# Patent

## Title
Humanized immunomodulatory monoclonal antibodies for the treatment of neoplastic disease or immunodeficiency

## Abstract

The present invention provides to a humanized monoclonal antibody having immunostimulatory effects. This antibody binds specifically to B lymphoblastoid cells, induces proliferation and activation of peripheral blood lymphocytes, and is capable of eliciting an anti-tumor effect upon administration to subjects suffering from cancer.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of International application PCT/IL03/00425 filed May 22, 2003, the entire content of which is expressly incorporated herein by reference thereto.


FIELD OF THE INVENTION
The present invention relates to the field of immunotherapy and more specifically concerns humanized monoclonal antibodies useful for therapy of a variety of indications, particularly in the treatment of cancer.
BACKGROUND OF THE INVENTION
Cancer in its different forms is a major cause of death in humans. The most widely used therapeutic treatments of cancer are surgery, radiation and chemotherapy. The rapid increase of knowledge in recent years about the molecular and cellular bases of immune regulation, particularly at the level of T-cell responses, provides a new arsenal of immunotherapeutic approaches including the development of tumor vaccines. Certain monoclonal antibodies (MABS) were shown to have immunomodulatory activity including the ability to bind determinants on the surface of T cells and to induce proliferation, activation or differentiation of these cells.
Monoclonal antibodies derived from mouse hybridomas contain substantial stretches of amino acid sequences that are immunogenic when injected into a human patient, often eliminating the antibody's therapeutic efficacy after an initial treatment. While the production of so called “chimeric antibodies” (i. e. mouse variable regions joined to human constant. regions) has proven somewhat successful, a significant immunogenicity impediment remains.
Recombinant DNA technology has been utilized to produce immunoglobulins containing human framework regions (FRs) combined with complementarity determining regions (CDRs) from a donor mouse or rat immunoglobulin. These new proteins are called “reshaped” or “HUMANIZED” IMMUNOGLOBULINS and the process by which the donor immunoglobulin is converted into a human-like immunoglobulin by combining its CDRs with a human framework is called “humanization”. Humanized antibodies are important because they bind to the same antigen as the original antibodies, but are less immunogenic when injected into humans.
U.S. Pat. No. 6,294,654 discloses a modified immunoglobulin molecule or functional fragment or part thereof (Ig), having an antigenic peptide foreign to the Ig incorporated in one or more non-CDR loops, and wherein the main outline of the constant domain framework is maintained. Further disclosed is the use of the modified antibody for therapeutic or prophylactic use.
U.S. Pat. No. 6,074,635 discloses a method for antigen independent activation of T cells in vitro comprising contacting T cells in the absence of antigen with a combination of at least two cytokines selected from the group consisting of interleukin-2, interleukin-6, and tumor necrosis factor alpha, or functionally equivalent fragments thereof.
U.S. Pat. No. 5,658,741 discloses a method of inducing the activation and proliferation of T-cells, said method comprising: (a) conjugating a plurality of T-cell specific monoclonal antibodies to an aminodextran molecule having 7-20% by weight amine groups and a molecular weight of at least 100,000 daltons, wherein the molar ratio of said antibodies to said aminodextran is greater than or equal to two; and (b) reacting said conjugate with a sample containing said T-cells to effect the binding of said conjugated antibodies to said T-cells to induce activation and proliferation of said T-cells.
U.S. Pat. No. 5,585,089 of Queen et al. discloses a humanized immunoglobulin having complementarity determining regions (CDRs) from a donor immunoglobulin and heavy and light chain variable region frameworks from human acceptor immunoglobulin heavy and light chains, which humanized immunoglobulin specifically binds to an antigen with an affinity constant of at least 107 M−1 and no greater than about four-fold that of the donor immunoglobulin, wherein said humanized immunoglobulin comprises amino acids from the donor immunoglobulin framework outside the Kabat and Chothia CDRs, wherein the donor amino acids replace corresponding amino acids in the acceptor immunoglobulin heavy or light chain frameworks, and each of said donor amino acids: (I) is adjacent to a CDR in the donor immunoglobulin sequence, or (II) contains an atom within a distance of 4 Å of a CDR in said humanized immunoglobulin.
U.S. Pat. No. 5,225,539, of Winter, discloses an altered antibody or antigen-binding fragment thereof, wherein a variable domain of the antibody or antigen-binding fragment has the framework regions of a first immunoglobulin heavy or light chain variable domain and the complementarity determining regions of a second immunoglobulin heavy or light chain variable domain, wherein said second immunoglobulin heavy or light chain variable domain is different from said first immunoglobulin heavy or light chain variable domain in antigen binding specificity, antigen binding affinity, species, class or subclass.
U.S. Pat. Nos. 5,225,539 and 5,585,089 do not provide sufficient tools and comprehensive description for carrying out the synthesis of an altered antibody, particularly a humanized antibody, by a person skilled in the art.
U.S. Pat. No. 5,897,862 of one of the inventors of the present invention which is incorporated herein by reference, discloses a monoclonal antibody or an antigen binding fragment thereof, wherein the monoclonal antibody: (i) is secreted by the hybridoma cell line deposited at the Collection Nationale de Cultures de Microorganismes (CNCM), under Accession No. I-1397, or (ii) recognizes the same antigenic epitope as the antibody under (i). The monoclonal antibody disclosed in U.S. Pat. No. 5,897,862 is directed against “Daudi” cells, a human B lymphoblastoid cell line, and was shown to stimulate murine lymphocytes and human peripheral blood T cells (Hardy et al, Cell Immunol. 118:22, 1989). This murine antibody is also termed mBAT-1 hereinafter. mBAT-1 also exhibits anti-tumor and immunostimulatory effects in various types of tumors (Hardy et al., Int. J. Oncol. 19:897, 2001) including tumors of human origin (Hardy et al., Proc. Natl. Acad. Sci. USA 94:5756, 1997).
International Patent Application WO 00/58363 of one of the inventors of the present invention which is incorporated herein by reference, discloses a monoclonal antibody having a variable region comprising the heavy chain variable region and/or the Kappa light chain variable region of mBAT-1 or a heavy chain variable region and/or a Kappa light chain variable region having at least 70% identity to the heavy chain variable region and/or the Kappa light chain variable region of mBAT-1.
Nowhere in the background art is it taught or suggested that a humanized monoclonal antibody comprising CDRs of a murine origin and FRs of a human origin may elicit an immune response and may further exhibit anti-cancer activity. Moreover, there is an unmet need for reliable methods for designing functional humanized antibodies, as it is well known in the art that the synthesis of the humanized antibody of the present invention cannot be predictably or routinely based on the background art.
SUMMARY OF THE INVENTION
The present invention now provides a humanized monoclonal immunomodulatory antibody, also termed hereinafter hBAT-1, which binds to B lymphoblastoid cells and induces proliferation and activation of peripheral blood lymphocytes. Said hBAT-1 is based on the previously known murine monoclonal immunomodulatory antibody, also termed herein mBAT-1, which binds to B lymphoblastoid cells and induces proliferation and activation of peripheral blood lymphocytes and further elicits an anti-tumor effect when injected into a tumor-bearing subject.
The present invention also provides a comprehensive description of the humanization process of mBAT-1 along with the rationale for each synthesis step. Thus, the description of the humanization process provided in the present invention is suitable for humanization of BAT antibodies other than mBAT-1, by a person skilled in the art.
The administration of humanized BAT-1 antibody offers a method for therapeutic prevention, detection or treatment of cancer. Treatment of a subject in need thereof with the humanized form of the BAT-1 antibody, as provided by the present invention, is considerably more efficient than treatment with a chimeric BAT-1 antibody, and avoids adverse immunogenic responses.
The present invention is based in part on the unexpected finding that the humanized BAT-1 antibody appears to induce a greater anti-tumor effect than that induced by the parent murine BAT-1 antibody.
According to a first aspect, the present invention provides a humanized monoclonal antibody, such as a humanized monoclonal immunomodulatory antibody, comprising at least one CDR from a donor immunoglobulin and an FR from an acceptor immunoglobulin. Advantageously, the donor of CDRs is the murine monoclonal BAT-1 antibody (mBAT-1). Also, the acceptor from which the FR is derived is preferably a human immunoglobulin.
According to yet another embodiment, the present invention provides a monoclonal immunomodulatory antibody comprising at least one CDR from a donor murine monoclonal BAT-1 antibody (mBAT-1) and an FR derived from an acceptor human immunoglobulin wherein the humanized antibody retains the biological activity of mBAT-1 monoclonal antibody and is less immunogenic in a human subject than said murine antibody.
According to yet another embodiment, the light chain variable region of the humanized BAT-1 antibody is characterized by the formula:

FRL1-CDRL1-FRL2-CDRL2-FRL3-CDRL3-FRL4

wherein each FR is independently a framework region of a human antibody and each CDR is independently a complementarity determining region of the monoclonal mBAT-1 antibody.
According to yet another embodiment, the heavy chain variable region of the humanized BAT-1 antibody is characterized by the formula:

FRH1-CDRH1-FRH2-CDRH2-FRH3-CDRH3-FRH4

wherein each FR is independently a framework region of a human antibody and each CDR is independently a complementarity determining region of the monoclonal mBAT-1 antibody.
According to a specific embodiment, the present invention provides a monoclonal antibody comprising FRs derived from the light chain variable region of the human TEL9 antibody.
According to another specific embodiment, the present invention provides a monoclonal antibody comprising FRs amino acid sequences derived from the light chain variable region of the human TEL9 antibody selected from the group consisting of: FRL1, [EIVLT QSPSS LSASV GDRVT ITC; SEQ. ID NO. 1]; FRL2, [W (F or Y) QQKPG KAPKL (W or L) IY; SEQ. ID NO. 2]; FRL3, [GVPSR FSGSG SGT (D or S) (Y or F) (C or T) LTINS LQPED FATYY C; SEQ. ID NO. 3]; FRL4, [FGGGT KLEIK; SEQ. ID NO. 4].
According to yet another specific embodiment, the present invention provides a monoclonal antibody comprising FRs derived from the heavy chain variable region of the human hsighv1295 antibody.
According to yet another specific embodiment, the present invention provides a monoclonal antibody comprising FRs amino acid sequences derived from the heavy chain variable region of the human hsighv1295 antibody selected from the group consisting of: FRH1, [Q (I or V) QLV QSGSE LKKPG ASVKI SCKAS GY (T or S) F (T or S); SEQ. ID NO. 5]; FRH2, [WV (R OR K) QAPGQ GL (Q or K) WMG; SEQ. ID NO. 6]; FRH3, [RF (V or A) FSLDT SV (N or S) TAYLQ ITSL (T or N) AEDTG MYFC (V or A) (R or K); SEQ. ID NO. 7]; FRH4, [WGQGT LVTVS S; SEQ. ID NO. 8].
According to yet another preferred embodiment, the present invention provides a monoclonal antibody comprising a light chain variable region comprising the amino acid sequence selected from the group consisting of: CDRL1 [SARSS VSYMII; SEQ. ID NO.9]; CDRL2 [RTSNL AS; SEQ. ID NO. 10]; CDRL3 [QQRSS FPLT; SEQ. ID NO. 11], wherein the CDRs are derived from the murine BAT-1 antibody and the subscripts “L” and “H” refer to light and heavy chain regions, respectively.
According to yet another specific embodiment, the present invention provides a monoclonal antibody comprising a heavy chain variable region comprising the amino acid sequence selected from the group consisting of: CDRH1 [NYGMN; SEQ. ID NO. 12]; CDRH2 [WINTD SGEST YAEEF KG; SEQ. ID NO. 13]; CDRH3 [VGYDA LDY; SEQ. ID NO. 14].
According to yet another embodiment, the humanized monoclonal antibody of the invention is selected from the group consisting of: a full length antibody having a human immunoglobulin constant region, a monoclonal IgG particularly of subclasses γ1 or γ4, a single chain antibody, an antibody fragment including, but not limited to, an F(ab′)2 fragment or F(ab) or Fv, a labeled antibody, an immobilized antibody, an antibody conjugated with a heterologous compound.
According to yet another preferred embodiment, the present invention provides a monoclonal antibody comprising a light chain variable region selected from the group consisting of: BATRκA (SEQ. ID NO.15), BATRκB (SEQ. ID NO.16), BATRκC (SEQ. ID NO. 17), BATRκD (SEQ. ID NO. 18).
According to yet another preferred embodiment, the present invention provides a monoclonal antibody comprising a heavy chain variable region selected from the group consisting of: BATRHA (SEQ. ID NO. 20), BATRHB (SEQ. ID NO. 21), BATRHC (SEQ. ID NO. 22), BATRHD (SEQ. ID NO. 23) or BATRHE (SEQ. ID NO. 24).
According to yet another preferred embodiment, the present invention provides a monoclonal antibody comprising a variable region selected from the group consisting of: BATRHA/BATRκA (SEQ. ID NO. 20/SEQ. ID NO. 15), BATRHB/BATRκA (SEQ. ID NO. 21/SEQ. ID NO. 15), BATRHB/BATRκB (SEQ. ID NO. 21/SEQ. ID NO. 16), BATRHC/BATRκB (SEQ. ID NO. 22/SEQ. ID NO. 16), BATRHB/BATRκD (SEQ. ID NO. 21/SEQ. ID NO. 18), or BATRHC/BATRκD (SEQ. ID NO. 22/SEQ. ID NO. 18).
According to yet another embodiment, the humanized monoclonal antibody of the invention is generated by recombinant DNA technology, utilizing CDR grafting.
According to a second aspect, the present invention provides polynucleotides encoding the humanized antibody of the invention or fragments thereof. The polynucleotides may encode the whole humanized antibody or the light chain variable region or the heavy chain variable region or both chains of the variable region of the humanized antibody. The invention further provides vectors comprising polynucleotides encoding the humanized antibody of the invention or fragments thereof. Consequently, the humanized BAT-1 antibody may be expressed in a host cell following co-transfection of the heavy and light chain vectors or by transfection of a single vector comprising both light and heavy chain polynucleotide sequences.
According to another embodiment, the present invention provides polynucleotide sequences encoding the humanized monoclonal antibody of the invention or fragments thereof.
According to another preferred embodiment, the present invention provides a polynucleotide sequence encoding the kappa light chain variable region of the humanized antibody of the invention wherein the kappa light chain variable region is selected from the group consisting of: SEQ ID NO. 15, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18.
According to another preferred embodiment, the polynucleotide sequence encoding the light chain of the humanized antibody of the invention is selected from the group consisting of: SEQ ID NO. 87, SEQ ID NO. 88, SEQ ID NO. 89.
According to another preferred embodiment, the present invention provides a polynucleotide sequence encoding the heavy chain variable region of the humanized antibody of the invention wherein the heavy chain variable region is selected from the group consisting of: SEQ ID NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24.
According to yet another preferred embodiment, the polynucleotide sequences encoding the heavy chain of the humanized antibody of the invention are selected from the group consisting of: SEQ ID NO. 90, SEQ ID NO. 91, SEQ ID NO. 92.
According to yet another embodiment, the present invention provides a vector comprising the polynucleotide sequence encoding the humanized BAT-1 antibody or fragments thereof.
According to yet another embodiment, the present invention provides a vector comprising the polynucleotide sequence encoding the humanized antibody of the invention or fragments thereof.
According to yet another embodiment, the present invention provides a vector comprising the polynucleotide sequence encoding the humanized antibody of the invention or fragments thereof selected from the group consisting of: whole humanized antibody, the light chain variable region, the heavy chain variable region, both chains of the variable region.
According to yet another preferred embodiment, the present invention provides a vector comprising a polynucleotide sequence encoding the kappa light chain variable region of the humanized antibody of the invention, wherein the kappa light chain variable region is selected from the group consisting of: SEQ ID NO. 15, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18.
According to yet another embodiment, the vector further comprises at least one sequence encoding a component selected from the group consisting of: resistance genes, promoter, signal peptide, polyA transcription terminator, selection markers, genomic human kappa constant region.
According to yet another preferred embodiment, the components of the vector are selected from the group consisting of: Ampicillin resistance gene, Neomycin resistance gene, HCMV Immediate Early Promoter, the genomic human kappa constant region, a mouse immunoglobulin signal peptide sequence, Kozak sequence, a signal sequence intron, BGH polyA transcription terminator, a Neo/G418 selection marker, a hamster dhfr selection marker.
According to yet another preferred embodiment, the present invention provides a vector comprising a polynucleotide sequence encoding the heavy chain variable region of the humanized antibody of the invention, wherein the heavy chain variable region is selected from the group consisting of: SEQ ID NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24.
According to yet another embodiment, the vector further comprises at least one sequence encoding a component selected from the group consisting of: resistance genes, promoter, signal peptide, polyA transcription terminator, selection markers, the genomic human Ig constant region.
According to yet another preferred embodiment, the components of the vector are selected from the group consisting of: Ampicillin resistance gene, Neomycin resistance gene, HCMV Immediate Early Promoter, the genomic human IgG1 constant region, a mouse immunoglobulin signal peptide sequence, Kozak sequence, a signal sequence intron, BGH polyA transcription terminator, a Neo/G418 selection marker, a hamster dhfr selection marker.
According to yet another preferred embodiment, the present invention provides a vector comprising a polynucleotide sequence encoding the kappa light chain variable region of the humanized antibody of the invention selected from the group consisting of: pKN110-BATRκA, pKN110-BATRκB and pKN110-BATRκD.
According to yet another preferred embodiment, the present invention provides a vector comprising a polynucleotide sequence encoding the heavy chain variable region of the humanized antibody of the invention selected from the group consisting of: pG1D110-BATRHA, pG1D110-BATRHB, pG1D110-BATRHC.
According to yet another preferred embodiment, the present invention provides a vector comprising a polynucleotide sequence encoding the complete humanized antibody of the invention of SEQ ID NO. 93.
According to a third aspect, the present invention provides cells containing a vector comprising the polynucleotide sequence encoding the antibody of the invention or fragments thereof for the purposes of storage, propagation, antibody production and therapeutic applications.
According to another embodiment, the host cell may be selected from the group consisting of: CHO, CHOdhfr, NSO, COS, COS7.
According to yet another embodiment, the present invention provides a pharmaceutical composition comprising as an active ingredient the antibody of the invention, for use in diagnosis and therapy.
According to yet another embodiment, the pharmaceutical composition comprising as an active ingredient the antibody of the invention is preferably used for the treatment of cancer.
According to yet another embodiment, the pharmaceutical composition may be administered either following detection of primary or secondary tumors in a subject or as preventive therapy of a subject having a high risk of developing cancers.
According to yet another preferred embodiment, the humanized antibody of the invention elicits anti-tumor effects in a variety of tumors.
According to yet another embodiment, the present invention provides a method for diagnosis or treatment of a disease or a disorder, particularly cancer, comprising administering to a subject in need thereof, an effective amount of a pharmaceutical composition comprising the antibody of the invention as an active ingredient.
According to yet another embodiment, the antibody of the invention in administered together with, prior to, or following, the administration of other agents, which can act in an additive or synergistic manner with it.
According to yet another embodiment, the antibody of the invention in administered together with, prior to, or following, the administration of agents selected from the group consisting of: cytokines, IL-1 (Interleuken-1), IL-2, IL-6, IFN-α (Interferon-α), cell vaccines, antibodies, T-cell stimulatory antibodies, anti-tumor therapeutic antibodies.
According to a particular embodiment of the present invention the humanized BAT monoclonal antibodies are identical in their function or activity to those produced by cells deposited under ATCC # (PTA-5189).
Other objects, features and advantages of the present invention will become apparent from the following detailed description and appended claims.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the DNA (SEQ ID NO: 25) and peptide (SEQ ID NO: 19) sequences of the kappa light chain variable region (Vκ) of the murine BAT-1 antibody.
FIG. 2 depicts the canonical classes of CDRs in the murine BAT-1 Vκ region. “Chothia Canonical Classes” indicates where the canonical classes as defined by Chothia and his colleagues (Chothia et al., 1987, 1989, 1992 ibid; Tramontano et al., J. Mol. Biol. 215:175, 1990) were used while “Martin Canonical Classes” signifies where the canonical classes defined by Martin and Thornton (Martin et al., J. Mol. Biol. 263:800, 1996) were used. FR residues are highlighted in bold. These sequences include: SNDTE (SEQ ID NO: 165); DLYVISNFHGT (SEQ ID NO: 166): SNTKG (SEQ ID NO: 167); FYNAHSR (SEQ ID NO: 168); MLVIF (SEQ ID NO: 169); QSGFL (SEQ ID NO: 170); NFGSRDHTYV (SEQ ID NO: 171); NYWTSRQHAD (SEQ ID NO: 172); ENGHTSRAOHAD (SEQ ID NO: 173); DYTVLHNIWPS (SEQ ID NO: 174); PLYRIWF (SEQ ID NO: 175).
FIG. 3 presents the DNA (SEQ ID NO: 27) and peptide (SEQ ID NO: 26) sequences of the heavy chain variable region (VH) of the murine BAT-1 antibody.
FIG. 4 depicts the canonical classes of CDRs in the murine BAT-1 VH region. “Chothia Canonical Classes” indicates where the canonical classes as defined by Chothia and his colleagues (Chothia et al., 1987, 1989, 1992 ibid; Tramontano et al., ibid) were used while “Martin Canonical Classes” signifies where the canonical classes defined by Martin and Thornton (Martin et al., ibid) were used. FR residues are highlighted in bold. These sequences include: TAVGS (SEQ ID NO: 176); MIVLT (SEQ ID NO: 177); RTKHGL (SEQ ID NO: 178); IHYFTNCED (SEQ ID NO: 179); YAWGTLV (SEQ ID NO: 180); HENOSYT (SEQ ID NO: 181); LIVTSN (SEQ ID NO: 182); ILFMV (SEQ ID NO: 183); ALVYF (SEQ ID NO: 184); RKGSHN (SEQ ID NO: 185); YHVISDG (SEQ ID NO: 186); YWGATL (SEQ ID NO: 187); REWYGOVLNKA (SEQ ID NO: 188): DLNSY (SEQ ID NO: 189): AGYSKTN (SEQ ID NO: 190): NSTKDG (SEQ ID NO: 191): YREDGVSA (SEQ ID NO: 192): KNTSDRGFY (SEQ ID NO: 193).
FIG. 5 shows the amino acid sequences of the various versions of the humanized BAT-1 Vκ region that are proposed (SEQ ID NOS. 15-18). Where the BAT-1 Vκ region residues and the human TEL9 Vκ region sequence match a dot [.] is shown. Where no amino acid is present at a specific residue position a dash [-] is shown. Where an amino acid in the TEL9 FRs is changed in the humanized BAT-1 Vκ region, it is highlighted in bold. The CDRs are described by the use of the nomenclature [==L1==]. The numbering used is as according to Kabat (Kabat et al., Sequences of proteins of immunological interest, Fifth Edition, U.S. Department of Health and Human Services, U.S. Government Printing Office, 1991).
FIG. 6 presents the amino acid sequences of the various versions of the humanized BAT-1 VH region that are proposed (SEQ ID NOS. 20-24). Where the BAT-1 VH region residues and the human hsighv1295 VH region sequence match a dot [.] is shown. Where no amino acid is present at a specific residue position a dash [-] is shown. Where an amino acid in the hsighv1295 FRs is changed in the humanized BAT-1 VH region, it is highlighted in bold. The CDRs are described by the use of the nomenclature [==H1==], while [-----] denotes part of the H1 structural loop. The numbering used is as according to Kabat (Kabat et al., ibid).
FIG. 7 shows the DNA (SEQ ID NO. 87) and peptide (SEQ ID NO. 15) sequences of version A (BATRκA) of the reshaped human kappa light chain variable region of the humanized BAT-1 antibody.
FIG. 8 shows the DNA (SEQ ID NO. 88) and peptide (SEQ ID NO. 16) of version B (BATRκB) of the reshaped human kappa light chain variable region of the humanized BAT-1 antibody.
FIG. 9 presents the DNA (SEQ ID NO. 89) and peptide (SEQ ID NO. 18) sequences of version D (BATRκD) of the reshaped human kappa light chain variable region of the humanized BAT-1 antibody.
FIG. 10 is a diagrammatic representation of the pKN110-BATRκD vector construct.
FIG. 11 is a diagrammatic representation of the BAT-1 light chain cassette inserted into BAT-1 light chain expression vectors.
FIG. 12 is a diagrammatic representation of the pG1D110.BAT-1.RHC vector construct.
FIG. 13 is a diagrammatic representation of the BAT-1 heavy chain cassette inserted into BAT-1 heavy chain expression vectors.
FIG. 14 is a diagrammatic representation of the pG1D200 gamma-1 immunoglobulin heavy chain mammalian expression vector.
FIG. 15 is a diagrammatic representation of the pG1KD210.BAT-1.RHC/RKD single expression vector (SEQ ID NO. 93).
FIG. 16 is a diagrammatic representation of the BATRκD/BATRHC heavy and light chains cassette inserted into a single expression vector for the expression of the complete BAT-1 antibody.
FIG. 17 shows a Daudi cell ELISA of humanized BATRHB/BATRκB variant against BAT-1 chimeric antibody.
FIG. 18 shows a Daudi cell ELISA of humanized BATRHB/BATRκA and BATRHA/BATRκA variants against BAT-1 chimeric antibody.
FIG. 19 shows a Daudi cell ELISA of humanized BATRHC/BATRκB and BATRHC/BATRκD variants against BAT-1 chimeric antibody.
FIG. 20 shows a Daudi cell ELISA of humanized BATRHB/BATRκD variant against BAT-1 chimeric antibody.
FIG. 21 presents dose dependence binding curves to Daudi cells of the murine BAT-1 mAb and the humanized BATRHC/BATRκD γ1 mAb.
FIG. 22 illustrates the dose-dependent anti-metastatic activity of the humanized BATRHC/BATRκD γ1 mAb (hBAT) in murine B16 lung tumors, with respect to control (no treatment) and to treatment with the original murine BAT-1 mAb. All treatments were administered intravenously 14 days post tumor inoculation and lungs were examined 10 days post treatment.
FIG. 23 represents the inhibitory effect of the humanized BATRHC/BATRκD γ1 mAb on human melanoma (SK-28) in SCID mice engrafted with human lymphocytes. The effect of the humanized BAT-1 on tumor growth is compared with control (no treatment) or treatment with the murine BAT-1 mAb (mBAT-1).
FIG. 24 demonstrates the anti-metastatic activity of the humanized BATRHC/BATRκD γ1 mAb in a Murine Tumor Model (HM7) implanted in BALB/c nude mice.
FIG. 25 shows co-localization of the humanized BATRHC/BATRκD γ1 mAb (hBAT) with CD4 (A) and CD8 (B) determined by flow cytometry on gated lymphocytes.
FIG. 26 presents binding of the humanized BATRHC/BATRκD γ1 mAb to cellular markers CD19 (A) and CD20 (B) of B lymphocytes isolated from a normal donor.
FIG. 27 represents the binding of the humanized BAT mAb to non-activated (day 0, A; day 5, C) and activated (2 days, B; 5 days, D) CD4+ T cells.
FIG. 28 shows the binding of the humanized BAT mAb to CD69+ T cells activated with beads conjugated to anti-CD3 and anti-CD28 in a dose-dependent manner (no activation, A; 0.25 μl, B; 0.5 μl, C).
FIG. 29 presents co-localization of the humanized BATRHC/BATRκD γ1 mAb with CD25 marker of T cells in a time dependent manner: day 0, A; day 2 and day 5 of activation, B and D respectively; day 5 of no activation, C.
FIG. 30 shows co-localization of the humanized BATRHC/BATRκD γ1 mAb with CD40-Ligand marker of T cells in a time dependent manner: day 0, A; day 1, day 2 and day 5 of activation, B-C and E, respectively; day 5 of no activation, D.
FIG. 31 describes hBAT induced increase in the number of viable CD4+ cells, isolated from two separate donors (A and B).
FIG. 32 presents hBAT binding to Daudi (A) and Jurkat (B) cell lines.
FIG. 33 demonstrates hBAT binding to peripheral blood lymphocytes, namely CD4+ cells (A), CD8+ cells (B) and B cells (C), of cancer patients.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
I. Definitions
For convenience certain terms employed in the specifications, examples and claims are set forth.
The term “antibody” is used in the broadest sense and specifically covers monoclonal antibodies (including full length monoclonal antibodies) and antibody fragments so long as they exhibit the desired biological activity. “Antibody 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′)2, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules; and multispecific antibodies formed from antibody fragments.
The term “monoclonal antibody” as used herein refers to antibodies that are highly specific, being directed against a single antigenic site. The monoclonal antibodies to be used in accordance with the present invention may be made by recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567 of Cabilly et al.).
The term “framework region” or “FR” residues are those variable domain residues other than the hypervariable region residues as herein defined. The term “hypervariable region” when used herein refers to the amino acid residues of an antibody which are responsible for antigen binding. The hypervariable region comprises amino acid residues from a “complementarity determining region” or “CDR”. The CDRs are primarily responsible for binding to an epitope of an antigen. The extent of FRs and CDRs has been precisely defined (see, Kabat et al., ibid).
As used herein, the term “humanized antibody” refers to an antibody comprising a framework region from a human antibody and one or more CDRs from a non-human (usually a mouse or rat) immunoglobulin. Parts of a humanized immunoglobulin, except possibly the CDRs, are substantially identical to corresponding parts of natural human immunoglobulin sequences. Importantly, the humanized antibody is expected to bind to the same antigen as the donor antibody that provides the CDRs. For further details, see e.g. U.S. Pat. No. 5,225,539 assigned to Medical Research Council, UK.
The expression “human antibody” is intended to mean an antibody encoded by a gene actually occurring in a human, or an allele, variant or mutant thereof.
As used herein, the term “donor” or “parental” immunoglobulin refers to the non-human immunoglobulin providing the CDRs.
As used herein, the term “acceptor” immunoglobulin refers to the human immunoglobulin providing the framework.
The term “expression vector” as used herein refers to a recombinant DNA molecule containing a desired coding sequence and appropriate nucleic acid sequences necessary for the expression of the operably linked coding sequence in a particular host cell. It is contemplated that the present invention encompasses expression vectors that are integrated into host cell genomes, as well as vectors that remain unintegrated into the host genome.
The term “genetically modified cells” as referred to herein relates to cells being transfected or infected by a vector, as exemplified by a virus encoding a polypeptide of interest, said cells capable of expressing said polypeptide. Particularly in the context of this invention, the genetically modified cells are capable of expressing and secreting the antibody of the invention.
The term “transfection” refers to the introduction of DNA into a host cell. It is contemplated that coding sequences may be expressed in transfected cells. Numerous methods of transfection are known to the ordinary skilled artisan, for example, CaPO4 and electroporation.
The term “anti-tumor effect” as used herein, refers to a biological effect which can be manifested by a decrease in tumor volume, a decrease in the number of tumor cells, a decrease in the number of metastases, an increase in life expectancy, or amelioration of various physiological symptoms associated with the cancerous condition. An “anti-tumor effect” can also be manifested by the ability of the antibody of the invention in prevention of the occurrence of tumor in the first place. Given its properties, the antibody of the invention can be used both in the treatment of acute cancer as well as in cancer prophylaxis.
Herein the term “excipient” refers to an inert substance added to a pharmaceutical composition to further facilitate administration of a compound. Examples, without limitation, of excipients include calcium carbonate, calcium phosphate, various sugars and types of starch, cellulose derivatives, gelatin, vegetable oils and polyethylene glycols. Pharmaceutical compositions may also include one or more additional active ingredients.
The term “Polymerase Chain Reaction” (“PCR”) refers to the methods disclosed in U.S. Pat. Nos. 4,683,195; 4,683,202, and 4,965,188.
II. Preferred Modes for Carrying Out the Invention
a. Antibody Preparation
In order to humanize the BAT-1 antibody, the non-human antibody starting material, namely mBAT-1 is prepared, following the design and preparation of the humanized variants. Some aspects of this invention, including the selection of a donor non-human antibody variable domain, humanizing an antibody gene sequence and producing a desired humanized antibody, are described in the following sections.
(i) Preparation of the Non-Humanized Antibody
The murine BAT-1 monoclonal antibody was described previously in U.S. Pat. No. 5,897,862. Accordingly, a representative hybridoma cell line that produces monoclonal murine BAT-1 antibodies, was deposited at the Collection Nationale de Cultures de Microorganismes (CNCM), Institute Pasteur, 25, Rue du Docteur Roux, 75724, Paris, Cedex 15, under Deposit Accession No. I-1397, on Jan. 28, 1994.
Alternatively, the chimeric γ1/κ BAT-1 antibody as produced from the murine BAT-1 may be used for the preparation of a humanized BAT-1. The chimeric BAT-1 antibody and its production, have been described in PCT application No. WO 00/58363.
(ii) Design Strategy of the Humanized Antibody
The present invention discloses procedures for humanization of BAT-1 antibody via a process in which the donor antibody, preferably mouse antibody, is converted into a human-like antibody by combining the CDRs of the donor antibody with a human framework. In certain embodiments, it may be desirable to generate amino acid sequence variants of the humanized antibody, particularly where these improve the binding affinity or other properties of the humanized antibody. The methods applied to select sites for substitution, insertion or deletion, from both the donor BAT-1 antibody and the selected human acceptor antibody, including the selection of acceptor human antibodies are described in detail. The extensive analysis and guidelines for antibody humanization which is provided hereinbelow, is not disclosed in the background art and is crucial for the preparation of an active altered antibody.
The design of a humanized antibody is preferably initiated by sequence analysis of the heavy and light chains of the non-human antibody variable region, also termed hereinafter VH and VL, respectively. Such analysis includes a comparison between the amino acid sequence of VL and VH of the non-humanized antibody and other mouse variable regions. In a preferred embodiment, the comparison can be further conducted with consensus sequences of the subgroups into which the variable regions were subdivided in the Kabat database (Kabat et al., ibid). The classification of the different elements of the variable region facilitates selection of immunoglobulin variable regions which are similar to the VL and VH of the non-humanized antibody of the present invention and are structurally solved.
Selection of the human kappa light chain variable region, also termed hereinafter Vκ, and of VH that would serve as the basis of the variable region of the humanized antibody, also termed an acceptor antibody, is preferably initiated by classifying the VL and VH of the non human antibody according to consensus sequences of human immunoglobulins. Particularly, VL of the non-humanized antibody is compared with and consequently categorized according to the consensus sequences of the four human kappa light chain variable region subgroups as defined by Kabat (Kabat et al., ibid). Similarly, VH of the non-humanized antibody is compared and categorized according to the consensus sequences of the three human heavy chain variable region subgroups.
The selection of the acceptor human Vκ and VH is preferably proceeded by conducting a comparison between VL and VH of the parental non-human antibody of the invention and all the recorded examples of individual sequences of human variable regions publicly available. An appropriate human Vκ and VH are selected on the basis of closest match to the parental non-human antibody.
Analysis of the sequences of the donor and humanized antibodies and reference to appropriate molecular models can help to discern which residues might be involved in antigen binding or maintenance of proper antibody structure and which residues should be removed or substituted in order to improve the structure of the humanized antibody.
Molecular models of the variable regions of both the non-human and humanized antibodies are thus prepared to assist the design of the humanized antibody. The modeling of these structures are based on the classifications of the variable region elements that were determined in the analysis procedure and can be obtained, for example, by using homology and ab initio techniques. The corresponding X-ray crystallographic structures can be obtained from the Brookhaven database.
Elements within the variable region of the non-human antibody of the invention, such as FRs, CDRs, and loop structures, are modeled on elements from similar, structurally solved, immunoglobulin variable regions. Steric clashes are identified in the models and consequently mismatched side-chains are selected for substitution. A particularly preferred approach for structure conformation includes categorization of the structural elements according to canonical classes based on those described by Chothia and his colleagues (Chothia et al., 1987, 1989, 1992 ibid; Tramontano et al., ibid). A preferred approach for structure prediction includes a database search or CONGEN search (Bruccoleri, R. E. et al., Biopolymers 26:137, 1987). The selected human Vκ and VH that would serve as the basis of the humanized antibody are similarly modeled and their amino acid sequences are studied to determine if any of their residues are likely to adversely influence binding specificity.
Energy minimization is preferably applied after adjusting the models for obvious steric clashes. Energy minimization is implemented here both to relieve unfavorable atomic contacts and to optimize van der Waals and electrostatic interaction.
As a result of the above design procedure the humanized antibody variants of BAT-1 may comprise additional, or substituted conservative amino acid residues which are not found in the recipient antibody or in the donor antibody. Deletion of amino acid residues included in the original acceptor or donor antibodies may also be applied. These modifications are made to refine antibody performance and have substantially no effect on antigen binding or other immunoglobulin functions. The sites of greatest interest for modifications include the hypervariable loops, but FR alterations are also contemplated. Hypervariable region residues or FR residues involved in antigen binding are generally substituted in a relatively conservative manner. The conservative substitutions that may be applied in the present invention comprise the following options: Val, Ile; Ser, Thr; Lys, Arg; Phe, Tyr; Trp, Leu; Asp, Ser; Cys, Thr; Gln, Lys; Val, Ala; Asn, Ser; Thr, Asn.
(iii) Construction of the Humanized Antibody Variants
Generally, the BAT-1 antibody variants are conventionally prepared in recombinant cell culture, as described in more detail below. Recombinant synthesis is preferred here but it is known to prepare peptides by chemical synthesis or to purify them from natural sources.
Molecular biology techniques and CDR grafting protocols suitable to carrying out the invention as herein described are known to those skilled in the art. Suitable teachings are described in numerous manuals and primary publications, including inter alia, Sambrook et al., (Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989); Ausubel et al., (Protocols In Molecular Biology, Green Publishing Associates and Wiley-Interscience, John Wiley and Sons, New York 1987, 1988, 1989); U.S. Pat. Nos. 5,225,539 and 5,585,089 which are herein incorporated by reference in their entirety including supplements.
The amino acid sequences of BAT-1 light and heavy chain CDRs are herein identified and illustrated in FIGS. 5 and 6: CDRL1 (SEQ. ID NO. 9 and SEQ L1 in FIG. 5): SARSS VSYMH; CDRL2 (SEQ. ID NO. 10 and SEQ L2 in FIG. 5): RTSNL AS; CDRL3 (SEQ. ID NO. 11 and SEQ L3 in FIG. 5): QQRSS FPLT; CDRH1 (SEQ. ID NO. 12 and SEQ H1 in FIG. 6): NYGMN; CDRH2 (SEQ. ID NO. 13 and SEQ H2 in FIG. 6): WINTD SGEST YAEEF KG; CDRH3 (SEQ. ID NO. 14 and SEQ H3 in FIG. 6): VGYDA LDY.
Using these amino acid sequences, oligonucleotides encoding these CDRs can be synthesized for use in the present invention. Also, the oligonucleotides may contain nucleotides in addition to those of BAT-1 CDRs, to facilitate cloning or to introduce restriction sites, for instance. Oligonucleotide synthesis techniques suitable to this aspect of the invention are well known to the skilled artisan and may be carried out using any of several commercially available automated synthesizers. In addition, DNAs encoding the CDRs set forth herein can be obtained through the services of commercial DNA synthesis vendors. It is thus not necessary to reclone BAT-1 CDRs from a natural source.
mBAT-1 CDRs are grafted into a human antibody to produce the humanized BAT-1 variants. It will be understood that human antibody in this context refers to any antibody that occurs in a human or an engineered antibody that has been designed, in some respect, to be compatible with the human immune system. Particularly preferred for this purpose are antibodies that, broadly, do not engender an adverse immune response in a patient.
To construct CDR-grafted humanized BAT-1 antibodies, oligonucleotides encoding the BAT-1 CDRs can be integrated into other DNAs encoding antibody heavy and light chains and fragments thereof, using well-known recombinant techniques such as those described in the above references. Particularly, BAT-1 CDRs can be introduced into practically any set of FRs in accordance with the present invention. A variety of human antibody genes are available in the form of publicly accessible deposits and suitable antibody genes can be synthesized from these sequences much as described above. Preferred techniques employed in this regard, for cloning and manipulating polynucleotides are illustrated by the methods and examples set forth.
The amino acid sequences of mBAT-1 and reshaped BAT-1 light (FIG. 5) and heavy (FIG. 6) chain FRs and modified FRs are herein identified: FRL1 (SEQ. ID NO.1): EIVLT QSPSS LSASV GDRVT ITC; FRL2 (SEQ. ID NO. 2): WXaaQQK PGKAP KLXbbI Y, wherein Xaa=F, Y and Xbb=W, L; FRL3 (SEQ. ID NO. 3): GVPSR FSGSG SGTXaaXbb XccLTIN SLQPE DFATY YC, wherein Xaa=D, S; Xbb=Y, F and Xcc=C, T; FRL4 (SEQ. ID NO. 4): FGGGT KLEIK; FRH1 (SEQ. ID NO. 5): QXaaQLV QSGSE LKKPG ASVKI SCKAS GYXbbFXcc, wherein Xaa=I, V; Xbb=T, S; Xcc=T, S; FRH2 (SEQ. ID NO. 6): WVXaaQA PGQGL XbbWMG, wherein Xaa=R, K; Xbb=Q, K; FRH3 (SEQ. ID NO. 7): RFXaaFS LDTSV XbbTAYL QITSL XccAEDT GMYFC XddXee, wherein Xaa=V, A; Xbb=N, .S; Xcc=T, N; Xdd=V, A; Xee=R, K; FRH4 (SEQ. ID NO. 8): WGQGT LVTVS S.
The oligonucleotides encoding the BAT-1 CDRs and/or specific FR residues originated from human antibodies may be used to introduce codons into the DNA encoding Vκ or VH of the humanized BAT-1 variants. In accordance with this aspect of the invention the additional codons may include those not derived from BAT-1 CDR as well as those that make up the CDR. These additional bases may be included to facilitate joining the CDR to the FRs from a heterologous source. They may comprise restriction sites or overlapping complementary regions for this purpose. The template DNAs are typically single-stranded DNAs (ssDNAs) vectors.
The CDRs of the BAT-1 heavy and light chains may also be modified particularly after incorporation into a humanized antibody using well-known recombinant DNA techniques for deleting, inserting and altering bases in a cloned or synthetic DNA or RNA. Site-specific mutagenesis techniques suitable to this end are well known to those of skill in the art, and are illustrated in the foregoing references on recombinant DNA techniques. These methods can be used to introduce practically any desired alteration into polynucleotides that encode the BAT-1 CDRs or into other regions of a closed heavy or light chain gene.
The synthesis of longer, double-stranded DNAs from shorter, overlapping, single-stranded DNAs is well known to those of skill in the art. Likewise, well known is the end-to-end joining of DNAs, including blunt-ended DNAs and those with at least partially overlapping complementary termini. These techniques are illustrated in the foregoing references on recombinant DNA techniques, for instance.
The construction of all versions of the human BAT-1 variable region is preferably carried out as described by Stemmer (Stemmer et al., GENE 164:49, 1995). Essentially, this method is favored for the synthesis of long DNA sequences from large numbers of oligodeoxyribonucleotides (oligos). The method relies on DNA polymerase using conventional PCR technique, to build increasingly longer DNA fragments during assembly process. Once the new variable region gene is synthesized it is preferentially subcloned into a vector which is transformed into competent cells as described in the above references. Putative positive clones can be identified by PCR-screening using appropriate primers and/or by restriction digest. Individual clones selected from the confirmed positive clones may be sequenced to double-stranded-DNA (ds-DNA). Preferably, the resultant ds-DNAs can be rechecked for PCR-induced errors, by sequencing, and corrected by subcloning correct fragments from other clones.
DNA of selected clones, from the confirmed positive clone, containing the humanized Vκ or VH of the BAT-1 variant may be directly inserted into expression vectors which comprise human light and heavy constant regions, respectively. Once DNA encoding the humanized BAT-1 CDR-grafted complete antibody variant, or the light or the heavy chain regions of the humanized BAT-1 CDR-grafted antibody, has been assembled, it may be inserted into a vector for propagation and expression by conventional techniques. In this manner desired amounts of the antibody may be obtained.
(iv) Expression of the Humanized BAT-1 Antibody Variants
The invention also provides isolated polynucleotide sequences encoding the complete humanized BAT-1 antibody, the light chain complete or variable region, heavy chain complete or variable region sequence, as well as vectors and host cells comprising the coding nucleic acid.
For recombinant production of the BAT-1 antibody, the polynucleotide sequence encoding said antibody or its fragments, is isolated and inserted into a replicable vector for further cloning, amplification or for expression. DNA encoding the antibody is readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the antibody). Many vectors are available which 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.
For expression, the polynucleotide encoding the humanized BAT-1 antibody or fragments thereof, may be cloned into an expression vector. Such vectors are well known to those skilled in the art. An expression control sequence, such as an immunoglobulin or viral promoter, is introduced upstream of the polynucleotide. Selection markers such as the dhfr gene, or other suitable selectable marker well known to those skilled in the art, are included in the vector to allow selection of host cells which are expressing the said polynucleotide included on the vector.
In one embodiment, the host cell endogenously produces antibodies, while in an alternative embodiment, the cell is genetically modified to produce antibodies. Examples of cells that endogenously produce antibodies include, but are not limited to hybridomas, lymphomas, plasmacytomas and EBV transformed cells. A cell can be genetically modified to produce antibodies by conventional methods, such as by transfection with a vector encoding an antibody molecule.
In use, the expression vector comprising the polynucleotide encoding the humanized BAT-1 antibody or fragments thereof, is transfected into cells. Transfection methods are well known in the art and such methods are suitable for employment in the present invention. The cells expressing the expression vector are selected using the selectable marker incorporated into the expression vector or a vector used for co-transfection. Cells expressing the antibody can be screened by enzyme-linked immunoabsorbent assay (ELISA) assays or other suitable methods well known to those skilled in the art.
The humanized BAT-1 antibody variants are introduced into a host cell by transfection of a vector comprising polynucleotide encoding the complete or Fv fragment of the antibody. Humanized BAT-1 antibody variants is also introduced into a host cells by co-transfection of: (i) a vector comprising polynucleotide encoding the variable or complete light chain region of the antibody and (ii) a vector comprising polynucleotide encoding the variable or complete heavy chain region of the antibody.
In a most preferred embodiment, the antibody of the invention is produced by a transfection of a single vector comprising polynucleotide sequences encoding the light and heavy variable regions of the antibody. Most preferably, this vector further comprises two promoters, each operatively linked to the polynucleotide sequence encoding the light chain and the heavy chain regions of reshaped BAT-1. The resulting expression of the BAT-1 antibody is higher than its expression following co-transfection with two vectors, each encoding the light chain or heavy chain regions, of the antibody, whereas the transfection and co-transfection being conducted in a similar host cell.
The humanized BAT-1 antibody variants can be expressed in any suitable cell type, including but not limited to mammalian, avian, insect, bacterial or yeast cells. Examples of mammalian cells include, but are not limited to, human, rabbit, rodent (e.g., mouse, rat) and bovine cells. In preferred embodiments, the cell is a myeloma cell, a Chinese hamster ovary (CHO) cell, COS cell, COS7 cell or fibroblast.
Antibody-producing cell lines may be cultured using techniques well known to the skilled artisan. Such techniques are described in a variety of laboratory manuals and primary publications. For instance, techniques suitable for use in the invention as described below are described in current protocols in immunology, Coligan et al., (Green Publishing Associates and Wiley-Interscience, John Wiley & Sons, N.Y. 1991) which is herein incorporated by reference in its entirety, including supplements.
The humanized monoclonal antibodies of the invention can be frozen or lyophilized for storage and reconstituted in a suitable carrier prior to use. This technique has been shown to be effective with conventional immune globulins and art-known lyophilization and reconstitution techniques can be employed. It will be appreciated by those skilled in the art that lyophilization and reconstitution can lead to varying degrees of antibody activity loss and that use levels may have to be adjusted to compensate.
(v) Purification of Humanized BAT-1 Antibody
Using recombinant techniques, the antibody can be produced intracellularly, in the periplasmic space, or directly secreted into the medium. If the antibody is produced intracellularly, as a first step the particulate debris, either host cells or lysed fragments, is removed, for example, by centrifugation or ultrafiltration. Carter et al., (Biotechnology 10:163, 1992) describe a procedure for isolating antibodies which are secreted to the periplasmic space of E. coli. Briefly, cell paste is thawed in the presence of sodium acetate (pH 3.5), EDTA, and phenylmethylsulfonylfluoride (PMSF) over about 30 min. Cell debris can be removed by centrifugation.
In a most preferred embodiment, the antibody of the invention is secreted into the medium, supernatants from such expression systems are generally first concentrated using a commercially available protein concentration filter, for example, an Amicon or Millipore ultrafiltration unit. A protease inhibitor may be included in any of the foregoing steps to inhibit proteolysis and antibiotics may be included to prevent the growth of adventitious contaminants.
The antibody composition prepared from the cells can be purified using methods well known in the art, for example, hydroxyapatite chromatography, gel electrophoresis, dialysis, and affinity chromatography, with affinity chromatography particularly with protein A, being a preferred purification technique. The matrix to which the affinity ligand is attached is most often agarose, but other matrices are available. Mechanically stable matrices, such as controlled pore glass or poly(styrenedivinyl)benzene, allow for faster flow rates and shorter processing times than can be achieved with agarose. Where the antibody comprises a CH3 domain, the Bakerbond ABXTM resin (J. T. Baker, Phillipsburg, N.J.) is useful for purification. Other techniques for protein purification such as fractionation on an ion-exchange column, ethanol precipitation, reverse phase HPLC, chromatography on silica, chromatography on heparin SEPHAROSETM, chromatography on an anion or cation exchange resin (such as a polyaspartic acid column), chromatofocusing, SDS-page, and ammonium sulfate precipitation are also available depending on the antibody to be recovered.
(vi) Deposit of Cell Line
According to a representative embodiment of the present invention the humanized BAT monoclonal antibodies are identical in their function or activity to those produced by cells deposited under ATCC # (PTA-5189), on May 9, 2003.
III. Pharmacology
(i) Pharmaceutical Compositions
The invention also provides a composition comprising the antibody of the invention.
According to another embodiment, the present invention provides a pharmaceutical composition comprising as an active ingredient the antibody of the invention, for use in diagnosis and therapy. Said compositions may be in any pharmaceutical form suitable for administration to a patient, including but not limited to solutions, suspensions, lyophilized powders for reconstitution with a suitable vehicle or dilution prior to usage, capsules and tablets. The pharmaceutical compositions disclosed in this invention may further comprise any pharmaceutically acceptable diluent or carrier to provide a physiologically acceptable conjugates comprising the antibodies with therapeutic agents for diagnosis, prognosis and therapy, among others.
Pharmaceutical compositions of the present invention may be manufactured by processes well known in the art, e.g., by means of conventional mixing, dissolving, granulating, grinding, pulverizing, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes.
Pharmaceutical compositions for use in accordance with the present invention thus may be formulated in conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries, which facilitate processing of the active compounds into preparations which, can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen.
For injection, the compounds of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hank's solution, Ringer's solution, or physiological saline buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants, for example polyethylene glycol, are generally known in the art. Pharmaceutical compositions which can be used orally, include push-fit capsules.
For administration by inhalation, the molecules for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from a pressurized pack or a nebulizer with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichloro-tetrafluoroethane or carbon dioxide. In the case of a pressurized aerosol, the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin for use in an inhaler or insufflator, may be formulated containing a powder mix of the polypeptide and a suitable powder base such as lactose or starch.
Pharmaceutical compositions for parenteral administration include aqueous solutions of the active ingredients in water-soluble form. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable natural or synthetic carriers are well known in the art. Optionally, the suspension may also contain suitable stabilizers or agents, which increase the solubility of the compounds, to allow for the preparation of highly concentrated solutions. Alternatively, the active ingredient may be in powder form for reconstitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.
Pharmaceutical compositions suitable for use in context of the present invention include compositions wherein the active ingredients are contained in an amount effective to achieve the intended purpose. All formulations for administration should be in dosages suitable for the chosen route of administration. More specifically, a “therapeutically effective” dose means an amount of a compound effective to prevent, alleviate or ameliorate symptoms of a disease of the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein.
Toxicity and therapeutic efficacy of the compositions described herein can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., by determining the IC50 (the concentration which provides 50% inhibition) and the maximal tolerated dose for a subject compound. The data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage may vary depending upon the dosage form employed and the route of administration utilized. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. Depending on the severity and responsiveness of the condition to be treated, dosing can also be a single administration of a slow release composition, with course of treatment lasting from several days to several weeks or until cure is effected or diminution of the disease state is achieved. The amount of a composition to be administered will, of course, be dependent on the subject being treated, the severity of the affliction, the manner of administration, the judgment of the prescribing physician, and all other relevant factors.
(ii) Methods of Treatment
Antibodies in accordance with the invention, while being useful for a variety of therapeutic indications, are used, in accordance with a currently preferred embodiment of the invention, for the treatment of cancer. It has been found that a monoclonal antibody in accordance with the invention elicits anti-tumor effects in a variety of tumors. Within the scope of the present invention, methods are provided for the use of the novel hBAT-1 for the treatment of tumor by administering to a subject an effective amount of the antibody of the invention. The term “effective amount” should be understood as meaning an amount of an antibody required to achieve a therapeutic effect. The effective amount required to achieve the therapeutic end result may depend on a number of factors including, for example, the tumor type and the severity of the patient's condition (i.e. the cancerous state), and whether the antibody is co-administered together with another agent which acts together with the antibody in an additive or synergistic manner. The antibody may be administered either following detection of primary or secondary tumors in the subject or, as preventive therapy of a subject having a high risk of developing cancers, such as an individual exposed to radiation or such having a genetic pre-disposition.
The invention additionally provides a method of treating a subject in need thereof, with a humanized BAT-1 antibody variant or with a composition that comprises said antibody as an active ingredient.
According to yet another embodiment, the present invention provides a method for diagnosis or treatment of a disease or a disorder, particularly cancer, comprising administering to a subject in need thereof, an effective amount of a pharmaceutical composition comprising the antibody of the invention as an active ingredient.
The method of treatment comprises administering an antibody or composition of the invention to a subject. The method of treatment also comprises administration an antibody or composition of the invention to a subject in parallel to, prior to, or following treatment with an additional active composition comprising cytokines such as IL-1 (interleuken-1), IL -2, IL -6 and IFN-α (interferon-α) or other antibodies, such as any T-cell stimulatory antibody or other anti-tumor therapeutic antibody. In one embodiment, the subject is a human. In another embodiment the disease to be prevented, treated or detected is cancer.
The administration of said compositions can be typically achieved by means of parenteral administration, e.g., intravenously (i.v.) intraperitoneally (i.p.) or intramuscularly (i.m.). Methods of treatment may comprise pharmaceutical compositions of the antibodies according to the invention. Alternatively or additionally, methods of treatment may include cell therapy, ex-vivo or in-vivo wherein cells are autologous or allogeneic.
In order to boost the anti-tumor activity of the antibody, it is at times advantageous to administer the antibody of the invention together with, prior to, or following, the administration of other agents, which can act in an additive or synergistic manner with it. Examples comprise various cytokines, including but not limited to IL-1 (Interleuken-1), IL-2, IL-6 and IFN-α (Interferon-α), as well as cell vaccines or additional antibodies, including but not limited to T-cell stimulatory antibodies, or anti-tumor therapeutic antibodies.
The antibody of the invention may be useful in the therapy of a variety of diseases other than cancer where activation or other effects of the antibody on the immune system's proliferative, cytolytic or stimulatory activity may have a therapeutic effect, such as, for example, in early stages of HIV infection or in patients whose blood count shows a decrease in CD4+ T cells (the causative virus of AIDS, Acquired Immune Deficiency Syndrome), in various autoimmune disorders, or in some cases of genetic or acquired immune deficiencies. In AIDS patients, the antibody may be administered to infected individuals, which have not yet developed any symptoms of the disease, or in individuals at early stages of the HIV infection process.
The dose of the antibody or composition to be administrated to a subject, in the context of the present invention should be sufficient to effect a beneficial therapeutic response in the subject over time, or to inhibit tumor growth. Thus, the antibody or composition may be administered to a subject in an amount sufficient to alleviate, reduce, cure or at least partially arrest the disease.
The dose will be determined by the activity of the therapeutic composition produced and the condition of the subject, as well as the body weight or surface area of the subject to be treated. The size of the dose and the dosing regiment also will be determined by the existence, nature, and extent of any adverse side effects that accompany the administration of a particular therapeutic composition in a particular subject. In determining the effective amount of the therapeutic composition to be administered, the physician needs to evaluate circulating plasma levels, toxicity, and progression of the disease.
EXAMPLES
Having now generally described the invention, the same will be more readily understood through reference to the following examples, which are provided by way of illustration and are not intended to be limiting of the present invention.
Example 1
Sequence Analysis of the Mouse BAT-1 Kappa Light Chain Variable Region (Vκ)
The DNA and amino acid sequences of the BAT-1 Vκ region is shown in FIG. 1. The amino acid sequences were compared with other mouse variable regions and also with the consensus sequences of the subgroups that the variable regions were subdivided into in the Kabat database (Kabat et al., ibid). From this analysis the BAT-1 Vκ region was found to most closely match the consensus sequences of both mouse kappa subgroup IV (Identity=88.38%; Similarity=92.45) and mouse kappa subgroup VI (Identity=87.74%; Similarity=89.62). When only the FRs of the BAT-1 kappa light chain variable region (i.e. without the amino acids in the CDRs) were compared to mouse subgroups IV and VI, percentage identity increased to exactly 90.00% for both, while percentage similarity rose to 92.50%, again for both consensus sequences. However, despite the close similarities to both Kabat subgroups, it was decided that the murine BAT-1 Vκ region should be classed as mouse subgroup VI.
The reason for the selection of mouse subgroup VI was related to the canonical classes of the hypervariable loops of the BAT-1 Vκ region, as defined by Chothia and his co-workers (Chothia et al., J. Mol. Biol. 196:901, 1987; Nature 34:877, 1989; J. Mol. Biol. 227:799, 1992; Tramontano et al., ibid). According to Chothia, each of the CDRs: CDR1 (L1), CDR2 (L2) and CDR3 (L3), were canonical class 1 (FIG. 2). Crucially, the 10 amino acid canonical class 1 L1 hypervariable loop was only seen in mouse Vκ regions which fitted Kabat subgroup VI.
Most restrictive canonical classes for the CDR related loops structures have more recently been defined by Martin and Thornton (Martin et al, ibid) and these too are described in FIG. 2. The utility of these new canonical class definitions lies in their stringency, which in turn is related to the presence of a greater number of so-called framework canonical residues in each class. The importance of these “extra”, potentially key, residues was later considered when designing the humanized BAT-1 antibody. Loops L1 and L2 were easily assigned to Martins canonical classes 1/10A and 1/7A, respectively, however, the L3 loop did not perfectly match any of the classes available to it. The class that it most closely matched was class 1/9A, however, to fit this class there had to be residue at position 28 in the Vκ region of BAT-1, which is not actually present. The closest mouse kappa light chain variable region germline gene to BAT-1 Vκ was H4, which also contained a 10 amino acid L1 loop (Table 1). Only 12 mismatches were found between the H4 germline sequence and the BAT-1 Vκ region. The majority of these mismatches were positioned in the CDRs with only four differences located in the FRs. Most of these mismatches were highly conservative changes, except for the cysteine at position 72 (Kabat numbering) in FR3. Its location immediately adjacent to an important canonical residue (position 71) suggested that the cysteine may have a key role in antigen binding. Nevertheless, taken together, the above example clearly suggested that the BAT-1 sequence was typical of a mouse Vκ variable region.










