U.S. patent application number 14/065391 was filed with the patent office on 2014-06-19 for methods and compositions for antibody therapy.
This patent application is currently assigned to Pikamab, Inc.. The applicant listed for this patent is Pikamab, Inc.. Invention is credited to Vijay Ramakrishnan.
Application Number | 20140170670 14/065391 |
Document ID | / |
Family ID | 38616540 |
Filed Date | 2014-06-19 |
United States Patent
Application |
20140170670 |
Kind Code |
A1 |
Ramakrishnan; Vijay |
June 19, 2014 |
Methods and Compositions for Antibody Therapy
Abstract
Methods and materials are provided for determining the
responsiveness of a subject to a therapy, such as an antibody
therapy and for selecting and/or for treating a subject based on an
Fc.gamma.RIIA polymorphism, or an Fc.gamma.RIIIA polymorphism, or
both an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism, including where the treatment is an therapy, such as
rituximab. Methods and materials are also provided for designing,
making, screening, testing and/or administering antibodies as well
as for optimizing antibody therapies based upon a subject's
Fc.gamma.RIIA polymorphism, or Fc.gamma.RIIIA polymorphism, or both
the Fc.gamma.RIIA polymorphism and the Fc.gamma.RIIIA
polymorphism.
Inventors: |
Ramakrishnan; Vijay; (Palo
Alto, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Pikamab, Inc. |
Palo Alto |
CA |
US |
|
|
Assignee: |
Pikamab, Inc.
Palo Alto
CA
|
Family ID: |
38616540 |
Appl. No.: |
14/065391 |
Filed: |
October 28, 2013 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12298661 |
Jan 8, 2010 |
8592149 |
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PCT/US2007/067663 |
Apr 27, 2007 |
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14065391 |
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60795957 |
Apr 27, 2006 |
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Current U.S.
Class: |
435/7.1 |
Current CPC
Class: |
C12Q 2600/106 20130101;
C07K 2317/732 20130101; C12Q 2600/156 20130101; C07K 16/2887
20130101; C12Q 1/6883 20130101; G01N 33/57407 20130101 |
Class at
Publication: |
435/7.1 |
International
Class: |
G01N 33/574 20060101
G01N033/574 |
Claims
1. A method for predicting treatment response to an antibody
therapy for a human test subject having an ADCC treatable disease
or disorder, the method comprising: (a) classifying the test
subject into one of nine genotype groups for the combination of H/R
polymorphisms at amino acid position 131 of Fc.gamma.RIIA receptor;
and F/V polymorphisms at amino acid position 158 of Fc.gamma.RIIIA
receptor; (b) using a reference index that correlates more than
three categories of treatment response upon treatment with an
antibody therapy with the genotype groups; and (c) further
comprising determining the ADCC function of the test subject.
Description
CROSS-REFERENCES TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 12/298,661, filed Oct. 27, 2008, which is a
national stage application under 35 U.S.C. .sctn.371 of
International application PCT/US2007/067663, filed Apr. 27, 2007,
which claims benefit under 35 U.S.C. .sctn.119(e) of U.S.
provisional patent application No. 60/795,957, filed Apr. 27, 2006.
The entire contents of each cited application is incorporated
herein by reference.
REFERENCE TO SEQUENCE LISTING
[0002] The official copy of the sequence listing is submitted
concurrently with the specification as an ASCII formatted text file
via EFS-Web, with a file name of "PMI-001US_ST25.txt", a creation
date of Oct. 28, 2013, and a size of 59.4 kilobytes. The sequence
listing filed via EFS-Web is part of the specification and is
hereby incorporated in its entirety by reference herein.
BACKGROUND
[0003] A number of antibodies have been developed, including for
their use in therapies for a variety of diseases, disorders or
conditions. For example, in the fall of 1997, the anti-CD20
monoclonal antibody, rituximab (currently sold under the brand name
RITUXAN.RTM.), was approved for the treatment of refractory or
relapsed low-grade B-cell non-Hodgkin's lymphoma (NHL). Rituximab
has since become a mainstay of treatment for low-grade NHL and over
400,000 patients worldwide have been treated with rituximab.
Despite this extensive clinical experience, the mechanism of action
of rituximab remains unclear, as does the nature of resistance.
[0004] Rituximab is a chimeric antibody consisting of a murine
CD20-binding variable region linked to human IgG.sub.1 constant
region. CD20 is a cell surface protein expressed on B-lymphocytes.
CD20 has four transmembrane domains and has been proposed to act as
an ion channel; however, the function of CD20 remains poorly
understood. Phase II trials of rituximab in people with refractory
or relapsed low grade or follicular NHL demonstrated a 50% response
rate. While the nature of de novo resistance to rituximab is
unclear, such resistance is very rarely due to loss of the CD20
antigen, which cannot be shed or internalized and is rarely
down-regulated. Despite these properties of CD20, acquired
resistance to rituximab is common in that only half of patients
previously responding to rituximab will respond to a second course
of treatment.
[0005] An effective and practical diagnostic protocol which could
provide information as to whether a patient is or is not responsive
to a therapy, including an antibody therapy such as rituximab
therapy, would be desirable for a number of reasons, including
avoidance of delays in alternative treatments, elimination of
exposure to adverse effects of the therapy and reduction of
unnecessary expense. As such, there is interest in the development
of protocols that can accurately predict whether or not a patient
is responsive to such therapies. There is also an interest in the
development of antibodies and antibody therapies that would be
effective or more effective in patients that were non-responsive or
poorly responsive to a particular therapy.
SUMMARY
[0006] Methods and materials are provided for determining the
responsiveness of a subject to a therapy, such as an antibody
therapy and for selecting and/or for treating a subject based on an
Fc.gamma.RIIA polymorphism, or an Fc.gamma.RIIIA polymorphism, or
both an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism, including where the treatment is an therapy, such as
rituximab. Methods and materials are also provided for designing,
making, screening, testing and/or administering antibodies as well
as for optimizing antibody therapies based upon a subject's
Fc.gamma.RIIA polymorphism, or Fc.gamma.RIIIA polymorphism, or both
the Fc.gamma.RIIA polymorphism and the Fc.gamma.RIIIA
polymorphism.
[0007] Methods and compositions are provided for determining
whether a subject suffering from a neoplastic condition is
responsive to an antineoplastic therapy, such as antibody therapy,
e.g., rituximab therapy. In practicing the subject methods, the
subject is genotyped to determine whether the subject has at least
one favorable Fc.gamma.R polymorphism, e.g., the H/H.sup.131
genotype in Fc.gamma.RIIA or the V/V.sup.158 genotype in
Fc.gamma.RIIIA. In addition, reagents, devices and kits thereof,
that find use in practicing the subject methods are provided.
[0008] Methods are provided for determining the degree of
responsiveness that a subject having an ADCC-treatable disease or
disorder will have to an antibody therapy for the disease or
disorder by genotyping the subject for an Fc.gamma.RIIA
polymorphism to obtain a first result, genotyping the subject for
an Fc.gamma.RIIIA polymorphism to obtain a second result, assigning
the subject to one of more than three categories of treatment
response and/or employing the first and second results to determine
the degree of the responsiveness of the subject to the antibody
therapy.
[0009] Methods are provided for selecting a specific Fc variant
antibody therapy from a set of two or more Fc variant antibody
therapies for use in treating subjects having an ADCC-treatable
disease by genotyping the subjects for an Fc.gamma.RIIA
polymorphism to classify patient population into three groups
(e.g., H/H.sup.131, H/R.sup.131, R/R.sup.131), genotyping the
subjects for an Fc.gamma.RIIIA polymorphism to classify patient
population into three groups (e.g., V/V.sup.158, V/F.sup.158,
F/F.sup.158), classifying the subjects into nine patient groups
I-IX based on the first and second results, and employing the first
and second results to select a specific Fc variant antibody therapy
for the patient group such that the degree of treatment response to
antibody therapy in the patient group is improved. Subjects may be
classified into nine groups based on their genotype, including:
V/V.sup.158, H/H.sup.131 (Group-I); V/F.sup.158, H/H.sup.131
(Group-II); F/F.sup.158, H/H.sup.131 (Group-III); V/V.sup.158,
H/R.sup.131 (Group-IV); V/F.sup.158, H/R.sup.131 (Group-V);
F/F.sup.158, H/R.sup.131 (Group-VI); V/V.sup.158 R/R.sup.131
(Group-VII); V/F.sup.158, R/R.sup.131 (Group-VIII); and
F/F.sup.158, R/R.sup.131 (Group-IX).
[0010] Methods are also provided for making a set of related
antibodies by modifying the amino acid sequence of at least one Fc
region amino acid residue in a parent antibody, such that the
modified Fc region exhibits enhanced binding affinity to at least
one Fc receptor encoded by an Fc receptor gene of a first genotype,
compared to the Fc binding affinity of the parent antibody, to
generate a first Fc variant antibody; and/or modifying at least one
Fc region amino acid residue in a parent antibody, such that the
modified constant region exhibits enhanced binding affinity to at
least one Fc receptor encoded by an Fc receptor gene of a second
genotype, compared to the Fc binding affinity of the parent
antibody, to generate a second Fc variant antibody, wherein the
first and second Fc variant antibodies have the same antigen
specificity.
[0011] Also provided are kits for use in determining responsiveness
to an antibody therapy in a patient which include an element for
genotyping a sample to identify an Fc.gamma.RIIA polymorphism, an
element for genotyping the sample to identify an Fc.gamma.RIIIA
polymorphism, or an element for genotyping the sample to identify
an Fc.gamma.RIIIA polymorphism and an Fc.gamma.RIIA, and a
reference that correlates a genotype with predicted therapeutic
response to a therapeutic antibody.
[0012] Methods are provided for of treating an ADCC-treatable
disease or disorder in an individual by determining a category of
therapeutic responsiveness to an antibody therapy by genotyping the
individual for an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism, wherein the Fc.gamma.RIIA polymorphism and the
Fc.gamma.RIIIA polymorphism together indicate a degree of
therapeutic responsiveness; selecting an antibody from a set of
related antibodies, wherein members of the set of related
antibodies have the same antigen binding specificity, and wherein
the members of the set of related antibodies differ in binding
affinity to an Fc.gamma.RIIA and/or an Fc.gamma.RIIIA and/or differ
in in vitro ADCC function; and administering an effective amount of
the antibody to the individual.
[0013] Methods are provided for determining the degree of
responsiveness to an antibody-dependent cell-mediated cytotoxicity
antibody therapy by genotyping the subject for two or more
Fc.gamma. receptor polymorphisms and employing the first and second
Fc.gamma. receptor polymorphisms to determine the degree of the
responsiveness of the subject to the antibody therapy.
[0014] Methods are also provided for generating a set of Fc variant
antibodies by amplifying a nucleic acid comprising a nucleotide
sequence encoding an Fc region of an antibody, wherein the
amplifying is carried out with a set of primers that encode all
nineteen amino acid variants at a single residue of the Fc region,
to generate a set of variant nucleic acids encoding nineteen amino
acid substitution variants at the single residue of the Fc region;
transcribing and translating each of the variant nucleic acids in
vitro, to generate a set of Fc variants; and/or c) selecting from
the set an Fc variant having altered FcR binding activity compared
to a reference Fc, generating a set of selected Fc variants.
[0015] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/V.sup.158 genotype, the H/H.sup.131 genotype, or
both the V/V.sup.158 genotype, the H/H.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0016] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/F.sup.158 genotype, the H/H.sup.131 genotype, or
both the V/F.sup.158 genotype, the H/H.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0017] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the F/F.sup.158 genotype, the H/H.sup.131 genotype, or
both the F/F.sup.158 genotype, the H/H.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0018] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/V.sup.158 genotype, the H/R.sup.131 genotype, or
both the V/V.sup.158 genotype, the H/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0019] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/F.sup.158 genotype, the H/R.sup.131 genotype, or
both the V/F.sup.158 genotype, the H/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0020] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the F/F.sup.158 genotype, the H/R.sup.131 genotype, or
both the F/F.sup.158 genotype, the H/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0021] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/V.sup.158 genotype, the R/R.sup.131 genotype, or
both the V/V.sup.158 genotype, the R/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0022] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/F.sup.158 genotype, the R/R.sup.131 genotype, or
both the V/F.sup.158 genotype, the R/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0023] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the F/F.sup.158 genotype, the R/R.sup.131 genotype, or
both the F/F.sup.158 genotype, the R/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0024] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA V/V.sup.158
genotype, an Fc.gamma.RIIA H/H.sup.131 genotype; or both an
Fc.gamma.RIIIA V/V.sup.158 genotype and an Fc.gamma.RIIA
H/H.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0025] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA V/F.sup.158
genotype, an Fc.gamma.RIIA H/H.sup.131 genotype; or both an
Fc.gamma.RIIIA V/F.sup.158 genotype and an Fc.gamma.RIIA
H/H.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0026] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA F/F.sup.158
genotype, or an Fc.gamma.RIIA H/H.sup.131 genotype; or both an
Fc.gamma.RIIIA F/F.sup.158 genotype and an Fc.gamma.RIIA
H/H.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0027] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA V/V.sup.158
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype; or both an
Fc.gamma.RIIIA V/V.sup.158 genotype and an Fc.gamma.RIIA
H/R.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0028] Methods are also provided for treating a patient with an
antibody by (a) selecting a patient with an Fc.gamma.RIIIA
V/F.sup.158 genotype, an Fc.gamma.RIIA H/R.sup.131 genotype, or
both an Fc.gamma.RIIIA V/F.sup.158 genotype and an Fc.gamma.RIIA
H/R.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0029] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA F/F.sup.158
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype, or both an
Fc.gamma.RIIIA F/F.sup.158 genotype and an Fc.gamma.RIIA
H/R.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0030] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA V/V.sup.158
genotype, an Fc.gamma.RIIA R/R.sup.131 genotype, or both an
Fc.gamma.RIIIA V/V.sup.158 genotype and an Fc.gamma.RIIA
R/R.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0031] Methods are also provided for treating a patient with an
antibody by (a) selecting a patient with an Fc.gamma.RIIIA
V/F.sup.158 genotype, an Fc.gamma.RIIA R/R.sup.131 genotype, or
both an Fc.gamma.RIIIA V/F.sup.158 genotype and an Fc.gamma.RIIA
R/R.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0032] Methods are provided for treating a patient with an
antibody, comprising: (a) selecting a patient with an
Fc.gamma.RIIIA F/F.sup.158 genotype, an Fc.gamma.RIIA R/R.sup.131
genotype, or both an Fc.gamma.RIIIA F/F.sup.158 genotype and an
Fc.gamma.RIIA R/R.sup.131 genotype and (b) administering the
antibody to the patient selected in step (a).
[0033] Methods are also provided for classifying a subject having
an ADCC-treatable disease or disorder into one of more than three
categories of responsiveness to an antibody therapy by genotyping
subjects for an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism, wherein the subjects have or had the ADCC-treatable
disease or disorder and are or were administered antibody therapy
for the disease or disorder; classifying each subject based on its
Fc.gamma.RIIA polymorphism and Fc.gamma.RIIIA polymorphism to one
of three or more categories of responsiveness to the antibody
therapy; genotyping the subject for an Fc.gamma.RIIA polymorphism
and an Fc.gamma.RIIIA polymorphism; identifying a genotype from (a)
that is identical to the genotype from the subject in step (c),
wherein the subject is classified into a category of responsiveness
to the antibody therapy for the disease or disorder corresponding
with a subject having an identical Fc.gamma.RIIA polymorphism and
an identical Fc.gamma.RIIIA polymorphism.
[0034] Methods are provided for determining the degree of
responsiveness that a subject having an ADCC-treatable disease or
disorder will have to an antibody therapy for the disease or
disorder by genotyping the subject for an Fc.gamma.RIIA
polymorphism and an Fc.gamma.RIIIA polymorphism; and identifying a
genotype associated with a particular degree of responsiveness to
the antibody therapy from a reference that is identical to the
genotype from the test subject, wherein the test subject is
determined to have a degree of responsiveness to the antibody
therapy for the disease or disorder corresponding to the level of
responsiveness associated with the reference having an identical
Fc.gamma.RIIA polymorphism and an identical Fc.gamma.RIIIA
polymorphism.
[0035] Methods are also provided for determining the degree of
responsiveness that a test subject having an ADCC-treatable disease
or disorder will have to an antibody therapy for the disease or
disorder by (a) genotyping subjects for an Fc.gamma.RIIA
polymorphism and an Fc.gamma.RIIIA polymorphism, wherein the
subjects have or had the ADCC-treatable disease or disorder and are
or were administered antibody therapy for the disease or disorder;
(b) classifying each subject based on its Fc.gamma.RIIA
polymorphism and Fc.gamma.RIIIA polymorphism to one of more than
three categories of responsiveness to the antibody therapy; (c)
genotyping the test subject for an Fc.gamma.RIIA polymorphism and
an Fc.gamma.RIIIA polymorphism; and (d) identifying a genotype from
(a) that is identical to the genotype from the test subject in step
(c), wherein the test subject is determined to have a degree of
responsiveness to the antibody therapy for the disease or disorder
corresponding to the level of responsiveness associated with a
subject having an identical Fc.gamma.RIIA polymorphism and an
identical Fc.gamma.RIIIA polymorphism.
[0036] Also provided are kits for use in determining responsiveness
to an antibody therapy in a patient which include an element for
genotyping the sample to identify an Fc.gamma.RIIA polymorphism; an
element for genotyping the sample to identify an Fc.gamma.RIIIA
polymorphism; and a reference that correlates a genotype in the
patient with one of more than three predicted therapeutic responses
to the antibody therapy.
[0037] Methods are provided for selecting a specific variant
antibody therapy from a set of two or more variant antibody
therapies for use in treatment of subjects having an ADCC-treatable
disease by genotyping the subjects for an Fc.gamma.RIIA
polymorphism and an Fc.gamma.RIIIA polymorphism, classifying the
subjects into one of more than three categories of responsiveness
based on their Fc.gamma.RIIA polymorphism and their Fc.gamma.RIIIA
polymorphism, and selecting a specific variant antibody therapy for
the subjects such that the degree of responsiveness to the antibody
therapy in the subjects is improved from the degree of
responsiveness obtained with another variant antibody.
[0038] Methods are also provided for treating an ADCC-treatable
disease or disorder in a subject by genotyping the subject for an
Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA polymorphism,
classifying the subject into one of more than three categories of
therapeutic responsiveness to an antibody therapy based on the
Fc.gamma.RIIA polymorphism and the Fc.gamma.RIIIA polymorphism,
selecting an antibody with a preferred degree of therapeutic
responsiveness from a set of related antibodies, wherein members of
the set of related antibodies have the same antigen binding
specificity, and wherein the members of the set of related
antibodies differ in binding affinity to an Fc.gamma.RIIA and/or an
Fc.gamma.RIIIA and/or differ in in vitro ADCC function, and
administering a therapeutically effective amount of the antibody to
the subject, wherein, the antibody treats the ADCC-treatable
disease or disorder in the subject.
[0039] Methods are provided for making a set of related antibodies
capable of modulating the responsiveness of a subject having an
ADCC-treatable disease or disorder to an antibody therapy for the
disease or disorder by modifying the amino acid sequence of at
least one amino acid residue in a parent antibody, such that the
modified parent antibody exhibits enhanced binding affinity to at
least one Fc receptor encoded by an Fc receptor gene of a first
genotype, compared to the Fc binding affinity of the parent
antibody, to generate a first variant antibody; and modifying at
least one amino acid residue in a parent antibody, such that the
modified parent antibody exhibits enhanced binding affinity to at
least one Fc receptor encoded by an Fc receptor gene of a second
genotype, compared to the Fc binding affinity of the parent
antibody, to generate a second variant antibody, wherein the first
and second variant antibodies have the same antigen specificity and
are capable of modulating the responsiveness of a subject having an
ADCC-treatable disease or disorder to an antibody therapy for the
disease or disorder.
[0040] Methods are provided for generating a set of variant
antibodies capable of modulating the responsiveness of a subject
having an ADCC-treatable disease or disorder to an antibody therapy
for the disease or disorder by amplifying a nucleic acid comprising
a nucleotide sequence encoding a region of an antibody, wherein the
amplifying is carried out with a set of primers that encode all
nineteen amino acid variants at a single residue of the region, to
generate a set of variant nucleic acids encoding nineteen amino
acid substitution variants at the single residue of the region,
transcribing and translating each of the variant nucleic acids in
vitro, to generate a set of variants, and/or selecting from the set
an variant having altered FcR binding activity compared to a
reference region, generating a set of selected variants, wherein
the first and second variant antibodies have the same antigen
specificity and are capable of modulating the responsiveness of a
subject having an ADCC-treatable disease or disorder to an antibody
therapy for the disease or disorder. In some embodiments, the
method includes determining in vitro ADCC activity of the selected
variant.
[0041] Methods are also provided for modulating the responsiveness
of a subject having an ADCC-treatable disease or disorder to an
antibody therapy for the disease or disorder by genotyping the
subject for an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism, classifying the subject into one of more than three
categories of therapeutic responsiveness to an antibody therapy
based on the Fc.gamma.RIIA polymorphism and the Fc.gamma.RIIIA
polymorphism, selecting an antibody from a set of related
antibodies, wherein members of the set of related antibodies have
the same antigen binding specificity, and wherein the members of
the set of related antibodies differ in binding affinity to an
Fc.gamma.RIIA and/or an Fc.gamma.RIIIA and/or differ in in vitro
ADCC function, and administering a therapeutically effective amount
of the antibody to the subject, wherein the antibody modulates the
responsiveness of the subject having an ADCC-treatable disease or
disorder to an antibody therapy for the disease or disorder.
[0042] Methods are provided for enhancing antibody dependent cell
mediated cytotoxicity (ADCC) activity of an antibody for use in
treatment of a subject having an ADCC-treatable disease by
genotyping the subject for an Fc.gamma.RIIA polymorphism and an
Fc.gamma.RIIIA polymorphism, selecting an Fc nucleotide sequence
for the antibody that has optimal ADCC for the Fc.gamma.RIIA
polymorphism and Fc.gamma.RIIIA polymorphism, and modifying the
antibody to include the optimal Fc sequence for the subject's
genotype, wherein the ADCC activity of the antibody is enhanced by
using the optimal Fc.
BRIEF DESCRIPTION OF THE DRAWINGS
[0043] FIG. 1: Rituximab-induced antibody-dependent cell-mediated
cytotoxicity (ADCC). The scatter plot in the left column of each
Group represents the degree of rituximab-induced ADCC
(effector/target ratio at 30:1) of individual tumors. The bars
represent the mean and standard deviations in each Group. NR,
nonresponder; PR, partial responder; CR, complete responder or
complete response unconfirmed.
[0044] FIG. 2: Kaplan-Meier estimates of progression free survival
by IgG Fc receptor IIIA (Fc.gamma.RIIIA) 158 valine
(V)/phenylalanine (F) polymorphism. Progression-free survival (PFS)
curves were plotted by Fc.gamma.RIIIA V/F.sup.158 genotype on all
87 patients. F carriers represent patients with either V/F.sup.158
or F/F.sup.158 genotype. TTP, median time to progression.
[0045] FIG. 3: Kaplan-Meier estimates of progression-free survival
(PFS) by IgG Fc receptor HA (Fc.gamma.RIIA) 131 histidine
(H)/arginine (R) polymorphism. PFS curves were plotted by
Fc.gamma.RIIA H/R.sup.131 genotype on all 87 patients. R carriers
represent patients with either H/R.sup.131 or R/R.sup.131 genotype.
TTP, median time to progression.
[0046] FIG. 4: Progression free survival (PFS) by IgG Fc receptor
IIIa (Fc.gamma.RIIIA) V/F.sup.158 and Fc.gamma.RIIA H/R.sup.131
polymorphisms. PFS curves were plotted by Fc.gamma.RIIIA
V/F.sup.158 and Fc.gamma.RIIA H/R.sup.131 genotype. Others
represent patients without either Fc.gamma.RIIIA V/V.sup.158 or
Fc.gamma.RIIA H/H.sup.131 genotype. TTP, median time to
progression.
[0047] FIGS. 5, 6, 7, 8, 9, 10 and 11 provide Tables 1 to 7
referred to in the Experimental Section, below.
[0048] FIGS. 12A-D: Amino acid sequences of Fc receptors and IgGs.
FIG. 12A depicts an amino acid sequence alignment of Fc.gamma.RIIIA
(SEQ ID NO:26) and Fc.gamma.RIIA (SEQ ID NO:27) from residues
83-170. Identical residues between the receptors are aligned, and
the FcR residues that contact Fcl are in bold. According to the
numbering system used in crystal structure studies, the Valine at
position 155 of Fc.gamma.RIIIA is the residue referred to herein as
V.sup.158. The residues H/R.sup.131 and V/I.sup.158 are underlined.
FIG. 12B depicts an amino acid sequence of hIgG1 from residues
229-444 (SEQ ID NO:34). Key binding motifs in the Fc region are in
bold. FIG. 12C depicts a structure-based sequence alignment of
Fc.gamma.RIII (Fc.gamma.R1--SEQ ID NO:36, SEQ ID NO: 37, SEQ ID
NO:38; Fc.gamma.RIIa-HR--SEQ ID NO: 39, SEQ ID NO: 40, and SEQ ID
NO: 41; Fc.gamma.RIIa-LR--SEQ ID NO: 42, SEQ ID NO: 43, and SEQ ID
NO: 44; Fc.gamma.RIIb--SEQ ID NO: 45, SEQ ID NO: 46, and SEQ ID NO:
47; Fc.gamma.RIa--SEQ ID NO: 48, SEQ ID NO: 49, and SEQ ID NO: 50;
Fc.gamma.RIII-V--SEQ ID NO: 51, SEQ ID NO: 52, and SEQ ID NO: 53;
and Fc.gamma.RIII-F--SEQ ID NO: 54, SEQ ID NO: 55, and SEQ ID NO:
56) and hIgG1 (IgG.sub.1--SEQ ID NO: 57, SEQ ID NO: 58, and SEQ ID
NO: 59; IgG.sub.2--SEQ ID NO: 60, SEQ ID NO: 61, and SEQ ID NO: 62;
IgG.sub.3--SEQ ID NO: 63, SEQ ID NO: 64, and SEQ ID NO: 65;
IgG.sub.4--SEQ ID NO: 66, SEQ ID NO: 67, and SEQ ID NO: 68;
IgE--SEQ ID NO: 69, SEQ ID NO: 70, and SEQ ID NO: 71) with their
respective homologues. HR indicates high responders; LR indicates
low responders. Fc.gamma.RIIIA-V, V.sup.158 allele;
Fc.gamma.RIIIA-F, F.sup.158 allele. FIG. 12D depicts Fc Walking:
This involves bi-directional scanning saturation mutagenesis of
approximately 5-10 residues, one residue at a time, on both sides
of the "binding" motifs of the hFc regions namely lower hinge
region (SEQ ID NO:30), B/C loop (SEQ ID NO:31), C/E loop (SEQ ID
NO:32), and the F/G loop (SEQ ID NO:33).
[0049] FIG. 13: Table depicting an analysis of Fc.gamma.RIIIA and
Fc.gamma.RIIA polymorphisms in B-NHL patients.
[0050] FIG. 14: Table depicting prevalence of Fc.gamma.RIIIA and
Fc.gamma.RIIA polymorphisms in B-NHL patients (Weng), healthy U.S.
Caucasians (Lehrnbecher), healthy U.S. African Americans
(Lehrnbecher) and healthy Norwegians (Torkildsen).
[0051] FIG. 15: Alignment of Antibody Fc Regions: Table comparing
the nucleotide sequence of the Fc regions of Rituxan.RTM. (SEQ ID
NO:1), Remicade.RTM. (SEQ ID NO:12), Erbitux.RTM. (SEQ ID NO:13),
Campath.RTM. (SEQ ID NO:14) and Herceptin.RTM. (SEQ ID NO:15)
(Prepared with CLUSTAL W (1.83); Mismatches are indicated by the
absence of a "*" underneath the alignment.
[0052] FIG. 16: SSM in rituximab V.sub.L CDR2 region (SEQ ID
NO:18).
[0053] FIG. 17: Simultaneous SSM of the CDR regions of V.sub.L (SEQ
ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19) and V.sub.H (SEQ ID NO:
17, SEQ ID NO: 35, SEQ ID NO: 20) sequences of Rituximab. Optimal
mutations identified in the CDR regions are highlighted (V.sub.L
CDR1--SEQ ID NO:21; V.sub.L CDR2--SEQ ID NO:22; V.sub.H CDR3--SEQ
ID NO:23).
[0054] FIG. 18: Sequence Comparison of the Hinge Region of human
IgG.sub.3 and human IgG.sub.1. Numbers correspond to those of
IgG.sub.1 Eu-residues 215 to 254 (Edelman et. al., Proc. Natl.
Acad. Sci. USA 63:78, 1969). The IgG.sub.3 hinge region (SEQ ID
NO:24) is about 4 times larger than the counterpart region of
IgG.sub.1 (SEQ ID NO:25), IgG.sub.2, and IgG.sub.4. The insertion
sequence of the IgG.sub.3 hinge region consists of an N-terminal
17-residue segment followed by a 15-residue segment that is
identically and consecutively repeated three times (Michaelsen et.
al., J. Biol. Chem. 252:883, 1977).
DEFINITIONS
[0055] A polynucleotide has a certain percent "sequence identity"
to another polynucleotide, meaning that, when aligned, that
percentage of bases are the same, and in the same relative
position, when comparing the two sequences. Sequence similarity can
be determined in a number of different manners. To determine
sequence identity, sequences can be aligned using the methods and
computer programs, including BLAST, available over the world wide
web at ncbi.nlm.nih.gov/BLAST. See, e.g., Altschul et al., 1990, J.
Mol. Biol. 215:403-10. Another alignment algorithm is FASTA,
available in the Genetics Computing Group (GCG) package, from
Madison, Wis., USA, a wholly owned subsidiary of Oxford Molecular
Group, Inc. Other techniques for alignment are described in Methods
in Enzymology, vol. 266: Computer Methods for Macromolecular
Sequence Analysis (1996), ed. Doolittle, Academic Press, Inc., a
division of Harcourt Brace & Co., San Diego, Calif., USA. Of
particular interest are alignment programs that permit gaps in the
sequence. The Smith-Waterman is one type of algorithm that permits
gaps in sequence alignments. See, e.g., Meth. Mol. Biol. 70:
173-187 (1997). Also, the GAP program using the Needleman and
Wunsch alignment method can be utilized to align sequences. See,
e.g., J. Mol. Biol. 48: 443-453 (1970).
[0056] A nucleic acid is "hybridizable" to another nucleic acid,
such as a cDNA, genomic DNA, or RNA, when a single stranded form of
the nucleic acid can anneal to the other nucleic acid under the
appropriate conditions of temperature and solution ionic strength.
Hybridization and washing conditions are well known and exemplified
in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning:
A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory
Press, Cold Spring Harbor (1989), particularly Chapter 11 and Table
11.1 therein; and Sambrook, J. and Russell, W., Molecular Cloning:
A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory
Press, Cold Spring Harbor (2001). The conditions of temperature and
ionic strength determine the "stringency" of the hybridization.
Stringency conditions can be adjusted to screen for moderately
similar fragments, such as homologous sequences from distantly
related organisms, to highly similar fragments, such as genes that
duplicate functional enzymes from closely related organisms.
[0057] Hybridization conditions and post-hybridization washes are
useful to obtain the desired determine stringency conditions of the
hybridization. One set of illustrative post-hybridization washes is
a series of washes starting with 6.times.SSC (where SSC is 0.15 M
NaCl and 15 mM citrate buffer), 0.5% SDS at room temperature for 15
minutes, then repeated with 2.times.SSC, 0.5% SDS at 45.degree. C.
for 30 minutes, and then repeated twice with 0.2.times.SSC, 0.5%
SDS at 50.degree. C. for 30 minutes. Other stringent conditions are
obtained by using higher temperatures in which the washes are
identical to those above except for the temperature of the final
two 30 minute washes in 0.2.times.SSC, 0.5% SDS, which is increased
to 60.degree. C. Another set of highly stringent conditions uses
two final washes in 0.1.times.SSC, 0.1% SDS at 65.degree. C.
Another example of stringent hybridization conditions is
hybridization at 50.degree. C. or higher and 0.1.times.SSC (15 mM
sodium chloride/1.5 mM sodium citrate). Another example of
stringent hybridization conditions is overnight incubation at
42.degree. C. in a solution: 50% formamide, 5.times.SSC (150 mM
NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6),
5.times.Denhardt's solution, 10% dextran sulfate, and 20 .mu.g/ml
denatured, sheared salmon sperm DNA, followed by washing the
filters in 0.1.times.SSC at about 65.degree. C. Stringent
hybridization conditions and post-hybridization wash conditions are
hybridization conditions and post-hybridization wash conditions
that are at least as stringent as the above representative
conditions.
[0058] Hybridization requires that the two nucleic acids contain
complementary sequences, although depending on the stringency of
the hybridization, mismatches between bases are possible. The
appropriate stringency for hybridizing nucleic acids depends on the
length of the nucleic acids and the degree of complementation,
variables well known in the art. The greater the degree of
similarity or homology between two nucleotide sequences, the
greater the value of the melting temperature (Tm) for hybrids of
nucleic acids having those sequences. The relative stability
(corresponding to higher Tm) of nucleic acid hybridizations
decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For
hybrids of greater than 100 nucleotides in length, equations for
calculating Tm have been derived (See, e.g., Sambrook et al.,
supra, 9.50-9.51). For hybridizations with shorter nucleic acids,
i.e., oligonucleotides, the position of mismatches becomes more
important, and the length of the oligonucleotide determines its
specificity (See, e.g., Sambrook et al., supra, 11.7-11.8). In some
embodiments, the length for a hybridizable nucleic acid is at least
about 10 nucleotides. Illustrative minimum lengths for a
hybridizable nucleic acid are: at least about 15 nucleotides; at
least about 20 nucleotides; and at least about 30 nucleotides.
Furthermore, the skilled artisan will recognize that the
temperature and wash solution salt concentration may be adjusted as
necessary according to factors such as length of the probe.
[0059] A "biological sample" encompasses a variety of sample types
obtained from an individual and can be used in a diagnostic or
monitoring assay. The definition encompasses blood and other liquid
samples of biological origin, solid tissue samples such as a biopsy
specimen or tissue cultures or cells derived therefrom and the
progeny thereof. The definition also includes samples that have
been manipulated in any way after their procurement, such as by
treatment with reagents, solubilization, or enrichment for certain
components, such as polynucleotides or polypeptides. The term
"biological sample" encompasses a clinical sample, and also
includes cells in culture, cell supernatants, cell lysates, serum,
plasma, biological fluid, and tissue samples.
[0060] As used herein, the term "target nucleic acid region" or
"target nucleic acid" or "target molecules" refers to a nucleic
acid molecule with a "target sequence" to be detected (e.g., by
amplification). The target nucleic acid may be either
single-stranded or double-stranded and may or may not include other
sequences besides the target sequence (e.g., the target nucleic
acid may or may not include nucleic acid sequences upstream or 5'
flanking sequence, may or may not include downstream or 3' flanking
sequence, and in some embodiments may not include either upstream
(5') or downstream (3') nucleic acid sequence relative to the
target sequence. Where detection is by amplification, these other
sequences in addition to the target sequence may or may not be
amplified with the target sequence.
[0061] The term "target sequence" or "target nucleic acid sequence"
refers to the particular nucleotide sequence of the target nucleic
acid to be detected (e.g., through hybridization and/or
amplification). The target sequence may include a probe-hybridizing
region contained within the target molecule with which a probe will
form a stable hybrid under desired conditions. The "target
sequence" may also include the complexing sequences to which the
oligonucleotide primers complex and be extended using the target
sequence as a template. Where the target nucleic acid is originally
single-stranded, the term "target sequence" also refers to the
sequence complementary to the "target sequence" as present in the
target nucleic acid. If the "target nucleic acid" is originally
double-stranded, the term "target sequence" refers to both the plus
(+) and minus (-) strands. Moreover, where sequences of a "target
sequence" are provided herein, it is understood that the sequence
may be either DNA or RNA. Thus where a DNA sequence is provided,
the RNA sequence is also contemplated and is readily provided by
substituting "T" of the DNA sequence with "U" to provide the RNA
sequence.
[0062] The term "primer" or "oligonucleotide primer" as used
herein, refers to an oligonucleotide which acts to initiate
synthesis of a complementary nucleic acid strand when placed under
conditions in which synthesis of a primer extension product is
induced, e.g., in the presence of nucleotides and a
polymerization-inducing agent such as a DNA or RNA polymerase and
at suitable temperature, pH, metal concentration, and salt
concentration. Primers are in some embodiments of a length
compatible with their use in synthesis of primer extension
products, and are in some embodiments are in the range of between 8
nucleotides to 100 nucleotides in length, such as 10 to 75
nucleotides, 15 to 60 nucleotides, 15 to 40 nucleotides, 18 to 30
nucleotides, 20 to 40 nucleotides, 21 to 50 nucleotides, 22 to 45
nucleotides, or 25 to 40 nucleotides, and so on. In some
embodiments, a primer has a length in the range of between 18-40
nucleotides, 20-35 nucleotides, or 21-30 nucleotides, and any
length between the stated ranges. In some embodiments, primers are
in the range of between 10-50 nucleotides long, such as 15-45
nucleotides long, 18-40 nucleotides long, 20-30 nucleotides long,
21-25 nucleotides long and so on, and any length between the stated
ranges. In some embodiments, the primers are not more than about
10, 12, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45,
50, 55, 60, 65, or 70 nucleotides in length.
[0063] Primers are in some embodiments single-stranded for maximum
efficiency in amplification, but may alternatively be
double-stranded. If double-stranded, the primer is usually first
treated to separate its strands before being used to prepare
extension products. This denaturation step can be effected by heat,
but may alternatively be carried out using alkali, followed by
neutralization. Thus, a "primer" is complementary to a template,
and complexes by hydrogen bonding or hybridization with the
template to give a primer/template complex for initiation of
synthesis by a polymerase, which is extended by the addition of
covalently bonded bases linked at its 3' end complementary to the
template in the process of DNA synthesis.
[0064] A "primer pair" as used herein refers to first and second
primers having nucleic acid sequence suitable for nucleic
acid-based amplification of a target nucleic acid. Such primer
pairs generally include a first primer having a sequence that is
the same or similar to that of a first portion of a target nucleic
acid, and a second primer having a sequence that is complementary
to a second portion of a target nucleic acid to provide for
amplification of the target nucleic acid or a fragment thereof.
Reference to "first" and "second" primers herein is arbitrary,
unless specifically indicated otherwise. For example, the first
primer can be designed as a "forward primer" (which initiates
nucleic acid synthesis from a 5' end of the target nucleic acid) or
as a "reverse primer" (which initiates nucleic acid synthesis from
a 5' end of the extension product produced from synthesis initiated
from the forward primer). Likewise, the second primer can be
designed as a forward primer or a reverse primer.
[0065] As used herein, the term "probe" or "oligonucleotide probe",
used interchangeable herein, refers to a structure comprised of a
polynucleotide, as defined above, which contains a nucleic acid
sequence complementary to a nucleic acid sequence present in the
target nucleic acid analyte (e.g., a nucleic acid amplification
product). The polynucleotide regions of probes may be composed of
DNA, and/or RNA, and/or synthetic nucleotide analogs. Probes are in
some embodiments of a length compatible with its use in specific
detection of all or a portion of a target sequence of a target
nucleic acid, and are in some embodiments in the range of between 8
nucleotides to 100 nucleotides in length, such as 8 to 75
nucleotides, 10 to 74 nucleotides, 12 to 72 nucleotides, 15 to 60
nucleotides, 15 to 40 nucleotides, 18 to 30 nucleotides, 20 to 40
nucleotides, 21 to 50 nucleotides, 22 to 45 nucleotides, or 25 to
40 nucleotides, and so on. In some embodiments, a probe has a
length in the range of between 18-40 nucleotides, 20-35
nucleotides, or 21-30 nucleotides long, and any length between the
stated ranges. In some embodiments, a probe is in the range of
between 10-50 nucleotides long, such as 15-45 nucleotides, 18-40
nucleotides, 20-30 nucleotides, 21-28 nucleotides, or 22-25
nucleotides, and so on, and any length between the stated ranges.
In some embodiments, the primers are not more than about 10, 12,
15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55,
60, 65, or 70 nucleotides in length.
[0066] Probes contemplated herein include probes that include a
detectable label. As used herein, the terms "label" and "detectable
label" refer to a molecule capable of detection, including, but not
limited to, radioactive isotopes, fluorescers, chemiluminescers,
chromophores, enzymes, enzyme substrates, enzyme cofactors, enzyme
inhibitors, dyes, metal ions, metal sols, ligands (e.g., biotin,
avidin, streptavidin or haptens) and the like. The term
"fluorescer" refers to a substance or a portion thereof which is
capable of exhibiting fluorescence in the detectable range.
[0067] The terms "hybridize" and "hybridization" refer to the
formation of complexes between nucleotide sequences which are
sufficiently complementary to form complexes via Watson-Crick base
pairing. Where a primer "hybridizes" with target (template), such
complexes (or hybrids) are sufficiently stable to serve the priming
function required by, e.g., the DNA polymerase to initiate DNA
synthesis.
[0068] The term "stringent conditions" refers to conditions under
which a primer will hybridize preferentially to, or specifically
bind to, its complementary binding partner, and to a lesser extent
to, or not at all to, other sequences. Put another way, the term
"stringent hybridization conditions" as used herein refers to
conditions that are compatible to produce duplexes on an array
surface between complementary binding members, e.g., between probes
and complementary targets in a sample, e.g., duplexes of nucleic
acid probes, such as DNA probes, and their corresponding nucleic
acid targets that are present in the sample, e.g., their
corresponding mRNA analytes present in the sample.
[0069] Exemplary stringent conditions typically will be those in
which the salt concentration is at least about 0.01 to 1.0 M sodium
ion concentration (or other salts) at pH 7.0 to 8.3 and the
temperature is at least about 30.degree. C. for short probes (e.g.,
10 to 50 nucleotides). Stringent conditions may also be achieved
with the addition of destabilizing agents such as formamide.
[0070] In general, there is a tradeoff between hybridization
specificity (stringency) and signal intensity. Thus, in a preferred
embodiment, the wash is performed at the highest stringency that
produces consistent results and that provides a signal intensity
greater than approximately 10% of the background intensity. Thus,
in a preferred embodiment, the hybridized array may be washed at
successively higher stringency solutions and read between each
wash. Analysis of the data sets thus produced will reveal a wash
stringency above that the hybridization pattern is not appreciably
altered and which provides adequate signal for the particular
oligonucleotide probes of interest.
[0071] The term "assessing" includes any form of measurement, and
includes determining if an element is present or not. The terms
"determining," "measuring," "evaluating," "assessing," and
"assaying" are used interchangeably and includes quantitative and
qualitative determinations. Assessing may be relative or absolute.
"Assessing the presence of" includes determining the amount of
something present, and/or determining whether it is present or
absent. As used herein, the terms "determining," "measuring," and
"assessing," and "assaying" are used interchangeably and include
both quantitative and qualitative determinations.
[0072] The term "antibody-dependent cell-mediated cytotoxicity" or
"ADCC" is a term well understood in the art, and refers to a
cell-mediated reaction in which non-specific cytotoxic cells that
express Fc receptors (FcRs) recognize bound antibody on a target
cell and subsequently cause lysis of the target cell. Non-specific
cytotoxic cells that mediate ADCC include natural killer (NK)
cells, macrophages, monocytes, neutrophils, and eosinophils.
[0073] As used herein, the term "ADCC-dependent antibody therapy"
refers to a therapy involving use of antibody that comprises an
antigen-binding domain and an Fc region that binds an FcR of a
cytotoxic effector cell, where binding of the antibody to a target
cell results in killing of the target cell via ADCC, and where
killing of the target cell(s) provides for a therapeutic effect in
an individual.
[0074] An "ADCC-treatable disease, condition, or disorder," as used
herein, is a disease, condition, or disorder that is treated with a
therapeutic antibody that mediates ADCC, thereby treating the
disease, condition, or disorder. ADCC-treatable diseases,
conditions, and disorders include, but are not limited to, a
neoplastic disease; an autoimmune disease; a microbial infection;
and allograft rejection.
[0075] The Fc receptors, members of the immunoglobulin gene
superfamily of proteins, are surface glycoproteins that can bind
the Fc portion of immunoglobulin molecules. Each member of the
family recognizes immunoglobulins of one or more isotypes through a
recognition domain on the .gamma. chain of the Fc receptor. Fc
receptors are defined by their specificity for immunoglobulin
subtypes. Fc receptors for IgG are referred to as Fc.gamma.R, for
IgE as FcR, and for IgA as Fc.alpha.R. Different accessory cells
bear Fc receptors for antibodies of different isotype, and the
isotype of the antibody determines which accessory cells will be
engaged in a given response (Ravetch J. V. et al., 2001, Annu. Rev.
Immunol. 19:275-90). Fc.gamma.Rs, designated Fc.gamma.RI (CD64),
Fc.gamma.RII (CD32), and Fc.gamma.RIII (CD16), are encoded by
distinct genes although they share extensive sequence homology.
[0076] Fc.gamma.RII (CD32) is a 40 KDa integral membrane
glycoprotein which binds complexed IgG; and exhibits only low
affinity for monomeric Ig (appr. 10.sup.6 M.sup.-1).
[0077] Fc.gamma.RII is the most widely expressed Fc.gamma.R,
present on all hematopoietic cells, including monocytes,
macrophages, B cells, NK cells, neutrophils, mast cells, and
platelets (Cohen-Solal et al., 2004, Immunol. Lett. 92:199-205).
Fc.gamma.RII has only two immunoglobulin-like regions in its
immunoglobulin binding chain and hence a much lower affinity for
IgG than Fc.gamma.RI. There are three human Fc.gamma.RII genes
(Fc.gamma.RIIA, Fc.gamma.RIIB, Fc.gamma.RIIC), all of which bind
IgG in aggregates or immune complexes. Distinct differences within
the cytoplasmic domains of Fc.gamma.RIIA and Fc.gamma.RIIB create
two functionally heterogeneous responses to receptor ligation.
Fc.gamma.RIIA initiates intracellular signaling leading to cell
activation such as phagocytosis and respiratory burst, whereas
Fc.gamma.RIIB initiates inhibitory signals leading to the
inhibition of B-cell activation.
[0078] Fc.gamma.RIII (CD16) is a Type-I membrane protein that
exists as two isoforms: Fc.gamma.RIIIA and Fc.gamma.RIIIB. Both
Fc.gamma.RIIIA and Fc.gamma.RIIIB are low affinity receptors.
Fc.gamma.RIIIA, an activating receptor, is expressed on NK cells,
macrophages, monocytes, and dendritic cells; Fc.gamma.RIIIB, an
inhibitory form, is expressed on neutrophils. All Fc.gamma.Rs bind
the same region on IgG Fc, yet with differing high (Fc.gamma.RI)
and low (Fc.gamma.RII and Fc.gamma.RIII) affinities (Sondermann et
al., 2001, J. Mol. Biol. 309:737-749).
[0079] As used herein, the terms "treatment," "treating," and the
like, refer to obtaining a desired pharmacological and/or
physiological effect. The effect may be prophylactic in terms of
completely or partially preventing a disease or symptom thereof
and/or may be therapeutic in terms of a partial or complete cure
for a disease and/or adverse affect attributable to the disease.
"Treatment," as used herein, covers any treatment of a disease in a
mammal, particularly in a human, and includes: (a) increasing
survival time; (b) decreasing the risk of death due to the disease;
(c) preventing the disease from occurring in a subject which may be
predisposed to the disease but has not yet been diagnosed as having
it; (d) inhibiting the disease, i.e., arresting its development
(e.g., reducing the rate of disease progression); and (e) relieving
the disease, i.e., causing regression of the disease.
[0080] The terms "individual," "host," "subject," and "patient,"
used interchangeably herein, refer to a mammal, including primates,
rodents, livestock, pets, horses, etc. In some embodiments, an
individual is a human.
[0081] A "functional Fc region" possesses an "effector function" of
a native Fc region, e.g., ADCC activity. Although the boundaries of
the Fc region of an immunoglobulin heavy chain may vary, the human
IgG heavy chain Fc region is usually defined to stretch from an
amino acid residue at position Cys226, or from Pro230, to the
carboxyl-terminus. The Fc region of an immunoglobulin generally
comprises two constant domains, CH2 and CH3. A "native Fc region
sequence" comprises an amino acid sequence identical to the amino
acid sequence of an Fc region found in nature. Native human Fc
region sequences include, but are not limited to, the human IgG1 Fc
region (non-A and A allotypes); human IgG2 Fc region; human IgG3 Fc
region; and human IgG4 Fc region as well as naturally occurring
variants thereof.
[0082] The term "Fc Walking" as used herein refers to an antibody
engineering procedure by which the amino acid residues in the Fc
region are selectively mutated around one or more of the lower
hinge region, B/C loop, C'/E loop, and the F/G loop. Fc Walking
involves bi-directional mutagenesis of approximately 5-10 residues,
one residue at a time, on both sides of the Fc-FcR "binding" motifs
with an objective of enhancing the Fc-FcR binding affinity and the
ADCC activity of IgG variants. As an example, Fc Walking would
cover the sequence stretch, L.sup.234-S.sup.239, as well as the
residues upstream (C.sup.229-E.sup.233) and downstream
(V.sup.240-P.sup.245) of this stretch. One such antibody
engineering procedure that can be employed for Fc Walking is in
vitro scanning saturation mutagenesis.
[0083] The term "Fc variant antibody" refers to an antibody that
differs in amino acid sequence by at least one amino acid, compared
to a reference antibody (where a reference antibody is also
referred to as a "parent antibody"). In some embodiments, the Fc
variant antibody is a monoclonal antibody (MAb); in these
embodiments, the Fc variant antibody is referred to as an "Fc
variant MAb." An Fc variant antibody may have altered FcR binding
properties (e.g., enhanced FcR binding affinity), and/or altered
ADCC activity, and/or altered effector function.
[0084] The term "enhanced affinity" is used to denote the
significant increase in binding of the Fc variant antibody to one
or more FcRs, compared to the binding affinity of the parent
antibody for the same FcR(s). An increase of 10% or more in binding
affinity over the parent antibody is considered significant.
