be any amino acid except Alanine, Cysteine,
Glutamine and Lysine misc_feature (58)..(58) Xaa can be any amino
acid except Alanine, Cysteine and Phenylalanine misc_feature
(60)..(60) Xaa can be Aspartic Acid, Glycine, Lysine, Leucine,
Proline or Tryptophan misc_feature (61)..(61) Xaa can be Aspartic
Acid, Glycine, Glutamic Acid, Lysine, Asparagine, Proline,
Glutamine or Tyrosine misc_feature (62)..(62) Xaa can be Valine,
Glutamic Acid, Glycine, Lysine, Proline or Tyrosine misc_feature
(63)..(63) Xaa can be Glutamic Acid, Glycine, Histidine, Lysine,
Proline, Arginine, Tyrosine or Leucine misc_feature (64)..(64) Xaa
can be Valine, Aspartic Acid, Glutamic Acid, Leucine, Asparagine,
Glutamine, Threonine or Tyrosine misc_feature (65)..(65) Xaa can be
Histidine, Aspartic Acid, Glutamic Acid, Lysine, Glutamine,
Tryptophan or Tyrosine misc_feature (66)..(66) Xaa can be
Asparagine, Glutamic Acid, Glycine, Proline or Tyrosine
misc_feature (68)..(68) Xaa can be Lysine, Aspartic Acid, Glutamic
Acid or Tyrosine misc_feature (70)..(70) Xaa can be Lysine,
Aspartic Acid, Histidine, Leucine, Asparagine or Tryptophan
misc_feature (71)..(71) Xaa can be Proline, Aspartic Acid, Glutamic
Acid, Glycine, Histidinie, Isoleucine, Glutamine or Threonine
misc_feature (72)..(72) Xaa can be Arginine, Aspartic Acid,
Glutamic Acid, Threonine or Tyrosine misc_feature (73)..(73) Xaa
can be any amino acid except Alanine, Cysteine, Aspartic Acid,
Glutamine and Lysine misc_feature (74)..(74) Xaa can be any amino
acid except Alanine, Cysteine, Arginine, Aspartic Acid and
Glutamine misc_feature (75)..(75) Xaa can be any amino acid except
Alanine, Cysteine, Leucine and Lysine misc_feature (76)..(76) Xaa
can be any amino acid except Cysteine, Phenylalanine, Proline and
Tryptophan misc_feature (77)..(77) Xaa can be any amino acid except
Alanine and Cysteine misc_feature (78)..(78) Xaa can be any amino
acid except Alanine, Cysteine, Glycine, Leucine, Proline and Valine
misc_feature (79)..(79) Xaa can be any amino acid except Cysteine
misc_feature (80)..(80) Xaa can be any amino acid except Cysteine,
Isoleucine, Leucine and Phenylalanine misc_feature (81)..(81) Xaa
can be Arginine, Aspartic Acid, Glutamic Acid, Histidine or
Tyrosine misc_feature (82)..(82) Xaa can be Valine or Isoleucine
misc_feature (83)..(83) Xaa can be Valine, Aspartic Acid, Glutamic
Acid or Tyrosine misc_feature (84)..(84) Xaa can be Serine,
Aspartic Acid, Histidine, Leucine, Asparagine or Threonine
misc_feature (85)..(85) Xaa can be Valine, Gluatmic Acid, Threonine
or Tyrosine misc_feature (93)..(93) Xaa can be Tryptophan or
Phenylalanine misc_feature (97)..(97) Xaa can be Lysine, Gluatmic
Acid, or Glutamine misc_feature (98)..(98) Xaa can be Glutamic
Acid, Histidine, Leucine, Glutamine, Arginine or Tyrosine
misc_feature (100)..(100) Xaa can be any amino acid except Alanine,
Arginine, Cysteine, Glutamine, Glutamic Acid and Methionine
misc_feature (102)..(102) Xaa can be any amino acid except Alanine,
