US20150093783A1

US20150093783A1 - Humanized antibodies to ca215

Info

Publication number: US20150093783A1
Application number: US14/569,444
Authority: US
Inventors: Gregory Lee
Original assignee: Vancouver Biotech Ltd
Current assignee: Vancouver Biotech Ltd
Priority date: 2012-06-13
Filing date: 2014-12-12
Publication date: 2015-04-02
Also published as: WO2013186630A3; US8974786B2; CA2876796A1; WO2013186630A2; EP2861625A2; JP2015525075A; US20130340102A1

Abstract

Provided herein are humanized forms of murine RP215 monoclonal antibodies and methods of using the same. These humanized RP215 monoclonal antibodies were characterized in terms of their respective affinity and specificity to the corresponding tumor-associated antigen, CA215, and shown to be comparable to those of murine RP215.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No. 13/797,204 filed 12 Mar. 2013, now allowed, which claims priority of U.S. Ser. No. 61/659,354 filed 13 Jun. 2012. The contents of these documents are incorporated by reference herein in their entirety.

SUBMISSION OF SEQUENCE LISTING ON ASCII TEXT FILE

The content of the following submission on ASCII text file is incorporated herein by reference in its entirety: a computer readable form (CRF) of the Sequence Listing (file name: 616342000510SeqList.txt, date recorded: 11 Dec. 2014, size: 35,938 KB).

TECHNICAL FIELD

The invention relates to the field of humanization of RP215 monoclonal antibody which is of murine origin. RP215 is known to recognize specifically a carbohydrate-associated epitope of cancer cell-expressed glycoproteins, known as CA215. The primary structure of the humanized forms of RP215 can then be utilized for the therapeutic treatment of human cancers as antibody-based anticancer drugs.

BACKGROUND ART

RP215 monoclonal antibody described in U.S. Pat. No. 5,650,291 and PCT publication WO2008/138,139 is one of three thousand monoclonal antibodies which were generated in mice immunized against the extract of OC-3-VGH ovarian cancer cell. Through years of effort, it was documented that RP215 reacts specifically with cancer cell-expressed pan cancer biomarker or glycoproteins, designated as CA215. The amino acid sequence of the variable regions of RP215 is disclosed in the PCT publication. The contents of these documents as related to uses for antibodies that bind to CA215 are incorporated herein by reference.
Following comprehensive analysis of more than 100 CA215-derived tryptic peptides by MALDI-TOF MS, it was further demonstrated that CA215 is a mixture of glycoproteins expressed by cancer cells, each of which contains an RP215-specific carbohydrate-associated epitope. Among these glycoproteins are mainly immunoglobulin superfamily (IgSF) proteins including immunoglobulin heavy chains, T cell receptors and cell adhesion molecules as well as mucins and others.
Both in vitro and in vivo biochemical and immunological assays were performed to document that RP215 reacts with the surface of almost all of cancer cells or cancerous tissues in humans. Besides immunohistochemical studies, apoptosis as well as complement-dependent cytotoxicity can be induced to cancer cells in the presence of RP215 at concentrations on the order of μg/ml. Growth inhibition of implanted tumor cells in model systems by RP215 was also demonstrated in nude mouse experiments. In addition, rat anti-idiotypic (Aid) monoclonal antibodies against RP215 were generated. The Ab3 response upon immunizations of these Aid monoclonal antibodies in mice was successfully induced. The anti-aid (Ab3) anti-sera were shown to be functionally equivalent to RP215. Aid monoclonal antibodies may also be used for the development of anti-cancer vaccines for human applications.
To develop RP215-based anti-cancer drugs for human application, it is essential to modify the original murine RP215 monoclonal antibody into humanized form.