[0085] The terms "cancer," "neoplasm," "hyperproliferative cell,"
and "tumor" are used interchangeably herein to refer to cells which
exhibit relatively autonomous growth, so that they exhibit an
aberrant growth phenotype characterized by a significant loss of
control of cell proliferation. Cancerous cells can be benign or
malignant. Viral infections (e.g., HCV infection in B-cells) can
lead to hyper(lympho)proliferative disorders.
[0086] As used herein, the term immunological binding refers to the
non-covalent interactions that occur between an antibody molecule
and an antigen for which the antibody is specific. It also refers
to such interactions that occur between an antibody in its bound
state to an antigen and an Fc receptor in an effector cell. The
strength or affinity of immunological binding interactions can be
expressed in terms of the dissociation constant (K.sub.D) of the
interaction, wherein a smaller K.sub.D represents a greater
affinity. Immunological binding properties of selected polypeptides
can be quantified using methods well known in the art. One such
method entails measuring the rates of antigen-binding site/antigen
complex formation and dissociation, wherein those rates depend on
the concentrations of the complex partners, the affinity of the
interaction, and on geometric parameters that equally influence the
rate in both directions. Thus, both the on (k.sub.on) and the off
(k.sub.off) rate constants can be determined by calculation of the
concentrations and the actual rates of association and
dissociation. The ratio of k.sub.off/k.sub.on enables cancellation
of all parameters not related to affinity and is thus equal to the
dissociation constant K.sub.D (Davies et. al., 1990, Ann. Rev.
Biochem. 59: 439).
[0087] The term "in vitro scanning saturation mutagenesis" (SSM;
Monju.TM.) refers to a novel antibody engineering procedure,
analogous to somatic hypermutation in vivo, for exploring in vitro
antibody affinity evolution. An amino acid residue of interest in a
protein sequence is mutated to nineteen other possible
substitutions, and its effect on the structure and function of the
protein analyzed. Interesting single mutants can be used as a
starting point for subsequent rounds of SSM at other sites, so that
multiple mutations with synergistic effects on binding may be
identified. This same sequential mutation approach should be useful
to optimize properties such as affinity, potency, efficacy, altered
specificity, reduced immunogenicity, and removal of proteolytic
cleavage sites (Burks et. al., 1997, Proc. Natl. Acad. Sci. USA
94:412; Chen et. al., 1999, Prot. Eng. 12:349; U.S. Pat. No.
6,180,341).
[0088] The term "specifically binds to a protein" refers to a
binding reaction, which is determinative of the presence of the
protein in the presence of a heterogeneous population of proteins.
Thus, under designated immunoassay conditions, the specified
antibodies bind to a particular protein and do not bind in a
significant amount to other proteins present in the sample.
Specific binding to a protein under such conditions may require an
antibody that is selected for its specificity for a particular
protein (Harlow and Lane, Antibodies: A Laboratory Manual, Cold
Spring Harbor Publications, New York, N.Y. (1988)).
[0089] The terms "polypeptide", "peptide", or "protein" are used
interchangeably herein to designate a linear sequence of amino acid
residues by peptide bonds between the alpha amino and carboxyl
Groups of adjacent residues. The amino acid residues are in many
embodiments in the natural L-isomeric form. However, residues in
the D-isomeric form can be substituted for any L-amino acid
residue, as long as the desired functional property is retained by
the polypeptide.
[0090] The term "binding polypeptide" refers to a polypeptide that
specifically binds to a target molecule (for example, a cell
receptor) in a manner analogous to the binding of an antibody to an
antigen. Binding polypeptides can be derived from antibody genes or
fragments of antibody genes. Thus, Fc fragment that binds to Fc
receptor is an example of a binding polypeptide.
[0091] The substitutions, deletions, inversions, and/or insertions
of amino acids in an antibody (e.g., in an Fc variant antibody)
will occur in regions not essential to antigen binding. The
identification of essential and non-essential amino acids in the
antibody can be achieved by methods known in the art, such as by
site-directed mutagenesis (for example, SSM) and AlaScan analysis
(Moffison et. al., 2001, Chem. Biol. 5:302-307). Essential amino
acids have to be maintained or replaced by conservative
substitutions in the variants. Non-essential amino acids can be
deleted, or replaced by a spacer or by conservative or
non-conservative substitutions.
[0092] Antibody variants can be obtained by substitution of any of
the amino acids present in the antibody. For example, Fc variant
antibodies can be obtained by substitution of any of the amino
acids present in the Fc fragment. As can be appreciated, there are
positions in the sequence that are more tolerant to substitutions
than others, and some substitutions can improve the binding
activity of the parent antibody. The amino acids that are essential
should either be identical to the amino acids present in the parent
antibody, or substituted by conservative substitutions. The amino
acids that are non-essential can be identical to those in the
parent antibody, or can be substituted by conservative or
non-conservative substitutions, and/or can be deleted.
[0093] The term "conservative substitution" is used in reference to
proteins or peptides to reflect amino acid substitutions that do
not substantially alter the activity (specificity or binding
affinity) of the molecule. Where the side-chain of the amino acid
to be replaced is either polar or hydrophobic, the conservative
substitution should be with a naturally or non-naturally occurring
amino acid that is also polar or hydrophobic. Conservative amino
acid substitutions generally involve substitution of one amino acid
for another amino acid with similar chemical properties (e.g.,
charge or hydrophobicity). The following six Groups each contain
amino acids that are typical conservative substitutions for one
another: (1) Alanine (A), Serine (S), Threonine (T); (2) Aspartic
acid (D), Glutamic acid (E); (3) Asparagine (N), Glutamine (Q); (4)
Arginine (R), Lysine (K); (5) Isoleucine (I), Leucine (L),
Methionine (M), Valine (V); and (6) Phenylalanine (F), Tyrosine
(Y), Tryptophan (W).
[0094] A non-conservative substitution is a substitution in which
the substituting amino acid (naturally or non-naturally occurring)
has significantly different size, configuration and/or electronic
properties compared to the amino acid being substituted. Thus, the
side chain of the substituting amino acid can be significantly
lower (or smaller) than the side chain of the native amino acid
being substituted and/or can have functional groups with
significantly different electronic properties than the amino acid
being substituted.
[0095] The term "nucleic acid" refers to deoxyribonucleotides or
ribonucleotides and polymers thereof in either single- or
double-stranded form. Unless specifically limited, the term
encompasses nucleic acids containing known analogues of natural
nucleotides that have similar binding properties as the reference
nucleic acid and are metabolized in a manner similar to naturally
occurring nucleotides. Unless otherwise indicated, a particular
nucleic acid sequence also implicitly encompasses conservatively
modified variants thereof (e.g., degenerate codon substitutions)
and complementary sequences and as well as the sequence explicitly
indicated.
[0096] Specifically, degenerate codon substitutions may be achieved
by generating sequences in which the third position of one or more
selected (or all) codons is substituted with mixed-base and/or
deoxyinosine residues (Batzer et. al., 1991, Nucleic Acid Res.
19:5081; Ohtsuka et. al., 1985, J. Biol. Chem. 260:2605). The term
nucleic acid is used interchangeably with gene, cDNA, and the mRNA
encoded by a gene.
[0097] The term "heterologous nucleic acid" refers to a nucleic
acid that is not native to the cell in which it is found.
[0098] The term "detectable label" refers to any material having a
detectable physical or chemical property. Such detectable labels
have been well established in the field of immunoassays. Thus, a
label is any composition detectable by spectroscopic,
photochemical, biochemical, immunochemical, electrical, optical or
chemical means. Useful labels in the present disclosure include
magnetic beads (for example, DYNABEADS.TM.) fluorescent dyes
(example, fluorescein isothiocyanate, rhodamine), enzymes (example,
.beta.-galactosidase, chloramphenicol acetyltransferase, horse
radish peroxidase, alkaline phosphatase and others, commonly used
as detectable enzymes, either as marker gene products or in an
enzyme-linked immunosorbent assay (ELISA). Those detectable labels
that can be encoded by nucleic acids are referred to as `reporter
genes` or `reporter gene products`.
[0099] Functional or active regions of the antibody or antibody
fragment may be identified and/or improved by mutagenesis of a
specific region of the protein, followed by expression and testing
of the expressed polypeptide. For example, amino acid sequence
variants of antibodies or antibody fragments can be generated and
those that display equivalent or improved affinity for antigen can
be identified using standard techniques and/or those described
herein. One such example is generation of an Fc variant region with
an improved affinity for Fc.gamma.RIIIA comprising F/F.sup.158
allele. Methods for generating amino acid sequence variants are
readily apparent to a skilled practitioner in the art and can
include site-specific mutagenesis, directed evolution technologies
(U.S. Pat. No. 6,180,341) or random mutagenesis (e.g., by PCR) of
the nucleic acid encoding the antibody or antibody fragment
(Zoller, M. J., 1992, Curr. Opinion in Biotechnol. 3:348-354). Both
naturally occurring and non-naturally occurring amino acids may be
used to generate amino acid sequence variants of the antibodies and
antibody fragments of the disclosure.
[0100] The "percentage of sequence identity" or "sequence identity"
is determined by comparing two optimally aligned sequences or
subsequences over a comparison window or span, wherein the portion
of the polynucleotide sequence in the comparison window may
optionally comprise additions or deletions (i.e., gaps) as compared
to the reference sequence (which does not comprise additions or
deletions) for optimal alignment of the two sequences. The
percentage is calculated by determining the number of positions at
which the identical residue (e.g., nucleic acid base or amino acid
residue) occurs in both sequences to yield the number of matched
positions, dividing the number of matched positions by the total
number of positions in the window of comparison and multiplying the
result by 100 to yield the percentage of sequence identity.
Percentage sequence identity when calculated using the programs GAP
or BESTFIT (See, e.g., below) is calculated using default gap
weights.
[0101] Sequences corresponding to the antibodies in the present
disclosure may comprise at least about 70% sequence identity to the
sequence of the antibody deposited in GenBank, preferably about
75%, 80% or 85% or more preferably, about 90% or 95% or more
identity. Homology or identity is determined by BLAST (Basic Local
Alignment Search Tool) analysis using the algorithm employed by the
programs blastp, blastn, blastx, tblastn and tblastx (Karlin et
al., 1990, Proc Natl Acad Sci USA 87:2264-2268; and Altschul, 1993,
J Mol Evol 36:290-300) which are tailored for sequence similarity
searching. The approach used by the BLAST program is first to
consider similar segments between a query sequence and a database
sequence, then to evaluate the statistical significance of all
matches that are identified and finally to summarize only those
matches which satisfy a preselected threshold of significance. For
a discussion of basic issues in similarity searching of sequence
databases, See, e.g., Altschul et al., 1994, Nat Genet. 6:119-129).
The search parameters for histogram, descriptions, alignments,
expect (i.e., the statistical significance threshold for reporting
matches against database sequences), cutoff, matrix and filter are
at the default settings. The default scoring matrix used by blastp,
blastx, tblastn, and tblastx is the BLOSUM62 matrix (Henikoff et
al., 1992, Proc Natl Acad Sci USA 89:10915-10919). Four blastn
parameters were adjusted as follows: Q=10 (gap creation penalty);
R=10 (gap extension penalty); wink=-1 (generates word hits at every
wink.sup.th position along the query); and gapw=16 (sets the window
width within which gapped alignments are generated). The equivalent
Blastp parameter settings were Q=9; R=2; wink=1; and gapw=32. A
Bestfit comparison between sequences, available in the GCG package
version 10.0, uses DNA parameters GAP=50 (gap creation penalty) and
LEN=3 (gap extension penalty) and the equivalent settings in
protein comparisons are GAP=8 and LEN=2.
DETAILED DESCRIPTION
[0102] Methods and compositions are provided for determining
whether a subject suffering from a neoplastic condition is
responsive to an antineoplastic therapy, such as antibody therapy,
e.g., Rituximab therapy. In practicing the subject methods, the
subject is genotyped to determine whether the subject has at least
one favorable Fc.gamma.R polymorphism, e.g., the H/H.sup.131
genotype in Fc.gamma.RIIA or the V/V.sup.151 genotype in
Fc.gamma.RIIIA. In addition, reagents, devices and kits thereof
that find use in practicing the subject methods are provided.
[0103] Methods and compositions are provided for determining
whether a subject suffering from a neoplastic condition is
responsive to an antineoplastic therapy, such as antibody therapy,
e.g., rituximab therapy. In practicing the subject methods, the
subject is genotyped to determine whether the subject has at least
one favorable Fc.gamma.R polymorphism, e.g., the H/H.sup.131
genotype in Fc.gamma.RIIA or the V/V.sup.158 genotype in
Fc.gamma.RIIIA. In addition, reagents, devices and kits thereof,
that find use in practicing the subject methods are provided.
[0104] Methods are provided for determining the degree of
responsiveness that a subject having an ADCC-treatable disease or
disorder will have to an antibody therapy for the disease or
disorder by genotyping the subject for an Fc.gamma.RIIA
polymorphism to obtain a first result, genotyping the subject for
an Fc.gamma.RIIIA polymorphism to obtain a second result, assigning
the subject to one of more than three categories of treatment
response and/or employing the first and second results to determine
the degree of the responsiveness of the subject to the antibody
therapy.
[0105] For example, the Fc.gamma.RIIA polymorphism can be the
H/R.sup.131 polymorphism and the Fc.gamma.RIIIA polymorphism can be
the V/F.sup.158 polymorphism.
[0106] In some embodiments, the presence of both a H/H.sup.131
genotype and a V/V.sup.158 genotype indicates a high degree of
treatment response to the antibody therapy. In other embodiments,
the identification of i) a H/H.sup.131 genotype and ii) a
V/F.sup.158 or a F/F.sup.158 genotype indicates an intermediate
degree of treatment response to the antibody therapy. In yet
another embodiment, the identification of i) a V/V.sup.158 genotype
and ii) a H/R.sup.131 or a R/R.sup.131 genotype indicates an
intermediate degree of treatment response to the antibody therapy.
In some embodiments, the identification of: i) a V/F.sup.158
genotype and a H/R.sup.131 genotype; ii) a 158 V/F genotype and a
R/R.sup.131 genotype; iii) a F/F.sup.158 genotype and a H/R.sup.131
genotype; or iv) a F/F.sup.158 genotype and a R/R.sup.131 genotype
indicates a low degree of treatment response to the antibody
therapy.
[0107] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a microbial
infection, or an allograft rejection. In other embodiments, the
ADCC-treatable disease or disorder is a neoplastic disease. In
another embodiment, the neoplastic disease is non-Hodgkin's
lymphoma (NHL), e.g., follicular lymphoma.
[0108] In some embodiments, the antibody therapy includes the use
of a therapeutic antibody or mimetic thereof that specifically
binds to CD20. In other embodiments, the therapeutic antibody is a
monoclonal antibody, e.g., rituximab.
[0109] In some embodiments, the methods include developing
patient-group specific Fc variant antibodies based on the first and
second results such that the therapeutic response rate of the
patient group to the antibody therapy is improved.
[0110] Methods are provided for selecting a specific Fc variant
antibody therapy from a set of two or more Fc variant antibody
therapies for use in treating subjects having an ADCC-treatable
disease by genotyping the subjects for an Fc.gamma.RIIA
polymorphism to classify patient population into three groups
(e.g., H/H.sup.131, H/R.sup.131, R/R.sup.131), genotyping the
subjects for an Fc.gamma.RIIIA polymorphism to classify patient
population into three groups (e.g., V/V.sup.158, V/F.sup.158,
F/F.sup.158), classifying the subjects into nine patient groups
I-IX based on the first and second results, and employing the first
and second results to select a specific Fc variant antibody therapy
for the patient group such that the degree of treatment response to
antibody therapy in the patient group is improved.
[0111] For example, the Fc.gamma.RIIA polymorphism can be the
H/R.sup.131 polymorphism and the Fc.gamma.RIIIA polymorphism can be
the V/F.sup.158 polymorphism.
[0112] In some embodiments, the genotyping may identify a
H/H.sup.131 genotype and a V/V.sup.158 genotype. In this
embodiment, the Fc variant antibody may be selected for enhanced
binding and/or in vitro ADCC function to at least one of an
Fc.gamma.RIIA including a H/H.sup.131 allele and an Fc.gamma.RIIIA
including a V/V.sup.158 allele.
[0113] In other embodiments, the genotyping may identify a
H/H.sup.131 genotype and a V/F.sup.158 genotype. In this
embodiment, the Fc variant antibody can be selected for enhanced
binding and/or in vitro ADCC function to at least one of an
Fc.gamma.RIIA including a H/H.sup.131 allele and an Fc.gamma.RIIIA
including a V/F.sup.158 allele.
[0114] In some embodiments, the genotyping may identify a
H/H.sup.131 genotype and a F/F.sup.158 genotype. In this
embodiment, the Fc variant antibody may be selected for enhanced
binding and/or in vitro ADCC function to at least one of an
Fc.gamma.RIIA including a H/H.sup.131 allele and an Fc.gamma.RIIIA
including a F/F.sup.158 allele.
[0115] In other embodiments, the genotyping may identify a
V/F.sup.158 genotype and a H/R.sup.131 genotype. In this
embodiment, the Fc variant antibody may be selected for enhanced
binding and/or in vitro ADCC function to at least one of an
Fc.gamma.RIIA including a H/R.sup.131 allele and an Fc.gamma.RIIIA
including a V/F.sup.158 allele.
[0116] In other embodiments, the genotyping may identify a
V/F.sup.158 genotype and a R/R.sup.131 genotype. In this
embodiment, the Fc variant antibody may be selected for enhanced
binding and/or in vitro ADCC function to at least one of an
Fc.gamma.RIIA including a R/R.sup.131 allele and an Fc.gamma.RIIIA
including a V/F.sup.158 allele.
[0117] In other embodiments, the genotyping may identify a
F/F.sup.158 genotype and a H/R.sup.131 genotype. In this
embodiment, the Fc variant antibody may be selected for enhanced
binding and/or in vitro ADCC function to at least one of an
Fc.gamma.RIIA including a H/R.sup.131 allele and an Fc.gamma.RIIIA
including a F/F.sup.158 allele.
[0118] In some embodiments, the genotyping may identify a
F/F.sup.158 genotype and a R/R.sup.131 genotype. In this
embodiment, the Fc variant antibody can be selected for enhanced
binding and/or in vitro ADCC function to at least one of an
Fc.gamma.RIIA including a R/R.sup.131 and an Fc.gamma.RIIIA
including a F/F.sup.158 allele
[0119] In other embodiments, the genotyping may identify a
V/V.sup.158 genotype and a H/R.sup.131 genotype. In this
embodiment, the Fc variant antibody may be selected for enhanced
binding and/or in vitro ADCC function to at least one of an
Fc.gamma.RIIA including a H/R.sup.131 allele and an Fc.gamma.RIIIA
including a V/V.sup.158 allele.
[0120] In other embodiments, the genotyping may identify a
V/V.sup.158 genotype and a R/R.sup.131 genotype. In this
embodiment, the Fc variant antibody may be selected for enhanced
binding and/or in vitro ADCC function to at least one of an
Fc.gamma.RIIA including a R/R.sup.131 allele and an Fc.gamma.RIIIA
including a V/V.sup.158 allele.
[0121] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a microbial
infection, or an allograft rejection.
[0122] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a microbial
infection, or an allograft rejection. In some embodiments, the
ADCC-treatable disease or disorder is a neoplastic disease. In
other embodiments, the neoplastic disease is non-Hodgkin's lymphoma
(NHL), e.g., follicular lymphoma.
[0123] In some embodiments, the antibody therapy includes the use
of a therapeutic antibody or mimetic thereof that specifically
binds to CD20. In other embodiments, the therapeutic antibody is a
monoclonal antibody.
[0124] In other embodiments, the monoclonal antibody may include
one or more amino acid substitutions compared to rituximab, wherein
the one or more amino acid substitutions provide for enhanced
binding and/or in vitro ADCC function to at least one of an
Fc.gamma.RIIA comprising H/R.sup.131 or R/R.sup.131 alleles, and an
Fc.gamma.RIIIA comprising V/F.sup.158 or F/F.sup.158 alleles.
[0125] Methods are also provided for making a set of related
antibodies by modifying the amino acid sequence of at least one Fc
region amino acid residue in a parent antibody, such that the
modified Fc region exhibits enhanced binding affinity to at least
one Fc receptor encoded by an Fc receptor gene of a first genotype,
compared to the Fc binding affinity of the parent antibody, to
generate a first Fc variant antibody; and/or modifying at least one
Fc region amino acid residue in a parent antibody, such that the
modified constant region exhibits enhanced binding affinity to at
least one Fc receptor encoded by an Fc receptor gene of a second
genotype, compared to the Fc binding affinity of the parent
antibody, to generate a second Fc variant antibody, wherein the
first and second Fc variant antibodies have the same antigen
specificity.
[0126] For example, the first and the second Fc variant antibodies
can have one or more amino acid residue modifications in one or
more locations of a lower hinge region, a CH2 domain, and/or a CH3
domain.
[0127] In some embodiments, the wild-type antibody is a therapeutic
antibody used in therapy of an ADCC-treatable disease or disorder.
In some embodiments, the wild-type antibody is a therapeutic
antibody used in therapy of a neoplastic disease. In another
embodiment, the neoplastic disease is non-Hodgkin's lymphoma (NHL),
e.g., follicular lymphoma.
[0128] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a viral
infection, a parasitic infection, or an allograft rejection.
[0129] In some embodiments, the first and second Fc variant
antibodies bind specifically binds to CD20. In some embodiments,
the first and second Fc variant antibodies are monoclonal
antibodies, e.g., rituximab.
[0130] Also provided are kits for use in determining responsiveness
to an antibody therapy in a patient which include an element for
genotyping a sample to identify an Fc.gamma.RIIA polymorphism, an
element for genotyping the sample to identify an Fc.gamma.RIIIA
polymorphism, or an element for genotyping the sample to identify
an Fc.gamma.RIIIA polymorphism and an Fc.gamma.RIIA, and a
reference that correlates a genotype with predicted therapeutic
response to a therapeutic antibody.
[0131] In some embodiments, the Fc.gamma.RIIA genotype may be a
H/H.sup.131 genotype and the Fc.gamma.RIIIA genotype may be a
V/V.sup.158 genotype. In this embodiment, the reference indicates a
high degree of responsiveness to the therapeutic antibody.
[0132] In other embodiments, the Fc.gamma.RIIA genotype may be a
H/H.sup.131 genotype and the Fc.gamma.RIIIA genotype may be a
V/F.sup.158 or a F/F.sup.158 genotype. In this embodiment, the
reference indicates an intermediate degree of responsiveness to the
therapeutic antibody.
[0133] In another embodiment, the Fc.gamma.RIIIA genotype is a
V/V.sup.158 genotype and the Fc.gamma.RIIA genotype is a
H/R.sup.131 or a R/R.sup.131 genotype. In this embodiment, the
reference indicates an intermediate degree of responsiveness to the
reference therapeutic antibody.
[0134] In some embodiments, the reference may indicate choosing an
Fc variant antibody that exhibits enhanced binding to an
Fc.gamma.RIIA and/or an Fc.gamma.RIIIA that exhibits enhanced in
vitro ADCC function.
[0135] In some embodiments, the genotype is a V/F.sup.158 genotype
and a H/R.sup.131 genotype, a V/F.sup.158 genotype and a
R/R.sup.131 genotype, a F/F.sup.158 genotype and a H/R.sup.131
genotype, or a F/F.sup.158 genotype and a R/R.sup.131* In this
embodiment, the reference indicates a low degree of responsiveness
to the therapeutic antibody.
[0136] In some embodiments, the therapeutic antibody is used for
treating an ADCC-treatable disease or disorder. In some
embodiments, the ADCC-treatable disease or disorder may be a
neoplastic disease, an autoimmune disease, a microbial infection,
or an allograft rejection.
[0137] Methods are provided for of treating an ADCC-treatable
disease or disorder in an individual by determining a category of
therapeutic responsiveness to an antibody therapy by genotyping the
individual for an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism, wherein the Fc.gamma.RIIA polymorphism and the
Fc.gamma.RIIIA polymorphism together indicate a degree of
therapeutic responsiveness; selecting an antibody from a set of
related antibodies, wherein members of the set of related
antibodies have the same antigen binding specificity, and wherein
the members of the set of related antibodies differ in binding
affinity to an Fc.gamma.RIIA and/or an Fc.gamma.RIIIA and/or differ
in in vitro ADCC function; and administering an effective amount of
the antibody to the individual.
[0138] In some embodiments, the genotyping may identify a
H/H.sup.131 genotype and a V/V.sup.158 genotype. In this
embodiment, the antibody is selected for binding to at least one of
an Fc.gamma.RIIA having a H/H.sup.131 allele and an Fc.gamma.RIIIA
having a V/V.sup.158 allele.
[0139] In other embodiments, the genotyping may identify an
H/H.sup.131 genotype and a V/F.sup.158 or a F/F.sup.158 genotype.
In this embodiment, the antibody can be selected for binding to at
least one of an Fc.gamma.RIIA having a His.sup.131 and an
Fc.gamma.RIIIA having a Val.sup.158 or F.sup.158.
[0140] In another embodiment, the genotyping may identify a
V/F.sup.158 genotype and a H/R.sup.131 genotype; a V/F.sup.158
genotype and a R/R.sup.131 genotype; a F/F.sup.158 genotype and a
H/R.sup.131 genotype; or a F/F.sup.158 genotype and a R/R.sup.131
genotype. In this embodiment, the antibody may be selected for
binding to at least one of an Fc.gamma.RIIA having a Arg.sup.131
and an Fc.gamma.RIIIA having a Phe.sup.158.
[0141] In other embodiments, the genotyping may identify a
H/H.sup.131 genotype and a V/F.sup.158 genotype. In this
embodiment, the antibody may be an Fc variant antibody selected for
enhanced binding and/or in vitro ADCC function to at least one of
an Fc.gamma.RIIA having a H/H.sup.131 allele and an Fc.gamma.RIIIA
having a V/F.sup.158 allele.
[0142] In some embodiment, the genotyping identifies a H/H.sup.131
genotype and a F/F.sup.158 genotype. In this embodiment, the
antibody may be an Fc variant antibody selected for enhanced
binding and/or in vitro ADCC function to at least one of an
Fc.gamma.RIIA having a H/H.sup.131 allele and an Fc.gamma.RIIIA
having a F/F.sup.158 allele.
[0143] In some embodiments, the genotyping may identify a
V/F.sup.158 genotype and a H/R.sup.131 genotype. In this
embodiment, the antibody can be an Fc variant antibody selected for
enhanced binding and/or in vitro ADCC function to at least one of
an Fc.gamma.RIIA having a H/R.sup.131 allele and an Fc.gamma.RIIIA
having a V/F.sup.158 allele.
[0144] In some embodiments, the genotyping may identify a
V/F.sup.158 genotype and a R/R.sup.131 genotype. In this
embodiment, the antibody can be an Fc variant antibody selected for
enhanced binding and/or in vitro ADCC function to at least one of
an Fc.gamma.RIIA having a R/R.sup.131 allele and an Fc.gamma.RIIIA
having a V/F.sup.158 allele.
[0145] In some embodiments, the genotyping may identify a
F/F.sup.158 genotype and a H/R.sup.131 genotype. In this
embodiment, the antibody can be an Fc variant antibody selected for
enhanced binding and/or in vitro ADCC function to at least one of
an Fc.gamma.RIIA having a H/R.sup.131 allele and an Fc.gamma.RIIIA
having a F/F.sup.158 allele.
[0146] In some embodiments, the genotyping may identify a
F/F.sup.158 genotype and a R/R.sup.131 genotype. In this
embodiment, the antibody can be an Fc variant antibody selected for
enhanced binding and/or in vitro ADCC function to at least one of
an Fc.gamma.RIIA having a R/R.sup.131 and an Fc.gamma.RIIIA having
a F/F.sup.158 allele.
[0147] In other embodiments, the genotyping may identify a
V/V.sup.158 genotype and a H/R.sup.131 genotype. In this
embodiment, the antibody may be an Fc variant antibody selected for
enhanced binding and/or in vitro ADCC function to at least one of
an Fc.gamma.RIIA having a H/R.sup.131 allele and an Fc.gamma.RIIIA
having a V/V.sup.158 allele.
[0148] In some embodiments, the genotyping may identify a
V/V.sup.158 genotype and a R/R.sup.131 genotype. In this
embodiment, the antibody is an Fc variant antibody selected for
enhanced binding and/or in vitro ADCC function to at least one of
an Fc.gamma.RIIA having a R/R.sup.131 allele and an Fc.gamma.RIIIA
having a V/V.sup.158 allele.
[0149] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a microbial
infection, or an allograft rejection.
[0150] Methods are provided for determining the degree of
responsiveness to an antibody-dependent cell-mediated cytotoxicity
antibody therapy by genotyping the subject for two or more
Fc.gamma. receptor polymorphisms and employing the first and second
Fc.gamma. receptor polymorphisms to determine the degree of the
responsiveness of the subject to the antibody therapy.
[0151] In some embodiments, the Fc.gamma. receptor polymorphisms
include an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism.
[0152] For example, an amino acid residue in the Fc region is
selectively substituted by nineteen other natural amino acids.
[0153] Methods are also provided for generating a set of Fc variant
antibodies by amplifying a nucleic acid comprising a nucleotide
sequence encoding an Fc region of an antibody, wherein the
amplifying is carried out with a set of primers that encode all
nineteen amino acid variants at a single residue of the Fc region,
to generate a set of variant nucleic acids encoding nineteen amino
acid substitution variants at the single residue of the Fc region;
transcribing and translating each of the variant nucleic acids in
vitro, to generate a set of Fc variants; and/or c) selecting from
the set an Fc variant having altered FcR binding activity compared
to a reference Fc, generating a set of selected Fc variants.
[0154] In some embodiments, the methods include determining in
vitro ADCC activity of the selected Fc variant.
[0155] In other embodiments, the methods include: d) repeating step
(a) at a second residue of the Fc region, generating a second set
of Fc variant; and/or e) repeating steps (b) and (c) on the second
set, generating a second set of selected Fc variants.
[0156] In some embodiments, the transcribing and translating is
carried out using a prokaryotic expression system.
[0157] In other embodiments, the Fc-encoding nucleotide sequence is
under the transcriptional control of a phage promoter.
[0158] In some embodiments, FcR binding activity is assessed using
an enzyme-linked immunosorbent assay.
[0159] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/V.sup.158 genotype, the H/H.sup.131 genotype, or
both the V/V.sup.158 genotype, the H/H.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0160] In some embodiments, the patient has a hyperproliferative
disorder. In some embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0161] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0162] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/F.sup.158 genotype, the H/H.sup.131 genotype, or
both the V/F.sup.158 genotype, the H/H.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0163] In a some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0164] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0165] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the F/F.sup.158 genotype, the H/H.sup.131 genotype, or
both the F/F.sup.158 genotype, the H/H.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0166] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0167] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0168] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/V.sup.158 genotype, the H/R.sup.131 genotype, or
both the V/V.sup.158 genotype, the H/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0169] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0170] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0171] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/F.sup.158 genotype, the H/R.sup.131 genotype, or
both the V/F.sup.158 genotype, the H/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0172] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0173] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0174] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the F/F.sup.158 genotype, the H/R.sup.131 genotype, or
both the F/F.sup.158 genotype, the H/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0175] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0176] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0177] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/V.sup.158 genotype, the R/R.sup.131 genotype, or
both the V/V.sup.158 genotype, the R/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0178] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0179] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0180] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the V/F.sup.158 genotype, the R/R.sup.131 genotype, or
both the V/F.sup.158 genotype, the R/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0181] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0182] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0183] Methods are also provided for selecting a patient for
treatment with an antibody by (a) determining if the patient has
(i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA
V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158 genotype; or (ii.)
determining if the patient has an Fc.gamma.RIIA H/H.sup.131
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA
R/R.sup.131 genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype or an Fc.gamma.RIIIA
F/F.sup.158, Fc.gamma.RIIA R/R.sup.131 genotype; (b) selecting the
patient with the F/F.sup.158 genotype, the R/R.sup.131 genotype, or
both the F/F.sup.158 genotype, the R/R.sup.131 genotype for
treatment with the antibody based on the genotype determination of
steps (i), (ii) or (iii); and (c) administering the antibody to the
patient selected in step (b).
[0184] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0185] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0186] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA V/V.sup.158
genotype, an Fc.gamma.RIIA H/H.sup.131 genotype; or both an
Fc.gamma.RIIIA V/V.sup.158 genotype and an Fc.gamma.RIIA
H/H.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0187] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0188] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0189] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA V/F.sup.158
genotype, an Fc.gamma.RIIA H/H.sup.131 genotype; or both an
Fc.gamma.RIIIA V/F.sup.158 genotype and an Fc.gamma.RIIA
H/H.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0190] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0191] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0192] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA F/F.sup.158
genotype, or an Fc.gamma.RIIA H/H.sup.131 genotype; or both an
Fc.gamma.RIIIA F/F.sup.158 genotype and an Fc.gamma.RIIA
H/H.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0193] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0194] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0195] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA V/V.sup.158
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype; or both an
Fc.gamma.RIIIA V/V.sup.158 genotype and an Fc.gamma.RIIA
H/R.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0196] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0197] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0198] Methods are also provided for treating a patient with an
antibody by (a) selecting a patient with an Fc.gamma.RIIIA
V/F.sup.158 genotype, an Fc.gamma.RIIA H/R.sup.131 genotype, or
both an Fc.gamma.RIIIA V/F.sup.158 genotype and an Fc.gamma.RIIA
H/R.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0199] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0200] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0201] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA F/F.sup.158
genotype, an Fc.gamma.RIIA H/R.sup.131 genotype, or both an
Fc.gamma.RIIIA F/F.sup.158 genotype and an Fc.gamma.RIIA
H/R.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0202] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0203] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0204] Methods are provided for treating a patient with an antibody
by (a) selecting a patient with an Fc.gamma.RIIIA V/V.sup.158
genotype, an Fc.gamma.RIIA R/R.sup.131 genotype, or both an
Fc.gamma.RIIIA V/V.sup.158 genotype and an Fc.gamma.RIIA
R/R.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0205] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0206] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0207] Methods are also provided for treating a patient with an
antibody by (a) selecting a patient with an Fc.gamma.RIIIA
V/F.sup.158 genotype, an Fc.gamma.RIIA R/R.sup.131 genotype, or
both an Fc.gamma.RIIIA V/F.sup.158 genotype and an Fc.gamma.RIIA
R/R.sup.131 genotype and (b) administering the antibody to the
patient selected in step (a).
[0208] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0209] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0210] Methods are provided for treating a patient with an
antibody, comprising: (a) selecting a patient with an
Fc.gamma.RIIIA F/F.sup.158 genotype, an Fc.gamma.RIIA R/R.sup.131
genotype, or both an Fc.gamma.RIIIA F/F.sup.158 genotype and an
Fc.gamma.RIIA R/R.sup.131 genotype and (b) administering the
antibody to the patient selected in step (a).
[0211] In some embodiments, the patient has a hyperproliferative
disorder. In other embodiments, the hyperproliferative disorder is
cancer, e.g., non-Hodgkin's lymphoma.
[0212] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0213] Methods are also provided for classifying a subject having
an ADCC-treatable disease or disorder into one of more than three
categories of responsiveness to an antibody therapy by genotyping
subjects for an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism, wherein the subjects have or had the ADCC-treatable
disease or disorder and are or were administered antibody therapy
for the disease or disorder; classifying each subject based on its
Fc.gamma.RIIA polymorphism and Fc.gamma.RIIIA polymorphism to one
of three or more categories of responsiveness to the antibody
therapy; genotyping the subject for an Fc.gamma.RIIA polymorphism
and an Fc.gamma.RIIIA polymorphism; identifying a genotype from (a)
that is identical to the genotype from the subject in step (c),
wherein the subject is classified into a category of responsiveness
to the antibody therapy for the disease or disorder corresponding
with a subject having an identical Fc.gamma.RIIA polymorphism and
an identical Fc.gamma.RIIIA polymorphism.
[0214] In one embodiment, the subjects are classified into one of
nine categories of responsiveness to the antibody therapy.
[0215] For example, the Fc.gamma.RIIA polymorphism may be the
H/R.sup.131 polymorphism and the Fc.gamma.RIIIA polymorphism may be
the V/F.sup.158 polymorphism.
[0216] In some embodiments, the presence of both a H/H.sup.131
genotype and a V/V.sup.158 genotype indicates a high degree of
treatment response to the antibody therapy.
[0217] In other embodiments, the identification of i) a H/H.sup.131
genotype and ii) a V/F.sup.158 or a F/F.sup.158 genotype indicates
an intermediate degree of treatment response to the antibody
therapy.
[0218] In other embodiments, the identification of i) a V/V.sup.158
genotype and ii) a H/R.sup.131 or a R/R.sup.131 genotype indicates
an intermediate degree of treatment response to the antibody
therapy.
[0219] In some embodiments, the identification of: i) a V/F.sup.158
genotype and a H/R.sup.131 genotype; ii) a 158 V/F genotype and a
R/R.sup.131 genotype; iii) a F/F.sup.158 genotype and a H/R.sup.131
genotype; or iv) a F/F.sup.158 genotype and a R/R.sup.131 genotype
indicates a low degree of treatment response to the antibody
therapy.
[0220] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a microbial
infection, or an allograft rejection. In some embodiments, the
ADCC-treatable disease or disorder may be a neoplastic disease. In
some embodiments, the neoplastic disease is non-Hodgkin's lymphoma
(NHL), e.g., follicular lymphoma.
[0221] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0222] Methods are provided for determining the degree of
responsiveness that a subject having an ADCC-treatable disease or
disorder will have to an antibody therapy for the disease or
disorder by genotyping the subject for an Fc.gamma.RIIA
polymorphism and an Fc.gamma.RIIIA polymorphism; and identifying a
genotype associated with a particular degree of responsiveness to
the antibody therapy from a reference that is identical to the
genotype from the test subject, wherein the test subject is
determined to have a degree of responsiveness to the antibody
therapy for the disease or disorder corresponding to the level of
responsiveness associated with the reference having an identical
Fc.gamma.RIIA polymorphism and an identical Fc.gamma.RIIIA
polymorphism.
[0223] In some embodiments, the subjects may be classified into one
of nine categories of responsiveness to the antibody therapy.
[0224] In some embodiments, the Fc.gamma.RIIA polymorphism is the
H/R.sup.131 polymorphism and the Fc.gamma.RIIIA polymorphism is the
V/F.sup.158 polymorphism. In other embodiments, the presence of
both a H/H.sup.131 genotype and a V/V.sup.158 genotype indicates a
high degree of treatment response to the antibody therapy. In other
embodiments, the identification of i) a H/H.sup.131 genotype and
ii) a V/F.sup.158 or a F/F.sup.158 genotype indicates an
intermediate degree of treatment response to the antibody therapy.
In other embodiments, the identification of i) a V/V.sup.158
genotype and ii) a H/R.sup.131 or a R/R.sup.131 genotype indicates
an intermediate degree of treatment response to the antibody
therapy. In yet other embodiments, the identification of: i) a
V/F.sup.158 genotype and a H/R.sup.131 genotype; ii) a 158 V/F
genotype and a R/R.sup.131 genotype; iii) a F/F.sup.158 genotype
and a H/R.sup.131 genotype; or iv) a F/F.sup.158 genotype and a
R/R.sup.131 genotype indicates a low degree of treatment response
to the antibody therapy.
[0225] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a microbial
infection, or an allograft rejection. In some embodiments, the
ADCC-treatable disease or disorder may be a neoplastic disease. In
some embodiments, the neoplastic disease is non-Hodgkin's lymphoma
(NHL), e.g., follicular lymphoma.
[0226] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0227] For example, the reference may be an index including the
genotypes for subjects that had an ADCC-treatable disease or
disorder and were administered antibody therapy for the disease or
disorder and wherein the subjects were classified into one of more
than three categories of responsiveness to the antibody
therapy.
[0228] Methods are also provided for determining the degree of
responsiveness that a test subject having an ADCC-treatable disease
or disorder will have to an antibody therapy for the disease or
disorder by (a) genotyping subjects for an Fc.gamma.RIIA
polymorphism and an Fc.gamma.RIIIA polymorphism, wherein the
subjects have or had the ADCC-treatable disease or disorder and are
or were administered antibody therapy for the disease or disorder;
(b) classifying each subject based on its Fc.gamma.RIIA
polymorphism and Fc.gamma.RIIIA polymorphism to one of more than
three categories of responsiveness to the antibody therapy; (c)
genotyping the test subject for an Fc.gamma.RIIA polymorphism and
an Fc.gamma.RIIIA polymorphism; and (d) identifying a genotype from
(a) that is identical to the genotype from the test subject in step
(c), wherein the test subject is determined to have a degree of
responsiveness to the antibody therapy for the disease or disorder
corresponding to the level of responsiveness associated with a
subject having an identical Fc.gamma.RIIA polymorphism and an
identical Fc.gamma.RIIIA polymorphism.
[0229] For example, the subjects may be classified into one of nine
categories of responsiveness to the antibody therapy.
[0230] For example, the Fc.gamma.RIIA polymorphism may be the
H/R.sup.131 polymorphism and the Fc.gamma.RIIIA polymorphism may be
the V/F.sup.158 polymorphism.
[0231] In some embodiments, the presence of both a H/H.sup.131
genotype and a V/V.sup.158 genotype indicates a high degree of
treatment response to the antibody therapy. In other embodiments,
the identification of i) a H/H.sup.131 genotype and ii) a
V/F.sup.158 or a F/F.sup.158 genotype indicates an intermediate
degree of treatment response to the antibody therapy. In other
embodiments, the identification of i) a V/V.sup.158 genotype and
ii) a H/R.sup.131 or a R/R.sup.131 genotype indicates an
intermediate degree of treatment response to the antibody therapy.
In other embodiments, the identification of: i) a V/F.sup.158
genotype and a H/R.sup.131 genotype; ii) a 158 V/F genotype and a
R/R.sup.131 genotype; iii) a F/F.sup.158 genotype and a H/R.sup.131
genotype; or iv) a F/F.sup.158 genotype and a R/R.sup.131 genotype
indicates a low degree of treatment response to the antibody
therapy.
[0232] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a microbial
infection, or an allograft rejection. In some embodiments, the
ADCC-treatable disease or disorder may be a neoplastic disease. In
some embodiments, the neoplastic disease is non-Hodgkin's lymphoma
(NHL), e.g., follicular lymphoma.
[0233] In some embodiments, the antibody is a therapeutic antibody,
e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0234] Also provided are kits for use in determining responsiveness
to an antibody therapy in a patient which include an element for
genotyping the sample to identify an Fc.gamma.RIIA polymorphism; an
element for genotyping the sample to identify an Fc.gamma.RIIIA
polymorphism; and a reference that correlates a genotype in the
patient with one of more than three predicted therapeutic responses
to the antibody therapy.
[0235] For example, the reference may correlate a genotype in the
patient with one of nine predicted therapeutic responses to the
antibody therapy.
[0236] In some embodiments, the Fc.gamma.RIIA genotype is a
H/H.sup.131 genotype, wherein the Fc.gamma.RIIIA genotype is a
V/V.sup.158 genotype, and wherein the reference indicates a high
degree of responsiveness to the therapeutic antibody.
[0237] In other embodiments, the Fc.gamma.RIIA genotype is a
H/H.sup.131 genotype, wherein the Fc.gamma.RIIIA genotype is a
V/F.sup.158 or a F/F.sup.158 genotype, and wherein the reference
indicates an intermediate degree of responsiveness to the
therapeutic antibody.
[0238] In some embodiments, the Fc.gamma.RIIIA genotype is a
V/V.sup.158 genotype, wherein the Fc.gamma.RIIA genotype is a
H/R.sup.131 or a R/R.sup.131 genotype, and wherein the reference
indicates an intermediate degree of responsiveness to the reference
therapeutic antibody.
[0239] In other embodiments, the genotype is i) a V/F.sup.158
genotype and a H/R.sup.131 genotype; ii) a V/F.sup.158 genotype and
a R/R.sup.131 genotype; iii) a F/F.sup.158 genotype and a
H/R.sup.131 genotype; or iv) a F/F.sup.158 genotype and a
R/R.sup.131, and wherein the reference indicates a low degree of
responsiveness to the therapeutic antibody.
[0240] In some embodiments, the reference indicates choosing an
variant antibody that exhibits enhanced binding to an Fc.gamma.RIIA
and/or an Fc.gamma.RIIIA and/or that exhibits enhanced in vitro
ADCC function.
[0241] In some embodiments, the therapeutic antibody is used for
treating an ADCC-treatable disease or disorder. In some
embodiments, the ADCC-treatable disease or disorder may be a
neoplastic disease, an autoimmune disease, a microbial infection,
or an allograft rejection. In some embodiments, the neoplastic
disease is non-Hodgkin's lymphoma (NHL), e.g., follicular
lymphoma.
[0242] Methods are provided for selecting a specific variant
antibody therapy from a set of two or more variant antibody
therapies for use in treatment of subjects having an ADCC-treatable
disease by genotyping the subjects for an Fc.gamma.RIIA
polymorphism and an Fc.gamma.RIIIA polymorphism, classifying the
subjects into one of more than three categories of responsiveness
based on their Fc.gamma.RIIA polymorphism and their Fc.gamma.RIIIA
polymorphism, and selecting a specific variant antibody therapy for
the subjects such that the degree of responsiveness to the antibody
therapy in the subjects is improved from the degree of
responsiveness obtained with another variant antibody.
[0243] In some embodiments, the subjects are classified into one of
nine categories of responsiveness to the antibody therapy.
[0244] For example, the Fc.gamma.RIIA polymorphism can be the
H/R.sup.131 polymorphism and the Fc.gamma.RIIIA polymorphism can be
the V/F.sup.158 polymorphism.
[0245] In some embodiments, the presence of both a H/H.sup.131
genotype and a V/V.sup.158 genotype indicates a high degree of
treatment response to the antibody therapy. In other embodiments,
the identification of i) a H/H.sup.131 genotype and ii) a
V/F.sup.158 or a F/F.sup.158 genotype indicates an intermediate
degree of treatment response to the antibody therapy. In other
embodiments, the identification of i) a V/V.sup.158 genotype and
ii) a H/R.sup.131 or a R/R.sup.131 genotype indicates an
intermediate degree of treatment response to the antibody therapy.
In yet other embodiments, the identification of: i) a V/F.sup.158
genotype and a H/R.sup.131 genotype; ii) a 158 V/F genotype and a
R/R.sup.131 genotype; iii) a F/F.sup.158 genotype and a H/R.sup.131
genotype; or iv) a F/F.sup.158 genotype and a R/R.sup.131 genotype
indicates a low degree of treatment response to the antibody
therapy.
[0246] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a microbial
infection, or an allograft rejection. In some embodiments, the
ADCC-treatable disease or disorder may be a neoplastic disease. In
some embodiments, the neoplastic disease is non-Hodgkin's lymphoma
(NHL), e.g., follicular lymphoma.
[0247] In some embodiments, the antibody may be a therapeutic
antibody, e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM.,
HERCEPTIN.RTM., XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM.,
REMICADE.RTM., HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM.,
SYNAGIS.RTM., VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM.,
REOPRO.RTM., LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0248] For example, the monoclonal antibody may include one or more
amino acid substitutions compared to Rituximab, wherein the one or
more amino acid substitutions provide for enhanced binding and/or
in vitro ADCC function to at least one of an Fc.gamma.RIIA
comprising H/R.sup.131 or R/R.sup.131 alleles, and an
Fc.gamma.RIIIA comprising V/F.sup.158 or F/F.sup.158 alleles.
[0249] Methods are also provided for treating an ADCC-treatable
disease or disorder in a subject by genotyping the subject for an
Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA polymorphism,
classifying the subject into one of more than three categories of
therapeutic responsiveness to an antibody therapy based on the
Fc.gamma.RIIA polymorphism and the Fc.gamma.RIIIA polymorphism,
selecting an antibody with a preferred degree of therapeutic
responsiveness from a set of related antibodies, wherein members of
the set of related antibodies have the same antigen binding
specificity, and wherein the members of the set of related
antibodies differ in binding affinity to an Fc.gamma.RIIA and/or an
Fc.gamma.RIIIA and/or differ in in vitro ADCC function, and
administering a therapeutically effective amount of the antibody to
the subject, wherein, the antibody treats the ADCC-treatable
disease or disorder in the subject.
[0250] In some embodiments, the subject is classified into one of
nine categories of therapeutic responsiveness.
[0251] For example, the Fc.gamma.RIIA polymorphism may be the
H/R.sup.131 polymorphism, and the Fc.gamma.RIIIA polymorphism may
be the V/F.sup.158 polymorphism.
[0252] In some embodiments, the genotyping identifies a H/H.sup.131
genotype and a V/V.sup.158 genotype, and the antibody is selected
for binding to at least one of an Fc.gamma.RIIA comprising
H/H.sup.131 allele and an Fc.gamma.RIIIA comprising V/V.sup.158
allele.
[0253] In some embodiments, the genotyping identifies a H/H.sup.131
genotype and a V/F.sup.158 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/H.sup.131 allele and an
Fc.gamma.RIIIA comprising V/F.sup.158 allele.
[0254] In some embodiments, the genotyping identifies a H/H.sup.131
genotype and a F/F.sup.158 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/H.sup.131 allele and an
Fc.gamma.RIIIA comprising F/F.sup.158 allele.
[0255] In some embodiments, the genotyping identifies a V/V.sup.158
genotype and a H/R.sup.131 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/R.sup.131 allele and an
Fc.gamma.RIIIA comprising V/V.sup.158 allele.
[0256] In some embodiments, the genotyping identifies a V/V.sup.158
genotype and a R/R.sup.131 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising R/R.sup.131 allele and an
Fc.gamma.RIIIA comprising V/V.sup.158 allele.
[0257] In other embodiments, the genotyping identifies a
V/F.sup.158 genotype and a H/R.sup.131 genotype, and the variant
antibody is selected for enhanced binding and/or in vitro ADCC
function to at least one of an Fc.gamma.RIIA comprising H/R.sup.131
allele and an Fc.gamma.RIIIA comprising V/F.sup.158 allele.
[0258] In other embodiments, the genotyping identifies a
V/F.sup.158 genotype and a R/R.sup.131 genotype, and the variant
antibody is selected for enhanced binding and/or in vitro ADCC
function to at least one of an Fc.gamma.RIIA comprising R/R.sup.131
allele and an Fc.gamma.RIIIA comprising V/F.sup.158 allele.
