HK1164338B - Human anti-pd-1, pd-l1, and pd-l2 antibodies and uses therefor - Google Patents

Description

Human anti-PD-1, PD-L1 and PD-L2 antibodies and uses thereof

RELATED APPLICATIONS

This application claims priority to U.S. provisional application No. 61/100,534 filed on 26.9.2008, which is incorporated herein by reference in its entirety.

Background

In response to exogenous polypeptides, at least two signals must be provided by Antigen Presenting Cells (APC) to quiescent T lymphocytes (Jenkins, M.and Schwartz, R. (1987) J.exp.Med.165: 302-. The first signal, which confers immune response specificity, is transduced via the T Cell Receptor (TCR) upon recognition of foreign antigenic peptides present in the Major Histocompatibility Complex (MHC). The second signal, which is called co-stimulation, induces T cell proliferation and is functional (Lenschow et al (1996) Annu. Rev. Immunol.14: 233). Costimulation is neither antigen-specific nor MHC-restricted and is provided by different cell surface molecules expressed by APCs. (Jenkins, M.K. et al, (1988) J.Immunol.140: 3324-3330; Linsley, P.S. et al, (1991) J.Exp.Med.173: 721-.

Proteins B7-1(CD80) and B7-2(CD86) are important costimulatory molecules (Freeman et al (1991) J.Exp.Med.174: 625; Freeman et al (1989) J.Immunol.143: 2714; Azuma et al (1993) Nature 366: 76; Freeman et al (1993) Science 262: 909). B7-2 plays a major role in the primary immune response, while B7-1, which is upregulated later in the immune response, may be important to prolong the primary T cell response or to co-stimulate the secondary T cell response (Bluestone (1995) Immunity 2: 555).

CD28 is a ligand for B7-1 and B7-2, which is constitutively expressed by quiescent T cells and increases in expression upon T cell activation. Ligation of CD28 that binds TCR signals results in costimulatory signal transduction that induces T cells to proliferate and secrete IL-2(Linsley, P.S. et al, (1991) J.exp.Med.173: 721-. The second B7-1 and B7-2 ligands, CTLA4(CDl52), were homologous to CD28, but were not expressed by resting T cells. CTLA4 expression occurs following T cell activation (Brunet, J.F. (1987) Nature 328: 267-270). The linkage of CTLA4 results in inhibitory signal transduction that prevents T cell proliferation and cytokine secretion. Thus, CTLA4 is an important negative regulator of T cell response (Waterhouse et al (1995) Science 270: 985) (Allison and Krummel (1995) Science 270: 932). The third member of the CD28 family found was ICOS (Hutloff et al (1999) Nature 397: 263; WO 98/38216). ICOS causes high levels of cytokine expression by ligation of its ligands (ICOS-L), but limited T cell expansion (Riley J.L. et al, (2001) J.Immunol.166: 4943-48; Aicher A. et al, (2000) J.Immunol.164: 4689-96; Mages H.W. et al, (2000) Eur.J.Immunol.30: 1040-7; Brodie D. et al, (2000) curr.biol.10: 333-6; Ling V. et al, (2000) J.Immunol.164: 3-7; Yoshinaga S.K. et al, (165) Nature 402: 827-32). If a T cell is stimulated through a T cell receptor in the absence of a costimulatory signal, it becomes unresponsive, anergic, or dead.

B7 has been demonstrated in vitro and in several in vivo model systems: importance of the CD28/CTLA4/ICOS costimulatory pathway. Blockade of this costimulatory pathway results in the development of antigen-specific tolerance in both murine and human systems (Harding, F.A. et al. (1992) Nature 356: 607609; Lenschow, D.J. et al. (1992) Science 257: 789792; Turka, L.A. et al. (1992) Proc.Natl.Acad.Sci.USA 89: 1110211105; Gimmi, C.D. et al. (1993) Proc.Natl.Acad.Sci.USA 90: 65866590; Boussiosotis, V. et al. (1993) J.Exp.Med.178: 17531763). In contrast, B7 expression of B7 negative murine tumor cells induces T cell-mediated specific immunity that is associated with tumor rejection and long-term sustained protection against tumor invasion (Chen, L. et al (1992) cells 71: 10931102; Townsend, S.E. and Allison, J.P. (1993) Science 259: 368370; Baskar, S. et al, (1993) Proc.Natl.Acad.Sci.90: 56875690.). Thus, control of the co-stimulatory pathway offers tremendous potential to stimulate or suppress human immune responses.

The discovery of more members of the B7-1 and CD28 families has revealed additional pathways that provide co-stimulatory and inhibitory secondary signals to T cells. One of the newer pathways is represented by the programmed death 1 (PD-1; also known as CD279) receptor and its ligand PD-L1 (B7-H1; CD274) and PD-L2 (B7-DC; CD 273). PD-1 is a member of the CD28/CTLA4 family, which is expressed on activated, but not quiescent, T cells (Nishimura et al (1996) int. Immunol.8: 773). PD-1 ligation by its ligand mediates inhibitory signals that result in decreased cytokine production and decreased survival of T cells (Nishimura et al (1999) Immunity 11: 141; Nishimura et al (2001) Science 291: 319; Chemnitz et al (2004) J.Immunol.173: 945).

PD-L1 is a member of the B7 family, which is expressed on a variety of cell types, including APC and activated T cells (Yamazaki et al (2002) J.Immunol.169: 5538). PD-L1 binds to PD-1 and B7-1. Binding of B7-1 expressed by PD-L1 to T cells and binding of PD-L1 expressed by B7-1 to T cells resulted in the suppression of T cells (button et al (2007) Immunity 27: 111). There is also evidence that: as with other B7 family members, PD-L1 also provides co-stimulatory signals to T cells (Subudhi et al (2004) J. Clin. invest.113: 694; Tamura et al (2001) Blood 97: 1809).

PD-L2 is a member of the B7 family expressed on different APCs, including dendritic cells, macrophages, and myeloid-derived mast cells (Zhong et al (2007) eur.j.immunol.37: 2405). PD-L2 expressed by APC can inhibit T cell activation by ligation of PD-1 and co-stimulate T cell activation by a PD-1 independent mechanism (Shin et al (2005) J.Exp.Med.201: 1531). Furthermore, ligation of PD-L2 expressed by dendritic cells results in increased dendritic cell cytokine expression and survival (Radhakrishnan et al, (2003) J.Immunol.37: 1827; Nguyen et al, (2002) J.exp.Med.196: 1393). The structure and expression of PD-1, PD-L1, and PD-L2, as well as the signaling characteristics and function (e.g., therapeutic effect) of these molecules in regulating T cell activation and tolerance profiles are described in Kier et al (2008) ann. 677, which is hereby incorporated by reference in its entirety. Control of this and other costimulatory pathways offers tremendous potential for stimulating or suppressing human immune responses, and there is a need for compositions and methods for achieving such control.

Summary of The Invention

The present invention is based on the generation and isolation of novel composite human monoclonal antibodies that specifically bind to human PD-1, human PD-L1, and human PD-L2, as well as the characterization of such novel antibodies and their therapeutic value in treating a variety of conditions mediated by PD-1, PD-L1, and/or PD-L2. Common techniques for humanizing murine antibodies typically produce humanized antibodies that: reduced antigen binding affinity compared to the original murine antibody (Almagro and Fransson (2008) Frontiers in bioscience 13: 1619-1633; Foote and Winter (1992) J.mol.biol.224: 487-499; Hwang et al (2005) Methods 36: 35-42). Surprisingly, the human composite antibodies of the invention have been shown to bind PD-1, PD-L1 or PD-L2 with an affinity very close to that of murine antibodies. In addition, conventional humanization techniques generate humanized antibodies that retain some murine sequences. Thus, such antibodies may retain immunogenicity when administered to humans. For example, the humanized antibody CAMPATHImmunogenicity is induced in about 50% of patients. On the other hand, the composite human antibody of the present invention is completely derived from a human sequence. Thus, it may have significantly reduced immunogenicity and be therapeutically more effective and useful when administered to human patients than other anti-human PD-1, PD-L1, and/or PD-L2 antibodies. Thus, the composite human antibodies of the invention provide improved methods for the treatment and prevention of diseases mediated by PD-1, PD-L1, and/or PD-L2, due in part to their unique specificity, affinity, structure, functional activity, and the fact that they are derived from human antibody sequences. The invention is also based on the discovery of novel therapeutic applications, including the treatment of persistent infectious diseases, asthma, inflammatory diseases, and cancer, by administering the human, multi-modal antibodies described herein.

One embodiment of the invention is an antibody or antigen-binding fragment thereof isolated as follows: which binds to a PD-1 protein, PD-L1 protein, or PD-L2 protein (such as human PD-1, PD-L1, or PD-L2 protein), wherein the isolated antibody or antigen-binding fragment thereof is chimeric, humanized, complexed, human, or human, and contains one, two, three, four, five, or six amino acid sequences selected from the group consisting of SEQ ID NOs: 7-24.

The invention also provides an isolated antibody or antigen-binding fragment thereof as follows: which binds to a PD-1 protein (such as a PD-1 protein comprising the amino acid sequence of SEQ ID NO: 2), wherein the isolated antibody or antigen-binding fragment thereof is chimeric, humanized, composite, human, or human and comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 7-9 (CDR 1 sequence of SEQ ID NO: 7, CDR2 sequence of SEQ ID NO: 8 and CDR3 sequence of SEQ ID NO: 9) and/or a light chain variable region sequence comprising the amino acid sequence of SEQ ID NO: 10-12 (CDR 1 sequence of SEQ ID NO: 10, CDR2 sequence of SEQ ID NO: 11 and CDR3 sequence of SEQ ID NO: 12).

The invention also provides an isolated antibody or antigen-binding fragment thereof as follows: which binds to a PD-L1 protein (e.g., a PD-L1 protein comprising the amino acid sequence of SEQ ID NO: 4), wherein the isolated antibody or antigen-binding fragment thereof is chimeric, humanized, composite, human, or human and comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 13-15 (the CDR1 sequence of SEQ ID NO: 13, the CDR2 sequence of SEQ ID NO: 14 and the CDR3 sequence of SEQ ID NO: 15) and/or a light chain variable region comprising the amino acid sequence of SEQ ID NO: 16-18 (the CDR1 sequence of SEQ ID NO: 16, the CDR2 sequence of SEQ ID NO: 17 and the CDR3 sequence of SEQ ID NO: 18).

The invention also provides an isolated antibody or antigen-binding fragment thereof as follows: which binds to a PD-L2 protein (e.g., a PD-L2 protein comprising the amino acid sequence of SEQ ID NO: 6), wherein the isolated antibody or antigen-binding fragment thereof is chimeric, humanized, composite, human, or human and comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 19-21 (CDR 1 sequence of SEQ ID NO: 19, CDR2 sequence of SEQ ID NO: 20 and CDR3 sequence of SEQ ID NO: 21) and/or a light chain variable region comprising the amino acid sequence of SEQ ID NO: 22-24 (the CDR1 sequence of SEQ ID NO: 22, the CDR2 sequence of SEQ ID NO: 23 and the CDR3 sequence of SEQ ID NO: 24).

The invention also includes an isolated antibody or antigen-binding fragment thereof as follows: which binds to a PD-1 protein, PD-L1 protein, or PD-L2 protein (e.g., human PD-1, PD-L1, or PD-L2 protein), wherein the isolated antibody or antigen-binding fragment thereof is chimeric, humanized, complexed, and/or human, and comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 25-29, 34-38, or 43-47, or a light chain sequence identical to SEQ ID NO: 25-29, 34-38, or 43-47, or a sequence having at least about 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, or more, identity; and/or is selected from SEQ ID NO: 30-33, 39-42 or 48-51, or a light chain sequence identical to SEQ ID NO: 30-33, 39-42, or 48-51, or a sequence having at least about 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9% or more identity.

The invention also provides an isolated antibody or antigen-binding fragment thereof as follows: which binds to a polypeptide comprising SEQ ID NO: 2, wherein the isolated antibody or antigen-binding fragment thereof is chimeric, humanized, complexed or human and comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 25-29, or a heavy chain sequence identical to SEQ ID NO: 25-29, or a sequence having at least about 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9% or more identity or homology; and/or is selected from seq id NO: 30-33, or a sequence identical to SEQ ID NO: 30-33 have at least about 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9% or more identity or homology. For example, an antibody or antigen-binding fragment thereof comprises seq id NO: 27 or 28 and the heavy chain variable region sequence of SEQ ID NO: 32 or 33, or a light chain variable region sequence. In some embodiments, the antibody or antigen-binding fragment thereof comprises SEQ ID NO: 28 and SEQ ID NO: 32, and a light chain variable region sequence.

The invention also provides an isolated antibody or antigen-binding fragment thereof as follows: which binds to a polypeptide comprising SEQ ID NO:4, wherein the isolated antibody or antigen-binding fragment thereof is chimeric, humanized, composite, or human and comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:34-38, or a sequence identical to SEQ ID NO: 34-38, or a sequence having at least about 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9% or more identity or homology; and/or is selected from seq id NO: 39-42, or a sequence that is identical to SEQ ID NO: 39-42, or a sequence having at least about 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9% or more identity or homology thereto. For example, an antibody or antigen-binding fragment thereof comprises seq id NO:35 or 37 and the variable heavy chain region sequence of SEQ ID NO: 39. 40 or 42, or a light chain variable region sequence. In some embodiments, the antibody or antigen-binding fragment thereof comprises SEQ ID NO:35 and the heavy chain variable region sequence of SEQ ID NO: 42, light chain variable region sequence.

The invention also provides an isolated antibody or antigen-binding fragment thereof as follows: which binds to a polypeptide comprising SEQ ID NO: 6, wherein the isolated antibody or antigen-binding fragment thereof is chimeric, humanized, composite, or human and comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 43-47, or a sequence identical to SEQ ID NO: 43-47 have at least about 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9% or more identity or homology; and/or is selected from seq id NO: 48-51, or a sequence identical to SEQ ID NO: 48-51 have at least about 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9% or more identity or homology. For example, an antibody or antigen-binding fragment thereof comprises seq id NO: 44 or 46 and the heavy chain variable region sequence of SEQ ID NO: 49. 50 or 51 in the presence of a heavy chain variable region. In some embodiments, the antibody or antigen-binding fragment thereof comprises SEQ ID NO: 46 and the heavy chain variable region sequence of SEQ ID NO: 51, and a light chain variable region sequence.