TABLE 1







Seq.
Seq.
1Id.



Name
ID NO
Res
2Residues 1-50 of murine BAT Vκ Vs. mouse germline Vκ













BAT
94
106
QIVLTQSPAIMSASPGEKVTITCSARS------SVSYMHWQQKPGTSPKL


 


H4
95
83
.....................S...S.............Y.Y.....S...


 


H3/O
96
83
....................M....S...............Y...S.....


x1


 


R9
97
83
....................M....S.........I.....Y.........


 


H13
98
81
.........L..........M....S.............Y.Y....RS...


 


H8
99
81
..........L.........M....S.............X.......S...


 


H1
100
81
....................M......S.....V.S..LY.Y.....S...


 


H9
101
81
..L.................M....S...............Y.....S...


 


R2
102
76
E.L.......IA.............S.............N.Y.....S...


 


T3B
103
75
---.......A..L.....M....S.S.....V.S..L..Y...S......


 


R11
104
74
EN.........A........M....S.S.....V.S.NL..Y...S...T.


 


H6/X
105
74
E.........TA..L.Q........S...............Y...S.....


24


 


L8
106
74
EN.........A..L.....M....S.S.....V.S..L..Y...S.....


 


R1/s1
107
72
EN.........A..L.Q...M....S.S.....V.S..L..Y...S.A...


07b


 


R13
108
72
EN............L.....MS.R.S..........N..Y.Y...SDA...


 


H2
109
67
G.......TT.T.F...N.......S.........IN.I..Y...S.NT..













Seq
Seq.
1Id.



Name
ID NO
Res.
Residues 51-99 of murine BAT Vκ Vs. mouse germline Vκ













BAT
94
106
WIYRTSNLASGVPARFSGSGSGTSYCLTISRMEAEDAATYYCQQRSSFP


 


H4
95
83
PS........................S....S.............YH.Y.


 


H3/O
96
83
R...D..K..................S....S.............W..N.


x1


 


R9
97
83
R...D..K..................S....S...........H....Y.


 


H13
98
81
P...L.....................S....S.............W..N.


 


H8
99
81
....SI....................S....SVK...........W..S.


 


H1
100
81
....S.....................S....S........F....Y.QY.


 


H9
101
81
P...D.......F.............S.I..S...........H....Y.


 


R2
102
76
I...GI...................FSF..NS.....V..........Y.


 


T3B
103
75
P...G.........V...........S....S.............W..Y.


 


R11
104
74
F..........E...P..........S....SV............W.GY.


 


H6/X
105
74
P...EI.K..................S....S.......I.....WNYPL


24


 


L8
106
74
....G................A.I..S....S....ND.......W.GY.


 


R1/s1
107
72
PL.H......................S....SV....D.......W.GY.


07b


 


R13
108
72
....Y.....P............N..S....S..G..........FT.S.


 


H2
109
67
QK..K..D.P....TL..........S....SV............W.GY.





1No. of identical residues to the BAT sequence.


2A dot [.] refers to a match between BAT Vκ and the mouse germline Vκ and a line [-] refers to the absence of amino acid






Example 2
Sequence Analysis of the Mouse BAT-1 Heavy Chain Variable Region
The DNA and amino acid sequences of the BAT-1 VH region is shown in FIG. 3. An analysis similar to that given in Example 1 was conducted for the BAT-1 VH region which determined that it exhibited the closest match to the consensus sequence of the mouse heavy chain miscellaneous subgroup in the Kabat database (Kabat et al., ibid). Identity between the mouse heavy chain variable region amino acid sequence of mBAT-1 and the consensus sequences of the miscellaneous subgroup was measured at 60.64% while the similarity was calculated to be 69.23%, with the next closest Kabat subgroup consensus sequences being subgroup IIa (Identity=59.83%; Similarity=66.67%). However, when only the FRs of the BAT-1 VH region was compared to mouse subgroup IIa, percentage identity decreased to 54.02% while the similarity dropped to 62.06%. Conversely, the same comparisons carried out against the mouse miscellaneous subgroup found the FRs of the BAT-1 VH region exhibited a 65.52% identity and a 74.71% similarity.
When the canonical classes of the hypervariable loops of the BAT-1 VH region, as defined by Chothia and his co-workers, were analyzed (FIG. 4) the CDR1 and CDR2 loops (H1) matched Chothia canonical class 1 loops. However, no class was assigned to the CDR3 loop structure (H3) due to the wide range of size and amino acid make-up that H3 loops can display.
Using the more stringent canonical classes for CDR loop structures defined by Martin and Thornton (Martin et al., ibid) it was a straight forward matter to determine that the H1 loop matched Martin canonical class 1/10A. However, for the H2 loop it was more difficult to assign class, although the closest Martin canonical class was Class 2/10A. Unfortunately, since the amino acid Asp53 in the H2 loop did not match the expected residues for this position (i.e. Ala, Gly, Tyr, Ser, Lys, Thr or Asn), the match was also not perfect. The closest mouse heavy chain variable region germline gene to mBAT-1 VH identified was VMS2/VGK4 (Table 2). Thus the above example clearly suggested that the mBAT-1 sequence was typical of a mouse VH variable region.









TABLE 2







Seq. Name/
Seq.



1Id. Res.
ID NO
2Residues 1-50 of murine BAT VH Vs. mouse germline VH





BAT/117
110
QIQLVQSGPELKKPGETVKISCKASGYTFTNYGMN-WVKQAPGKGLKWMG


 


VMS2/VGK4/
111
...................................................


92


 


VMS9/VGK1A/
112
...................................................


251/90


 


VGK6/89
113
...................................................


 


VFM11/VGK1
114
...................................................


B/89


264/88
115
..............................T...S................


 


VFM1/281/VG
116
..............................D.S.H................


K7/87


 


VMS1/141/VG
117
................................A.H................


K3/84


 


161/84
118
...................................................


 


VGK5/79
119
--............................TA..Q....QKM.......I.


 


VGK2/77
120
---..............R............TA..Q....QKM.......I.


 


V104A/VAR10
121
.V..Q......VR..TS............LT.W.......XM..Q..E.I.


4A/57


 


VH105/57
122
.V..Q......V...AS.............S.YIH......R..Q..E.I.


 


VAR104/56
123
.V..Q......VR..TS............LT.W.......XR.AQ..E.I.


 


J558-43y/56
124
.V..Q......V...AS.R...........S.NIH......R..Q..E.I.


 


J558-122B/55
125
.V..Q......VR..TS............IT.W.......XR..Q.XE.I.


 


37A11/55
126
.V..L...A..M...AS.......T....SS.WIE......R..H..E.I.


 


VH104A/55
127
.V..Q......VR..TS............LT.W.......XM..Q..E.I.


 


VAR100/54
128
.V..Q......VR..LS..L.......I.IT.W........R..Q..E.I.





Seq. Name/
Seq



1Id. Res.
ID NO
2Residues 51-101 of murine BAT VH Vs. mouse germline VH





BAT/117
110
WINTDSG--ESTYAEEFKGRFAFSLETSANTAYLQINNLNNEDTATYFCVR


 


VMS2/VGK4/
111
....NT....P..................S.........K.........A.


92


 


VMS9/VGK1A/
112
....YT....P...DD.............S.........K.........A.


251/90


 


VGK6/89
113
....ET....P...DD.............S.........K.........--


 


VFM11/VGK1
114
....YT....P...DD.............S.........K...M.....A.


B/89


 


264/88
115
....Y....VP...DD.............S.........K.........A.


 


VFM1/281/VG
116
....ET....P...DD.............S.........K.........A.


K7/87


 


VMS1/141/VG
117
.KY.NT....P..GDD.............S.........K...M.....A.


K3/84


 


161/84
118
....YT....P...DD...........C.S.........K.Q....-----


 


VGK5/79
119
....H....VPK...D.............S.........K...M.....--


 


VGK2/77
120
....H....VPK...D.............S......S..K.........--


 


V104A/VAR10
121
Q.FPA....STN.N.M...KATLTVD..SS...M.LSS.TS..S.V...A.


4A/57


 


VH105/57
122
Y.YPRD...STN.N.K...KATLTAD..SS...M.LSS.TS..S.V...A.


 


VAR104/56
123
Q.FPA....STN.N.M...KATLTVD..SS...M.LSS.TS........A.


 


J558-43y/56
124
..YPGD...NTK.N.K...KTTLTADK.SS...M.LSS.TS..S.V...A.


 


J558-122B/55
125
Q.FPA....STN.N.M...KATLTVD..SS...M.LSS.TS..S.VH..A.


 


37A11/55
126
K.LPG....STN.N.K...KAK.TADI.S....M.LSS.TS..S.V.Y.A.


 


VH104A/55
127
A.FPAG...STN.NQM...KATLTVD..SS...M.LSS.TS..S.V...A.


 


VAR100/54
128
Q.FPA....STN.N.M.E.KATLTVD..SS...M.LSS.TS..S.V.Y.A.





1No. of identical residues to the BAT sequence.