[0259] In some embodiments, the genotyping identifies a F/F.sup.158
genotype and a H/R.sup.131 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/R.sup.131 allele and an
Fc.gamma.RIIIA comprising F/F.sup.158 allele.
[0260] In other embodiments, the genotyping identifies a
F/F.sup.158 genotype and a R/R.sup.131 genotype, and the variant
antibody is selected for enhanced binding and/or in vitro ADCC
function to at least one of an Fc.gamma.RIIA comprising R/R.sup.131
and an Fc.gamma.RIIIA comprising F/F.sup.158 allele.
[0261] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a microbial
infection, or an allograft rejection. In some embodiments, the
ADCC-treatable disease or disorder may be a neoplastic disease. In
some embodiments, the neoplastic disease is non-Hodgkin's lymphoma
(NHL), e.g., follicular lymphoma.
[0262] In some embodiments, the antibody may be a therapeutic
antibody, e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM.,
HERCEPTIN.RTM., XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM.,
REMICADE.RTM., HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM.,
SYNAGIS.RTM., VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM.,
REOPRO.RTM., LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0263] In another embodiment, the monoclonal antibody includes one
or more amino acid substitutions compared to Rituximab, wherein the
one or more amino acid substitutions provide for enhanced binding
and/or in vitro ADCC function to at least one of an Fc.gamma.RIIA
comprising H/R.sup.131 or R/R.sup.131 alleles, and an
Fc.gamma.RIIIA comprising V/F.sup.158 or F/F.sup.158 alleles.
[0264] Methods are provided for making a set of related antibodies
capable of modulating the responsiveness of a subject having an
ADCC-treatable disease or disorder to an antibody therapy for the
disease or disorder by modifying the amino acid sequence of at
least one amino acid residue in a parent antibody, such that the
modified parent antibody exhibits enhanced binding affinity to at
least one Fc receptor encoded by an Fc receptor gene of a first
genotype, compared to the Fc binding affinity of the parent
antibody, to generate a first variant antibody; and modifying at
least one amino acid residue in a parent antibody, such that the
modified parent antibody exhibits enhanced binding affinity to at
least one Fc receptor encoded by an Fc receptor gene of a second
genotype, compared to the Fc binding affinity of the parent
antibody, to generate a second variant antibody, wherein the first
and second variant antibodies have the same antigen specificity and
are capable of modulating the responsiveness of a subject having an
ADCC-treatable disease or disorder to an antibody therapy for the
disease or disorder.
[0265] For example, the first and the second variant antibodies may
include one or more amino acid residue modifications in one or more
locations of a lower hinge region, a CH2 domain, and/or a CH3
domain.
[0266] In some embodiments, the parent antibody may be a
therapeutic antibody used in therapy of an ADCC-treatable disease
or disorder.
[0267] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a viral
infection, a parasitic infection, or an allograft rejection. In
some embodiments, the neoplastic disease is non-Hodgkin's lymphoma
(NHL), e.g., follicular lymphoma.
[0268] In some embodiments, the parent antibody is a therapeutic
antibody, e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM.,
HERCEPTIN.RTM., XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM.,
REMICADE.RTM., HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM.,
SYNAGIS.RTM., VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM.,
REOPRO.RTM., LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0269] In other embodiments, the parent antibody is modified in its
Fc domain. In another embodiment, the parent antibody is modified
in its CDR.
[0270] Methods are provided for generating a set of variant
antibodies capable of modulating the responsiveness of a subject
having an ADCC-treatable disease or disorder to an antibody therapy
for the disease or disorder by amplifying a nucleic acid comprising
a nucleotide sequence encoding a region of an antibody, wherein the
amplifying is carried out with a set of primers that encode all
nineteen amino acid variants at a single residue of the region, to
generate a set of variant nucleic acids encoding nineteen amino
acid substitution variants at the single residue of the region,
transcribing and translating each of the variant nucleic acids in
vitro, to generate a set of variants, and/or selecting from the set
an variant having altered FcR binding activity compared to a
reference region, generating a set of selected variants, wherein
the first and second variant antibodies have the same antigen
specificity and are capable of modulating the responsiveness of a
subject having an ADCC-treatable disease or disorder to an antibody
therapy for the disease or disorder. In some embodiments, the
method includes determining in vitro ADCC activity of the selected
variant.
[0271] In some embodiments, the methods include, repeating step
amplifying a nucleic acid comprising a nucleotide sequence encoding
a region of an antibody, wherein the amplifying is carried out with
a set of primers that encode all nineteen amino acid variants at a
single residue of the region at a second residue of the region,
generating a second set of variants and generating a second set of
selected variants.
[0272] In some embodiments, the transcribing and translating are
carried out using a prokaryotic expression system. For example, the
region-encoding nucleotide sequence may be under the
transcriptional control of a phage promoter.
[0273] In some embodiments, FcR binding activity is assessed using
an enzyme-linked immunosorbent assay.
[0274] In some embodiments, the parent antibody is modified in its
Fc domain. In other embodiments, the parent antibody is modified in
its CDR.
[0275] Methods are also provided for modulating the responsiveness
of a subject having an ADCC-treatable disease or disorder to an
antibody therapy for the disease or disorder by genotyping the
subject for an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism, classifying the subject into one of more than three
categories of therapeutic responsiveness to an antibody therapy
based on the Fc.gamma.RIIA polymorphism and the Fc.gamma.RIIIA
polymorphism, selecting an antibody from a set of related
antibodies, wherein members of the set of related antibodies have
the same antigen binding specificity, and wherein the members of
the set of related antibodies differ in binding affinity to an
Fc.gamma.RIIA and/or an Fc.gamma.RIIIA and/or differ in in vitro
ADCC function, and administering a therapeutically effective amount
of the antibody to the subject, wherein the antibody modulates the
responsiveness of the subject having an ADCC-treatable disease or
disorder to an antibody therapy for the disease or disorder.
[0276] For example, the subject may be classified into one of nine
categories of therapeutic responsiveness.
[0277] In some embodiments, the antibody increases responsiveness
to the antibody therapy. In other embodiments, the antibody
decreases responsiveness to the antibody therapy.
[0278] For example, the Fc.gamma.RIIA polymorphism may be the
H/R.sup.131 polymorphism, and the Fc.gamma.RIIIA polymorphism may
be the V/F.sup.158 polymorphism.
[0279] In some embodiments, the genotyping identifies a H/H.sup.131
genotype and a V/V.sup.158 genotype, and the antibody is selected
for enhanced binding to at least one of an Fc.gamma.RIIA comprising
an H/H.sup.131 allele and an Fc.gamma.RIIIA comprising an
V/V.sup.158 allele.
[0280] In other embodiments the genotyping identifies a H/H.sup.131
genotype and a V/F.sup.158 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/H.sup.131 allele and an
Fc.gamma.RIIIA comprising an V/F.sup.158 allele.
[0281] In some embodiments, the genotyping identifies a H/H.sup.131
genotype and a F/F.sup.158 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/H.sup.131 allele and an
Fc.gamma.RIIIA comprising an F/F.sup.158 allele.
[0282] In some embodiments, the genotyping identifies a V/V.sup.158
genotype and a H/R.sup.131 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/R.sup.131 allele and an
Fc.gamma.RIIIA comprising an V/V.sup.158 allele.
[0283] In some embodiments, the genotyping identifies a V/V.sup.158
genotype and a R/R.sup.131 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising R/R.sup.131 allele and an
Fc.gamma.RIIIA comprising an V/V.sup.158 allele.
[0284] In some embodiments, the genotyping identifies a V/F.sup.158
genotype and a H/R.sup.131 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/R.sup.131 allele and an
Fc.gamma.RIIIA comprising an V/F.sup.158 allele.
[0285] In some embodiments, the genotyping identifies a V/F.sup.158
genotype and a R/R.sup.131 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising R/R.sup.131 allele and an
Fc.gamma.RIIIA comprising an V/F.sup.158 allele.
[0286] In some embodiments, the genotyping identifies a F/F.sup.158
genotype and a H/R.sup.131 genotype, and the variant antibody is
selected for enhanced binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/R.sup.131 allele and an
Fc.gamma.RIIIA comprising an F/F.sup.158 allele.
[0287] In some embodiments, the genotyping identifies or a
F/F.sup.158 genotype and a R/R.sup.131 genotype, and the variant
antibody is selected for enhanced binding and/or in vitro ADCC
function to at least one of an Fc.gamma.RIIA comprising R/R.sup.131
and an Fc.gamma.RIIIA comprising an F/F.sup.158 allele.
[0288] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a microbial
infection, or an allograft rejection. In some embodiments, the
neoplastic disease may be non-Hodgkin's lymphoma (NHL), e.g.,
follicular lymphoma.
[0289] In some embodiments, the antibody may be a therapeutic
antibody, e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM.,
HERCEPTIN.RTM., XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM.,
REMICADE.RTM., HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM.,
SYNAGIS.RTM., VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM.,
REOPRO.RTM., LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0290] For example, the related antibodies may include one or more
amino acid substitutions compared to Rituximab, wherein the one or
more amino acid substitutions provide for enhanced binding and/or
in vitro ADCC function to at least one of an Fc.gamma.RIIA
comprising H/R.sup.131 or R/R.sup.131 alleles, and an
Fc.gamma.RIIIA comprising V/F.sup.158 or F/F.sup.158 alleles.
[0291] In some embodiments, the genotyping identifies a H/H.sup.131
genotype and a V/V.sup.158 genotype, and the antibody is selected
for decreased binding to at least one of an Fc.gamma.RIIA
comprising H/H.sup.131 allele and an Fc.gamma.RIIIA comprising an
V/V.sup.158 allele.
[0292] In other embodiments, the genotyping identifies a
H/H.sup.131 genotype and a V/F.sup.158 genotype, and the variant
antibody is selected for decreased binding and/or in vitro ADCC
function to at least one of an Fc.gamma.RIIA comprising H/H.sup.131
allele and an Fc.gamma.RIIIA comprising an V/F.sup.158 allele.
[0293] In some embodiments, the genotyping identifies a H/H.sup.131
genotype and a F/F.sup.158 genotype, and the variant antibody is
selected for decreased binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/H.sup.131 allele and an
Fc.gamma.RIIIA comprising an F/F.sup.158 allele.
[0294] In some embodiments, the genotyping identifies a V/V.sup.158
genotype and a H/R.sup.131 genotype, and the variant antibody is
selected for decreased binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/R.sup.131 allele and an
Fc.gamma.RIIIA comprising an V/V.sup.158 allele.
[0295] In some embodiments, the genotyping identifies a V/V.sup.158
genotype and a R/R.sup.131 genotype, and the variant antibody is
selected for decreased binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising R/R.sup.131 allele and an
Fc.gamma.RIIIA comprising an V/V.sup.158 allele.
[0296] In some embodiments, the genotyping identifies a V/F.sup.158
genotype and a H/R.sup.131 genotype, and the variant antibody is
selected for decreased binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/R.sup.131 allele and an
Fc.gamma.RIIIA comprising an V/F.sup.158 allele.
[0297] In other embodiments, the genotyping identifies a
V/F.sup.158 genotype and a R/R.sup.131 genotype, and the variant
antibody is selected for decreased binding and/or in vitro ADCC
function to at least one of an Fc.gamma.RIIA comprising R/R.sup.131
allele and an Fc.gamma.RIIIA comprising an V/F.sup.158 allele.
[0298] In some embodiments, the genotyping identifies a F/F.sup.158
genotype and a H/R.sup.131 genotype, and the variant antibody is
selected for decreased binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising H/R.sup.131 allele and an
Fc.gamma.RIIIA comprising an F/F.sup.158 allele.
[0299] In some embodiments, the genotyping identifies a F/F.sup.158
genotype and a R/R.sup.131 genotype, and the variant antibody is
selected for decreased binding and/or in vitro ADCC function to at
least one of an Fc.gamma.RIIA comprising R/R.sup.131 and an
Fc.gamma.RIIIA comprising an F/F.sup.158 allele.
[0300] In some embodiments, the ADCC-treatable disease or disorder
may be a neoplastic disease, an autoimmune disease, a microbial
infection, or an allograft rejection. In some embodiments, the
neoplastic disease is non-Hodgkin's lymphoma (NHL), e.g.,
follicular lymphoma.
[0301] In some embodiments, the antibody may be a therapeutic
antibody, e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM.,
HERCEPTIN.RTM., XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM.,
REMICADE.RTM., HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM.,
SYNAGIS.RTM., VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM.,
REOPRO.RTM., LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0302] In some embodiments, the related antibodies include one or
more amino acid substitutions compared to Rituximab, wherein the
one or more amino acid substitutions provide for decreased binding
and/or in vitro ADCC function to at least one of an Fc.gamma.RIIA
comprising H/R.sup.131 or R/R.sup.131 alleles, and an
Fc.gamma.RIIIA comprising V/F.sup.158 or F/F.sup.158 alleles.
[0303] Methods are provided for enhancing antibody dependent cell
mediated cytotoxicity (ADCC) activity of an antibody for use in
treatment of a subject having an ADCC-treatable disease by
genotyping the subject for an Fc.gamma.RIIA polymorphism and an
Fc.gamma.RIIIA polymorphism, selecting an Fc nucleotide sequence
for the antibody that has optimal ADCC for the Fc.gamma.RIIA
polymorphism and Fc.gamma.RIIIA polymorphism, and modifying the
antibody to include the optimal Fc sequence for the subject's
genotype, wherein the ADCC activity of the antibody is enhanced by
using the optimal Fc.
[0304] For example, the Fc.gamma.RIIA polymorphism may be the
H/R.sup.131 polymorphism, and the Fc.gamma.RIIIA polymorphism may
be the V/F.sup.158 polymorphism.
[0305] In some embodiments, the patient may have a
hyperproliferative disorder. In other embodiments, the
hyperproliferative disorder may be cancer, e.g., non-Hodgkin's
lymphoma.
[0306] In some embodiments the antibody may be a therapeutic
antibody, e.g., RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM.,
HERCEPTIN.RTM., XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM.,
REMICADE.RTM., HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM.,
SYNAGIS.RTM., VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM.,
REOPRO.RTM., LUCENTIS.RTM., SOLIRIS.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM..
[0307] The genotypes determined by any of the above-disclosed
methods may include (i.) an Fc.gamma.RIIIA V/V.sup.158 genotype, an
Fc.gamma.RIIIA V/F.sup.158 or an Fc.gamma.RIIIA F/F.sup.158
genotype; or (an Fc.gamma.RIIA H/H.sup.131 genotype, an
Fc.gamma.RIIA H/R.sup.131 genotype or an Fc.gamma.RIIA R/R.sup.131
genotype, or (iii.) an Fc.gamma.RIIIA V/V.sup.158, Fc.gamma.RIIA
H/H.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158, Fc.gamma.RIIA
H/H.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158, Fc.gamma.RIIA
H/H.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158, Fc.gamma.RIIA
H/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158, Fc.gamma.RIIA
H/R.sup.131 genotype, an Fc.gamma.RIIIA F/F.sup.158, Fc.gamma.RIIA
H/R.sup.131 genotype, an Fc.gamma.RIIIA V/V.sup.158, Fc.gamma.RIIA
R/R.sup.131 genotype, an Fc.gamma.RIIIA V/F.sup.158, Fc.gamma.RIIA
R/R.sup.131 genotype or an Fc.gamma.RIIIA F/F.sup.158,
Fc.gamma.RIIA R/R.sup.131 genotype.
[0308] It is to be understood that the terminology used herein is
for the purpose of describing particular embodiments only, and is
not intended to be limiting, since the scope of the present
disclosure will be limited only by the appended claims.
[0309] Where a range of values is provided, it is understood that
each intervening value, to the tenth of the unit of the lower limit
unless the context clearly dictates otherwise, between the upper
and lower limit of that range and any other stated or intervening
value in that stated range, is encompassed within the disclosure.
The upper and lower limits of these smaller ranges may
independently be included in the smaller ranges and are also
encompassed within the disclosure, subject to any specifically
excluded limit in the stated range. Where the stated range includes
one or both of the limits, ranges excluding either or both of those
included limits are also included in the disclosure.
[0310] Unless defined otherwise, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this disclosure belongs.
Although any methods and materials similar or equivalent to those
described herein can also be used in the practice or testing of the
present disclosure, representative illustrative methods and
materials are now described.
[0311] All publications and patents cited in this specification are
herein incorporated by reference as if each individual publication
or patent were specifically and individually indicated to be
incorporated by reference and are incorporated herein by reference
to disclose and describe the methods and/or materials in connection
with which the publications are cited. The citation of any
publication is for its disclosure prior to the filing date and
should not be construed as an admission that the present disclosure
is not entitled to antedate such publication by virtue of prior
disclosure. Further, the dates of publication provided may be
different from the actual publication dates which may need to be
independently confirmed.
[0312] It is noted that, as used herein and in the appended claims,
the singular forms "a", "an", and "the" include plural referents
unless the context clearly dictates otherwise. It is further noted
that the claims may be drafted to exclude any optional element. As
such, this statement is intended to serve as antecedent basis for
use of such exclusive terminology as "solely," "only" and the like
in connection with the recitation of claim elements, or use of a
"negative" limitation.
[0313] As will be apparent to those of skill in the art upon
reading this disclosure, each of the individual embodiments
described and illustrated herein has discrete components and
features which may be readily separated from or combined with the
features of any of the other several embodiments without departing
from the scope or spirit of the present disclosure. Any recited
method can be carried out in the order of events recited or in any
other order which is logically possible.
[0314] The publications discussed herein are provided solely for
their disclosure prior to the filing date of the present
application. Nothing herein is to be construed as an admission that
the present disclosure is not entitled to antedate such publication
by virtue of prior disclosure. Further, the dates of publication
provided may be different from the actual publication dates which
may need to be independently confirmed.
[0315] As summarized above, the subject disclosure is directed to
methods of determining whether a subject suffering from a
neoplastic condition is responsive to a particular therapy, such as
antibody therapy, as well as reagents and kits thereof (and
devices) for use in practicing the subject methods. In further
describing the disclosure, the subject methods are described first,
followed by a review of the reagents, kits and devices for use in
practicing the subject methods.
Methods of Determining Whether a Subject Suffering from a
Neoplastic Condition is Responsive to a Particular Therapy
[0316] Methods are provided for determining whether a patient or
subject suffering from a neoplastic disease, i.e.,
hyperproliferative disorder, is responsive to a particular therapy,
such as antibody therapy. Hyperproliferative disorders, or
malignancies, are conditions in which there is unregulated cell
growth. The methods of the present disclosure are directed at
hyperproliferative disorders and particularly whether such a
disorder will or will not be responsive to a particular
antineoplastic therapy, e.g., antibody therapy. The disorder may be
characterized by the presence or absence of solid tumors.
[0317] In certain embodiments, the subject methods are directed to
determining whether a B-cell hyperproliferative disorder, e.g.,
NHL, is responsive to therapeutic antibody therapy. B-cell
hyperproliferative disorders are those disorders that derive from
cells in the B cell lineage, typically including hematopoietic
progenitor cells expressing B lineage markers, pro-B cells, pre-B
cells, B-cells and memory B cells; and that express markers
typically found on such B lineage cells.
[0318] Of particular interest are non-Hodgkin's lymphomas (NHLs),
which are a heterogeneous group of lymphoproliferative malignancies
with different patterns of behavior and responses to treatment.
Like Hodgkin's disease, NHL usually originates in lymphoid tissues
and can spread to other organs, however, NHL is much less
predictable than Hodgkin's disease regarding their responses to
therapy and has a far greater predilection to disseminate to
extranodal sites. The NHLs can be divided into 2 prognostic groups:
the indolent lymphomas and the aggressive lymphomas. Indolent NHL
types have a relatively good prognosis, with median survival as
long as 10 years, but they usually are not curable in advanced
clinical stages. The aggressive type of NHL has a shorter natural
history. A number of these patients can be cured with intensive
combination chemotherapy regimens, but there is a significant
number of relapses, particularly in the first 2 years after
therapy.
[0319] Among the NHL are a variety of B-cell neoplasms, including
precursor B-lymphoblastic leukemia/lymphoma; peripheral B-cell
neoplasms, e.g., B-cell chronic lymphocytic leukemia;
prolymphocytic leukemia; small lymphocytic lymphoma; mantle cell
lymphoma; follicle center cell lymphoma; marginal zone B-cell
lymphoma; splenic marginal zone lymphoma; hairy cell leukemia;
diffuse large B-cell lymphoma; T-cell rich B-cell lymphoma,
Burkitt's lymphoma; high-grade B-cell lymphoma, (Burkitt-like);
etc.
[0320] Follicular lymphoma comprises 70% of the indolent lymphomas
reported in American and European clinical trials. Most patients
with follicular lymphoma are over age 50 and present with
widespread disease at diagnosis. Nodal involvement is most common,
often accompanied by splenic and bone marrow disease. The vast
majority of patients are diagnosed with advanced stage follicular
lymphoma and are not cured with current therapeutic options, and
the rate of relapse is fairly consistent over time, even in
patients who have achieved complete responses to treatment.
Subtypes include follicular small cleaved cell (grade 1) and
follicular mixed small cleaved and large cell (grade 2). Another
subtype of interest is follicular large cell (grade 3 or FLC)
lymphoma which can be divided into grades 3a and 3b.
[0321] Marginal zone lymphomas were previously included among the
diffuse small lymphocytic lymphomas. When marginal zone lymphomas
involve the nodes, they are called monocytoid B-cell lymphomas, and
when they involve extranodal sites (gastrointestinal tract,
thyroid, lung, breast, skin), they are called mucosa-associated
lymphatic tissue (MALT) lymphomas. Many patients have a history of
autoimmune disease, such as Hashimoto's thyroiditis or Sjogren's
syndrome, or of Helicobacter gastritis. Most patients present with
stage I or II extranodal disease, which is most often in the
stomach. When disseminated to lymph nodes, bone marrow, or blood,
this entity behaves like other low-grade lymphomas. Large B-cell
lymphomas of MALT sites are classified and treated as diffuse large
cell lymphomas.
[0322] Splenic marginal zone lymphoma is an indolent lymphoma that
is marked by massive splenomegaly and peripheral blood and bone
marrow involvement, usually without adenopathy. This type of
lymphoma is otherwise known as splenic lymphoma with villous
lymphocytes, an uncommon variant of B-cell chronic lymphocytic
leukemia. Management of this entity usually starts with splenectomy
which is different than other low-grade lymphomas. If/when the
disease progresses after splenectomy, it tends to be managed like
other low grade lymphomas.
[0323] Among the aggressive forms of NHL is diffuse large B-cell
lymphoma, which is the most common of the non-Hodgkin's lymphomas,
comprising 30% of newly-diagnosed cases. Most patients present with
rapidly enlarging masses, often with symptoms both locally and
systemically. Relapses after treatment are not uncommon, depending
on the presence of various risk factors. Lymphomatoid
granulomatosis is an EBV positive large B-cell lymphoma with a
predominant T-cell background. The histology shows association with
angioinvasion and vasculitis, usually manifesting as pulmonary
lesions or paranasal sinus involvement. Patients are managed like
others with diffuse large cell lymphoma.
[0324] Primary mediastinal B-cell lymphoma is a subset of diffuse
large cell lymphoma characterized by significant fibrosis on
histology. Patients are usually female and young. Patients present
with a locally invasive anterior mediastinal mass which may cause
respiratory symptoms or superior vena cava syndrome. Therapy and
prognosis are the same as for other comparably-staged patients with
diffuse large cell lymphoma, except for advanced-stage patients
with a pleural effusion, who have an extremely poor prognosis
(progression-free survival is less than 20%) whether the effusion
is cytologically positive or negative.
[0325] Mantle cell lymphoma is found in lymph nodes, the spleen,
bone marrow, blood, and sometimes the gastrointestinal system
(lymphomatous polyposis). Mantle cell lymphoma is characterized by
CD5-positive mantle zone B cells, a translocation of chromosomes 11
and 14, and an overexpression of the cyclin D1 protein. The median
survival is significantly shorter (3-5 years) than that of other
lymphomas, and this histology is now considered to be an aggressive
lymphoma. A diffuse pattern and the blastoid variant have an even
more aggressive course with shorter survival, while the mantle zone
type may have a more indolent course. Refractoriness to
chemotherapy is a usual feature.
[0326] Lymphoblastic lymphoma is a very aggressive form of NHL. It
often occurs in young patients, but not exclusively. It is commonly
associated with large mediastinal masses and has a high
predilection for disseminating to bone marrow and the central
nervous system (CNS). Treatment is usually patterned after that for
acute lymphoblastic leukemia (ALL). Since these forms of NHL tend
to progress so quickly, combination chemotherapy is instituted
rapidly once the diagnosis has been confirmed. Careful review of
the pathologic specimens, bone marrow aspirate and biopsy specimen,
cerebrospinal fluid cytology, and lymphocyte marker constitute the
most important aspects of the pretreatment staging work-up.
[0327] Burkitt's lymphoma/diffuse small noncleaved cell lymphoma
typically involves younger patients and represents the most common
type of pediatric non-Hodgkin's lymphoma. These aggressive
extranodal B-cell lymphomas are characterized by translocation and
deregulation of the c-myc gene on chromosome 8. A subgroup of
patients with dual translocation of c-myc and bcl-2 appear to have
an extremely poor outcome despite aggressive therapy. Treatment of
Burkitt's lymphoma/diffuse small noncleaved cell lymphoma involves
aggressive multidrug regimens similar to those used for the
advanced-stage aggressive lymphomas.
[0328] Patients who undergo transplantation of the heart, lung,
liver, kidney, or pancreas usually require life-long
immunosuppression. Life-long immunosuppression may result in
post-transplantation lymphoproliferative disorder (PTLD), which
appears as an aggressive lymphoma. Pathologists can distinguish a
polyclonal B-cell hyperplasia from a monoclonal B-cell lymphoma;
both are almost always associated with EBV. In some cases, usually
for the polyclonal forms of the disease, withdrawal of
immunosuppression results in eradication of the lymphoma. When this
is unsuccessful or not feasible, a combination chemotherapy is
usually used. EBV-negative post-transplantation lymphoproliferative
disorders occur late and have a particularly poor prognosis.
Chronic lymphocytic leukemia (CLL) is a disorder of morphologically
mature but immunologically less mature lymphocytes and is
manifested by progressive accumulation of these cells in the blood,
bone marrow, and lymphatic tissues. Lymphocyte counts in the blood
are usually equal to or higher than 10,000 per cubic millimeter. At
present there is no curative therapy. CLL occurs primarily in
middle-aged and elderly individuals, with increasing frequency in
successive decades of life. The clinical course of this disease
progresses from an indolent lymphocytosis without other evident
disease to one of generalized lymphatic enlargement with
concomitant pancytopenia. Complications of pancytopenia, including
hemorrhage and infection, represent a major cause of death in these
patients. Immunological aberrations, including Coombs-positive
hemolytic anemia, immune thrombocytopenia, and depressed
immunoglobulin levels may all complicate the management of CLL. CLL
lymphocytes coexpress the B-cell antigens CD19 and CD20 along with
the T-cell antigen CD5. CLL B cells express relatively low levels
of surface-membrane immunoglobulin (compared with normal peripheral
blood B cells). CLL is diagnosed by an absolute increase in
lymphocytosis and/or bone marrow infiltration coupled with the
characteristic features of morphology and immunophenotype.
[0329] AIDS-related lymphomas are comprised of a narrow spectrum of
histologic types consisting almost exclusively of B-cell tumors of
aggressive type. These include diffuse large cell lymphoma;
B-immunoblastic; and small non-cleaved, either Burkitt's or
Burkitt's like. The HIV-associated lymphomas can be categorized
into: primary central nervous system lymphoma (PCNSL); systemic
lymphoma; and primary effusion lymphoma. All of these lymphomas
differ from non-HIV-related lymphomas in their molecular
characteristics, presumed mechanism of pathogenesis, treatment, and
clinical outcome. All three pathologic types are equally
distributed and represent aggressive disease. In general, the
clinical setting and response to treatment of patients with
AIDS-related lymphoma is very different from the non-HIV patients
with lymphoma. The HIV-infected individual with aggressive lymphoma
usually presents with advanced-stage disease that is frequently
extranodal. The clinical course is more aggressive, and the disease
is both more extensive and less responsive to chemotherapy.
Immunodeficiency and cytopenias, common in these patients at the
time of initial presentation, are exacerbated by the administration
of chemotherapy. Therefore, treatment of the malignancy increases
the risk of opportunistic infections that, in turn, further
compromise the delivery of adequate treatment.
[0330] Acute lymphocytic leukemia (ALL) generally has an aggressive
course, depending in part on the presence of the Philadelphia (Ph)
chromosome. Patients with Ph chromosome-positive ALL are rarely
cured with chemotherapy. Many patients who have molecular evidence
of the bcr-abl fusion gene, which characterizes the Ph chromosome,
have no evidence of the abnormal chromosome by cytogenetics.
[0331] Although the methods of the disclosure are primarily applied
to NHL, in some cases treatment may be used in cases of Hodgkin's
lymphoma, which is a lymphoma characterized by a pleomorphic
lymphocytic infiltrate with malignant multinucleated giant cells.
Most cases of Hodgkin's disease probably arise from germinal center
B cells that are unable to synthesize immunoglobulin. The majority
of cases in developing countries and about one third of those in
the United States are associated with the presence of Epstein-Barr
virus in the Reed-Sternberg cells. Treatment strategies depend on a
number of factors including the presence of B symptoms, the
histologic subtype, gender, and sexual maturity. To date there are
several published studies demonstrating the effectiveness of
Rituxan for CD20-positive Hodgkin's disease, particularly the
lymphocyte predominant variant.
[0332] Other neoplastic disease conditions whose responsiveness to
antibody therapy can be evaluated according to the subject methods
include, but are not limited to: colorectal cancer, non-small cell
lung cancer, small cell lung cancer, ovarian cancer, breast cancer,
head and neck cancer, renal cell carcinoma, and the like.
[0333] As summarized above, the subject methods may be used to
evaluate the responsiveness of a subject to a given antineoplastic
therapy. Antineoplastic therapies of interest include, but are not
limited to: chemotherapy, radiation therapy, antibody therapy,
etc.
[0334] By therapeutic antibody therapy is meant a treatment
protocol or regimen that includes administration of a therapeutic
antibody agent. Representative therapeutic antibody agents
specifically bind to antigens present on B cells, particularly
hyperproliferative B cells, e.g., B lineage lymphomas and
leukemias, and the like. The term "antibody" is used in the
broadest sense and specifically covers monoclonal antibodies
(including full length monoclonal antibodies), polyclonal
antibodies, multispecific antibodies (e.g., bispecific antibodies),
antibody fragments, and Fc:fusion proteins so long as they exhibit
the desired biological activity. Fragments comprise a portion of a
full-length antibody, generally the antigen binding or variable
region thereof. Examples of antibody fragments include Fab, Fab',
F(ab').sub.2, and Fv fragments; diabodies; linear antibodies;
single-chain antibody molecules; and multispecific antibodies
formed from antibody fragments. In some aspects of the disclosure,
a combination of one or more antibodies with different
specificities, either for epitopes of a single antigen, or for
multiple antigens, may be used.
[0335] Markers that are specifically found on B-cells include
CD45R, which is an exon specific epitope found on essentially all
B-cells, and is maintained throughout B cell development (Coffman
et al., 1982, Immunol. Rev. 69:5-23). The B-cell markers CD19,
CD20; CD22; CD23 are selectively expressed on B-cells and have been
associated with B-cell malignancies (Kalil and Cheson, 2000, Drugs
Aging 16(1):9-27; U.S. Pat. No. 6,183,744, herein incorporated by
reference). Surface immunoglobulin, including epitopes present on
the constant regions or idiotypic determinants, is a specific
marker for B-cells and has been utilized in immunotherapy (Caspar
et al., 1997, Blood 90(9):3699-706). The MB-1 antigen is found on
all normal immunoglobulin (Ig)-expressing cells, but not on
T-cells, thymocytes, granulocytes, or platelets, and expressed by
virtually all Ig-expressing B-cell tumors (Link et al., 1986, J.
Immunol. 137(9):3013-8). Other B cell antigens of interest known to
be expressed, for example, on non-Hodgkin's lymphomas, are Muc-1;
B5; BB1; and T9 (Freedman et al., 1987, Leukemia 1(1):9-15).
[0336] Of particular interest is the CD20 antigen, also known as
"Bp35". (Note that CD20 was called B1 early in the course of
research on B-cell markers). CD20 is a human B cell marker that is
expressed during early pre-B cell development and remains until
plasma cell differentiation. The CD20 molecule may regulate a step
in the activation process that is required for cell cycle
initiation and differentiation, and is usually expressed at very
high levels on neoplastic B cells. Thus, the CD20 surface antigen
can be targeted for treating B cell lymphomas. U.S. Pat. No.
5,736,137, herein incorporated by reference, describes the chimeric
antibody "C2B8" that binds the CD20 antigen and its use to treat
B-cell lymphoma (antibody is also known as Rituxan.RTM., rituximab,
Mabthera (this is a trademark in Europe)).
[0337] In an embodiment, the antibody is a monoclonal antibody.
Monoclonal antibodies are highly specific, being directed against a
single antigenic site, and each monoclonal antibody is directed
against a single determinant on the antigen. For example, the
monoclonal antibodies to be used in accordance with the present
disclosure may be made by the hybridoma method first described by
Kohler et al., 1975, Nature 256:495, or may be made by recombinant
DNA methods (see, e.g., U.S. Pat. No. 4,816,567). The monoclonal
antibodies may also be isolated from phage antibody libraries using
the techniques described in Clackson et al., 1991, Nature
352:624-628, and Marks et al., 1991, J. Mol. Biol. 222:581-597, for
example. For clinical use, the monoclonal antibodies may be
humanized forms of non-human antibodies. These are chimeric
antibodies that contain sequences derived from both human and
non-human immunoglobulin. For the most part, humanized antibodies
are human immunoglobulins in which residues from a hypervariable
region of the recipient are replaced by residues from a
hypervariable region of a non-human species having the desired
specificity, affinity, and capacity.
[0338] Specificity, as used herein, refers to the affinity of the
antibody, and to the cross-reactivity with other antigens. In order
to consider an antibody interaction to be "specific", the affinity
will be at least about 10.sup.-7 M, usually about 10.sup.-8 to
10.sup.-9 M, and may be up to 10.sup.-11 M or higher for the
epitope of interest. It will be understood by those of skill in the
art that the term "specificity" refers to such a high affinity
binding, and is not intended to mean that the antibody cannot bind
to other molecules as well. One may find cross-reactivity with
different epitopes, due, e.g., to a relatedness of antigen sequence
or structure, or to the structure of the antibody binding pocket
itself. Antibodies demonstrating such cross-reactivity are still
considered specific for the purposes of the present disclosure.
[0339] In practicing the subject methods, a subject or patient
sample, e.g., cells or collections thereof, e.g., tissues, is
assayed to determine whether the host or subject from which the
assayed sample was obtained is responsive to a given therapy, e.g.,
therapeutic antibody therapy. The sample obtained from the host is
assayed to determine the genotype of the host or subject from which
the sample was obtained with respect to at least two or more,
polymorphisms, where polymorphisms of interest are referred to
herein as target polymorphisms.
[0340] In certain embodiments, the target polymorphisms are
Fc.gamma.R polymorphisms. An Fc.gamma.R polymorphism is a
polymorphism present in an Fc.gamma.R (Fc receptor) protein.
Fc.gamma.R proteins of interest include, but are not limited to,
Fc.gamma.RII proteins (e.g., Fc.gamma.RIIA, also known as CD32
(whose amino acid and nucleotide sequence is present at Genbank
accession NOs. NM.sub.--021642 or M28697)); Fc.gamma.RIII proteins
(e.g., Fc.gamma.RIIIA, also known as CD16 (whose amino acid and
nucleotide sequence is present at Genbank accession NOs. BCO36723;
BCO33678; BC017865 and NM.sub.--000569)).
[0341] In certain embodiments, the sample is assayed to determine
the genotype of a subject with respect to two or more different
target polymorphisms, where the two or more different target
polymorphisms include at least one Fc.gamma.R polymorphism. In
certain of these embodiments, at least two of the target
polymorphisms are different Fc.gamma.R polymorphisms, such as an
Fc.gamma.RII and an Fc.gamma.RIII polymorphism.
[0342] In some embodiments, the sample is assayed to determine the
genotype of the subject with respect to at least two or more target
polymorphisms, where, the target polymorphisms are an Fc.gamma.RII
polymorphism and an Fc.gamma.RIII polymorphism. In certain
embodiments, the Fc.gamma.RIIA polymorphism is the Fc.gamma.RIIA
H/R.sup.131 polymorphism (where the nucleotide codons encoding the
H and R residues of the polymorphism are CAT and CGT,
respectively). In certain embodiments, the Fc.gamma.RIIIA
polymorphism is the Fc.gamma.RIIIA V/F.sup.158 polymorphism (where
the nucleotide codons encoding the V and F residues of the
polymorphism are GTT and TTT, respectively).
[0343] In practicing the subject methods, a subject or patient
sample, e.g., cells or collections thereof, e.g., tissues, is
assayed to determine whether the host or subject from which the
assayed sample was obtained is responsive to a given therapy, e.g.,
therapeutic antibody therapy. In practicing the subject diagnostic
methods, the sample obtained from the host is assayed to determine
the genotype of the host or subject from which the sample was
obtained with respect to at least one, i.e., one or more,
polymorphisms, where polymorphisms of interest are referred to
herein as target polymorphisms. In certain embodiments, the at
least one target polymorphism is an Fc.gamma.R polymorphism. An
Fc.gamma.R polymorphism is a polymorphism present in an Fc.gamma.R
(Fc receptor) protein. Fc.gamma.R proteins of interest include, but
are not limited to, Fc.gamma.RII proteins (e.g., Fc.gamma.RIIA,
also known as CD32 (whose amino acid and nucleotide sequence is
present at Genbank accession nos. NM.sub.--021642 or M28697));
Fc.gamma.RIII proteins (e.g., Fc.gamma.RIIIA, also known as CD16
(whose amino acid and nucleotide sequence is present at Genbank
accession nos. BCO36723; BCO33678; BC017865 and NM 000569)), and
the like. In certain embodiments, the sample is assayed to
determine the genotype of the host with respect to a single target
polymorphism, where in these embodiments, the single target
polymorphism is an Fc.gamma.RII polymorphism, such as an
Fc.gamma.RIIA polymorphism, where a specific representative
Fc.gamma.RIIA polymorphism of interest is the Fc.gamma.RIIA
H/R.sup.131 polymorphism (where the nucleotide codons encoding the
H and R residues of the polymorphism are CAT and CGT,
respectively). In certain embodiments, the sample is assayed to
determine the genotype of the host with respect to two or more
different target polymorphisms, where in these embodiments, the two
or more different target polymorphisms include at least one
Fc.gamma.R polymorphism. In certain of these embodiments, at least
two of the target polymorphisms are different Fc.gamma.R
polymorphisms, such as an Fc.gamma.RII and an Fc.gamma.RIII
polymorphism. In certain embodiments, the sample is assayed for
both an Fc.gamma.RII polymorphism, such as the specific
Fc.gamma.RIIA polymorphisms described above, and an Fc.gamma.RIII
polymorphism, such as an Fc.gamma.RIIIA polymorphism, including the
Fc.gamma.RIIIA V/F.sup.158 polymorphism (where the nucleotide
codons encoding the V and F residues of the polymorphism are GTT
and TTT, respectively).
[0344] Any convenient protocol for assaying a sample for the above
one or more target polymorphisms may be employed in the subject
methods. In certain embodiments, the target polymorphism will be
detected at the protein level, e.g., by assaying for a polymorphic
protein. In yet other embodiments, the target polymorphism will be
detected at the nucleic acid level, e.g., by assaying for the
presence of nucleic acid polymorphism, e.g., a single nucleotide
polymorphism (SNP) that cause expression of the polymorphic
protein.
[0345] For example, polynucleotide samples derived from (e.g.,
obtained from) an individual may be employed. Any biological sample
that comprises a polynucleotide from the individual is suitable for
use in the methods of the disclosure. The biological sample may be
processed so as to isolate the polynucleotide. Alternatively, whole
cells or other biological samples may be used without isolation of
the polynucleotides contained therein. Detection of a target
polymorphism in a polynucleotide sample derived from an individual
can be accomplished by any means known in the art, including, but
not limited to, amplification of a sequence with specific primers;
determination of the nucleotide sequence of the polynucleotide
sample; hybridization analysis; single strand conformational
polymorphism analysis; denaturing gradient gel electrophoresis;
mismatch cleavage detection; and the like. Detection of a target
polymorphism can also be accomplished by detecting an alteration in
the level of a mRNA transcript of the gene; aberrant modification
of the corresponding gene, e.g., an aberrant methylation pattern;
the presence of a non-wild-type splicing pattern of the
corresponding mRNA; an alteration in the level of the corresponding
polypeptide; and/or an alteration in corresponding polypeptide
activity.
[0346] Detection of a target polymorphism by analyzing a
polynucleotide sample can be conducted in a number of ways. A test
nucleic acid sample can be amplified with primers which amplify a
region known to comprise the target polymorphism(s). Genomic DNA or
mRNA can be used directly. Alternatively, the region of interest
can be cloned into a suitable vector and grown in sufficient
quantity for analysis. The nucleic acid may be amplified by
conventional techniques, such as a polymerase chain reaction (PCR),
to provide sufficient amounts for analysis. The use of the
polymerase chain reaction is described in a variety of
publications, including, e.g., "PCR Protocols (Methods in Molecular
Biology)" J. M. S. Bartlett and D. Stirling, eds, Humana Press
(2000); and "PCR Applications: Protocols for Functional Genomics"
Innis, Gelfand, and Sninsky, eds., Academic Press (1999). Once the
region comprising a target polymorphism has been amplified, the
target polymorphism can be detected in the PCR product by
nucleotide sequencing, by SSCP analysis, or any other method known
in the art. In performing SSCP analysis, the PCR product may be
digested with a restriction endonuclease that recognizes a sequence
within the PCR product generated by using as a template a reference
sequence, but does not recognize a corresponding PCR product
generated by using as a template a variant sequence by virtue of
the fact that the variant sequence no longer contains a recognition
site for the restriction endonuclease. PCR may also be used to
determine whether a polymorphism is present by using a primer that
is specific for the polymorphism. Such methods may comprise the
steps of collecting from an individual a biological sample
comprising the individual's genetic material as template,
optionally isolating template nucleic acid (genomic DNA, mRNA, or
both) from the biological sample, contacting the template nucleic
acid sample with one or more primers that specifically hybridize
with a target polymorphic nucleic acid molecule under conditions
such that hybridization and amplification of the template nucleic
acid molecules in the sample occurs, and detecting the presence,
absence, and/or relative amount of an amplification product and
comparing the length to a control sample. Observation of an
amplification product of the expected size is an indication that
the target polymorphism contained within the target polymorphic
primer is present in the test nucleic acid sample. Parameters such
as hybridization conditions, polymorphic primer length, and
position of the polymorphism within the polymorphic primer may be
chosen such that hybridization will not occur unless a polymorphism
present in the primer(s) is also present in the sample nucleic
acid. Those of ordinary skill in the art are well aware of how to
select and vary such parameters. See, e.g., Saiki et al., 1986,
Nature 324:163; and Saiki et al, 1989, Proc. Natl. Acad. Sci. USA
86:6230. As one non-limiting example, a PCR primer comprising the
T78C variation described in Example 1 may be used.
[0347] Alternatively, various methods are known in the art that
utilize oligonucleotide ligation as a means of detecting
polymorphisms. See, e.g., Riley et al., 1990, Nucleic Acids Res.
18:2887-2890; and Delahunty et al., 1996, Am. J. Hum. Genet.
58:1239-1246.
[0348] A detectable label may be included in an amplification
reaction. Suitable labels include fluorochromes, e.g., fluorescein
isothiocyanate (FITC), rhodamine, Texas Red, phycoerythrin,
allophycocyanin, 6-carboxyfluorescein (6-FAM),
2',7'-dimethoxy-4',5'-dichloro-6-carboxyfluorescein (JOE),
6-carboxy-X-rhodamine (ROX),
6-carboxy-2',4',7',4,7-hexachlorofluorescein (HEX),
5-carboxyfluorescein (5-FAM) or
N,N,N',N'-tetramethyl-6-carboxyrhodamine (TAMRA), radioactive
labels, e.g., .sup.32P, .sup.355, .sup.3H; etc. The label may be a
two stage system, where the amplified DNA is conjugated to biotin,
haptens, etc. having a high affinity binding partner, e.g., avidin,
specific antibodies, etc., where the binding partner is conjugated
to a detectable label. The label may be conjugated to one or both
of the primers. Alternatively, the pool of nucleotides used in the
amplification is labeled, so as to incorporate the label into the
amplification product.
[0349] The sample nucleic acid may be sequenced by a dideoxy chain
termination method or other well-known methods. Genomic DNA or mRNA
may be used directly. If mRNA is used, a cDNA copy may first be
made. If desired, the sample nucleic acid can be amplified using a
PCR. A variety of sequencing reactions known in the art can be used
to directly sequence the relevant gene, or a portion thereof in
which a specific polymorphism is known to occur, and detect
polymorphisms by comparing the sequence of the sample nucleic acid
with a reference polynucleotide that contains a target
polymorphism. Any of a variety of automated sequencing procedures
can be used. See, e.g., WO 94/16101; Cohen et al., 1996, Adv.
Chromatography 36:127-162.
[0350] Hybridization with the variant sequence may also be used to
determine the presence of a target polymorphism. Hybridization
analysis can be carried out in a number of different ways,
including, but not limited to Southern blots, Northern blots, dot
blots, microarrays, etc. The hybridization pattern of a control and
variant sequence to an array of oligonucleotide probes immobilized
on a solid support, as described in U.S. Pat. No. 5,445,934, or in
WO 95/35505, may also be used as a means of detecting the presence
of variant sequences. Identification of a polymorphism in a nucleic
acid sample can be performed by hybridizing a sample and control
nucleic acids to high density arrays containing hundreds or
thousands of oligonucleotide probes. Cronin et al., 1996, Human
Mutation 7:244-255; and Kozal et al., 1996, Nature Med.
2:753-759.
[0351] Single strand conformational polymorphism (SSCP) analysis;
denaturing gradient gel electrophoresis (DGGE); mismatch cleavage
detection; and heteroduplex analysis in gel matrices can also be
used to detect polymorphisms. Alternatively, where a polymorphism
creates or destroys a recognition site for a restriction
endonuclease (restriction fragment length polymorphism, RFLP), the
sample is digested with that endonuclease, and the products size
fractionated to determine whether the fragment was digested.
Fractionation is performed by gel or capillary electrophoresis,
particularly acrylamide or agarose gels. The aforementioned
techniques are well known in the art. Detailed description of these
techniques can be found in a variety of publications, including,
e.g., "Laboratory Methods for the Detection of Mutations and
Polymorphisms in DNA" G. R. Taylor, ed., CRC Press (1997), and
references cited therein.
[0352] A number of methods are available for determining the
expression level of a polymorphic nucleic acid molecule, e.g., a
polymorphic mRNA, or polymorphic polypeptide in a particular
sample. Diagnosis may be performed by a number of methods to
determine the absence or presence or altered amounts of normal or
abnormal mRNA in a patient sample. For example, detection may
utilize staining of cells or histological sections with labeled
antibodies, performed in accordance with conventional methods.
Cells are permeabilized to stain cytoplasmic molecules. The
antibodies of interest are added to the cell sample, and incubated
for a period of time sufficient to allow binding to the epitope,
usually at least about 10 minutes. The antibody may be labeled with
radioisotopes, enzymes, fluorescers, chemiluminescers, or other
labels for direct detection. Alternatively, a second stage antibody
or reagent is used to amplify the signal. Such reagents are well
known in the art. For example, the primary antibody may be
conjugated to biotin, with horseradish peroxidase-conjugated avidin
added as a second stage reagent. Alternatively, the secondary
antibody conjugated to a fluorescent compound, e.g., fluorescein,
rhodamine, Texas red, etc. Final detection uses a substrate that
undergoes a color change in the presence of the peroxidase. The
absence or presence of antibody binding may be determined by
various methods, including flow cytometry of dissociated cells,
microscopy, radiography, scintillation counting, etc. The presence
and/or the level of a polymorphic polypeptide may also be detected
and/or quantitated in any of a variety of published procedures.
[0353] Alternatively, one may focus on the expression of mRNA.
Biochemical studies may be performed to determine whether a
sequence polymorphism in a coding region or control regions is
associated with disease. Disease associated polymorphisms may
include deletion or truncation of the gene, mutations that alter
expression level, that affect the activity of the protein, etc.
[0354] Screening for mutations in a polymorphic polypeptide may be
based on the functional or antigenic characteristics of the
protein. Protein truncation assays are useful in detecting
deletions that may affect the biological activity of the protein.
Various immunoassays designed to detect polymorphisms in
polymorphic polypeptides may be used in screening. Where many
diverse genetic mutations lead to a particular disease phenotype,
functional protein assays have proven to be effective screening
tools. The activity of the encoded a polymorphic polypeptide may be
determined by comparison with a reference polypeptide lacking a
specific polymorphism.
[0355] Diagnostic methods of the subject disclosure in which the
level of polymorphic gene expression is of interest will typically
involve comparison of the relevant nucleic acid abundance of a
sample of interest with that of a control value to determine any
relative differences, where the difference may be measured
qualitatively and/or quantitatively, which differences are then
related to the presence or absence of an abnormal gene expression
pattern. A variety of different methods for determining the nucleic
acid abundance in a sample are known to those of skill in the art,
where particular methods of interest include those described in:
Pietu et al., 1996, Genome Res. 6:492-503; Zhao et al., Gene (Apr.
24, 1995) 156: 207-213; Soares, 1997, Curr. Opin. Biotechnol. 8:
542-546; Raval, J., 1994, Pharmacol. Toxicol. Methods 32:125-127;
Chalifour et al., 1994, Anal. Biochem. 216:299-304; Stolz &
Tuan, 1996, Mol. Biotechnol. 6:225-230; Hong et al., 1982,
Bioscience Reports 2: 907; and McGraw, 1984, Anal. Biochem. 143:
298. Also of interest are the methods disclosed in WO 97/27317, the
disclosure of which is herein incorporated by reference.
[0356] Additional references describing various protocols for
detecting the presence of a target polymorphism include, but are
not limited to, those described in: U.S. Pat. Nos. 6,703,228;
6,692,909; 6,670,464; 6,660,476; 6,653,079; 6,632,606; and
6,573,049; the disclosures of which are herein incorporated by
reference.