Another embodiment of the invention is an isolated antibody or antigen-binding fragment thereof as described herein: which binds to PD-1 protein, wherein the isolated antibody inhibits the binding of biotinylated EH12.2H7 antibody to Fc-PD-1 in a competition ELISA assay. Another embodiment is an isolated antibody or antigen-binding fragment thereof as described herein: it binds to PD-L1 protein, wherein the isolated antibody inhibits binding of biotinylated 29E2A3 antibody to Fc-PD-L1 in a competition ELISA assay. Another embodiment is an isolated antibody or antigen-binding fragment thereof as described herein: which binds to PD-L2 protein, wherein the isolated antibody inhibits binding of biotinylated 24f.10c12 antibody to Fc-PD-L2 in a competition ELISA assay.

Another embodiment of the invention is an isolated antibody or antigen-binding fragment thereof as described herein: which bind to the PD-1 protein, wherein the isolated antibody inhibits PD-1 mediated signaling. Another embodiment is an isolated antibody or antigen-binding fragment thereof as described herein: which binds to the PD-L1 protein, wherein the isolated antibody inhibits PD-L1-mediated signaling. Another embodiment is an isolated antibody or antigen-binding fragment thereof as described herein: which binds to the PD-L2 protein, wherein the isolated antibody inhibits PD-L2-mediated signaling.

In particular, an embodiment of the invention is an isolated nucleic acid encoding a polypeptide, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ id nos: 25-51, or a sequence that is identical to SEQ ID NO: 25-51 have at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identity or homology. Another embodiment is a vector, host cell or animal comprising one or more of these nucleic acids. Another aspect is a nucleic acid that hybridizes under stringent conditions to the complement (complement) of: the nucleic acid encodes a polypeptide selected from the group consisting of SEQ ID NO: 25-51 or a polypeptide corresponding to seq id NO: 25-51 have at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical homology.

The invention also provides an isolated nucleic acid encoding the heavy chain variable region and/or the light chain variable region of any of the antibodies or antigen binding fragments thereof described herein. In some embodiments, the nucleic acid is in a vector, e.g., an expression vector. The invention also provides host cells containing one or more nucleic acids encoding the heavy and/or light chains of the antibodies or antigen-binding fragments described herein. In some embodiments, the host cell produces an antibody or antigen-binding fragment. The invention also provides methods of producing an antibody or antigen-binding fragment described herein, comprising culturing a cell that produces the antibody or antigen-binding fragment and recovering the antibody or antigen-binding fragment from the cell culture.

The invention further includes a pharmaceutical composition comprising an isolated antibody or antigen-binding fragment thereof described herein and a pharmaceutically acceptable carrier.

The invention includes a method of reactivating depleted T cells comprising contacting a population of T cells, at least some of which express PD-, PD-L1, and/or PD-L2, with an antibody or antigen binding fragment thereof described herein in vitro, ex vivo, or in vivo.

The invention further relates to methods of treating an individual suffering from a persistent infection, including a viral infection, a bacterial infection, a helminth infection, or a protozoal infection, comprising administering to the individual a composition comprising an effective amount of an isolated antibody or antigen-binding fragment thereof described herein.

The invention further includes methods of treating cancer comprising administering to an individual a composition comprising an effective amount of an isolated antibody or antigen-binding fragment thereof described herein, including wherein the isolated antibody induces antibody-mediated cytotoxicity, or is modified to induce antibody-mediated cytotoxicity, or is conjugated to an agent (agent) selected from a toxin and an imaging agent. In some embodiments, an antibody or antigen-binding fragment that binds to PD-L1 is administered to an individual having a cancer that overexpresses PD-L1. In some embodiments, an antibody or antigen-binding fragment that binds to PD-L2 is administered to an individual having a cancer that overexpresses PD-L2.

The invention further relates to a method of treating an individual suffering from asthma comprising administering to the individual a composition comprising an effective amount of an isolated antibody or antigen-binding fragment thereof that binds to PD-L2 protein described herein.

The invention also includes a method of treating an individual suffering from an inflammatory disease or transplant rejection comprising administering to the individual a composition comprising an effective amount of an isolated antibody or antigen-binding fragment thereof that binds PD-L1 protein or PD-L2 protein as described herein.

The invention also includes an antibody, antigen-binding fragment, or polypeptide described herein for use in any of the methods described herein. The invention also includes the use of an antibody, antigen-binding fragment, or polypeptide described herein for the manufacture of a medicament, such as a medicament for treating any of the diseases described herein in an individual.

Brief Description of Drawings

FIG. 1 shows a schematic representation of an expression vector for cloning assembled human immunoglobulin sequences according to the invention.

FIGS. 2A-2E show composite human heavy chain (FIG. 2A, VH 1; FIG. 2B, VH 2; FIG. 2C, VH 3; and FIG. 2D, VH 4; FIG. 2E, VH5) variable region sequences designed to correspond to the heavy chain variable region sequence of murine anti-human PD-1 antibody EH12.2H7.

FIGS. 3A-3D show the composite human light chain (FIG. 3A, V.kappa.1; FIG. 3B, V.kappa.2; FIG. 3C, V.kappa.3; FIG. 3D, V.kappa.4) variable region sequence designed to correspond to the light chain variable region sequence of murine anti-human PD-1 antibody EH12.2H7.

FIGS. 4A-4E show composite human heavy chain (FIG. 4A, VH 1; FIG. 4B, VH 2; FIG. 4C, VH 3; FIG. 4D, VH 4; FIG. 4E, VH5) variable region sequences designed to correspond to the heavy chain variable region sequence of murine anti-human PD-L1 antibody 29 E.2A3.

FIGS. 5A-5D show the composite human light chain (FIG. 5A, V.kappa.1; FIG. 5B, V.kappa.2; FIG. 5C, V.kappa.3; FIG. 5D, V.kappa.4) variable region sequence designed to correspond to the light chain variable region sequence of murine anti-human PD-L1 antibody 29 E.2A3.

FIGS. 6A-6E show composite human heavy chain (FIG. 6A, VH 1; FIG. 6B, VH 2; FIG. 6C, VH 3; FIG. 6D, VH 4; FIG. 6E, VH5) variable region sequences designed to correspond to the heavy chain variable region sequence of murine anti-human PD-L2 antibody 24 F.10C12.

FIGS. 7A-7D show the composite human light chain (FIG. 7A, V.kappa.1; FIG. 7B, V.kappa.2; FIG. 7C, V.kappa.3; FIG. 7D, V.kappa.4) variable region sequence designed to correspond to the light chain variable region sequence of the murine anti-human PD-L2 antibody 24 F.10C12.

FIGS. 8A-8C show SDS-PAGE results of 1. mu.g of the composite human antibodies corresponding to murine anti-human antibodies EH12.2H7, 29E.2A3, and 24F.10C12, respectively.

FIGS. 9A-9C show ELISA competition results for human antibodies corresponding to and relative to the murine anti-human antibodies EH12.2H7, 29E.2A3, and 24F.10C12, respectively. In fig. 9A, purified antibodies were tested for binding to human PD-1 by competition ELISA. Different concentrations of each antibody (0.06. mu.g/ml to 8. mu.g/ml) were mixed with a fixed concentration of biotinylated EH12.2H7(40ng/ml) and bound to PD-1 coated immulon maxisorb plates. Binding was detected by streptavidin-HRP and OPD substrate. The absorbance at 490nm was measured on a plate reader (plate reader) and plotted against test antibody concentration. In fig. 9B, the purified antibody was tested for binding to human PD-L1 by competition ELISA. Different concentrations of each antibody (0.02. mu.g/ml to 8. mu.g/ml) were mixed with a fixed concentration of biotinylated 29E.2A3(40ng/ml) and bound to a PD-L1 coated immulon maxisorb plate. Binding was detected by streptavidin-HRP and OPD substrate. The absorbance at 490nm was measured on a plate reader and plotted against test antibody concentration. In fig. 9C, the purified antibody was tested for binding to human PD-L2 by competition ELISA. Various concentrations of each antibody (0.02. mu.g/ml to 8. mu.g/ml) were mixed with a fixed concentration of biotinylated 24F.10C12(40ng/ml) and bound to PD-L2-coated immulon maxisorb plates. Binding was detected by streptavidin-HRP and OPD substrate. The absorbance at 490nm was measured on a plate reader and plotted against test antibody concentration.

FIGS. 10A-10C show IC generated by ELISA competition assay of composite human antibodies₅₀Binding data, the composite human antibodies were formed from different combinations of composite human heavy and light chains designed to correspond to those of murine anti-human antibody EH12.2H7 (FIG. 10A), 29E.2A3 (FIG. 10B), and 24F.10C12 (FIG. 10C), respectively. The analysis was performed as shown in fig. 3. IC of each combination of heavy and light chains₅₀IC relative to murine antibody₅₀And (6) standardizing. ND means no data.

FIG. 11 shows the amino acid sequences of PD-1, PD-L1 and PD-L2.

FIG. 12 shows the amino acid sequences of the CDR regions of some of the human multi-modal antibodies described herein.

FIG. 13 shows the amino acid sequences of the variable regions of some of the human composite antibodies described herein.

FIGS. 14A and 14B show the effect of humanized anti-PD-1 and humanized anti-PD-L1 antibodies on the proliferative capacity of SIV Gag-specific CD 8T cells in vitro. Each mark represents a macaque. The numbers in parentheses indicate fold increase in proliferation in the presence of blocking Ab relative to that in the absence of blocking Ab.

Figure 15 shows that blockade of PD-L1 restores intrahepatic CD 8T cell antigen driven proliferation (representative data from animal 1564).

Detailed Description

The present invention provides novel antibody-based therapeutics for the treatment and diagnosis of a variety of diseases mediated by PD-1, PD-L1, and/or PD-L2 (e.g., treatment of persistent infectious disease, asthma, inflammatory diseases, transplant rejection, and cancer).

In order to make the invention more comprehensible, certain terms are first defined. Additional definitions are set forth throughout the detailed description.

As used herein, unless otherwise specifically defined, the terms "PD-1", "PD-L1" and "PD-L2" include any variant or isoform naturally expressed by a cell and/or a fragment thereof that possesses at least one biological activity of the full-length polypeptide. Furthermore, the term "PD-1 ligand" includes one or both of PD-L1(Freeman et al, (2000) J.Exp.Med.192: 1027) and PD-L2(Latchman et al (2001) nat. Immunol.2: 261) as well as any variant or isoform naturally expressed by a cell and/or fragments thereof that possess at least one biological activity of the full-length polypeptide. For example, PD-1, PD-L1, and PD-L2 sequences from different species, including human, are well known in the art (see, e.g., Honjo et al, U.S. Pat. No. 5,629,204, which discloses human and mouse PD-1 sequences, Wood et al, U.S. Pat. No. 7,105,328, which discloses human PD-1 sequences, Chen et al, U.S. Pat. No. 6,803,192, which discloses human and mouse PD-L1 sequences, Wood et al, U.S. Pat. No. 7,105,328, which discloses human PD-L1 sequences, Freeman et al, U.S. Pat. Pub. No. 20020164600, which discloses human and mouse PD-L2 sequences).

As used herein, the term "antibody" includes whole antibodies and any antigen-binding fragment (i.e., "antigen-binding portion") or single chain thereof. An "antibody" refers to a glycoprotein or antigen-binding portion thereof comprising at least two heavy (H) chains and two light (L) chains interconnected by disulfide bonds. Each heavy chain is composed of a heavy chain variable region (abbreviated herein as V)_H) And a heavy chain constant region. The heavy chain constant region consists of three domains, CH1, CH2, and CH 3. Each light chain is composed of a light chain variable region (abbreviated herein as V)_L) And a light chain constant region. The light chain constant region consists of one domain CL. V_HRegion and V_LThe regions may be further subdivided into hypervariable regions, termed Complementarity Determining Regions (CDRs), interspersed with more conserved regions, termed Framework Regions (FRs). Each V_HAnd V_LConsists of three CDRs and four FRs, arranged in the following order from amino-terminus to carboxy-terminus: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR 4. The variable regions of the heavy and light chains comprise binding domains that interact with an antigen. "inactivated antibody" refers to an antibody that does not induce the complement system.

The terms "hypervariable region", "HVR" or "HV" when used herein refer to a region of an antibody variable domain which is hypervariable in sequence and/or forms structurally defined loops. Generally, antibody packsComprises six HVRs; three in VH (H1, H2, H3) and three in VL (L1, L2, L3). Among natural antibodies, H3 and L3 showed the most diversity among six HVRs, and H3 was particularly thought to have a unique role in conferring subtle specificity to antibodies. See, e.g., Xu et al, Immunity 13: 37-45 (2000); johnson and Wu in Methods in Molecular Biology248: 1-25(Lo, ed., HumanPress, Totowa, NJ, 2003). In fact, naturally occurring camel (camelid) antibodies, which consist of only the heavy chain, are functional and stable in the absence of the light chain. See, e.g., Hamers-Casterman et al, Nature363: 446, 448(1993) and Sheriff et al, Nature struct. biol.3：733-736(1996)。

A number of hypervariable region descriptions are used and included herein. Kabat Complementarity Determining Regions (CDRs) are based on sequence variability and are most commonly used (Kabat et al, Sequences of Proteins of Immunological Interest, 5th Ed. public Health Service, National Institutes of Health, Bethesda, Md. (1991)). Chothia conversely refers to the position of the structural loops (Chothia and Lesk J.mol.biol.196: 901-917 (1987)). The ends of Chothia CDR-H1 loops when numbered using Kabat numbering convention vary between H32 and H34 (see below) depending on loop length (since Kabat numbering scheme is characterized by insertions at H35A and H35B; if neither 35A nor 35B is present, the loop ends at 32; if only 35A is present, the loop ends at 33; if both 35A and 35B are present, the loop ends at 34). The AbM hypervariable regions represent a compromise between Kabat CDRs and Chothia structural loops and were applied by Oxford Molecular's AbM antibody simulation software. The "Contact" hypervariable region is based on an analysis of the available complex crystal structure. The residues for each of these hypervariable regions are noted below.

The hypervariable regions may comprise the following "extended hypervariable regions": 24-36 or 24-34(L1), 46-56 or 50-56(L2) and 89-97(L3) in VL and 26-35B (H1), 50-65, 47-65 or 49-65(H2) and 93-102, 94-102 or 95-102(H3) in VH. These extended hypervariable regions are typical combinations of Kabat and Chothia definitions, which may optionally further comprise residues identified using the Contact definition. For each of these definitions, the variable domain residues are numbered according to Kabat et al, supra.