DISCLOSURE OF THE INVENTION

The invention is directed to the humanized forms of RP215 monoclonal antibody. The humanized versions of RP215 of the invention were shown to have affinity and specificity to CA215 comparable to, or equivalent to, those of original murine RP215. Thus, in one aspect, the invention is directed to humanized antibodies or fragments that bind CA215 with specificities and affinities substantially equivalent to that of RP215. In particular, the antibodies or fragments with variable regions shown in FIG. 8 are part of the invention.
For complete antibodies of the invention, it is preferred that the constant region of the heavy chain be IgG and the constant region of the light chain be kappa. However, other Ig forms, including IgM, for example, are included as well as those embodiments that have lambda constant regions in their light chains.
In still other aspects, the invention is directed to methods to use the antibodies of the invention in the treatment of cancer in human subjects.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows antigen binding curves of various humanized and chimeric forms of RP215 monoclonal antibodies.

FIG. 2 shows the results of an ELISA to determine the low cross-reactivity of various humanized RP215 monoclonal antibodies to human IgG.

FIG. 3 shows sequence analysis of VL: 3CDR of murine RP215 loops which are highlighted in primary amino acid sequence with key residues (C-W-C-F) identified and with no free Cys and N-linked glycosylation sites.

FIG. 4 shows human framework donors considered.

FIG. 5 is a template antibody structure model of murine RP215 (VL shown on left-hand side, VH on right-hand side, and CDR loops shown as spheres with van der Waals radii).

FIG. 6 is a template antibody structure model of murine RP215. Residues in close proximity to CDR loops are shown as sticks. These residue positions are candidates for back-mutation.

FIG. 7 shows humanized sequences that exhibit high homology to human antibody sequences. hRP215_VH1 has ˜97% sequence identity to its closest human FR donor (germline) outside of CDR regions hRP215 ˜99% identity to germline FR Alignment of Humanized VH with Human VH Framework Donors regions, while hRP215_VH2 has donor outside of CDRs. Different residues are mostly located within or adjacent to CDRs, with the exception of Loop 3 in VH.

FIG. 8 shows comparison of amino acid sequences of heavy chain and light chain of humanized forms of RP215 with those of murine RP215.

FIG. 9A and 9B shows the nucleotide sequences that encode the amino acid sequences of FIG. 8.

MODES OF CARRYING OUT THE INVENTION

The humanized antibodies of the present invention may be in a variety of forms—including whole antibodies, fragments that are immunoreactive with CA215, including Fab, Fab', and F(ab')₂fragments as well as recombinantly produced single-chain antibodies. The resulting humanized forms as noted below are of equivalent affinity and specificity to the murine RP215 and contain substantially similar or identical CDR regions.
The CDR regions of the variable region of both heavy and light chains can be determined by a number of art-known methods, including the numbering system of Kabat which defines, in the light chain CDR1 as residues 24-34, CDR2 as residues 50-56, CDR3 as residues 89-97 and in the heavy chain CDR1 as residues 31-35, CDR2 as residues 50-65 and CDR3 as residues 95-102 (Wu, T. T., and Kabat, E. A., Exp. Med. (1970) 132:211-250). CDRs can also be determined according to the system of Clothia which gives slightly different results (Clothia, C., et al., Nature (1989) 342:877-883; Al-Laziken, et al., J. Mol. Biol. (1997) 273:927-948). Various subsequent authors have suggested some minor modifications. The CDRs as assigned by both Kabat and Clothia systems are included within the scope of the present invention.
Sandwich and/or binding immunoassays were used to demonstrate the substantial equivalence between the humanized forms and murine RP215. Their respective affinity and specificity to the cognate antigen, the cancer cell-expressed CA215, are two important parameters to establish their substantial equivalence.
General Approach For Humanization
Based on the published sequence of the RP215 variable chain, it was determined that five of the CDRs (excluding H3) fall into one of the canonical structure classes indicated as follows:


CDR	L1	L2	L3	H1	H2

Canonical Structure class	3/17A	1/7A	1/9A	1/10A	2/10A

Human framework donor selection was made through a search of germline followed by rearrangement of human IgG data base using VL and VH sequences with or without CDRs. To obtain human IgG results, normally, we go through each hit to eliminate inappropriate donors (such as mouse sequence or humanized sequence, etc.). For VL and VH sequences, the best hits in each group were aligned. Finally, one germline FR donor and one rearranged (mature) FR donor based on sequence similarity and other factors are selected. These factors included CDR length (except for CDR-H3), CDR canonical structure, proline residues at key positions or factors which may affect proper folding of humanized antibody.
Homology modeling was used to obtain template antibody structure by searching the PDB data base for the template antibody VL and VH sequences with or without CDR. The following conditions are taken into consideration:

- (1) Sequence homology
- (2) CDR length
- (3) CDR canonical structure, and
- (4) Model with correct disulfide linkage

The antigen binding region of the antibody structure model can then be optimized through the CDR loop data base and canonical structure class as well as comparison to the template structure.
Structural modeling was used to identify residues outside of the CDR loops that might affect CDR configurations. The following binding or interaction factors should be taken into consideration: hydrogen bonding, steric hindrance and other interactions to main chain and side chains of CDR residues.
Back mutation was performed to those residues that are predicted to significantly affect CDR loop structure. Other critical residues were also verified including those in (1) the heterodimer interface in FR donors for proper VL and VH interactions, (2) the intra-chain domain interface and (3) direct interactions to antigen/epitopes in the known structure.
Therefore, based on the above considerations, combinations of different back mutations were designed to balance the minimal need of such process. As a result, low immunogenicity to humans can be obtained and the maximal preservations of antigen-binding affinity can be preserved.
The following examples are offered to illustrate but not to limit the invention.

EXAMPLE 1

Characterization of Humanized RP215 Monoclonal Antibodies

Humanized RP215 monoclonal antibodies with heavy and light chains designated 0021-0023 (VH1-VH3 and VL1-VL2) and the parent murine chains 0024 were generated, expressed and affinity-purified. Various heavy chain/light chain combinations were used to construct antibodies FY1-FY6 as shown in Table 1. ChRP215 is a murine chimera with human IgG.

TABLE 1

VL1	VL2	L0024

VH1	FY1	FY4
VH2	FY2	FY5
VH3	FY3	FY6
H0024			ChRP215

The titers and amounts of FY1-FY6 from CHO cells are shown in Table 2.

TABLE 2

	Apparent titer	Production yield
Name of antibody	(ng/ml)	(N = 1)

Neg. control	NA	305
RP215 chimera	4.2	219
(with human IgG)
FY1	5.7	287
FY2	13.1	166
FY3	8.4	152
FY4	4.4	351
FY5	9.6	158
FY6	7.1	350

Binding immunoassays were performed using affinity-purified CA215 coated on microwells, to determine the binding affinities of these humanized RP215 to CA215 and to compare with that of the original murine RP215. The results of such comparative binding assays are presented in FIG. 1. As shown, all of FY1-FY6 have comparable affinities to RP215.
Previously, RP215 was established to have no cross-reactivity to normal human IgG. It reacts only with CA215 expressed by cancer cells that contain RP215-specific carbohydrate-associated epitope. Therefore, the humanized RP215 monoclonal antibodies should also show no cross-reactivity to normal human IgG. This lack-of-cross reactivity result was demonstrated, as humanized RP215 FY1, FY4 and FY5 (similar to the murine chimera) revealed no binding to human IgG as shown in FIG. 2.
FIG. 8 shows the complete amino acid sequences of both heavy and light chains of the humanized antibodies. The complete nucleotide sequences for these chains is shown in FIG. 9A and Figure B.
As a matter of interest, FIGS. 3-7 show various additional structural features of these antibodies.

Claims

1. A recombinant expression system which comprises a nucleotide sequence encoding a humanized monoclonal antibody (mAb) or antigen-binding fragment thereof that reacts specifically with a CA215, and

that binds to the CA215 with an affinity substantially equivalent to that of RP215,

which mAb comprises the CDR regions inherent in one of the heavy chain variable regions set forth in SEQ ID NOS:24-26 and in one of the light chain variable regions set forth in SEQ ID NO:28 or 29 according to the numbering system of either Kabat or Clothia;

said encoding nucleotide sequence operably linked to a heterologous promoter.