[0357] Following obtainment of the genotype from the sample being
assayed, the genotype is evaluated to determine whether the subject
is responsive to the antineoplastic therapy of interest. In certain
embodiments, the obtained genotype may be compared with a reference
or control to make a diagnosis regarding the therapy responsive
phenotype of the cell or tissue, and therefore host, from which the
sample was obtained/derived. The terms "reference" and "control" as
used herein mean a standardized genotype to be used to interpret
the genotype of a given patient and assign a prognostic class
thereto. The reference or control may be a genotype that is
obtained from a cell/tissue known to have the desired phenotype,
e.g., responsive phenotype, and therefore may be a positive
reference or control genotype. In addition, the reference/control
genotype may be from a cell/tissue known to not have the desired
phenotype, and therefore be a negative reference/control
genotype.
[0358] In certain embodiments, the obtained genotype is compared to
a single reference/control genotype to obtain information regarding
the phenotype of the cell/tissue being assayed. In yet other
embodiments, the obtained genotype is compared to two or more
different reference/control profiles to obtain more in depth
information regarding the phenotype of the assayed cell/tissue. For
example, the obtained genotype may be compared to a positive and
negative genotype to obtain confirmed information regarding whether
the cell/tissue has the phenotype of interest.
[0359] Representative examples of genotypes associated with therapy
responsiveness, particularly Rituximab responsive include, but are
not limited to: the Fc.gamma.RIIA H/H.sup.131 genotype and the
Fc.gamma.RIIIA V/V.sup.158 genotype. Representative examples of
genotypes associated with therapy non-responsiveness, particularly
Rituximab-non responsiveness include, but are not limited to: the
Fc.gamma.RIIA H/R.sup.131 genotype; the Fc.gamma.RIIA R/R.sup.131
genotype; the Fc.gamma.RIIIA V/F.sup.158 genotype; and the
Fc.gamma.RIIIA F/F.sup.158 genotype.
[0360] In certain embodiments, the above-obtained information about
the cell/tissue being assayed is employed to diagnose a host,
subject or patient with respect to responsive to therapeutic
antibody therapy, as described above. In certain embodiments, the
above-obtained information is employed to give a refined
probability determination as to whether a subject will or will not
respond to a particular therapy. For example, an identification of
the Fc.gamma.RIIA H/H.sup.131 genotype and/or the Fc.gamma.RIIIA
V/V.sup.158 genotype may be employed to determine that the subject
has at least a 70% chance, such as at least a 75% chance, including
at least an 80% chance of responding to antibody, e.g., Rituximab,
therapy. Likewise, an identification of the Fc.gamma.RIIA
H/R.sup.131 or R/R.sup.131 genotype and/or the Fc.gamma.RIIIA
V/F.sup.158 or F/F.sup.158 genotype may be employed to determine
that the subject has less than 50% chance, such as a less than 45%
chance, including a less than 40% chance of responding to antibody,
e.g., Rituximab, therapy.
[0361] The subject methods further find use in pharmacogenomic
applications. In these applications, a subject is first diagnosed
for the presence of absence of a responsive phenotype using a
protocol such as the diagnostic protocol described in the preceding
section.
[0362] The subject is then treated using a pharmacological
protocol, where the suitability of the protocol for a particular
subject/patient is determined using the results of the diagnosis
step. More specifically, where the identified phenotype is
responsive, an appropriate therapeutic antibody treatment protocol
is then employed to treat the patient. Alternatively, where a
patient is identified as having a non-responsive phenotype, other
treatment options are sought.
Methods for Selecting a Patient for Treatment with an Antibody
[0363] Methods are provided for selecting a patient for treatment
with an antibody or antibody fragment based on the patient's
Fc.gamma.RIIA and Fc.gamma.RIIIA polymorphism. For example, a
patient with a particular Fc.gamma.RIIA (H/R.sup.131) polymorphism
and an Fc.gamma.RIIIA (V/F.sup.158) polymorphism is selected for
treatment with one or more antibody therapies.
[0364] Methods are provided for selecting a patient for treatment
with an antibody, comprising: (a) determining if the patient has an
Fc.gamma.RIIIA V/V.sup.158 genotype, an Fc.gamma.RIIIA V/F.sup.158
or an Fc.gamma.RIIIA F/F.sup.158 genotype; (b) determining if the
patient has an Fc.gamma.RIIA H/H.sup.131 genotype, an Fc.gamma.RIIA
H/R.sup.131 genotype or an Fc.gamma.RIIA R/R.sup.131 genotype; (c)
selecting the patient with a particular genotype for treatment with
the antibody based on the genotype determination of steps (a) and
(b); and (d) administering the antibody to the patient selected in
step (c).
[0365] A patient is assigned to one of nine Groups according to
their Fc.gamma.RIIA(H/R.sup.131) polymorphism and an Fc.gamma.RIIIA
(V/F.sup.158) polymorphism. Genotypes include: V/V.sup.158,
H/H.sup.131 (Group-I); V/F.sup.158, H/H.sup.131 (Group-II);
F/F.sup.158, H/H.sup.131 (Group-III); V/V.sup.158, H/R.sup.131
(Group-IV); V/F.sup.158, H/R.sup.131 (Group-V); F/F.sup.158,
H/R.sup.131 (Group-VI); V/V.sup.158, R/R.sup.131 (Group-VII);
V/F.sup.158, R/R.sup.131 (Group-VIII); and F/F.sup.158, R/R.sup.131
(Group-IX). Accordingly, a patient with one of the above-described
genotypes is selected for treatment with one or more antibody
therapies.
[0366] In some embodiments, the antibody, variable region of an
antibody or Fc variant antibody is selected from the Group
RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM.,
LUCENTIS.RTM., SOURIS.RTM., OKT3.RTM., BEXXAR.RTM. ZEVALIN.RTM.,
ENBREL.RTM. or AMEVIVE.RTM..
Methods of Determining a Degree of Responsiveness
[0367] Methods are provided for determining the degree of treatment
response that an individual having an ADCC-treatable disease or
disorder will have to an antibody therapy for the disease or
disorder. The methods generally involve: a) genotyping an
individual having a disease or disorder that is treatable with an
ADCC-based antibody therapy, to determine an Fc.gamma.RIIA
polymorphism to obtain a first result; b) genotyping the individual
to determine an Fc.gamma.RIIIA polymorphism to obtain a second
result; and c) employing the first and second results to determine
the degree of responsiveness of the individual to the antibody
therapy.
[0368] Diseases and disorders that are treatable with an ADCC-based
antibody therapy include, but are not limited to, neoplastic
diseases; autoimmune diseases; allograft rejection, and microbial
infections.
[0369] Thus, e.g., in some embodiments, methods are provided for
determining the degree of responsiveness that an individual having
a neoplastic disease will have to an antibody therapy. The methods
generally involve: a) genotyping an individual having a neoplastic
disease, to determine an Fc.gamma.RIIA polymorphism to obtain a
first result; b) genotyping the individual to determine an
Fc.gamma.RIIIA polymorphism to obtain a second result; and c)
employing the first and second results to determine the degree of
responsiveness of the individual to the antibody therapy.
[0370] In other embodiments, methods are provided for determining
the degree of responsiveness that a subject having an
ADCC-treatable disease or disorder will have to an antibody therapy
for the disease or disorder, the method comprising: (a) genotyping
the subject for an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism; and (b) identifying a genotype associated with a
particular degree of responsiveness to the antibody therapy from a
reference that is identical to the genotype from the test subject,
wherein the test subject is determined to have a degree of
responsiveness to the antibody therapy for the disease or disorder
corresponding to the level of responsiveness associated with the
reference having an identical Fc.gamma.RIIA polymorphism and an
identical Fc.gamma.RIIIA polymorphism.
[0371] In a further embodiment, methods are provided for
determining the degree of responsiveness that a test subject having
an ADCC-treatable disease or disorder will have to an antibody
therapy for the disease or disorder, the method comprising: (a)
genotyping subjects for an Fc.gamma.RIIA polymorphism and an
Fc.gamma.RIIIA polymorphism, wherein the subjects have or had the
ADCC-treatable disease or disorder and are or were administered
antibody therapy for the disease or disorder; (b) classifying each
subject based on its Fc.gamma.RIIA polymorphism and Fc.gamma.RIIIA
polymorphism to one of more than three categories of responsiveness
to the antibody therapy; (c) genotyping the test subject for an
Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA polymorphism; and
(d) identifying a genotype from (a) that is identical to the
genotype from the test subject in step (c), wherein the test
subject is determined to have a degree of responsiveness to the
antibody therapy for the disease or disorder corresponding to the
level of responsiveness associated with a subject having an
identical Fc.gamma.RIIA polymorphism and an identical
Fc.gamma.RIIIA polymorphism.
[0372] The predicted responsiveness of an individual to an antibody
therapy may be categorized into a plurality of different categories
based on first and second results, such as three or more different
categories, e.g., a) "high degree of responsiveness": the
individual has at least a 65% chance, at least a 70% chance, at
least a 75% chance, or at least an 80% chance, or greater, of
responding to the antibody therapy; b) "intermediate degree of
responsiveness": the individual has from about a 35% chance to
about a 65% chance, or from about a 50% chance to about a 70%
chance, of responding to the antibody therapy; and c) "low degree
of responsiveness": the individual has a less than 50% chance, less
than 45% chance, or less than 40% chance, of responding to the
antibody therapy.
[0373] Responsiveness may be determined at various times after
treatment with a given antibody therapy, e.g., 1-3 months, 3-6
months, 6-9 months, or 9-12 months following treatment, e.g.,
following initiation of treatment. Thus, e.g., responsiveness can
be expressed with a time component.
[0374] For example, in some embodiments, predicted responsiveness
of an individual to an antibody therapy may be categorized into a
plurality of different categories based on first and second
results, such as three or more different categories, e.g., a) "high
degree of responsiveness": the individual has at least a 65%
chance, at least a 70% chance, at least a 75% chance, or at least
an 80% chance, or greater, of responding to the antibody therapy at
one month following initiation of treatment; b) "intermediate
degree of responsiveness": the individual has from about a 35%
chance to about a 65% chance, or from about a 50% chance to about a
70% chance, of responding to the antibody therapy at one month
following initiation of treatment; and c) "low degree of
responsiveness": the individual has a less than 50% chance, less
than 45% chance, or less than 40% chance, of responding to the
antibody therapy at one month following initiation of
treatment.
[0375] In other embodiments, predicted responsiveness of an
individual to an antibody therapy may be categorized into a
plurality of different categories based on first and second
results, such as three or more different categories, e.g., a) "high
degree of responsiveness": the individual has at least a 65%
chance, at least a 70% chance, at least a 75% chance, or at least
an 80% chance, or greater, of responding to the antibody therapy at
three months following initiation of treatment; b) "intermediate
degree of responsiveness": the individual has from about a 35%
chance to about a 65% chance, or from about a 50% chance to about a
70% chance of responding to the antibody therapy at three months
following initiation of treatment; and c) "low degree of
responsiveness": the individual has a less than 50% chance, less
than 45% chance, or less than 40% chance, of responding to the
antibody therapy at three months following initiation of
treatment.
[0376] In other embodiments, predicted responsiveness of an
individual to an antibody therapy may be categorized into a
plurality of different categories based on first and second
results, such as three or more different categories, e.g., a) "high
degree of responsiveness": the individual has at least a 65%
chance, at least a 70% chance, at least a 75% chance, or at least
an 80% chance, or greater, of responding to the antibody therapy at
six months following initiation of treatment; b) "intermediate
degree of responsiveness": the individual has from about a 35%
chance to about a 65% chance, or from about a 50% chance to about a
70% chance of responding to the antibody therapy at six months
following initiation of treatment; and c) "low degree of
responsiveness": the individual has a less than 50% chance, less
than 45% chance, or less than 40% chance, of responding to the
antibody therapy at six months following initiation of
treatment.
[0377] In other embodiments, predicted responsiveness of an
individual to an antibody therapy may be categorized into a
plurality of different categories based on first and second
results, such as three or more different categories, e.g., a) "high
degree of responsiveness": the individual has at least a 65%
chance, at least a 70% chance, at least a 75% chance, or at least
an 80% chance, or greater, of responding to, the antibody therapy
at 12 months following initiation of treatment; b) "intermediate
degree of responsiveness": the individual has from about a 35%
chance to about a 65% chance, or from about a 50% chance to about a
70% chance of responding to the antibody therapy at 12 months
following initiation of treatment; and c) "low degree of
responsiveness": the individual has a less than 50% chance, less
than 45% chance, or less than 40% chance, of responding to the
antibody therapy at 12 months following initiation of
treatment.
[0378] Responsiveness to an antibody therapy for a neoplastic
disease can include one or more of: antibody-dependent
cell-mediated cytotoxicity (ADCC) response to tumor cells;
reduction in tumor mass; reduction in number of tumor cells; etc.
Responsiveness to an antibody therapy for an autoimmune disease can
include one or more of: reduction in a symptom associated with the
autoimmune disorder; reduction in the number and/or activity of an
autoreactive B-cell; reduction in the number and/or activity of an
autoreactive T-cell; etc. Responsiveness to an antibody therapy for
allograft rejection can include one or more of: reduction in the
amount of immunosuppressive drug that must be administered to an
individual who is the recipient of an allograft and still maintain
the allograft; duration of maintenance of the allograft; function
of the allograft; reduction in the number and/or activity of
alloreactive T-cells in the allograft recipient. Responsiveness to
an antibody therapy for a viral infection can include one or more
of: reduction in the number of viral genomes in a tissue, fluid, or
other specimen from an individual; reduction in one or more
symptoms of a viral infection; etc. Responsiveness can also be
assessed using an in vitro ADCC assay, e.g., as described in the
Examples.
[0379] For example, where an Fc.gamma.RIIIA polymorphism can be one
of A/A, A/a, and a/a, and where an Fc.gamma.RIIA polymorphism can
be one of B/B, B/b, and b/b, responsiveness to a given antibody
therapy at a given time point after treatment may be categorized as
shown in Tables A and B, below. A/A, a/a, B/B, and b/b represent
homozygous alleles for the respective Fc.gamma.R polymorphisms,
while A/a and B/b represent heterozygous alleles for the respective
Fc.gamma.R polymorphisms.
TABLE-US-00001 TABLE A Fc.gamma.RIIIA Fc.gamma.RIIIA Fc.gamma.RIIIA
Genotype A/A Genotype A/a Genotype a/a Fc.gamma. RIIA 70%-100%
50%-70% 50%-70% Genotype B/B Fc.gamma. RIIA 50%-70% <50% <50%
Genotype B/b Fc.gamma. RIIA 50%-70% <50% <50% Genotype
b/b
TABLE-US-00002 TABLE B Allelic expression patterns based on
Fc.gamma.RIIIA and Fc.gamma.RIIA polymorphisms in various patient
Groups Fc.gamma. RIIIA Fc.gamma. RIIIA Fc.gamma. RIIIA Genotype A/A
Genotype A/a Genotype a/a Fc.gamma. RIIA Group I Group II Group III
Genotype B/B 70%-100% 50%-70% 50%-70% A, A; B, B A, a; B, B a, a;
B, B Fc.gamma. RIIA Group IV Group V <50% Group VI <50%
Genotype B/b 50%-70% A, a; B, b a, a; B, b A, A; B, b Fc.gamma.
RIIA Group VII Group VIII <50% Group IX <50% Genotype b/b
50%-70% A, a; b, b a, a; b, b A, A; b, b
[0380] For a given antibody (a "reference antibody") with
responsiveness categories as set forth in Table A or Table B, Table
A or Table B is an exemplary reference chart. A person with unknown
responsiveness to therapy with the reference antibody is genotyped
for Fc.gamma.RIIA and Fc.gamma.RIIIA polymorphisms; and the
person's genotype is compared with the reference chart; and the
degree of predicted responsiveness is determined from the reference
chart. In some embodiments, where the predicted degree of
responsiveness is high, the individual will be treated with an
antibody that is the same as the reference antibody. In other
embodiments, where the predicted degree of responsiveness is
intermediate (e.g., 50%-70%) or low (e.g., <50%), a therapeutic
antibody will be selected that has the same antigen binding
specificity as the reference antibody, but has enhanced in vitro
ADCC activity to an Fc.gamma.RIIA and/or an Fc.gamma.RIIIA, as
described in more detail below. The nature of allelic expression
for the above genotypes can be best described by codominance. For
example, for the Patient Group-V (Table B) with genotypes
Fc.gamma.RIIIA (A/a) and Fc.gamma.RIIA (B/b) will have equal
phenotypic expression of both alleles A,a for Fc.gamma.RIIIA and
B,b for Fc.gamma.RIIA. In some embodiments, individuals of category
(a) will have an Fc.gamma.RIIA H/H.sup.131 genotype and an
Fc.gamma.RIIIA V/V.sup.158 genotype. In some embodiments,
individuals of category (b) will have an Fc.gamma.RIIA H/H.sup.131
genotype or an Fc.gamma.RIIIA V/V.sup.158 genotype, but not both.
For example, individuals of category (b) will have one of: i) an
Fc.gamma.RIIA H/H.sup.131 genotype and an Fc.gamma.RIIIA
V/F.sup.158 genotype; ii) an Fc.gamma.RIIA H/H.sup.131 genotype and
an Fc.gamma.RIIIA 158 F/F genotype; iii) an Fc.gamma.RIIA
H/R.sup.131 genotype and an Fc.gamma.RIIIA V/V.sup.158 genotype; or
iv) an Fc.gamma.RIIA R/R.sup.131 genotype and an Fc.gamma.RIIIA
V/V.sup.158 genotype. Individuals of category (c) will have neither
an Fc.gamma.RIIA H/H.sup.131 genotype nor an Fc.gamma.RIIIA
V/V.sup.158 genotype. Thus, e.g., in some embodiments, individuals
of category (c) will have one of: i) an Fc.gamma.RIIA H/R.sup.131
genotype and an Fc.gamma.RIIIA V/F.sup.158 genotype; ii) an
Fc.gamma.RIIA R/R.sup.131 genotype and an Fc.gamma.RIIIA
V/F.sup.158 genotype; iii) an Fc.gamma.RIIA H/R.sup.131 genotype
and an Fc.gamma.RIIIA F/F.sup.158 genotype; or iv) an Fc.gamma.RIIA
R/R.sup.131 genotype and an Fc.gamma.RIIIA F/F.sup.158 genotype.
The nature of allelic expression for the above genotypes can be
best described by codominance. For example, for the Patient Group-V
(Table B) with genotypes Fc.gamma.RIIIA (V/F) and Fc.gamma.RIIA
(H/R) will have equal phenotypic expression of both alleles V,F for
Fc.gamma.RIIIA and H,R for Fc.gamma.RIIA. Both Fc.gamma.RIIIA and
Fc.gamma.RIIA are monomers under physiological conditions, and the
number of these receptors can be .about.15,000-35,000 per cell
(Guyre et al., 1983, J. Clin. Invest. 72:393-397). Individuals with
an Fc.gamma.RIIIA V/F.sup.158 genotype will express equal number of
V.sup.158 and F.sup.158 alleles. Similarly, individuals with an
Fc.gamma.RIIA 131H/R genotype will express equal number of
H.sup.131 and R.sup.131 alleles. As an example, a reference chart
with various combinations of Fc.gamma.RIIA and Fc.gamma.RIIIA
polymorphisms, and corresponding categories of anticipated
responsiveness to a monoclonal antibody therapy (e.g., Rituxan),
are shown in Table C, below.
TABLE-US-00003 TABLE C Fc.gamma.RIIIA 158 V/V Fc.gamma.RIIIA V IF
Fc.gamma.RIIIA F/F Fc.gamma.RIIA 131 H/H 70%-100% 50%-70% 50%-70%
Fc.gamma.RIIA 131 H/R 50%-70% <50% <50% Fc.gamma.RIIA 131 R/R
50%-70% <50% <50%
TABLE-US-00004 TABLE D Allelic expression patterns based on
Fc.gamma.RIIIA and Fc.gamma.RIIA polymorphisms in various patient
Groups (n = 87) Fc.gamma.RIIIA V/V.sup.158 Fc.gamma.RIIIA
V/F.sup.158 Fc.gamma.RIIIA F/F.sup.158 Total (%) Fc.gamma.RIIA
Group-I 70%-100% Group-II 50%-70% Group-III 50%-70% 20 (23).sup.
H/H.sup.131 V, V; H, H V, F; H, H F, F; H, H 3 (3.4) 14 (16.1) 3
(3.4) Fc.gamma.RIIA Group-IV 50%-70% Group-V <50% Group-VI
<50% 19 (21.8) H/R.sup.131 V, V; H, R V, F; H, R F, F; H, R 8
(9.2) 16 (18.4) 19 (21.8) Fc.gamma.RIIA Group-VII 50%-70%
Group-VIII <50% Group-IX <50% 12 (13.8) R/R.sup.131 V, V; R,
R V, F; R, R F, F; R, R 2 (2.3) 10 (11.8) 12 (13.8) Total (%) 13
(14.9) 40 (46) 34 (39.1) 87 (100)
[0381] Table D is another example of a reference chart. The
V.sup.158 allele in Fc.gamma.RIIIA is a
high-affinity/high-responder receptor while the F.sup.158 allele is
a low-affinity/low-responder receptor. Similarly, the H.sup.131
allele in Fc.gamma.RIIA is a high-affinity/high-responder receptor
while the R.sup.131 allele is a low-affinity/low-responder
receptor. The polymorphisms were determined in an expanded Group of
87 patients with follicular lymphoma (Table D; FIG. 13). The
allelic frequencies are: pV=0.38, pF=0.62; pH=0.48; pR=0.52.
[0382] Further, Fc.gamma.RIIIA and Fc.gamma.RIIA were determined
for populations of healthy U.S. Caucasians, healthy U.S. African
Americans and healthy Norwegians. Interestingly, these groups
exhibited a similar allelic expression pattern as the patient group
with B-NHL (FIG. 14).
[0383] As an example, a reference chart with various combinations
of Fc.gamma.RIIA and Fc.gamma.RIIIA polymorphisms, and
corresponding categories of anticipated responsiveness to a
monoclonal antibody therapy (e.g., Rituxan), are shown in Table D,
above.
[0384] In some embodiments, an Fc.gamma.RIIIA genotype and an
Fc.gamma.RIIA genotype are determined using a nucleic acid probe
that hybridizes under stringent hybridization conditions to
Fc.gamma.RIIA-encoding and Fc.gamma.RIIIA-encoding nucleic acids
comprising polymorphisms associated with an altered response to
treatment with a therapeutic antibody. Fc.gamma.RIIA-encoding and
Fc.gamma.RIIIA-encoding nucleic acids (referred to collectively
herein as "target nucleic acids") are in some embodiments genomic
DNA that comprise nucleotide sequences encoding all or part of an
Fc.gamma.RIIA or an Fc.gamma.RIIIA, and that include a polymorphism
associated with a response to an antibody therapeutic.
[0385] In other embodiments, an Fc.gamma.RIIIA genotype and an
Fc.gamma.RIIA genotype are determined using nucleic acid primer
pairs that, in the presence of an appropriate polymerase and other
reagents (e.g., dNTPs, ions such as magnesium ions, etc.), prime
the synthesis of an amplification product using the target nucleic
acids as templates, using, e.g., a polymerase chain reaction. The
target nucleic acids are chosen such that they include at least one
polymorphic region. For example, a first primer pair primes
amplification of an Fc.gamma.RIIA target nucleic acid that
comprises the polymorphism that gives rise to H/H.sup.131,
H/R.sup.131, or R/R.sup.131; and a second primer pair primes
amplification of an Fc.gamma.RIIIA target nucleic acid that
comprises a polymorphism that gives rise to V/V.sup.158,
V/F.sup.158, or F/F.sup.158. A nucleic acid primer will in some
embodiments include a detectable label, which detectable label is
incorporated into the amplification product, giving rise to a
detectably labeled amplification product. A nucleic acid primer
will in some embodiments include a restriction endonuclease
recognition site not found in the template or in other nucleic acid
primers, such that an amplification product is generated which
includes a restriction endonuclease recognition site that provides
for its identification.
ADCC Mediated by NK-Cells and Macrophages
[0386] The presence of infiltrating NK cells and macrophages in
surgically removed tumors from MAb-treated patients has been
extensively documented (Adams et al., 1984, Proc. Natl. Acad. Sic.
USA 81:3506; Shetye et al., 1988, Cancer Immunol. Immunother.
27:154). Although both ADCC and CDC may play a role in tumor cell
destruction in vivo, as substantiated by several in vitro studies,
the main anti-tumor mechanism of therapeutic antibodies in vivo is
considered to be ADCC (See, e.g., Velders et al., 1998, British J.
Cancer 78:478).
[0387] ADCC can be classified into two types: NK-cell mediated ADCC
(NK-ADCC) and macrophage-mediated ADCC (M-ADCC). Both mechanisms
either independently or together can be viewed to play significant
roles in mediating cytotoxicities, and have direct relevance in
determining the clinical efficacy of MAb therapies (Carton et al.,
2002, Blood 99:754; Weng and Levy, 2003, J. Clin. Oncol. 21:3940;
Cheung et al., 2006, J. Clin. Oncol. 24:2885).
[0388] Most tumor cells appear to secrete chemoattractants which
actively recruit monocytes to tumor sites (Graves et al., 1989,
Science 245:1490; Bottazzi et al., 1983, Science 220:210). The
mechanism of ADCC by these MDM (monocyte-derived macrophages)
appears to involve phagocytosis of intact tumor cells (Munn and
Cheung, 1990, J. Exp. Med. 172:231; Munn et al., 1991, Cancer
Research 51:1117). Thus, in one embodiment, macrophages are
important in immunotherapeutic regimens involving anti-tumor
ADCC.
[0389] Macrophages express three Fc.gamma.Rs for IgG: the
high-affinity receptor, F.gamma.RI, and the two low-affinity
receptors, Fc.gamma.RIIA and Fc.gamma.RIIIA Fc.gamma.RI avidly
binds monomeric human IgG (K.sub.a.about.2.times.10.sup.8
M.sup.-1), and therefore the binding of monoclonal antibody is
competitively inhibited by serum immunoglobulin.
[0390] Fc.gamma.RIIIA is present in NK cells
(Fc.gamma.RIIIA.sub.NK) and macrophages (Fc.gamma.RIIIA.sub.M).
Fc.gamma.RIIA is preferentially expressed on macrophages and
neutrophils, and not on lymphocytes. Although Fc.gamma.RIIIA.sub.NK
and Fc.gamma.RIIIA.sub.M have identical protein cores, they each
undergo differential cell type-specific glycosylation:
Fc.gamma.RIIIA.sub.NK is glycosylated with high mannose- and
complex-type oligosaccharides, while Fc.gamma.RIIIA.sub.M has no
high mannose-type oligosaccharides. Because of this,
Fc.gamma.RIIIA.sub.NK exhibits higher affinity for IgG.sub.1 and
this feature is not influenced by VF.sup.158 allelic polymorphism
(Edberg and Kimberly, 1997, J. Immunol. 159:3849). In normal whole
blood or plasma (containing 8-11 mg/ml IgG), Fc.gamma.RIIIA.sub.NK
was fully blocked, but Fc.gamma.RIIIA.sub.M showed approximately
60% blockade of the binding of mAB 3G8, which binds in or near the
ligand binding site. The ligand binding site of
Fc.gamma.RIIIA.sub.NK was blocked with as little as 2 mg/ml of
human IgG.sub.1 while Fc.gamma.RIIIA.sub.M was only partially (30%)
blocked at this concentration. In contrast, plasma containing
approximately 26 mg/ml of IgG (obtained from Immune
Thrombocytopenic Purpura patients receiving therapeutic g-globulin)
showed complete saturation of Fc.gamma.RIIIA.sub.M with blockade of
3G8 binding. Binding of mAB IV.3, an Fc.gamma.RIIA-specific MAb, to
the low affinity Fc.gamma.RIIA on monocytes was unaltered by
exposure of the cells to the same ITP patient plasmas. Thus, in one
embodiment, the ligand binding properties of Fc.gamma.RIIIA.sub.NK
and Fc.gamma.RIIIA.sub.M are distinctly different (Edberg and
Kimberly, supra). In another embodiment, therefore, the ADCC levels
mediated by the Fc.gamma.RIIIA.sub.NK and Fc.gamma.RIIIA.sub.M are
expected to be significantly different.
[0391] The Fc.gamma.RIIIA VF.sup.158 polymorphism is a clinically
relevant phenotype that has a direct impact on human biology (Wu et
al., 1997, J. Clin. Invest. 100:1059). Compared with FF.sup.158
homozygotes, Fc.gamma.RIIIA expressed on NK cells and monocytes in
VV.sup.158 homozygotes bound more IgG.sub.1 and IgG.sub.3 despite
identical levels of receptor expression. In response to a standard
aggregated human IgG stimulus, Fc.gamma.RIIIA engagement on NK
cells from VV.sup.158 (high binding) homozygotes led to a larger
rise in [Ca.sup.2+].sub.i, a greater level of NK cell activation,
and a more rapid induction of activation-induced cell death (by
apoptosis). Investigation of an independently phenotyped normal
cohort revealed that all donors with a low binding phenotype are
FF.sup.158 homozygotes, while all phenotypic high binding donors
have at least one V.sup.158 allele (either VV or VF). Initial
analyses of 200 patients with systemic lupus erythematosus (SLE)
indicates a strong association of the low-binding phenotype
(FF.sup.158) with disease, especially in patients with nephritis
who have an underrepresentation of the homozygous high binding
(VV.sup.158) phenotype (FF, 44%; VF, 46%; VV, 10%). This VF.sup.158
polymorphism based variations in IgG binding was further correlated
to the earlier observations that some patients have "high" NK-cell
mediated ADCC (Vance et al., 1993, J. Immunol. 151:6429).
[0392] Some forms of macrophage ADCC have been reported to be
inhibited by serum IgG.sub.1 which competes with monoclonal
antibodies for binding to Fc.gamma.RI. Hybridoma cells bearing
surface antibody directed against either of Fc.gamma.Rs (II and
III) were efficiently phagocytosed by MDM (Munn et. al., 1991,
Cancer Research 51:1117). Soluble anti-receptor antibodies against
Fc.gamma.RII and Fc.gamma.RIII were able to inhibit ADCC but only
when both antibodies were simultaneously present suggesting that
either Fc.gamma.R is capable of functioning independently to
mediate phagocytosis of tumor cells. Consistent with the mechanism
involving the low-affinity receptors rather than Fc.gamma.RI,
antibody-dependent phagocytosis occurred in the presence of human
serum and purified human IgG. Greater than 75% of the MDM were able
to ingest tumor cells when a suitable target cell was available
(Munn et. al., supra). Optimal phagocytosis occurred at monoclonal
antibody concentrations of 10-100 ng/ml. Because Fc.gamma.RI is
normally occupied in vivo by serum IgG.sub.1 the participation of
both low-affinity Fc.gamma.Rs in tumor cell phagocytosis is
potentially important in establishing the in vivo applicability of
this efficient form of toxicity (Munn et. al., supra).
[0393] C-reactive protein (CRP) is involved in host defense,
regulation of inflammation, and modulation of autoimmune disease.
CRP shares several functional activities with IgG including binding
to Fc.gamma.Rs (Crowell et al., 1991, J. Immunol. 147:3445; Marvell
et al., 1995, J. Immunol. 155:2185). Direct genetic evidence for
Fc.gamma.RIIA as the functional, high affinity CRP receptor on
monocytes/leukocytes has been provided, and this study emphasized
the reciprocal relationship between IgG and CRP avidities (Stein
et. al., 2000, J. Clin. Invest. 105:369). Fc.gamma.RIA binds CRP
with low affinity, whereas Fc.gamma.RIIA binds CRP with high
affinity. CRP bound with high avidity to monocytes and neutrophils
from Fc.gamma.RIIA-RR.sup.131 homozygotes. CRP showed decreased
binding to cells from Fc.gamma.RIIA-HH.sup.131 homozygotes. That
is, both IgG.sub.1, for instance, an antibody therapy such as
rituximab, and CRP will compete for the same binding site in
Fc.gamma.RIIA, and is further influenced by the HR.sup.131
polymorphism. Fc.gamma.RIIA-HR.sup.131 heterozygotes showed
intermediate binding. These findings provide direct genetic
evidence for Fc.gamma.RIIA as the functional, high affinity CRP
receptor on leukocytes while emphasizing the reciprocal
relationship between IgG and CRP binding avidities (Stein et al.
supra). Thus, in one embodiment, the M-ADCC is the sum of ADCC
mediated by the Fc.gamma.RIIIA and Fc.gamma.RIIA. In another
embodiment, the M-ADCC is influenced by both VF.sup.158 and HR131
polymorphisms.
[0394] The murine IgG.sub.3 anti-GD2 MAb 3F8 is being used in the
clinic for its antitumor activity in high-risk neuroblastoma
patients. The MAb exhibits potent in vitro ADCC activity (Kushner
et. al., 1989, Blood 73:1936), and its phagocyte-mediated ADCC is
markedly increased in the presence of GM-CSF. ELISA studies showed
3F8 has preferential binding to Fc.gamma.RIIA-R.sup.131 over
Fc.gamma.RIIA-H.sup.131. The role of Fc.gamma.RIIA-HR.sup.131 and
Fc.gamma.RIIIA-VF.sup.158 polymorphisms with clinical outcome of
high-risk neuroblastoma patients (N=136) treated with 3F8 and
GM-CSF was investigated (Cheung et. al., 2006, J. Clin. Oncol.
24:2885). Fc.gamma.RIIA-RR.sup.131 genotype correlated with
progression-free survival for the entire cohort (P=0.049), and also
correlated with marrow remission 2.5 months after treatment
initiation. This finding is in stark contrast to what was shown for
rituximab in B-NHL patients (Weng and Levy, supra), and can only be
attributed to the fact that 3F8 is a mouse IgG.sub.3 (Yan and
Davis, 2006, Pharmacogenomics 7:961), whose hinge region is about
four times longer than that of IgG.sub.1 (Michaelsen et. al., 1977,
J. Biol. Chem. 252:883, FIG. 18). Thus, in one embodiment, based on
the H/R.sup.131 polymorphisms, Fc variant IgG.sub.3 antibodies can
be generated with enhanced ADCC activity.
[0395] Therefore, in some embodiments, the Fc engineering is
focused on optimizing both NK-ADCC and M-ADCC. In other
embodiments, the Fc engineering is focused on optimizing the ADCC
mediated by Fc.gamma.RIIIA.sub.NK and Fc.gamma.RIIIA.sub.M. In some
other embodiments, the Fc engineering is attempted to optimize the
ADCC based on HR.sup.131 polymorphism in Fc.gamma.RIIA. In other
embodiments, the Fc engineering is attempted to optimize the ADCC
based on VF.sup.158 polymorphism in Fc.gamma.RIIIA.
Structure of Fc Region, Fc Receptors (FcR), and Fc-FcR
Complexes
[0396] All known Fc receptors are members of the Ig super family,
except for FccRII. The crystal structures of the extracellular
domains of Fc.gamma.RII (Maxwell et al., 1999, Nature Struct. Biol.
6:437-442; Sondermann et al., 1999, Biochemistry 29:8469-77) and
Fc.gamma.RIII (Zhang et al., 2000, Immunity 13:387-395) show
remarkable similarities. The receptors consist of two extracellular
Ig-like domains, D1 and D2, with acute interdomain hinge angles of
50-55.degree., unique to Fc receptors. The Fc-binding region is
located in the D2 domain. Additional crystal structures (Sondermann
et al., 2000, Nature 406:267-73; Radaev et al., 2001, J. Biol.
Chem. 276:16469-77; Sondermann et al., 2001, J. Mol. Biol.
309:737-749) have revealed that the receptor-ligand interface
consists of the BC, C'E, FG loops and the C.beta.. strand of the D2
domain, the hinge loop between the D1 and D2 domains of the
receptor providing additional interactions with Fc.gamma.R (FIG.
12C).
[0397] In the complex structure, the receptor is asymmetrically
bound between the two C.gamma.2 domains of the Fc fragment creating
a 1:1 receptor ligand stoichiometry. Only D2 of the sFc.gamma.RIII
and two residues from the linker connecting this domain with D1
interact in the complex with different regions of both C.gamma.2
domains (C.gamma.2-A and C.gamma.2-B) and the preceding hinge
regions of hFc1 (Fc from human IgG1; Sondermann et al., 2000,
Nature 406:267-73; Sondermann et al., 2001, J. Mol. Biol.
309:737-749). Both Fc.gamma.RIII and Fc components undergo
substantial domain rearrangements upon binding but are restricted
to the loops involved in the complex formation.
[0398] Fc Region-sFc.gamma.RIII Contact Interface: sFc.gamma.RIII
binds hFc1 with the B/C loop (W.sup.110-A.sup.114) the F/G loop
(V.sup.155-K.sup.158), the C strand (H.sup.116-T.sup.119) and C'
strand (D.sup.126-H.sup.132) on its carboxyl-terminal D2 (FIG.
12-C). Additionally, R.sup.152 and the connector between the
N-terminal D1 and D2 (I.sup.85-W.sup.87) is involved in binding.
These regions interact with loops on the hFc1 within C.gamma.2-B
(B/C: D.sup.265-E.sup.269, C/E: N.sup.297-T.sup.299), with the F/G
loop of C.gamma.2A (A.sup.327-I.sup.332), with the carbohydrate
residue N-acetyl-D-glucosamine (NAG)1 of C.gamma.2-B and with the
hinge region of both heavy chains (L.sup.234-S.sup.239). N.sup.297
is the glycosylation site in the Fc region.
[0399] Two main contact areas exist. First, P.sup.329 of
C.gamma.2-A is encaged tightly by W.sup.87 and W.sup.110 of the
Fc.gamma.RIII (`proline sandwich`). Second, residues
L.sup.234-S.sup.239 of the lower hinge of both hFc1 chains are
engaged in sFc.gamma.RIII binding. These residues were disordered
in the hFc1 crystal structures but are defined in the complex.
[0400] The receptor and the Fc fragment are in very close contact
at the hinge region. G.sup.237 of C.gamma.2-A and G.sup.236 of
C.gamma.2-B adopt Phi/Psi angles in the complex not allowed for
other residues. The hinge residues L.sup.234-S.sup.239 of
C.gamma.2-A are in contact with residues T.sup.113, A.sup.114 and
V.sup.155-K.sup.158 of Fc.gamma.RIII. The main contact is mediated
by L.sup.235 which binds in a shallow hydrophobic groove with
V.sup.155 at its bottom and the A.sup.114 of the B/C loop, and
T.sup.113 C.gamma.2 at its rim (FIG. 12-C).
[0401] The hinge residues of the C.gamma.2-B domain are bound in a
narrow channel of sFc.gamma.RIII lined by H.sup.116 and H.sup.132
on one side and K.sup.117 on the other. The residues G.sup.236 and
G.sup.237 of the hinge peptide bind into this channel and Y.sup.129
and H.sup.131 form additional contacts to the hinge peptide. In
this arrangement, the residues H.sup.116, H.sup.131, and H.sup.132
are potential hydrogen bond partners to hinge residues. L.sup.235
is in contact with H.sup.116 and H.sup.132; this region is
considerably more hydrophobic in other receptors.
[0402] The Fc.gamma.RIII contacts the interstrand loops of the
C.gamma.2-B domain and the terminal residues of the .beta.-strands.
The side chains of the residues D.sup.126-H.sup.131 (C' strand) are
bound to the residues D.sup.265-E.sup.269, and N.sup.297-T.sup.299
of C.gamma.2-B. R.sup.152 of the F strand could potentially form a
hydrogen bond to the carbohydrate residue NAG1 that is directly
attached to N.sup.297 of C.gamma.2-B. Some more distant contacts to
this sugar residue are formed by K.sup.117, T.sup.119, D.sup.126,
and Y.sup.129 (See, e.g., FIG. 12-C). Substitution of Asparagine at
position N.sup.297 should lead to aglycosylated Fc form, which
lacks ADCC activity but other functions such as CDC and FcRn
binding are retained (Dorai et al., 1991, Hybridoma 10:211-217;
Vaccaro et al., 2005, Nature Biotechnol. 23:1283-1287).
[0403] A sequence comparison of sFc.gamma.RIII with other
Fc.gamma.Rs and the FccRI.alpha. shows a high degree of similarity
(FIG. 12C). Mutagenesis studies with Fc.gamma.RI (Canfield and
Morrison, 1991, J. Exp. Med. 173:1483-91), Fc.gamma.RII (Lund et
al., 1991, J. Immunol. 147:2657-2662; Hulett et al., 1994, J. Biol.
Chem. 269:15287-93; Hulett et al., 1995, J. Biol. Chem. 270:21188;
Maxwell et al., 1999, Nature Struct. Biol. 6:437) and
Fc.epsilon.RI.alpha.(Hulett et al., 1999, J. Biol. Chem. 274:13345)
indicate that the same regions are involved in complex formation as
are defined here for sFc.gamma.RIII. Therefore, based on several
crystallographic and mutagenic studies, a common model describing
the principal interactions within the various complexes can be
proposed.
[0404] The proline sandwich appears as the primary binding motif in
all FcR-Ig complexes. The two tryptophan residues (W.sup.87 and
W.sup.110) are conserved in the FcRs including Fc.epsilon.RI.alpha.
and the proline occurs in all IgGs and IgE. Further conserved
contacts are observed between K.sup.117 and D.sup.265, T.sup.119
and NAG1, and K.sup.128 and E.sup.269 (the numbers in all Igs and
FcRs refer to the homologous position in IgG1 and sFc.gamma.RIII,
respectively; FIG. 12C).
[0405] The hinge peptide is a second central recognition site. The
sequence variation in this region is likely to be the main reason
for the differing affinities in the FcR-Ig pairs. The interactions
seem to be modulated in different receptor Ig pairings in a
productive or destructive way by the non-conserved regions of the
binding loops.
[0406] Fc.gamma.RII and Fc.gamma.RIII are 50% identical and the
differences affect the loops in contact with the hinge, but not the
contact regions to C.gamma.2-A and C.gamma.2-B. The residues
G.sup.236 and G.sup.237 of the C.gamma.2-B domain hinge peptide are
bound in the narrow channel between V.sup.116, L.sup.132, L.sup.132
and K.sup.117. These exchanges at positions V.sup.116 and L.sup.132
create a small hydrophobic patch to which L.sup.235 may bind and
allow a tighter contact of receptor and hinge peptide.
[0407] Therefore, in some embodiments, amino acid sequence changes
(e.g., insertions, deletions, substitutions, etc.) in one or more
of the following conserved regions of IgG1-Fc region are expected
to alter its binding properties to Fc.gamma.RIIIA and
Fc.gamma.RIIA: L.sup.234LGGPS.sup.239; R.sup.255TPEVT.sup.260;
D.sup.265VSHE.sup.269; N.sup.297ST.sup.299; A.sup.327LPAPI.sup.332.
In other embodiments, based on the V/F and H/R polymorphisms, Fc
variant antibodies can be generated with enhanced binding, potency,
efficacy, and ADCC function specific to the patient Groups as
exemplified in this disclosure. In some other embodiments,
modification of additional residues involved in Fc engineering is
accomplished through Fc Walking.
Methods of Making Sets of Related Antibodies
[0408] Methods are provided for making a set of related antibodies.
The method generally involves:
[0409] a) modifying at least one Fc region amino acid residue in a
parent antibody, such that the modified Fc region exhibits enhanced
binding affinity to at least one Fc receptor encoded by an Fc
receptor gene of a first genotype, compared to the Fc binding
affinity of the parent antibody, to generate a first Fc region
modified antibody (also referred to as an "Fc variant antibody");
and
[0410] b) modifying at least one Fc region amino acid residue in a
parent antibody, such that the modified Fc region exhibits enhanced
binding affinity to at least one Fc receptor encoded by an Fc
receptor gene of a second genotype, compared to the Fc binding
affinity of the parent antibody, to generate a second Fc region
modified antibody.
[0411] In other embodiments, methods are provided to modify the Fc
region of an antibody to reduce its binding affinity to at least
one Fc receptor compared to the Fc binding affinity of the parent
antibody.
[0412] The parent antibody is a reference antibody. The first and
second Fc region modified antibodies each differ in Fc region amino
acid sequence by at least one amino acid from the Fc region amino
acid sequence of the parent antibody, e.g., the first and the
second Fc variant antibodies each independently comprise an Fc
region amino acid sequence that differs in amino acid sequence from
the Fc region of the parent antibody by 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, or more, amino acids. In some embodiments,
the first and the second Fc variant antibodies each independently
comprise an Fc region amino acid sequence that differs in amino
acid sequence from the Fc region of the parent antibody by from 1
amino acid to 5 amino acids, or from 5 amino acids to 10 amino
acids. Changes in amino acid sequence are accomplished by one or
more of amino acid substitution, deletion, insertion, etc.
[0413] In some embodiments, the parent antibody is a wild-type
antibody, e.g., a naturally-occurring antibody. In other
embodiments, the parent antibody is a synthetic antibody, a
recombinant antibody, a chimeric antibody, etc. In some
embodiments, an Fc region modified antibody ("Fc variant antibody")
is a monoclonal antibody (e.g., an "Fc variant MAb").
[0414] In some embodiments, a subject method of making a set of
related antibodies comprises one or more of:
[0415] a) substituting at least one amino acid residue in the Fc
region of a parent antibody, generating an Fc variant antibody,
such that the Fc variant antibody exhibits enhanced in vitro ADCC
function to at least one Fc.gamma. receptor encoded by an Fc.gamma.
receptor gene of a first genotype, compared to the Fc.gamma.R in
vitro ADCC function of the parent antibody, to generate a first Fc
variant antibody;
[0416] b) substituting at least one amino acid residue in the Fc
region of a parent antibody, generating an Fc variant antibody,
such that the Fc variant antibody exhibits enhanced in vitro ADCC
function to at least one Fc.gamma. receptor encoded by an Fc.gamma.
receptor gene of a second genotype, compared to the Fc.gamma.R in
vitro ADCC function of the parent antibody, to generate a second Fc
variant antibody;
[0417] c) substituting more than one amino acid residue in the Fc
region of a parent antibody, generating an Fc variant antibody,
such that the Fc variant antibody exhibits enhanced in vitro ADCC
function to both Fc.gamma. receptors encoded by the Fc.gamma.
receptor genes, compared to the Fc.gamma.R in vitro ADCC function
of the parent antibody;
[0418] d) combining the amino acid substitutions of the first and
second Fc variant antibodies to generate a third Fc variant
antibody such that the third Fc variant antibody exhibit enhanced
in vitro ADCC function to both Fc.gamma. receptors encoded by the
Fc.gamma. receptor genes, compared to the Fc.gamma.R in vitro ADCC
function of the parent antibody; and
[0419] e) generating patient Group-specific Fc variant antibodies
such that the degree of treatment response to antibody therapy in
the patient Groups is increased.
[0420] In certain embodiments, first and second Fc variant
antibodies have the same antigen specificity, and have the same
antigen specificity as the parent antibody. Antibodies that are
members of a set of related antibodies include monoclonal
antibodies, chimeric antibodies, bi-specific antibodies,
recombinant antibodies, synthetic antibodies, semi-synthetic
antibodies, tetravalent (multivalent) antibodies, Fc:fusion
proteins, and chemically modified intact antibodies.
[0421] The parent antibody, the first Fc variant antibody, and the
second Fc variant antibody constitute a set of related antibodies.
In certain embodiments, the set of related antibodies are
therapeutic antibodies suitable for treating an ADCC-treatable
disease, condition, or disorder. In some embodiments, a set of
related therapeutic antibodies are antibodies that bind a
tumor-associated antigen; such a set of related antibodies is
useful for treating an individual having a neoplastic disease. In
other embodiments, a set of related therapeutic antibodies are
antibodies that bind an antigen on an autoreactive immune cell;
such a set of related antibodies is useful for treating an
individual having an autoimmune disorder. In other embodiments, a
set of related therapeutic antibodies are antibodies that bind an
antigen on an alloreactive T-cell; such a set of related antibodies
is useful for treating allograft rejection. In other embodiments, a
set of related therapeutic antibodies are antibodies that bind a
viral antigen expressed on the surface of a virus-infected cell;
such a set of related antibodies is useful for treating a virus
infection. In other embodiments, a set of related therapeutic
antibodies are antibodies that bind an antigen expressed on the
surface of a parasite; such a set of related antibodies is useful
for treating a parasite infection.
[0422] Any convenient method of modifying the amino acid sequence
of the Fc region can be used. In some embodiments, residues that
are proximal to residues that are known to bind or contact an Fc
receptor are modified. For example, based on the crystal structure
of an Fc portion of an antibody, an amino acid residue that, if
substituted, enhances binding to an Fc receptor, is an amino acid
residue that is within about 30 .ANG., within about 15 .ANG.,
within about 10 .ANG., or within about 5 .ANG., of an amino acid
residue that is known to contact an Fc receptor. In other
embodiments, residues of the Fc region that are proximal to other
Fc residues on a three-dimensional space, if substituted, enhance
binding to an Fc receptor. Such examples include interactions
between T.sup.256 and K.sup.290, and K.sup.338 and E.sup.43.degree.
(e.g., Shields et al., supra). These residues may be involved in
van der Waals contacts, hydrogen bonding, and salt bridge
formation.
[0423] The Fc fragment including the hinge can be successfully
produced as a dimer in E. coli (Kim et al., 1994, Eur. J. Immunol.
24:542). Soluble Fc.gamma.RIII and Fc.gamma.RII can also be
expressed in E. coli (Sondermann and Jacob, 1999, Biol. Chem.
380:717-721; Sondermann et al., 2000, Nature 406:267-273), and
through binding and crystallographic studies it is shown that the
Fc fragment binds to FcR domain. Thus, in one embodiment, a) in
vitro ADCC is a function of Fc-FcR binding, and b) ADCC-dependent
therapeutic response is a function of in vitro ADCC. In another
embodiment, in vitro Fc-FcR binding studies and in vitro ADCC
assays can be employed to develop Fc variant MAbs specific for
patient Groups I-IX as exemplified in this disclosure based on the
differences in Fc.gamma.R polymorphisms.