"framework" or "FR" residues are those variable domain residues other than the HVR residues as defined herein.

The expression "variable domain residue numbering as in Kabat" or "amino acid position numbering as in Kabat" and variants thereof refers to the numbering system used in antibody compilation for heavy or light chain variable domains as in Kabat et al above. Using this numbering system, the actual linear amino acid sequence may comprise fewer amino acids or additional amino acids corresponding to the FR or HVR shortening or insertion of the variable domain. For example, a heavy chain variable domain may comprise one inserted amino acid after residue 52 of H2 (residue 52a according to Kabat), may comprise an inserted residue after heavy chain FR residue 82 (e.g., residues 82a, 82b, and 82c, etc. according to Kabat). Kabat residue numbering for a given antibody can be determined by aligning regions of homology of the antibody sequence with "standard" Kabat-numbered sequences.

The term "Fc region" is used herein to define the C-terminal region of an immunoglobulin heavy chain, including native sequence Fc regions and variant Fc regions. Although the boundaries of the Fc region of an immunoglobulin heavy chain may vary, it is generally defined that the Fc region of a human IgG heavy chain extends from Cys226 or from the amino acid residue at Pro230 to its carboxy terminus. The C-terminal lysine of the Fc region (residue 447 according to the EU numbering system) may be removed, for example, during antibody production or purification, or by recombinantly engineering nucleic acid encoding the heavy chain of an antibody. Thus, the composition of a whole antibody may comprise a population of antibodies with all K447 residues removed, a population of antibodies without K447 residues removed, and a population of antibodies with a mixture of antibodies having K447 residues and no K447 residues. Suitable native sequence Fc regions for use in the antibodies of the invention include human IgG1, IgG2(IgG2A, IgG2B), IgG3 and IgG 4.

"Fc receptor" or "FcR" describes a receptor that binds to the Fc region of an antibody. Preferred FcR is a native sequenceA human FcR. In addition, a preferred FcR is one that binds an IgG antibody (gamma receptor) and includes receptors of the Fc γ RI, Fc γ RII, and Fc γ RIII subclasses, including allelic variants and alternatively spliced forms of these receptors. Fc γ RII receptors include Fc γ RIIA ("activating receptor") and Fc γ RIIB ("inhibiting receptor"), which have similar amino acid sequences that differ primarily in their cytoplasmic domains. The activation receptor Fc γ RIIA comprises in its cytoplasmic domain an immunoreceptor tyrosine-based activation motif (ITAM). The inhibitory receptor Fc γ RIIB contains an immunoreceptor tyrosine-based inhibitory motif (ITIM) in its cytoplasmic domain. (see M.Annu.Rev.Immunol.15: 203-234(1997)). FcR is in ravatch and Kinet, annu.9: 457-92 (1991); capel et al, immunolmethods4: 25-34 (1994); and de Haas et al, j.lab.clin.med.126: 330-41 (1995). Other fcrs, including those identified in the future, are also encompassed by the term "FcR" herein.

The term "CDR" and its plural "CDRs" refer to Complementarity Determining Regions (CDRs), three of which constitute the binding characteristics of a light chain variable region (CDRL1, CDRL2, and CDRL3) and three of which constitute the binding characteristics of a heavy chain variable region (CDRH1, CDRH2, and CDRH 3). The CDRs contribute to the functional activity of the antibody molecule and are separated by amino acid sequences comprising a scaffold or framework region. The exact definition of CDR boundaries and lengths is subject to different classification and numbering systems. The CDRs may thus be referred to by Kabat, Chothia, contact, or any other boundary definition, including the numbering system described herein. Each of these systems has a degree of overlap in the variable sequence in the formation of so-called "hypervariable regions", although the boundaries are different. The CDR definitions according to these systems may thus differ in length and boundary area with respect to adjacent framework regions. See, e.g., Kabat, Chothia, and/or MacCallum et al (Kabat et al, in Sequences of Proteins of Immunological Interest, "5)^thEdition, U.S. department of Health and Human Services, 1992; chothia et al, j.mol.biol., 1987, 196: 901; and MacCallum et alBiol., 1996, 262: 732, each of which is incorporated herein by reference in its entirety).

As used herein, the term "antigen-binding portion" of an antibody (or simply "antibody portion") refers to one or more fragments of an antibody that retain the ability to specifically bind to an antigen (e.g., PD-1, PD-L1, and/or PD-L2). It has been shown that the antigen binding function of an antibody can be performed by fragments of a full-length antibody. Examples of binding fragments encompassed within the term "antigen-binding portion" of an antibody include (i) Fab fragments consisting of V_H、V_LA monovalent fragment consisting of the CL and CH1 domains; (ii) f (ab')₂A fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) fd fragment of from V_HAnd a CH1 domain; (iv) fv fragment, V monobrachial of antibody_HAnd V_LDomain composition; (v) dAb fragments (Ward et al (1989) Nature 341: 544546), consisting of V_HDomain composition; and (vi) an isolated Complementarity Determining Region (CDR) or (vii) a combination of two or more isolated CDRs, which may optionally be linked by a synthetic linker. Furthermore, although the two domains V of the Fv fragment_HAnd V_LEncoded by a separate gene, but can be joined by recombinant means via a synthetic linker which allows it to form a single protein chain, in which V_HAnd V_LThe regions pair to form monovalent molecules (known as single chain fv (scfv)); see, e.g., Bird et al (1988) Science 242: 423426, respectively; and Huston et al, (1988) Proc.Natl.Acad.Sci.USA 85: 58795883). Such single chain antibodies are also intended to be encompassed within the term "antigen-binding portion" of an antibody. These antibody fragments are obtained using conventional techniques known to those skilled in the art, and useful fragments are screened in the same manner as for intact antibodies.

The antibody may be polyclonal or monoclonal; xenogeneic, allogeneic or allogeneic isogeneic; or modified forms thereof (e.g., humanized, chimeric, etc.). The antibody may also be fully human. Preferably, the antibodies of the invention specifically bind or substantially specifically bind to PD-1, PD-L1 or PD-L2 polypeptides. The term "monoclonal antibody" as used herein refers to an antibody that exhibits a single binding specificity and affinity for a particular epitope. Thus, the term "human monoclonal antibody" refers to an antibody that exhibits a single binding specificity and has variable and constant regions derived from human germline or non-germline immunoglobulin sequences. In one embodiment, the human monoclonal antibody is produced by a hybridoma comprising a B cell obtained from a transgenic non-human animal, e.g., a transgenic mouse, having a genome comprising a human heavy chain transgene and a light chain transgene fused to an immortalized cell.

As used herein, the term "isolated antibody" is intended to refer to an antibody that is substantially free of other antibodies having different antigen specificities (e.g., an isolated antibody that specifically binds PD-1, PD-L1, or PD-L2 is substantially free of antibodies that do not bind PD-1, PD-L1, or PD-L2, respectively). However, an isolated antibody that specifically binds to an epitope of PD-1, PD-L1, and/or PD-L2 may have cross-reactivity with other PD-1, PD-L1, and/or PD-L2 proteins, respectively, of different species. However, antibodies always preferably bind to human PD-1, PD-L1 and/or PD-L2. Furthermore, isolated antibodies are generally substantially free of other cellular material and/or chemicals. In one embodiment of the invention, combinations of "isolated" monoclonal antibodies with different specificities for PD-1, PD-L1 and/or PD-L2 are combined in well-defined compositions.

The term "humanized antibody" as used herein refers to an antibody composed of the CDRs of an antibody obtained from a mammal other than a human and the FR regions and constant regions of a human antibody. The humanized antibody can be used as an effective component of the therapeutic agent according to the present invention because the antigenicity of the humanized antibody in human body is reduced.

As used herein, the term "complex antibody" refers to an antibody that: having variable regions comprising germline or non-germline immunoglobulin sequences from two or more unrelated variable regions. Furthermore, the term "composite human antibody" refers to an antibody that: having constant regions derived from human germline or non-germline immunoglobulin sequences and variable regions comprising human germline or non-germline sequences from two or more unrelated human variable regions. The composite human antibody can be used as an effective component of the therapeutic agent according to the present invention because the antigenicity of the composite human antibody in a human body is reduced.

As used herein, the term "recombinant human antibody" includes all human antibodies prepared, expressed, produced or isolated by recombinant means, such as: (a) antibodies isolated from transgenic or transchromosomal animals (e.g., mice) of human immunoglobulin genes or hybridomas made therefrom (further described below in section I); (b) antibodies isolated from host cells transformed to express the antibodies, e.g., from transfectomas; (c) antibodies isolated from a library of recombinant combinatorial human antibodies; and (d) an antibody prepared, expressed, produced or isolated by any other means, including splicing of human immunoglobulin gene sequences to other DNA sequences. Such recombinant human antibodies have variable and constant regions derived from human germline and/or non-germline immunoglobulin sequences. In certain embodiments, however, such recombinant human antibodies can be subjected to in vitro mutagenesis (or in vivo somatic mutagenesis in the case of transgenic animals employing human Ig sequences), and thus the V of the recombinant antibody_HAnd V_LThe amino acid sequence of the region is such that: albeit from the human germline V_HAnd V_LSequence and human reproductive system V_HAnd V_LSequences are related, but may not naturally occur in vivo in human antibody germline repertoire systems.

As used herein, the term "heterologous antibody" is defined in relation to the production of such an antibody by a transgenic non-human organism. This term refers to antibodies that: having an amino acid sequence or coding nucleic acid sequence corresponding to a sequence found in an organism other than that consisting of the transgenic non-human animal, and is generally from a species other than the transgenic non-human animal.

As used herein, the term "K_DBy "is meant the dissociation equilibrium constant for a particular antibody-antigen interaction.

The term "specifically binds" as used herein refers to the binding of an antibody to a pre-antibodyAntigen binding is determined. Typically, the antibody is less than about 10% when measured by Surface Plasmon Resonance (SPR) techniques in a BIACORE 3000 instrument using recombinant human PD-1, PD-L1 or PD-L2 as the analyte and the antibody as the ligand^-7M-e.g. less than about 10^-8M、10^-9M or 10^-10M or less-affinity (K)_D) Binds, and binds to a predetermined antigen with an affinity as follows: is at least 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 6.0, 7.0, 8.0, 9.0, or 10.0 times greater than its affinity for binding to a non-specific antigen (e.g., BSA, casein) other than the predetermined antigen or closely related antigen. The phrases "an antibody that recognizes an antigen" and "an antibody specific for an antigen" are used interchangeably herein with the term "an antibody that specifically binds an antigen".

As used herein, the term "isotype" refers to the class of antibodies (e.g., IgM or IgG1) encoded by the heavy chain constant region gene.

As used herein, the term "glycosylation pattern" is defined as a pattern of sugar units covalently linked to a protein, more specifically to an immunoglobulin protein. The glycosylation pattern of the heterologous antibody can be characterized as being substantially similar to the glycosylation pattern naturally occurring on antibodies produced in non-human transgenic animal species, where one skilled in the art would know that the glycosylation pattern of the heterologous antibody is more similar to that described in non-human transgenic animal species than to the species from which the transgenic CH gene was derived.

As used herein, the term "naturally occurring" as applied to a substance refers to the fact that: this substance can be found in nature. For example, a polypeptide or polynucleotide sequence that is present in an organism (including viruses), that can be isolated from a natural source, and that has not been purposefully modified in the laboratory by humans, is naturally-occurring.

As used herein, the term "rearranged" refers to the configuration of such heavy or light chain immunoglobulin loci: wherein the V segments are located and are each substantially encodedIntegral V_HAnd V_LThe D-J or J segments of the conformation of the domains are directly adjacent. By comparison with germline DNA, rearranged immunoglobulin gene loci can be identified; the rearranged locus will have at least one recombinant heptamer/nonamer homology component.

As used herein, the term "unrearranged" or "germline configuration" with respect to a V segment refers to a configuration that is: wherein the V segments are not recombined and are thus immediately adjacent to the D or J segments.

As used herein, the term "nucleic acid molecule" is meant to include DNA molecules and RNA molecules. The nucleic acid molecule may be single-stranded or double-stranded, but is preferably double-stranded DNA.

As used herein with respect to antibodies or antibody portions (e.g., V) encoding binding to PD-1, PD-L1 or PD-L2_H、V_LCDR3) to nucleic acid the term "isolated nucleic acid molecule" means a nucleic acid molecule that: wherein the nucleotide sequence encoding the antibody or antibody portion is free of other nucleotide sequences encoding antibodies or antibody portions that bind to antigens other than PD-1, PD-L1, or PD-L2, respectively, which other sequences may naturally flank (flank) nucleic acids in human genomic DNA. FIGS. 2-7 correspond to heavy chains (V) comprising human anti-PD-1, PD-L1 or PD-L2 antibodies of the invention, respectively_H) And light chain (V)_L) Nucleotide and amino acid sequences of the variable region.

The present invention also includes "conservative sequence modifications" of the sequences shown in the figures (e.g., fig. 2-7), including nucleotide and amino acid sequence modifications that do not significantly affect or alter the binding characteristics of the antibody encoded by the nucleotide sequence or an antibody containing the amino acid sequence, such conservative sequence modifications include nucleotide and amino substitutions, additions and deletions, the modifications may be introduced into the sequences shown in the figures (e.g., fig. 2-7) by standard techniques known in the art, such as site-directed mutagenesis and PCR-mediated mutagenesis, conservative amino acid substitutions include substitutions in which amino acid residues are substituted with amino acid residues having similar side chains, families of amino acid residues having similar side chains have been defined in the art, these families include amino acids having basic side chains (e.g., lysine, arginine, histidine), amino acids having acidic side chains (e.g., aspartic acid, glutamic acid), amino acids having no polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine, tryptophan), amino acids having nonpolar side chains (e.g., alanine, valine, proline, phenylalanine, tyrosine, tryptophan.

Alternatively, in another embodiment, mutations may be introduced randomly along all or part of the human anti-PD-1, PD-L1, or PD-L2 antibody coding sequence, such as by saturation mutagenesis, and the resulting modified human anti-PD-1, anti-PD-L1, or anti-PD-L2 antibodies are screened for binding activity.