2A dot [.] refers to a match between BAT VH and the mouse germline VH and a line [-] refers to the absence of amino acid






Example 3
Design of the Humanized BAT-1 Vκ Antibody Variants
The first step in the design of the humanized variable regions of the BAT-1 antibody was the selection of the human kappa light chain variable region that would serve as the basis of the humanized BAT-1 Vκ region. As an aid to this process the BAT-1 Vκ region was initially compared to the consensus sequences of the four human kappa light chain variable region subgroups as defined by Kabat and his coworkers (Kabat et al., ibid).
The mouse BAT-1 light chain variable region was most similar to the consensus sequences of human kappa light chain subgroup I and human kappa light chain subgroup III. In the case of human kappa light chain subgroup I the mouse BAT-1 Vκ region displayed a 63.21% identity over the whole variable region and a 70.00% identity within the FRs alone. When measured with respect to similarity, these values increased to 71.70% overall and 80.00% within the FRs alone. In the case of human kappa light chain subgroup III the mouse BAT-1 Vκ region displayed a 65.09% identity over the whole variable region and a 68.75% identity within the FRs alone. When measured with respect to similarity, these values increased to 74.53% overall and 80.00% within the FRs alone. Consequently, it generally appeared to match well a broad range of human kappa light chain variable region sequences, however, with respect to FRs in particular, it was marginally more identical to those found within human kappa light chain subgroup I.
The mouse BAT-1 Vκ region was then compared to all the recorded examples of individual sequences of human variable regions publicly available. Table 3 shows the best fifteen matches to the mouse BAT-1 Vκ region which were identified through this analysis. Overall, the search algorithm selected the human Vκ region from antibody TEL9 (Marks et al., J. Mol. Biol. 222:581, 1991) as the closest match to the mouse BAT-1 Vκ region (Table 4). This human sequence had an overall identity to the BAT-1 Vκ region of 67.93% overall and 72.50% within the FRs alone. When measured with respect to similarity, these values increased to 77.36% overall and 82.50% within the FRs alone. Consequently, the TEL9 kappa light chain variable region FR was selected as the human acceptor sequence for the humanization of the BAT-1 antibody kappa light chain variable region. This then became the basis of the first humanized version of the BAT-1 kappa light chain (BATRκA), which essentially comprised the CDRs of the BAT-1 Vκ region and the FRs of the TEL9 Vκ region.
The next step in the design process was to study the amino acid sequences of the human acceptor TEL9 Vκ region FRs to determine if any of these amino acid residues were likely to adversely influence binding to antigen, either directly through interactions with antigen, or indirectly by altering the conformation or orientation of the CDR loops. This was a difficult process which was only made possible through the availability of a model of the BAT-1 variable regions i.e. both the Vκ and VH regions. The modeling procedure will be given in detail in Example 5. Nevertheless, any amino acid in the mouse BAT-1 FRs which did appear to affect antigen binding were then considered for conservation in the humanized BAT-1 antibody. In deciding which murine residues to conserve the following points were addressed:










TABLE 3






SEQ




Name
ID NO
1ID
2MURINE BAT Vκ VS. MOST HOMOLOGUES 15 HUMAN Vκ


















RESIDUES
129

 3SCSCCcccsCccccsccscccCCscssscscsssscccccCC


1-36


          1         2               3





0123456789012345678901234567ABCDEF890123456





  4v v                  =======L1========vv


BAT
129
100
-QIVLTQSPAIMSASPGEKVTITCSARS-------SVSYMWF


TEL9
130
64.8
 E.......SSL...V.DR.....R.SQ      SISN.LN.Y


Vlclone47
131
63.3
 D..M....SSL...V.DR.....R.SQ      SIS..LN.Y


SiP055
132
63.3
 E........TL.L....RA.LS.R.SQ      SVS..LA.Y


039741
133
63.9
 E........TL.L....RA.LS.R.SQ      SVS..LA.Y


AC32
134
63.9
 E........TL.L....RA.LS.R.SQ      SVS..LA.Y


AC21B
135
64.5
 E........TL.L....RA.LS.R.SQ      SVS..LA.Y


B9601(Vg-
136
62.7
 E........TL.L....RA.LS.R.SQ      SVS..LA.Y


Jk2)


LS1
137
62.4
 E........TL.L....RA.LS.R.SQ      SVS..LA.Y


TR1.21
138
63.0
 EL.M....SSL...V.DR.....R.SQ      SIS..LN.Y


AC18
139
63.0
 E........TL.L....RA.LS.R.SQ      SVSG.LA.Y


19.E7
140
63.6
 E........TL.L....RA.LS.R.SQ      SVS..LA.Y


STRAb SA-1A
141
63.0
 D.QM....SSL...V.DR.....R.SQ      SIS..LN.Y


Vlclone49
142
62.4
 D..M....SSL...V.DR.....R.SQ      SIS..LN.Y


MP6
143
62.4
 D.QM....SSL...V.DR.....R.SQ      SIS..LN.Y


AC33
144
63.6
 E........TL.L....RA.LS.R.SQ      SVG.SLA.Y


 


Residues


cccssccCsCCCCcccsccsSCCScCCCCCSCCSCccccccccs


37-80


   4         5         6         7         8





78901234567890123456789012345678901234567890





        vvvv==L2===       v v vv v


BAT

100
QQKPGTSPKLWIYRTSNLASGVPARFSGSGSGTSYCLTISRMEA


TEL9
130
64.8
.....KA...L..AA.T.Q....S.........DFT...NSLQP


Vlclone47
131
63.3
.....KA...L..AA.S.QS...S.........DFT....SLQP


SiP055
132
63.3
.....QA.R.L..DA..R.T.I...........DFT....SL.P


039741
133
63.9
.....QA.R.L..DA..K.T.............DFT....SL.P


AC32
134
63.9
.....QA.R.L..DA..R.T.I...........DFT....SL.P


AC21B
135
64.5
.....QA.R.L..DA..R.T.I...........DFT....SL.P


B9601(Vg-
136
62.7
.....QA.R.L..DA..R.T.I...........DFT....SL.P


Jk2)


LS1
137
62.4
..R..QA.R.L..DA..R.T.I...........DFT....SL.P


TR1.21
138
63.0
.....KA...L..AA...Q....S.........DFT....SLQP


AC18
139
63.0
.....QA.R.L..D.F.R.T.I...........DFT....SL.P


19.E7
140
63.6
.....QA.R.L..DA..R.T.I...........DFT....SL.P


STRAb SA-1A
141
63.0
.....KA...L..AA.S.Q....S.........DFT....SLQP


Vlclone49
142
62.4
.....KA...L..AA.S.Q....S.........DFT....SLQP


MP6
143
62.4
.....KA...L..AA.S.Q....S.........DFT....SLQP


AC33
144
63.6
.....QA.R.LV.D...R.T.I...........DFT....SL.P


 


RESIDUES


scccccCCccccc      ccccCcsccccc


81-107


         9               10





123456789012345ABCDEF67890123456A7





        =======L3=======v


BAT
129
100
EDAATYYCQ QRSSFP------LTFGSGTKLEI-K


TEL9
130
64.8
..F.......TN...      ....G...... .


Vlclone47
131
63.3
..F.......SY.T.      ....G...V.. .


SiP055
132
63.3
..F.V.......NW.      R...Q...... .


039741
133
63.9
..F.V.....S.KW.      ....G...V.. .


AC32
134
63.9
..F.V.......NW.P     ....G...V.. .


AC21B
135
64.5
..F.V.......NW.      ....G...V.. .


B9601(Vg-
136
62.7
..F.V.......NW.P     Y...Q...... .


Jk2)


LS1
137
62.4
..F.V.......NW.      ....G...V.. .


TR1.21
138
63.0
..F.......SY.T.      F...G...V.. .


AC18
139
63.0
..F.V......Y.W.P     ....G...V.. .


19.E7
140
63.6
..F.V.......NW.      ....P...VD. .


STRAb SA-1A
141
63.0
..F.......SY.T.      ....G...V.. .


Vlclone49
142
62.4
..F.......SY.T.      R...Q...V.. .


MP6
143
62.4
..F.......SY.P.PV    Y...Q...... .


AC33
144
63.6
..F.D.......EW.      ....G...V.. .





1ID - percentage identity of the human Vκ sequences to the murine BAT Vκ region


2A dot [.] refers to a match between BAT Vκ and the mouse germline Vκ, a line [-] refers to the absence of amino acid, underlined residues in the human Vκ sequences differ from their closest human Vκ gene


3S/C refers to amino acids positioned within 5Å of a CDR on the Surface or Core of Fv and s/c to amino acids positioned further away than 5Å of a CDR on the surface or core of Fv


4v refers to Vernier residues (Footer et al., J. Mol. Biol. 224:487, 1992) located in the FRs























TABLE 4








SEQ




4Kabat

3FR
4FR
6FR near


Name
ID NO
1ID
2All
3Surface
Core
CDR
5FR
Surface
Core
CDR





BAT Vκ
129
100.0
106
23
81
26
80
17
63
32


TEL9
130
64.8
70
11
59
13
58
10
50
26


VI clone47
131
63.3
69
11
59
13
57
10
50
26


SiP055
132
63.3
69
11
59
13
57
10
50
26


039741
133
63.9
69
11
59
13
57
10
50
26


AC32
134
63.9
69
11
59
13
57
10
50
26


AC21B
135
64.5
69
11
59
13
57
10
50
26


B9601 (Vg-Jk2)
136
62.7
69
11
59
13
57
10
50
26


LS1
137
62.4
68
11
59
13
57
10
50
26


TR1.21
138
63.0
68
11
58
13
57
10
50
26


AC18
139
63.0
68
11
58
13
57
10
50
26


19.E7
140
63.6
68
11
58
12
57
10
50
26


STRAb SA-1A
141
63.0
68
11
58
12
57
10
49
26


VIclone49
142
62.4
68
11
58
12
57
10
49
26


MP6
143
62.4
68
11
58
12
57
10
49
25


AC33
144
63.6
68
11
58
12
57
10
49
25


























Close









SEQ



Human
9L1
L2
L3
10L1
L2
L3


Name
ID NO
7Vernier
8Vκ
8J
Germline
Size
Size
Size
Class
Class
Class





BAT Vκ
129
14
94
12

10
7
9
?
1/7A
?


TEL9
130
12
60
10
DPK8-Vd+
11
Same
Same
2/11A
Same
?


VIclone47
131
12
60
10
V3b+
11
Same
Same
2/11A
Same
1/9A


SiP055
132
12
60
10
3A7
11
Same
Same
2/11A
Same
1/9A


039741
133
12
59
10
3A7


AC32
134
12
59
10
3A7
11
Same
10
2/11A
Same
?


AC21B
135
12
59
10
3A7
11
Same
Same
2/11A
Same
1/9A


B9601 (Vg-Jk2)
136
12
59
10
3A7
11
Same
10
2/11A
Same
?


LS1
137
12
59
10
3A7
11
Same
Same
2/11A
Same
1/9A


TR1.21
138
12
59
10
V3b+
11
Same
Same
?
Same
1/9A


AC18
139
12
59
10
3A7
11
Same
10
2/11A
Same
?


19.E7
140
12
59
10
3A7
11
Same
Same
2/11A
Same
1/9A


STRAb SA-1A
141
12
59
10
V3b+
11
Same
Same
2/11A
Same
1/9A


VIclone49
142
12
59
10
V3b+
11
Same
Same
2/11A
Same
1/9A


MP6
143
12
59
10
V3b+
11
Same
11
2/11A
Same
?


AC33
144
12
59
10
3A7
11
Same
Same
2/11A
Same
1/9A





1ID - percentage identity of the human Vκ sequences to the murine BAT Vκ region


2All - number of identical residues in the whole of the human Vκ region when compared to the whole of the murine BAT Vκ region


3Surface (FR Surface) - number of identical (FR) residues on the surface


4Core (FR Core) - number of identical residues within the (FR) core of the Fv domain


5CDR/FR - number of identical residues within the CDRs or the FRs;


6FR Near CDR - represents the number of identical residues amongst the FR amino acids within 5Å of a CDR;


7Vernier - number of identical residues amongst the 14 Vernier amino acids (Foote et al., ibid);


8Vκ (J Chain) - number of identical residues within the Vκ (J Chain) gene


9L1 to L3 Size - number of residues in each CDR


10L1 to L3 Class - Canonical class of the CDR according to Martin & Thornton (Martin et al., ibid)






    a. It was of great importance that the canonical structures for the hypervariable loops (Chothia et al., 1987, 1989, 1992 ibid; Tramontano et al., ibid) were conserved. Consequently, it was crucial to conserve in the humanized BAT-1 variable regions all the mouse FR residues that were part of these canonical structures.
    b. The sequences of the mBAT-1 antibody variable regions were compared to similar sequences from other mouse antibodies to identify unusual or rare residues—which may have indicated an important role in antigen binding. This was then investigated using the model of the BAT-1 variable region genes.
    c. A direct analysis of the model was also made to try and predict whether any of the other mouse FR residues not present in the humanized FRs could influence antigen binding in some way.
    d. Comparisons of the individual human acceptor sequences for the kappa light and heavy chain variable regions to the consensus sequence of human variable regions subgroups to which the acceptor sequences belonged were also made. The identification of any idiosyncratic amino acids in the human donor sequences was important as these could have adversely affected antigen binding.
    e. Since the human light and heavy chain variable regions selected would be derived from two different human antibodies (see Example 4 for the selection of the human VH acceptor sequence), a careful analysis of the interdomain packing residues of both the donor and acceptor kappa light variable regions should be carried out. This was because any miss-packing in this region could have had a dramatic affect upon antigen binding, irrespective of the conformation of the CDR loop structures of the humanized BAT-1 antibody.
    f. By following this design process, a number of amino acids in the murine BAT-1 Vκ FRs were identified for conservation in the second version (BATRκB) of the humanized BAT-1 antibody (Table 5). Table 5 provides alignment of amino acid sequences leading to the design of the first (BATRκA) and second (BATRκB) reshaped human versions of the BAT-1 antibody kappa light chain variable region. There were 21 amino acid differences between the FRs of the donor mouse BAT-1 Vκ region and the acceptor human TEL9 Vκ region. However, there were only five residues in the humanized FRs where it was considered necessary to change the amino acid present in the human FRs to the amino acid present in the original mouse FRs.


The Vκ region amino acids, located at the Vκ/VH interface as defined by Chothia and colleagues (Chothia et al., J. Mol. Biol. 186:651, 1985), were checked for unusual or rare residues. From this analysis, the only residue position that raised any level of concern was the Phe at position 36 (Phe36) in FR2. Tyr (as found in TEL9) was normally seen at this position, however, in mBAT-1 Phe was present. In addition, position 36 was a recognized position for a Vernier amino acid (Foote et al., ibid). Vernier residues were thought to be important for maintaining CDR loop conformation. Moreover, Phe was not commonly seen in Kabat mouse subgroup VI (21/153) while Tyr was very commonly seen in both mouse subgroup VI (131/153) and human subgroup I (66/74) (Kabat et al., ibid). Consequently, a Tyr36Phe change was thought to be appropriate, both to mimic the interdomain packing found in BAT-1, between the two heterologous human acceptor variable regions, and also to maintain CDR loop conformation.

















TABLE 5











Human








FR or
Mouse
Mouse
Human
acceptor
Surface
BAT
BAT


Kabat
#
CDR
BAT Vκ
κ-VI
κ-I
TEL9
or Core
RκA
RκB
Comment







SEQ


129
161
162
130

15
16



ID NO


1
1
FR1
Q
Q
D
E
S
E
E


2
2

I
I
I*
.
C
I
I
Chothia Canonical (L1);












Martin Canonical (L1/L3);












Vernier


3
3

V
V*
Q
.
S
V
V
Martin Canonical (L3);


4
4

L
L*
M
.
C
L
L
Chothia Canonical (L1/L3);












Martin Canonical (L1/L3);












Vernier


5
5

T
T
T*
.
C
T
T


6
6

Q
Q*
Q
.
c
Q
Q


7
7

S
S*
S*
.
c
S
S


8
8

P
P*
P*
.
c
P
P


9
9

A
A*
S*
S
s
S
S


10
10

I
I*
S
S
C
S
S


11
11

M
M
L
L
c
L
L


12
12

S
S
S*
.
c
S
S


13
13

A
A*
A
.
c
A
A


14
14

S
S*
S
.
c
S
S


15
15

P
P
V*
V
s
V
V


16
16

G
G*
G*
.
c
G
G


17
17

E
E
D
D
c
D
D


18
18

K
K*
R
R
s
R
R


19
19

V
V*
V
.
c
V
V


20
20

T
T*
T*
.
c
T
T


21
21

I
M
I*
.
c
I
I


22
22

T
T*
T
.
C
T
T


23
23
FR1
C
C*
C*
.
C
C
C
Martin Canonical (L1/L2)


24
24
CDR1
S
S
R
R
s
S
S


25
25
|
A
A*
A
.
c
A
A
Chothia Canonical (L1);












Martin Canonical (L1)


26
26
|
R
S*
S
S
s
R
R


27
27
|
S
S*
Q
Q
s
S
S


 27A 

|
—
—
S
—
s
—
—


 27B

|
—
—
L
—
c
—
—


 27C

|
—
—
V
—
s
—
—


 27D

|
—
—
x
—
c
—
—


 27E

|
—
—
x
—
s
—
—


 27F

|
—
—
—
—
s
—
—


28

|
—
—
S
S
s
—
—
Martin Canonical (L3);












There is no amino acid












here in BAT Vκ


29
28
|
S
S*
I
I
s
S
S
Martin Canonical (L3)


30
29
|
V
V
S
S
c
V
V
Chothia Canonical (L1);












Martin Canonical (L1)


31
30
|
S
S
N
N
c
S
S
Martin Canonical (L3)


32
31
|
Y
Y*
Y
.
c
Y
Y
Martin Canonical (L3)


33
32
|
M
M
L*
L
c
M
M
Chothia Canonical (L1);












Martin Canonical (L1/L3)


34
33
CDR1
H
H
A
N
c
H
H
Packing AA


35
34
FR2
W
W*
W*
.
C
W
W
Martin Canonical (L1);












Vernier


36
35

 
 
 
 
C
Y
F
Packing AA; Vernier;












Mouse germline = Tyr;












(Δ1)


37
36

Q
Q*
Q
.
c
Q
Q


38
37

Q
Q*
Q
.
c
Q
Q
Packing AA


39
38

K
K*
K
.
c
K
K


40
39

P
S
P*
.
s
P
P


41
40

G
G
G
.
s
G
G


42
41

T
T
K
K
c
K
K
Mouse germline = Ser


43
42

S
S*
A
A
c
A
A


44
43

P
P*
P*
.
C
P
P
Core packing AA


45
44

K
K*
K
.
s
K
K


46
45

L
R
L
.
C
L
L
Vernier; Packing AA;












Mouse germline = Pro


47
46

 
 
 *
 
C
L
W
Vernier; (Δ2)


48
47

I
I*
I*
.
C
I
I
Chothia Canonical (L2);












Vernier


49
48
FR2
Y
Y*
Y
.
C


Vernier


50
49
CDR2
R
D
A
A
c
R
R


51
50
|
T
T
A
A
c
T
T
Chothia Canonical (L2)


52
51
|
S
S*
S
.
c
S
S
Chothia Canonical (L2)


53
52
|
N
K
S
T
s
N
N


54
53
|
L
L*
L*
.
c
L
L


55
54
|
A
A
E
Q
c
A
A


56
55
CDR2
S
S*
S′
.
s
S
S


57
56
FR3
G
G*
G*
.
S
G
G


58
57

V
V*
V
.
C
V
V


59
58

P
P*
P*
.
C
P
P


60
59

A
A
S*
S
S
S
S


61
60

R
R*
R*
.
c
R
R


62
61

F
F*
F*
.
C
F
F


63
62

S
S*
S
.
C
S
S


64
63

G
G*
G*
.
C
G
G
Chothia Canonical (L2);












Vernier


65
64

S
S*
S
.
C
S
S


66
65

G
G*
G*
.
C
G
G
Vernier


67
66

S
S*
S
.
S
S
S


68
67

G
G*
G*
.
C
G
G
Vernier


69
68

T
T
T
.
C
T
T
Vernier


70
69

S
S*
D
D
S
D
D


71
70

 
Y
F
F
C
F
Y
Chothia Canonical (L1);












Martin Canonical (L1);












Vernier; (Δ3)


72
71

 
S*
T
T
c
T
T
Mouse germline = Ser


73
72

L
L*
L
.
c
L
L


74
73

T
T*
T
.
c
T
T


75
74

I
I*
I
.
c
I
I


76
75

S
S
S
N
c
N
N


77
76

R
S
S
S
c
S
S
Mouse germline = Ser


78
77

M
M
L*
L
c
L
L


79
78

E
E*
Q
Q
c
Q
Q


80
79

A
A*
P
P
s
P
P


81
80

E
E*
E
.
s
E
E


82
81

D
D*
D
.
c
D
D


83
82

A
A
F
F
c
F
F


84
83

A
A*
A*
.
c
A
A


85
84

T
T
T
.
c
T
T


86
85

Y
Y*
Y*
.
c
Y
Y


87
86

Y
Y*
Y*
.
C
Y
Y
Packing AA


88
87
FR3
C
C*
C*
.
C
C
C
Martin Canonical (L3)


89
88
CDR3
Q
Q
Q
.
c
Q
Q
Martin Canonical (L3);












Packing AA


90
89
|
Q
Q*
Q
.
c
Q
Q
Chothia Canonical (L3);












Martin Canonical (L3)


91
90
|
R
W
Y
T
c
R
R
Martin Canonical (L3);












Packing AA


92
91
|
S
S
N
N
c
S
S
Martin Canonical (L3)


93
92
|
S
S
S
.
c
S
S
Martin Canonical (L3)


94
93
|
F
N
L
.
c
F
F
Martin Canonical (L3)


95
94
|
P
P
P
.
c
P
P
Chothia Canonical (L3);












Martin Canonical (L3)


 95A

|
—
P
E
—

—
—


 95B

|
—
M
—
—

—
—


 95C

|
—
P
—
—

—
—


 95D

|
—
—
—
—

—
—


 95E

|
—
—
—
—

—
—


 95F

|
—
—
E
—

—
—


96
95
|
L
L
W
.
c
L
L
Martin Canonical (L3);












Core packing AA


97
96
CDR3
T
T*
T
.
c
T
T
Martin Canonical (L3)


98
97
FR4
F
F*
F*
.
C
F
F
Martin Canonical












(L3); Vernier;












Core packing AA.


99
98

G
G*
G*
.
c
G
G


100
99

S
A
Q
G
s
G
G


101
100

G
G*
G*
.
c


102
101

T
T*
T*
.
c


103
102

K
K*
K
.
c
K
K


104
103

L
L*
V
.
c
V
V


105
104

E
E*
E
.
c
E
E


106
105

I
L
I
.
c
I
I


106A


—
—
—
—

—
—


107
106
FR4
K
K*
K
.
s
K
K









A second change was also decided upon at position 47 in FR2. The highly conserved Leu found in the human TEL9 kappa light chain variable region was changed to a Trp, as found in the mouse BAT-1 kappa light chain variable region. Position 47 was another recognized Vernier residue position and was also located near the VH interface according to the molecular model. In particular, it was close to Ala55 in H2 and may have been interacting with it. Therefore, although Trp was never seen at this core residue position in human VH sequences, it was felt prudent to conserve it in BATRκB by making the Leu47Trp modification.
The third FR change introduced into BATRκB was located at position 71, which as well as being identified as a Vernier residue position (Foote et al., ibid), was also recognized as being one of the important canonical residue positions for the L1 loop structure. These canonical residues were defined by Chothia and his co-workers (Chothia et al., 1987, 1989, 1992 ibid; Tramontano et al., ibid) as being vital for the conservation of the CDR loop structure. Many of the canonical amino acids were located within the CDRs, however, a number (such as 71Tyr) were also positioned within the FRs. Although the amino acid change was conservative, the Phe71Tyr change was considered critical for the successful humanization of the BAT-1 kappa light chain.
Other versions of the humanized Vκ region are:
BATRκC: Cys and Ser are similar in size and character, and from the model both amino acids at position 72 in FR3 appeared to be reasonably buried and pointing away from the L1 loop. However, in the case of the Cys amino acid the sulphur side-chain is exposed, according to the model, whereas according to the Kabat database (Kabat et al., ibid) the presence of Cys at this position is a unique event and Ser is commonly seen at this position (421/1234). Consequently, BATRκC contained the changes at Tyr36Phe, Leu47Trp and Phe71Tyr (as in BATRκB) plus the Ser72Cys modification to the Vκ FRs residues of the acceptor TEL9 antibody.

BATRκD: Evidence from the murine BAT-1 Fv model suggests that the surface exposed 69Ser is a residue which may interact with the L1 loop. In the human TEL9 kappa light chain the amino acid at this position is Asp, which is larger than Ser and positively charged. Ser is never seen at this position in human Vκ regions (Asp being by far the most common amino acid). The proximity to the L1 loop and the surface exposed nature of 69Ser tentatively suggested that it may be either interacting with L1 or even the antigen directly. Consequently, it was decided to make the Asp69Ser change in BATRκD, which was otherwise identical to BATRκC.