[0424] Fc variant antibodies of interest include antibodies that
have at least about 10%, at least about 20%, at least about 30%, at
least about 40%, at least about 50%, at least about 60%, at least
about 70%, at least about 80%, at least about 90%, or at least
about 100%, or 2-fold, increased binding affinity to an Fc receptor
and/or enhanced in vitro ADCC activity, compared to the binding
affinity of the parent antibody to the Fc receptor and/or in vitro
ADCC activity. In some embodiments, Fc variant Abs of interest
include antibodies that have at least about 10%, at least about
20%, at least about 30%, at least about 40%, at least about 50%, at
least about 60%, at least about 70%, at least about 80%, at least
about 90%, or at least about 100%, or 2-fold, increased binding
affinity and/or enhanced in vitro ADCC activity to an Fc.gamma.RIIA
comprising Arg.sup.131, compared to the binding affinity or ADCC
activity of the parent antibody to the Fc.gamma.RIIA comprising
Arg.sup.131. In some embodiments, Fc variant Abs of interest
include antibodies that have at least about 10%, at least about
20%, at least about 30%, at least about 40%, at least about 50%, at
least about 60%, at least about 70%, at least about 80%, at least
about 90%, or at least about 100%, or 2-fold, increased binding
affinity and/or enhanced in vitro ADCC activity to an
Fc.gamma.RIIIA comprising Phe.sup.158, compared to the binding
affinity or ADCC activity of the parent antibody to an
Fc.gamma.RIIIA comprising Phe.sup.158.
[0425] Fc variant antibodies of interest will comprise one or more
amino acid sequence modifications (substitutions, insertions,
deletions, etc.) that provide for enhanced binding affinity and/or
enhanced in vitro ADCC activity to an Fc.gamma.RIIA and/or an
Fc.gamma.RIIIA; and will in some embodiments comprise one or more
amino acid substitutions in a hinge region, and/or a CH2 region,
and/or a CH3 region. See, e.g., Wines et al., 2000, J. Immunol.
164:5313; Lazar et al., 2006, Proc. Natl. Acad. Sci. USA
103:4005-4010. In some embodiments, Fc variant antibodies of
interest will comprise one or more amino acid substitutions in the
lower hinge region, e.g., amino acids L.sup.234-S.sup.239 (the
numbering of the residues in an immunoglobulin heavy chain is that
of the EU index as in Kabat et al., Sequences of Proteins of
Immunological Interest, 5th Ed. Public Health Service, National
Institutes of Health, Bethesda, Md. (1991). The "EU index as in
Kabat" refers to the residue numbering of the human IgG1 EU
antibody. In some embodiments, Fc variant antibodies of interest
will comprise one or more amino acid substitutions in one or more
of the following regions: R.sup.255-T.sup.260; D.sup.265-E.sup.269;
N.sup.297-T.sup.299; A.sup.327-I.sup.332 (See, e.g., FIG. 12-C). In
some embodiments, Fc variant antibodies of interest will comprise
one or more amino acid substitutions in the CH3 domain, which when
substituted, make considerable improvements in FcR binding (e.g.,
K.sup.338 and E.sup.430).
[0426] Fc variant antibodies of interest will comprise one or more
amino acid substitutions that provide for enhanced binding affinity
and/or enhanced in vitro ADCC activity to an Fc.gamma.RIIA and/or
an Fc.gamma.RIIIA For example, a human IgG1 constant region
comprising a T256A or a K290A substitution has enhanced binding
affinity to Fc.gamma.RIIA and Fc.gamma.RIIIA, compared to wild-type
human IgG1. A human IgG1 constant region comprising a E333A, K334A,
or A339T substitution has enhanced binding affinity to
Fc.gamma.RIIIA, compared to wild-type human IgG1. Similarly, a
human IgG1 constant region comprising the following triple
mutations has enhanced binding affinity to Fc.gamma.RIIIA: S298A,
E333A; K334A. See, e.g., Shields et al., 2001, J. Biol. Chem.
276:6591-6604; and Presta et al., 2002, Biochem. Soc. Trans.
30:487-490.
[0427] In some embodiments, an Fc variant antibody exhibits
enhanced binding affinity and/or enhanced in vitro ADCC activity
between the Fc region of the antibody and an Fc.gamma. receptor,
compared to the binding affinity and ADCC activity between the Fc
region of a parent antibody and the Fc.gamma. receptor. In some
embodiments, an Fc variant antibody exhibits an at least 10%, at
least 15%, at least 25%, at least 50%, at least 75%, at least 100%
(or two-fold), at least 5-fold, at least 10-fold, at least 50-fold,
at least 100-fold, or more, higher affinity and/or enhanced in
vitro ADCC activity for an Fp.gamma. receptor than the
corresponding parent antibody.
[0428] In some embodiments, a method of generating an Fc variant
antibody that exhibits enhanced binding affinity and/or enhanced in
vitro ADCC activity to an Fc receptor involves modifying a codon in
a nucleic acid that comprises a nucleotide sequence that encodes an
antibody constant region (including, e.g., hinge region, CH2, and
CH3 domains). In some embodiments, a nucleic acid comprising a
nucleotide sequence encoding an Fc region is amplified by PCR,
using a set of primers that encode all nineteen naturally-occurring
amino acid variants at a single residue of the constant region, to
generate a set of variant nucleic acids encoding nineteen amino
acid substitution variants at the single residue of the constant
region. Each of the variants is expressed in an in vitro
transcription/translation system, to generate a set of Fc variant
antibodies. Each of the Fc variant antibodies is then tested for
binding affinity to an Fc receptor. The variants are generated
using any known method, including, e.g., the method described in
U.S. Pat. No. 6,180,341. Assessing binding to Fc receptors is
carried out using any known method, including a method as described
in Shields et al., 2001, J. Biol. Chem. 276:6591-6604.
[0429] In other embodiments, a method of generating an Fc variant
antibody that exhibits enhanced binding affinity to an Fc receptor
involves generating a set of variant nucleic acids encoding
nineteen amino acid substitution variants at the single residue of
the constant region, as described above; expressing each of the
encoded Fc variant antibodies on the surface of a host cell; and
selecting a host cell that expresses an Fc variant antibody that
exhibits enhanced binding and/or enhanced in vitro ADCC activity to
an Fc receptor. See, e.g., U.S. Patent Publication No.
2003/0036092.
[0430] The present disclosure further provides sets of related
antibodies, as described above. In many embodiments, the antibodies
are isolated.
Antigen-Binding Specificity
[0431] A set of related antibodies includes member antibodies that
share antigen-binding specificity; and that differ in binding
affinity to an Fc.gamma.R. An antibody that is a member of a set of
related antibodies will have an antigen-binding domain; and an Fc
domain. Antigen-binding domains (ABD) include ABD specific for an
epitope on the surface of a tumor cell; ABD specific for a
virally-encoded epitope on the surface of a virus-infected cell;
ABD specific for an epitope on the surface of an autoreactive cell;
ABD specific for an epitope on the surface of an alloreactive cell;
and ABD specific for an epitope expressed on the surface of a
eukaryotic parasite, e.g., a helminth. An ABD from any known
antibody can be linked to an Fc fragment, e.g., a native Fc
fragment, or a variant Fc fragment that exhibits enhanced binding
to one or more Fc.gamma.Rs, in generating a set of related
antibodies.
[0432] Sequences of exemplary Fc fragments (e.g., RITUXAN.RTM.,
REMICADE.RTM., ERBITUX.RTM. CAMPATH.RTM., and HERCEPTIN.RTM.) are
shown in FIG. 15.
[0433] In some embodiments, antigen binding domains may be obtained
from any one of the following antibodies: RITUXAN.RTM.,
CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM., XOLAIR.RTM.,
RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM., HUMIRA.RTM.,
ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM., VECTIBIX.RTM.,
TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM., OKT3.RTM., BEXXAR.RTM. or
ZEVALIN.RTM., ENBREL.RTM. or AMEVIVE.RTM.
[0434] Antigen-binding domains will in some embodiments comprise a
V.sub.H-C.sub.H1 region and a V.sub.L-C.sub.L region.
Antigen-binding domains will in some embodiments be a V.sub.H or
V.sub.L domains (domain antibodies), Fv, Fab, scFv, F(ab).sub.2
fragments, tetravalent (multivalent) antibodies, Fc:fusion
proteins, or engineered Fc:fusion constructs (e.g., SMIPs; Trubion
Pharmaceuticals). The antigen-binding domain will in some
embodiments have the amino acid sequence of an antigen-binding
domain of a naturally-occurring antibody. The antigen-binding
domain will in some embodiments be recombinant, synthetic, or
semi-synthetic. "Humanized" ABD are also suitable for use; see,
e.g., U.S. Pat. No. 6,180,370.
Enhanced Antigen Affinity Improves ADCC
[0435] The impact of antigen density and antibody affinity on the
efficacy of tumor cell elimination via has been studied
extensively. The low-affinity Ep-CAM MAb 17-1A
(K.sub.a=5.times.10.sup.7 M.sup.-1) and the high affinity MAb
323/A3 (K.sub.a=2.times.10.sup.9 M.sup.-1) were compared in ADCC
experiments against murine and human tumor target cells (Velders et
al. supra). The high-affinity MAb mediated ADCC killing of tumor
cells with low antigen expression levels. Even at comparable
MAb-binding levels, ADCC mediated by the high-affinity MAb was more
effective. The kinetics of ADCC was also found to be determined by
the level of antigen expression, and by the affinity and
concentration of the MAb used (Velders et al. supra).
[0436] Additionally, the heterogeneity of a target antigen
expression is a common feature of all tumors, and some tumor cells
express very low levels of antigen. For example, the CD20 antigen
density varies in various NHL types (antigens per cell): normal
B-cells, 94,000; mantle cell leukemia, 123,000; pro-lymphocytic
leukemia, 129,000; splenic lymphoma, 167,000; hairy cell lymphoma,
312,000; chronic lymphocytic leukemia, 65,000; B-cell (peripheral
blood) CLL patients, 9,000; bone marrow and lymph nodes, 4,000
(Manshouri et al., 2003, Blood 101:2507).
[0437] Affinity improvements in antibodies are primarily
accomplished through CDR engineering, and it is a function of
association and dissociation rate constants, k.sub.on, and
k.sub.off (Schier et al., 1996, J. Mol. Biol. 263:551; Wu et al.,
1998, Proc. Natl. Acad. Sci. USA 95:6037). Thus, improved ADCC in
high-affinity antibodies can be due to a) retention of MAbs bound
to the antigens for such long periods in a conformationally locked
position that facilitates Fc binding to Fc.gamma.Rs, and b) reduced
internalization of antibodies as has been shown for anti-Her2/neu
antibody variants (for example, McCall et al., 2001, J Immunol.
166:6112; Tang et al., "High affinity promotes more effective ADCC
by anti-HER2/neu monocloncal antibodies," Abstract No: 2538,
American Society of Clinical Oncology, 2006 ASCO Annual
Meeting).
[0438] In one embodiment, affinity improvement through CDR
engineering improves the affinity of the IgG Fc region to
Fc.gamma.RIIIA and Fc.gamma.RIIA. In another embodiment, affinity
improvement through CDR engineering improves the binding of the IgG
Fc region to Fc.gamma.RIIIA and Fc.gamma.RIIA. In yet another
embodiment, affinity improvement through CDR engineering improves
the in vitro ADCC mediated by NK cells and/or macrophages. In
another embodiment, affinity improvement through CDR engineering
improves the clinical efficacy of an ADCC-mediated antibody
therapy.
Cancer Cell Antigens
[0439] Examples of antigens that are expressed on the surface of
cancer cells and to which an ABD binds include, but are not limited
to, p185.sup.HER2; CD20; CD19; CD21; CD22; CD23; epidermal growth
factor (EGF) receptor; vascular endothelial growth factor (VEGF)
receptor; CD33; CD52; epithelial cell adhesion molecule (Ep-CAM);
carcinoembryonic antigen (CEA); B-cell idiotypes; CD40; CD80; MHC
Class-II; CTLA-4; G250 antigen; GD2; and the like. Such antigens
are suitable targets for an ADCC-based antibody therapy.
[0440] The p185.sup.HER2 antigen has been described. See, e.g.,
Coussens, L. et al., 1985, Science 230:1132-1139; Yamamoto, T. et
al., 1986, Nature 319:230-234; King, C. R. et al., 1985, Science
229:974-976). HER2 is also known in the field as c-erbB-2, and
sometimes by the name of the rat homolog, neu. Amplification and/or
overexpression of HER2 is associated with multiple human
malignancies and appears to be integrally involved in progression
of 25-30% of human breast and ovarian cancers (Slamon et al., 1987,
Science 235:177-182; Slamon et al., 1989, Science 244:707-712).
Furthermore, the extent of amplification is inversely correlated
with the observed median patient survival time (Slamon, supra).
Antibodies that bind HER2 are known in the art, and an ABD of any
known anti-HER2 antibody can be used. The murine monoclonal
antibody known as muMAb4D5 (Fendly et al., 1990, Cancer Res.
50:1550-1558), directed against the extracellular domain (ECD) of
p185.sup.HER2, specifically inhibits the growth of tumor cell lines
overexpressing p185.sup.HER2 in monolayer culture or in soft agar
(Hudziak et al., 1989, Mol. Cell. Biol. 9:1165-1172; Lupu et al.,
1990, Science 249:1552-1555). MuMAb4D5 also has the potential of
enhancing tumor cell sensitivity to tumor necrosis factor, an
important effector molecule in macrophage-mediated tumor cell
cytotoxicity (Hudziak, supra, 1989; Shepard, H. M. and Lewis, G.
D., 1988, J. Clinical Immunology 8:333-395). The ABD of muMAb4D5 is
useful in the treatment of cancer cells in which p185.sup.HER2 is
overexpressed. The muMAb4D5 antibody is described in PCT
application WO 89/06692 published 27 Jul. 1989. This murine
antibody was deposited with the ATCC and designated ATCC CRL 10463.
A "humanized" version of MAb4D5 is discussed in U.S. Pat. No.
6,800,738.
[0441] Antibodies to CD20 are known in the art and include
Rituximab (as discussed above). Antibodies to CD52 include, e.g.,
Alemtuzumab (Campath-1H) (see, e.g., U.S. Pat. No. 5,545,403).
Antibodies to CD33 include, e.g., gemtuzumab (Myelotarg); humanized
M195 (Caron et al., 1994, Blood 83:1760-1768; and Co et al., 1992,
J. Immunol. 148:1149). Antibodies to EGF receptor include, e.g.,
cetuximab (Erbitux); and panitumumab (Abgenix/Immunex). Antibodies
to GD2 (expressed on neuroblastoma cells) include, e.g., Ch14.18
(NCI). Antibodies to G250 antigen (expressed on renal cancer cells)
include, e.g., Rencarex (WX-9250; Wilex). Antibodies to MHC
class-II (expressed on non-Hodgkins lymphoma cells) include, e.g.,
Remitogen (Hu1D10; Protein Design Labs).
Autoreactive Immune Cell Antigens
[0442] Antigens expressed on the surface of autoreactive immune
cells that are suitable as targets of an ADCC-based antibody
therapy include, but are not limited to, CD3.
Antigens Expressed on Alloreactive T-Cells
[0443] Antigens on alloreactive T-cells that are suitable as
targets of an ADCC-based antibody therapy include, but are not
limited to, CD3, CD2, CD4, CD5, CD6, CD8, CD28, and CD44.
Microbial Antigens
[0444] Viral antigens that are suitable as targets of an ADCC-based
antibody therapy include virus-encoded antigens expressed on the
surface of a virus-infected cell. Viral antigens are from any of a
variety of DNA and RNA viruses. Although HCV is primarily a
hepatotropic virus, HCV infection is frequently associated with
mixed cryoglobulinemia, non-Hodgkin's B-cell lymphoma, and
Sjogren's syndrome, all of which involve B-cell proliferation
(Selva-O'Callaghan et. al., 1999, Arthritis Rheum. 42:2489),
suggesting that HCV may infect B-cells or affect B-cell functions
in natural infection. Minus-strand HCV RNA has been detected by
reverse transcriptase PCR in peripheral lymphocytes, bone marrow,
lymph nodes, and central nervous system of some HCV patients
(Radkowski et. al., 2002, J. Virol. 76:600).
[0445] Parasitic antigens that are suitable targets for ADCC-based
antibody therapy include antigens expressed on the surface of a
parasite that is the etiologic agent of a parasitic disorder.
Bacterial antigens that are suitable targets for ADCC-based
antibody therapy include antigens expressed on the surface of a
bacterium that is the etiologic agent of a bacterial infection.
Preparation of Antibodies
[0446] Variant antibodies are produced by modifying the nucleic
acid of a parent antibody, inserting the modified nucleic acid into
an appropriate cloning vector and expressing the modified nucleic
acid to produce variant antibodies. Representative protocols are
described below:
[0447] 1. Making Variant Antibody Nucleic Acid
[0448] Variant antibodies will comprise one or more amino acid
sequence modifications (substitutions, insertions, deletions, etc.)
relative to a parent antibody sequence that provide for enhanced
binding affinity and/or enhanced in vitro ADCC activity to an
Fc.gamma.RIIA and/or an Fc.gamma.RIIIA.
[0449] In some embodiments, an Fc variant antibodies will comprise
one or more amino acid substitutions in a hinge region, and/or a
CH2 region, and/or a CH3 region (See, e.g., Wines et al., 2000, J.
Immunol. 164:5313; Lazar et al., 2006, Proc. Natl. Acad. Sci. USA
103:4005-4010). In other embodiments, Fc variant antibodies of
interest will comprise one or more amino acid substitutions in the
lower hinge region, e.g., amino acids L.sup.234-S.sup.239 (the
numbering of the residues in an immunoglobulin heavy chain is that
of the EU index as in Kabat et al., Sequences of Proteins of
Immunological Interest, 5th Ed. Public Health Service, National
Institutes of Health, Bethesda, Md. (1991). The "EU index as in
Kabat" refers to the residue numbering of the human IgG1 EU
antibody. In yet further embodiments, Fc variant antibodies of
interest will comprise one or more amino acid substitutions in one
or more of the following regions: R.sup.255-T.sup.260;
D.sup.265-E.sup.269; N.sup.297-T.sup.299; A.sup.327-I.sup.332 (See,
e.g., FIG. 12-C). In some embodiments, Fc variant antibodies of
interest will comprise one or more amino acid substitutions in the
CH3 domain, which when substituted, make considerable improvements
in FcR binding (e.g., K.sup.338 and E.sup.430).
[0450] Fc variant antibodies of interest will comprise one or more
amino acid substitutions that provide for enhanced binding affinity
and/or enhanced in vitro ADCC activity to an Fc.gamma.RIIA and/or
an Fc.gamma.RIIIA. For example, a human IgG1 constant region
comprising a T256A or a K290A substitution has enhanced binding
affinity to Fc.gamma.RIIA and Fc.gamma.RIIIA, compared to wild-type
human IgG1. A human IgG1 constant region comprising a E333A, K334A,
or A339T substitution has enhanced binding affinity to
Fc.gamma.RIIIA, compared to wild-type human IgG1. Similarly, a
human IgG1 constant region comprising the following triple
mutations has enhanced binding affinity to Fc.gamma.RIIIA: S298A,
E333A; K334A (See, e.g., Shields et al., 2001, J. Biol. Chem.
276:6591-6604; and Presta et al., 2002, Biochem. Soc. Trans.
30:487-490).
[0451] In some embodiments, an Fc variant antibody exhibits
enhanced binding affinity and/or enhanced in vitro ADCC activity
between the Fc region of the antibody and an Fc.gamma. receptor,
compared to the binding affinity and ADCC activity between the Fc
region of a parent antibody and the Fc.gamma. receptor. In some
embodiments, an Fc variant antibody exhibits an at least 10%, at
least 15%, at least 25%, at least 50%, at least 75%, at least 100%
(or two-fold), at least 5-fold, at least 10-fold, at least 50-fold,
at least 100-fold, or more, higher affinity and/or enhanced in
vitro ADCC activity for an F.gamma. receptor than the corresponding
parent antibody.
[0452] In some embodiments, a method of generating an Fc variant
antibody that exhibits enhanced binding affinity and/or enhanced in
vitro ADCC activity to an Fc receptor involves modifying a codon in
a nucleic acid that comprises a nucleotide sequence that encodes an
antibody constant region (including, e.g., hinge region, CH2, and
CH3 domains). In some embodiments, a nucleic acid comprising a
nucleotide sequence encoding an Fc region is amplified by PCR,
using a set of primers that encode all nineteen naturally-occurring
amino acid variants at a single residue of the constant region, to
generate a set of variant nucleic acids encoding nineteen amino
acid substitution variants at the single residue of the constant
region.
[0453] The antibody variants are generated using any known method,
including, e.g., the method described in U.S. Pat. No.
6,180,341.
[0454] In other embodiments, a method of generating an Fc variant
antibody that exhibits enhanced binding affinity to an Fc receptor
involves generating a set of variant nucleic acids encoding
nineteen amino acid substitution variants at the single residue of
the constant region, as described above; expressing each of the
encoded Fc variant antibodies on the surface of a host cell; and
selecting a host cell that expresses an Fc variant antibody that
exhibits enhanced binding and/or enhanced in vitro ADCC activity to
an Fc receptor (See, e.g., U.S. Patent Publication No.
2003/0036092).
[0455] In other embodiments, antibody variants may comprise one or
more amino acid substitutions in a complementarity determining
region (CDR). Such modifications may be generated by any of the
methods describe above concerning Fc variants.
[0456] In designing amino acid sequence antibody variants, the
location of the mutation site and the nature of the mutation will
depend on the target antibody characteristic(s) to be modified. The
sites for mutation can be modified individually or in series, e.g.,
by (1) substituting first with conservative amino acid choices and
then with more radical selections depending upon the results
achieved, (2) deleting the target residue, or (3) inserting
residues of the same or a different class adjacent to the located
site, or combinations of options 1-3.
[0457] A useful method for identification of certain residues or
regions of the antibody that are preferred locations for
mutagenesis is called "alanine scanning mutagenesis" as described
by Cunningham and Wells, 1989, Science, 244: 1081-1085. Here, a
residue or Group of target residues are identified (e.g., charged
residues such as arg, asp, his, lys, and glu) and replaced by a
neutral or negatively charged amino acid (most preferably alanine
or polyalanine) to affect the interaction of the amino acids with
the surrounding aqueous environment in or outside the cell. Those
domains demonstrating functional sensitivity to the substitutions
then are refined by introducing further or other variants at or for
the sites of substitution. Thus, while the site for introducing an
amino acid sequence variation is predetermined, the nature of the
mutation per se need not be predetermined. For example, to optimize
the performance of a mutation at a given site, ala scanning or
random mutagenesis may be conducted at the target codon or region
and the expressed antibody variants are screened for the optimal
combination of desired activity.
[0458] There are two principal variables in the construction of
amino acid sequence variants: the location of the mutation site and
the nature of the mutation. In general, the location and nature of
the mutation chosen will depend upon the antibody characteristic to
be modified.
[0459] Amino acid sequence deletions of antibodies are generally
not preferred, as maintaining the generally configuration of an
antibody is believed to be necessary for its activity. Any
deletions will be selected so as to preserve the structure of the
antibody.
[0460] Amino acid sequence insertions include amino- and/or
carboxyl-terminal fusions ranging in length from one residue to
polypeptides containing a hundred or more residues, as well as
intra-sequence insertions of single or multiple amino acid
residues. Intrasequence insertions (i.e., insertions within the
antibody sequence) may range generally from about 1 to 10 residues,
more preferably 1 to 5, most preferably 1 to 3. Examples of
terminal insertions include the antibody with an N-terminal
methionyl residue, an artifact of the direct expression of target
polypeptide in bacterial recombinant cell culture, and fusion of a
heterologous N-terminal signal sequence to the N-terminus of the
target polypeptide molecule to facilitate the secretion of the
mature target polypeptide from recombinant host cells. Such signal
sequences generally will be obtained from, and thus homologous to,
the intended host cell species. Suitable sequences include STII or
Ipp for E. coli, alpha factor for yeast, and viral signals such as
herpes gD for mammalian cells.
[0461] Another group of variants are amino acid substitution
variants. These variants have at least one amino acid residue in
the antibody molecule removed and a different residue inserted in
its place. The sites of greatest interest for substitutional
mutagenesis include sites identified as the active site(s) of the
antibody, and sites where the amino acids found in the antibody
from various species are substantially different in terms of
side-chain bulk, charge, and/or hydrophobicity. Other sites for
substitution are described infra, considering the effect of the
substitution of the antigen binding, affinity and other
characteristics of a particular target antibody.
[0462] Other sites of interest are those in which particular
residues of the antibody obtained from various species are
identical. These positions may be important for the biological
activity of the antibody. These sites, especially those falling
within a sequence of at least three other identically conserved
sites, are substituted in a relatively conservative manner. If such
substitutions result in a change in biological activity, then other
changes are introduced and the products screened until the desired
effect is obtained.
[0463] Substantial modifications in function or immunological
identity of the antibody are accomplished by selecting
substitutions that differ significantly in their effect on
maintaining (a) the structure of the polypeptide backbone in the
area of the substitution, for example, as a sheet or helical
conformation, (b) the charge or hydrophobicity of the molecule at
the target site, or (c) the bulk of the side chain. Naturally
occurring residues are divided into Groups based on common side
chain properties: [0464] hydrophobic: norleucine, met, ala, val,
leu, ile; [0465] neutral hydrophilic: cys, ser, thr; [0466] acidic:
asp, glu; [0467] basic: asn, gin, his, lys, arg; [0468] residues
that influence chain orientation: gly, pro; and [0469] aromatic:
trp, tyr, phe.
[0470] Non-conservative substitutions will entail exchanging a
member of one of these classes for another. Such substituted
residues may be introduced into regions of the antibody that are
homologous with other antibodies of the same class or subclass, or,
more preferably, into the non-homologous regions of the
molecule.
[0471] Any cysteine residues not involved in maintaining the proper
conformation of the antibody also may be substituted, generally
with serine, to improve the oxidative stability of the molecule and
prevent aberrant crosslinking.
[0472] DNA encoding amino acid sequence variants of the antibody
are prepared by a variety of methods known in the art. These
methods include, but are not limited to, isolation from a natural
source (in the case of naturally occurring amino acid sequence
variants) or preparation by oligonucleotide-mediated (or
site-directed) mutagenesis, PCR mutagenesis, and cassette
mutagenesis of an earlier prepared variant or a non-variant version
of the target polypeptide. A particularly preferred method of gene
conversion mutagenesis is described below in Example 1. These
techniques may utilized antibody nucleic acid (DNA or RNA), or
nucleic acid complementary to the antibody nucleic acid.
Oligonucleotide-mediated mutagenesis is a preferred method for
preparing substitution, deletion, and insertion variants of
antibody DNA. This technique is well known in the art as described
by Adelman et al., 1983, DNA, 2: 183. Briefly, the antibody DNA is
altered by hybridizing an oligonucleotide encoding the desired
mutation to a DNA template, where the template is the
single-stranded form of a plasmid or bacteriophage containing the
unaltered or native DNA sequence of the target polypeptide. After
hybridization, a DNA polymerase is used to synthesize an entire
second complementary strand of the template that will thus
incorporate the oligonucleotide primer, and will code for the
selected alteration in the target polypeptide DNA.
[0473] Generally, oligonucleotides of at least 25 nucleotides in
length are used. An optimal oligonucleotide will have 12 to 15
nucleotides that are completely complementary to the template on
either side of the nucleotide(s) coding for the mutation. This
ensures that the oligonucleotide will hybridize properly to the
single-stranded DNA template molecule. The oligonucleotides are
readily synthesized using techniques known in the art such as that
described by Crea et al., 1978, Proc. Natl. Acad. Sci. USA, 75:
5765.
[0474] Single-stranded DNA template may also be generated by
denaturing double-stranded plasmid (or other) DNA using standard
techniques.
[0475] For alteration of the native DNA sequence (to generate amino
acid sequence variants, for example), the oligonucleotide is
hybridized to the single-stranded template under suitable
hybridization conditions. A DNA polymerizing enzyme, usually the
Klenow fragment of DNA polymerase I, is then added to synthesize
the complementary strand of the template using the oligonucleotide
as a primer for synthesis. A heteroduplex molecule is thus formed
such that one strand of DNA encodes the mutated form of the
antibody, and the other strand (the original template) encodes the
native, unaltered sequence of the antibody. This heteroduplex
molecule is then transformed into a suitable host cell, usually a
prokaryote such as E. coli JM 101. After the cells are grown, they
are plated onto agarose plates and screened using the
oligonucleotide primer radiolabeled with 32-phosphate to identify
the bacterial colonies that contain the mutated DNA. The mutated
region is then removed and placed in an appropriate vector for
protein production, generally an expression vector of the type
typically employed for transformation of an appropriate host. The
method described immediately above may be modified such that a
homoduplex molecule is created wherein both strands of the plasmid
contain the mutation(s). The modifications are as follows: The
single-stranded oligonucleotide is annealed to the single-stranded
template as described above. A mixture of three
deoxyribonucleotides, deoxyriboadenosine (dATP), deoxyriboguanosine
(dGTP), and deoxyribothymidine (dTTP), is combined with a modified
thio-deoxyribocytosine called dCTP-(aS) (which can be obtained from
Amersham Corporation). This mixture is added to the
template-oligonucleotide complex.
[0476] Upon addition of DNA polymerase to this mixture, a strand of
DNA identical to the template except for the mutated bases is
generated. In addition, this new strand of DNA will contain
dCTP-(aS) instead of dCTP, which serves to protect it from
restriction endonuclease digestion.
[0477] After the template strand of the double-stranded
heteroduplex is nicked with an appropriate restriction enzyme, the
template strand can be digested with ExoIII nuclease or another
appropriate nuclease past the region that contains the site(s) to
be mutagenized. The reaction is then stopped to leave a molecule
that is only partially single-stranded. A complete double-stranded
DNA homoduplex is then formed using DNA polymerase in the presence
of all four deoxyribonucleotide triphosphates, ATP, and DNA ligase.
This homoduplex molecule can then be transformed into a suitable
host cell such as E. coli JM101, as described above.
[0478] DNA encoding antibody variants with more than one amino acid
to be substituted may be generated in one of several ways. If the
amino acids are located close together in the polypeptide chain,
they may be mutated simultaneously using one oligonucleotide that
codes for all of the desired amino acid substitutions. If, however,
the amino acids are located some distance from each other
(separated by more than about ten amino acids), it is more
difficult to generate a single oligonucleotide that encodes all of
the desired changes. Instead, one of two alternative methods may be
employed.
[0479] In the first method, a separate oligonucleotide is generated
for each amino acid to be substituted. The oligonucleotides are
then annealed to the single-stranded template DNA simultaneously,
and the second strand of DNA that is synthesized from the template
will encode all of the desired amino acid substitutions.
[0480] The alternative method involves two or more rounds of
mutagenesis to produce the desired mutant antibody. The first round
is as described for the single antibody mutants: wild-type DNA is
used for the template, an oligonucleotide encoding the first
desired amino acid substitution(s) is annealed to this template,
and the heteroduplex DNA molecule is then generated. The second
round of mutagenesis utilizes the mutated DNA produced in the first
round of mutagenesis as the template. Thus, this template already
contains one or more mutations. The oligonucleotide encoding the
additional desired amino acid substitution(s) is then annealed to
this template, and the resulting strand of DNA now encodes
mutations from both the first and second rounds of mutagenesis.
This resultant DNA can be used as a template in a third round of
mutagenesis, and so on.
[0481] PCR mutagenesis is also suitable for making amino acid
antibody variants. While the following discussion refers to DNA, it
is understood that the technique also finds application with RNA.
The PCR technique generally refers to the following procedure (See,
e.g., Erlich, supra, the chapter by R. Higuchi, p. 61-70). When
small amounts of template DNA are used as starting material in a
PCR, primers that differ slightly in sequence from the
corresponding region in a template DNA can be used to generate
relatively large quantities of a specific DNA fragment that differs
from the template sequence only at the positions where the primers
differ from the template. For introduction of a mutation into a
plasmid DNA, one of the primers is designed to overlap the position
of the mutation and to contain the mutation; the sequence of the
other primer must be identical to a stretch of sequence of the
opposite strand of the plasmid, but this sequence can be located
anywhere along the plasmid DNA. It is preferred, however, that the
sequence of the second primer is located within 200 nucleotides
from that of the first, such that in the end the entire amplified
region of DNA bounded by the primers can be easily sequenced. PCR
amplification using a primer pair like the one just described
results in a population of DNA fragments that differ at the
position of the mutation specified by the primer, and possibly at
other positions, as template copying is somewhat error-prone.
[0482] If the ratio of template to product material is extremely
low, the vast majority of product DNA fragments incorporate the
desired mutation(s). This product material is used to replace the
corresponding region in the plasmid that served as PCR template
using standard DNA technology. Mutations at separate positions can
be introduced simultaneously by either using a mutant second
primer, or performing a second PCR with different mutant primers
and ligating the two resulting PCR fragments simultaneously to the
vector fragment in a three (or more)-part ligation.
[0483] In a specific example of PCR mutagenesis, template plasmid
DNA (1 .mu.g) is linearized by digestion with a restriction
endonuclease that has a unique recognition site in the plasmid DNA
outside of the region to be amplified. Of this material, 100 ng is
added to a PCR mixture containing PCR buffer, which contains the
four deoxynucleotide tri-phosphates and is included in the
GeneAmp.RTM. kits (obtained from Perkin-Elmer Cetus, Norwalk, Conn.
and Emeryville, Calif.), and 25 pmole of each oligonucleotide
primer, to a final volume of 50 .mu.l. The reaction mixture is
overlayed with 35 .mu.l mineral oil. The reaction is denatured for
5 minutes at 100.degree. C., placed briefly on ice, and then 1
.mu.l Thermus aquaticus (Taq) DNA polymerase (5 units/4 purchased
from Perkin-Elmer Cetus, Norwalk, Conn. and Emeryville, Calif.) is
added below the mineral oil layer. The reaction mixture is then
inserted into a DNA Thermal Cycler (purchased from Perkin-Elmer
Cetus) programmed as follows: 2 min. at 55.degree. C., then 30 sec.
at 72.degree. C., then 19 cycles of the following: 30 sec. at
94.degree. C., 30 sec. at 55.degree. C., and 30 sec. at 72.degree.
C.
[0484] At the end of the program, the reaction vial is removed from
the thermal cycler and the aqueous phase transferred to a new vial,
extracted with phenol/chloroform (50:50:vol), and ethanol
precipitated, and the DNA is recovered by standard procedures. This
material is subsequently subjected to the appropriate treatments
for insertion into a vector.
[0485] Another method for preparing variants, cassette mutagenesis,
is based on the technique described by Wells et al., 1985, Gene,
34:315. The starting material is the plasmid (or other vector)
comprising the antibody DNA to be mutated. The codon(s) in the
antibody DNA to be mutated are identified. There must be a unique
restriction endonuclease site on each side of the identified
mutation site(s). If no such restriction sites exist, they may be
generated using the above-described oligonucleotide-mediated
mutagenesis method to introduce them at appropriate locations in
the target polypeptide DNA. After the restriction sites have been
introduced into the plasmid, the plasmid is cut at these sites to
linearize it. A double-stranded oligonucleotide encoding the
sequence of the DNA between the restriction sites but containing
the desired mutation(s) is synthesized using standard procedures.
The two strands are synthesized separately and then hybridized
together using standard techniques. This double-stranded
oligonucleotide is referred to as the cassette. This cassette is
designed to have 3' and 5' ends that are compatible with the ends
of the linearized plasmid, such that it can be directly ligated to
the plasmid. This plasmid now contains the mutated antibody DNA
sequence.
[0486] 2. Insertion of DNA into a Cloning Vehicle
[0487] The cDNA or genomic DNA encoding the antibody is inserted
into a replicable vector for further cloning (amplification of the
DNA) or for expression. Many vectors are available, and selection
of the appropriate vector will depend on 1) whether it is to be
used for DNA amplification or for DNA expression, 2) the size of
the DNA to be inserted into the vector, and 3) the host cell to be
transformed with the vector. Each vector contains various
components depending on its function (amplification of DNA or
expression of DNA) and the host cell for which it is compatible.
The vector components generally include, but are not limited to,
one or more of the following: a signal sequence, an origin of
replication, one or more marker genes, an enhancer element, a
promoter, and a transcription termination sequence.
[0488] (a) Signal Sequence Component
[0489] In general, the signal sequence may be a component of the
vector, or it may be a part of antibody DNA that is inserted into
the vector.
[0490] The therapeutic antibody may be expressed not only directly,
but also as a fusion with a heterologous polypeptide, preferably a
signal sequence or other polypeptide having a specific cleavage
site at the N-terminus of the mature protein or polypeptide. In
general, the signal sequence may be a component of the vector, or
it may be a part of the antibody DNA that is inserted into the
vector. Included within the scope of this disclosure are antibody
with any native signal sequence deleted and replaced with a
heterologous signal sequence. The heterologous signal sequence
selected should be one that is recognized and processed (i.e.
cleaved by a signal peptidase) by the host cell. For prokaryotic
host cells that do not recognize and process the native antibody
signal sequence, the signal sequence is substituted by a
prokaryotic signal sequence selected, for example, from the group
of the alkaline phosphatase, penicillinase, Ipp, or heat-stable
enterotoxin II leaders. For yeast secretion the native target
polypeptide signal sequence may be substituted by the yeast
invertase, alpha factor, or acid phosphatase leaders. In mammalian
cell expression the native signal sequence is satisfactory,
although other mammalian signal sequences may be suitable.
[0491] (b) Origin of Replication Component
[0492] Both expression and cloning vectors contain a nucleic acid
sequence that enables the vector to replicate in one or more
selected host cells. Generally, in cloning vectors this sequence is
one that enables the vector to replicate independently of the host
chromosomal DNA, and includes origins of replication or
autonomously replicating sequences. Such sequences are well known
for a variety of bacteria, yeast, and viruses. The origin of
replication from the plasmid pBR322 is suitable for most
Gram-negative bacteria, the 2.mu., plasmid origin is suitable for
yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or
BPV) are useful for cloning vectors in mammalian cells. Generally,
the origin of replication component is not needed for mammalian
expression vectors (the SV40 origin may typically be used only
because it contains the early promoter).
[0493] Most expression vectors are "shuttle" vectors, i.e. they are
capable of replication in at least one class of organisms but can
be transfected into another organism for expression. For example, a
vector is cloned in E. coli and then the same vector is,
transfected into yeast or mammalian cells for expression even
though it is not capable of replicating independently of the host
cell chromosome.
[0494] DNA may also be amplified by insertion into the host genome.
This is readily accomplished using Bacillus as a host, for example,
by including in the vector a DNA sequence that is complementary to
a sequence found in Bacillus genomic DNA. Transfection of Bacillus
with this vector results in homologous recombination with the
genome and insertion of the antibody DNA. However, the recovery of
genomic DNA encoding the antibody is more complex than that of an
exogenously replicated vector because restriction enzyme digestion
is required to excise the antibody DNA.
[0495] (c) Selection Gene Component
[0496] Expression and cloning vectors should contain a selection
gene, also termed a selectable marker. This gene encodes a protein
necessary for the survival or growth of transformed host cells
grown in a selective culture medium. Host cells not transformed
with the vector containing the selection gene will not survive in
the culture medium. Typical selection genes encode proteins that
(a) confer resistance to antibiotics or other toxins, e.g.,
ampicillin, neomycin, methotrexate, or tetracycline, (b) complement
auxotrophic deficiencies, or (c) supply critical nutrients not
available from complex media, e.g., the gene encoding D-alanine
racemase for Bacilli.
[0497] One example of a selection scheme utilizes a drug to arrest
growth of a host cell. Those cells that are successfully
transformed with a heterologous gene express a protein conferring
drug resistance and thus survive the selection regimen. Examples of
such dominant selection use the drugs neomycin (Southern et al.,
1982, J. Molec. Appl. Genet. 1:327), mycophenolic acid (Mulligan et
al., 1980, Science, 209:1422) or hygromycin (Sugden et al., 1985,
Mol. Cell. Biol., 5:410-413). The three examples given above employ
bacterial genes under eukaryotic control to convey resistance to
the appropriate drug G418 or neomycin (geneticin), xgpt
(mycophenolic acid), or hygromycin, respectively. Another example
of suitable selectable markers for mammalian cells are those that
enable the identification of cells competent to take up the
antibody nucleic acid, such as dihydrofolate reductase (DHFR) or
thymidine kinase. The mammalian cell transformants are placed under
selection pressure which only the transformants are uniquely
adapted to survive by virtue of having taken up the marker.
Selection pressure is imposed by culturing the transformants under
conditions in which the concentration of selection agent in the
medium is successively changed, thereby leading to amplification of
both the selection gene and the DNA that encodes antibody.
Amplification is the process by which genes in greater demand for
the production of a protein critical for growth are reiterated in
tandem within the chromosomes of successive generations of
recombinant cells. Increased quantities of the antibody are
synthesized from the amplified DNA.
[0498] For example, cells transformed with the DHFR selection gene
are first identified by culturing all of the transformants in a
culture medium that contains methotrexate (Mtx), a competitive
antagonist of DHFR. An appropriate host cell when wild-type DHFR is
employed is the Chinese hamster ovary (CHO) cell line deficient in
DHFR activity, prepared and propagated as described by Urlaub and
Chasin, 1980, Proc. Natl. Acad. Sci. USA, 77:4216. The transformed
cells are then exposed to increased levels of methotrexate. This
leads to the synthesis of multiple copies of the DHFR gene, and,
concomitantly, multiple copies of other DNA comprising the
expression vectors, such as the DNA encoding the antibody.
[0499] This amplification technique can be used with any otherwise
suitable host, e.g., ATCC No. CCL61 CHO-K1, notwithstanding the
presence of endogenous DHFR if, for example, a mutant DHFR gene
that is highly resistant to Mtx is employed (EP 117,060).
Alternatively, host cells (particularly wild-type hosts that
contain endogenous DHFR) transformed or co-transformed with DNA
sequences encoding the antibody, wild-type DHFR protein, and
another selectable marker such as aminoglycoside 3'
phosphotransferase (APH) can be selected by cell growth in medium
containing a selection agent for the selectable marker such as an
aminoglycosidic antibiotic, e.g., kanamycin, neomycin, or G418
(See, e.g., U.S. Pat. No. 4,965,199).
[0500] A suitable selection gene for use in yeast is the trp1 gene
present in the yeast plasmid YRp7 (Stinchcomb et al., 1979, Nature,
282: 39; Kingsman et al., 1979, Gene, 7:141; or Tschemper et al.,
1980, Gene, 10:157). The trp1 gene provides a selection marker for
a mutant strain of yeast lacking the ability to grow in tryptophan,
for example, ATCC No. 44076 or PEP4-1 (Jones, 1977, Genetics,
85:12). The presence of the trp1 lesion in the yeast host cell
genome then provides an effective environment for detecting
transformation by growth in the absence of tryptophan. Similarly,
Leu2-deficient yeast strains (ATCC 20,622 or 38,626) are
complemented by known plasmids bearing the Leu2 gene.
[0501] (d) Promoter Component
[0502] Expression and cloning vectors usually contain a promoter
that is recognized by the host organism and is operably linked to
the antibody nucleic acid. Promoters are untranslated sequences
located upstream (5') to the start codon of a structural gene
(generally within about 100 to 1000 bp) that control the
transcription and translation of a particular nucleic acid
sequence, such as that encoding the antibody, to which they are
operably linked. Such promoters typically fall into two classes,
inducible and constitutive. Inducible promoters are promoters that
initiate increased levels of transcription from DNA under their
control in response to some change in culture conditions, e.g., the
presence or absence of a nutrient or a change in temperature. At
this time a large number of promoters recognized by a variety of
potential host cells are well known. These promoters are operably
linked to DNA encoding the target polypeptide by removing the
promoter from the source DNA by restriction enzyme digestion and
inserting the isolated promoter sequence into the vector. Both the
native antibody promoter sequence and many heterologous promoters
may be used to direct amplification and/or expression of the
antibody DNA. However, heterologous promoters are preferred, as
they generally permit greater transcription and higher yields of
expressed antibody as compared to the native antibody promoter.
[0503] Promoters suitable for use with prokaryotic hosts include
the .beta.-lactamase and lactose promoter systems (Chang et al.,
1978, Nature, 275: 615; and Goeddel et al., 1979, Nature, 281:
544), alkaline phosphatase, a tryptophan (trp) promoter system
(Goeddel, 1980, Nucleic Acids Res., 8: 4057 and EP 36,776) and
hybrid promoters such as the tac promoter (deBoer et al., 1983,
Proc. Natl. Acad. Sci. USA, 80:21-25). However, other known
bacterial promoters are suitable. Their nucleotide sequences have
been published, thereby enabling a skilled worker operably to
ligate them to DNA encoding the target polypeptide (Siebenlist et
al., 1980, Cell, 20:269) using linkers or adaptors to supply any
required restriction sites. Promoters for use in bacterial systems
also generally will contain a Shine-Dalgarno (S.D.) sequence
operably linked to the DNA encoding the target polypeptide.
[0504] Suitable promoting sequences for use with yeast hosts
include the promoters for 3-phosphoglycerate kinase (Hitzeman et
al., 1980, J. Biol. Chem. 255:2073) or other glycolytic enzymes
(Hess et al, 1968, J. Adv. Enzyme Reg. 7:149; and Holland, 1978,
Biochemistry 17:4900), such asenolase, glyceraldehyde-3-phosphate
dehydrogenase, hexokinase, pyruvate decarboxylase,
phosphofructokinase, glucose-6-phosphate isomerase,
3-phosphoglycerate mutase, pyruvate kinase, triosephosphate
isomerase, phosphoglucose isomerase, and glucokinase.
[0505] Other yeast promoters, which are inducible promoters having
the additional advantage of transcription controlled by growth
conditions, are the promoter regions for alcohol dehydrogenase 2,
isocytochrome C, acid phosphatase, degradative enzymes associated
with nitrogen metabolism, met allothionein,
glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible
for maltose and galactose utilization. Suitable vectors and
promoters for use in yeast expression are further described in
Hitzeman et al., EP 73,657A. Yeast enhancers also are
advantageously used with yeast promoters.
[0506] Promoter sequences are known for eukaryotes. Virtually all
eukaryotic genes have an AT-rich region located approximately 25 to
30 bases upstream from the site where transcription is initiated.
Another sequence found 70 to 80 bases upstream from the start of
transcription of many genes is a CXCAAT region where X may be any
nucleotide. At the 3' end of most eukaryotic genes is an AATAAA
sequence that may be the signal for addition of the poly A tail to
the 3' end of the coding sequence. All of these sequences are
suitably inserted into mammalian expression vectors.
[0507] Antibody transcription from vectors in mammalian host cells
is controlled by promoters obtained from the genomes of viruses
such as polyoma virus, fowlpox virus (UK 2,211,504 published Jul.
5, 1989), adenovirus (such as Adenovirus 2), bovine papilloma
virus, avian sarcoma virus, cytomegalovirus, a retrovirus,
hepatitis-B virus and most preferably Simian Virus 40 (SV40), from
heterologous mammalian promoters, e.g., the actin promoter or an
immunoglobulin promoter, from heat-shock promoters, and from the
promoter normally associated with the antibody sequence, provided
such promoters are compatible with the host cell systems.
[0508] The early and late promoters of the SV40 virus are
conveniently obtained as an SV40 restriction fragment that also
contains the SV40 viral origin of replication. Fiers et al., 1978,
Nature, 273:113; Mulligan and Berg, 1980, Science, 209: 1422-1427;
Pavlakis et al., 1981, Proc. Natl. Acad. Sci. USA, 78: 7398-7402.
The immediate early promoter of the human cytomegalovirus is
conveniently obtained as a HindIII E restriction fragment.
Greenaway et al., 1982, Gene, 18: 355-360. A system for expressing
DNA in mammalian hosts using the bovine papilloma virus as a vector
is disclosed in U.S. Pat. No. 4,419,446. A modification of this
system is described in U.S. Pat. No. 4,601,978. See, e.g., Gray et
al., 1982, Nature, 295: 503-508 on expressing cDNA encoding immune
interferon in monkey cells; Reyes et al., 1982, Nature, 297:
598-601 on expression of human .beta.-interferon cDNA in mouse
cells under the control of a thymidine kinase promoter from herpes
simplex virus, Canaani and Berg, 1982, Proc. Natl. Acad. Sci. USA,
79: 5166-5170 on expression of the human interferon-131 gene in
cultured mouse and rabbit cells, and Gorman et al., 1982, Proc.
Natl. Acad. Sci. USA, 79: 6777-6781 on expression of bacterial CAT
sequences in CV-1 monkey kidney cells, chicken embryo fibroblasts,
Chinese hamster ovary cells, HeLa cells, and mouse NIH-3T3 cells
using the Rous sarcoma virus long terminal repeat as a
promoter.
[0509] (e) Enhancer Element Component
[0510] Transcription of DNA encoding the antibody of this
disclosure by higher eukaryotes is often increased by inserting an
enhancer sequence into the vector. Enhancers are cis-acting
elements of DNA, usually about from 10-300 bp, that act on a
promoter to increase its transcription. Enhancers are relatively
orientation and position independent having been found 5' (Laimins
et al., 1981, Proc. Natl. Acad. Sci. USA 78:993) and 3' (Lusky et
al., 1983, Mol. Cell. Bio. 3:1108) to the transcription unit,
within an intron (Banerji et al., 1983, Cell 33:729) as well as
within the coding sequence itself (Osborne et al., 1984, Mol. Cell.
Bio. 4:1293). Many enhancer sequences are now known from mammalian
genes (globin, elastase, albumin, -fetoprotein and insulin).
Typically, however, one will use an enhancer from a eukaryotic cell
virus. Examples include the SV40 enhancer on the late side of the
replication origin (bp 100-270), the cytomegalovirus early promoter
enhancer, the polyoma enhancer on the late side of the replication
origin, and adenovirus enhancers. See, e.g., Yaniv, 1982, Nature
297:17-18 on enhancing elements for activation of eukaryotic
promoters. The enhancer may be spliced into the vector at a
position 5' or 3' to the antibody DNA, but is preferably located at
a site 5' from the promoter.
[0511] (f) Transcription Termination Component
[0512] Expression vectors used in eukaryotic host cells (yeast,
fungi, insect, plant, animal, human, or nucleated cells from other
multicellular organisms) will also contain sequences necessary for
the termination of transcription and for stabilizing the mRNA. Such
sequences are commonly available from the 5' and, occasionally 3'
untranslated regions of eukaryotic or viral DNA or cDNAs. These
regions contain nucleotide segments transcribed as polyadenylated
fragments in the untranslated portion of the mRNA encoding the
target polypeptide. The 3' untranslated regions also include
transcription termination sites.