Arginine, Asparagine, Cysteine, Glutamine, Glutamic Acid, Leucine,
and Methionine misc_feature (103)..(103) Xaa can be Valine or
Isoleucine misc_feature (104)..(104) Xaa can be any amino acid
except for Alanine, Cysteine, Asparagine, Glutamine, Glutamic Acid
and Lysine misc_feature (105)..(105) Xaa can be any amino acid
except for Cysteine misc_feature (106)..(106) Xaa can be Lysine,
Isoleucine, Leucine, Proline or Threonine misc_feature (107)..(107)
Xaa can be any amino acid except Cysteine, Glutamine and Glycine
misc_feature (108)..(108) Xaa can be any amino acid except Cysteine
misc_feature (109)..(109) Xaa can be any amino acid except Alanine
and Cysteine misc_feature (110)..(110) Xaa can be any amino acid
except Aspartic Acid, Cysteine, Glutamine and Lysine misc_feature
(111)..(111) Xaa can be any amino acid except Alanine, Asparagine,
Cysteine, Glutamic Acid, Glycine, Lysine and Serine misc_feature
(112)..(112) Xaa can be any amino acid except Cysteine and Glycine
misc_feature (113)..(113) Xaa can be Glutamic Acid, Phenylalanine,
Histidine, Isoleucine, Leucine, Methionine, Asparagine, Proline,
Threonine or Tyrosine misc_feature (114)..(114) Xaa can be Lysine,
Phenylalanine, Isoleucine, Leucine, Proline or Threonine
misc_feature (115)..(115) Xaa can be any amino acid except Alanine,
Cysteine, Glutamine, Glutamic Acid and Lysine misc_feature
(116)..(116) Xaa can be Isoleucine, Glutamic Acid, Lysine or
Tyrosine misc_feature (117)..(117) Xaa can be Serine, Glutamic
Acid, Histidine or Asparagine 8 Xaa Xaa Xaa Xaa Xaa Cys Xaa Xaa Cys
Xaa Xaa Xaa Xaa Xaa Xaa Xaa 1 5 10 15 Xaa Xaa Xaa Xaa Xaa Leu Xaa
Xaa Xaa Xaa Xaa Lys Xaa Thr Leu Met 20 25 30 Ile Ser Xaa Thr Pro
Xaa Val Xaa Cys Xaa Xaa Xaa Xaa Xaa Xaa Xaa 35 40 45 Xaa Xaa Xaa
Xaa Xaa Xaa Xaa Xaa Trp Xaa Val Xaa Xaa Xaa Xaa Xaa 50 55 60 Xaa
Xaa Ala Xaa Thr Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa 65 70
75 80 Xaa Xaa Xaa Xaa Xaa Leu Thr Val Leu His Gln Asp Xaa Leu Asn
Gly 85 90 95 Xaa Xaa Tyr Xaa Cys Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa
Xaa Xaa Xaa 100 105 110 Xaa Xaa Xaa Xaa Xaa 115 9 5 PRT Artificial
Synthetic 9 Gly Ser Gly Gly Ser 1 5 10 5 PRT Artificial Synthetic
10 Gly Gly Gly Gly Ser 1 5 11 4 PRT Artificial Synthetic 11 Gly Gly
Gly Ser 1 12 5 PRT Homo sapiens 12 Thr Leu Met Ile Ser 1 5 13 7 PRT
Homo sapiens 13 Leu Thr Val Leu His Gln Asp 1 5 14 5 PRT Artificial
Synthetic MISC_FEATURE (1)..(1) Xaa can be threonine MISC_FEATURE
(2)..(2) Xaa can be leucine MISC_FEATURE (3)..(3) Xaa can be
methionine MISC_FEATURE (4)..(4) Xaa can be isoleucine MISC_FEATURE
(5)..(5) Xaa can be serine 14 Xaa Xaa Xaa Xaa Xaa 1 5 15 7 PRT
Artificial Synthetic MISC_FEATURE (1)..(1) Xaa can be leucine
MISC_FEATURE (2)..(2) Xaa can be threonine MISC_FEATURE (3)..(3)
Xaa can be valine MISC_FEATURE (4)..(4) Xaa can be leucine
MISC_FEATURE (5)..(5) Xaa can be histidine MISC_FEATURE (6)..(6)
Xaa can be glutamine MISC_FEATURE (7)..(7) Xaa can be aspartic acid
15 Xaa Xaa Xaa Xaa Xaa Xaa Xaa 1 5
* * * * *