Thus, antibodies encoded by and/or comprising the heavy and light chain variable region nucleotide sequences disclosed herein (e.g., fig. 2-7) include substantially similar antibodies encoded by or comprising conservatively modified similar sequences. Further discussion of how such substantially similar antibodies can be generated based on the sequences disclosed herein (i.e., heavy and light chain variable regions) (e.g., fig. 2-7) is provided below.

In addition, there is a known and unambiguous correspondence between the amino acid sequence of a particular protein and the nucleotide sequence that can encode that protein, as defined by the genetic code (shown below). Also, as defined by the genetic code, there is a known and unambiguous correspondence between the nucleotide sequence of a particular nucleic acid and the amino acid sequence encoded by that nucleic acid.

Genetic code

An important and well-known feature of the genetic code is its redundancy, i.e., more than one coding nucleotide triplet (described above) may be utilized for most of the amino acids used to make up a protein. Thus, a plurality of different nucleotide sequences may encode a given amino acid sequence. Such nucleotide sequences are considered functionally equivalent, as they result in the production of the same amino acid sequence in all organisms (although some organisms may translate some sequences more efficiently than others). In addition, methylated variants of purines or pyrimidines may sometimes be found in a given nucleotide sequence. This methylation does not affect the coding relationship between the trinucleotide codon and the corresponding amino acid.

The term "substantial homology" with respect to nucleic acids means that at least about 80% of the nucleotides, usually at least about 90%, 91%, 92%, 93%, 94%, 95%, 96% or more of the nucleotides, and more preferably at least about 97%, 98%, 99% or more of the nucleotides are identical when optimally aligned and compared between two nucleic acids or designated sequences thereof with appropriate nucleotide insertions or deletions. Alternatively, substantial homology exists when the segment will hybridize to a complement under selective hybridization conditions.

The percent identity between two sequences is a function of the number of identical positions shared by the sequences (i.e.,% identity ═ identical position #/total position # × 100), which, taking into account the number of null bits and the length of each null bit, needs to be introduced to optimally align the two sequences. Sequence comparisons between two sequences and percent identity determinations can be accomplished using mathematical algorithms, as described in the following non-limiting examples.

The percentage identity between two nucleotide sequences can be determined using the GAP program of the GCG software package (from the web GCG company website), using the nwsgapdna. cmp matrix, and GAP weights (GAP weight)40, 50, 60, 70 or 80 and length weights (length weight)1, 2,3, 4,5 or 6. Percent identity between two nucleotide or amino acid sequences can also be determined using the algorithm e.meyersa and w.miller (cabaos, 4: 1117 (1989)), which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table (weight residual), a gap length penalty of 12 and a gap penalty of 4. Furthermore, percent identity between two amino acid sequences can be determined using the Needleman and Wunsch (J.mol.biol. (48): 444453 (1970)) algorithm of the GAP program which has been incorporated into the GCG software package (from the GCG company website on the world Wide Web), using the Blosum 62 or PAM250 matrix with GAP weights 16, 14, 12, 10, 8, 6 or 4 and length weights 1, 2,3, 4,5 or 6.

The nucleic acid and protein sequences of the invention may further be used as "query sequences" to perform searches of public databases, e.g., to identify related sequences. Such a search may be applied to Altschul, et al, (1990) j.mol.biol.215: 40310 NBLAST and XBLAST programs (version 2.0). BLAST nucleotide searches can be performed using NBLAST program, score 100, word length 12, to obtain nucleotide sequences homologous to the nucleic acid molecules of the invention. BLAST protein searches can be performed using the XBLAST program with a score of 50 and a word length of 3 to obtain amino acid sequences homologous to the protein molecules of the present invention. For comparison purposes, gap alignments can be obtained, for example, by Altschul et al, (1997) Nucleic Acids Res.25 (17): 33893402, Gapped BLAST was used. When BLAST and Gapped BLAST programs are used, the default parameters (available from the world Wide Web NCBI website) for each program (e.g., XBLAST and NBLAST) can be used.

The nucleic acid may be present in the whole cell, a cell lysate, or in a partially purified or substantially pure form. Nucleic acids are "isolated" or "substantially pure" when purified from other cellular components or other impurities, e.g., other cellular nucleic acids or proteins, by standard techniques, including alkali/SDS treatment, CsCl banding, column chromatography, agarose gel electrophoresis, and other techniques well known in the art. See, F.Ausubel, et al, current Protocols in molecular Biology, Greene Publishing and Wiley Interscience, New York (1987).

Nucleic acid components from a cDNA, genome or mixture thereof according to the invention, typically in the native sequence (except for modified cleavage sites and the like), may be mutated according to standard techniques to provide a gene sequence. For coding sequences, these mutations can affect the amino acid sequence as desired. In particular, DNA sequences that are substantially homologous to or derived from native V, D, J, constant sequences (constants), switch sequences (switches), and other such sequences described herein (wherein "derived" means that the sequence is identical to or modified from another sequence) are contemplated.

A nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence. For example, a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence. With respect to transcriptional regulatory sequences, operably linked means that the DNA sequences being linked are contiguous and, where necessary, bind to both protein coding regions, contiguous and in reading frame. For switching sequences, operably linked refers to sequences that are capable of effecting switching recombination.

The term "vector" as used herein means a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid," which refers to a circular double-stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. In addition, certain vectors are capable of directing the expression of genes to which they are operably linked. Such vectors are referred to herein as "recombinant expression vectors" (or simply "expression vectors"). In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, "plasmid" and "vector" are used interchangeably, as plasmids are the most commonly used form of vector. However, the present invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses, and adeno-associated viruses) that serve equivalent functions.

As used herein, the term "recombinant host cell" (or simply "host cell") means a cell into which a recombinant expression vector has been introduced. It is understood that such terms are intended to refer not only to the particular subject cell, but also to the progeny of such a cell. Since certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term "host cell" as used herein.

As used herein, the term "subject" includes any human or non-human animal. For example, the methods and compositions described herein can be used to treat a subject having an inflammatory disease, such as arthritis, e.g., rheumatoid arthritis. The term "non-human animal" includes all vertebrates, e.g., mammals and non-mammals, such as non-human primates, sheep, dogs, cows, chickens, amphibians, reptiles, and the like.

As used herein, the term "modulate" includes both up-and down-regulation, e.g., enhancing or inhibiting a response.

As used herein, the term "inhibit" includes, for example, a reduction, limitation, or blocking of a particular effect, function, or interaction.

As used herein, the term "immune cell" refers to a cell that plays a role in an immune response. Immune cells are of hematopoietic origin, including: lymphocytes, such as B cells and T cells; natural killer cells; bone marrow cells, such as monocytes, macrophages, eosinophils, mast cells, basophils and granulocytes.

As used herein, the term "T cell" includes CD4+ T cells and CD8+ T cells. The term T cell also includes T helper type 1T cells, T helper type 2T cells, T helper type 17T cells, and suppressor T cells. The term "antigen presenting cell" includes specialized antigen presenting cells (e.g., B lymphocytes, monocytes, dendritic cells, langerhans cells) and other antigen presenting cells (e.g., keratinocytes, epithelial cells, astrocytes, fibroblasts, oligodendrocytes).

As used herein, the term "immune response" includes T cell-mediated and/or B cell-mediated immune responses affected by modulation of T cell co-stimulation. Exemplary immune responses include T cell responses-e.g., cytokine production-and cytotoxicity. Furthermore, the term immune response includes immune responses that are indirectly influenced by T cell activation, e.g., the production of antibodies (humoral responses) and the activation of cytokine-responsive cells, e.g., macrophages.

As used herein, the term "co-stimulatory" as used with respect to an activated immune cell includes the ability of the co-stimulatory polypeptide to provide a second non-activated receptor mediated signal ("co-stimulatory signal") that induces proliferation and/or effector effects. For example, co-stimulatory signals, e.g., in T cells that have received T cell receptor-mediated signals, can result in cytokine secretion. For example, an immune cell that receives a signal mediated by a cellular receptor through an activation receptor is referred to herein as an "activated immune cell".

As used herein, the term "inhibitory signal" refers to a signal transmitted by an inhibitory receptor (e.g., CTLA4 or PD-1) of a polypeptide on an immune cell. Such signaling antagonizes signaling conducted through an activated receptor (e.g., via a TCR or CD3 polypeptide), and can result in-e.g., inhibition of second messenger production; inhibition of proliferation; inhibition of effector functions in immune cells, e.g., decreased phagocytosis, decreased antibody production, decreased cytotoxicity, immune cell non-production mediators (such as cytokines (e.g., IL-2) and/or allergic reaction mediators); or development of no reactivity.

As used herein, the term "unresponsive" includes the refractive power of immune cells to stimulation, e.g., stimulation by activating receptors or cytokines. Unresponsiveness may exist, for example, due to exposure to immunosuppressive agents or exposure to high doses of antigen. As used herein, the term "anergy" or "tolerance" includes refractive power to stimuli mediated by activating receptors. This refractive power is generally antigen-specific and persists after exposure to tolerizing antigens has ceased. For example, T cell anergy (relative to anergy) is characterized by the absence of cytokine production, e.g., IL-2. T cell anergy exists when T cells are exposed to an antigen and receive a first signal (T cell receptor or CD-3 mediated signal) in the absence of a second signal (costimulatory signal). Under these conditions, re-exposure of the cells to the same antigen (even if re-exposure occurs in the presence of the co-stimulatory polypeptide) results in no cytokine production and thus no proliferation. However, if cultured with cytokines (e.g., IL-2), non-allergic T cells are able to proliferate. For example, T cell anergy can also be observed by T lymphocytes not producing IL-2, as determined by ELISA or by proliferation assays using indicator cell lines. Alternatively, reporter gene constructs may be utilized. For example, anergic T cells are unable to initiate transcription of the IL-2 gene induced by a heterologous promoter under the control of a 5' IL-2 gene enhancer or by multimers of AP1 sequences that may be found in enhancers (Kang et al (1992) Science 257: 1134).

As used herein, the term "activity" when applied in reference to a polypeptide, e.g., a PD-1, PD-L1, or PD-L2 polypeptide, includes activity inherent in the structure of the protein. For example, with respect to PD-1 ligands, the term "activity" includes the ability to modulate co-stimulation of immune cells (e.g., by modulating a co-stimulatory signal in an activated immune cell) or the ability to modulate inhibition by modulating an inhibitory signal in an immune cell (e.g., by attaching a native receptor to an immune cell). One skilled in the art will recognize that when a PD-1 ligand polypeptide binds to a costimulatory receptor, a costimulatory signal can be generated in an immune cell. When the PD-1 ligand polypeptide binds to an inhibitory receptor, an inhibitory signal is generated in the immune cell. Similarly, an inhibitory signal may be generated when a PD-1 ligand binds to a B7-1 polypeptide (button et al (2007) Immunity 27: 111).

With respect to PD-1, the term "activity" includes the ability of a PD-1 polypeptide to modulate an inhibitory signal in an immune cell, e.g., by linking a native PD-1 ligand to an antigen presenting cell. PD-1 transmits inhibitory signals to immune cells in a manner similar to CTLA 4. Modulation of inhibitory signals in immune cells results in modulation of immune cell proliferation and/or cytokine secretion by immune cells. Thus, the term "PD-1 activity" includes the ability of a PD-1 polypeptide to bind its natural ligand(s), to modulate an immune cell costimulatory signal or inhibitory signal, and to modulate an immune response.

As used herein, the term "interaction," when referring to an interaction between two molecules, refers to physical contact (e.g., binding) of the molecules to each other. Typically, this interaction results in the activity of one or both of the molecules (which results in a biological effect). The activity may be a direct activity (e.g., signal transduction) of one or both of the molecules. Alternatively, one or both of the interacting molecules may block binding to the ligand, thereby being inactive with respect to ligand binding activity (e.g., binding to its ligand and initiating or inhibiting co-stimulation). Inhibition of this interaction results in the disruption of the activity of one or more molecules involved in the interaction. Enhancing this interaction is prolonging or increasing the likelihood of said physical contact and prolonging or increasing the likelihood of said activity.

As used herein, the singular forms "a", "an" and "the" include plural referents unless the context clearly dictates otherwise.

It is to be understood that the aspects and embodiments of the invention described herein include "consisting of and/or" consisting essentially of aspects and embodiments.

Various aspects of the invention are described in more detail in the following subsections.

I.Isolated nucleic acid molecules

One aspect of the invention relates to isolated nucleic acid molecules encoding a polypeptide of the invention (e.g., the polypeptides in FIGS. 2-7) or biologically active portions thereof, as well as nucleic acid fragments sufficient for use as hybridization probes to identify nucleic acid molecules encoding such polypeptides and fragments, for use as PCR primers to perform amplification or mutation of the nucleic acid molecules. As used herein, the term "nucleic acid molecule" is meant to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs. The nucleic acid molecule may be single-stranded or double-stranded, but is preferably double-stranded DNA.

The term "isolated nucleic acid molecule" includes nucleic acid molecules that are isolated from other nucleic acid molecules that are present in the natural source of the nucleic acid. For example, with respect to genomic DNA, the term "isolated" includes nucleic acid molecules that are isolated from chromosomes with which genomic DNA is naturally associated. Preferably, an "isolated" nucleic acid molecule does not contain a sequence: which naturally flank the nucleic acid (i.e., sequences located at the 5 'and 3' ends of the nucleic acid molecule) in the genomic DNA of the organism from which the nucleic acid is obtained. For example, an "isolated" nucleic acid molecule, such as a cDNA molecule, can be substantially free of other cellular material or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.

The nucleic acid molecules of the invention (e.g., the nucleic acid molecules in fig. 2-7), or portions thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein. For example, nucleic acid molecules comprising all or part of the sequences shown in FIGS. 2-7 can be isolated by Polymerase Chain Reaction (PCR) using synthetic oligonucleotide primers designed based on the sequences shown in FIGS. 2-7.

The nucleic acid molecules of the invention can be amplified according to standard PCR amplification techniques using cDNA, mRNA or alternatively genomic DNA as template and appropriate oligonucleotide primers. The nucleic acid molecules thus amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis. Furthermore, oligonucleotides corresponding to the nucleic acid sequences of the invention can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.

In another embodiment, an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule complementary to a nucleic acid molecule of the invention (e.g., the nucleic acid molecules in fig. 2-7) or a portion thereof. A nucleic acid molecule that is complementary to a nucleic acid molecule of the invention (e.g., the nucleic acid molecule of fig. 2-7) or a portion thereof is a nucleic acid molecule that is sufficiently complementary to the nucleotide sequence set forth in fig. 2-7 that it can hybridize to each of the nucleotide sequences set forth in fig. 2-7 to form a stable duplex.