[0513] Construction of suitable vectors containing one or more of
the above listed components the desired coding and control
sequences employs standard ligation techniques. Isolated plasmids
or DNA fragments are cleaved, tailored, and religated in the form
desired to generate the plasmids required.
[0514] For analysis to confirm correct sequences in plasmids
constructed, the ligation mixtures are used to transform E. coli
K12 strain 294 (ATCC 31,446) and successful transformants selected
by ampicillin or tetracycline resistance where appropriate.
Plasmids from the transformants are prepared, analyzed by
restriction endonuclease digestion, and/or sequenced by the method
of Messing et al., 1981, Nucleic Acids Res. 9:309 or by the method
of Maxam et al., 1980, Methods in Enzymology. 65:499.
[0515] Particularly useful in the practice of this disclosure are
expression vectors that provide for the transient expression in
mammalian cells of DNA encoding the antibody. In general, transient
expression involves the use of an expression vector that is able to
replicate efficiently in a host cell, such that the host cell
accumulates many copies of the expression vector and, in turn,
synthesizes high levels of a desired antibody encoded by the
expression vector. Transient expression systems, comprising a
suitable expression vector and a host cell, allow for the
convenient positive identification of polypeptides encoded by
cloned DNAs, as well as for the rapid screening of such
polypeptides for desired biological or physiological properties.
Thus, transient expression systems are particularly useful in the
disclosure for purposes of identifying analogs and variants of the
antibody that have antibody-like activity.
[0516] Other methods, vectors, and host cells suitable for
adaptation to the synthesis of the target polypeptide in
recombinant vertebrate cell culture are described in Gething et
al., 1981, Nature 293:620-625; Mantei et al., 1979, Nature
281:40-46; Levinson et al.; EP 117,060; and EP 117,058. A
particularly useful plasmid for mammalian cell culture expression
of the antibody is pRK5 (EP pub. no. 307,247) or pSVI6B. Selection
and
[0517] 3. Transformation of Host Cells
[0518] Suitable host cells for cloning or expressing the vectors
herein are the prokaryote, yeast, or higher eukaryote cells
described above. Suitable prokaryotes include eubacteria, such as
Gram-negative or Gram-positive organisms, for example, E. coli,
Bacilli such as B. subtilis, Pseudomonas species such as P.
aeruginosa, Salmonella typhimurium, or Serratia marcescens. One
preferred E. coli cloning host is E. coli 294 (ATCC 31,446),
although other strains such as E. coli B, E. coli .chi.1776 (ATCC
31,537), and E. coli W3110 (ATCC 27,325) are suitable.
[0519] These examples are illustrative rather than limiting.
Preferably the host cell should secrete minimal amounts of
proteolytic enzymes. Alternatively, in vitro methods of cloning,
e.g., PCR or other nucleic acid polymerase reactions, are
suitable.
[0520] In addition to prokaryotes, eukaryotic microbes such as
filamentous fungi or yeast are suitable hosts for target
polypeptide-encoding vectors. Saccharomyces cerevisiae, or common
baker's yeast, is the most commonly used among lower eukaryotic
host microorganisms. However, a number of other genera, species,
and strains are commonly available and useful herein, such as
Schizosaccharomyces pombe (Beach and Nurse, 1981, Nature 290:140;
EP 139,383 published May 2, 1985, Kluyveromyces hosts (U.S. Pat.
No. 4,943,529) such as, e.g., K. lactis (Louvencourt et al., 1983,
J. Bacteriol., 737), K. fragilis, K. bulgaricus, K. thermotolerans,
and K. marxianus, yarrowia (EP 402,226), Pichia pastoris (EP
183,070; Sreekrishna et al., 1988, J. Basic Microbiol., 28:
265-278), Candida, Trichoderma reesei (EP 244,234), Neurospora
crassa (Case et al., 1979, Proc. Natl. Acad. Sci. USA, 76:
5259-5263), and filamentous fungi such as, e.g., Neurospora,
Penicillium, Tolypocladium (WO 91/00357 published Jan. 10, 1991),
and Aspergillus hosts such as A. nidulans (Ballance et al., 1983,
Biochem. Biophys. Res. Commun. 112:284-289); Tilburn et al., 1983,
Gene 26:205-221); Yelton et al., 1984, Proc. Natl. Acad. Sci. USA
81:1470-1474) and A. niger (Kelly and Hynes, 1985, EMBO J.
4:475-479).
[0521] Suitable host cells for the expression of glycosylated
target polypeptide are derived from multicellular organisms. Such
host cells are capable of complex processing and glycosylation
activities. In principle, any higher eukaryotic cell culture is
workable, whether from vertebrate or invertebrate culture. Examples
of invertebrate cells include plant and insect cells. Numerous
baculoviral strains and variants and corresponding permissive
insect host cells from hosts such as Spodoptera frugiperda
(caterpillar), Aedes aegypti (mosquito), Aedes albopictus
(mosquito), Drosophila melanogaster (fruitfly), and Bombyx mori
host cells have been identified. See, e.g., Luckow et al., 1988,
Bio/Technology 6:47-55; Miller et al., in Genetic Engineering,
Setlow, J. K. et al., eds., Vol. 8, Plenum Publishing, pp. 277-279
(1986); and Maeda et al., 1985, Nature 315:592-594). A variety of
such viral strains are publicly available, e.g., the L-1 variant of
Autographa californica NPV and the Bm-5 strain of Bombyx mori NPV,
and such viruses may be used as the virus herein according to the
present disclosure, particularly for transfection of Spodoptera
frugiperda cells. Plant cell cultures of cotton, corn, potato,
soybean, petunia, tomato, and tobacco can be utilized as hosts.
Typically, plant cells are transfected by incubation with certain
strains of the bacterium Agrobacterium tumefaciens, which has been
previously manipulated to contain the antibody DNA. During
incubation of the plant cell culture with A. tumefaciens, the DNA
encoding antibody is transferred to the plant cell host such that
it is transfected, and will, under appropriate conditions, express
the antibody DNA. In addition, regulatory and signal sequences
compatible with plant cells are available, such as the nopaline
synthase promoter and polyadenylation signal sequences. See,
Depicker et al., 1982, J. Mol. Appl. Gen. 1:561. In addition, DNA
segments isolated from the upstream region of the T-DNA 780 gene
are capable of activating or increasing transcription levels of
plant-expressible genes in recombinant DNA-containing plant tissue.
See, e.g., EP 321,196 published Jun. 21, 1989.
[0522] However, interest has been greatest in vertebrate cells, and
propagation of vertebrate cells in culture (tissue culture) has
become a routine procedure in recent years (Tissue Culture,
Academic Press, Kruse and Patterson, editors (1973)). Examples of
useful mammalian host cell lines are monkey kidney CV1 line
transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney
line (293 or 293 cells subcloned for growth in suspension culture,
Graham et al., 1977, J. Gen Virol. 36:59); baby hamster kidney
cells (BHK, ATCC CCL 10); Chinese hamster ovary cells/-DHFR (CHO,
Urlaub and Chasin, 1980, Proc. Natl. Acad. Sci. USA 77:4216); mouse
sertoli cells (TM4, Mather, 1980, Biol. Reprod. 23:243-251); monkey
kidney cells (CV1 ATCC CCL 70); African green monkey kidney cells
(VERO-76, ATCC CRL-1587); human cervical carcinoma cells (HELA,
ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat
liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC
CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor
(MMT 060562, ATCC CCL51); TRI cells (Mather et al., 1982, Annals
N.Y. Acad. Sci. 383:44-68); MRC 5 cells; FS4 cells; and a human
hepatoma cell line (Hep G2). Preferred host cells are human
embryonic kidney 293 and Chinese hamster ovary cells.
[0523] Host cells are transfected and preferably transformed with
the above-described expression or cloning vectors of this
disclosure and cultured in conventional nutrient media modified as
appropriate for inducing promoters, selecting transformants, or
amplifying the genes encoding the desired sequences.
[0524] Transfection refers to the taking up of an expression vector
by a host cell whether or not any coding sequences are in fact
expressed. Numerous methods of transfection are known to the
ordinarily skilled artisan, for example, CaPO.sub.4 and
electroporation. Successful transfection is generally recognized
when any indication of the operation of this vector occurs within
the host cell.
[0525] Transformation means introducing DNA into an organism so
that the DNA is replicable, either as an extrachromosomal element
or by chromosomal integrant. Depending on the host cell used,
transformation is done using standard techniques appropriate to
such cells. The calcium treatment employing calcium chloride, as
described in section 1.82 of Sambrook et al., supra, is generally
used for prokaryotes or other cells that contain substantial
cell-wall barriers. Infection with Agrobacterium tumefaciens is
used for transformation of certain plant cells, as described by
Shaw et al., 1983, Gene 23:315 and WO 89/05859 published Jun. 29,
1989. For mammalian cells without such cell walls, the calcium
phosphate precipitation method described in sections 16.30-16.37 of
Sambrook et al., supra, is preferred. General aspects of mammalian
cell host system transformations have been described by Axel in
U.S. Pat. No. 4,399,216 issued Aug. 16, 1983. Transformations into
yeast are typically carried out according to the method of Van
Solingen et al., 1977, J. Bact. 130:946 and Hsiao et al., 1979,
Proc. Natl. Acad. Sci. USA 76:3829. However, other methods for
introducing DNA into cells such as by nuclear injection,
electroporation, or protoplast fusion may also be used. Culturing
the Host Cells
[0526] Prokaryotic cells used to produce the target polypeptide of
this disclosure are cultured in suitable media as described
generally in Sambrook et al., supra.
[0527] The mammalian host cells used to produce the target
polypeptide of this disclosure may be cultured in a variety of
media. Commercially available media such as Ham's F10 (Sigma),
Minimal Essential Medium (MEM, Sigma), RPMI-1640 (Sigma), and
Dulbecco's Modified Eagle's Medium (DMEM, Sigma) are suitable for
culturing the host cells. In addition, any of the media described
in Ham and Wallace, 1979, Meth. Enz. 58:44; Barnes and Sato, 1980,
Anal. Biochem. 102:255; U.S. Pat. No. 4,767,704; U.S. Pat. No.
4,657,866; U.S. Pat. No. 4,927,762; or U.S. Pat. No. 4,560,655; WO
90/03430; WO 87/00195; U.S. Pat. Re. No. 30,985, may be used as
culture media for the host cells. Any of these media may be
supplemented as necessary with hormones and/or other growth factors
(such as insulin, transferrin, or epidermal growth factor), salts
(such as sodium chloride, calcium, magnesium, and phosphate),
buffers (such as HEPES), nucleosides (such as adenosine and
thymidine), antibiotics (such as Gentamycin.TM. drug), trace
elements (defined as inorganic compounds usually present at final
concentrations in the micromolar range), and glucose or an
equivalent energy source. Any other necessary supplements may also
be included at appropriate concentrations that would be known to
those skilled in the art. The culture conditions, such as
temperature, pH, and the like, are those previously used with the
host cell selected for expression, and will be apparent to the
ordinarily skilled artisan.
[0528] The host cells referred to in this disclosure encompass
cells in in vitro culture as well as cells that are within a host
animal.
[0529] It is further envisioned that the antibody of this
disclosure may be produced by homologous recombination, or with
recombinant production methods utilizing control elements
introduced into cells already containing DNA encoding the antibody
currently in use in the field. For example, a powerful
promoter/enhancer element, a suppressor, or an exogenous
transcription modulatory element is inserted in the genome of the
intended host cell in proximity and orientation sufficient to
influence the transcription of DNA encoding the desired antibody.
The control element does not encode the antibody of this
disclosure, but the DNA is present in the host cell genome. One
next screens for cells making the antibody of this disclosure, or
increased or decreased levels of expression, as desired.
Enhancement of Antibody Effector Functions
[0530] Methods are provided for using a subject's Fc.gamma.RIIA
and/or Fc.gamma.RIIIA genotype to select a specific Fc nucleotide
sequence associated with optimal effector function for an antibody
therapy.
[0531] It is contemplated that the Fc nucleotide sequence from an
antibody, including, for example, a variant antibody with one or
more optimal effector functions for a particular Fc.gamma.RIIA and
Fc.gamma.RIIIA genotype can be used to optimize one or more
effector functions of other antibodies used to treat the same or
other subjects with the Fc.gamma.RIIA and Fc.gamma.RIIIA
genotype.
[0532] In a preferred embodiment, the effector function is ADCC. In
other embodiments, the effector function is selected from the Group
consisting of: phagocytosis, opsonization, opsonophagocytosis, Clq
binding, and complement dependent cell mediated cytotoxicity
(CDC).
[0533] Generally, methods are provided for enhancing one or more
effector functions of an antibody used to treat a subject having an
ADCC-treatable disease or disorder, comprising: a) genotyping the
subject for an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism; b) classifying the subject into one of more than
three categories of ADCC activity for the antibody based on their
Fc.gamma.RIIA polymorphism and Fc.gamma.RIIIA polymorphism; and c)
selecting an Fc nucleotide sequence that has at least one optimized
effector function for the Fc.gamma.RIIA polymorphism and
Fc.gamma.RIIIA polymorphism, wherein at least one effector function
of the antibody is enhanced by using the optimized Fc nucleotide
sequence.
[0534] Fc cassettes are optimized for each of the nine distinct
Fc.gamma.RIIA and Fc.gamma.RIIIA genotypes, including: V/V.sup.158,
H/H.sup.131 (Group-I); V/F.sup.158, H/H.sup.131 (Group-II);
F/F.sup.158, H/H.sup.131 (Group-III); V/V.sup.158, H/R.sup.131
(Group-IV); V/F.sup.158, H/R.sup.131 (Group-V); F/F.sup.158,
H/R.sup.131 (Group-VI); V/V.sup.158, R/R.sup.131 (Group-VII);
V/F.sup.158, R/R.sup.131 (Group-VIII); and F/F.sup.158, R/R.sup.131
(Group-IX) as previously described in the above methods.
[0535] Antibody effector functions, such as ADCC, may be optimized
for a particular Fc.gamma.RIIA and Fc.gamma.RIIIA genotype by
altering the nucleotide sequence of the Fc portion of the antibody,
to an Fc nucleotide sequence associated with optimal effector
functions for the genotype. The nucleotide sequence of the Fc
region of an antibody is engineered by techniques commonly known in
the art to derive the same nucleotide sequence of Fc that has
optimized ADCC activity for a subject with a particular
Fc.gamma.RIIA and Fc.gamma.RIIIA genotype.
[0536] In other embodiments, the ADCC activity of an antibody used
to treat a subject with a particular Fc.gamma.RIIA and
Fc.gamma.RIIIA genotype can be optimized by fusing an Fc nucleotide
sequence from another antibody molecule which has optimized
effector functions for the given genotype to the antibody.
[0537] Therapeutic antibodies used to treat a particular
.gamma.RIIA (H/R.sup.131) Fc.gamma.RIIIA (V/F.sup.158) genotype may
be modified to exhibit optimal ADCC activity. For instance the
therapeutic antibody RITUXAN.TM. has optimal ADCC activity for
subjects exhibiting a V/V.sup.158, H/H.sup.131 genotype. Hence, the
Fc nucleotide sequence of RITUXAN.RTM. may be used to optimize ADCC
activity of other antibodies used to treat subjects exhibiting a
V/V.sup.158, H/H.sup.131 genotype. For instance, the Fc nucleotide
sequence of RITUXAN.RTM. may be used to in place of the Fc
nucleotide sequence present in ZENAPAX.RTM. to optimize ADCC
activity in subjects exhibiting a V/V.sup.158, H/H.sup.131
genotype.
[0538] Examples of other therapeutic antibodies, variable regions
of an antibody, or Fc variant antibodies that can be engineered to
have enhanced ADCC activity for a particular Fc.gamma.RIIA and
Fc.gamma.RIIIA genotype, include but are not limited to:
RITUXAN.RTM., CAMPATH.RTM., ZENAPAX.RTM., HERCEPTIN.RTM.,
XOLAIR.RTM., RAPTIVA.RTM., AVASTIN.RTM., REMICADE.RTM.,
HUMIRA.RTM., ERBITUX.RTM., SIMULECT.RTM., SYNAGIS.RTM.,
VECTIBIX.RTM., TYSABRI.RTM., MYLOTARG.RTM., REOPRO.RTM., OKT3.RTM.,
BEXXAR.RTM. or ZEVALIN.RTM..
[0539] Optimized fusion antibodies can be produced by standard
recombinant DNA techniques or by protein synthetic techniques,
e.g., by use of a peptide synthesizer. For example, a nucleic acid
molecule encoding an optimized antibody fusion can be synthesized
by conventional techniques including automated DNA
synthesizers.
[0540] Alternatively, PCR amplification of gene fragments (i.e. the
optimized Fc and antigen binding domain) can be carried out using
anchor primers which give rise to complementary overhangs between
two consecutive gene fragments which can subsequently be annealed
and reamplified to generate a chimeric gene sequence (See, e.g.,
Current Protocols in Molecular Biology, Ausubel et al., eds., John
Wiley & Sons, 1992).
[0541] Moreover, a nucleic acid encoding an antigen binding domain
can be cloned into an expression vector containing an genotype
optimized Fc region such that the antigen binding domain is linked
in-frame to the optimized Fc region.
[0542] Methods for fusing or conjugating antigen binding domains to
a genotype optimized Fc are known in the art (See, e.g., U.S. Pat.
Nos. 5,336,603, 5,622,929, 5,359,046, 5,349,053, 5,447,851,
5,723,125, 5,783,181, 5,908,626, 5,844,095, and 5,112,946; EP
307,434; EP 367, 166; EP 394,827; International Publication Nos. WO
91/06570, WO 96/04388, WO 96/22024, WO 97/34631, and WO 99/04813;
Ashkenazi et al., 1991, Proc. Natl. Acad. Sci. USA 88:10535-10539;
Traunecker et al., 1988, Nature 331:84-86; Zheng et al., 1.995, J.
Immunol. 154:5590-5600; and Vil et al., 1992, Proc. Natl. Acad.
Sci. USA 89:11337-11341).
[0543] The nucleotide sequences encoding a antigen binding domain
and an Fc domain may be obtained from any information available to
those of skill in the art (i.e., from Genbank, the literature, or
by routine cloning) (See, e.g., Xiong et al., 2001, Science
294(5541):339-45). The nucleotide sequence coding for an antibody
fusion protein can be inserted into an appropriate expression
vector, i.e., a vector that contains the necessary elements for the
transcription and translation of the inserted protein-coding
sequence. A variety of host-vector systems may be utilized in the
present disclosure to express the protein-coding sequence. These
include but are not limited to mammalian cell systems infected with
virus (e.g., vaccinia virus, adenovirus, etc.); insect cell systems
infected with virus (e.g., baculovirus); microorganisms such as
yeast containing yeast vectors; or bacteria transformed with
bacteriophage, DNA, plasmid DNA, or cosmid DNA. The expression
elements of vectors vary in their strengths and specificities.
Depending on the host-vector system utilized, any one of a number
of suitable transcription and translation elements may be used.
Functional Assays for Antibodies
[0544] Antibodies, including, for example, variant antibodies may
be characterized in a variety of ways. For example, antibody
variants may be assayed for the ability to specifically bind to a
ligand, (e.g., Fc.gamma.RIIIA, Fc.gamma.RIIB, Clq). Such an assay
may be performed in solution (e.g., Houghten, 1992, Bio/Techniques
13:412-421), on beads (Lam, 1991, Nature 354:82-84), on chips
(Fodor, 1993, Nature 364:555-556), on bacteria (U.S. Pat. No.
5,223,409), 011 plasmids (Cull et al., 1992, Proc. Natl. Acad. Sci.
USA 89:1865-1869) or on phage (Scott and Smith, 1990, Science
249:386-390; Devlin, 1990, Science 249:404-406; Cwirla et al.,
1990, Proc. Natl. Acad. Sci. USA 87:6378-6382; and Felici, 1991, J.
Mol. Biol. 222:301-310). Molecules that have been identified to
specifically bind to a ligand, (e.g., Fc.gamma.RIIIA,
Fc.gamma.RIIB, Clq or to an antigen) can then be assayed for their
affinity for the ligand.
[0545] Antibody variants may be assayed for specific binding to a
molecule such as an antigen (e.g., cancer antigen and
cross-reactivity with other antigens) or a ligand (e.g.,
Fc.gamma.R) by any method known in the art, Immunoassays which can
be used to analyze specific binding and cross-reactivity include,
but are not limited to, competitive and non-competitive assay
systems using techniques such as western blots, radioimmunoassays,
ELISA (enzyme linked immunosorbent assay), "sandwich" immunoassays,
immunoprecipitation assays, precipitin reactions, gel diffusion
precipitin reactions, immunodiffusion assays, agglutination assays,
complement-fixation assays, immunoradiometric assays, fluorescent
immunoassays, protein A immunoassays, to name but a few. Such
assays are routine and well known in the art (See, e.g., Ausubel et
al., eds, Current Protocols in Molecular Biology, Vol. 1, John
Wiley & Sons, Inc., New York (1994).
[0546] The binding affinity of the antibody variants to a molecule
such as an antigen or a ligand, (e.g., Fc.gamma.R) and the off-rate
of the interaction can be determined by competitive binding assays.
One example of a competitive binding assay is a radioimmunoassay
comprising the incubation of labeled ligand, such as Fc.gamma.R
(e.g., .sup.3H or .sup.1251) with a molecule of interest (e.g.,
antibody variants) in the presence of increasing amounts of
unlabeled ligand, such as Fc.gamma.R, and the detection of the
molecule bound to the labeled ligand. The affinity of the molecule
of the present disclosure for the ligand and the binding off-rates
can be determined from the saturation data by scatchard
analysis.
[0547] The kinetic parameters of an antibody variant may also be
determined using any surface plasmon resonance (SPR) based assays
known in the art (e.g., BIAcore kinetic analysis). For a review of
SPR-based technology, See, e.g., Mullet et al., 2000, Methods
22:77-91; Dong et al., 2002, Review in Mol. Biotech., 82:303-23;
Fivash et al., 1998, Current Opinion in Biotechnology 9:97-101;
Rich et al., 2000, Current Opinion in Biotechnology 11:54-61.
[0548] Additionally, any of the SPR instruments and SPR based
methods for measuring protein-protein interactions described in
U.S. Pat. Nos. 6,373,577; 6,259,286 5,322,798; 5,341,215; 6,268,125
are contemplated in the methods of the disclosure.
[0549] Fluorescence activated cell sorting (FACS), using any of the
techniques known to those skilled in the art, can be used for
characterizing the binding of antibody variants to a molecule
expressed on the cell surface (e.g., Fc.gamma.RIIA, Fc.gamma.RIIIA)
Flow sorters are capable of rapidly examining a large number of
individual cells that contain library inserts (e.g., 10-100 million
cells per hour) (Shapiro et al, Practical Flow cytometry, 1995).
Flow cytometers for sorting and examining biological cells are well
known in the art. Known flow cytometers are described, for example,
in U.S. Pat. Nos. 4,347,935; 5,464,581; 5,483,469; 5,602,039;
5,643,796; and 6,211,477. Other known flow cytometers are the FACS
Vantage.TM. system manufactured by Becton Dickinson and Company,
and the COPAS.TM. system manufactured by Union Biometrica.
[0550] The antibody variants can be characterized by their ability
to mediate Fc.gamma.R-mediated effector cell function. Examples of
effector cell functions that can be assayed include, but are not
limited to, antibody-dependent cell mediated cytotoxicity (ADCC),
phagocytosis, opsonization, opsonophagocytosis, Clq binding, and
complement dependent cell mediated cytotoxicity (CDC).
[0551] Any cell-based or cell free assay known to those skilled in
the art for determining effector cell function activity can be used
(For effector cell assays, See, e.g., Perussia et al., 2000,
Methods Mol. Biol. 121:179-92; Baggiolini et al., 1998, Experientia
44(10): 841-8; Lehmann et al., 2000, J. Immunol, Methods
243(1-2):229-42; Brown E J., 1994, Methods Cell Biol. 45:147-64;
Munn et al., 1990, J. Exp. Med. 172:231-237, Abdul-Majid et al.,
2002, Scand. J. Immunol. 55:70-81; Ding et al., 1998, Immunity
8:403-411).
[0552] For example, the antibody variants can be assayed for
Fc.gamma.R-mediated ADCC activity in effector cells, (e.g., natural
killer cells) using any of the standard methods known to those
skilled in the art (See e.g., Perussia et al., 2000, Methods Mol.
Biol.).
[0553] An exemplary assay for determining ADCC activity of the
molecules of the disclosure is based on a .sup.51Cr release assay
comprising of: labeling target cells with Na.sub.2CrO.sub.4 (this
cell-membrane permeable molecule is commonly used for labeling
since it binds cytoplasmic proteins and although spontaneously
released from the cells with slow kinetics, it is released
massively following target cell necrosis); osponizing the target
cells with the antibody variants of the disclosure; combining the
opsonized radiolabeled target cells with effector cells in a
microtitre plate at an appropriate ratio of target cells to
effector cells; incubating the mixture of cells for 16-18 hours at
37.degree. C.; collecting supernatants; and analyzing
radioactivity. The cytotoxicity of the molecules of the disclosure
can then be determined, for example using the following formula: %
lysis(experimental cpm-target leak cpm)/(detergent lysis cpm-target
leak cpm).times.100%. Alternatively, % lysis=(ADCC-AICC)/(maximum
release-spontaneous release). Specific lysis can be calculated
using the formula: specific lysis % lysis with the molecules of the
disclosure-% lysis in the absence of the molecules of the
disclosure. A graph can be generated by varying either the target:
effector cell ratio or antibody concentration.
[0554] Methods to characterize the ability of the antibody variants
to bind Clq and mediate complement dependent cytotoxicity (CDC) are
well known in the art. For example, to determine Clq binding, a Clq
binding ELISA may be performed. An exemplary assay may comprise the
following: assay plates may be coated overnight at 4.degree. C.
with polypeptide variant or starting polypeptide (control) in
coating buffer. The plates may then be washed and blocked.
Following washing, an aliquot of human Clq may be added to each
well and incubated for 2 hrs at room temperature. Following a
further wash, 100 .mu.L of a sheep anti-complement Clq peroxidase
conjugated antibody may be added to each well and incubated for 1
hour at room temperature. The plate may again be washed with wash
buffer and 100 .mu.l of substrate buffer containing OPD
(O-phenylenediamine dihydrochloride (Sigma)) may be added to each
well. The oxidation reaction, observed by the appearance of a
yellow color, may be allowed to proceed for 30 minutes and stopped
by the addition of 100 .mu.l of 4.5 NH.sub.2SO.sub.4. The
absorbance may then read at (492-405) nm. Specific methods are also
disclosed in the section entitled "Examples," infra.
[0555] To assess complement activation, a complement dependent
cytotoxicity (CDC) assay may be performed, (e.g., as described in
Gazzano-Santoro et al., 1996, J. Immunol. Methods 202:163).
Briefly, various concentrations of antibody variant and human
complement may be diluted with buffer. Cells which express the
antigen to which the Fc variant binds may be diluted to a density
of about I > 10 cells/ml. Mixtures of the Fc variant, diluted
human complement and cells expressing the antigen may be added to a
flat bottom tissue culture 96 well plate and allowed to incubate
for 2 hrs at 37.degree. C. and 5% CO.sub.2 to facilitate complement
mediated cell lysis. 50 .mu.L of alamar blue (Accumed
International) may then be added to each well and incubated
overnight at 37.degree. C. The absorbance is measured using a
96-well fluorometer with excitation at 530 nm and emission at 590
nm. The results may be expressed in relative fluorescence units
(RFU). The sample concentrations may be computed from a standard
curve and the percent activity, relative to a comparable
molecule.
[0556] Complement assays may be preformed with guinea pig, rabbit
or human serum. Complement lysis of target cells maybe detected by
monitoring the release of intracellular enzymes such as lactate
dehydrogenase (LDH), as described in Korzeniewski et al., 1983.
Immunol. Methods 64(3):313-20; and Decker et at., 1988, Immunol.
Methods 115(1):61-9; or the release of an intracellular label such
as europium, chromium 51 or indium 111 in which target cells are
labeled.
Treatment Methods
[0557] Methods are provided for treating a disease or disorder that
is treatable with an ADCC-based antibody therapy in an individual.
The methods generally involve: a) determining a category of
responsiveness to an antibody therapy by genotyping the individual
for an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA
polymorphism; b) selecting an antibody from a set of related
antibodies, where members of the set of related antibodies have the
same antigen binding specificity, and differ in binding affinity to
an Fc.gamma.RIIA and/or an Fc.gamma.RIIIA receptor; and c)
administering an effective amount of the antibody to the
individual.
[0558] Diseases and disorders that are treatable with an ADCC-based
antibody therapy include, but are not limited to, neoplastic
diseases; autoimmune diseases; allograft rejection; viral
infections; bacterial infections; and parasitic infections.
[0559] Thus, in some embodiments, methods are provided for treating
a neoplastic disease in an individual. The methods generally
involve: a) determining a category of responsiveness to an antibody
therapy for a neoplastic disease by genotyping the individual for
an Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA polymorphism;
b) selecting an antibody from a set of related antibodies, where
members of the set of related antibodies have the same antigen
binding specificity, and differ in binding affinity and/or in vitro
ADCC activity to an Fc.gamma.RIIA and/or an Fc.gamma.RIIIA
receptor; and c) administering an effective amount of the antibody
to the individual.
[0560] The methods are useful for treating a wide variety of
cancers, including carcinomas, sarcomas, leukemias, and
lymphomas.
[0561] Carcinomas that can be treated using a subject method
include, but are not limited to, esophageal carcinoma,
hepatocellular carcinoma, basal cell carcinoma (a form of skin
cancer), squamous cell carcinoma (various tissues), bladder
carcinoma, including transitional cell carcinoma (a malignant
neoplasm of the bladder), bronchogenic carcinoma, colon carcinoma,
colorectal carcinoma, gastric carcinoma, lung carcinoma, including
small cell carcinoma and non-small cell carcinoma of the lung,
adrenocortical carcinoma, thyroid carcinoma, pancreatic carcinoma,
breast carcinoma, ovarian carcinoma, prostate carcinoma,
adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma,
papillary carcinoma, papillary adenocarcinoma, cystadenocarcinoma,
medullary carcinoma, renal cell carcinoma, ductal carcinoma in situ
or bile duct carcinoma, choriocarcinoma, seminoma, embryonal
carcinoma, Wilm's tumor, cervical carcinoma, uterine carcinoma,
testicular carcinoma, osteogenic carcinoma, epithelial carcinoma,
and nasopharyngeal carcinoma, etc.
[0562] Sarcomas that can be treated using a subject method include,
but are not limited to, fibrosarcoma, myxosarcoma, liposarcoma,
chondrosarcoma, chordoma, osteogenic sarcoma, osteosarcoma,
angiosarcoma, endotheliosarcoma, lymphangiosarcoma,
lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's
sarcoma, leiomyosarcoma, rhabdomyosarcoma, and other soft tissue
sarcomas.
[0563] Other solid tumors that can be treated using a subject
method include, but are not limited to, glioma, astrocytoma,
medulloblastoma, craniopharyngioma, ependymoma, pinealoma,
hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma,
melanoma, neuroblastoma, and retinoblastoma.
[0564] Leukemias that can be treated using a subject method
include, but are not limited to, a) chronic myeloproliferative
syndromes (neoplastic disorders of multipotential hematopoietic
stem cells); b) acute myelogenous leukemias (neoplastic
transformation of a multipotential hematopoietic stem cell or a
hematopoietic cell of restricted lineage potential; c) chronic
lymphocytic leukemias (CLL; clonal proliferation of immunologically
immature and functionally incompetent small lymphocytes), including
B-cell CLL, T-cell CLL prolymphocytic leukemia, and hairy cell
leukemia; and d) acute lymphoblastic leukemias (characterized by
accumulation of lymphoblasts). Lymphomas that can be treated using
a subject method include, but are not limited to, B-cell lymphomas
(e.g., Burkitt's lymphoma); Hodgkin's lymphoma; non-Hodgkin's
lymphoma; and the like.
[0565] In other embodiments, methods are provided for treating an
autoimmune disease in an individual. The methods generally involve:
a) determining a category of responsiveness to an antibody therapy
for an autoimmune disease by genotyping the individual for an
Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA polymorphism; b)
selecting an antibody from a set of related antibodies, where
members of the set of related antibodies have the same antigen
binding specificity, and differ in binding affinity and/or in vitro
ADCC activity to an Fc.gamma.RIIA and/or an Fc.gamma.RIIIA
receptor; and c) administering an effective amount of the antibody
to the individual.
[0566] Autoimmune disorders include autoimmune hemolytic anemia,
antiphospholipid syndrome, dermatitis, allergic encephalomyelitis,
glomerulonephritis, Crohn's Disease, Goodpasture's Syndrome,
Graves' Disease, multiple sclerosis, myasthenia gravis, neuritis,
ophthalmia, bullous pemphigoid, pemphigus, acute disseminated
encephalomyelitis, polyendocrinopathies, purpura, Reiter's Disease,
stiff-Man syndrome, inflammation, Guillain-Barre Syndrome, insulin
dependent diabetes mellitus (also referred to as Type 1 diabetes),
rheumatoid arthritis, autoimmune inflammatory eye disease, adult
respiratory distress syndrome, inflammatory bowel disease,
dermatitis, immune thrombocytopenic purpura (ITP), Sjogren's
syndrome, Waldenstrom's macroglobulinemia, encephalitis, uveitis,
leukocyte adhesion deficiency, psoriatic arthritis, progressive
systemic sclerosis, primary biliary cirrhosis, pemphigus,
pemphigoid, necrotizing vasculitis, systemic lupus erythematosus,
polymyositis, sarcoidosis, granulomatosis, Wegener's Granulomatosis
(vasculitis), Type-II mixed cryoglobulinemia, pernicious anemia,
CNS inflammatory disorder, antigen-antibody complex mediated
diseases, Hashimoto's thyroiditis, habitual spontaneous abortions,
Reynard's syndrome, glomerulonephritis, dermatomyositis, chronic
active hepatitis, celiac disease, tissue specific autoimmunity,
degenerative autoimmunity delayed hypersensitivities, autoimmune
complications of acquired immunodeficiency syndrome (AIDS),
atrophic gastritis, ankylosing spondylitis and Addison's
disease.
[0567] In other embodiments, methods are provided for treating
allograft rejection in an individual. The methods generally
involve: a) determining a category of responsiveness to an antibody
therapy for allograft rejection by genotyping the individual for an
Fc.gamma.RIIA polymorphism and an Fc.gamma.RIIIA polymorphism; b)
selecting an antibody from a set of related antibodies, where
members of the set of related antibodies have the same antigen
binding specificity, and differ in binding affinity and/or in vitro
ADCC activity to an Fc.gamma.RIIA and/or an Fc.gamma.RIIIA
receptor; and c) administering an effective amount of the antibody
to the individual.
[0568] In other embodiments, methods are provided for treating a
viral infection in an individual. The methods generally involve: a)
determining a category of responsiveness to an antibody therapy for
a viral infection by genotyping the individual for an Fc.gamma.RIIA
polymorphism and an Fc.gamma.RIIIA polymorphism; b) selecting an
antibody from a set of related antibodies, where members of the set
of related antibodies have the same antigen binding specificity,
and differ in binding affinity and/or in vitro ADCC activity to an
Fc.gamma.RIIA and/or an Fc.gamma.RIIIA receptor; and c)
administering an effective amount of the antibody to the
individual.
[0569] As discussed above, the presence of a particular Fc.gamma.
receptor polymorphism predicts an individual's degree of
responsiveness to an antibody therapy. Based on the individual's
Fc.gamma. receptor genotype, an antibody is chosen from a set of
related antibodies. The set of related antibodies comprises members
that have the same antigen binding specificity, and differ in
binding affinity and/or in vitro ADCC activity to Fc.gamma.
receptors. Where the degree of responsiveness is predicted to be
intermediate or low, an antibody is selected for enhanced binding
to a given Fc.gamma. receptor.
[0570] In some embodiments, the genotyping step identifies an
Fc.gamma.RIIA H/H.sup.131 genotype and an Fc.gamma.RIIIA
V/V.sup.158 genotype, and the Fc variant antibody is selected for
enhanced binding and/or in vitro ADCC function to at least one of
an Fc.gamma.RIIA comprising His/His.sup.131 allele and an
Fc.gamma.RIIIA comprising Val/Val.sup.158 allele. In other
embodiments, the genotyping step identifies: a) a H/H.sup.131
genotype and a V/F.sup.158 genotype, and wherein the Fc variant
antibody is selected for enhanced binding and/or in vitro ADCC
function to at least one of an Fc.gamma.RIIA comprising H/H.sup.131
allele and an Fc.gamma.RIIIA comprising V/F.sup.158 allele, and b)
a H/H.sup.131 genotype and a F/F.sup.158 genotype, and wherein the
Fc variant antibody is selected for enhanced binding and/or in
vitro ADCC function to at least one of an Fc.gamma.RIIA comprising
H/H.sup.131 allele and an Fc.gamma.RIIIA comprising F/F.sup.158
allele.
[0571] In other embodiments, the genotyping step identifies one
of:
[0572] a) a V/F.sup.158 genotype and a H/R.sup.131 genotype, and
wherein the Fc variant antibody is selected for enhanced binding
and/or in vitro ADCC function to at least one of an Fc.gamma.RIIA
comprising H/R.sup.131 allele and an Fc.gamma.RIIIA comprising
V/F.sup.158 allele;
[0573] b) a V/F.sup.158 genotype and a R/R.sup.131 genotype, and
wherein the Fc variant antibody is selected for enhanced binding
and/or in vitro ADCC function to at least one of an Fc.gamma.RIIA
comprising R/R.sup.131 allele and an Fc.gamma.RIIIA comprising
V/F.sup.158 allele;
[0574] c) a F/F.sup.158 genotype and a H/R.sup.131 genotype, and
wherein the Fc variant antibody is selected for enhanced binding
and/or in vitro ADCC function to at least one of an Fc.gamma.RIIA
comprising H/R.sup.131 allele and an Fc.gamma.RIIIA comprising
F/F.sup.158 allele;
[0575] d) a F/F.sup.158 genotype and a R/R.sup.131 genotype, and
wherein the Fc variant antibody is selected for enhanced binding
and/or in vitro ADCC function to at least one of an Fc.gamma.RIIA
comprising R/R.sup.131 and an Fc.gamma.RIIIA comprising F/F.sup.158
allele;
[0576] e) a V/V.sup.158 genotype and a H/R.sup.131 genotype, and
wherein the Fc variant antibody is selected for enhanced binding
and/or in vitro ADCC function to at least one of an Fc.gamma.RIIA
comprising H/R.sup.131 allele and an Fc.gamma.RIIIA comprising
V/V.sup.158 allele; or f) a V/V.sup.158 genotype and a R/R.sup.131
genotype, and wherein the Fc variant antibody is selected for
enhanced binding and/or in vitro ADCC function to at least one of
an Fc.gamma.RIIA comprising R/R.sup.131 allele and an
Fc.gamma.RIIIA comprising V/V.sup.158 allele.
[0577] Routes of administration, formulations, as well as dosages,
of therapeutic antibodies are well known to those skilled in the
art.
[0578] A therapeutic antibody is in some embodiments formulated
into a preparation suitable for injection (e.g., subcutaneous,
intravenous, intramuscular, intradermal, transdermal, intratumoral,
peritumoral, intrathecal, or other injection routes) by dissolving,
suspending or emulsifying the antibody in an aqueous solvent (e.g.,
saline, and the like) or a nonaqueous solvent, such as vegetable or
other similar oils, synthetic aliphatic acid glycerides, esters of
higher aliphatic acids or propylene glycol; and if desired, with
conventional additives such as solubilizers, isotonic agents,
suspending agents, emulsifying agents, stabilizers and
preservatives.
[0579] A therapeutic antibody is formulated with one or more
pharmaceutically acceptable excipients. A wide variety of
pharmaceutically acceptable excipients are known in the art and
need not be discussed in detail herein. Pharmaceutically acceptable
excipients have been amply described in a variety of publications,
including, for example, A. Gennaro, "Remington: The Science and
Practice of Pharmacy," 20th edition, Lippincott, Williams, &
Wilkins (2000); Pharmaceutical Dosage Forms and Drug Delivery
Systems, H. C. Ansel et al., eds., 7.sup.th Ed., Lippincott,
Williams, & Wilkins (1999); and Handbook of Pharmaceutical
Excipients, A. H. Kibbe et al., eds., 3.sup.rd ed. Amer.
Pharmaceutical Assoc. (2000).
[0580] The pharmaceutically acceptable excipients, such as
vehicles, adjuvants, carriers or diluents, are readily available to
the public. Moreover, pharmaceutically acceptable auxiliary
substances, such as pH adjusting and buffering agents, tonicity
adjusting agents, stabilizers, wetting agents and the like, are
readily available to the public.
[0581] A therapeutic antibody can be administered as an injectable
formulation. Typically, injectable compositions are prepared as
liquid solutions or suspensions; solid forms suitable for solution
in, or suspension in, liquid vehicles prior to injection may also
be prepared. The preparation may also be emulsified or the active
ingredient encapsulated in liposome vehicles.
[0582] In some embodiments, a therapeutic antibody is delivered by
bolus injection. In other embodiments, a therapeutic antibody is
delivered by a continuous delivery system. The term "continuous
delivery system" is used interchangeably herein with "controlled
delivery system" and encompasses continuous (e.g., controlled)
delivery devices (e.g., pumps) in combination with catheters,
injection devices, and the like, a wide variety of which are known
in the art. In other embodiments, a therapeutic antibody is
administered by intravenous infusion.
[0583] In some embodiments, a therapeutic antibody is administered
in an amount of from about 10 mg to about 1000 mg per dose, e.g.,
from about 10 mg to about 20 mg, from about 20 mg to about 25 mg,
from about 25 mg to about 50 mg, from about 50 mg to about 75 mg,
from about 75 mg to about 100 mg, from about 100 mg to about 125
mg, from about 125 mg to about 150 mg, from about 150 mg to about
175 mg, from about 175 mg to about 200 mg, from about 200 mg to
about 225 mg, from about 225 mg to about 250 mg, from about 250 mg
to about 300 mg, from about 300 mg to about 350 mg, from about 350
mg to about 400 mg, from about 400 mg to about 450 mg, from about
450 mg to about 500 mg, from about 500 mg to about 750 mg, or from
about 750 mg to about 1000 mg per dose.
[0584] In some embodiments, the dose of a therapeutic antibody is a
weight-based dose, e.g., from about 50 mg/m.sup.2 to about 100
mg/m.sup.2, from about 100 mg/m.sup.2 to about 150 mg/m.sup.2, from
about 150 mg/m.sup.2 to about 200 mg/m.sup.2, from about 200
mg/m.sup.2 to about 250 mg/m.sup.2, from about 250 mg/m.sup.2 to
about 300 mg/m.sup.2, from about 300 mg/m.sup.2 to about 350
mg/m.sup.2, from about 350 mg/m.sup.2 to about 400 mg/m.sup.2, or
from about 400 mg/m.sup.2 to about 500 mg/m.sup.2.
[0585] In some embodiments, multiple doses are administered. For
example, in some embodiments, a therapeutic antibody is
administered once per month, twice per month, three times per
month, every other week (qow), once per week (qw), twice per week
(biw), three times per week (tiw), four times per week, five times
per week, six times per week, every other day (qod), daily (qd),
twice a day (qid), or three times a day (tid).
[0586] In some embodiments, a therapeutic antibody is administered
over a period of time ranging from about one day to about one week,
from about two weeks to about four weeks, from about one month to
about two months, from about two months to about four months, from
about four months to about six months, from about six months to
about eight months, from about eight months to about 1 year, from
about 1 year to about 2 years, or from about 2 years to about 4
years, or more.
[0587] Therapeutic formulations of an antibody may be prepared for
storage as lyophilized formulations or aqueous solutions by mixing
an antibody having the desired degree of purity with optional
"pharmaceutically-acceptable" carriers, excipients or stabilizers
typically employed in the art (all of which are termed
"excipients"), i.e., buffering agents, stabilizing agents,
preservatives, isotonifiers, non-ionic detergents, antioxidants,
and other miscellaneous additives. See, e.g., Remington's
Pharmaceutical Sciences, 16th edition, Osol, Ed. (1980). Such
additives must be nontoxic to the recipients at the dosages and
concentrations employed.
[0588] Buffering agents help to maintain the pH in the range which
approximates physiological conditions. They are preferably present
at concentration ranging from about 2 mM to about 50 mM. Suitable
buffering agents include both organic and inorganic acids and salts
thereof such as citrate buffers (e.g., monosodium citrate-disodium
citrate mixture, citric acid-trisodium citrate mixture, citric
acid-monosodium citrate mixture, etc.), succinate buffers (e.g.,
succinic acid-monosodium succinate mixture, succinic acid-sodium
hydroxide mixture, succinic acid-disodium succinate mixture, etc.),
tartrate buffers (e.g., tartaric acid-sodium tartrate mixture,
tartaric acid-potassium tartrate mixture, tartaric acid-sodium
hydroxide mixture, etc.), fumarate buffers (e.g., fumaric
acid-monosodium fumarate mixture, etc.), fumarate buffers (e.g.,
fumaric acid-monosodium fumarate mixture, fumaric acid-disodium
fumarate mixture, monosodium fumarate-disodium fumarate mixture,
etc.), gluconate buffers (e.g., gluconic acid-sodium glyconate
mixture, gluconic acid-sodium hydroxide mixture, gluconic
acid-potassium glyuconate mixture, etc.), oxalate buffer (e.g.,
oxalic acid-sodium oxalate mixture, oxalic acid-sodium hydroxide
mixture, oxalic acid-potassium oxalate mixture, etc.), lactate
buffers (e.g., lactic acid-sodium lactate mixture, lactic
acid-sodium hydroxide mixture, lactic acid-potassium lactate
mixture, etc.) and acetate buffers (e.g., acetic acid-sodium
acetate mixture, acetic acid-sodium hydroxide mixture, etc.).
Additionally, there may be mentioned phosphate buffers, histidine
buffers and trimethylamine salts such as Tris.
[0589] Preservatives may be added to retard microbial growth, and
may be added in amounts ranging from 0.2%-1% (w/v). Suitable
preservatives include phenol, benzyl alcohol, meta-cresol, methyl
paraben, propyl paraben, octadecyldimethylbenzyl ammonium chloride,
benzalconium halides (e.g., chloride, bromide, iodide),
hexamethonium chloride, and alkyl parabens such as methyl or propyl
paraben, catechol, resorcinol, cyclohexanol, and 3-pentanol.
[0590] "Stabilizers" may be added to ensure isotonicity of liquid
compositions of antibodies and include polyhydric sugar alcohols,
preferably trihydric or higher sugar alcohols, such as glycerin,
erythritol, arabitol, xylitol, sorbitol and mannitol. Stabilizers
refer to a broad category of excipients which can range in function
from a bulking agent to an additive which solubilizes the
therapeutic agent or helps to prevent denaturation or adherence to
the container wall. Typical stabilizers can be polyhydric sugar
alcohols (enumerated above); amino acids such as arginine, lysine,
glycine, glutamine, asparagine, histidine, alanine, ornithine,
L-leucine, 2-phenylalanine, glutamic acid, threonine, etc., organic
sugars or sugar alcohols, such as lactose, trehalose, stachyose,
mannitol, sorbitol, xylitol, ribitol, myoinisitol, galactitol,
glycerol and the like, including cyclitols such as inositol;
polyethylene glycol; amino acid polymers; sulfur containing
reducing agents, such as urea, glutathione, thioctic acid, sodium
thioglycolate, thioglycerol, alpha.-monothioglycerol and sodium
thio sulfate; low molecular weight polypeptides (i.e. <10
residues); proteins such as human serum albumin, bovine serum
albumin, gelatin or immunoglobulins; hydrophylic polymers, such as
polyvinylpyrrolidone monosaccharides, such as xylose, mannose,
fructose, glucose; disaccharides such as lactose, maltose, sucrose
and trisaccacharides such as raffinose; and polysaccharides such as
dextran. Stabilizers may be present in the range from 0.1 to 10,000
weights per part of weight active protein.
[0591] Non-ionic surfactants or detergents (also known as "wetting
agents") may be added to help solubilize the therapeutic agent as
well as to protect a therapeutic antibody against agitation-induced
aggregation, which also permits the formulation to be exposed to
shear surface stressed without causing denaturation of the protein.
Suitable non-ionic surfactants include polysorbates (20, 80, etc.),
polyoxamers (184, 188 etc.), Pluronic.TM. polyols, and
polyoxyethylene sorbitan monoethers (TWEEN-20.RTM., TWEEN-80.RTM.,
etc.). Non-ionic surfactants may be present in a range of about
0.05 mg/ml to about 1.0 mg/ml, preferably about 0.07 mg/ml to about
0.2 mg/ml.
[0592] Additional miscellaneous excipients include bulking agents,
(e.g., starch), chelating agents (e.g., EDTA), antioxidants (e.g.,
ascorbic acid, methionine, vitamin E), and cosolvents. The
formulation may also contain more than one active compound as
necessary for the particular indication being treated, preferably
those with complementary activities that do not adversely affect
each other. Such molecules are suitably present in combination in
amounts that are effective for the purpose intended. The active
ingredients may also be entrapped in microcapsule prepared, for
example, by coacervation techniques or by interfacial
polymerization, for example, hydroxymethylcellulose or
gelatin-microcapsule and poly-(methylmethacylate) microcapsule,
respectively, in colloidal drug delivery systems (for example,
liposomes, albumin micropheres, microemulsions, nano-particles and
nanocapsules) or in macroemulsions. Such techniques are disclosed
in Remington's Pharmaceutical Sciences, 16th edition, Osal, Ed.
(1980).
[0593] Formulations to be used for in vivo administration must be
sterile. This is readily accomplished, for example, by filtration
through sterile filtration membranes. Sustained-release
preparations may be prepared. Suitable examples of
sustained-release preparations include semi-permeable matrices of
solid hydrophobic polymers containing an antibody, 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),
poly(vinylalcohol)), polylactides (U.S. Pat. No. 3,773,919),
copolymers of L-glutamic acid and ethyl-L-glutamate, non-degradable
ethylene-vinyl acetate, degradable lactic acid-glycolic acid
copolymers such as the LUPRON DEPOT.TM. (injectable microspheres
composed of lactic acid-glycolic acid copolymer and leuprolide
acetate), and poly-D-(-)-3-hydroxybutyric acid. While polymers such
as ethylene-vinyl acetate and lactic acid-glycolic acid enable
release of molecules for over 100 days, certain hydrogels release
proteins for shorter time periods. When encapsulated antibodies
remain in the body for a long time, they may denature or aggregate
as a result of exposure to moisture at 37.degree. C. resulting in a
loss of biological activity and possible changes in immunogenicity.