A description of the amino acid sequences of all the humanized BAT-1 antibody Vκ region variants proposed above is given in FIG. 5.
Although potential N-linked glycosylation sites i.e. Asn-Xaa-(Ser/Thr)-Xaa (Gavel et al., Protein Eng. 3:43, 1990) were searched for in both the donor mouse and acceptor human Vκ regions, as well as the humanized constructs themselves, none were identified.
Example 4
Design of the Humanized BAT-1 VH Antibody Variants
Again, the first step in the design of the humanized VH region of the mouse BAT-1 antibody was the selection of the acceptor human heavy chain variable region that would serve as the basis of the humanized BAT-1 VH region. When the mBAT-1 VH region was initially compared to the consensus sequences of the three human heavy chain variable region subgroups it was found to be most similar to the consensus sequence for human heavy chain subgroup I with a 61.54% identity overall and a 67.82% identity between the FRs alone. When measured with respect to similarity, these values also increased to 70.09% overall and 77.01% within the FRs alone.










TABLE 6






SEQ




Name
ID NO
ID
Murine BAT V11 Vs.most homologues 15 human VH


















Residues


scsCccccscScssccccsccCccccCSCCs  ccccCCCccsss


1-43


         1         2         3            4





12345678901234567890123456789012345AB67890123





  v                       -vvvv===H1==


BAT
145
100
QIQLVQSGPELKKPGETVKISCKASGYTFTNYGMN--WVKQAPG


hsighvl295
146
65.0
.V......S......AS..........S.SSHAI.  ..R....


R2C5H
147
60.3
.V......S......AS.........N..ST.AL.  .MRR...


030805
148
56.8
.V......A.V....AS..V..........S.DI.  ..R..T.


WIL2
149
57.7
.V......A.V....AS..V..E...V...GHY.H  ..R....


21/28
150
59.7
.V......A.V....AS..V..........S.A.H  ..R....


UC
151
57.7
.V.............AS..V..E.......GHY.H  ..R....


030802
152
58.2
.V......A.V....AS..V..........S.A.H  ..R....


039734
153
57.7
.V......A.V....AS..V..E.......GHY.H  ..G....


030812
154
56.3
.V.............AS..V..........S.Y.H  ..R....


030810
155
57.9
.V......A.V....AS..V..........S.Y.H  ..R....


4d275a
156
71.4
.V......S......AS..V..........S.A..  ..G....


030811
157
56.0
.V......A.V....AS..V..........S.Y.H  ..R....


IF10
158
59.3
.V......A.V....AS..V..........S.DI.  ..R....


GD9
159
71.4
.V......S......AS..V..........S.A..  ..R....


039232
160
59.3
.VH.....S.F....AS..V..........SSVI.  ..R....


 


Residues


cCCCCCcccccsc csccccsscssCCCCCCcSscccccccccsc


44-82


      5            6         7         8





456789012ABC345678901234567890123456789012ABC





    vvv=====H2=====-Kabat- v v v v   v


BAT
145
100
KGLKWMGWINT-DSGESTYAEEFKGRFAFSLETSANTAYLQINNL


hsighvl295
146
65.0
Q..Q....... NT.SP...QG.T...V...D..VS......TS.


R2C5H
147
60.3
Q.........L NT.NP...QD.T...V...D..V...F...SS.


030805
148
56.8
Q..E....M.P N..NTG..QK.Q..VTMTRN..IS...MELSS.


WIL2
149
57.7
Q..E......P N..GTN...K.Q..VTITRD..I....MELSR.


21/28
150
59.7
QR.E......A GN.NTK.SQK.Q..VTITRD...S...MELSS.


UC
151
57.7
Q..E......P N..GTN..QK.Q..VTITRD..I....MELSR.


030802
152
58.2
QR.E......A GN.NTK.SQK.Q..VTITRD...S...MELSS.


039734
153
57.7
Q..E......P N..GTN..QK.Q..VTITRD..I....MELSR.


030812
154
56.3
Q..E...I..P SG.STS..QK.Q..VTMTRD..TS.V.MELSS.


030810
155
57.9
Q..E...I..P SG.STS..QK.Q..VTMTRD..TS.V.MELSS.


4d275a
156
71.4
Q..E....... NT.NP...QG.T...V...D..VS......CS.


030811
157
56.0
Q..E...I..P SG.STS..QK.Q..VTMTRD..TS.V.MELSS.


IF10
158
59.3
Q..E....M.P N..NTG..QK.Q..VTMTRN..IS...MELSS.


GD9
159
71.4
Q..E....... NT.DP...QG.T...V...D..VS......SS.


039232
160
59.3
Q..E....... NT.NP...QG.T...V...D..VT.T.....S.


 


Residues


csscccccCCCCccsscccccc cccc ccCcsccccc


83-113


       9        10                   11





345678901234567890ABCDEFGHIJK1234567890123





     vv========H3=========v


BAT
145
100
NNEDTATYFCVRVGYDA-----------LDYWGQGTSVTVSS


hsighvl295
146
65.0
TA...GM...AKESHSSALDL       -.......L.....


R2C5H
147
60.3
QA....V.Y.AKPKRGTYRRGYYYYP  M.V.....T.....


030805
148
56.8
RS....V.Y.A.G..VWGSYRYTA   AF.I.....M.....


WIL2
149
57.7
RSD...V.Y.A.AS.CGYDCYY     FF.......L.....


21/28
150
59.7
RS....V.Y.A.G..YGSGS        -N......L.....


UC
151
57.7
RSD...V.Y.A.AS.CGYDCYY     FF.......L.....


030802
152
58.2
RS....V.Y.A..KWEQPIDAP      F.......L.....


039734
153
57.7
RSD...V.Y.A.AS.CGYDCYYF     F.......L.....


030812
154
56.3
RS....V.Y.A.D..YYDSNGYYSG  YF.......L.....


030810
155
57.9
RS....V.Y.A..QWLGLTGPN      -.......L.....


4d275a
156
71.4
KA....V.Y.A.-----           --------------


030811
157
56.0
RS....V.Y.A.D.IVVVPAAIPH   YF.......L.....


IF10
158
59.3
RS....V.Y.A.NNGSY          YF.......L.....


GD9
159
71.4
KA....V.Y.A.-----           --------------


039232
160
59.3
KA....V.Y.A.ELRNDHYVWXNYRPPLS-....--------









The mouse BAT-1 VH region was then compared to all the recorded examples of individual sequences of human variable regions publicly available. Tables 6 and 7 show the best fifteen matches to the mouse BAT-1 VH region which were identified through this analysis. Overall, the search algorithm selected the human VH region from antibody hsighv1295 (Fang et al., J. Exp. Med. 179:1445, 1994) as the closest match to the mouse BAT-1 VH region. This human VH region had an overall identity to the BAT-1 VH region of 69.23% (Table 7), a value which increased to 74.71% when the FRs alone were compared. When measured with respect to similarity, these values increased to 75.21% overall and 79.31% within the FRs alone. This human FR thus became the basis of the humanized version of the BAT-1 heavy chain.

















TABLE 7








SEQ




Kabat

FR
FR
FR Near


Name
ID NO
ID
All
Surface
Core
CDR
FR
Surface
Core
CDR





BAT VH
145
100
117
26
86
30
87
18
68
27


Hsighvl2
146
65.0
78
17
63
17
65
14
51
22


95


R2C5H
147
60.3
76
16
59
17
64
14
49
20


030805
148
56.8
71
16
56
14
59
13
47
19


WIL2
149
57.7
71
15
56
13
59
13
46
19


21/28
150
59.7
71
15
55
13
59
13
46
19


UC
151
57.7
71
15
55
13
59
13
46
19


030802
152
58.2
71
15
55
13
59
13
46
19


039734
153
57.7
71
15
55
13
57
13
46
19


030812
154
56.3
71
15
55
13
58
13
46
18


030810
155
57.9
70
15
55
13
58
13
46
17


4d275a
156
71.4
70
15
54
13
58
13
46
18


030811
157
56.0
70
15
54
13
58
13
46
18


IF10
158
59.3
70
15
54
13
58
13
46
18


GD9
159
71.4
70
15
54
11
58
13
46
18


039232
160
59.3
70
15
54
13
58
13
46
18





















SEQ



Close Human
H1
H2
H3
H1
H2


Name
ID NO
Vernier
VH
J
Germline
Size
Size
Size
Class
Class





BAT VH
145
16
98
19

5
17
8
?
?


Hsighvl2
146
13
70
14
VI-4.1b+
Same
Same
11
1/10A
2/10A


95


R2C5H
147
13
70
14
VI-4.1b+
Same
Same
17
Same
Same


030805
148
11
66
14
DP-15-V18+


WIL2
149
11
65
14
DP-8+
Same
Same
14
1/10A
Same


21/28
150
11
64
14
DP-25-VI3b+
Same
Same
10
1/10A
Same


UC
151
11
62
14
DP-8+
Same
Same
14
1/10A
Same


030802
152
11
62
14
DP-25-VI3b+


039734
153
11
62
14
DP-8+


030812
154
11
60
14
hv1fl0t


030810
155
11
59
14
hv1fl0t


4d275a
156
11
59
14
DP-21-4d275a+
Same
Same
0
Same
Same


030811
157
11
59
14
hv1fl0t


IF10
158
11
59
14
DP-15-V18+
Same
Same
9
Same
Same


GD9
159
11
58
14
VI-4.1b+
Same
Same
0
Same
2/10A


039232
160
11
58
14
VI-4.1b+





1ID—percentage identity of the human VH sequences to the murine BAT VH region


2All—number of identical residues in the whole of the human VH region when compared to the whole of the murine BAT VH region


3Surface (FR Surface)—number of identical (FR) residues on the surface


4Core (FR Core)—number of identical residues within the (FR) core of the Fv domain


5CDR/FR—number of identical residues within the CDRs or the FRs;


6FR Near CDR—represents the number of identical residues amongst the FR amino acids within 5Å of a CDR;


7Vernier—number of identical residues amongst the 14 Vernier amino acids (Foote et al., ibid);


8VH (J Chain)—number of identical residues within the VH (J Chain) gene


9L1 to L3 Size—number of residues in each CDR


10L1 to L3 Class—Canonical class of the CDR according to Martin & Thornton (Martin et al., ibid)






The next step in the design process was to study the amino acid sequences of the human acceptor hsighv1295 VH region FRs to determine if any of these amino acid residues were likely adversely influence binding to antigen. Once again, the molecular models built by OML (see Example 5) were crucial to this design process, from which a number of amino acids in the murine BAT-1 VH region FRs were identified for conservation in the first (BATRHA) and subsequent versions of the humanized BAT-1 antibody (Table 8). There were 22 amino acid differences between the FRs of the donor mouse BAT-1 and the acceptor human hsighv1295 VH regions and up to nine murine residues were considered for conservation in the humanized FRs.
BATRHA therefore consisted of the CDRs of the mouse BAT-1 antibody VH region genetically inserted into the FRs of the human hsighv1295 antibody VH region. This was the CDR-grafted version of the VH region of the humanized BAT-1 antibody and contained no FR amino acid changes whatsoever.
In BATRHB, the amino acids at positions 28 and 30 in FR1 of the mouse BAT-1 sequence (i.e. Thr and Thr, respectively) replaced the corresponding human hsighv1295 amino acids (i.e. Ser, and Ser, respectively) in the humanized BAT-1 heavy chain variable region. This was done because they represented some of the canonical residues important for the H1 hypervariable loop conformation (Chothia et al., 1992 ibid). Canonical residues were considered critical for the correct orientation and structure of hypervariable loops and were generally always conserved in a humanized variable region. Moreover, residue positions 27-30 were considered part of the H1 loop itself and so were even more critical to the correct conformation and orientation of this loop—justifying their conservation even more strongly. Thus, these two residue positions represented the sum of the changes made to the FRs of the human hsighv1295 sequence in BATRHB.
The next step in the design process was to study the amino acid sequences of the human acceptor hsighv1295 VH region FRs to determine if any of these amino acid residues were likely to adversely influence binding to antigen. Once again, the molecular models built by OML (see Example 5) were crucial to this design process, from which a number of amino acids in the murine BAT-1 VH region FRs were identified for conservation in the first (BATRHA) and subsequent versions of the humanized BAT-1 antibody (Table 8). There were 22 amino acid differences between the FRs of the donor mouse BAT-1 and the acceptor human hsighv1295 VH regions and up to nine murine residues were considered for conservation in the humanized FRs.
BATRHA therefore consisted of the CDRs of the mouse BAT-1 antibody VH region genetically inserted into the FRs of the human hsighv1295 antibody VH region. This was the CDR-grafted version of the VH region of the humanized BAT-1 antibody and contained no FR amino acid changes whatsoever.
In BATRHB, the amino acids at positions 28 and 30 in FR1 of the mouse BAT-1 sequence (i.e. Thr and Thr, respectively) replaced the corresponding human hsighv1295 amino acids (i.e. Ser, and Ser, respectively) in the humanized BAT-1 heavy chain variable region. This was done because they represented some of the canonical residues important for the H1 hypervariable loop conformation (Chothia et al., 1992 ibid). Canonical residues were considered critical for the correct orientation and structure of hypervariable loops and were generally always conserved in a humanized variable region. Moreover, residue positions 27-30 were considered part of the H1 loop itself and so were even more critical to the correct conformation and orientation of this loop—justifying their conservation even more strongly. Thus, these two residue positions represented the sum of the changes made to the FRs of the human hsighv1295 sequence in BATRHB.


















TABLE 8











Human









FR



Accep.
Surf.




or
Mouse
Mouse
Human
hsighv
or
BAT
BAT
BAT


Kabat
#
CDR
BAT VH
Misc.
I
1295
Core
RHA
RHB
RHC
Comment


























SEQ


145
163
164
146

20
21
22



ID


NO


















1
1
FR1
Q
E
Q
.
s
Q
Q
Q



2
2
|
I
V*
V
V
c
V
V
V
Martin Canonical (H1);













Vernier


3
3
|
Q
Q
Q
.
s
Q
Q
Q


4
4
|
L
L
L*
.
C
L
L
L
Martin Canonical (H1)


5
5
|
V
Q*
V
.
c
V
V
V


6
6
|
Q
Q*
Q
.
c
Q
Q
Q


7
7
|
S
S
S*
.
c
S
S
S


8
8
|
G
G
G*
.
c
G
G
G


9
9
|
P
A*
A
S
s
S
S
S


10
10
|
E
E
E
.
c
E
E
E


11
11
|
L
L*
V
.
S
L
L
L


12
12
|
K
V*
K
.
c
K
K
K


13
13
|
K
K
K*
.
s
K
K
K


14
14
|
P
P*
P*
.
s
P
P
P


15
15
|
G
G
G*
.
c
G
G
G


16
16
|
E
A
A
A
c
A
A
A


17
17
|
T
S*
S*
S
c
S
S
S


18
18
|
V
V*
V
.
c
V
V
V


19
19
|
K
K*
K
.
s
K
K
K


20
20
|
I
L
V
.
c
I
I
I
Martin Canonical (H1)


21
21
|
S
S
S
.
c
S
S
S


22
22
|
C
C
C*
.
C
C
C
C
Martin Canonical (H1)


23
23
|
K
T
K
.
c
K
K
K


24
24
|
A
A*
A
.
c
A
A
A
Chothia Canonical (H1);













Martin Canonical (H1)


25
25
|
S
S
S*
.
c
S
S
S


26
26
|
G
G
G*
.
c
G
G
G
Chothia Canonical (H1);













Martin Canonical (H1)


27
27
|
Y
P*
Y
.
C
Y
Y
Y
Chothia Canonical (H1);













Vernier


28
28
|
T
N
T
S
S
S
T
T
Vernier; (Δ1)


29
29
|
F
I*
F*
.
C
F
F
F
Chothia Canonical (H1);













Martin Canonical (H1);













Vernier


30
30
FR1
T
K
T
S
C
S
T
T
Vernier; (Δ2)


31
31
CDR1
N
D
S
S
s
N
N
N


32
32
|
Y
T
Y
H
c
Y
Y
Y
Martin Canonical (H1)


33
33
|
G
Y*
A
A
c
G
G
G
Martin Canonical (H1/H2)


34
34
|
M
M
I
I
c
M
M
M
Chothia Canonical (H1)













Martin Canonical (H1)


35
35
|
N
H
S
.
c
N
N
N
Martin Canonical (H1);













Packing AA.


35a 

|
—
—
—
—
—
—
—
—


35b 

CDR1
—
—
—
—
—
—
—
—


36
36
FR2
W
W
W*
.
C
W
W
W
Martin Canonical (H1)


37
37
|
V
V*
V
.
C
V
V
V
Packing AA.


38
38
|
K
K
R*
R
C
R
R
R


39
39
|
Q
Q
Q*
.
c
Q
Q
Q
Packing AA.


40
40
|
A
R
A
.
c
A
A
A


41
41
|
P
P
P
.
s
P
P
P


42
42
|
G
E*
G*
.
s
G
G
G


43
43
|
K
Q*
Q
Q
s
Q
Q
Q


44
44
|
G
G*
G
.
c
G
G
G


45
45
|
L
L
L*
.
C
L
L
L
Core packing AA.


46
46
|
K
E
E*
Q
C
Q
Q
Q


47
47
|
W
W
W*
.
C
W
W
W
Martin Canonical (H2);













Packing AA.


48
48
|
M
I*
M
.
C
M
M
M
Martin Canonical (H1)


49
49
FR2
G
G*
G*
.
C
G
G
G


50
50
CDR2
W
R
W
.
c
W
W
W
Martin Canonical (H2)


51
51
|
I
I
I
.
c
I
I
I
Martin Canonical (H1/H2)


52
52
|
N
D*
N
.
c
N
N
N
Martin Canonical (H2)


52a 
53
|
T
P*
P
.
c
T
T
T
Chothia Canonical (H2)













Martin Canonical (H2)


52b 

|
—
—
Y
—
—
—
—
—
Martin Canonical (H2)


52c 

|
—
—
—
—
—
—
—
—
Martin Canonical (H2)


53
54
|
D
A
G
N
s
D
D
D
Martin Canonical (H2)


54
55
|
S
N
N
T
c
S
S
S
Martin Canonical (H2)


55
56
|
G
G
G
.
c
G
G
G
Chothia Canonical (H2);













Martin Canonical (H2)


56
57
|
E
N
D
S
s
E
E
E
Martin Canonical (H2)


57
58
|
S
T
T
P
c
S
S
S


58
59
|
T
K
N
.
c
T
T
T
Martin Canonical (H2)


59
60
|
Y
Y
Y
.
c
Y
Y
Y
Martin Canonical (H2)


60
61
|
A
D
A
.
c
A
A
A


61
62
|
E
P*
Q
Q
s
E
E
E


62
63
|
E
K*
K
G
s
E
E
E


63
64
|
F
F*
F
.
c
F
F
F


64
65
|
K
Q*
Q
T
s
K
K
K


65
66
CDR2
G
G
G
.
s
G
G
G


66
67
FR3
R
K
R
.
C
R
R
R


67
68
|
F
A
V
.
C
F
F
F


68
69
|
A
T*
T
V
C
V
V
V


69
70
|
F
I
I
.
C
F
F
F
Martin Canonical (H1/H2)


70
71
|
S
T*
T
.
C
S
S
S


71
72
|
L
A*
A
.
C
L
L
L
Chothia Canonical (H2);













Martin Canonical (H2)


72
73
|
E
D
D
D
c
D
D
D


73
74
|
T
T*
T
.
S
T
T
T


74
75
|
S
S*
S*
.
s
S
S
S


75
76
|
A
S*
T
V
c
V
V
V


76
77
|
N
N*
S
S
c
S
S
N
(Δ3)


77
78
|
T
T*
T
.
c
T
T
T


78
79
|
A
A*
A
.
c
A
A
A
Martin Canonical (H1/H2)


79
80
|
Y
Y*
Y
.
c
Y
Y
Y


80
81
|
L
L
M
.
c
L
L
L
Martin Canonical (H1)


81
82
|
Q
Q*
E
.
c
Q
Q
Q


82
83
|
I
L*
L
.
c
I
I
I


82a 
84
|
N
S*
S
T
c
T
T
T


82b 
85
|
N
S*
S
S
s
S
S
S


82c 
86
|
L
L
L*
.
c
L
L
L


83
87
|
N
T*
R
T
c
T
T
T


84
88
|
N
S*
S
A
s
A
A
A


85
89
|
E
E*
E
.
s
E
E
E


86
90
|
D
D*
D*
.
c
D
D
D


87
91
|
T
T*
T
.
c
T
T
T


88
92
|
A
A
A
G
c
G
G
G


89
93
|
T
V
V
M
c
M
M
M


90
94
|
Y
Y
Y*
.
c
Y
Y
Y
Martin Canonical (H1)


91
95
|
F
Y*
Y
.
C
F
F
F
Packing AA.


92
96
|
C
C
C*
.
C
C
C
C
Martin Canonical (H1)


93
97
|
V
A
A*
A
C
V
V
A
Packing AA; (Δ4)


94
98
FR3
R
R
R
K
C
R
R
K
Chothia Canonical (H1);













Martin Canonical (H1);













(Δ5)


95
99
CDR3
V
G
A
E
c
V
V
V
Packing AA.


96
100
|
G
Y
P
S
c
G
G
G


97
101
|
Y
L
G
H
s
Y
Y
Y


98
102
|
D
R
Y
S
s
D
D
D


99
103
|
A
R
G
S
c
A
A
A


100

|
—
D
S
A

—
—
—


100 a 

|
—
—
G
L

—
—
—


100 b 

|
—
—
G
D

—
—
—


100 c 

|
—
—
G
—

—
—
—


100 d 

|
—
—
C
—

—
—
—


100 e 

|
—
—
Y
—

—
—
—


100 f 

|
—
—
R
—

—
—
—


100 g 

|
.
—
G
—

.
.
.


100 h 

|
.
—
D
—

.
.
.


100 i 

|
.
—
Y
—

.
.
.


100 j 

|
.
—
x
—

.
.
.


100 k 
104
|
L
—
F
.
c
L
L
L
Core packing AA.


101
105
|
D
D
D
.
c
D
D
D


102
106
CDR3
Y
Y
Y
.
c
Y
Y
Y
Martin Canonical (H1)


103
107
FR4
W
W
W*
.
C
W
W
W
Core packing AA.


104
108
|
G
G
G
.
c
G
G
G


105
109
|
Q
Q
Q
.
s
Q
Q
Q


106
110
|
G
G
G*
.
c
G
G
G


107
111
|
T
T*
T
.
c
T
T
T


108
112
|
S
S
L
L
c
L
L
L


109
113
|
V
V
V*
.
c
V
V
V


110
114
|
T
T
T
.
c
T
T
T


111
115
|
V
V*
V*
.

V
V
V


112
116
|
S
S
S*
.

S
S
S


113
117
FR4
S
S
S*
.