In yet another embodiment, an isolated nucleic acid molecule of the invention comprises a nucleotide sequence that is at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to the full length of the nucleotide sequence set forth in fig. 2-7 or a portion of any of these nucleotide sequences.

Furthermore, a nucleic acid molecule of the invention may comprise only a portion of a nucleic acid molecule of the invention (e.g., the nucleic acid molecule in fig. 2-7) or a portion thereof, e.g., a fragment that can be used as a probe or primer or a fragment that encodes a portion of a polypeptide of the invention, e.g., the polypeptide in fig. 2-7. Probes/primers typically comprise substantially purified oligonucleotides. Oligonucleotides generally include nucleotide sequence regions that: which react under stringent conditions with a nucleic acid molecule of the invention (e.g., the nucleic acid molecules in FIGS. 2-7); an antisense sequence of a nucleic acid molecule of the invention (e.g., the nucleic acid molecules in FIGS. 2-7); or mutants of a nucleic acid molecule of the invention (e.g., the nucleic acid molecules in fig. 2-7), hybridize over at least about 12 or 15, preferably about 20 or 25, and more preferably about 30, 35, 40, 45, 50, 55, 60, 65, or 75 consecutive nucleotides.

Probes based on the nucleic acid molecules of the invention (e.g., the nucleic acid molecules in FIGS. 2-7) can be used to detect transcripts or genomic sequences encoding the same or homologous polypeptides. In one embodiment, the probe further comprises a set of labels attached thereto, for example, the set of labels can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme cofactor.

A nucleic acid fragment encoding a "biologically active portion of a polypeptide of the invention" can be prepared by: isolating a partial nucleotide sequence of a nucleic acid molecule of the invention (e.g., the nucleic acid molecule of fig. 2-7) that encodes a polypeptide having a biological activity of a polypeptide of the invention (e.g., the ability to bind to its antigenic target); expressing the encoded portion of the polypeptide of the invention (e.g., by in vitro recombinant expression); and assessing the activity of the encoded portion of the polypeptide of the invention.

The invention further includes nucleic acid molecules that: differs from the nucleotide sequence(s) shown in figures 2-7 due to the degeneracy of the genetic code and thus encodes the same polypeptide as that encoded by each of the nucleotide sequences shown in figures 2-7. In another embodiment, an isolated nucleic acid molecule of the invention has a nucleotide sequence encoding a polypeptide of the invention (e.g., the polypeptide in FIGS. 2-7).

The cDNA disclosed herein or portions thereof can be used as hybridization probes under stringent hybridization conditions according to standard hybridization techniques to isolate nucleic acid molecules corresponding to homologues (homologue) of the nucleic acid molecules described herein (e.g., the nucleic acid molecules in fig. 2-7) based on their homology to the nucleic acids disclosed herein.

Thus, in another embodiment, an isolated nucleic acid molecule of the invention is at least 15, 20, 25, 30 or more nucleotides in length and hybridizes under stringent conditions to a nucleic acid molecule comprising a nucleic acid molecule of the invention (e.g., the nucleic acid molecule in fig. 2-7).

As used herein, the term "hybridizes under stringent conditions" means conditions that specify hybridization and washing under which nucleotide sequences that are significantly identical or homologous to each other remain hybridized to each other. Preferably, the conditions are such that: at least about 70%, more preferably at least about 80%, even more preferably at least about 85% or more of each otherSequences that are 90% identical remain hybridized to each other. Such stringent conditions are well known to those skilled in the art and can be found in Current protocols in Molecular Biology, Ausubel et al, eds., John Wiley&Sons, inc. (1995), sections 2, 4 and 6. Additional stringent conditions can be found in Molecular Cloning: a Laboratory Manual, Sambrook et al, Cold Spring harborPress, Cold Spring Harbor, N.Y. (1989), chapters 7, 9 and 11. Non-limiting examples of stringent hybridization conditions include: hybridization is carried out in 4 XSSC or 6 XSSC (SSC) at about 65-70 deg.C (or in 4 XSSC and 50% formamide at about 42-50 deg.C), followed by one or more washes in 1 XSSC at about 65-70 deg.C. Further non-limiting examples of stringent hybridization conditions include: hybridization was performed in 6 XSSC at 45 ℃ followed by one or more washes in 0.2 XSSC, 0.1% SDS at 65 ℃. Non-limiting examples of high stringency hybridization conditions include: hybridization is performed in 1 XSSC at about 65-70 deg.C (or in 1 XSSC and 50% formamide at about 42-50 deg.C), followed by one or more washes in 0.3 XSSC at about 65-70 deg.C. Non-limiting examples of reduced stringency hybridization conditions include: hybridization is performed in 4 × or 6 × SSC at about 50-60 deg.C (or alternatively in 6 × SSC and 50% formamide at about 40-45 deg.C), followed by one or more washes in 2 × SSC at about 50-60 deg.C. Intermediate ranges of the above values, for example at 65-70 ℃ or at 42-50 ℃, are also intended to be encompassed by the present invention. In hybridization and washing buffer, SSPE (1 XSSSPE is 0.15M NaCl, 10mM NaH)₂PO₄And 1.25mM EDTA, pH 7.4) alternative SSC (1 XSSC is 0.15M NaCl and 15mM sodium citrate); after completion of hybridization, washing was carried out for 15 minutes each. It is expected that hybridization temperatures for hybrid molecules less than 50 base pairs in length should be higher than the melting temperature (T) of the hybrid molecule_m) 5-10 ℃ lower, where T is determined according to the following equation_m. For hybrid molecules less than 18 base pairs in length, T_m(° C) + 2 (# of a + T bases) +4 (# of G + C bases). For hybrid molecules between 18 and 49 base pairs in length, T_m(℃)＝81.5+16.6(log₁₀[Na⁺])+0.41(％G+C)-(600/N), where N is the number of bases in the hybrid molecule, [ Na ]⁺]Is the sodium ion concentration in the hybridization buffer (1 XSSC [ Na ] of⁺]0.165M). The skilled artisan will also appreciate that additional reagents may be added to the hybridization and/or wash buffers to reduce non-specific hybridization of nucleic acid molecules to membranes, e.g., nitrocellulose or nylon membranes, including, but not limited to, blockers (e.g., BSA or salmon or herring sperm carrier DNA), detergents (e.g., SDS), chelators (e.g., EDTA), Ficoll, PVP, and the like. Another non-limiting example of stringent hybridization conditions, particularly when using nylon membranes, is 0.25-0.5M NaH at about 65 deg.C₂PO₄Hybridization in 7% SDS, followed by 0.02MNaH at 65 ℃₂PO₄One or more washes in 1% SDS, see: for example, Church and Gilbert (1984) proc.natl.acad.sci.usa 81: 1991-1995 (or alternatively, 0.2 XSSC, 1% SDS).

The skilled artisan will further appreciate that alterations can be introduced into the nucleic acid molecules of the invention (e.g., the nucleic acid molecules of FIGS. 2-7) by mutation, thereby resulting in alteration of the amino acid sequence of the encoded polypeptide of the invention, without altering the functional capability of the polypeptide. For example, nucleotide substitutions may be made in nucleic acid molecules of the invention (e.g., the nucleic acid molecules in FIGS. 2-7) that result in amino acid substitutions at "nonessential" amino acid residues. A "nonessential" amino acid residue is a residue that can be converted from a nucleic acid molecule of the invention (e.g., the nucleic acid molecules in FIGS. 2-7) without altering the biological activity, but the biological activity requires an "essential" amino acid residue. For example, it is contemplated that amino acid residues conserved among polypeptides of the invention, e.g., amino acid residues required for binding of a polypeptide to its antigen of interest, are particularly unamenable to alteration.

Thus, another aspect of the invention relates to a nucleic acid molecule encoding a polypeptide of the invention (e.g., the polypeptide in fig. 2-7) comprising an amino acid residue alteration that is not essential for activity. The amino acid sequence of this polypeptide differs from the sequences in FIGS. 2-7 and still retains biological activity. In one embodiment, an isolated nucleic acid molecule comprises a nucleotide sequence encoding a polypeptide, wherein the polypeptide comprises an amino acid sequence that is at least about 71%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to the sequence in figures 2-7.

In one embodiment, conservative amino acid substitutions are made at one or more predicted nonessential amino acid residues in the nucleic acid molecules described herein (e.g., the nucleic acid molecules of FIGS. 2-7) by standard techniques such as site-directed mutagenesis and PCR-mediated mutagenesis, "conservative amino acid substitutions" are substitutions of amino acid residues by amino acid residues having a similar side chain in one or more predicted nonessential amino acid residues.A family of amino acid residues having a similar side chain has been defined in the art.these families include amino acids having a basic side chain (e.g., lysine, arginine, histidine), amino acids having an acidic side chain (e.g., aspartic acid, glutamic acid), amino acids having an uncharged polar side chain (e.g., asparagine, glutamine, serine, threonine, tyrosine, cysteine), amino acids having a non-polar side chain (e.g., lysine, arginine, histidine), amino acids having an acidic side chain (e.g., aspartic acid, glutamic acid), amino acids having a non-polar side chain (e.g., aspartic acid, phenylalanine, tryptophan.

In one embodiment, the mutant polypeptides of the invention can be analyzed for the following ability: bind to and/or modulate the activity of native PD-1 (e.g., PD-1 ligand) or a partner of PD-1 ligand (e.g., PD-1 and B7-1), modulate intracellular or intercellular signaling, modulate the activation of T lymphocytes, and/or modulate the immune response of an organism.

Yet another aspect of the invention relates to an isolated nucleic acid molecule encoding a fusion protein. Such a nucleic acid molecule can be prepared by standard recombinant DNA techniques and comprises at least a first nucleotide sequence encoding a polypeptide of the invention (e.g., the polypeptide of fig. 2-7) operably linked to a second nucleotide sequence encoding a polypeptide of the invention (e.g., the polypeptide of fig. 2-7).

The expression profile of a nucleic acid molecule of the invention (e.g., the nucleic acid molecule in fig. 2-7) in a cell line or microorganism can be altered by inserting a heterologous DNA regulatory element into the genome of a stable cell line or a cloned microorganism, thereby operably linking the inserted regulatory element to a nucleic acid molecule of the invention (e.g., the nucleic acid molecule in fig. 2-7). For example, heterologous regulatory elements can be inserted into a stable cell line or cloned microorganism to be operably linked to a nucleic acid molecule of the invention (e.g., the nucleic acid molecules of FIGS. 2-7) using techniques such as targeted homologous recombination, which are well known to those skilled in the art and are described below: for example, Chappel, U.S. Pat. No. 5,272,071; PCT publication No. WO 91/06667, published in 1991, 5, 16.

II.Isolated polypeptide molecules

One aspect of the invention pertains to isolated polypeptides of the invention (including antibodies and antigen-binding fragments thereof described herein and the polypeptides in figures 2-7) and biologically active portions thereof. In one embodiment, the polypeptides of the invention (e.g., the polypeptides in fig. 2-7) and biologically active portions thereof can be isolated from a cell or tissue source by an appropriate purification scheme using standard protein purification techniques. In another embodiment, the polypeptides of the invention (e.g., the polypeptides in FIGS. 2-7) and biologically active portions thereof are produced by recombinant DNA techniques. Alternatively, the polypeptides of the invention (e.g., the polypeptides in FIGS. 2-7) and biologically active portions thereof can be chemically synthesized using standard peptide synthesis techniques.

An "isolated" or "purified" polypeptide or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue from which the polypeptide of the invention (e.g., the polypeptide of FIGS. 2-7) is obtained, or substantially free of chemical precursors or other chemicals when chemically synthesized. The expression "substantially free of cellular material" includes preparations of the polypeptide(s) of the invention (e.g., the polypeptides in figures 2-7) and biologically active portions thereof, wherein the polypeptide is isolated or recombinantly produced from a cellular component of the cell in which the polypeptide is isolated. In one embodiment, the expression "substantially free of cellular material" includes preparations of such polypeptide(s) of the invention (e.g., the polypeptides in fig. 2-7) and biologically active portions thereof: it has less than about 30% (by dry weight) of non-protein of the invention (also referred to herein as "impurity protein"), more preferably less than about 20% of non-protein of the invention, still more preferably less than about 10% of non-protein of the invention, and most preferably less than about 5% of non-protein of the invention. When a polypeptide of the invention (e.g., the polypeptide in FIGS. 2-7) or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium comprises less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of protein produced.

The expression "substantially free of chemical precursors or other chemicals" includes preparations of the polypeptide(s) of the invention (e.g., the polypeptides in fig. 2-7) or biologically active portions thereof, wherein the polypeptide is isolated from the chemical precursors or other chemicals involved in the synthesis of the polypeptide. In one embodiment, the expression "substantially free of chemical precursors or other chemicals" includes preparations of such polypeptide(s) of the invention (e.g., the polypeptides in fig. 2-7) or biologically active portions thereof: has less than about 30% (dry weight) of chemical precursors or non-proteins of the invention, more preferably less than about 20% of chemical precursors or non-proteins of the invention, still more preferably less than about 10% of chemical precursors or non-proteins of the invention, and most preferably less than about 5% of chemical precursors or non-proteins of the invention.

As used herein, a "biologically active portion" of a polypeptide(s) of the invention (e.g., a polypeptide in fig. 2-7) includes polypeptides that participate in the interaction between PD-1 and non-PD-1 molecules, PD-L1 and non-PD-L1 molecules, or PD-L2 and non-PD-L2 molecules, respectively, such as: natural ligands for PD-1-e.g., PD-1 ligands; or a natural ligand for a PD-1 ligand-for example, PD-1 or B7-1. Biologically active portions of the polypeptide(s) of the invention (e.g., the polypeptides in fig. 2-7) include such peptides: which contains an amino acid sequence that is sufficiently identical to or derived from the amino acid sequence of the polypeptide(s) of the invention (e.g., the polypeptides in figures 2-7), which comprises fewer amino acids than the respective full-length polypeptide(s) of the invention (e.g., the polypeptides in figures 2-7), and which exhibits at least one activity of the respective polypeptide(s) of the invention (e.g., the polypeptides in figures 2-7). In one embodiment, the biologically active portion comprises a domain or motif that: has the ability to specifically bind to PD-1 or PD-L1 ligand, respectively, according to the antigen to which it is proposed or designed to bind. Biologically active portions of the polypeptide(s) of the invention (e.g., the polypeptides in figures 2-7) can be used as targets for a spreading agent that modulates an activity mediated by PD-1, PD-L1, or PD-L2, e.g., immune cell activation or inhibition.