Rational strategies can be devised for stabilization depending on
the mechanism involved. For example, if the aggregation mechanism
is discovered to be intermolecular S---S bond formation through
thio-disulfide interchange, stabilization may be achieved by
modifying sulfhydryl residues, lyophilizing from acidic solutions,
controlling moisture content, using appropriate additives, and
developing specific polymer matrix compositions.
Reagents, Devices and Kits
[0594] Also provided are reagents, devices and kits thereof for
practicing one or more of the above-described methods. The subject
reagents, devices and kits thereof may vary greatly. Reagents and
devices of interest include those mentioned above with respect to
the methods of identifying the presence of the target
polymorphisms, where such reagents may include nucleic acid
primers, arrays of nucleic acid probes, antibodies to polymorphic
polypeptides (e.g., immobilized on a substrate), signal producing
system reagents, etc., depending on the particular detection
protocol to be performed.
[0595] In some embodiments, a subject kit comprises: i) an element
for genotyping a sample to identify an Fc.gamma.RIIA polymorphism;
ii) an element for genotyping a sample to identify an
Fc.gamma.RIIIA polymorphism; and iii) a reference that correlates a
genotype with predicted response to a therapeutic antibody. In some
embodiments, the reference is a chart or table that correlates
predicted degrees of responsiveness to a given therapeutic antibody
to Fey receptor polymorphisms. Elements for genotyping include,
e.g., nucleic acid probes, and nucleic acid primer sets. A sample
will in some embodiments be a biological sample obtained from an
individual, e.g., a blood sample or other sample that includes
nucleic acid (e.g., genomic DNA) from the individual.
[0596] In some embodiments, the reference indicates a high degree
of responsiveness to a given therapeutic antibody. In these
embodiments, therapeutic antibody may be selected for
administration to the individual. In other embodiments, the
reference indicates an intermediate or low responsiveness; and
choosing an Fc variant antibody that exhibits enhanced binding
and/or in vitro ADCC function to an Fc.gamma.RIIA and/or an
Fc.gamma.RIIIA is indicated. In some embodiments, a subject kit
includes a set of related antibodies.
[0597] In addition to the above components, the subject kits may
further include instructions for practicing the subject methods.
These instructions may be present in the subject kits in a variety
of forms, one or more of which may be present in the kit. One form
in which these instructions may be present is as printed
information on a suitable medium or substrate, e.g., a piece or
pieces of paper on which the information is printed, in the
packaging of the kit, in a package insert, etc. Yet another means
would be a computer readable medium, e.g., diskette, CD, etc., on
which the information has been recorded. Yet another means that may
be present is a website address which may be used via the internet
to access the information at a removed site. Any convenient means
may be present in the kits.
[0598] The following examples are offered by way of illustration
and not by way of limitation.
EXPERIMENTAL
Example 1
Polymorphisms in Fc.gamma.RIIA and Fc.gamma.RIIIA; and Response to
Rituximab
[0599] I. Materials and Methods
[0600] A. Patient Population
[0601] This study included 87 patients with follicular lymphoma,
who were treated with rituximab at Stanford Medical Center between
1993 and 2003. They were selected because of the availability of
their lymphoma tumor cells, peripheral blood or serum samples, and
their known clinical response to rituximab. The pathology of all
patient cases was reviewed. There were 47 patients with follicular
small cleaved, 35 patients with follicular mixed, and five patients
with follicular large-cell lymphoma. Fifteen patients had received
rituximab as their first-line therapy. Seventy-two patients had
received chemotherapy before rituximab, including 10 patients who
had prior bone marrow transplantation. No patients received
chemotherapy within the 2 months before rituximab treatment.
Eighty-one patients had four weekly infusions of rituximab at 375
mg/m.sup.2, five patients had eight weekly infusions of 375
mg/m.sup.2, and one patient had four weekly infusions of 250
mg/m.sup.2. Clinical responses were determined by physical
examination and computed tomography scans between 1 and 3 months
after last rituximab infusion and every 3 months thereafter. These
responses were scored according to the Cheson criteria (Cheson B D
et al., 1999, "Report of an international workshop to standardize
response criteria for non-Hodgkin's lymphoma," J. Clin. Oncol.
17:1244-1253). Maximal clinical responses were observed at 1 to 3
months in all but three patients, who had partial responses at 1 to
3 months and showed additional tumor shrinkage at later time
points. Pretreatment tumor cells were available in 43 patients and
were used for in vitro ADCC assay. Fc.gamma.R polymorphisms were
analyzed in all 87 patients. This study was conducted according to
a protocol approved by the institutional review board of our
institution, and informed consent was obtained from all patients
for the use of tissue samples and the analysis of clinical
information.
[0602] B. Tumor Cells
[0603] Suspensions of pretreatment tumor cells isolated from lymph
nodes were cryopreserved in liquid nitrogen. For ADCC assay, the
tumor cells were thawed and subjected to Ficoll-Paque PLUS
(Amersham Pharmacia Biotech, Piscataway, N.J.) gradient
centrifugation to remove dead cells. The viability of tumor cells,
determined by trypan blue dye exclusion at the time of assay,
always exceeded 90%. The percentage of tumor cells in each sample
was estimated by staining with antibodies specific for kappa or
lambda light chains.
[0604] C. ADCC Assay
[0605] Lymphoma cells were labeled with chromium-51 (.sup.51Cr) by
incubating 3.times.10.sup.6 cells with 450 .mu.Ci of .sup.51Cr
(Amersham Pharmacia Biotech) for 2 hours at 37.degree. C. Cells
were washed with RPMI-1640, and then incubated for 30 minutes at
37.degree. C. with antibodies (at 10 mg/mL) Excess antibodies were
removed by washing with medium. Mononuclear cells were obtained by
Ficoll-Hypaque centrifugation of peripheral blood of a healthy
donor (with Fc.gamma.RIIIA V/V.sup.158 genotype) and used as
effector cells. 1.times.10.sup.4 51Cr-labeledtarget cells were
incubated for 4 hours at 37.degree. C. with the indicated number of
effector cells in 200 .mu.L of RPMI-5 medium (RPMI-1640, 10 mmol/L
HEPES, 5% heat-inactivated human AB serum, 1% L-glutamine). Fifty
microliters of medium was collected after 4 hours of incubation and
counted in a MicroBeta 1450 scintillation counter (Wallac, Turku,
Finland). Spontaneous .sup.51Cr release was determined in the
absence of effector cells. Maximal .sup.51Cr release was determined
by lysis with 0.5% Triton X-100. All samples were assayed in
triplicate. The specific .sup.51Cr release was determined by
subtracting the spontaneous .sup.51Cr release from that of the
treatment wells, then dividing the result by the maximal .sup.51Cr
release minus spontaneous .sup.51Cr release. All the tumor samples
had coexistent T-cells of variable degree (Table-1). To compare
different tumor samples, the specific ADCC is calculated by
dividing the specific .sup.51Cr release in rituximab-treated
samples minus .sup.51Cr release in control IgG1-treated samples by
the percentage of CD20-positive cells in individual samples.
[0606] D. Analysis of Fc.gamma.RIIIA and Fc.gamma.RIIA
Polymorphisms
[0607] Genomic DNA was prepared from tumor cells or from
peripheral-blood mononuclear cells using a DNA extraction kit
(Qiagen, Valencia, Calif.). In six patients, DNA was prepared from
the serum using a described method (Kopreski M S, Benko F A, Kwee
C, et al., 1997, "Detection of mutant K-ras DNA in plasma or serum
of patients with colorectal cancer," Br. J. Cancer 76:1293-1299).
Genotyping of Fc.gamma.RIIIA V/F.sup.158 and Fc.gamma.RIIA
H/R.sup.131 polymorphisms was performed by a polymerase chain
reaction followed by allele-specific restriction enzyme digestion
(Koene H R, Kleijer M, Algra J, et al., 1997, "Fc-gamma-RIIIA-158
V/F polymorphism influences the binding of IgG by natural killer
cell Fc-gamma-RIIIA, independently of the Fc-gamma-RIIIA-48 L/R/H
phenotype," Blood 90:1109-1114; Jiang X-M, Arepally G, Poncz M, et
al., 1996, "Rapid detection of the Fc-gamma-RIIA-H/R131
ligand-binding polymorphism using an allele-specific restriction
enzyme digestion (ASRED)," J. Immunol. Methods 199:55-59). All
genotyping of Fc.gamma.RIIIA polymorphism was confirmed by direct
sequencing of the region of interest.
[0608] E. Statistical Analysis
[0609] Differences in the means of ADCC killing were tested by
single-factor analysis of variance test and checked by the
Kruskal-Wallis (nonparametric) test. The clinical responses of the
patients were compared using a two-tailed Fisher's exact test
(PRISM for Macintosh; GraphPad Software, San Diego, Calif.). A
logistic regression analysis including age (.gtoreq. or <60
years), stage (III.nu. IV), presence of bulky disease, number of
extranodal sites (.gtoreq.two or <two), prior bone marrow
transplantation, and Fc.gamma.RIIA and Fc.gamma.RIIIA genotype was
used to identify independent prognostic variables influencing the
clinical responses (StatView 5.0.1; SAS Inc, Cary, N.C.).
[0610] II. Results
[0611] A. Rituximab-Mediated ADCC in Follicular Lymphoma Cells
[0612] The ability of rituximab to mediate ADCC in follicular
lymphoma cells was determined. Pretreatment lymphoma cells from 43
patients were tested using effector cells isolated from one healthy
donor. Rituximab-mediated ADCC was detected in all 43 patient
samples (range, 13.5% to 100%). As expected, the murine antibody of
rituximab, 2B8, which contains a mouse .beta.1 Fc portion and binds
lymphoma cells identically to rituximab, did not mediate ADCC (data
not shown).
[0613] The relation of the observed ADCC susceptibility of lymphoma
cells from individual patients to their clinical response to
rituximab therapy was then evaluated. Patients were subdivided into
nonresponders (NR), partial responders (PR), and complete
responders (CR) according to their response to rituximab at the
first evaluation at 1 to 3 months (Table 1, FIG. 5). The range of
ADCC varied widely in all three Groups (NR, 16.9% to 80.6%; PR,
13.5% to 57.0%; CR, 20.9% to 100.0%; FIG. 1). However, there was no
difference of rituximab-mediated ADCC between the three
[0614] Groups (means.+-.standard deviations: NR, 44.6%.+-.18%; PR,
40.0%.+-.12%; CR, 53.6%.+-.23%). Additional analysis showed no
relationship between rituximab-mediated ADCC and response when
clinical response was scored at 6, 9, or 12 months after treatment,
nor did the susceptibility to ADCC correlate with the duration of
remission (data not shown). In a subGroup of 29 patients whose
tumors were studied in a report on complement-mediated
cytotoxicity, (Weng W- K, Levy R, 2001, "Expression of complement
inhibitors CD46, CD55, and CD59 on tumor cells does not predict
clinical outcome after rituximab treatment in follicular
non-Hodgkin lymphoma," Blood 98:1352-1357) the expression of CD20
on their lymphoma cells had previously been determined by flow
cytometric staining. Within this subGroup, there was no correlation
between the expression of CD20 and rituximab-mediated ADCC
(r=-0.03; P=0.88).
[0615] B. Clinical Response to Rituximab Therapy and Fc.gamma.RIIIA
V/F.sup.158 Polymorphism
[0616] The Fc.gamma.RIIIA (CD16) of V allele demonstrates higher
affinity to IgG1 than the F allele and mediates ADCC more
effectively. Recently, Cartron et al., (Cartron G, Dacheux L,
Salles G, et al., 2002, "Therapeutic activity of humanized
anti-CD20 monoclonal antibody and polymorphism in IgG Fc receptor
Fc-gamma-R IIIA gene," Blood 99:754-758) have shown an association
between Fc.gamma.RIIIA V/V.sup.158 genotype and higher response
rate in patients treated with first-line rituximab. This
association was assayed in the subject patient Group, the majority
of whom were treated for relapsed disease. The study Group was
expanded to 87 by acquiring peripheral blood or serum samples from
additional rituximab-treated patients.
[0617] In this sample set, 13 patients (15%) had homozygous VN
(V/V.sup.158), 40 (46%) had heterozygous V/F (V/F.sup.158), and 34
(39%) had homozygous F/F (F/F.sup.158). The three groups were not
different in terms of average age at the time of treatment, number
of prior chemotherapy courses, or time between diagnosis and
treatment (Table 2, FIG. 6). The response rate in patients with
V/F.sup.158 and in patients with F/F.sup.158 was similar at all
four time points (Table 3, FIG. 7). For that reason, we Grouped
V/F.sup.158 and F/F.sup.158 together as the F carrier for
statistical analysis. A significant difference was detected between
the response rates of V/V.sup.158 and F carriers (Table 3, FIG. 7).
The progression-free survival (PFS) at 2 years was 45% for patients
with 158 VN, 12% for 158 V/F, 16% for 158 F/F, and 14% for F
carriers, using the Kaplan-Meier estimation, with median time to
progression (TTP) of 534, 148, 250, and 170 days for each Group,
respectively. The PFS estimate of patients with V/V.sup.158 was
significantly longer than that for patients with V/F.sup.158,
F/F.sup.158, or F carriers (FIG. 2).
[0618] C. Clinical Response to Rituximab Therapy and Fc.gamma.RIIA
H/R.sup.131 Polymorphism
[0619] The Fc.gamma.RIIA (CD32) is another activating Fc.gamma.R
that is expressed only on macrophages but not on natural killer
(NK) cells. An H/R polymorphism at position 131 of Fc.gamma.RIIA
has been found to affect its affinity to human IgG (Jiang X- M,
Arepally G, Poncz M, et al., 1996, "Rapid detection of the
Fc-gamma-RIIA-H/R131 ligand-binding polymorphism using an
allele-specific restriction enzyme digestion (ASRED)," J. Immunol.
Methods 199:55-59). Of the 87 patients in the Group, 20 (23%) had
homozygous H/H(H/H.sup.131), 43 (49%) had heterozygous
H/R(H/R.sup.131), and 24 (28%) had homozygous R/R(R/R.sup.131).
Once again, the three Groups were not different in terms of average
age at the time of treatment, number of prior chemotherapy
treatments, or time between diagnosis and treatment (Table 2).
Although there was no difference in the response rate at 1 to 3
months between the three Groups, patients with H/H.sup.131 showed a
significantly higher response rate than the other two Groups
combined (H/R and R/R (R carrier)) at 6, 9, and 12 months (Table 4,
FIG. 8). This higher response rate also translated to longer
remission: the PFS at 2 years was 37% for patients with
H/H.sup.131, 13% for H/R.sup.131, 19% for R/R.sup.131, and 14% for
R carrier using the Kaplan-Meier estimation with TTP of 445, 162,
158, and 158 days for each Group, respectively. The PFS estimate
for patients with H/H.sup.131 was significantly longer than for
patients with other genotypes (FIG. 3).
[0620] The possibility of an association between Fc.gamma.RIIIA and
Fc.gamma.RIIA genotypes that might explain the correlation of the
two with response rate was examined. As shown in Table 5, FIG. 9,
there was no significant difference in the fraction of V/V.sup.158
or F carrier in three H/R.sup.131 genotypes. The combination of
Fc.gamma.RIIIA V/V.sup.158 and/or Fc.gamma.RIIA H/H.sup.131 was
then analyzed, and their relationship to rituximab response. As
shown in Table 6, FIG. 10, patients with V/V.sup.158 and/or
H/H.sup.131 (total of 30 patients) had a significantly higher
response rate than patients without either genotype at all four
time points (83% .nu. 54%, P=0.009 at 1 to 3 months; 80% .nu. 34%,
P=0.0001 at 6 months; 69% .nu. 26%, P=0.0003 at 9 months; 59% .nu.
18%, P=0.0004 at 12 months). The PFS estimate of patients with
V/V.sup.158 and/or H/H.sup.131 was also significantly longer
(P=0.001), with TTP of 445 and 140 days for the two Groups,
respectively (FIG. 4). By logistic regression analysis,
Fc.gamma.RIIIA V/V.sup.158 genotype emerged as the only predictive
factor for response at 1 to 3 months, whereas both the
Fc.gamma.RIIIA V/V.sup.158 genotype and Fc.gamma.RIIA H/H.sup.131
genotype were identified as independent predictive factors for
response at 6, 9, and 12 months (Table 7, FIG. 11).
[0621] III. Discussion
[0622] In this study, the observation of Cartron et al., supra,
that V/V.sup.158 genotype is associated with higher response rate
to rituximab treatment was confirmed. However, there were
significant differences between the present and prior studies.
First, the response rate in the patient Group of the present study
was lower than that in the previous report, especially at 12 months
after treatment. This observation is consistent with previous
observations of a lower response rate when rituximab is used as
second-line treatment. In addition, the patients of the present
study probably had higher tumor burden because 53% of them had
bulky (5 cm) disease compared with the previous study in patients
with nonbulky disease. Second, although F carriers (V/F and F/F)
showed a significantly lower response rate, the response rate in
patients with F/F.sup.158 was slightly higher than that in patients
with V/F.sup.158. The biologic explanation of this phenomenon is
unclear, given that patients with V/F.sup.158 would be expected to
have an intermediate response rate. Third, consistent with the
previous report, we detected a difference between V/V.sup.158 and F
carrier. However, one interesting observation in this study is that
the difference became more pronounced after longer times from the
treatment. The antibody is known to persist for up to 6 months, and
its effect may be cumulative.
[0623] The most unexpected result came from the analysis of
Fc.gamma.RIIA polymorphism. The allele of H/H.sup.131 binds to
human IgG2 better than that of R/R.sup.131. However, no significant
difference in the affinity of these two allelic forms for human
IgG1 has been noted. (Parren P W, Warmerdam P A, Boeije L C, et
al., 1992, "On the interaction of IgG subclasses with the low
affinity Fc-gamma-RIIA (CD32) on human monocytes, neutrophils, and
platelets: Analysis of a functional polymorphism to human IgG2," J.
Clin. Invest. 90:1537-1546). Therefore, it was unexpected to find a
higher rituximab response rate associated with H/H.sup.131 genotype
(Table 4, FIG. 8). Similar to the Fc.gamma.RIIIA V/F.sup.158
polymorphism, a gene dosage effect of the 131H allele was not
observed. Instead, the response rate in patients with H/R.sup.131
was similar to that of R/R.sup.131 at 6, 9, and 12 months. The
biologic explanation of this observation is not clear. The
association between Fc.gamma.RIIA H/H.sup.131 and higher response
rate was not a result of a linkage disequilibrium of Fc.gamma.RIIIA
V/F.sup.158 polymorphism (Table 5, FIG. 9). There is a random
distribution of combinations of variant genotypes of Fc.gamma.RIIA
and Fc.gamma.RIIIA in the normal population. (Lehrnbecher T, Foster
C B, Zhu S, et al., 1999, "Variant genotypes of the low-affinity
Fc-gamma receptor in two control populations and a review of
low-affinity Fc-gamma receptor polymorphisms in control and disease
populations," Blood 94:4220-4232).
[0624] The Fc.gamma.RIIA H/R.sup.131 polymorphism is an independent
predictive factor for clinical response: In the subGroup of
patients with 158 F carrier, Fc.gamma.RIIA H/H.sup.131 genotype was
associated with higher response rate at 6, 9, and 12 months
(H/H=76% .nu. R carrier=34%, P=0.004 at 6 months; H/H=65% .nu. R
carrier=26%, P=0.007 at 9 months; H/H=47% .nu. R carrier=18%,
P=0.026 at 12 months). Furthermore, all three patients with both
V/V.sup.158 and H/H.sup.131 genotypes had long-lasting remissions
(Table 6, FIG. 10). Patients with V/V.sup.158 and/or H/H.sup.131
genotypes showed a higher response rate and a longer remission than
did patients without either of these two genotypes (Table 6, FIG.
10). Lastly, the logistic regression analysis showed that the
V/V.sup.158 and H/H.sup.131 were independent predictive factors for
response at 6, 9, and 12 months. The report of Cartron et al.,
supra, also analyzed the Fc.gamma.RIIA H/R.sup.131 polymorphism and
concluded that the Fc.gamma.RIIA polymorphism did not influence the
clinical response. However, it is important to point out that
Cartron et al., analyzed a smaller Group of patients (N=45) and
scored the clinical responses only at 1 and 12 months. In this
study, the most prominent differences were observed at 6 and 9
months (Table 4, FIG. 8).
[0625] To reiterate, this study established a) for the first time a
clear role for ADCC in the clinical effects (treatment response and
freedom of progression) of rituximab at the level of the effector
cell was established through in vitro ADCC assays and by
correlating this to specific Fc.gamma.RIIIA polymorphism, b)
through a rigorous time-course analysis, an unequivocal proof that
Fc.gamma.RIIA H/R.sup.131 polymorphism is independently associated
with the therapeutic response rate, and c) both the Fc.gamma.RIIIA
V/F.sup.158 and the Fc.gamma.RIIA H/R.sup.131 polymorphisms are
independently and collectively associated with the therapeutic
response rate and freedom from progression, which is to say that
details of both polymorphisms are absolutely essential to make a
meaningful prediction of the therapeutic response rate. This work
has provided a sequential correlation between Fc.gamma.RIIIA
V/F.sup.158 polymorphism, in vitro ADCC, and the clinical effect of
rituximab. Although similar in vitro ADCC experiments were not
conducted to test such a relationship for Fc.gamma.RIIA H/R.sup.131
polymorphism in these patients, the direct correlation between the
H/R.sup.131 polymorphism and the clinical effect of rituximab is
unequivocally established in this study. Thus, given the central
role for these two receptors in ADCC, a) patients can be classified
into nine Groups based on these polymorphisms, b) it is possible to
generate Fc variant antibodies specific for Fc.gamma.RIIIA and
Fc.gamma.RIIA alleles by selecting for enhanced binding and/or in
vitro ADCC function, c) it is comprehended that, like rituximab,
many other antibodies exert their therapeutic efficacy through ADCC
as the major mechanism of action, and therefore, d) the patient
Group specific Fc variants contemplated in this disclosure can be
used to enhance the therapeutic response of these antibodies to
treat ADCC-treatable diseases or disorders.
Example 2
Construction of Patient Group Specific Fc Variant Antibodies
[0626] Throughout this example, methods are described to generate
Fc variants optimized for Fc.gamma.RIIIA F/F.sup.158 and
Fc.gamma.RIIA R/R.sup.131 genotypes (Patient Group-IX; See, e.g.,
Table D). While Rituximab is shown as an example, any other
ADCC-dependent antibody can be used in these experiments with
appropriate modifications in the procedures. For preliminary
binding studies which involve SSM and Fc Walking, aglycosylated Fc
fragment including the hinge as well as the soluble domains of
Fc.gamma.RIIIA and Fc.gamma.RIIA are expressed in vitro or through
bacterial expression by established procedures (Kim et al., 1994,
Eur. J. Immunol. 24:542; Sondermann and Jacob, 1999, Biol. Chem.
380:717-721).
[0627] FC ENGINEERING AND BINDING STUDIES: For each chosen residue,
in vitro scanning saturation mutagenesis (SSM) is carried out (U.S.
Pat. No. 6,180,341). Briefly, at each site, twenty-one genes
encoding all possible amino acid substitutions as well as a double
stop codon (control) are constructed by overlap extension PCR. The
following conserved stretches of the Fc region will be subjected to
both SSM and Fc Walking, one residue at a time, in order to
generate single mutants: L.sup.234-S.sup.239 (6.times.20=120
variants), R.sup.255-T.sup.260 (6.times.20=120 variants);
D.sup.265-E.sup.269 (5.times.20=100 variants); N.sup.297-T.sup.299
(3.times.20=60 variants); A.sup.327-I.sup.332 (6.times.20=120
variants) (See, e.g., FIG. 12-C). In addition, approximately 5-10
residues upstream and downstream of the conservative stretches will
also be subjected to Fc Walking (FIG. 12-D). Taken together, this
generates <2000 Fc variants. Similarly, double and triple
mutants are generated by combining the single mutants and
additionally selecting for the binding properties (Yang et al.,
1995, J. Mol. Biol. 254:392; Wu et al., 1998, Proc Natl. Acad. Sci.
USA 95:6037). This is accomplished by simultaneous SSM at 3-5
different positions. The final products of the overlap extension
PCR reaction contain a T7 promoter and ribosome binding site in
front of the Fc fragment gene. An HSV sequence is also present at
the C-terminal end of the Fc fragment gene, so that the MAb
fragment protein can be detected by ELISA using an anti-HSV
monoclonal antibody. The PCR overlap extension products are used as
templates for coupled in vitro transcription-translation reactions
to produce Fc variants. An E. coli S30 ribosomal extract is used
for in vitro translation.
[0628] The protein products from the coupled in vitro
transcription-translation step are analyzed by ELISA. In ELISA,
96-well microtiter plates are coated with the BSA conjugate of
soluble Fc.gamma.RIIIA F.sup.158 or Fc.gamma.RIIA R.sup.131. The
plates are then incubated with equal amounts from each of the in
vitro synthesis reactions. In order to provide accurate
calibration, the construct prepared with the Fc wild-type sequence
is used on each ELISA plate. The Fc wild-type construct is produced
by the overlapping PCR method alongside the mutants, thereby
providing an accurate calibration for all stages of the procedure.
Heterogeneity of the transcribed/translated products is verified by
DNA/protein sequencing protocols, or matrix-assisted laser
desorption/ionization time-of-flight mass spectrometry
(MALDI-TOF-MS). The ELISA results for the different mutants are
recorded and the promising Fc variants in terms of binding and
affinity are subjected to in vitro ADCC assays (See, e.g.,
below).
[0629] Construction, Expression, and Purification of Fc Variant
Antibodies and Fc.gamma.Rs:
[0630] The wild-type Fc region of rituximab is substituted with Fc
variants generated through Fc engineering, cloned and expressed in
293T cells, and purified by using protein-A chromatography.
Fc.gamma.Rs are constructed as C-terminal 6.times.His-GST fusions,
expressed in 293T (human Fc.gamma.Rs) or NIH 3T3 (mouse
Fc.gamma.RIII) cells, and purified by using nickel affinity
chromatography. Heterogeneity of the translated products is tested
by any one of the following analytical procedures: SDS-PAGE, gel
filtration, MALDI-TOF-MS.
[0631] Binding Assays: AlphaScreen assays use untagged Ab to
compete the interaction between biotinylated IgG bound to
streptavidin donor beads and Fc.gamma.R-His-GST bound to anti-GST
acceptor beads. Competition SPR (Harvey et al., 2004, Proc. Natl.
Acad. Sci. USA 101:9193) experiments measured capture of free Ab
from a preequilibrated Ab:receptor analyte mixture to
Fc.gamma.RIIIA V.sup.158-His-GST bound to an immobilized anti-GST
surface. Equilibrium dissociation constants (K.sub.D values) are
calculated by using the proportionality of initial binding rate on
free Ab concentration in the Ab:receptor equilibrium (Schier et
al., 1996, J. Mol. Biol. 255:28; Daugherty et al., 1998, Protein
Engg. 11:825-832).
[0632] in vitro ADCC is measured by .sup.51Cr release assay (Weng
and Levy, 2003, J. Clin. Oncol. 21:3940). Human PBMCs are purified
from leukopacks by using a Ficoll gradient and allotyped for
Fc.gamma.RIIIA F/F.sup.158 and Fc.gamma.RIIA R/R.sup.131 by PCR. NK
cells are isolated from human PBMCs by negative selection using a
magnetic bead NK cell isolation kit (Miltenyi Biotech, Auburn,
Calif.). All the necessary target cell lines are obtained from
American Type Culture Collection. As a second format, ADCC assay
using PBMC as effector cells is measured based on lactate
dehydrogenase activity released from the dead or plasma membrane
damaged cells (Shields et al., 2001, J. Biol. Chem. 276:6591).
[0633] For phagocytosis experiments, monocytes are isolated from
PBMCs of individuals belonging to the Patient Group-IX
(Fc.gamma.RIIIA F/F.sup.158 and Fc.gamma.RIIA R/R.sup.131) by using
a Percoll gradient and differentiated into macrophages by culturing
in a medium supplemented with 0.1 ng/ml granulocyte macrophage
colony-stimulating factor for 1 week. For imaging, WIL2-S target
cells are labeled with PKH67 (Sigma) and cocultured for 24 h with
macrophages at an effector:target cell ratio of 3:1 in the presence
of 100 ng/ml Fc variant rituximab optimized for the Patient
Group-IX. Cells are then treated with secondary antibodies
anti-CD11-RPE and anti-CD14-RPE (DAKO) for 15 minutes before live
cell imaging using a fluorescence microscope. For quantitative ADCP
(antibody-dependent cell-mediated phagocytosis), WIL2-S target
cells are labeled with PKH67, seeded in a 96-well plate at
20.times.10.sup.3 cells per well, and treated with WT or the Fc
variant rituximab at the designated final concentrations.
Macrophages are labeled with PKH26 (Sigma) and added to the
opsonized labeled target cells at 20.times.10.sup.3 cells per well,
and the cells are cocultured for 18 h. Fluorescence is measured by
using dual-label flow cytometry. Fc variant antibodies with
increased potency and efficacy are selected. CDC assays are
performed according to published procedures (Gazzano-Santoro et
al., 1997, J. Immunol. Meth. 202:163; Uchida et al., 2004, J. Exp.
Med. 199:1659).
[0634] In Vivo B-Cell Depletion: Cynomolgus monkeys (Macaca
fascicularis) will be injected intravenous once daily for 4
consecutive days with wild-type or the Fc variant rituximab
optimized for the Patient Group-IX (Reff et al., 1994, Blood
83:435-445). The test animals will be allotyped for the Fc.gamma.R
polymorphisms, and if required, the animals corresponding to
F/F.sup.158 and R/R.sup.131 genotypes will be used for the
experiment. The experiment is comprised of six treatment Groups of
.about.0.1, 0.2, 2, 7, or 30 .mu.g/kg (Group-IX specific variant
rituximab) or .about.2 or 30 .mu.g/kg (wild-type control), with
three monkeys per treatment Group. Blood samples are acquired on
two separate days before dosing (baseline) and at days 1, 2, 5, 15,
and 28 after initiation of dosing. For each sample, cell
populations are quantified by flow cytometry by using specific
antibodies against the representative marker antigens. Percent
B-cell depletion is calculated by comparing B-cell counts on the
given day with the average of the two baseline measures for each
animal.
Example 3
ADCC Improvement Through CDR Engineering
[0635] Antibodies or antibody fragments are specifically optimized
to a patient Group according to their Fc.gamma.RIIA and
Fc.gamma.RIIIA polymorphism as described in Example 2. However,
instead of introducing amino acid modifications (i.e., insertions,
substitutions, deletions, etc.) into the Fc portion of the
antibody, as described in Example 2, modifications are introduced
in the complementarity determining regions (CDRs) of the
antibody.
[0636] CDR engineering of Rituxan is shown here as an example. FIG.
16 shows the codon-based mutagenesis of the light chain CDR2 region
(APSNLAS). Scanning saturation mutagenesis (Burks et al., 1997,
Proc. Natl. Acad. Sci. USA 94:412; Chen et al., 1999, Protein Eng.
12:349) is used in a stepwise fashion to rapidly improve the
affinity of the CD20-binding fragment by greater than 50-100 fold.
The focused library of V.sub.L CDR2 region will have 140 variants.
In the absence of structural information about the Rituxan-CD20
interactions, in vitro translated antibody libraries for all six
light and heavy chain CDRs will be screened by a quantitative assay
(k.sub.on, k.sub.off, K.sub.d, in vitro ADCC assay) to identify
variants with improved binding to CD20. The Rituxan variants in
these libraries each contains a single mutation, and all 20 amino
acids are introduced at each CDR residue, resulting in a library
consisting of 1,320 unique variants. Multiple clones displaying 2-
to >10 fold improved affinity are identified. The CDR residues
identified as "critical" (optimal) residues for engineering (FIG.
16) will be subjected to second round of scanning saturation
mutagenesis. Where necessary, simultaneous mutations of 3-4 changes
in multiple CDR sequences are made. Promising scFv variants were
converted into IgG1 format, cloned, and expressed in 293T cells,
and purified by standard procedures. Binding assays and in vitro
ADCC assays are carried out essentially as described in Example
II.
Example 4
Engineering, Screening and Selection of Optimized Patient Group
Variant Rituximab Antibodies
[0637] Antibodies or antibody fragments are specifically optimized
for a patient Group based on their Fc.gamma.RIIA and Fc.gamma.RIIIA
polymorphism. For example, patients are categorized into Groups
according to their Fc.gamma.RIIA (H/R.sup.131) polymorphism and
their Fc.gamma.RIIIA (V/F.sup.158) polymorphism. Consequently,
patients can be divided into nine genotypic Groups, including:
V/V.sup.158, H/H.sup.131 (Group-I); V/F.sup.158, H/H.sup.131
(Group-II); F/F.sup.158, H/H.sup.131 (Group-III); V/V.sup.158,
H/R.sup.131 (Group-IV); V/F.sup.158, H/R.sup.131 (Group-V);
F/F.sup.158, H/R.sup.131 (Group-VI); V/V.sup.158, R/R.sup.131
(Group-VII); V/F.sup.158, R/R.sup.131 (Group-VIII); and
F/F.sup.158, R/R.sup.131 (Group-IX) (See, e.g., Table D). Notably,
an antibody can be optimized for each patient Group except for the
Group or Groups that exhibit the highest degree of responsiveness
to the antibody therapy.
[0638] A variant antibody specific for a particular patient Group
(genotype) is engineered such that the variant antibody exhibits
responsiveness optimized to the patient Groups (genotypes) which
exhibit a higher degree of responsiveness to the parent antibody.
In some embodiments, a variant antibody specific for a particular
patient Group (genotype) is engineered such that the variant
antibody exhibits responsiveness optimized to the patient Group
which exhibits the highest degree of responsiveness to the parent
antibody.
[0639] Responsiveness to an antibody therapy for a neoplastic
disease can include one or more of: antibody-dependent
cell-mediated cytotoxicity (ADCC) response to tumor cells;
reduction in tumor mass; reduction in number of tumor cells.
[0640] Responsiveness to an antibody therapy for an autoimmune
disease can include one or more of: reduction in a symptom
associated with the autoimmune disorder; reduction in the number
and/or activity of an autoreactive B-cell; reduction in the number
and/or activity of an autoreactive T-cell; etc.
[0641] Responsiveness to an antibody therapy for allograft
rejection can include one or more of: reduction in the amount of
immunosuppressive drug that must be administered to an individual
who is the recipient of an allograft and still maintain the
allograft; duration of maintenance of the allograft; function of
the allograft; reduction in the number and/or activity of
alloreactive T-cells in the allograft recipient.
[0642] Responsiveness to an antibody therapy for a viral infection
can include one or more of: reduction in the number of viral
genomes in a tissue, fluid, or other specimen from an individual;
reduction in one or more symptoms of a viral infection; etc.
[0643] Responsiveness may be determined at various times after
treatment with a given antibody therapy, e.g., 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11 and 12 months following treatment, e.g., following
initiation of treatment. Thus, e.g., responsiveness can be
expressed with a time component.
[0644] For example, when Rituximab is the antibody of interest, a
variant Rituximab antibody is engineered for each patient Group,
except the Group associated with the highest degree of
responsiveness to Rituximab (Group-I). Variant Rituximab antibodies
are then optimized for each patient Group such that each Group
exhibits an increased degree of responsiveness to the variant
antibody. In some embodiments, the variant Rituximab antibodies are
optimized for each patient Group exhibit a similar degree of
responsiveness as exhibited by the patients of Group-I to
Rituxamab. Given that Group-I genotype is associated with the
highest degree of responsiveness to Rituxamab, variant Rituximab
antibodies are only engineered and optimized for patient Groups
II-IX.
[0645] While the example described below are directed toward the
V/F.sup.158, H/H.sup.131 genotype, it will be understood that the
same protocols may be employed to engineer optimized antibodies for
the F/F.sup.158, H/R.sup.131 genotype (Group-III); the V/V.sup.158,
H/R.sup.131 genotype (Group-IV); the V/F.sup.158, H/R.sup.131
genotype (Group-V); the F/F.sup.158, H/R.sup.131 genotype
(Group-VI); the V/V.sup.158, R/R.sup.131 genotype (Group-VII); the
V/F.sup.158, R/R.sup.131 genotype (Group-VIII); and the
F/F.sup.158, R/R.sup.131 genotype (Group-IX) (See, e.g., Table
D).
[0646] A. Patient Group-II (V/F.sup.158, H/H.sup.131 Genotype)
[0647] Variant Rituximab antibodies engineered for Group-II
(V/F.sup.158, H/H.sup.131 genotype) are optimized to exhibit an
increased degree of responsiveness comparable to any other Group
with a higher responsiveness to the antibody. In some embodiments,
variant Rituximab antibodies engineered for Group-II (V/F.sup.158,
H/H.sup.131) are optimized to exhibit a degree of responsiveness
comparable to the level of H/H.sup.131) to Rituxamab.
[0648] 1. Engineering Variant Rituximab Antibodies for Patient
Group-II (V/F.sup.158, H/H.sup.131 Genotype)
[0649] The Fc region and CDRs of Rituximab may be engineered to
create variant Rituximab antibodies. Antibody variants can be
obtained by substitution, deletion, inversion, and/or insertion of
any of the amino acids present in the antibody. For example, Fc
variant antibodies can be obtained by substitution of any of the
amino acids present in the Fc fragment. Likewise, CDR variant
antibodies can be obtained by deletion of any of the amino acids
present in the CDRs. As can be appreciated, there are positions in
the sequence that are more tolerant to substitutions, deletions,
inversions, and/or insertions than others, and with some amino acid
modifications improving the binding activity of the parent
antibody. The amino acids that are essential should either be
identical to the amino acids present in the parent antibody, or
substituted by conservative substitutions. The amino acids that are
non-essential can be identical to those in the parent antibody, or
can be substituted by conservative or non-conservative
substitutions, and/or can be deleted.
[0650] The substitutions, deletions, inversions, and/or insertions
of amino acids in an Fc variant antibody will occur in regions not
essential to antigen binding. The identification of essential and
non-essential amino acids in the antibody can be achieved by
methods known in the art, such as by site-directed mutagenesis (for
example, SSM) and AlaScan analysis (Moffison et. al., 2001, Chem.
Biol. 5:302-307).
[0651] Essential amino acids have to be maintained or replaced by
conservative substitutions in the variants. Non-essential amino
acids can be deleted, or replaced by a spacer or by conservative or
non-conservative substitutions.
[0652] The following conserved stretches (bolded and underlined) in
the Fc region of Rituximab (SEQ ID NO: 1) may be subjected to both
SSM (See, e.g., U.S. Pat. No. 6,180,341) and Fc Walking, one
residue at a time, in order to generate single mutants:
L234-S.sup.239 (6.times.20=120 variants), R.sup.255-T.sup.260
(6.times.20=120 variants); D.sup.265-E.sup.269 (5.times.20=100
variants); N.sup.297-T.sup.299 (3.times.20=60 variants);
A.sup.327-I.sup.332 (6.times.20=120 variants) (See, e.g., FIG.
12-C). Briefly, at each site, twenty-one genes encoding all
possible amino acid substitutions as well as a double stop codon
(control) are constructed by overlap extension PCR. In addition,
approximately 5-10 residues upstream and downstream of the lower
hinge, B/C loop, C'/E loop and F/G loop are also subjected to Fc
Walking (FIG. 12-D). Taken together, this generates <2000 Fc
variants.
[0653] Similarly, the Fc region in REMICADE.RTM. (SEQ ID NO: 5),
ERBITUX.RTM. (SEQ ID NO: 7), HERCEPTIN.RTM. (SEQ ID NO: 9) and
CAMPATH.RTM. (SEQ ID NO: 11) may be subjected to Fc walking.
[0654] For example, the first conserved stretch (from the
N-terminus) in the Fc region of RITUXAN begins with an lysine (as
shown below). This arginine residue may be altered with any of the
other known 21 amino acid residues, for instance, tyrosine.
Additionally, an antibody molecule may comprise two or more
modifications in one or more conserved regions of the Fc.
TABLE-US-00005 Rituximab Heavy Chain (Fc-amino acid residues 232-
448) (SEQ ID NO: 1)
PELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAP
IEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEW
ESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEA
LHNHYTQKSLSLSPGK
[0655] Similarly, double and triple mutants are generated by
combining the single mutants and additionally selecting for binding
properties (Yang et al., 1995, J. Mol. Biol. 254:392; Wu et al.,
1998, Proc Natl. Acad. Sci. USA 95:6037). This is accomplished by
simultaneous SSM at 3-5 different positions.
[0656] The final products of the overlap extension PCR reaction
contain a T7 promoter and ribosome binding site in front of the
antibody fragment gene. An HSV sequence is also present at the
C-terminal end of the antibody fragment gene so that the MAb
fragment protein can be detected by ELISA using an anti-HSV
monoclonal antibody. The PCR overlap extension products are used as
templates for coupled in vitro transcription-translation reactions
to produce antibody variants. An E. coli S30 ribosomal extract is
used for in vitro translation.
[0657] Alternatively or in addition to the modification(s) made to
the Fc region of rituximab, the antibody may be modified in one or
more of its complementarity determining regions (CDRs) by the
methods described above for the Fc region. Specifically, one or
more modifications are made to one or more of the heavy or light
chain CDRs in rituximab (SEQ ID NO: 2 and 3, respectively). Any one
or more of the CDR sequences presented below (bolded and
underlined) from the Rituximab heavy or light chain may be modified
by the SSM procedure.
[0658] Similarly, one or more of the above-described modifications
may be made to the CDRs regions of REMICADE.RTM. (SEQ ID NO: 4 and
5), ERBITUX.RTM. (SEQ ID NO: 6 and 7), HERCEPTIN.RTM. (SEQ ID NO: 8
and 9) and CAMPATH.RTM. (SEQ ID NO: 10 and 11).
TABLE-US-00006 Rituximab Light Chain
QIVLSQSPAILSASPGEKVTMTCRASSSVSYMHVVYQQKPGSSPKPWIYAPSNL
ASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSFNPPTFGAG
TKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVD
NALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGL SSPVTKSFNR (SEQ
ID NO: 2) Rituximab Heavy Chain
QAYLQQSGAELVRPGASVKMSCKASGYTFTSYNMHVVVKQTPRQGLEWIG
AIYPGNGDTSYNQKFKGKATLTVDKSSSTAYMQLSSLTSEDSAVYFCARVVYY
SNSYWYFDVWGTGTTVTVSGPSVFPLAPSSKSTSGGTAALGCLVKDYF
PEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYIC
NVNHKPSNTKVDKKAEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDT
LMISRTPEVTCVVVDVSHEDPEVKFNVVYVDGVEVHNAKTKPREEQYNSTY
RVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYT
LPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDS
DGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK (SEQ ID NO: 3)
[0659] For example, the first CDR (from the N-terminus) in the
light chain molecule begins with an arginine (as shown below). This
arginine residue may be altered with any of the other known 21
amino acid residues, for instance, tyrosine. Additionally, an
antibody molecule may comprise two or more modifications in its
CDR. When two or more amino acid modifications are present, all may
be located in the CDR of a light chain molecule. Alternatively, all
the modification may be located in the CDR of a heavy chain
molecule. Moreover, the two or more modifications may be present in
both the heavy chain molecule and the light chain molecule.
[0660] 2. Screening Variant Rituximab Antibodies Specific for
Group-II (V/F.sup.158, H/H.sup.131 Genotype)
[0661] Variant Rituximab antibodies or antibody fragments
engineered for Group-II are screened using any of the functional
assays described supra. Exemplary screening methods are described
below.
[0662] For example, variant antibodies or antibody fragments may be
analyzed by ELISA. In ELISA, 96-well microtiter plates are coated
with the BSA conjugate of soluble Fc.gamma.RIIIA V/F.sup.158 or
Fc.gamma.RIIA H/H.sup.131. The plates are then incubated with equal
amounts of variant Rituximab antibodies or antibody fragments from
each of the in vitro synthesis reactions. Heterogeneity of the
transcribed/translated products is verified by DNA/protein
sequencing protocols, or matrix-assisted laser
desorption/ionization time-of-flight mass spectrometry
(MALDI-TOF-MS). The ELISA results for the different mutants are
recorded and the promising variant Rituximab antibodies or antibody
fragments in terms of binding and affinity are subjected to in
vitro ADCC assays (See, e.g., below).
[0663] Additionally, variant Rituximab antibodies or antibody
fragments engineered for Group-II are screened for binding affinity
to Fc.gamma.RIIA and Fc.gamma.RIIIA. One such affinity assay,
AlphaScreen, uses untagged antibody to compete the interaction
between biotinylated IgG bound to streptavidin donor beads and
Fc.gamma.R-His-GST bound to anti-GST acceptor beads. Competition
SPR (Harvey et al., 2004, Proc. Natl. Acad. Sci. USA 101:9193)
experiments measured capture of free antibody from a
pre-equilibrated Ab:receptor analyte mixture to Fc.gamma.RIIIA
V.sup.158-His-GST bound to an immobilized anti-GST surface.
Equilibrium dissociation constants (K.sub.D values) are then
calculated by using the proportionality of initial binding rate on
free antibody concentration in the Ab:receptor equilibrium (Schier
et al., 1996, J. Mol. Biol. 255:28; Daugherty et al., 1998, Protein
Eng. 11:825-832).
[0664] Further, variant Rituximab antibodies or antibody fragments
may be screened for ADCC activity. To assess ADCC activity an
antibody of interest is added to target cells in combination with
immune effector cells, which may be activated by the antigen
antibody complexes resulting in cytolysis of the target cell.
Cytolysis is generally detected by the release of label (e.g.,
radioactive substrates, fluorescent dyes or natural intracellular
proteins) from the lysed cells. Useful effector cells for such
assays include peripheral blood mononuclear cells (PBMC) and
Natural Killer (NK) cells. Specific examples of in vitro ADCC
assays are described in Wisecarver et al., 1985, 79:277; Bruggemann
et al., 1987, J Exp Med 166:1351; Wilkinson et al., 2001, J Immunol
Methods 258:183; Patel et al., 1995, J Inzinunoi Methods 184:29 and
herein (see, e.g., section entitled "Characterization and
Functional Assays" infra). Alternatively, or additionally, ADCC
activity of the antibody may be assessed in vivo, e.g., in an
animal model such as that disclosed in Clynes et al., 1998, Proc.
Nat'l Acad. Sci. USA 95:652.
[0665] Additionally, variant Rituximab antibodies or antibody
fragments may be screened for ADCP activity. For the phagocytosis
experiments involved in this assay, monocytes are isolated from
PBMCs of individuals belonging to patient Group-II (Fc.gamma.RIIIA
V/F.sup.158 and Fc.gamma.RIIA H/H.sup.131) by using a Percoll
gradient and differentiated into macrophages by culturing in a
medium supplemented with 0.1 ng/ml granulocyte macrophage
colony-stimulating factor for 1 week. For imaging, WIL2-S target
cells are labeled with PKH67 (Sigma) and co-cultured for 24 hours
with macrophages at an effector:target cell ratio of 3:1 in the
presence of 100 ng/ml variant Rituximab. Cells are then treated
with secondary antibodies anti-CD11-RPE and anti-CD14-RPE (DAKO)
for 15 minutes before live cell imaging using a fluorescence
microscope. For quantitative ADCP (i.e., antibody-dependent
cell-mediated phagocytosis; macrophage mediated ADCC), WIL2-S
target cells are labeled with PKH67, seeded in a 96-well plate at
20.times.10.sup.3 cells per well, and treated with WT or the
variant Rituximab at the designated final concentrations.
Macrophages are labeled with PKH26 (Sigma) and added to the
opsonized labeled target cells at 20.times.10.sup.3 cells per well,
and the cells are co-cultured for 18 h. Fluorescence is measured by
using dual-label flow cytometry. Variant antibodies or antibody
fragments with increased potency and efficacy are selected. CDC
assays are performed according to published procedures
(Gazzano-Santoro et al., J. Immunol. Meth. 202:163, 1997; Uchida et
al., 2004, J. Exp. Med. 199:1659).
[0666] Also, variant Rituximab antibodies or antibody fragments may
be screened for those variant antibodies or antibody fragments that
are capable of depleting B-cells in a subject. For instance, in
vivo B-cell depletion assays may be employed. In such assays,
Cynomolgus monkeys (Macaca fascicularis) are injected intravenous
once daily for 4 consecutive days with wild-type or the variant
rituximab antibody (Reff et al., 1994, Blood 83:435-445). The test
animals will be allotyped for the Fc.gamma.R polymorphisms, and if
required, the animals corresponding to V/F.sup.158 and H/H.sup.131
genotypes will be used for the experiment. The experiment is
comprised of six treatment Groups of .about.0.1, 0.2, 2, 7, or 30
.mu.g/kg (variant Rituximab antibody) or .about.2 or 30 .mu.g/kg
(wild-type control), with three monkeys per treatment Group. Blood
samples are acquired on two separate days before dosing (baseline)
and at days 1, 2, 5, 15, and 28 after initiation of dosing. For
each sample, cell populations are quantified by flow cytometry by
using specific antibodies against the representative marker
antigens. Percent B-cell depletion is calculated by comparing
B-cell counts on the given day with the average of the two baseline
measures for each animal.
[0667] 3. Selection of Variant Rituximab Antibodies Optimized for
Group-II (V/F.sup.158, H/H.sup.131 Genotype)
[0668] Variant Rituximab antibodies or antibody fragments are
considered optimized for Group-II when they exhibit properties
(e.g., binding affinity, ADCC activity, etc.) similar to those
properties exhibited by Groups (genotypes) associated with a higher
degree of responsiveness to Rituxamab. In other embodiments,
variant Rituximab antibodies or antibody fragments are considered
optimized for Group-II when they exhibit properties (i.e. binding
affinity, ADCC activity, etc.) similar to those properties
exhibited by the Group associated with the highest degree of
responsiveness to Rituximab (i.e. Group-1).