S
s
S









The third version of the humanized BAT-1 VH region (BATRHC) incorporated all the substitutions made in BATRHB and, in addition contained a further three murine amino acids, which were inserted into the human FRs in place of the corresponding human residues. The first of these was the Asn amino acid located at position 76 in FR3. According to the molecular model of the BAT-1 Fv region, the Asn residue was close to CDR H1 and may have been supporting the loop structure. In addition, in the mouse BAT-1 VH region, the Asn was surface exposed and larger than the Ser in the human hsighv1295 FRs. Consequently, a Ser76Asn substitution was made to the FR.
A further change was made to the amino acid at position 94 in FR3 of the VH region, a residue position which had been previously identified by Chothia et al. (Chothia et al., 1992 ibid) as well as by Martin and Thornton (Martin et al., ibid), as important for H3 loop conformation. Moreover, the molecular model indicated that the Arg94 could form a salt bridge with Asp101 in CDR H3, stabilizing the loop structure. Consequently, the Arg in the mouse replaced the Lys in the human at this residue position. A final modification was also made at position 93 in FR3 where the human Ala was replaced by the murine Val amino acid. This residue was considered a packing residue, as defined by Chothia (Chothia et al., 1985 ibid), important for the correct packing of the Vκ and VH regions. In addition, this was identified as a Vernier residue position, and therefore important for maintaining CDR loop conformation, a classification confirmed by an analysis of the molecular model. Taken together, all the data and molecular analysis suggested that it was appropriate to conserve these three murine residues in the humanized VH region of BATRHC, i.e. Ser76Asn, Ala93Val and Lys94Arg.
The construction of the next two humanized variants of the BAT-1 VH region depended upon the binding affinity of these first three humanized versions i.e. BATRHA, BATRHB and BATRHC. If all three failed to display an adequate level of binding, then versions BATRHD and BATRHE would be synthesized and tested.
Version D of the humanized BAT-1 VH region (BATRHD) incorporated all the substitutions made in BATRHC and, in addition, contained one further mouse amino acid located at position 2 in FR1. This location was defined as both a canonical (Martin et al, ibid) and Vernier (Foote et al., ibid) residue position. In addition, from the model of the BAT-1 variable region, the murine Ile amino acid was close to Tyr27 in FR1, which is itself part of the H1 loop structure. Conversely, the murine Ile and human Val amino acids, at this location in the mouse and human FRs, were similar in character and only slightly different in size, i.e. Ile has an extra methyl group. Therefore, it was decided to make the Val21Ile change only at this stage of the humanization procedure and incorporate the mutation into version BATRHD.
The final version of the humanized BAT-1 heavy chain variable region (BATRHE) incorporated all the mouse FR substitutions made in BATRHD along with three additional amino acid changes at positions 38 (FR2), 46 (FR2) and 68 (FR3).
The Arg38Lys modification was made because the model suggested that the Arg, deeply buried in the core of the VH region, was close to Phe63 in CDR H2. However, this was not a previously identified canonical or Vernier residue position. In addition, Arg and Lys are relatively similar in structure, although Arg is bulkier, and so the significance of any amino acid change was hard to judge. Consequently, this was considered as only a tentative possibility and the substitution was only going to be made if the binding affinity of the humanized BAT-1 antibody was found to be poor. The same rationale was also behind the selection of the Gln46Lys modification. The Lys amino acid was half-buried, according to the molecular model, but close to Glu62 and Phe63 in CDR H2. There was a faint possibility that the larger, charges Lys46 residue could interact with the antigen directly, therefore it was conserved in BATRHE. The case for preserving the murine 68Ala amino acid was related to its proximity to CDR H2, particularly to residue Tyr59 in the H2 loop, and to the chance of it therefore influencing loop structure. The Ala was unlikely to be important due to its small size, however the larger Val, found in the human hsighv1295 FRs could have adversely affected H2 loop structure, and so was replaced with the murine Ala residue.
A description of the amino acid sequences of all the humanized VH region variants proposed above is given in FIG. 6.
Although potential N-linked glycosylation sites i.e. Asn-Xaa-(Ser/Thr)-Xaa (Gavel et al., ibid) were searched for in both the donor mouse and acceptor human VH regions, as well as the humanized constructs themselves, none were identified.
Example 5
Molecular Modeling of the Murine and Humanized BAT-1 Fv Domain
To assist the design of the humanized variable regions of the BAT-1 antibody, a molecular model of the variable regions of both the murine and the humanized antibodies were built. The modeling of these structures was achieved using both the established methods of modeling by homology and ab initio techniques. This was done using AbM molecular modeling package, which was supplied and utilized by Oxfored Molecular Limited (OML). Antibody X-ray crystallographic structures from the Brookhaven database available were formatted to allow them to be used for modeling with AbM.
The FRs of the BAT-1 variable regions were modeled on FRs from similar, structurally solved immunoglobulin variable regions. While identical amino acid side-chains were kept in their original orientation, mismatched side-chains were substituted as in the original BAT-1 Fv region. The backbone atoms of the FAB17-1A Vκ region were used for the model of the BAT-1 Vκ region, while the FRs of the 409.5.3 VH region were used to model the BAT-1 VH region (Brookhaven PDB codes 1for and 1iai, respectively). These sequences both represented good matches for the variable region sequences of murine BAT-1 antibody, and their humanized variants. The identities for the mBAT-1 and humanized sequences ranged from 73% to 92% for Vκ region sequences and between 65% and 79% for VH region sequences. Testing of AbM with known structures has shown that FR backbone homology is an important factor in the quality of any model, since the use of FR structures that poorly match a sequence being modeled can significantly and adversely affect the position and orientation of the CDR loop structure.
For the backbone structure of the L1 loop, the loop conformations of the murine BAT-1 Vκ region and the humanized BATRκB sequence (FIG. 5) were taken from canonical classes used by AbM. These canonical classes are based on those described by Chothia and his colleagues, but they have been modified to take into consideration structures that have become available since the original articles were published (Chothia et al., 1987, 1989, 1992 ibid; Tramontano et al., ibid). Testing the performance of AbM predictions for known loop structures has shown that CDR loops which are created in this way are usually modeled very accurately, i.e. to within 1-1.5 Å RMS deviation. For the Vκ region sequence BATRκA, the substitution of Phe for Tyr at position 71 (in FR3) meant that it no longer fitted the canonical class (Class 1) seen in the murine Vκ region and the humanized BATRκB Vκ region. Tyr71 had an important role in the conformation of the L1 loop, however, analysis of the modeled structures suggested that it was the packing of the L1 loop against the aromatic ring of Tyr which was the key feature of the residue. Thus, there was reason to believe that Phe could also perform this function. In addition, from the models there did not seem to be any strong interactions with the hydroxyl group of Tyr71. Consequently, there was a possibility that the substitution of Tyr with Phe could well have had no affect the actual conformation of the L1 loop.
For the backbone structures of CDRs L2, L3, H1 and H2, conformations for all the models were taken from canonical classes defined by AbM without modification.
The H3 loop in the BAT-1 VH region was eight residues long, so two methods were used for predicting the H3 loop structure. A database search for the backbone conformations was used for both methods, but in addition, the conformation of the central five residues in the model were searched more thoroughly using a CONGEN search (Bruccoleri, ibid). Although this took longer to compute, it reassuringly produced a conformation which was very similar to those identified from the database search.
After adjusting the whole of the model for obvious steric clashes it was finally subjected to energy minimization, as implemented in MACROMODEL, both to relieve unfavorable atomic contacts and to optimize van der Waals and electrostatic interactions.
Example 6
Construction of Humanized BAT-1 Light Chain Variants
As with all examples, a strict PCR-cloning and sequencing protocol was followed. This was done to minimize the possibility of introducing errors into the humanized versions. The construction of the humanized BAT-1 kappa light chain variable region genes (i.e. BATRκA, BATRκB, and BATRκD) produced an approximately 425 bp product which was then subcloned in pCR2.1TM. The PCR reactions were set up using the primers described in Tables 9 and 10.










TABLE 9







Oligonucleotide used in the construction of





the various humanized versions of the BAT-1


Primer
SEQ
antibody kappa light chain variable region


Name
ID NO
gene (5′→ 3′)

















BATRκ.1
30
CCCAAGCTTGCCGCCACCATG GACATGAGGGTCCCCGCTCAG C


 


BATRκ.2
31
TCCTGGGGCTCCTGCTGCTCT GGCTCCCAGGTGCCAAATG


 


BATRκ.3
32
TGAAATTGTGTTGACGCAGTC TCCATCCTCCCTGTCTGCA


 


BATRκ.4
33
TCTGTAGGAGACAGAGTCACC ATCACTTGCAGTGCCAGGT


 


BATRκ.5
34
CAAGTGTAAGTTACATGCACT GGTATCAGCAGAAACCAGG


 


BATRκ.6
35
GAAAGCCCCTAAGCTCCTGAT CTATAGGACATCCAACCTG


 


BATRκ.7
36
GCTTCTGGGGTCCCATCTAGA TTCAGCGGCAGTGGATCTG


 


BATRκ.8
37
GGACAGATTTCACTCTCACCA TCAACAGCCTGCAGCCTGA


 


BATRκ.9
38
AGATTTTGCAACTTACTATTG CCAGCAAAGGAGTAGTTTC


 


BATRκ.10
39
CCACTCACGTTCGGCGGAGGG ACCAAGCTGGAGATCAAACGT




GAGTGGATCCGCG


 


BATRK.11
40
GAGCAGCAGGAGCCCCAGGAG CTGAGCGGGGACCCTCATG


 


BATRK.12
41
ACTGCGTCAACACAATTTCAC ATTTGGCACCTGGGAGCCA


 


BATRK.13
42
GTGACTCTGTCTCCTACAGAT GCAGACAGGGAGGATGGAG


 


BATRK.14
43
GTGCATGTAACTTACACTTGACCTGGCACTGCAAGTGATG


 


BATRK.15
44
TCAGGAGCTTAGGGGCTTTCCCTGGTTTCTGCTGATACCA


 


BATRK.16
45
CTAGATGGGACCCCAGAAGCCAGGTTGGATGTCCTATAGA


 


BATRK.17
46
GGTGAGAGTGAAATCTGTCCCAGATCCACTGCCGCTGAAT


 


BATRK.18
47
AATAGTAAGTTGCAAAATCTTCAGGCTGCAGGCTGTTGAT


 


BATRK.19
48
CCTCCGCCGAACGTGAGTGGGAAACTACTCCTTTGCTGGC


 


BATRK.20
49
CGCGGATCCACTCACGTTTGATCTCCAGCTTGGTC


 


BATRK.5B
50
CAAGTGTAAGTTACATGCACTGGTTCCAGCAGAAACCAGG


 


BATRK.6B
51
GAAAGCCCCTAAGCTCTGGATCTATAGGACATCCAACCTG


 


BATRK.8B
52
GGACAGATTACACTCTCACCATCAACAGCCTGCAGCCTGA


 


BATRK.15B
53
TCCAGAGCTTAGGGGCTTTCCCTGGTTTCTGCTGGAACCA


 


BATRK.17B
54
GGTGAGAGTGTAATCTGTCCCAGATCCACTGCCGCTGAAC


 


BATRK.17D
55
GGTGAGACAGTAAGATGTCCCAGATCCACTGCCGCTGAAC


 


BATRK.8D
56
GGACATCTTACTGTCTCACCATCAACAGCCTGCAGCCTGA

















TABLE 10





Humanized



BAT-1
Oligonucleotide primer1 combinations used for the construction of


variant
the kappa light chain of each variant2




















BATRκA
BATRκ.1
BATRκ.2
BATRκ.3
BATRκ.4
BATRκ.5



BATRκ.6
BATRκ.7
BATRκ.8
BATRκ.9
BATRκ.10



BATRκ.11
BATRκ.12
BATRκ.13
BATRκ.14
BATRκ.15



BATRκ.16
BATRκ.17
BATRκ.18
BATRκ.19
BATRκ.20


BATRκB
BATRκ.1
BATRκ.2
BATRκ.3
BATRκ.4
BATRκ.5B



BATRκ.6B
BATRκ.7
BATRκ.8B
BATRκ.9
BATRκ.10



BATRκ.11
BATRκ.12
BATRκ.13
BATRκ.14
BATRκ.15B



BATRκ.16
BATRκ.17B
BATRκ.18
BATRκ.19
BATRκ.20


BATRκD
BATRκ.1
BATRκ.2
BATRκ.3
BATRκ.4
BATRκ.5B



BATRκ.6B
BATRκ.7
BATRκ.8D
BATRκ.9
BATRκ.10



BATRκ.11
BATRκ.12
BATRκ.13
BATRκ.14
BATRκ.15B



BATRκ.16
BATRκ.17D
BATRκ.18
BATRκ.19
BATRκ.20





1Oligonucleotide sequences are given in Table 9.


2Oligonuclotide primers BATRκ.1 and BATRκ.20 were also used as the outer amplification


primers.






Putative positive transformants were identified using the PCR-screening assay, restriction digest and then ds-DNA sequenced. The humanized Vκ genes (FIGS. 7-9; SEQ ID NOS. 15, 16 and 18) were then subcloned into expression plasmids.
The light chain pKN110 construct included Ampicillin and Neomycin resistance genes. The humanized Vκ gene variants of BAT-1 (i.e. BATRκA, BATRκB and BATRκD) were inserted between the HCMV Immediate Early Promoter and the genomic human kappa constant region resulting in the following expression vectors: pKN110-BATRκA, pKN110-BATRκB and pKN110-BATRκD, respectively (see FIG. 10 for a representative pKN 110-BATRκD vector).
The BAT-1 light chain expression cassette inserted into an expression vector included a DNA fragment encoding a mouse immunoglobulin signal peptide sequence, Kozak sequence and a signal sequence intron which was added to both sides of the humanized Vκ gene variants of BAT-1 (FIG. 11). This cassette was inserted between the HCMV Immediate Early Promoter and the genomic human kappa constant region. The complete light chain expression vector also included a BGH polyA transcription terminator and a Neo/G418 selection marker. All constructs were restriction enzyme digested and ds-DNA sequenced to confirm the presence of the correct insert.
Example 7
Construction of Humanized BAT-1 Heavy Chain Variants
The construction of the various versions of the reshaped human BAT-1 heavy chain variable region genes (i.e. BATRHA, BATRHB, BATRHC) produced an approximately 450 bp product which was then subcloned into pCR2.1TM. The PCR reactions were set up using the primers described in Tables 11 and 12.
Putative positive transformants were again identified in a PCR screen and then ds-DNA sequenced. The humanized VH genes (SEQ ID NOS. 20-22) were then subcloned into expression vectors.
The heavy chain pG1D110 construct included Ampicillin resistance gene and the hamster dhfr as the selectable marker. The humanized VH gene variants of BAT-1 were inserted between the HCMV Immediate Early Promoter and the genomic human IgG1 constant region resulting in the following expression vectors: pG1D110-BATRHA, pG1D110-BATRHB, pG1D110-BATRHC (see FIG. 12 for a representative pG1D110.BAT-1.RHC vector).
The BAT-1 heavy chain expression cassette inserted into an expression vector which included a DNA fragment encoding a mouse immunoglobulin signal peptide sequence, Kozak sequence and a signal sequence intron which was added to both sides of the humanized Vκ gene variants of BAT-1 (FIG. 13). This cassette was inserted between the HCMV Immediate Early Promoter and the genomic human IgG1 constant region. The complete light chain expression vector also included a BGH polyA transcription terminator and a dhfr selection marker.
The resulting expression vectors were restriction enzyme digested to confirm the presence of the correct insert.










TABLE 11







Oligonucleotide used in the construction



Primer
SEQ
of the various humanized BAT-1 antibody


Name
ID NO
heavy chain variable region gene (5′→3′)


















BATRH.1
57
CCCAAGCTTGCCGCCACCATG GACTGGACCTGGAGGATCC



 


BATRH.2
58
TCTTCTTGGTGGCAGCAGCAA CAGGTGCCCACT


 


BATRH.3
59
CCCAGGTGCAGCTGGTGCAAT CTGGGTCTGAGCTTAAGAA


 


BATRH.4
60
GCCTGGGGCCTCAGTGAAGAT CTCCTGCAAGGCTTCTGGA


 


BATRB.5
61
TATAGCTTCAGTAACTATGGA ATGAACTGGGTGCGACAGG


 


BATRH.6
62
CCCCTGGACAAGGGCTTCAGT GGATGGGATGGATAAACAC


 


BATRH.7
63
CGACAGTGGAGAGTCAACATA TGCTGAAGAGTTCAAGGGA


 


BATRH.8
64
CGGTTTGTCTTCTCCTTGGAC ACCTCTGTCAGCACGGCAT


 


BATRH.9
65
ATCTGCAGATCACCAGCCTCA CGGCTGAGGACACTGGCAT


 


BATRH.10
66
GTATTTCTGTGCGAAAGTCGG CTACGATGCTTTGG


 


BATRH.11
67
ACTACTGGGGCCAGGGAACCC TGGTCACCGTCTCCTCAGGTG




AGTGGATCCGCG


 


BATRH.12
68
TGCTGCCACCAAGAAGAGGAT CCTTCCAGGTGGAGTCCATGG




TGG


 


BATRH.13
69
TTGCACCAGCTGCACCTGGGA GTGGGCACCTGTTGC


 


BATRH.14
70
T CTTCACTGAGGCCCCAGGCT TCTTAAGCTCAGACCCAGA


 


BATRH.15
71
CCATAGTTACTGAAGCTATAT CCAGAAGCTTGCAGGAGA


 


BATRH.16
72
CTGAAGCCCTTGTCCAGGGGC CTGTCGCACCCAGTTCATT


 


BATRH.17
73
ATGTTGACTCTCCACTGTCGG TGTTTATCCATCCCATCCA


 


BATRH.18
74
TCCAAGGAGAAGACAAACCGT CCCTTGAACTCTTCAGCAT


 


BATRH.19
75
GAGGCTGGTGATCTGCAGATA TGCCGTGCTGACAGAGGTG


 


BATRH.20
76
CGACTTTCGCACAGAAATACA TGCCAGTGTCCTCAGCCGT


 


BATRH.21
77
TTCCCTGGCCCCAGTAGTCCA AAGCATCGTAGC


 


BATRH.22
78
CGCGGATCCACTCACCTGAGG AGACGGTGACCAGGG


 


BATRH.5B
79
TATACTTTCACAAACTATGGA ATGAACTGGGTGCGACAGG


 


BATRH.15B
80
CCATAGTTTGTGAAAGTATAT CCAGAAGCCTTGCAGGAGA


 


BATRH.8C
81
CGGTTTGTCTTCTCCTTGGAC ACCTCTGTCAACACGGCAT


 


BATRH.10C
82
GTATTTCTGTGTGAGAGTCGG CTACGATGCTTTGG


 


BATRH.20C
83
CGACTCTCACACAGAAATACATG CCAGTGTCCTCAGCCGT


 


BATRH.9C
84
ATCTGCAGATCACCAGCC TC AACGCTGAGGACACTGGCAT


 


BATRH.19C
85
GAGGCTGGTGATCTGCAGAT ATGCCGTGTTGACAGAGGTG


 


BATRH.5C
86
TATACTTTCACAAACTATGG AATGAACTGGGTGAAGCAGG

















TABLE 12





Humanized



BAT-1
Oligonucleotide primer1 combinations used for the construction of


variant
the heavy chain of each variant2




















BATRHA
BATRH.1
BATRH.2
BATRH.3
BATRH.4
BATRH.5



BATRH.6
BATRH.7
BATRH.8
BATRH.9
BATRH.10



BATRH.11
BATRH.12
BATRH.13
BATRH.14
BATRH.15



BATRH.16
BATRH.17
BATRH.18
BATRH.19
BATRH.20



BATRH.21
BATRH.22


BATRHB
BATRH.1
BATRH.2
BATRH.3
BATRH.4
BATRH.5B



BATRH.6
BATRH.7
BATRH.8
BATRH.9
BATRH.10



BATRH.11
BATRH.12
BATRH.13
BATRH.14
BATRH.15B



BATRH.16
BATRH.17
BATRH.18
BATRH.19
BATRH.20



BATRH.21
BATRH.22


BATRHC
BATRH.1
BATRH.2
BATRH.3
BATRH.4
BATRH.5C



BATRH.6
BATRH.7
BATRH.8C
BATRH.9
BATRH.10



BATRH.11
BATRH.12
BATRH.13
BATRH.14
BATRH.15C



BATRH.16
BATRH.17
BATRH.18
BATRH.19
BATRH.20



BATRH.21
BATRH.22





1Oligonucleotide sequences are given in Table 11.


2Oligonuclotide primers BATRH.1 and BATRH.22 were also used as the outer amplification primers.






Example 8
Construction of BAT-1 RHC/RκD γ1 Complete Antibody in a Single Expression Vector
In order to maximize the achievable expression levels for the BAT-1 γ1 antibody it was decided to remove an intron from the pG1D110.BAT-1.RHC construct (described in Example 7, see FIG. 12) before making the BAT-1 γ1 single vector construct. This procedure was carried out as follows.
pG1D200 is another γ1 immunoglobulin heavy chain mammalian expression vector (AERES Biomedical; FIG. 14). This vector is a VH:CH γ1 intron minus version of the pG1D110 vector (i.e. it does not have the 71 bp intron at the VH:CH junction).
In order to convert the pG1D110.BAT-1.RHC construct into a construct, a BstEII fragment (219 bp) was excised from the pG1D200 vector and gel purified using a Qiagen gel extraction/purification kit. This fragment contained the intron minus VH:CH junction.
The pG1D110.BAT-1.RHC construct (FIG. 12) was also restriction digested with BstEII, releasing a 290 bp fragment which contained the intron plus VH:CH junction. The remaining vector fragment ( ̃7207 bp) was gel purified using a Qiagen gel extraction/purification kit.
The intron minus BstEII fragment (219 bp) from the pG1D200 vector digest was then ligated into the  ̃7207 bp BstEII digested pG1D110.BAT-1.RHC vector. 2 μl of ligated DNA was transformed into DH5α cells (Stratagene) according to the manufacturers instructions. Plasmid DNA was prepared from 10 colonies and each plasmid DNA was analyzed for the presence of the correct BstEII fragment by DNA sequence analysis.
Following identification of a perfect clone, the new intron minus construct (pG1D210.BAT-1.RHC) and the light chain construct pKN110.BAT.RκD (see FIG. 10) were used to construct the pG1KD210.BAT-1.RHC/RκD single expression vector (SEQ ID NO. 93).
The component of this pG1KD210.BAT-1.RHC/RκD single expression vector within SEQ ID NO 93 are localized as follows:

    
    
        1. Nucleotide range: 1 to 2502—pBR322 (pBR322 based sequence including the Amp-resistance gene and ColEI origin plus the SV40 origin and crippled SV40 early promoter)
        2. Nucleotide range: 206 to 1067—Amp (Ampicillin resistance gene)
        3. Position: 1824—ColE1
        4. Nucleotide range: 2502 to 3227—DHFR (Dihydrofolate reductase gene)
        5. Nucleotide range: 3233 to 4074—SV40 polyA (SV40 poly A sequence etc)
        6. Nucleotide range: 4109 to 5649—HCMVi (HCMVi promoter)
        7. Nucleotide range: 5662 to 6067—BAT rKd
    
    


Reshaped BAT Kappa Light Chain Variable Region.