In another embodiment, the polypeptide(s) of the invention (e.g., the polypeptides in figures 2-7) have the amino acid sequences shown in figures 2-7. In other embodiments, the polypeptide is substantially identical to the polypeptide(s) shown in figures 2-7, and retains the functional activity of each polypeptide(s) shown in figures 2-7 but differs in amino acid sequence due to mutagenesis, as described in detail in section I above. Thus, in another embodiment, the polypeptide(s) of the invention are polypeptides that: comprising an amino acid sequence that is at least about 71%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or 99.9% or more identical to the polypeptide(s) set forth in figures 2-7.

To determine the percent identity of two amino acid sequences or two nucleic acid sequences, the sequences are aligned for optimal comparison (e.g., gaps can be introduced in one or both of the first and second amino acid or nucleic acid sequences for optimal alignment, and non-identical sequences can be disregarded for comparison). In one embodiment, the length of a reference sequence aligned for comparison is at least 30%, preferably at least 40%, more preferably at least 50%, even more preferably at least 60%, or even more preferably at least 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 99.9% of the length of the reference sequence. The amino acid residues or nucleotides at the corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein, amino acid or nucleic acid "identity" is equivalent to amino acid or nucleic acid "homology"). The percent identity between two sequences is a function of the number of identical positions shared by the two sequences, taking into account the number of empty positions and the length of each empty position that need to be introduced for optimal alignment of the two sequences.

The invention also provides chimeric or fusion proteins. As used herein, a "chimeric protein" or "fusion protein" comprises a polypeptide(s) of the invention (e.g., the polypeptides in fig. 2-7) operably linked to a polypeptide(s) of the invention. "polypeptide(s) of the invention" refers to a polypeptide having an amino acid sequence corresponding to the polypeptide shown in FIGS. 2-7, whereas "non-polypeptide of the invention" refers to a polypeptide which: do not have an amino acid sequence corresponding to a polypeptide that is not substantially homologous to the polypeptide shown in figures 2-7, e.g., a polypeptide that is different from the polypeptide shown in figures 2-7, derived from the same or a different organism. In a fusion protein, the term "operably linked" means that the polypeptide(s) of the invention and the non-polypeptide(s) of the invention are fused to each other in frame. The polypeptide(s) not of the invention may be fused to the N-or C-terminus of the polypeptide(s) of the invention, corresponding to a moiety that alters the solubility, binding affinity, stability or potency (valency) of the polypeptide(s) of the invention.

For example, in one embodiment, the fusion protein is a GST fusion protein with the polypeptide(s) of the invention. Such fusion proteins facilitate the purification of the recombinant polypeptides of the invention. In another embodiment, the fusion protein comprises a heterologous signal sequence at its N-terminus. In certain host cells (e.g., mammalian host cells), expression and/or secretion of the polypeptide(s) of the invention may be enhanced by the use of heterologous signal sequences.

The chimeric or fusion polypeptide(s) of the invention (e.g., the polypeptides in fig. 2-7) can be produced by standard recombinant DNA techniques. For example, DNA fragments encoding different polypeptide sequences are ligated together in frame according to conventional techniques, e.g., by ligation using blunt or ragged ends, providing appropriate ends using restriction enzyme digestion, filling with cohesive ends as an appropriate alkaline phosphatase treatment to prevent unwanted ligation, and using enzymatic ligation. In another embodiment, the fusion gene may be synthesized by conventional techniques, including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be performed using anchor primers that result in complementary overhangs between two consecutive gene fragments that can then be annealed and re-amplified to generate a chimeric gene sequence (see, e.g., Current Protocols in molecular biology, Ausubel et al, eds., John Wiley & Sons: 1992). In addition, a variety of expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide).

The amino acid sequences of the polypeptide(s) of the invention identified herein (e.g., the polypeptides in figures 2-7) enable one skilled in the art to make a polypeptide corresponding to the polypeptide(s) of the invention (e.g., the polypeptides in figures 2-7). Such a polypeptide can be produced in a prokaryotic or eukaryotic host cell by expression of a polynucleotide encoding the polypeptide(s) of the present invention (e.g., the polypeptides in FIGS. 2-7). Alternatively, such peptides may be synthesized by chemical methods. Methods for the expression of heterologous polypeptides in recombinant hosts, methods for the chemical synthesis of polypeptides and methods for in vitro translation are well known in the art and described in Maniatis et al, Molecular Cloning: a Laboratory Manual (1989), 2nd ed., Cold Spring Harbor, n.y.; berger and Kimmel, Methods in Enzymology, Volume 152, Guide to Molecular cloning technologies (1987), Academic Press, Inc., San Diego, Calif.; merrifield, j. (1969) j.am.chem.soc.91: 501; chaiken I.M (1981) CRC crit. rev. biochem.11: 255; kaiser et al (1989) Science 243: 187; merrifield, b. (1986) Science 232: 342; kent, s.b.h. (1988) annu.rev.biochem.57: 957 (a); and Offord, R.E, (1980) semi synthetic Proteins, Wileypublishing, which are incorporated herein by reference.

III.PD-1, PD-L1 and/or PD-L2 antibodies

Antibodies to PD-1, PD-L1, or PD-L2 described herein can be prepared using any of the methods described herein or known in the art. Monoclonal antibodies (e.g., human antibodies) of the invention can be prepared using a variety of known techniques, such as those described by Kohler and milstein, Nature 256: 495(1975) by standard somatic hybridization techniques. Although a somatic hybridization procedure is preferred, in principle other techniques for the preparation of monoclonal antibodies can also be applied, e.g. viral or oncogenic transformation of B lymphocytes, phage display technology (phase display technology) using human antibody gene banks.

One method of hybridoma production that produces a monoclonal antibody of the invention is the mouse system. The generation of hybridomas in mice is well known in the art and includes immunization protocols and techniques for the isolation and fusion of immune spleen cells.

By immunizing an appropriate subject with a polypeptide immunogen, polyclonal antibodies can be prepared as described above. The titer of the polypeptide antibody in the immunized subject can be monitored over time using the immobilized polypeptide by standard techniques, e.g., by enzyme-linked immunosorbent assay (ELISA). If desired, antibodies to the antigen can be isolated from the mammal (e.g., from blood) by well-known techniques, such as protein A chromatography, and further purified to provide IgG fractions. At a suitable time after immunization, for example, when antibody titers are highest, antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as those originally developed by Kohler and Milstein (1975) Nature 256: 495-497) (see also Brown et al (1981) j. immunol.127: 539-46; brown et al (1980) j.biol.chem.255: 4980-83; yeh et al, (1976) Proc.Natl.Acad.Sci.76: 2927-31; and Yeh et al (1982) int.J. cancer 29: 269-75), the more recent human B cell hybridoma technology (Kozbor et al (1983) immunol. today 4: 72) EBV-hybridoma technology (Cole et al (1985) Monoclonal Antibodies and Cancer Therapy, Alan R.Liss, Inc., pp.77-96)) or triple hybridoma (trioma) technology. Techniques for preparing Monoclonal antibody hybridomas are well known (see generally Kenneth, R.H.in Monoclonal Antibodies: A New Dimension In biologica analytes, Plenum Publishing Corp., New York, New York (1980); Lerner, E.A. (1981) Yale J.biol.Med.54: 387-402; Gefter, M.L. et al (1977) physical Cell Gene.3: 231-36). Briefly, and particularly preferably, an immortal cell line (typically a myeloma) is fused to lymphocytes (typically spleen cells) from a mammal immunized with an immunogen as described above, and the culture supernatants of the resulting hybridoma cells are screened to identify a hybridoma that produces a monoclonal antibody that binds to the polypeptide antigen.

Any of a variety of well-known protocols for fusing lymphocytes and immortalized cell lines can be used to generate monoclonal antibodies against PD-1, PD-L1, or PD-L2 (see, e.g., Galfre, G., et al (1977) Nature 266: 55052; the above-mentioned Gefter et al (1977); the above-mentioned Lerner (1981); the above-mentioned Kenneth (1980)). Furthermore, one of ordinary skill will appreciate that numerous variations of this approach will also be available. Typically, the immortalized cell line (e.g., a myeloma cell line) is derived from the same mammalian species as the lymphocytes. For example, murine hybridomas can be prepared by fusing lymphocytes from a mouse immunized with an immunogenic preparation of the invention with an immortal murine cell line. A preferred immortalized cell line is a mouse myeloma cell line sensitive to a medium containing hypoxanthine, aminopterin and thymidine ("HAT medium"). Any of a variety of myeloma cell lines may be used as fusion partners according to standard techniques, for example, the P3-NS1/1-Ag4-1, P3-x63-Ag8.653, or Sp2/O-Ag14 myeloma lines. These myeloma lines are available from American Type Culture Collection (ATCC), Rockville, Md. Typically, HAT-sensitive mouse myeloma cells are fused to mouse spleen cells using polyethylene glycol ("PEG"). Hybridoma cells resulting from fusion are then selected using HAT medium, which kills unfused and inefficiently fused myeloma cells (unfused splenocytes die after several days because they are not transformed). For example, hybridoma cells producing a monoclonal antibody of the invention are detected by screening hybridoma culture supernatants for antibodies that bind to a given polypeptide using a standard ELISA assay.

Alternatively, for the preparation of monoclonal antibody-secreting hybridomas, a monoclonal specific for one of the polypeptides described above can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with the appropriate polypeptide to isolate immunoglobulin library members that bind the polypeptide. Commercially available kits for generating and screening Phage display libraries (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and Stratagene SurfZAP^TMPhage Display Kit, Catalog No. 240612). Furthermore, examples of methods and reagents that are particularly useful for generating and screening antibody display libraries can be found in: for example, Ladner et al, U.S. Pat. nos. 5,223,409; kang et al, International publication No. WO 92/18619; dower et al, international publication No. WO 91/17271; winter et al, International publication No. WO 92/20791; markland et al, International publication No. WO 92/15679; breitling et al, International publication WO 93/01288; McCafferty et al,international publication nos. WO 92/01047; garrrard et al, International publication No. WO 92/09690; ladner et al, international publication No. WO 90/02809; fuchs et al (1991) Biotechnology (NY) 9: 1369-; hay et al, (1992) hum.antibody.hybridoma 3: 81-85; huse et al (1989) Science 246: 1275-1281; griffiths et al, (1993) EMBO J.12: 725-; hawkins et al, (1992) J.mol.biol.226: 889-896; clarkson et al (1991) Nature 352: 624-; gram et al, (1992) proc.natl.acad.sci.usa 89: 3576-3580; garrrard et al (1991) Biotechnology (NY) 9: 1373-1377; hoogenboom et al (1991) Nucleic acids sRes.19: 4133-4137; barbas et al, (1991) proc.natl.acad.sci.usa 88: 7978-7982; and McCafferty et al, (1990) Nature 348: 552 and 554.

In addition, recombinant anti-PD-1, PD-L1, or PD-L2 antibodies, such as chimeric, composite, and humanized monoclonal antibodies, can be generated that can be prepared using standard recombinant DNA techniques. Such chimeric, composite and humanized monoclonal antibodies can be prepared by recombinant DNA techniques known in the art, for example, using the methods described in: robinson et al, International patent publication No. PCT/US 86/02269; akira et al, European patent application 184,187; taniguchi, m. european patent application 171,496; morrison et al, European patent application 173,494; neuberger et al, PCT application WO 86/01533; cabilly et al, U.S. Pat. No. 4,816,567; cabilly et al, European patent application 125,023; better et al (1988) Science 240: 1041-1043; liu et al, (1987) Proc.Natl.Acad Sci.USA 84: 3439-; liu et al (1987) j. immune l.139: 3521-3526; sun et al, (1987) Proc.Natl.Acad.Sci.84: 214-218; nishimura et al (1987) cancer Res.47: 999-; wood et al (1985) Nature 314: 446- > 449; and Shaw et al (1988) j.natl.cancer inst.80: 1553 1559); morrison, s.l. (1985) Science 229: 1202-1207; oi et al (1986) Biotechniques 4: 214; winter U.S. Pat. Nos. 5,225,539; jones et al (1986) Nature 321: 552-525; verhoeyan et al (1988) Science 239: 1534; and Beidler et al (1988) j.immunol.141: 4053-4060.

In addition, humanized antibodies can be prepared according to standard protocols, such as those disclosed in U.S. Pat. No. 5,565,332. In another embodiment, an antibody chain or specific binding pair member can be prepared by recombination between a vector comprising a nucleic acid molecule encoding a fusion of a polypeptide chain of a specific binding pair member with a replicable species display package (generic display package) component and a vector comprising a nucleic acid molecule encoding a second polypeptide chain of a single binding pair member, using techniques known in the art, e.g., as described below: U.S. Pat. No. 5,565,332, 5,871,907 or 5,733,743. The use of intrabodies to inhibit the function of proteins in cells is also known in the art (see, for example, Carlson, J.R et seq., 1988) mol. cell. biol. 8: 2638. 2646; Biocca, S. et al (1990) EMBO J. 9: 101. 108; Wege, T. M. et al. (1990) FEBS Lett. 274: 198; Carlson, J.R. Sci. 1993) Proc. Natl. Acad. Sci. USA 90: 7427. 7428; Marasco, W.A. et al, (1993) Proc. Natl. Acad. Sci. USA 90: 7889. 7893; Biocca, S. et al. (1994) Biotechniques. NY 12: 396. 399; Chen, S-Y. et al., Hum. 1994; Biotech. J. 92. Nath. 75. 19851. J. Natl. Sci. J. 19851. J. Nat. Sci. J. 19851. J. Nat. J. Nat. Sci. J. 19851. J. 19851. Biotech. J. 19851. 92; Biotech. J. 92. Nat. J. Nath. 19851. Nat. 92. 19851. 92. Biotech. J. 92. J. Biotech. 92. Biotech. 92. Nat. J. 92. J. Nature. 92. Nature J. 92; Biotech. J. Nat. D. J. D. 5975. J. Nat. D, PCT publication nos. WO 94/02610; and Duan et al, PCT publication No. WO 95/03832).