[0669] In some embodiments, variant antibodies or antibody
fragments are considered optimized for Group-II when they exhibit a
binding affinity to Fc.gamma.RIIA and Fc.gamma.RIIIA that is
increased to a level exhibited by Groups with a higher degree of
responsiveness to Rituximab. In other embodiments, variant
antibodies or antibody fragments are considered optimized for
Group-II when they exhibit a binding affinity to Fc.gamma.RIIA and
Fc.gamma.RIIIA that is increased to the level exhibited by the
Group with the highest degree of responsiveness to Rituximab
(Group-I).
[0670] In some embodiments, variant antibodies or antibody
fragments are considered optimized for Group-II when they have ADCC
activity similar to the ADCC activity exhibited by Groups with a
higher degree of responsiveness to Rituximab. In other embodiments,
variant antibodies or antibody fragments are considered optimized
for Group-II when they exhibit ADCC activity similar to the ADCC
activity exhibited by the Group with the highest degree of
responsiveness to Rituximab (Group-I).
[0671] Variant Rituximab antibodies or antibody fragments that
exhibit a similar degree of responsiveness in the patients of
Group-II as compared to the responsiveness of Rituximab in the
patients of Group-I are considered patient Group optimized. Variant
antibodies optimized for a Group-II are selected for use in the
treatment of patients of Group-II.
Example 5
Enhancement of an Antibody's Effector Functions with a Genotype
Optimized Fc
[0672] The Fc nucleotide sequence (Fc cassette) from an antibody
optimized for responsiveness for a particular Fc.gamma.RIIA and
Fc.gamma.RIIIA genotype (e.g., by the methods described in the
above examples) can be used to optimize the responsiveness of other
antibodies used to treat the same or other subjects with the
particular Fc.gamma.RIIA and Fc.gamma.RIIIA genotype.
[0673] Fc cassettes with optimized responsiveness for each
Fc.gamma.RIIA (H/R.sup.131) polymorphism and Fc.gamma.RIIIA
(V/F.sup.158) polymorphism are used to optimize the responsiveness
exhibited by other antibodies. As such, an Fc cassette that is
optimized for the V/F.sup.158, H/H.sup.131 (Group-II) genotype can
be used to optimize the responsiveness of patients of the same
genotype to another antibody. For example, the optimized Fc
cassette for the V/F.sup.158, H/H.sup.131 (Group-II) genotype,
engineered to optimize responsiveness to Rituximab, is used to
optimize the responsiveness in patients of the same genotype to any
other therapeutic antibody, such as HERCEPTIN.RTM..
[0674] While the example described in detail below is directed
toward optimizing HERCEPTIN.RTM. for the V/F.sup.158, H/H.sup.131
genotype, it will be understood that the same protocol may be
employed to engineer optimized antibodies for any other
Fc.gamma.RIIA and Fc.gamma.RIIIA genotype.
[0675] Optimizing HERCEPTIN.RTM. for Group-II (V/F.sup.158,
H/H.sup.131)
[0676] HERCEPTIN.RTM. may be optimized for a patient with a
Group-II genotype (V/F.sup.158, H/H.sup.131) by fusion of the
antigen binding domain of HERCEPTIN.RTM. to a Group-II optimized Fc
cassette. Specifically, an Fc cassette engineered to optimize
responsiveness to an antibody (other than S HERCEPTIN.RTM.) for
Group-II patients is used to optimize responsiveness to
HERCEPTIN.RTM..
[0677] As previously described, a variant Rituximab antibody is
engineered for optimized responsiveness in a patient with a
Group-II genotype (V/F.sup.158, H/H.sup.131). The optimized Fc
portion of Rituximab is fused to the antigen binding domain of
HERCEPTIN.RTM. by recombinant techniques. Specifically, the
Group-II optimized Rituximab Fc cassette is fused in frame with the
antigen binding domain of HERCEPTIN.RTM. and inserted into an
vector. The vector may be transfected into an appropriate host cell
and expressed to produce the optimized Fc-HERCEPTIN.RTM.fusion. Any
methods for generating an antibody fusion, such as, for example,
those previously discussed, may be employed.
[0678] Although the foregoing disclosure has been described in some
detail by way of illustration and example for purposes of clarity
of understanding, it is readily apparent to those of ordinary skill
in the art in light of the teachings of this disclosure that
certain changes and modifications may be made thereto without
departing from the spirit or scope of the appended claims.
[0679] Accordingly, the preceding merely illustrates the principles
of the disclosure. It will be appreciated that those skilled in the
art will be able to devise various arrangements which, although not
explicitly described or shown herein, embody the principles of the
disclosure and are included within its spirit and scope.
Furthermore, all examples and conditional language recited herein
are principally intended to aid the reader in understanding the
principles of the disclosure and the concepts contributed by the
inventors to furthering the art, and are to be construed as being
without limitation to such specifically recited examples and
conditions. Moreover, all statements herein reciting principles,
aspects, and embodiments of the disclosure as well as specific
examples thereof, are intended to encompass both structural and
functional equivalents thereof. Additionally, it is intended that
such equivalents include both currently known equivalents and
equivalents developed in the future, i.e., any elements developed
that perform the same function, regardless of structure. The scope
of the present disclosure, therefore, is not intended to be limited
to the exemplary embodiments shown and described herein. Rather,
the scope and spirit of present disclosure is embodied by the
appended claims.
Sequence CWU 1
1
711216PRTArtificial Sequencesynthetic polypeptide--Rituximab
Fc-amino acid residues 1Pro Glu Leu Leu Gly Gly Pro Ser Val Phe Leu
Phe Pro Pro Lys Pro 1 5 10 15 Lys Asp Thr Leu Met Ile Ser Arg Thr
Pro Glu Val Thr Cys Val Val 20 25 30 Val Asp Val Ser His Glu Asp
Pro Glu Val Lys Phe Asn Trp Tyr Val 35 40 45 Asp Gly Val Glu Val
His Asn Ala Lys Thr Lys Pro Arg Glu Glu Gln 50 55 60 Tyr Asn Ser
Thr Tyr Arg Val Val Ser Val Leu Thr Val Leu His Gln 65 70 75 80 Asp
Trp Leu Asn Gly Lys Glu Tyr Lys Cys Lys Val Ser Asn Lys Ala 85 90
95 Leu Pro Ala Pro Ile Glu Lys Thr Ile Ser Lys Ala Lys Gly Gln Pro
100 105 110 Arg Glu Pro Gln Val Tyr Thr Leu Pro Pro Ser Arg Asp Glu
Leu Thr 115 120 125 Lys Asn Gln Val Ser Leu Thr Cys Leu Val Lys Gly
Phe Tyr Pro Ser 130 135 140 Asp Ile Ala Val Glu Trp Glu Ser Asn Gly
Gln Pro Glu Asn Asn Tyr 145 150 155 160 Lys Thr Thr Pro Pro Val Leu
Asp Ser Asp Gly Ser Phe Phe Leu Tyr 165 170 175 Ser Lys Leu Thr Val
Asp Lys Ser Arg Trp Gln Gln Gly Asn Val Phe 180 185 190 Ser Cys Ser
Val Met His Glu Ala Leu His Asn His Tyr Thr Gln Lys 195 200 205 Ser
Leu Ser Leu Ser Pro Gly Lys 210 215 2210PRTArtificial
Sequencesynthetic polypeptide--Rituximab light chain 2Gln 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 Met 20 25
30 His Trp Tyr Gln Gln Lys Pro Gly Ser Ser Pro Lys Pro Trp Ile Tyr
35 40 45 Ala Pro Ser Asn Leu Ala Ser Gly Val Pro Ala 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
Ser Phe Asn Pro Pro Thr 85 90 95 Phe Gly Ala Gly Thr Lys Leu Glu
Leu 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 210 3447PRTArtificial
Sequencesynthetic polypeptide--Rituximab Heavy chain 3Gln Ala Tyr
Leu Gln Gln Ser Gly Ala Glu Leu Val Arg 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 Arg Gln 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 Val 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 Phe Cys 85 90 95 Ala Arg Val Val Tyr Tyr Ser Asn
Ser Tyr Trp Tyr Phe Asp Val Trp 100 105 110 Gly Thr Gly Thr Thr Val
Thr Val Ser Gly Pro Ser Val Phe Pro Leu 115 120 125 Ala Pro Ser Ser
Lys Ser Thr Ser Gly Gly Thr Ala Ala Leu Gly Cys 130 135 140 Leu Val
Lys Asp Tyr Phe Pro Glu Pro Val Thr Val Ser Trp Asn Ser 145 150 155
160 Gly Ala Leu Thr Ser Gly Val His Thr Phe Pro Ala Val Leu Gln Ser
165 170 175 Ser Gly Leu Tyr Ser Leu Ser Ser Val Val Thr Val Pro Ser
Ser Ser 180 185 190 Leu Gly Thr Gln Thr Tyr Ile Cys Asn Val Asn His
Lys Pro Ser Asn 195 200 205 Thr Lys Val Asp Lys Lys Ala Glu Pro Lys
Ser Cys Asp Lys Thr His 210 215 220 Thr Cys Pro Pro Cys Pro Ala Pro
Glu Leu Leu Gly Gly Pro Ser Val 225 230 235 240 Phe Leu Phe Pro Pro
Lys Pro Lys Asp Thr Leu Met Ile Ser Arg Thr 245 250 255 Pro Glu Val
Thr Cys Val Val Val Asp Val Ser His Glu Asp Pro Glu 260 265 270 Val
Lys Phe Asn Trp Tyr Val Asp Gly Val Glu Val His Asn Ala Lys 275 280
285 Thr Lys Pro Arg Glu Glu Gln Tyr Asn Ser Thr Tyr Arg Val Val Ser
290 295 300 Val Leu Thr Val Leu His Gln Asp Trp Leu Asn Gly Lys Glu
Tyr Lys 305 310 315 320 Cys Lys Val Ser Asn Lys Ala Leu Pro Ala Pro
Ile Glu Lys Thr Ile 325 330 335 Ser Lys Ala Lys Gly Gln Pro Arg Glu
Pro Gln Val Tyr Thr Leu Pro 340 345 350 Pro Ser Arg Asp Glu Leu Thr
Lys Asn Gln Val Ser Leu Thr Cys Leu 355 360 365 Val Lys Gly Phe Tyr
Pro Ser Asp Ile Ala Val Glu Trp Glu Ser Asn 370 375 380 Gly Gln Pro
Glu Asn Asn Tyr Lys Thr Thr Pro Pro Val Leu Asp Ser 385 390 395 400
Asp Gly Ser Phe Phe Leu Tyr Ser Lys Leu Thr Val Asp Lys Ser Arg 405
410 415 Trp Gln Gln Gly Asn Val Phe Ser Cys Ser Val Met His Glu Ala
Leu 420 425 430 His Asn His Tyr Thr Gln Lys Ser Leu Ser Leu Ser Pro
Gly Lys 435 440 445 4211PRTArtificial Sequencesynthetic
polypeptide--Remicade Mouse-human chimeric chain 1 4Ser Ile Val Met
Thr Gln Thr Pro Lys Phe Leu Leu Val Ser Ala Gly 1 5 10 15 Asp Arg
Val Thr Ile Thr Cys Thr Ala Ser Gln Ser Val Ser Asn Asp 20 25 30
Val Val Trp Tyr Gln Gln Lys Pro Gly Gln Ser Pro Lys Met Leu Met 35
40 45 Tyr Ser Ala Phe Asn Arg Tyr Thr Gly Val Pro Asp Arg Phe Thr
Gly 50 55 60 Arg Gly Tyr Gly Thr Asp Phe Thr Phe Thr Ile Ser Ser
Val Gln Ala 65 70 75 80 Glu Asp Leu Ala Val Tyr Phe Cys Gln Gln Asp
Tyr Asn Ser Pro Arg 85 90 95 Thr Phe Gly Gly Gly Thr Lys Leu Glu
Ile Lys Arg Thr Val Ala Ala 100 105 110 Pro Ser Val Phe Ile Phe Pro
Pro Ser Asp Glu Gln Leu Lys Ser Gly 115 120 125 Thr Ala Ser Val Val
Cys Leu Leu Asn Asn Phe Tyr Pro Arg Glu Ala 130 135 140 Lys Val Gln
Trp Lys Val Asp Asn Ala Leu Gln Ser Gly Asn Ser Gln 145 150 155 160
Glu Ser Val Thr Glu Gln Asp Ser Lys Asp Ser Thr Tyr Ser Leu Ser 165
170 175 Ser Thr Leu Thr Leu Ser Lys Ala Asp Tyr Glu Lys His Lys Val
Tyr 180 185 190 Ala Cys Glu Val Thr His Gln Gly Leu Ser Ser Pro Val
Thr Lys Ser 195 200 205 Phe Asn Arg 210 5443PRTArtificial
Sequencesynthetic polypeptide--Remicade mouse-human chimeric chain
1 5Gln Ile Gln Leu Val Gln Ser Gly Pro Glu Leu Lys Lys Pro Gly Glu
1 5 10 15 Thr Val Lys Ile Ser Cys Lys Ala Ser Gly Tyr Thr Phe Thr
His Tyr 20 25 30 Gly Met Asn Trp Val Lys Gln Ala Pro Gly Lys Gly
Leu Lys Trp Met 35 40 45 Gly Trp Ile Asn Thr Tyr Thr Gly Glu Pro
Thr Tyr Ala Asp Asp Phe 50 55 60 Lys Glu His Phe Ala Phe Ser Leu
Glu Thr Ser Ala Ser Thr Val Phe 65 70 75 80 Leu Gln Ile Asn Asn Leu
Lys Asn Glu Asp Thr Ala Thr Tyr Phe Cys 85 90 95 Ala Arg Glu Arg
Gly Asp Ala Met Asp Tyr Trp Gly Gln Gly Thr Ser 100 105 110 Val Thr
Val Ser Ser Gly Pro Ser Val Phe Pro Leu Ala Pro Ser Ser 115 120 125
Lys Ser Thr Ser Gly Gly Thr Ala Ala Leu Gly Cys Leu Val Lys Asp 130
135 140 Tyr Phe Pro Glu Pro Val Thr Val Ser Trp Asn Ser Gly Ala Leu
Thr 145 150 155 160 Ser Gly Val His Thr Phe Pro Ala Val Leu Gln Ser
Ser Gly Leu Tyr 165 170 175 Ser Leu Ser Ser Val Val Thr Val Pro Ser
Ser Ser Leu Gly Thr Gln 180 185 190 Thr Tyr Ile Cys Asn Val Asn His
Lys Pro Ser Asn Thr Lys Val Asp 195 200 205 Lys Lys Ala Glu Pro Lys
Ser Cys Asp Lys Thr His Thr Cys Pro Pro 210 215 220 Cys Pro Ala Pro
Glu Leu Leu Gly Gly Pro Ser Val Phe Leu Phe Pro 225 230 235 240 Pro
Lys Pro Lys Asp Thr Leu Met Ile Ser Arg Thr Pro Glu Val Thr 245 250
255 Cys Val Val Val Asp Val Ser His Glu Asp Pro Glu Val Lys Phe Asn
260 265 270 Trp Tyr Val Asp Gly Val Glu Val His Asn Ala Lys Thr Lys
Pro Arg 275 280 285 Glu Glu Gln Tyr Asn Ser Thr Tyr Arg Val Val Ser
Val Leu Thr Val 290 295 300 Leu His Gln Asp Trp Leu Asn Gly Lys Glu
Tyr Lys Cys Lys Val Ser 305 310 315 320 Asn Lys Ala Leu Pro Ala Pro
Ile Glu Lys Thr Ile Ser Lys Ala Lys 325 330 335 Gly Gln Pro Arg Glu
Pro Gln Val Tyr Thr Leu Pro Pro Ser Arg Asp 340 345 350 Glu Leu Thr
Lys Asn Gln Val Ser Leu Thr Cys Leu Val Lys Gly Phe 355 360 365 Tyr
Pro Ser Asp Ile Ala Val Glu Trp Glu Ser Asn Gly Gln Pro Glu 370 375
380 Asn Asn Tyr Lys Thr Thr Pro Pro Val Leu Asp Ser Asp Gly Ser Phe
385 390 395 400 Phe Leu Tyr Ser Lys Leu Thr Val Asp Lys Ser Arg Trp
Gln Gln Gly 405 410 415 Asn Val Phe Ser Cys Ser Val Met His Glu Ala
Leu His Asn His Tyr 420 425 430 Thr Gln Lys Ser Leu Ser Leu Ser Pro
Gly Lys 435 440 6213PRTArtificial Sequencesynthetic
polypeptide--Erbitux light chain 1 6Asp Ile Leu Leu Thr Gln Ser Pro
Val Ile Leu Ser Val Ser Pro Gly 1 5 10 15 Glu Arg Val Ser Phe Ser
Cys Arg Ala Ser Gln Ser Ile Gly Thr Asn 20 25 30 Ile His Trp Tyr
Gln Gln Arg Thr Asn Gly Ser Pro Arg Leu Leu Ile 35 40 45 Lys Tyr
Ala Ser Glu Ser Ile Ser Gly Ile Pro Ser Arg Phe Ser Gly 50 55 60
Ser Gly Ser Gly Thr Asp Phe Thr Leu Ser Ile Asn Ser Val Glu Ser 65
70 75 80 Glu Asp Ile Ala Asp Tyr Tyr Cys Gln Gln Asn Asn Asn Trp
Pro Thr 85 90 95 Thr Phe Gly Ala Gly Thr Lys Leu Glu Leu Lys Arg
Thr Val Ala Ala 100 105 110 Pro Ser Val Phe Ile Phe Pro Pro Ser Asp
Glu Gln Leu Lys Ser Gly 115 120 125 Thr Ala Ser Val Val Cys Leu Leu
Asn Asn Phe Tyr Pro Arg Glu Ala 130 135 140 Lys Val Gln Trp Lys Val
Asp Asn Ala Leu Gln Ser Gly Asn Ser Gln 145 150 155 160 Glu Ser Val
Thr Glu Gln Asp Ser Lys Asp Ser Thr Tyr Ser Leu Ser 165 170 175 Ser
Thr Leu Thr Leu Ser Lys Ala Asp Tyr Glu Lys His Lys Val Tyr 180 185
190 Ala Cys Glu Val Thr His Gln Gly Leu Ser Ser Pro Val Thr Lys Ser
195 200 205 Phe Asn Arg Gly Ala 210 7452PRTArtificial
Sequencesynthetic polypeptide--Erbitux heavy chain 1 7Gln Val Gln
Leu Lys Gln Ser Gly Pro Gly Leu Val Gln Pro Ser Gln 1 5 10 15 Ser
Leu Ser Ile Thr Cys Thr Val Ser Gly Phe Ser Leu Thr Asn Tyr 20 25
30 Gly Val His Trp Val Arg Gln Ser Pro Gly Lys Gly Leu Glu Trp Leu
35 40 45 Gly Val Ile Trp Ser Gly Gly Asn Thr Asp Tyr Asn Thr Pro
Phe Thr 50 55 60 Ser Arg Leu Ser Ile Asn Lys Asp Asn Ser Lys Ser
Gln Val Phe Phe 65 70 75 80 Lys Met Asn Ser Leu Gln Ser Asn Asp Thr
Ala Ile Tyr Tyr Cys Ala 85 90 95 Arg Ala Leu Thr Tyr Tyr Asp Tyr
Glu Phe Ala Tyr Trp Gly Gln Gly 100 105 110 Thr Leu Val Thr Val Ser
Ala Ala Ser Thr Lys Gly Pro Ser Val Phe 115 120 125 Pro Leu Ala Pro
Ser Ser Lys Ser Thr Ser Gly Gly Thr Ala Ala Leu 130 135 140 Gly Cys
Leu Val Lys Asp Tyr Phe Pro Glu Pro Val Thr Val Ser Trp 145 150 155
160 Asn Ser Gly Ala Leu Thr Ser Gly Val His Thr Phe Pro Ala Val Leu
165 170 175 Gln Ser Ser Gly Leu Tyr Ser Leu Ser Ser Val Val Thr Val
Pro Ser 180 185 190 Ser Ser Leu Gly Thr Gln Thr Tyr Ile Cys Asn Val
Asn His Lys Pro 195 200 205 Ser Asn Thr Lys Val Asp Lys Arg Val Glu
Pro Lys Ser Pro Lys Ser 210 215 220 Cys Asp Lys Thr His Thr Cys Pro
Pro Cys Pro Ala Pro Glu Leu Leu 225 230 235 240 Gly Gly Pro Ser Val
Phe Leu Phe Pro Pro Lys Pro Lys Asp Thr Leu 245 250 255 Met Ile Ser
Arg Thr Pro Glu Val Thr Cys Val Val Val Asp Val Ser 260 265 270 His
Glu Asp Pro Glu Val Lys Phe Asn Trp Tyr Val Asp Gly Val Glu 275 280
285 Val His Asn Ala Lys Thr Lys Pro Arg Glu Glu Gln Tyr Asn Ser Thr
290 295 300 Tyr Arg Val Val Ser Val Leu Thr Val Leu His Gln Asp Trp
Leu Asn 305 310 315 320 Gly Lys Glu Tyr Lys Cys Lys Val Ser Asn Lys
Ala Leu Pro Ala Pro 325 330 335 Ile Glu Lys Thr Ile Ser Lys Ala Lys
Gly Gln Pro Arg Glu Pro Gln 340 345 350 Val Tyr Thr Leu Pro Pro Ser
Arg Asp Glu Leu Thr Lys Asn Gln Val 355 360 365 Ser Leu Thr Cys Leu
Val Lys Gly Phe Tyr Pro Ser Asp Ile Ala Val 370 375 380 Glu Trp Glu
Ser Asn Gly Gln Pro Glu Asn Asn Tyr Lys Thr Thr Pro 385 390 395 400
Pro Val Leu Asp Ser Asp Gly Ser Phe Phe Leu Tyr Ser Lys Leu Thr 405
410 415 Val Asp Lys Ser Arg Trp Gln Gln Gly Asn Val Phe Ser Cys Ser
Val 420 425 430 Met His Glu Ala Leu His Asn His Tyr Thr Gln Lys Ser
Leu Ser Leu 435 440 445 Ser Pro Gly Lys 450 8214PRTArtificial
Sequencesynthetic polypeptide--Herceptin light chain 1 8Asp Ile Gln
Met Thr Gln Ser Pro Ser Ser Leu Ser Ala Ser Val Gly 1 5 10 15 Asp
Arg Val Thr Ile Thr Cys Arg Ala Ser Gln Asp Val Asn Thr Ala 20
25 30 Val Ala Trp Tyr Gln Gln Lys Pro Gly Lys Ala Pro Lys Leu Leu
Ile 35 40 45 Tyr Ser Ala Ser Phe Leu Tyr Ser Gly Val Pro Ser Arg
Phe Ser Gly 50 55 60 Ser Arg Ser Gly Thr Asp Phe Thr Leu Thr Ile
Ser Ser Leu Gln Pro 65 70 75 80 Glu Asp Phe Ala Thr Tyr Tyr Cys Gln
Gln His Tyr Thr Thr Pro Pro 85 90 95 Thr Phe Gly Gln Gly Thr Lys
Val Glu Ile Lys Arg Thr Val Ala Ala 100 105 110 Pro Ser Val Phe Ile
Phe Pro Pro Ser Asp Glu Gln Leu Lys Ser Gly 115 120 125 Thr Ala Ser
Val Val Cys Leu Leu Asn Asn Phe Tyr Pro Arg Glu Ala 130 135 140 Lys
Val Gln Trp Lys Val Asp Asn Ala Leu Gln Ser Gly Asn Ser Gln 145 150
155 160 Glu Ser Val Thr Glu Gln Asp Ser Lys Asp Ser Thr Tyr Ser Leu
Ser 165 170 175 Ser Thr Leu Thr Leu Ser Lys Ala Asp Tyr Glu Lys His
Lys Val Tyr 180 185 190 Ala Cys Glu Val Thr His Gln Gly Leu Ser Ser
Pro Val Thr Lys Ser 195 200 205 Phe Asn Arg Gly Glu Cys 210
9451PRTArtificial Sequencesynthetic polypeptide--Herceptin heavy
chain 1 9Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro
Gly Gly 1 5 10 15 Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Phe Asn
Ile Lys Asp Thr 20 25 30 Tyr Ile His Trp Val Arg Gln Ala Pro Gly
Lys Gly Leu Glu Trp Val 35 40 45 Ala Arg Ile Tyr Pro Thr Asn Gly
Tyr Thr Arg Tyr Ala Asp Ser Val 50 55 60 Lys Gly Arg Phe Thr Ile
Ser Ala Asp Thr Ser Lys Asn Thr Ala Tyr 65 70 75 80 Leu Gln Met Asn
Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys 85 90 95 Ser Arg
Trp Gly Gly Asp Gly Phe Tyr Ala Met Asp Tyr Trp Gly Gln 100 105 110
Gly Thr Leu Val Thr Val Ser Ser Ala Ser Thr Lys Gly Pro Ser Val 115
120 125 Phe Pro Leu Ala Pro Ser Ser Lys Ser Thr Ser Gly Gly Thr Ala
Ala 130 135 140 Leu Gly Cys Leu Val Lys Asp Tyr Phe Pro Glu Pro Val
Thr Val Ser 145 150 155 160 Trp Asn Ser Gly Ala Leu Thr Ser Gly Val
His Thr Phe Pro Ala Val 165 170 175 Leu Gln Ser Ser Gly Leu Tyr Ser
Leu Ser Ser Val Val Thr Val Pro 180 185 190 Ser Ser Ser Leu Gly Thr
Gln Thr Tyr Ile Cys Asn Val Asn His Lys 195 200 205 Pro Ser Asn Thr
Lys Val Asp Lys Lys Val Glu Pro 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
10211PRTArtificial Sequencesynthetic polypeptide--Campath light
chain 10Asp Ile Gln Met Thr Gln Ser Pro Ser Ser Leu Ser Ala Ser Val
Gly 1 5 10 15 Asp Arg Val Thr Ile Thr Cys Lys Ala Ser Gln Asn Ile
Asp Lys Tyr 20 25 30 Leu Asn Trp Tyr Gln Gln Lys Pro Gly Lys Ala
Pro Lys Leu Leu Ile 35 40 45 Tyr Asn Thr Asn Asn Leu Gln Thr Gly
Val Pro Ser Arg Phe Ser Gly 50 55 60 Ser Gly Ser Gly Thr Asp Phe
Thr Phe Thr Ile Ser Ser Leu Gln Pro 65 70 75 80 Glu Asp Ile Ala Thr
Tyr Tyr Cys Leu Gln His Ile Ser Arg Pro Arg 85 90 95 Thr Phe Gly
Gln Gly Thr Lys Val Glu Ile Lys Arg Thr Val Ala Ala 100 105 110 Pro
Ser Val Phe Ile Phe Pro Pro Ser Asp Glu Gln Leu Lys Ser Gly 115 120
125 Thr Ala Ser Val Val Cys Leu Leu Asn Asn Phe Tyr Pro Arg Glu Ala
130 135 140 Lys Val Gln Trp Lys Val Asp Asn Ala Leu Gln Ser Gly Asn
Ser Gln 145 150 155 160 Glu Ser Val Thr Glu Gln Asp Ser Lys Asp Ser
Thr Tyr Ser Leu Ser 165 170 175 Ser Thr Leu Thr Leu Ser Lys Ala Asp
Tyr Glu Lys His Lys Val Tyr 180 185 190 Ala Cys Glu Val Thr His Gln
Gly Leu Ser Ser Pro Val Thr Lys Ser 195 200 205 Phe Asn Arg 210
11451PRTArtificial Sequencesynthetic polypeptide--Campath heavy
chain 11Gln Val Gln Leu Gln Glu Ser Gly Pro Gly Leu Val Arg Pro Ser
Gln 1 5 10 15 Thr Leu Ser Leu Thr Cys Thr Val Ser Gly Phe Thr Phe
Thr Asp Phe 20 25 30 Tyr Met Asn Trp Val Arg Gln Pro Pro Gly Arg
Gly Leu Glu Trp Ile 35 40 45 Gly Phe Ile Arg Asp Lys Ala Lys Gly
Tyr Thr Thr Glu Tyr Asn Pro 50 55 60 Ser Val Lys Gly Arg Val Thr
Met Leu Val Asp Thr Ser Lys Asn Gln 65 70 75 80 Phe Ser Leu Arg Leu
Ser Ser Val Thr Ala Ala Asp Thr Ala Val Tyr 85 90 95 Tyr Cys Ala
Arg Glu Gly His Thr Ala Ala Pro Phe Asp Tyr Trp Gly 100 105 110 Gln
Gly Ser Leu Val Thr Val Ser Ser 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 Val 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
12216PRTArtificial Sequencesynthetic polypeptide--Remicade Fc
Region 12Pro Glu Leu Leu Gly Gly Pro Ser Val Phe Leu Phe Pro Pro
Lys Pro 1 5 10 15 Lys Asp Thr Leu Met Ile Ser Arg Thr Pro Glu Val
Thr Cys Val Val 20 25 30 Val Asp Val Ser His Glu Asp Pro Glu Val
Lys Phe Asn Trp Tyr Val 35 40 45 Asp Gly Val Glu Val His Asn Ala
Lys Thr Lys Pro Arg Glu Glu Gln 50 55 60 Tyr Asn Ser Thr Tyr Arg
Val Val Ser Val Leu Thr Val Leu His Gln 65 70 75 80 Asp Trp Leu Asn
Gly Lys Glu Tyr Lys Cys Lys Val Ser Asn Lys Ala 85 90 95 Leu Pro
Ala Pro Ile Glu Lys Thr Ile Ser Lys Ala Lys Gly Gln Pro 100 105 110
Arg Glu Pro Gln Val Tyr Thr Leu Pro Pro Ser Arg Asp Glu Leu Thr 115
120 125 Lys Asn Gln Val Ser Leu Thr Cys Leu Val Lys Gly Phe Tyr Pro
Ser 130 135 140 Asp Ile Ala Val Glu Trp Glu Ser Asn Gly Gln Pro Glu
Asn Asn Tyr 145 150 155 160 Lys Thr Thr Pro Pro Val Leu Asp Ser Asp
Gly Ser Phe Phe Leu Tyr 165 170 175 Ser Lys Leu Thr Val Asp Lys Ser
Arg Trp Gln Gln Gly Asn Val Phe 180 185 190 Ser Cys Ser Val Met His
Glu Ala Leu His Asn His Tyr Thr Gln Lys 195 200 205 Ser Leu Ser Leu
Ser Pro Gly Lys 210 215 13216PRTArtificial Sequencesynthetic
polypeptide--Erbitux Fc Region 13Pro Glu Leu Leu Gly Gly Pro Ser
Val Phe Leu Phe Pro Pro Lys Pro 1 5 10 15 Lys Asp Thr Leu Met Ile
Ser Arg Thr Pro Glu Val Thr Cys Val Val 20 25 30 Val Asp Val Ser
His Glu Asp Pro Glu Val Lys Phe Asn Trp Tyr Val 35 40 45 Asp Gly
Val Glu Val His Asn Ala Lys Thr Lys Pro Arg Glu Glu Gln 50 55 60
Tyr Asn Ser Thr Tyr Arg Val Val Ser Val Leu Thr Val Leu His Gln 65
70 75 80 Asp Trp Leu Asn Gly Lys Glu Tyr Lys Cys Lys Val Ser Asn
Lys Ala 85 90 95 Leu Pro Ala Pro Ile Glu Lys Thr Ile Ser Lys Ala
Lys Gly Gln Pro 100 105 110 Arg Glu Pro Gln Val Tyr Thr Leu Pro Pro
Ser Arg Asp Glu Leu Thr 115 120 125 Lys Asn Gln Val Ser Leu Thr Cys
Leu Val Lys Gly Phe Tyr Pro Ser 130 135 140 Asp Ile Ala Val Glu Trp
Glu Ser Asn Gly Gln Pro Glu Asn Asn Tyr 145 150 155 160 Lys Thr Thr
Pro Pro Val Leu Asp Ser Asp Gly Ser Phe Phe Leu Tyr 165 170 175 Ser
Lys Leu Thr Val Asp Lys Ser Arg Trp Gln Gln Gly Asn Val Phe 180 185
190 Ser Cys Ser Val Met His Glu Ala Leu His Asn His Tyr Thr Gln Lys
195 200 205 Ser Leu Ser Leu Ser Pro Gly Lys 210 215
14216PRTArtificial Sequencesynthetic polypeptide--Campath Fc Region
14Pro Glu Leu Leu Gly Gly Pro Ser Val Phe Leu Phe Pro Pro Lys Pro 1
5 10 15 Lys Asp Thr Leu Met Ile Ser Arg Thr Pro Glu Val Thr Cys Val
Val 20 25 30 Val Asp Val Ser His Glu Asp Pro Glu Val Lys Phe Asn
Trp Tyr Val 35 40 45 Asp Gly Val Glu Val His Asn Ala Lys Thr Lys
Pro Arg Glu Glu Gln 50 55 60 Tyr Asn Ser Thr Tyr Arg Val Val Ser
Val Leu Thr Val Leu His Gln 65 70 75 80 Asp Trp Leu Asn Gly Lys Glu
Tyr Lys Cys Lys Val Ser Asn Lys Ala 85 90 95 Leu Pro Ala Pro Ile
Glu Lys Thr Ile Ser Lys Ala Lys Gly Gln Pro 100 105 110 Arg Glu Pro
Gln Val Tyr Thr Leu Pro Pro Ser Arg Asp Glu Leu Thr 115 120 125 Lys
Asn Gln Val Ser Leu Thr Cys Leu Val Lys Gly Phe Tyr Pro Ser 130 135
140 Asp Ile Ala Val Glu Trp Glu Ser Asn Gly Gln Pro Glu Asn Asn Tyr
145 150 155 160 Lys Thr Thr Pro Pro Val Leu Asp Ser Asp Gly Ser Phe
Phe Leu Tyr 165 170 175 Ser Lys Leu Thr Val Asp Lys Ser Arg Trp Gln
Gln Gly Asn Val Phe 180 185 190 Ser Cys Ser Val Met His Glu Ala Leu
His Asn His Tyr Thr Gln Lys 195 200 205 Ser Leu Ser Leu Ser Pro Gly
Lys 210 215 15216PRTArtificial Sequencesynthetic
polypeptide--Herceptin Fc Region 15Pro Glu Leu Leu Gly Gly Pro Ser
Val Phe Leu Phe Pro Pro Lys Pro 1 5 10 15 Lys Asp Thr Leu Met Ile
Ser Arg Thr Pro Glu Val Thr Cys Val Val 20 25 30 Val Asp Val Ser
His Glu Asp Pro Glu Val Lys Phe Asn Trp Tyr Val 35 40 45 Asp Gly
Val Glu Val His Asn Ala Lys Thr Lys Pro Arg Glu Glu Gln 50 55 60
Tyr Asn Ser Thr Tyr Arg Val Val Ser Val Leu Thr Val Leu His Gln 65
70 75 80 Asp Trp Leu Asn Gly Lys Glu Tyr Lys Cys Lys Val Ser Asn
Lys Ala 85 90 95 Leu Pro Ala Pro Ile Glu Lys Thr Ile Ser Lys Ala
Lys Gly Gln Pro 100 105 110 Arg Glu Pro Gln Val Tyr Thr Leu Pro Pro
Ser Arg Asp Glu Leu Thr 115 120 125 Lys Asn Gln Val Ser Leu Thr Cys
Leu Val Lys Gly Phe Tyr Pro Ser 130 135 140 Asp Ile Ala Val Glu Trp
Glu Ser Asn Gly Gln Pro Glu Asn Asn Tyr 145 150 155 160 Lys Thr Thr
Pro Pro Val Leu Asp Ser Asp Gly Ser Phe Phe Leu Tyr 165 170 175 Ser
Lys Leu Thr Val Asp Lys Ser Arg Trp Gln Gln Gly Asn Val Phe 180 185
190 Ser Cys Ser Val Met His Glu Ala Leu His Asn His Tyr Thr Gln Lys
195 200 205 Ser Leu Ser Leu Ser Pro Gly Lys 210 215
1610PRTArtificial Sequencesynthetic peptide--Rituximab CDR1
Variable Light Chain (VL) 16Arg Ala Ser Ser Ser Val Ser Tyr Met His
1 5 10 1710PRTArtificial Sequencesynthetic peptide--Rituximab CDR1
Variable Heavy Chain (VH) 17Gly Tyr Thr Phe Thr Ser Tyr Asn Met His
1 5 10 187PRTArtificial Sequencesynthetic peptide--Rituximab CDR2
Variable Light Chain (VL) 18Ala Pro Ser Asn Leu Ala Ser 1 5
199PRTArtificial Sequencesynthetic peptide--Rituximab CDR3
Variable
Light Chain (VL) 19Gln Gln Trp Ser Phe Asn Pro Pro Thr 1 5
2013PRTArtificial Sequencesynthetic peptide--Rituximab CDR3
Variable Heavy Chain (VH) 20Val Val Tyr Tyr Ser Asn Ser Tyr Trp Tyr
Phe Asp Val 1 5 10 2110PRTArtificial Sequencesynthetic
peptide--Rituximab CDR1 Variable Light Chain (VL) 21Arg Ala Ser Ser
Ser Val Ser Tyr Met His 1 5 10 229PRTArtificial Sequencesynthetic
peptide--Rituximab CDR3 Variable Heavy Chain (VH) 22Gln Gln Trp Ser
Phe Asn Pro Pro Thr 1 5 2313PRTArtificial Sequencesynthetic
peptide--Rituximab CDR3 Variable Heavy Chain (VH) 23Val Val Tyr Tyr
Ser Asn Ser Tyr Trp Tyr Phe Asp Val 1 5 10 2486PRTHomo
sapiensmisc_featureHinge Region of IgG3 24Val Asp Leu Lys Thr Pro
Leu Gly Asp Thr Thr His Thr Cys Pro Arg 1 5 10 15 Cys Pro Glu Pro
Lys Ser Cys Asp Thr Pro Pro Pro Cys Pro Arg Cys 20 25 30 Pro Glu
Pro Lys Ser Cys Asp Thr Pro Pro Pro Cys Pro Arg Cys Pro 35 40 45
Glu Pro Lys Ser Cys Thr Pro Pro Pro Cys Pro Arg Cys Pro Ala Pro 50
55 60 Glu Leu Leu Gly Gly Pro Ser Val Phe Leu Phe Pro Pro Lys Pro
Lys 65 70 75 80 Asp Thr Leu Met Ile Ser 85 2540PRTHomo
sapiensmisc_featureHinge region of IgG1 25Val Glu Pro Lys Ser Cys
Asp Lys Thr His Thr Cys Pro Pro Cys Pro 1 5 10 15 Ala Pro Glu Leu
Leu Gly Gly Pro Ser Val Phe Leu Phe Pro Pro Lys 20 25 30 Pro Lys
Asp Thr Leu Met Ile Ser 35 40 2688PRTHomo sapiensmisc_featureFc
RIIIa 26Val His Ile Gly Trp Leu Leu Leu Gln Ala Pro Arg Trp Val Phe
Lys 1 5 10 15 Glu Glu Asp Pro Ile His Leu Arg Cys His Ser Trp Lys
Asn Thr Ala 20 25 30 Leu His Lys Val Thr Tyr Leu Gln Asn Gly Lys
Asp Arg Lys Tyr Phe 35 40 45 His His Asn Ser Asp Phe His Ile Pro
Lys Ala Thr Leu Lys Asp Ser 50 55 60 Gly Ser Tyr Phe Cys Arg Gly
Leu Val Gly Ser Lys Asn Val Ser Ser 65 70 75 80 Glu Thr Val Asn Ile
Thr Ile Thr 85 2788PRTHomo sapiensmisc_featureFc RIIa 27Val Leu Ser
Glu Trp Leu Val Leu Gln Thr Pro His Leu Glu Phe Gln 1 5 10 15 Glu
Gly Glu Thr Ile Met Leu Arg Cys His Ser Trp Lys Asp Lys Pro 20 25
30 Leu Val Lys Val Thr Phe Phe Gln Asn Gly Lys Ser Gln Lys Phe Ser
35 40 45 Arg Leu Asp Pro Thr Phe Ser Ile Pro Gln Ala Asn His Ser
His Ser 50 55 60 Gly Asp Tyr His Cys Thr Gly Asn Ile Gly Tyr Thr
Leu Phe Ser Ser 65 70 75 80 Lys Pro Val Thr Ile Thr Val Gln 85
28107PRTHomo sapiensmisc_feature12b-1 28Cys Pro Ala Pro Glu Leu Leu
Gly Gly Pro Ser Val Phe Leu Phe Pro 1 5 10 15 Pro Lys Pro Lys Asp
Thr Leu Met Ile Ser Arg Thr Pro Glu Val Thr 20 25 30 Cys Val Val
Val Asp Val Ser His Glu Asp Pro Gln Val Lys Phe Asn 35 40 45 Trp
Tyr Val Asp Gly Val Gln Val His Asn Ala Lys Thr Lys Pro Arg 50 55
60 Glu Gln Gln Tyr Asn Ser Thr Tyr Arg Val Val Ser Val Leu Thr Val
65 70 75 80 Leu His Gln Asn Trp Leu Asp Gly Lys Glu Tyr Lys Cys Lys
Val Ser 85 90 95 Asn Lys Ala Leu Pro Ala Pro Ile Glu Lys Thr 100
105 29109PRTHomo sapiensmisc_feature12b-2 29Ile Ser Lys Ala Lys Gly
Gln Pro Arg Glu Pro Gln Val Tyr Thr Leu 1 5 10 15 Pro Pro Ser Arg
Glu Glu Met Thr Lys Asn Gln Val Ser Leu Thr Cys 20 25 30 Leu Val
Lys Gly Phe Tyr Pro Ser Asp Ile Ala Val Glu Trp Glu Ser 35 40 45
Asn Gly Gln Pro Glu Asn Asn Tyr Lys Thr Thr Pro Pro Val Leu Asp 50
55 60 Ser Asp Gly Ser Phe Phe Leu Tyr Ser Lys Leu Thr Val Asp Lys
Ser 65 70 75 80 Arg Trp Gln Gln Gly Asn Val Phe Ser Cys Ser Val Met
His Glu Ala 85 90 95 Leu His Asn His Tyr Thr Gln Lys Ser Leu Ser
Leu Ser 100 105 3017PRTHomo sapiensmisc_featureFc lower hinge
region 30Cys Pro Ala Pro Glu Leu Leu Gly Gly Pro Ser Val Phe Leu
Phe Pro 1 5 10 15 Pro 3122PRTHomo sapiensmisc_featureFc BC Loop
Region 31Glu Val Thr Cys Val Val Val Asp Val Ser His Glu Asp Pro
Gln Val 1 5 10 15 Lys Phe Asn Trp Tyr Val 20 3218PRTHomo
sapiensmisc_featureFc CE Loop Region 32Pro Arg Glu Gln Gln Tyr Asn
Ser Thr Tyr Arg Val Val Ser Val Leu 1 5 10 15 Thr Val 3324PRTHomo
sapiensMISC_FEATUREFc FG loop Region 33Lys Glu Tyr Lys Cys Lys Val
Ser Asn Lys Ala Leu Pro Ala Pro Ile 1 5 10 15 Glu Lys Thr Ile Ser
Lys Ala Lys 20 34216PRTHomo sapiensmisc_featurehIgG1 from residues
229-444 (Figure 12B) 34Cys Pro Ala Pro Glu Leu Leu Gly Gly Pro Ser
Val Phe Leu Phe Pro 1 5 10 15 Pro Lys Pro Lys Asp Thr Leu Met Ile
Ser Arg Thr Pro Glu Val Thr 20 25 30 Cys Val Val Val Asp Val Ser
His Glu Asp Pro Gln Val Lys Phe Asn 35 40 45 Trp Tyr Val Asp Gly
Val Gln Val His Asn Ala Lys Thr Lys Pro Arg 50 55 60 Glu Gln Gln
Tyr Asn Ser Thr Tyr Arg Val Val Ser Val Leu Thr Val 65 70 75 80 Leu
His Gln Asn Trp Leu Asp Gly Lys Glu Tyr Lys Cys Lys Val Ser 85 90
95 Asn Lys Ala Leu Pro Ala Pro Ile Glu Lys Thr Ile Ser Lys Ala Lys
100 105 110 Gly Gln Pro Arg Glu Pro Gln Val Tyr Thr Leu Pro Pro Ser
Arg Glu 115 120 125 Glu Met Thr Lys Asn Gln Val Ser Leu Thr Cys Leu
Val Lys Gly Phe 130 135 140 Tyr Pro Ser Asp Ile Ala Val Glu Trp Glu
Ser Asn Gly Gln Pro Glu 145 150 155 160 Asn Asn Tyr Lys Thr Thr Pro
Pro Val Leu Asp Ser Asp Gly Ser Phe 165 170 175 Phe Leu Tyr Ser Lys
Leu Thr Val Asp Lys Ser Arg Trp Gln Gln Gly 180 185 190 Asn Val Phe
Ser Cys Ser Val Met His Glu Ala Leu His Asn His Tyr 195 200 205 Thr
Gln Lys Ser Leu Ser Leu Ser 210 215 3517PRTHomo
sapiensmisc_featureCDR2 VH 35Ala Ile Tyr Pro Gly Asn Gly Asp Thr
Ser Tyr Asn Gln Lys Phe Lys 1 5 10 15 Gly 3610PRTArtificial
sequencesynthetic peptide--FcGammaR1 B/C loop 36Trp Lys Asp Lys Leu
Val Tyr Asn Val Leu 1 5 10 377PRTArtificial sequencesynthetic
peptide--FcGammaR1 C/E loop 37Ala Phe Lys Phe Phe His Trp 1 5
384PRTArtificial sequencesynthetic peptide--FcGammaR1 F/G loop
38Met Gly Lys His 1 3910PRTArtificial sequencesynthetic
peptide--FcGammaRIIa-HR B/C loop 39Trp Lys Asp Lys Pro Leu Val Lys
Val Thr 1 5 10 407PRTArtificial sequencesynthetic
peptide--FcGammaRIIa-HR C/E loop 40Ser Gln Lys Phe Ser Arg Leu 1 5
414PRTArtificial sequencesynthetic peptide--FcGammaRIIa-HR F/G loop
41Ile Gly Tyr Thr 1 4210PRTArtificial sequencesynthetic
peptide--FcGammaRIIa-LR B/C loop 42Trp Lys Asp Lys Pro Leu Val Lys
Val Thr 1 5 10 437PRTArtificial sequencesynthetic
peptide--FcGammaRIIa-LR C/E loop 43Ser Gln Lys Phe Ser His Leu 1 5
444PRTArtificial sequencesynthetic peptide--FcGammaRIIa-LR F/G loop
44Ile Gly Tyr Thr 1 4510PRTArtificial sequencesynthetic
peptide--FcGammaRIIb B/C loop 45Trp Lys Asp Lys Pro Leu Val Lys Val
Thr 1 5 10 467PRTArtificial sequencesynthetic peptide--FcGammaRIIb
C/E loop 46Ser Lys Lys Phe Ser Arg Ser 1 5 474PRTArtificial
sequencesynthetic peptide--FcGammaRIIb F/G loop 47Ile Gly Tyr Thr 1
4810PRTArtificial sequencesynthetic peptide--FcEpsilonR1alpha B/C
loop 48Trp Arg Asn Trp Asp Val Tyr Lys Val Ile 1 5 10
497PRTArtificial sequencesynthetic peptide--FcEpsilonR1alpha C/E
loop 49Ala Leu Lys Tyr Trp Tyr Glu 1 5 504PRTArtificial
sequencesynthetic peptide--FcEpsilonR1alpha F/G loop 50Val Trp Gln
Leu 1 5110PRTArtificial sequencesynthetic peptide--FcGammaRIII-V
B/C loop 51Trp Lys Asn Thr Ala Leu His Lys Val Thr 1 5 10
527PRTArtificial sequencesynthetic peptide--FcGammaRIII-V C/E loop
52Asp Arg Lys Tyr Phe His His 1 5 534PRTArtificial
sequencesynthetic peptide--FcGammaRIII-V F/G loop 53Val Gly Ser Lys
1 5410PRTArtificial sequencesynthetic peptide--FcGammaRIII-F B/C
loop 54Trp Lys Asn Thr Ala Leu His Lys Val Thr 1 5 10
557PRTArtificial sequencesynthetic peptide--FcGammaRIII-F C/E loop
55Asp Arg Lys Tyr Phe His His 1 5 564PRTArtificial
sequencesynthetic peptide--FcGammaRIII-F F/G loop 56Phe Gly Ser Lys
1 576PRTArtificial sequencesynthetic peptide--IgG1 lower hinge
57Leu Leu Gly Gly Pro Ser 1 5 585PRTArtificial sequencesynthetic
peptide--IgG1 B/C loop 58Asp Val Ser His Glu 1 5 596PRTArtificial
sequencesynthetic peptide--IgG1 F/G loop 59Ala Leu Pro Ala Pro Ile
1 5 606PRTArtificial sequencesynthetic peptide--IgG2 lower hinge
60Pro Val Ala Gly Pro Ser 1 5 615PRTArtificial sequencesynthetic
peptide--IgG21 B/C loop 61Asp Val Ser His Glu 1 5 626PRTArtificial
sequencesynthetic peptide--IgG2 F/G loop 62Gly Leu Pro Ala Pro Ile
1 5 636PRTArtificial sequencesynthetic peptide--IgG3 lower hinge
63Leu Leu Gly Gly Pro Ser 1 5 645PRTArtificial sequencesynthetic
peptide--IgG3 B/C loop 64Asp Val Ser His Glu 1 5 656PRTArtificial
sequencesynthetic peptide--IgG3 F/G loop 65Ala Leu Pro Ala Pro Ile
1 5 666PRTArtificial sequencesynthetic peptide--IgG4 lower hinge
66Phe Leu Gly Gly Pro Ser 1 5 675PRTArtificial sequencesynthetic
peptide--IgG4 B/C loop 67Asp Val Ser Gln Glu 1 5 686PRTArtificial
sequencesynthetic peptide--IgG4 F/G loop 68Gly Leu Pro Ser Ser Ile
1 5 696PRTArtificial sequencesynthetic peptide--IgGE lower hinge
69Asn Pro Arg Gly Val Ser 1 5 705PRTArtificial sequencesynthetic
peptide--IgGE B/C loop 70Asp Leu Ala Pro Ser 1 5 716PRTArtificial
sequencesynthetic peptide--IgGE F/G loop 71His Leu Pro Arg Ala Leu
1 5
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