    
    
        8. Nucleotide range: 6073 to 6720—HuK (cDNA copy of human kappa constant region (Km(3)) gene)
        9. Nucleotide range: 6726 to 6943—spaC2 Artificial spaC2 termination sequence
        10. Nucleotide range: 6949 to 8489—HCMVi (HCMVi promoter)
        11. Nucleotide range: 8502 to 8923—BAT rHc
    
    


Reshaped BAT Heavy Chain Variable Region

    
    
        12. Nucleotide range: 8924 to 10297—HG1 (Human gamma-1 constant regions preceded by a 60 bp intron and followed by the ‘Arnie’ termination sequence)
    
    


The BAT-1 kappa light chain expression cassette which contained the HCMVi promoter, the BAT-1 kappa light chain variable region gene, and the kappa light chain constant region gene, was restriction enzyme digested (EcoRI/SpeI) out of the pKN110.BAT-1.RκD construct and subsequently ligated into the pG1D210.BAT-1.RHC construct via the unique EcoRI and SpeI restriction sites. This ligation resulted in the construction of the single expression vector pG1KD210.BAT-1.RHC/RκD, containing both the heavy and kappa light chains of the BAT-1 humanized antibody RHC/RKD (FIG. 15). 2 μl of ligated DNA was transformed into DH5α cells (Stratagene) according to the manufacturers instructions. Mini prep DNA was prepared from ten colonies and each plasmid DNA was analyzed for the presence of the correct single expression construct by restriction digest analysis. One clone of a correct single expression construct was chosen for the transient expression of the BAT-1 gamma-1 antibody in COS cells as will be illustrated in Example 11.
Example 9
Construction of the BAT-1.RHC/RκD Gamma-1 (γ1) Complete Antibody Variant in a Single Expression Vector
The BATRHC heavy chain variable region was transferred to the combined (single) expression vector as an XhoI to HindIII fragment. The BATRκD light chain variable region was transferred to the combined (single) expression vector as an XbaI to BamHI fragment. The internal XbaI site in the light chain gene was removed without changing the amino acid sequence. The sequences of the BAT-1.RκD/BAT-1.RHC heavy and light chain variable regions in this vector were confirmed. The vector includes genomic human IgG1 and Kappa constant regions. Both heavy and light chain genes were placed under the control of the HCMV Immediate Early promoter. The vector includes a mouse dhfr gene as the selectable marker (see FIG. 16). The same Kozak sequence, signal peptide sequence and intron were added as for the two vector expression system (see Examples 6 and 7).
Example 10
Construction of the BAT-1 Gamma-4 (γ4) PG4KD110.BAT-1. RHC/RKD in a Single Vector
The first step in the construction of the BAT-1 γ4 single expression vector construct was the cloning of the modified BAT-1.RHC gene out of the pG1D110.BAT-1.RHC construct by BamHI and HindIII restriction digest, and ligation of this 430 bp fragment into the gamma-4 immunoglobulin heavy chain expression vector pG4D110, again via BamHI and HindIII restriction sites.
2 μl of ligated DNA was transformed into DH5α cells (Stratagene) according to the manufacturers instructions. Plasmid DNA was prepared from 10 colonies and each plasmid DNA was analyzed for the presence of the correct BAT-1.RHC BamHI/HindIII fragment by DNA sequence analysis.
Following identification of a perfect clone, the new gamma-4 construct (pG4D110.BAT-1.RHC) and the light chain construct pKN110.BAT-1.RKD (FIG. 10) were used to construct the pG4KD110.BAT-1.HRC/RκD single expression vector in the following way.
The BAT-1 kappa light chain expression cassette which contained the HCMVi promoter, the BAT-1 kappa light chain variable region gene, and the kappa light chain constant region gene, was restriction enzyme digested (EcoRI/SpeI) out of the pKN110.BAT-1.RκD construct and subsequently ligated into pG4D110.BAT-1.RHC construct via the unique EcoRI and SpeI restriction sites. This ligation resulted in the construction of a single expression vector construct pG4KD110.BAT-1.RHC/RκD, containing both the heavy and kappa light chains of the BAT-1 humanized antibody RHC/RκD variant. 2 μl of ligated DNA was transformed into DH5α cells (Stratagene) according to the manufacturers instructions. Mini prep DNA was prepared from ten colonies and each plasmid DNA was analyzed for the presence of the correct single expression vector construct by restriction digest analysis. The correct single expression vector construct digested with BamHI and with HindIII released a 2864 bp fragment and the HindIII digest released a 2840 bp fragment. One clone was chosen for the transient expression of the BAT-1 gamma-4 antibody in COS cells.
Example 11
Co-transfection of Humanized BAT-1 Light and Heavy Chain Vectors, and Transient Expression of the Humanized BAT-1 Variants in COS7 Cells
The humanized BAT-1 heavy (pG1D110) and light (pKN110; Example 7) chain expression vectors were co-transfected, at various combinations, into COS7 cells and after 72 hr incubation, the medium was collected, spun to remove cell debris, filtered and analyzed by ELISA for humanized antibody production. The concentration of humanized antibody in the COS7 cell supernatants varied with each combination of reshaped human BAT-1 antibody constructs that were tested (Table 13). For example, version BATRHB/BATRκA expressed the highest antibody levels (4800 ng/ml) whilst the BATRHB/BATRκD version was the poorest expresser (357 ng/ml).
Example 12
Purification of the Humanized BAT-1 Variants from COS7 Cells
Harvesting approximately 8 ml per co-transfection (see Example 11), a series of transfections were carried out until in excess of 200 ml of COS7 supernatant had been collected. The volume of this supernatant was reduced to 10 ml by passing the supernatant through a stirred ultra-filtration cell with a PM30 filter membrane—which had a molecular weight cut-off of 30 kDa.
The IMMUNOPURETM IgG purification kit essentially comprised of a 2 ml column of immobilized Protein A Sepharose column. The antibody was eluted from the column with 5 ml of elution buffer, the eluate of which was collected in 1 ml fractions. The concentration of humanized BAT-1 antibody in each fraction was then assayed using ELISA methods. Table 13 describes the final concentrations of the Protein A purified antibodies. On average the purification step increased the antibody concentration by approximately 150-fold.










TABLE 13









Chimeric and hBAT-1 antibody




concentrations in COS7



cells supernatants (transient



expression experiments)












Antibody chain


After Protein A













Kappa
Raw supernatants
Purification



Heavy
Light
(μg/ml)
(μg/ml)
















BATCH
BATRκ
0.358
50



BATRHA
BATRκA
2.350
110



BATRHB
BATRκA
4.800
211



BATRHB
BATRκB
0.757
149



BATRHC
BATRκB
1.250
137



BATRHB
BATRκD
0.357
112



BATRHC
BATRκD
0.718
122










Example 13
Analysis of Daudi Cell Binding to the Humanized BAT-1 Variants Produced in COS7 Cells
Using the Daudi cell ELISA it was clear that the different versions of the Protein A purified humanized BAT-1 antibody bound to Daudi cells to various degrees. FIGS. 17-20 show typical examples for these binding experiments. Sigmoidal dose-response curves of Daudi cell binding by the recombinant antibodies were also plotted and the hill slopes of these binding curves were calculated. The combination of the hill slope data and the positions of the dose-response curves relative to the chimeric antibody dose-response curves suggested a qualitative hierarchy with respect to Daudi cell binding among the various humanized BAT-1 antibody constructs tested (Table 14). At the top of this hierarchy was clearly construct BATRHC/BATRκD, which exhibited a hill slope (i.e. 0.8818±0.1107) very similar to its chimeric BAT-1 antibody control (i.e. 0.8248±0.1210) and closely tracked the dose-response curve of the chimeric control. Although construct BATRHC/BATRκB displayed a steeper hill slope (i.e. 0.6408±0.1622) than the same chimeric BAT-1 antibody control (i.e. 0.8248±0.1210), as calculated from the available binding data, the difference was no statistically significant. In addition, it is clear from FIG. 19 that the dose-response curve for this construct is not as good as for the BATRHC/BATRκD construct and was therefore ranked second in the binding hierarchy.
Conversely, construct BATRHA/BATRκA clearly has the poorest binding characteristics of all the humanized BAT-1 antibody constructs tested (Table 14) and so was ranked sixth in the binding hierarchy. Although the calculated hill slope for this version (i.e. 1.2730±0.2688) is apparently better than the very similar humanized construct BATRHB/BATRκA (i.e. 1.7710±0.6461) this difference is again not statistically significant. In addition, it is clear from FIG. 18 that the CDR-grafted BATRHA/BATRκA BAT-1 antibody is reaching its maximum binding response at much lower level than the humanized construct BATRHB/BATRκA—which was ranked fifth in the binding hierarchy.
Constructs BATRHB/BATRκB (FIG. 17; ranked fourth) and BATRHB/BATRκD (FIG. 20; ranked third) display intermediate levels of binding between these two sets of extremes. Again these rankings were mainly based upon a subjective interpretation of the binding data available and previous experience.







TABLE 14







Relative binding affinities of Protein A purified humanized


versus chimeric BAT-1 antibodies constructs harvested following


transient expression in COS cells















Binding




Kappa

hierarchy


Experiment
Heavy
Light
Hill slope
from hill


Number
Chain
Chain
±SEMa
slope analysis





1
BATRH
BATRκ
0.5422 ± 0.2911
—



BATRHA
BATRκA
 1.273 ± 0.2688
6



BATRHB
BATRκA
 1.771 ± 0.6461
5


2
BATRH
BATRκ
0.8057 ± 0.0849
—



BATRHB
BATRκD
0.6555 ± 0.1252
3


3
BATRH
BATRκ
0.8248 ± 0.1210
—



BATRHC
BATRκB
0.6408 ± 0.1622
2



BATRHC
BATRκD
0.8818 ± 0.1107
1


4
BATRH
BATRκ
0.7090 ± 0.2768
—



BATRHB
BATRκB
0.7796 ± 0.3420
4





aStandard error mean of 3 duplicate Daudi cell ELISA calculated after fitting ELISA data onto a sigmoidal dose-response curve.






Example 14
Transient Expression of the BAT-1 RκD/RHC Variant by Co-transfection or by Single Transfection of COS Cells
The method of Kettleborough (Kettleborough et al., Eur. J. Immunol. 23:206, 1993) was followed to transfect the mammalian expression constructs into COS cells. Briefly, the DNA (10 μg each of the kappa light chain expression construct pKN110.BAT-1.RκD and the heavy chain expression construct pG1D210.BAT-1.RHC, or 13 μg of the single vector construct pG1KD210.BAT-1.RHC/RκD) was added to a 0.7 ml aliquot of 107 cells/ml in PBS and pulsed at 1900 V, 25 μF capacitance using a Bio-Rad Gene Pulser apparatus. Following a 10 minute recovery at room temperature, the electroporated cells were transferred to petri-dishes containing 8 ml of DMEM containing 10% FCS and incubated for 72 hrs in 5% CO2 at 37° C. After 72 hrs incubation, the medium was collected, spun to remove cell debris, and analyzed by capture ELISA for antibody production. The co-transfections, with light chain expression vector and heavy chain expression vector, and transfections with a single-vector expressing both light and heavy chains, were carried out in triplicate. The results are presented in Table 15. The results indicate that expression levels from the single vector are  ̃6 fold higher than the expression levels observed for the co-transfections.









TABLE 15







Transient COS cell


Trans-

expression levels


fection
Construct
for the BAT-1 γ1


no.
transfected
antibody (μg/ml)*

















1
Single vector
55.451


2
′′
49.009


3
′′
66.018


1
Light and heavy chain vectors
9.06


2
′′
10.232


3
′′
9.536





*Trasfection levels of humanized RHC/RκD BAT-1 variant, from co-trasfection using pG1D110 and pKN110 vectors, were 0.718 μg/ml






Example 15
Stable Transfection of CHOdhfr− Mammalian Cells with the Single Vector pG1KD210.BAT-1.RHC/RκD and Production of Stable Cell Lines
CHOdhfr− cells were propagated in a non-selective media consisting of α-MEM with ribonucleosides and deoxyribonucleosides, supplemented with 10% Fetal Clone II and 50 μg/ml Gentamicin. Aliquot, 0.7 ml, of 107 cells/ml in PBS was transfected with 13 μg of pG1KD210.BAT-1.RHC/RκD at 1900 V, 25 μF capacitance using a Bio-Rad Gene Pulser. The cells were allowed to recover for 10 minutes at RT before being transferred to 10 cm petri-dishes in 8 ml of non-selective media and then incubated in 5% CO2 at 37° C. for 48 hours.
Two days after transfection, the cells were trypsinized, spun down and resuspended in 150 ml of prewarmed selective media (α-MEM without ribonucleosides and deoxyribonucleosides, supplemented with 10% dialyzed FBS and 50 μg/ml Gentamicin, and containing either 10 nM, 50 nM, 100 nM or 500 nM Methotrxate) before being divided equally between fifteen 10 cm petri-dishes. These were then incubated in 5% CO2 at 37° C. for 20-30 days, the selective media being changed every 3-4 days until foci were clearly visible. After 2 weeks from the initial transfection, foci began to develop on the 10 nM plates. Eight days later, one focus developed on the 50 nM plates. No other foci developed after 35 days, on the 50 nM plates and no foci developed on the 100 nM or 500 nM plates.
To “pick” foci, 1 mm squares of Whatman 1 MM filter paper were first immersed in 0.05% trypsin, 0.02% EDTA solution. The selective media was carefully removed from the culture dishes, which were then washed carefully with 5 ml of PBS. The PBS was then removed and, using sterile forceps, the squares of pre-soaked filter paper were carefully placed onto individual focus of cells. The squares were left on the foci for 15 seconds before being transferred into individual wells of a 24-well tissue culture plate containing 1 ml of the appropriate selective media.
A total of 31 gamma-1 foci were picked, 30 were from the 10 nM MTX plates and one was from the 50 nM plates. These cells were allowed to grow in selective media until almost confluent and the media from individual wells was tested for antibody production. Those clones producing human antibody were then selected for expansion and specific production analysis. The results of the specific production assays are presented in Table 16.









TABLE 16









Specific CHO cell production levels for the RHC/RKD



BAT-1 γ1 whole antibody variant (ng/106 cells/day)










Clone
ASSAY NO. 1
Assay No. 2
Assay No. 3













γ1 B9
3284.7
2921.5
1227.1


γ1 B10
297
1288
268.3


γ1 B13
12443
5425.2
7731.53


γ1 B18
6.5
10.4
4.9


γ1 B19
199.7
26.9
43


γ1 B15
5978.6
1657.1
3015.43


γ1 D6
2539.2
1605.5
2072.40









The three cell lines (B9, B13 and B15) which showed the best specific productivity levels were further analyzed and monitored for accurate doubling times. (see Table 17).









TABLE 17





Cell
Production levels of the best γ1
Doubling time of the best γ1


line
CHO cell lines (μg/106 cells/day)
CHO cell lines (hours)

















B9
3.5
22.5


B13
7.7
31.5


B15
3
21









Based on specific productivity levels and doubling times it was decided to begin production of the 500 μg quantity of the BAT-1 γ1 antibody using the B15 cell line.
Example 16
Transient Expression of BAT-1 γ4 RHC/RκD Variant in COS Cells by Single- and Co-transfections
The method of Kettleborough et al. was followed to transfect the mammalian expression constructs into COS cells. Briefly, the DNA (10 kg each of the kappa light chain expression construct pKN110.BAT-1.RκD and the heavy chain expression construct pG4D110.BAT-1.RHC, or 13 μg of the supervector construct pG4D110.BAT-1.RHC/RκD) was added to a 0.7 ml aliquot of 107 cells/ml in PBS and pulsed at 1900 V, 25 μF capacitance using a Bio-Rad Gene Pulser apparatus. Following a 10 minute recovery at RT, the electroporated cells were transferred to petri-dishes containing 8 ml of DMEM containing 10% FCS and incubated for 72 hrs in 5% CO2 at 37° C. After 72 hrs incubation, the medium was collected, spun to remove cell debris, and analyzed by capture ELISA for antibody production.
Both the co-transfections and single transfections were carried out in triplicate. The results are presented in Table 18. The results indicate that expression levels from this single expression vector are  ̃4 fold higher than the expression levels observed for the co-transfections.









TABLE 18







Transient COS cell


Trans-

expression levels


fection

for the BAT-1 γ4


No.
Construct transfected
antibody (ng/ml)

















1
Single vector
519.3


2
′′
522


3
′′
567.2


1
Light and heavy chain vectors
65.6


2
′′
152.3


3
′′
129.9









Example 17
Stable Transfection of CHOdhfr− Mammalian Cells with the Single Vector pG4KD210.BAT-1.RHC/RκD and Production of Stable Cell Lines
CHOdhfr− cells were propagated in a non-selective media consisting of α-MEM with ribonucleosides and deoxyribonucleosides, supplemented with 10% Fetal Clone II and 50 μg/ml Gentamicin. Aliquot, 0.7 ml, of 107 cells/ml in PBS was transfected with 13 μg of pG4KD110.BAT-1.RHC/RκD at 1900 V, 25 μF capacitance using a Bio-Rad Gene Pulser. The cells were allowed to recover for 10 minutes at room temperature before being transferred to 10 cm petri-dishes in 8 ml of non-selective media and then incubated in 5% CO2 at 37° C. for 48 hours. Two days following this incubation, the cells were trypsinized, spun down and resuspended in 150 ml of prewarmed selective media (α-MEM without ribonucleosides and deoxyribonucleosides, supplemented with 10% dialyzed FBS and 50 μg/ml Gentamicin, and containing either 10 nM, 50 nM, 100 nM or 500 nM Methotrexate) before being divided equally between fifteen 10 cm petri-dishes. These were then incubated in 5% CO2 at 37° C. for 20-30 days, the selective media being changed every 3-4 days until foci were clearly visible.
After 2 weeks, foci began to develop on the 10 nM plates. No foci developed after 35 days on the 50 nM plates and on the 100 nM or 500 nM plates. Foci were picked as described earlier (Example 15) and those selected clones producing human antibody were then selected for expansion and specific production analysis. The results of the specific production assays are presented in Table 19.









TABLE 19









CHO cell production levels for the



BAT-1 γ4 whole antibody (ng/106 cells/day)












Clone
ASSAY NO. 1
ASSAY NO. 2
ASSAY NO. 3
















γ4 A9
4.8
6.08
5.7



γ4 A13
48.5
14.8
68.8



γ4 A12
60.7
77.0
52.7



γ4 C4
66.0
141.7
104.4



γ4 C8
41.7
52.4
77.6



γ4 C9
30.7
30.6
32.2



γ4 F2
40.7
17.9
29.30










Example 18
Co-transfection of NSO Cells with BATHC Heavy Chain and BATκD Light Chain Amplification Vectors and Selection of Antibody Producing Cell Lines
Expression vectors containing the BATRHC heavy chain cassette (FIG. 13) and the BATRκD light chain cassettes (FIG. 11) were mixed and transfected into the NSO host cell line by electroporation.
Transfected cells were distributed into 10 96-well plates in Dulbecco's Modified Eagles medium (DMEM) supplemented with 10% Foetal Bovine Serum (FBS) and 1 mg/ml G418 (Gentamicin) medium. After 10 to 14 days when colonies of transfected cells have developed, samples of conditioned medium from the wells were assayed for humanized BAT-1 antibody. Cells from the highest producing wells were picked, and expanded in medium including G418.
The transfection was repeated after one week as a back up and to provide more transfected cell clones for selection. After 10 days visible colonies of transfected cells had developed, and conditioned medium from the wells was screened for antibody production. ELISA plates were coated with sheep anti-human κ antibody. 25 μl samples of medium from the wells were transferred to the ELISA plate and diluted to 100 μl in PBS Tween (PBST). The secondary antibody was HRP-conjugated sheep anti-human IgG (γ chain specific) and color was developed with o-Phenylene Diamine (OPD). Positive wells were examined microscopically and the cells from the highest producing wells were picked into 1.5 ml of DMEM supplemented with 10% FBS and 1 mg/ml G418 in 24 well plates. A total of 15 high producing colonies were picked from the two transfections (Table 20). Two independent cell lines gave antibody production levels around 40 μg/ml or greater.
For amplification using the dhfr gene in the heavy chain vector, an initial two high producing cell lines have been transferred to medium (DMEM with 10% FCS and 1 mg/ml G418) with 0.02 μM Methotrexate added.
Example 19
Transfection of NSO Host Cell Line with a Single Amplification Vector Containing BAT-1.RHC/RκD γ1 Gene and Selection of Antibody Producing Cell Lines
The combined (single) antibody expression vector described in Example 9, was transfected into the NSO host cell line by electroporation.
Transfected cells were distributed into 10 96-well plates in DMEM with 10% FBS. After 2 days an equal amount of medium with 0.1 μM Methotrexate was added. Half the medium was changed with the same volume of 0.1 μM MTX-containing medium every 2 days until the 8th day post transfection. The transfection was repeated after one week as a back up and to provide more transfected cell clones for selection. After 14-21 days visible colonies of transfected cells had developed, and conditioned medium from the wells was screened for antibody production as described in the above Example. Positive wells were examined microscopically and the cells from the highest producing wells were picked into 1.5 ml of DMEM supplemented with 10% FBS and 0.1 μM Methotrexate in 24 well plates. A total of 13 high producing colonies were picked from the two transfections and kept frozen in liquid nitrogen (Table 20). Six independent cell lines gave antibody production levels above 40 μg/ml. Due to the different selection, the cell lines containing the single vector were slower to develop than those containing the antibody genes on 2 different vectors.