In another embodiment, human monoclonal antibodies to PD-1, PD-L1, or PD-L2 can be generated using transgenic or transchromosomal mice carrying portions of the human immune system rather than the mouse system. In one embodiment, a transgenic mouse, also referred to herein as a "HuMAb mouse," comprises a human immunoglobulin gene minilocus encoding unrearranged human heavy (μ and γ) and kappa light chain immunoglobulin sequences, together with a targeted mutation that inactivates the endogenous μ and kappa chain sites (Lonberg, n. et al, (1994) Nature 368 (6474): 856859). Thus, mice display reduced expression of mouse IgM or kappa, and in response to immunization, the introduced human heavy and light chain transgenes undergo type conversion and somatic mutation, thereby generating high affinity human IgG kappa monoclonal antibodies (Lonberg, N.et al (1994), supra; Lonberg, N. (1994) described in Handbook of Experimental Pharmacology 113: 49101; Lonberg, N.and Huszar, D. (1995) Intern.Rev.Immunol.Vol.13: 6593 and Harding, F. and Lonberg, N. (1995) Ann.N.YAcad.Sci 764: 536546). Preparation of HuMAb mice is described below: taylor, L.et al, (1992) nucleic acids Research 20: 62876295, respectively; chen, J.et al, (1993) International Immunology 5: 647656, respectively; tuaillon et al, (1993) Proc.Natl.Acad.Sci USA 90: 37203724, respectively; choi et al, (1993) Naturegenetics 4: 117123, respectively; chen, J.et al, (1993) EMBO J.12: 821830, respectively; tuaillon et al (1994) J.Immunol.152: 29122920, respectively; lonberg et al, (1994) Nature 368 (6474): 856859, respectively; lonberg, N. (1994) Handbook of Experimental Pharmacology 113: 49101, respectively; taylor, L. et al (1994) International Immunology 6: 579591, respectively; lonberg, n. and Huszar, d. (1995) intern.rev.immunol.vol.13: 6593; harding, f, and Lonberg, n. (1995) ann.n.y.acad.sci764: 536546, respectively; fishwild, D. et al, (1996) Nature Biotechnology 14: 845851. see, further, U.S. Pat. nos. 5,545,806; 5,569,825; 5,625,126, respectively; 5,633,425, respectively; 5,789,650, respectively; 5,877,397, respectively; 5,661,016, respectively; 5,814, 318; 5,874,299, respectively; and 5,770,429, all belonging to Lonberg and Kay, and GenPharmInternational; U.S. Pat. No. 5,545,807, Surani et al; international publication No. WO 98/24884, published on 11/6/1998; WO 94/25585, published on month 11 and 10 of 1994; WO 93/1227, published at 24.6.1993; WO 92/22645, published on 23.12.1992; WO 92/03918, published on 3/19 1992.

In another embodiment, the antibody used in the present invention is a bispecific antibody. Bispecific antibodies have two different antigen binding sites in one antibody polypeptide. Antigen binding may be performed simultaneously or sequentially. Triomas (trioma) and mixed hybridomas are two examples of bispecific antibody-secreting cell lines. Us patent 4,474,893 discloses examples of bispecific antibodies produced by mixed or triple hybrid hybridomas. Bispecific antibodies have been constructed by chemical methods (Staerz et al (1985) Nature 314: 628; and Perez et al (1985) Nature 316: 354) and hybridoma technology (Staerz and Bevan (1986) Proc. Natl.Acad.Sci.USA, 83: 1453; and Staerz and Bevan (1986) immunol. Today7: 241). U.S. patent 5,959,084 also describes bispecific antibodies. U.S. patent 5,798,229 describes bispecific antibody fragments. Bispecific agents can be generated by: heterohybridomas (heterohybridomas) are made by fusing hybridomas or other cells that produce different antibodies, and clones that produce and co-assemble the two antibodies are then identified. They can also be generated by chemical or genetic association of the complete immunoglobulin chain or parts thereof, such as Fab and Fv sequences. The antibody component can bind to a PD-1, PD-L1, and/or PD-L2 polypeptide. In one embodiment, the bispecific antibody can specifically bind a PD-1 ligand and a PD-1 polypeptide.

Yet another aspect of the invention relates to an anti-PD-1, PD-L1 or PD-L2 polypeptide antibody obtainable by: comprising immunizing an animal with an immunogenic PD-1, PD-L1 or PD-L2 polypeptide, or immunogenic portion thereof, respectively; and then isolating an antibody that specifically binds to the polypeptide from the animal.

In yet another aspect of the invention, partial or known antibody sequences may be used to generate and/or express novel antibodies. Antibodies interact with the antigen of interest primarily through amino acid residues located in the six heavy and light chain Complementarity Determining Regions (CDRs). Thus, the amino acid sequences in the CDRs are more diverse between the individual antibodies than outside the CDRs. Since CDR sequences cause most antibody-antigen interactions, it is possible to express recombinant antibodies that mimic the properties of a particular naturally occurring antibody by constructing expression vectors that contain the CDR sequences of the particular naturally occurring antibody grafted onto the framework sequences of different antibodies with different properties (see, e.g., Riechmann, L. et al, 1998, Nature 332: 323327; Jones, P. et al, 1986, Nature 321: 522525; and Queen, C. et al, 1989, Proc. Natl. Acad. see, U.S. Pat. No. 86: 1002910033). Such framework sequences can be obtained from published DNA databases comprising germline or non-germline antibody gene sequences. These germline sequences will differ from the mature antibody gene sequences in that they will not include the fully assembled variable genes that are generated by v (d) J junctions during B cell maturation. Germline gene sequences will also differ from the sequences of high affinity secondary repertoire antibodies each evenly distributed in the variable region. For example, somatic mutations are relatively rare in the amino-terminal portion of the framework region. For example, somatic mutations are relatively rare in the amino-terminal portion of framework region 1 and the carboxy-terminal portion of framework region 4. Furthermore, various somatic mutations do not significantly alter the binding properties of the antibody. Thus, it is not necessary to obtain the entire DNA sequence of a particular antibody to reconstitute an entire recombinant antibody having similar binding properties to the original antibody (see PCT/US99/05535 filed 3/12 1999). Portions of the heavy and light chain sequences encompassing the CDR regions are generally sufficient for this purpose. The partial sequence is used to determine which germline and/or non-germline variable and to link gene segments that contribute to the recombination of antibody variable genes. The germline and/or non-germline sequences are then used to fill in the deleted portion of the variable region. The heavy and light chain leader sequences are cleaved during protein maturation and do not contribute to the properties of the final antibody. To add missing sequences, the cloned cDNA sequence can be combined with synthetic oligonucleotides by ligation or PCR amplification. Alternatively, the entire variable region can be synthesized as a set of short overlapping oligonucleotides and combined by PCR amplification to generate a fully synthesized variable region clone. This approach has certain advantages, such as elimination or inclusion of or specific restriction sites, or optimization of specific codons. The method can also be used to screen libraries of specific immunoglobulin coding sequences of one species (e.g., human) to design homologous immunoglobulin coding sequences from known antibody sequences of another species (e.g., mouse) (see, e.g., the examples section below).

The nucleotide sequences of the hybridoma heavy and light chain transcripts were used to design overlapping sets of synthetic oligonucleotides, thereby generating synthetic V sequences with identical amino acid coding capabilities as the native sequences. Synthetic heavy and kappa chain sequences can differ from the natural sequence in three ways: interrupting the repetitive nucleotide base strings to facilitate oligonucleotide synthesis and PCR amplification; integration of optimal translation initiation sites according to the Kozak's rule (Kozak, 1991, j.biol.chem.266l19867019870); and a HindIII site engineered upstream of the translation start site.

For the heavy and light chain variable regions, the optimized coding and corresponding non-coding chain sequences are split into 30-50 nucleotides at the approximate midpoint of the corresponding non-coding oligonucleotide. Thus, for each strand, oligonucleotides can be assembled into overlapping double-stranded sets encompassing fragments of 150-400 nucleotides. This pool (pool) can then be used as a template to generate a PCR amplification product of 150-400 nucleotides. Typically, a variable region oligonucleotide set will be separated into two pools that are amplified separately to produce two overlapping PCR products. These overlapping products are then combined by PCR amplification to form the complete variable region. Overlapping fragments including heavy or light chain constant regions may also be required in PCR amplification to generate fragments that can be readily cloned into expression vector constructs.

The reconstructed heavy and light chain variable regions are then combined with a cloned promoter, leader sequence, translation initiation, leader sequence, constant region, 3' untranslated sequence, polyadenylation sequence, and transcription termination sequence to form an expression vector construct. The heavy and light chain expression constructs can be combined into separate vectors, co-transfected, sequentially transfected or separately transfected into a host cell, which is then fused, thereby generating a host cell expressing both chains.

Plasmids for this use are known in the art and include the plasmids provided in the examples section below. Fully human and chimeric antibodies of the invention also include IgG2, IgG3, IgE, IgA, IgM, and IgD antibodies. Similar plasmids can be constructed to express other heavy chain isotypes or to express lambda light chain-containing antibodies.

Thus, in another aspect of the invention, structurally related human anti-human PD-1, PD-L1, or PD-L2 antibodies that retain at least one of the functional properties of the antibodies of the invention, such as binding to PD-1, PD-L1, or PD-L2, are generated using the structural characteristics of known non-human or human antibodies (e.g., mouse anti-human anti-PD-1, PD-L1, or PD-L2 antibodies, such as antibodies EH12.2H7, 29e.2a3, and 24f.10c12, respectively). Another functional characteristic includes inhibiting EH12.2H7 binding to PD-1, 29E.2A3 binding to PD-L1 or 24F.10C12 binding to PD-L2 in a competition ELISA assay. In some embodiments, the structurally related anti-human PD-1, PD-L1, or PD-L2 antibody has lower binding affinity for antigen than antibody EH12.2H7, 29e.2a3, or 24f.10c12 as measured by IC50 values described in example 2 (e.g., the affinity of the murine reference antibody is not greater than any of 3.0, 2.0, 1.9, 1.8, 1.7, 1.6, 1.5, 1.4, 1.3, 1.2, or 1.1 fold greater than the affinity of the structurally related antibody). In some embodiments, a structurally related anti-human PD-1, PD-L1, or PD-L2 antibody has a higher affinity for antigen than antibody EH12.2H7, 29e.2a3, or 24f.10c12 as measured by the IC50 values described in example 2 (e.g., the affinity of the structurally related antibody is at least 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, or 2.0 fold that of the reference antibody). Furthermore, one or more CDRs or variable regions of the invention (e.g., figures 2-7) can be recombinantly combined with known human framework regions and CDRs to produce additional recombinantly engineered human anti-PD-1, PD-L1, or PD-L2 antibodies of the invention.

Since it is well known in the art that antibody heavy and light chain CDR3 domains play a particularly important role in the binding specificity/affinity of an antibody for an antigen, recombinant antibodies of the invention prepared as described above preferably comprise the heavy and light chain CDR3s of the variable regions of the invention (e.g., fig. 2-7). The antibody may further comprise CDR2s of a variable region of the invention (e.g., fig. 2-7). The antibody may further comprise CDR1s of a variable region of the invention (e.g., fig. 2-7). The antibody may further comprise any combination of CDRs.

The CDR1, CDR2, and/or CDR3 regions of the engineered antibodies described above can comprise the exact amino acid sequence(s) as the amino acid sequences of the variable regions of the invention disclosed herein (e.g., fig. 2-7). However, the ordinarily skilled artisan will appreciate that some deviation from the exact CDR sequences is possible (e.g., conservative sequence changes) while still maintaining the ability of the antibody to effectively bind PD-1, PD-L1, or PD-L2. Thus, in another embodiment, an engineered antibody may consist of one or more CDRs that are, e.g., 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to one or more CDRs of the invention (e.g., fig. 2-7).

In addition to simple binding to PD-1, PD-L1 or PD-L2, engineered antibodies-such as the above-described antibodies-can be selected for their retention of other functional properties as follows:

(1) (ii) binds to human PD-1, PD-L1, or PD-L2;

(2) inhibit EH12.2H7 from binding to PD-1, 29E.2A3 from binding to PD-L1 or 24F.10C12 from binding to PD-L2;

(3) the ability to bind to human PD-1, and inhibit binding of bound PD-1 to a PD-1 ligand (e.g., PD-L1 and/or PD-L2);

(4) binds to human PD-L1, and inhibits the ability of the bound PD-L1 to bind to a PD-L1 ligand (e.g., PD-1 and/or B7-1);

(5) binds human PD-L2, and inhibits the ability of the bound PD-L2 to bind a PD-L2 ligand (e.g., PD-1).

The variable region amino acid sequences of the heavy and light chains of antibodies EH12.2H7, 29e.2a3, and 24f.10c12 are shown below.

EH12.2H7 heavy chain variable region

QVQLQQSGAELAKPGASVQMSCKASGYSFTSSWIHWVKQRPGQGLEWIGYIYPSTGFTEYNQKFKDKATLTADKSSSTAYMQLSSLTSEDSAVYYCARWRDSSGYHAMDYWGQGTSVTVSS(SEQID NO：76)

EH12.2H7 light chain variable region

DIVLTQSPASLTVSLGQRATISCRASQSVSTSGYSYMHWYQQKPGQPPKLLIKFGSNLESGIPARFSGSGSGTDFTLNIHPVEEEDTATYYCQHSWEIPYTFGGGTKLEIK(SEQ ID NO：77)

29E.2A3 heavy chain variable region

EVQLQQSGPELVKPGASVKMSCKASGYTFTSYVMHWVKQKPGQGLEWIGYVNPFNDGTKYNEMFKGKATLTSDKSSSTAYMELSSLTSEDSAVYYCARQAWGYPWGQGTLVTVSA(SEQ ID NO：78)

29E.2A3 light chain variable region

DIVLTQSPASLAVSLGQRATISCRATESVEYYGTSLVQWYQQKPGQPPKLLIYAASSVDSGVPARFSGSGSGTDFSLTIHPVEEDDIAMYFCQQSRRVPYTFGGGTKLEIK(SEQ ID NO：79)

24F.10C12 heavy chain variable region

QVQLQQSAAELARPGASVKMSCKASGYTFTGYTMHWVKQRPGQGLEWIGYINPRSGYTEYNQKFKDKTTLTADKSSSTAYMQLSSLTSEDSAVYYCARPWFAYWGQGTLVTVSA(SEQ ID NO：80)

24F.10C12 light chain variable region

DIVMTQSPSSLTVTAGEKVTMSCKSSQSLLNSGNQKNYLTWYQQKPGQPPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDYSYPLTFGAGTKLELK(SEQ ID NO：81)

The activity of an antibody to inhibit the binding of PD-1, PD-L1 or PD-L2 to its ligand(s) can be determined by examining the ability of the antibody to block the binding of PD-1, PD-L1 or PD-L2 to its ligand. Competitive ELISA assays in the presence of labeled ligand and antibody can be used. For example, to determine whether an anti-PD-L1 antibody can block the interaction between PD-1 and PD-L1, a competitive binding assay was performed. Cells expressing PD-L1 were pre-incubated with anti-PD-L1 antibody, and biotinylated PD-1-Ig fusion protein was added. An anti-PD-L1 antibody is considered effective in inhibiting the interaction between PD-1 and PD-L1 if the anti-PD-L1 antibody blocks the binding of PD-1-Ig in a dose-dependent manner and with high affinity. Similar assays can be performed to test for antibodies that effectively inhibit the interaction of PD-1 with PD-L2.