2. The expression system of claim 1, wherein in said mAb or fragment:

a) the CDR1 region of the heavy chain is DYWMH (SEQ ID NO:1); and

b) the CDR2 region of the heavy chain is AIDTSDSYTRYAQKFQG (SEQ ID NO:2) or GIDTSDSYTRYAQKFQG (SEQ ID NO:3); and

c) the CDR3 region of the heavy chain is SIYD (SEQ ID NO:4); and

d) the CDR1 region of the light chain is KSSQSLLNSSNQKSYLA (SEQ ID NO:5); and

e) the CDR2 region of the light chain is FASTRES (SEQ ID NO:6); and

f) the CDR3 region of light chain is QGHYSTPST (SEQ ID NO:7).

3. A recombinant expression system which comprises a nucleotide sequence encoding an mAb or antigen-binding fragment thereof which comprises the variable regions of

VH1 (SEQ ID NO:24)+VL1 (SEQ ID NO:28); VH1 (SEQ ID NO:24)+VL2 (SEQ ID NO:29);

VH2 (SEQ ID NO:25)+VL1 (SEQ ID NO:28); VH2 (SEQ ID NO:25)+VL2 (SEQ ID NO:29);

VH3 (SEQ ID NO:26)+VL1 (SEQ ID NO:28); or VH3 (SEQ ID NO:26)+VL2 (SEQ ID NO:29);

said encoding nucleotide sequence operably linked to a heterologous promoter.

4. The expression system of claim 1 which encodes a complete antibody.

5. The expression system of claim 1 which encodes a single-chain antibody.

6. The expression system of claim 3 which encodes a complete antibody.

7. The expression system of claim 3 which encodes a single-chain antibody.

8. Recombinant host cells or immortalized cells that produce an mAb or antigen-binding fragment thereof that reacts specifically with a CA215, and

which mAb comprises the CDR regions inherent in one of the heavy chain variable regions set forth in SEQ ID NOS:24-26 and in one of the light chain variable regions set forth in SEQ ID NO:28 or 29 according to the numbering system of either Kabat or Clothia.

9. The cells of claim 8, wherein in said mAb or fragment:

a) the CDR1 region of the heavy chain is DYWMH (SEQ ID NO:1); and

c) the CDR3 region of the heavy chain is SIYD (SEQ ID NO:4); and

d) the CDR1 region of the light chain is KSSQSLLNSSNQKSYLA (SEQ ID NO:5); and

e) the CDR2 region of the light chain is FASTRES (SEQ ID NO:6); and

f) the CDR3 region of light chain is QGHYSTPST (SEQ ID NO:7).

10. The cells of claim 8 that are contained in a transgenic non-human animal or transgenic plant.

11. A method to produce a humanized mAb or fragment that reacts specifically with CA215 which method comprises culturing the cells of claim 8 and recovering said mAb or fragment.

12. Recombinant host cells or immortalized cells that produce an mAb or antigen-binding fragment which comprises the variable regions of

VH1 (SEQ ID NO:24)+VL1 (SEQ ID NO:28); VH1 (SEQ ID NO:24)+VL2 (SEQ ID NO:29);

VH2 (SEQ ID NO:25)+VL1 (SEQ ID NO:28); VH2 (SEQ ID NO:25)+VL2 (SEQ ID NO:29);

VH3 (SEQ ID NO:26)+VL1 (SEQ ID NO:28); or VH3 (SEQ ID NO:26)+VL2 (SEQ ID NO:29).

13. The cells of claim 12 that are contained in a transgenic non-human animal or transgenic plant.

14. A method to produce a humanized mAb or fragment that reacts specifically with CA215 which method comprises culturing the cells of claim 12 and recovering said mAb or fragment.