TABLE 20









Two Vector System

Single Vector System













Cell
Production level
Cell
Production level



line
(μg/ml)
line
(μg/ml)
















31E1
43
1B7
48



33E5
15
3E3
45



33B10
40
3H5
35



34F1
8
8H7
26



35C12
12.5
9D7
41



36G4
4
24B7
26



37H5
20
26A6
24



38E8
15
26D6
33



39A3
38
26E3
43



42G7
12
27B2
23



44F4
7
27C4
45



45C2
10
23E10
45



45H12
13
29E3
22



46A10
7



49H2
15










A representative example of the humanized BAT producing cells after transfection of an NSO host cell line with a single amplification vector containing BAT-1.RHC/RκD γ1 gene and selection of antibody producing cell lines, i.e., cloned cell line 1B7, was deposited at the ATCC Cell Bank using the Budapest Treaty Deposit Form on May 9, 2003 under accession number ATCC# (PTA-5189).
Example 20
Inhibition of Mouse BAT-1 by Humanized BAT-1.RHC/RκD γ1 Variant
To assure that the humanized BAT-1.RHC/RκD γ1 variant can recognize the same epitope as the original murine BAT-1, a competition assay of binding to Daudi cells that express the BAT-1-binding epitope was conducted.
Daudi cells were incubated with increasing amounts of the humanized BAT-1 or the mouse BAT-1 as control (0-80 μg/ml). Unbound antibody was discarded and biotinylated murine-BAT-1 (20 μg/ml) added to the cells and stained with streptavidin-FITC. FIG. 21 depicts a decreased binding of murine BAT-1 in the presence of increasing concentrations of both the humanized and original mouse mAb, supporting the recognition of the same epitope as expected. Both antibodies show a similar dose dependency, with an IC50 of approximately 10 μg/ml, suggesting a similar affinity of antigen binding.
Example 21
In Vivo Effect of Humanized BAT-1 in a Murine Tumor Model
As shown in Example 20, CDR grafting resulting in the formation of the humanized BAT-1.RHC/RκD γ1 mAb retained recognition of BAT-1 antigen. To examine whether this binding can transmit the biological effects characteristic of murine BAT-1, the efficacy of the humanized BAT-1 was studied in vivo. This is of particular importance in view of the isotype difference between the mouse and human mAbs.
C57BL mice were inoculated with B16 melanoma cells to induce lung metastases. Increasing amounts (1, 10 and 20 μg) of humanized mAb were injected on day 12 post tumor-inoculation and compared to an optimal dose of 10 μg murine-BAT-1. Lung weight measured on Day 24 post tumor inoculation is depicted in FIG. 22 and corresponds to the establishment of a tumor. Both non-treated mice and mice treated with an isotype-matched irrelevant human IgG1, had an average lung weight of 0.9 gr. The humanized BAT-1 exhibited a dose dependent inhibition of metastases growth with the highest inhibition occurring at a low dose of 1 μg/mouse. This resulted in a decrease of 67% in tumor mass and was similar to that achieved by an optimal dose of murine BAT-1 (62%). Importantly, this maximal effect was achieved by a ten-fold lower dose of the humanized mAb, suggesting a higher therapeutic efficacy of this antibody in comparison to the original murine BAT-1 mAb.
Example 22
Inhibition of Human Melanoma (SK-28) in SCID Mice by hBAT-1
Mouse-BAT-1 mAb has been shown to inhibit the formation of human-tumor metastases in the presence of human peripheral blood lymphocytes (hPBL). To estimate the efficacy of humanized BAT-1.RHC/RκD γ1 mAb in inhibition of human cancer, the humanized antibody was studied in a model combining both tumors and lymphocytes of human origin. Severe combined immune-deficient mice (SCID) were engrafted with hPBL to restore immune-competence. Mice were challenged with human melanoma cells (SK-28) and treated with increasing concentrations of the humanized antibody, administered in a single i.v. dose on day 11 post tumor inoculation. FIG. 23 depicts lung weight that correlates with the number of metastases observed, as measured on day 23. Both concentrations of the humanized antibody induced tumor inhibition in the presence of hPBL. As observed in the mouse tumor model described above, the humanized antibody could more efficiently inhibit tumor growth in vivo, in comparison to mouse BAT-1. A single dose of 1 μg of this humanized antibody inhibited tumor growth by 68% showing a higher efficacy than 10 μg of the mouse BAT-1 antibody (30%).
Example 23
Immunotherapy of Human Colorectal Cancer Hepatic Metastases by hBAT-1 Monoclonal Antibody in Nude Mice
LIM6 and HM7 are two sub-clones of the human CRC cell line LS174T that were selected for their high mucin synthesis and metastatic potential. The tumor cells were injected into the exposed spleen of anesthetized nude mice. After 1 minute, the spleens were removed and the excisions closed. Low doses of murine and humanized BAT-1 antibody were administered 12 days later and mice were sacrificed 35 days post tumor inoculation. The livers were weighed, the number of metastatic nodules was counted, and liver tissue was processed for histology and Immunohistochemistry study.
Treatment with BAT-1, murine and humanized antibodies, was found efficient in inhibition of liver metastases establishment in the murine model. Mouse BAT-1 antibody treatment prevented LIM-6 xenografts development. The average weight of xenografts from BAT-1 treated mice and controls were of 0.14±0.17 gr and 0.98±1.12 gr, respectively (P=0.004). HM7 cells injected to the nude mice resulted in large number of bulky metastatic lesions in the liver that were prevented by the single administration of murine BAT-1 and humanized BAT-1 (FIG. 24). A major (over 40%) decrease was observed in the number of metastatic nodules, namely from 134.5±34 in the control mice to 8.36±3 and 4.88±2 in mice treated with murine BAT-1 humanized BAT-1, respectively. Treatment with BAT-1 prevented the accumulation of lymphocytes in the tumor edge. The role of lymphocyte infiltration around the metastatic nodule may be related to outcome of the cancer and may suggest a mechanism for BAT-1 therapy.
Example 24
Co-localization of hBAT with CD4 and CD8
Mouse BAT-1 has been shown to bind human lymphocytes, recognizing both CD4+ and CD8+ subsets. To establish the binding specificity of the humanized BATRHC/BATRκD γ1 mAb (hBAT), human Peripheral Blood Lymphocytes (PBL) were isolated from the blood of normal donors, as described hereinbelow, and analyzed for co-localization of hBAT with known lymphocyte markers.
Peripheral blood mononuclear cells (PBMC) were isolated by ficoll and incubated in tissue culture plates to remove adherent cells. Isolated PBL were gated on lymphocytes by size and granularity and on live cells by propidium iodine (PI) exclusion. Binding was performed at 4° C. for 1 hr, and determined by flow cytometry on gated lymphocytes.
In all samples examined at least 20% of PBL exhibited binding to hBAT. FIG. 25 depicts an example of binding to lymphocytes of a selected donor in which 50% of the isolated PBL were positive for hBAT, including both CD4+ cells (25%) and CD8+ cells (15%). Within these subpopulations, the majority of CD4+ as well as CD8+ cells bound the hBAT mAb (58% and 71% respectively).
Example 25
Binding of HBAT to B Lymphocytes
The humanized BATRHC/BATRκD γ1 mAb (hBAT) was raised against the membranes of Daudi cells, a human B lymphoma cell-line. PBL from normal donors were isolated by ficoll, as described above, followed by adherence to tissue culture plates. Non-adherent cells were examined for the co-localization of hBAT with B-cell markers including CD19 and CD20. Binding was performed at 4° C. for 1 hr, and determined by flow cytometry on gated lymphocytes. FIG. 26 depicts the evaluation of binding to the cells of a representative normal donor.
25-29% of lymphocytes in the sample were positive for the humanized BAT mAb. These cells included the majority of B cells (70-75%) as demonstrated by both independent markers. 70% of CD20+ were positive for the humanized BAT mAb (Gated on R1 and PI negative; FIG. 26A) and 75% of CD19+ were positive for the humanized BAT mAb (Gated on R1 and PI negative). The results suggest that the BAT-binding moiety on the cell surface could be common to peripheral B cells.
Example 26
Binding of hBAT to CD4+ T Cells Increases Upon Activation of the Cells
Binding of the mouse BAT antibody has been formerly correlated with lymphocyte activation. This binding activity was further studied for the human mAb and the binding level of the human BAT mAB to human CD4+ T cells, subjected to activation, was examined. Cells were isolated from a normal donor by negative selection and stimulated with beads conjugated to anti-CD3 and anti-CD28 (5 μl/ml). This treatment was selected in order to exert polyclonal activation through the T-cell receptor and co-stimulatory molecules.
Cells were examined for binding of the humanized BATRHC/BATRκD γ1 mAb (hBAT) and anti-CD4 (4° C., 1 hr) on day 0, 2 and 5 following activation (FIGS. 27A, B and D). Analysis was performed by flow cytometry on cells negative for PI staining. Quadrants were determined by isotype controls.
The binding of the humanized BATRHC/BATRκD γ1 mAb to CD4+ cells increased dramatically following activation (FIG. 27). Whereas non-activated cells, at day 0 (FIG. 27A) and at day 5 (FIG. 27C), exhibited 17-20% positive binding to hBAT, 52% and 77% of CD4+ cells bound hBAT on day 2 (FIG. 27B) and day 5 (FIG. 27D) of activation, respectively. Similar results were obtained with multiple samples and could also be demonstrated for CD8+ cells. This demonstrates that hBAT binding to T cells is increased upon TCR activation.
The dose dependency of this activation was demonstrated by co-localization of hBAT with CD69. T cell activation is characterized by cell-surface expression of various molecules, some of which have been shown to be involved in the activation process. hBAT was studied for its co-expression with different markers including both early and late activation molecules. CD69, an early activation marker, is up-regulated on T cells upon activation. Four days following activation, cells were examined for binding of hBAT and anti-CD69 (4° C., 1 hr). Analysis was performed by flow cytometry on cells negative for PI staining. Quadrants were determined by isotype controls.
A dose-dependent activation of CD4+ T cells from a normal donor is demonstrated in FIG. 28. Upon strong activation (5 μl/ml of beads conjugated to anti-CD3 and anti-CD28; FIG. 28B) most of the cells, which were capable of binding to hBAT (93%), were activated cells and were identified by CD69 expression. Increased time of activation also resulted in increase binding to hBAT beginning at day one of activation. Time dependency of activation could also be demonstrated and resulted in an increase in hBAT binding beginning at day one of activation. Interestingly, hBAT binding to both CD4+ and CD8+ cells remained high even after CD69 decrease (day 5) suggesting a correlation of binding with multiple stages of lymphocyte activation. hBAT binding to CD69+ cells suggests that the expression of hBAT binding protein is correlated with early activation.
Example 27
Binding of HBAT to Activated T Cells Expressing CD25 and CD40-Ligand
CD25, the high-affinity receptor for IL2, is vital for T-cell expansion and is typically increased on the surface of activated cells. Chronologically it follows the appearance of CD69 and its expression is extended several days after the down-regulation of CD69.
CD4+ T cells were isolated from a normal donor by negative selection and stimulated for several days with beads conjugated to anti-CD3 and anti-CD28 (5 μl/ml). Cells were examined for binding of hBAT and anti-CD25 (4° C., 1 hr) on day 0 (FIG. 29A), day 1 (FIG. 29B), and day 5 (FIG. 29D) of activation with respect to controls (day 0, FIG. 29A and day 5 of no activation, FIG. 29C). Analysis was performed by flow cytometry on cells negative for PI staining. Quadrants were determined by isotype controls.
Both CD4+ and CD8+ T cells showed a time dependent increase in CD25 expression upon anti-CD3 and anti-CD28 stimulation, beginning at day 1 of stimulation. hBAT co-localized with CD25 on these activated cells (FIG. 29).
CD25 expression increased from 55% of the cells on day 1 (FIG. 29B) to 93% on day 5 (FIG. 29D) following activation. At both time points the majority of hBAT binding cells were CD25+ (85% and 98% respectively).
Correlation with activation markers was further extended to the late activation marker CD40-Ligand (FIG. 30). hBAT binding positively correlated with the expression of CD40-Ligand in CD4+ (FIG. 30) and CD8+ T cells in a time dependent manner. The results culminate to suggest that activation of T cells induces the expression of the hBAT binding protein in a manner that correlates with different activation stages.
Example 28
hBAT Increases Survival of activated CD4+ Cells
To examine whether activated T cells can be further stimulated by the hBAT, human CD4+ cells were isolated from normal donors by negative selection and activated with a suboptimal concentration (0.25 μl/ml) of anti-CD3/CD28 beads (FIG. 31). hBAT (0.5 μg/ml) was added 2 days following activation and its effect was evaluated by determining the number of viable cells. The results indicate that hBAT induced a significant increase in the number of viable CD4+ cells isolated from the two separate donors (FIGS. 31A and B). Control nonstimulated cells died within eight days of isolation whereas activated cells expanded in a manner that is typical of lymphocytes, commencing with cell proliferation followed by a stage of stable cell number leading to a stage dominated by cell death. The addition of hBAT enhanced the expansion of CD4+ cell and increased the number of cells by 1.5 folds with respect to cells in the absence of the mAb.
The fact that the efficacy of BAT antibody in vivo is increased in the presence of tumor together with the results herein, suggests that the increased efficacy may depend on the presence of activated BAT target cells. Lymphocytes directed against tumor antigens have been observed in cancer patients, albeit inefficient in the inhibition of tumor growth, and may serve as target cells for BAT activity. Thus, in view of the results it may be implied that hBAT activates CD4+ cells by stimulating cell proliferation and/or by inhibiting cell death.
Example 29
Binding of HBAT to Daudi and Jurkat Cell Lines
Mouse BAT-1 was raised against membranes of the Daudi B-cell line and has been shown to bind human T cells. To verify the specificity of the humanized antibody, hBAT was examined for its binding to two human cell lines of myeloid origin: Daudi cells—a human B cell lymphoma line and Jurkat cells—a human T cell leukemia line. hBAT conjugated to FITC was incubated with Daudi and Jurkat cells at a concentration of 150 ug/ml (4° C. for 1 hr). Binding was determined by flow cytometry.
Both cell lines, Daudi (FIG. 32A) and Jurkat (FIG. 32B) bound the humanized antibody. Moreover, most of the cells in culture of both lines were capable of binding the antibody. An isotype matched human-IgG1 served as a negative control (FIG. 32; isotype control) and established the reading threshold. Both cell lines demonstrated a similar intensity of antibody staining suggesting that they express a similar number of hBAT binding molecules.
Example 30
Binding of HBAT to PBL of Cancer Patients
Following the observation that hBAT is capable of binding human T cells from normal donors, we compared its ability to bind lymphocytes collected from cancer patients. PBL were isolated from the blood of a prostate cancer patient by ficoll followed by adherence to tissue culture plates. Non-adherent cells were examined for binding of hBAT and lymphocyte markers. Binding was performed at 4° C. for 1 hr, and determined by flow cytometry on gated lymphocytes. Isotype controls were used to determine the quadrants. These patients have formerly undergone therapy that often affects the presence and phenotype of lymphocytes. hBAT binding to these cells is a pre-requisite for its activity and as depicted in FIG. 33, resembles the binding to lymphocytes of normal donors. Although total lymphocyte numbers were low, hBAT could still bind a large proportion of the lymphocyte subpopulations which we examined including 39% of CD4+ cells, 60% of CD8+ cells and 68% of B cells.
Example 31
Cross Reactivity of HBAT with Human, Primate and Murine Tissues
The purpose of this study was to examine the cross reactivity of hBAT-1 monoclonal antibody with a range of normal human tissue. This study involved immunohistochemical testing of the monoclonal antibody against-a range of human tissues. A comparison of in vitro cross-reactivity in tissues from cynomologus monkey and CD-1 mice was also undertaken.
(i) Tissue Source
The tissues used in this study were each obtained from three unrelated donors to minimize the chances of donor specific factors affecting antibody binding. The human tissue was provided by an ethical source. The primate and murine tissues used in this study were obtained from two animals of each species, by an ethical source. The murine and primate are potential test systems that may be evaluated in pre-clinical toxicology Studies. The tissues selected were those specified in the FDA Points to Consider in the Manufacture and Testing of Monoclonal Antibody Products for Human Use (Office of Biologics Research and Review. Center for Biologics Evaluation and Research FDA. 1997) and the Rules Governing Medicinal Products in the European Community Vol. 3a (Production and Quality Control of Monoclonal Antibodies Dec. 1994, 3AB4a). All tissues used in this investigation were snap frozen in liquid nitrogen and stored at or below −70° C. until required. Cryostat sections were prepared at a nominal thickness of 5 μm to 8 μm. The positive control was Jurkat E6 cells. Samples of fresh blood were collected from 3 donors and smears prepared on the day of use.
(ii) FITC Conjugation
The humanized monoclonal hBAT-1 antibody was conjugated to FITC by the Custom Antibody Services Division of Serotec Ltd (ISO 9001, Certification) before the study was started. The final concentration of the conjugated antibody was 1.99 mg/ml.
Initial validation of the methodology was performed on control tissue (Jurkat E6 cell line) to determine the titer concentration for antibody-tissue binding with frozen sections and other conditions relevant to the proper performance of the antibody-tissue binding. Slides were microscopically examined and scored subjectively against the antibody specificity (Table 21). Based on these data, the concentrations of hBAT-1 that were used throughout the study were 1:100, 1:250 and 1:500.












TABLE 21







hBAT-1

Signal




dilution
1Specificity
Strength
Background









1:25
3
+++
3



1:50
3
+++
2



1:100
3
+++
1



1:250
3
+++
0



1:500
2
++
0



1:1000
1
+
0



1:2000
0
0
0



1:4000
0
0
0



1:8000
0
0
0



Negative
0
0
0







1Key: 3 refers to strong positive-staining, 2 refers to positive staining, 1 refers to weak positive staining and 0 refers to no staining/signal. +++ refers to strong visual signal, ++ refers to good visual signal and + refers to weak visual signal.






(iii) Controls.
Negative control reactions, in which the antibody was substituted with a buffer, were carried out for each tissue. Each detection reaction included positive control cells, Jurkat E6, reacted at the three predetermined dilutions of the antibody. This allowed the consistency of the reaction to be monitored. Sections of thyroid, incubated with anti actin antibody, were included in each assay run as controls for the detection system.
(iv) Cross-reactivity Assessment
Sections of each tissue were stained with Haematoxylin and Eosin (H&E) to confirm their identity and suitability for the study. Sections were also incubated with anti smooth muscle actin (SMA; Table 22) or rabbit anti human transferrin control sera, which showed the tissues were suitable for immunohistochemistry. Three sections of each of the tissues were prepared and incubated with the antibody, which had been conjugated to FITC, at concentrations of 1:100, 1:250 and 1:500 as determined during the validation phase. After washing in buffer and blocking with normal serum, the sections were incubated with the appropriate secondary and tertiary antibodies for alkaline-phosphatase detection, and counter-stained with haematoxylin before microscopical examination to determine sites of binding.
The FITC-conjugated staining method with Alkaline Phosphatase detection contained the following steps:
1. Air dry cryostat sections.
2. Fix by immersion in acetone, 10 minutes at room temperature
3. Air dry.
4. Buffer wash.
5. Normal serum, 1:5, at least 20 minutes.
6. Buffer wash
7. 1022292 test FITC conjugated antibody at 1:100, 1:250 and 1:500,:. overnight at 2-8° C.
8. Buffer wash.
9. Monoclonal anti FITC antibody, 1:50, 30 minutes.
10. Buffer wash.
11. Alkaline phosphatase conjugated antibody, 1:200, 2 hours.
12. Buffer wash.
13. Vector red and levamisole, 20 minutes.
14. Buffer wash.
15. Counterstain and mount.
Endogenous alkaline phosphatase was minimized by using Levamisole incorporated into the chromogen. In tissues where endogenous alkaline phosphatase activity could not be suppressed (human colon, ileum, placenta and endothelium, murine colon and pancreas, primate stomach, ileum and prostate), horseradish peroxidase conjugated antibody at 1:200 for 2 hours was used, followed by Diaminobenzidene (DAB) reagent for 20 minutes.
(v) Results
Samples of individual tissues stained with H&E were examined for quality of tissue, presence of normal histological features and adequacy of preservation. All samples that were tested were considered to be suitable for the purposes of this study. Positive staining was achieved in the Jurkat E6 cell line for hBAT-1 and in the thyroid sections treated with smooth muscle actin. As the controls gave the expected results, the test was considered valid.
Individual cross reactivity results for hBAT-1 and human tissues are shown in Tables 22. Positive staining was detected in blood vessels human endothelium at a dilution of 1:100 and was probably a result of hBAT-1 binding to lymphocytes. Positive staining indicates probable tissue binding of the humanized monoclonal hBAT-1 antibody. No staining, i.e. cross reactivity with hBAT-1, was observed in spleen sections, blood smears or other human tissues (except human endothelium-blood vessels). None of the murine and primate tissues showed evidence of cross reactivity with hBAT-1.










TABLE 22









hBAT-1 Antibody















Tissue
SMA
1:100
1:250
1:500
1:100







Adrenal
+
−
−
−
−



Bladder
+
−
−
−
−



Blood Cells
1N/A
−
−
−
−



Blood Vessel
+
+
−
−
−



(endothelium)



Bone Marrow
 N/A
−
−
−
−



Breast
+
−
−
−
−



Cerebellum
+
−
−



Cerebral Cortex
+
−
−
−
−



Colon
+
−
−
−
−



Eye (Retina)
+
−
−
−
−



Fallopian tube
+
−
−
−
−



Heart
+
−
−
−
−



Ileum (GI tract)
+
−
−
−
−



Kidney
+
−
−
−
−



Liver
+
−
−
−
−



Lung
+
−
−
−
−



Lymph node
+
−
−
−
−



Ovary
+
−
−
−
−



Pancreas
+
−
−
−
−



Parathyroid
+
−
−
−
−



Parotid
+
−
−
−
−



Pituitary
+
−
−
−
−



Placenta
+
−
−
−
−



Prostate
+
−
−
−
−



Skin
+
−
−
−
−



Spinal cord
+
−
−
−
−



Spleen
+
−
−
−
−



Stomach
+
−
−
−
−



Striated muscle
+
−
−
−
−



Testes
+
−
−
−
−



Thymus
+
−
−
−
−



Thyroid
+
−
−
−
−



Tonsil
+
−
−
−
−



Ureter
+
−
−
−
−



Uterus-cervix
+
−
−
−
−



Uterus-
+
−
−
−
−



endometrium







1N/A - result not applicable






The foregoing description of the specific embodiments will so fully reveal the general nature of the invention that others can, by applying current knowledge, readily modify and/or adapt for various applications such specific embodiments without undue experimentation and without departing from the generic concept, and, therefore, such adaptations and modifications should and are intended to be comprehended within the meaning and range of equivalents of the disclosed embodiments. It is to be understood that the phraseology or terminology employed herein is for the purpose of description and not of limitation. The means, materials, and steps for carrying out various disclosed functions may take a variety of alternative forms without departing from the invention. Thus the expressions “means to . . . ” and “means for . . . ”, or any method step language, as may be found in the specification above and/or in the claims below, followed by a functional statement, are intended to define and cover whatever structural, physical, chemical or electrical element or structure, or whatever method step, which may now or in the future exist which carries out the recited function, whether or not precisely equivalent to the embodiment or embodiments disclosed in the specification above, i.e., other means or steps for carrying out the same functions can be used; and it is intended that such expressions be given their broadest interpretation.

## Claims

1. A humanized antibody comprising the complementarity-determining regions (CDRs) of murine monoclonal antibody BAT-1 (mBAT-1), wherein the humanized antibody comprises:
a light chain variable region selected from the group consisting of: BATRKA (SEQ. ID NO. 15), BATRKB (SEQ. ID NO. 16), BATRKC (SEQ. ID NO. 17), and BATRKD (SEQ. ID NO. 18), and
a heavy chain variable region selected from the group consisting of: BATRHA (SEQ. ID NO. 20), BATRHB (SEQ. ID NO. 21), BATRHC (SEQ. ID NO. 22), BATRHD (SEQ. ID NO. 23) and BATRHE (SEQ. ID NO. 24); wherein the humanized antibody retains the anti-tumor activity of mBAT-1 and is less immunogenic in a human subject than mBAT-1.

2. The humanized antibody of claim 1, wherein the variable regions are selected from the group consisting of: BATRHA/BATRKA (SEQ. ID NO. 20/SEQ. ID NO. 15), BATRHB/BATRKA (SEQ. ID NO. 21/SEQ. ID NO. 15), BATRHB/BATRKB (SEQ. ID NO. 21/SEQ. ID NO. 16), BATRHC/BATRKB (SEQ. ID NO. 22/SEQ. ID NO. 16), BATRHB/BATRKD (SEQ. ID NO. 21/SEQ. ID NO. 18), and BATRHC/BATRKD (SEQ. ID NO. 22/SEQ. ID NO. 18).

3. An antibody fragment of the humanized antibody of claim 1, wherein the antibody fragment is selected from the group consisting of: Fv, F(ab′), F(ab′)2, and a single chain antibody.

4. A pharmaceutical composition comprising the humanized antibody according to claim 1, and a physiologically acceptable carrier, diluent, or stabilizer.

5. A method for treating cancer cells that express the BAT-1 antigen in a subject in need of such treatment which comprises the step of treating the subject with a therapeutically effective amount of a pharmaceutical composition containing as an active ingredient the humarized antibody of claim 1 and optionally including a physiologically acceptable carrier, diluent, or stabilizer.

6. The method of claim 5 further comprising treating the subject with an additional therapeutic agent.

7. The method of claim 6 wherein the additional therapeutic agent is selected from IL-1, IL-2, IL-6, IFN-α (interferon-α), T-cell stimulatory antibody, or anti-tumor therapeutic antibody.

8. The method of claim 6, wherein the humarized antibody and the additional agent is administered substantially at the same time in a single composition or sequentially in separate compositions.

9. The method of claim 6, further comprising applying a cell therapy treatment to the subject.

10. The method of claim 9, wherein the cells are autologous or allogeneic cells.

11. The method of claim 6 wherein the cancer is selected from the group consisting of melanoma, a lung tumor, colorectal cancer and hepatic metastasis.

12. A method for producing the humanized antibody of claim 1, which comprises:
a) transfecting a host cell with a vector comprising a polynucleotide sequence encoding the humanized antibody, or co-transfecting the host cell with 2 vectors each comprising a polynucleotide sequence encoding the heavy or light chain regions of the humanized antibody;
b) culturing the host cell so that said humanized antibody is expressed; and
c) recovering the humanized antibody from the host cell culture.