IV.Recombinant expression vectors and host cells

Another aspect of the invention relates to a vector, preferably an expression vector, comprising one, two or more nucleic acid molecules encoding one or more polypeptides of the invention (e.g., figures 2-7) (or portions thereof). The term "vector" as used herein refers to a nucleic acid molecule capable of transporting another nucleic acid to which it is linked. One type of vector is a "plasmid," which refers to a circular double-stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. In addition, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are also referred to herein as "expression vectors". In general, expression vectors useful in recombinant DNA techniques are usually in the form of plasmids. In the present specification, "plasmid" and "vector" are used interchangeably, as plasmids are the most commonly used form of vector. However, the present invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses, and adeno-associated viruses), which serve equivalent functions.

The recombinant expression vectors of the invention include the nucleic acids of the invention in a form suitable for expression of the nucleic acids in a host cell, meaning that the recombinant expression vectors include one or more regulatory sequences selected on the basis of the host cell used for expression, operably linked to the nucleic acid sequence being expressed. In a recombinant expression vector, "operably linked" means that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner that allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). The term "regulatory sequence" is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel (1990) methods Enzymol.185: 3-7 are mentioned. Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in a variety of host cells and those which direct expression of a nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). One skilled in the art will appreciate that the design of an expression vector may depend on the following factors: the choice of the host cell to be transformed, the level of expression of the desired protein, and the like. The expression vectors of the invention may be introduced into host cells to produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein.

The recombinant expression vectors of the invention can be designed to express the polypeptides of the invention in prokaryotic or eukaryotic cells (e.g., FIGS. 2-7). For example, the polypeptide can be expressed in bacterial cells, such as e.coli (e.coli), insect cells (using baculovirus expression vectors), yeast cells, or mammalian cells. Suitable host cells are further described in Goeddel (1990) supra. Alternatively, the recombinant expression vector may be transcribed and translated in vitro, for example, using T7 promoter regulatory sequences and T7 polymerase.

Polypeptide expression in prokaryotes is most often performed in e.coli: vectors having constitutive or inducible promoters containing promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to the polypeptide encoded therein, typically the amino terminus of a recombinant polypeptide. Such fusion vectors are generally used for three purposes: 1) increasing expression of the recombinant polypeptide; 2) increasing the solubility of the recombinant polypeptide; and 3) by assisting the purification of the recombinant polypeptide as a ligand in affinity purification. Typically, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant polypeptide to allow the recombinant polypeptide to be separated from the fusion moiety after purification of the fusion protein. Such enzymes and their cognate recognition sequences include factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D.B. and Johnson, K.S. (1988) Gene 67: 31-40), pMAL (New England Biolabs, Beverly, Mass.), and pRIT5(Pharmacia, Piscataway, N.J.), which respectively fuse glutathione S-transferase (GST), maltose E binding protein, or protein A to the recombinant polypeptide of interest.

Examples of suitable inducible non-fusion E.coli expression vectors include pTrc (Amann et al (1988) Gene 69: 301-315) and pET 1 Id (Studier et al (1990) Methods enzymol.185: 60-89). Expression of the target gene by the pTrc vector is dependent on transcription by the host RNA polymerase which hybridizes to the trp-lac fusion promoter. Target gene expression from the pET 11 d vector is dependent on transcription from the T7 gn10-lac fusion promoter mediated by co-expressed viral RNA polymerase (T7 gn 1). The viral polymerase is provided by host strain BL21(DE3) or HMS174(DE3) from a colonizing prophage having the T7 gn1 gene under the transcriptional control of the lacUV 5 promoter.

One strategy for maximizing recombinant polypeptide expression in E.coli is to express the polypeptide in host bacteria with a reduced ability to proteolytically cleave the recombinant polypeptide (Gottesman, S. (1990) Methods enzymol.185: 119-128). Another strategy is to alter the Nucleic acid sequence of the Nucleic acid inserted into the expression vector so that the respective codons for each amino acid are those preferentially used in E.coli (Wada et al (1992) Nucleic Acids Res.20: 2111-2118). Such changes can be made to the nucleic acid sequences of the invention by standard DNA synthesis techniques.

In another embodiment, the expression vector is a yeast expression vector. Examples of expression vectors in the yeast Saccharomyces cerevisiae (S.cerevisiae) include pYepSec1(Baldari et al, (1987) EMBO J.6: 229. 234), pMFa (Kurjan and Herskowitz (1982) Cell 30: 933. 943), pJRY88(Schultz et al, (1987) Gene 54: 113. 123), pYES2(Invitrogen Corporation, San Diego, Calif.) and picZ (Invitrogen Corp, San Diego, Calif.).

Alternatively, baculovirus expression vectors can be used to express polypeptides of the invention in insect cells (e.g., FIGS. 2-7). Baculovirus vectors useful for expressing polypeptides in cultured insect cells (e.g., Sf 9 cells) include the pAc series (Smith et al (1983) mol. CellBiol.3: 2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170: 31-39).

In yet another embodiment, a nucleic acid of the invention is expressed in a mammalian cell using a mammalian expression vector (e.g., FIGS. 2-7). Examples of mammalian expression vectors include pCDM8(Seed, B. (1987) Nature 329: 840) and pMT2PC (Kaufman et al (1987) EMBO J.6: 187-195). When used in mammalian cells, the control functions of the expression vector are typically provided by the regulatory elements of the virus. For example, commonly used promoters are derived from polyoma Virus (polyma), adenovirus 2, cytomegalovirus and monkey Virus (Simian Virus) 40. For other suitable prokaryotic and eukaryotic cell expression systems, see Sambrook, j, et al, Molecular Cloning: chapters 16 and 17 of A Laboratory Manual.2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.

In another embodiment, recombinant mammalian expression vectors are capable of directing the expression of nucleic acids preferentially in specific Cell types (e.g., expression of nucleic acids using tissue-specific regulatory elements). non-limiting examples of suitable tissue-specific promoters are well known in the art include the albumin promoter (liver-specific; Pinkert et al (1987) Genes Dev.1: 268-277), the lymph-specific promoter (Calame and Eaton (1988) adv.Immunol.43: 235-275), the specific promoter for the T-Cell receptor (Winto and BamHore (1989) EMJ.8: 729-733), and the specific promoter for immunoglobulin (Banerji et al (1983) Cell 33: 729-740; Queen and Baltimore (1983) Cell 33: 741-748), the neuron-specific promoter (e.g., neural filament promoter; Byrne and Ruddc.264) Natl.1990: 1983) promoter (1989) and the pancreatic gland-specific promoter (1989) 120: 741-166; e.g., bovine mammary gland-specific promoter; Japanese laid-on protein, USA; 1989) promoters including the mammary gland-specific promoters, USA, 35, USA, 1987, USA, 1989, and USA, 1989, 2000-specific promoters including the mammary gland-specific promoters, USA, 35, USA, 2000, and USA, 35, and USA, 2000-21, and USA, 2000-specific promoters, 2000-21, including the promoter (1989).

Another aspect of the invention relates to a host cell into which a nucleic acid molecule of the invention (e.g., FIGS. 2-7) has been introduced within a recombinant expression vector or nucleic acid molecule comprising a sequence that allows homologous recombination into a specific site in the genome of the host cell. The terms "host cell" and "recombinant host cell" are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell, but also to the progeny or potential progeny of such a cell. Because certain changes may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.

The host cell may be any prokaryotic or eukaryotic cell. For example, a polypeptide of the invention can be expressed in a bacterial cell, such as E.coli, insect cell, yeast, or mammalian cell, such as Chinese Hamster Ovary (CHO) or COS cells (e.g., FIGS. 2-7). Other suitable host cells are well known to those skilled in the art.

Vector DNA can be introduced into prokaryotic or eukaryotic cells by conventional transformation or transfection techniques. As used herein, the terms "transformation" and "transfection" refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in: sambrook et al (Molecular Cloning: A Laboratory Manual.2nd, ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989) and other Laboratory manuals.

For stable transfection of mammalian cells, it is known that, depending on the expression vector and transfection technique used, only a small fraction of cells can integrate the foreign DNA into their genome. To identify and select these integrants, a gene encoding a selectable marker (e.g., resistance to antibiotics) is typically introduced into the host cell along with the gene of interest. Preferred selectable markers include those that confer drug resistance, such as G418, hygromycin and methotrexate. The nucleic acid encoding the selectable marker may be introduced into the host cell on the same vector as that encoding the PD-L2 polypeptide, or on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have integrated the selectable marker gene will survive when other cells die).

Host cells of the invention, such as prokaryotic or eukaryotic host cells in culture, can be used to produce (i.e., express) a polypeptide of the invention (e.g., fig. 2-7). Accordingly, the invention further provides methods of producing a polypeptide of the invention (e.g., FIGS. 2-7) using a host cell of the invention. In one embodiment, the method comprises culturing a host cell of the invention, into which has been introduced a recombinant expression vector encoding a polypeptide of the invention (e.g., FIGS. 2-7), in a suitable culture medium to produce the polypeptide of the invention (e.g., FIGS. 2-7). In another embodiment, the method further comprises isolating the polypeptide of the invention from the culture medium or the host cell (e.g., FIGS. 2-7).

As described below, the host cells of the invention can also be used to produce non-human transgenic animals.

V.Preparation of transgenic and transchromosomal non-human animals producing Complex human PD-1, PD-L1 or PD-L2 antibodies

In yet another aspect, the invention provides transgenic and transchromosomal non-human animals, such as transgenic or transchromosomal mice, capable of expressing human monoclonal antibodies that specifically bind to PD-1, PD-L1, or PD-L2. In a particular embodiment, the invention provides transgenic or transchromosomal mice that: having a genome comprising a human heavy chain transgene such that upon immunization with a PD-1, PD-L1 or PD-L2 antigen and/or a cell expressing PD-1, PD-L1 or PD-L2, the mouse produces a human anti-PD-1, PD-L1 or PD-L2 antibody. The human heavy chain transgene may be integrated into the mouse chromosomal DNA as is the case for transgenes, e.g., HuMAb mice, according to methods well known in the art. Alternatively, the human heavy chain transgene is maintained extrachromosomally as in the case of transchromosomal (e.g., KM) mice as described in WO 02/43478. Such transgenic and transchromosomal mice are capable of producing multiple isotypes (e.g., IgG, IgA, and/or IgE) of human monoclonal antibodies to PD-1, PD-L1, or PD-L2 by undergoing V-D-J recombination and isotype switching. Isotype switching can occur by: for example, classical or non-classical isotype switching.

The design of transgenic or transchromosomal non-human animals in response to stimulation with exogenous antigens from a heterologous antibody repertoire requires that the heterologous immunoglobulin transgene contained in the transgenic animal functions correctly throughout the developmental pathway of the B cell. This includes: for example, isotype switching of heterologous heavy chain transgenes. Thus, transgenes were constructed to generate isotype switching and one or more of the following antibodies: (1) high level and cell type specific expression, (2) functional gene rearrangement, (3) activation and response of allelic exclusion, (4) expression of sufficient major repertoire, (5) signal transduction, (6) somatic hypermutation, and (7) control of transgenic antibody loci during immune response.

It is not necessary that all of the above criteria be met. For example, in those embodiments in which the endogenous immunoglobulin locus of the transgenic animal is functionally hindered, the transgene need not activate allelic exclusion. Further, in those embodiments in which the transgene comprises functionally rearranged heavy and/or light chain immunoglobulin genes, the second criterion of functional gene rearrangement, at least for the transgene that has been rearranged, is not necessary. For background on molecular Immunology, see Fundamental Immunology, 2nd edition (1989), Paul William e.

In certain embodiments, the transgenic or transchromosomal non-human animals used to produce the human monoclonal antibodies of the invention comprise a rearranged heterologous immunoglobulin heavy and light chain transgene, an unrearranged heterologous immunoglobulin heavy and light chain transgene, or a combination of rearranged and unrearranged heterologous immunoglobulin heavy and light chain transgenes in the germline of the transgenic animal. Each heavy chain transgene includes at least one CH gene. In addition, the heavy chain transgene may comprise functional isotype switching sequences that are capable of supporting isotype switching of heterologous transgenes encoding multiple CH genes in B cells of transgenic animals. Such a transition sequence may be a sequence naturally occurring in the germline immunoglobulin locus of the species from which the transgenic CH gene was derived, or such a transition sequence may be derived from a sequence occurring in the species (transgenic animal) that received the transgenic construct. For example, a human transgene construct used to prepare transgenic mice can produce a higher frequency of isotype switching events if it incorporates switching sequences similar to those naturally occurring in the mouse heavy chain locus, presumably because the mouse switching sequences are optimized to function with the mouse switch recombinase enzyme system, while the human switching sequences do not. The switching sequences can be isolated and cloned by conventional cloning methods or synthesized de novo starting from: overlapping synthetic oligonucleotides designed based on published sequence information on immunoglobulin transition region sequences (Mills et al, Nucl. acids Res.15: 73057316 (1991); Sideras et al, Intl. Immunol.1: 631642 (1989)). For each of the foregoing transgenic animals, functionally rearranged heterologous heavy and light chain immunoglobulin transgenes were found in a substantial portion (at least 10%) of the transgenic animal B cells.

The transgenes used to generate the transgenic animals of the invention include heavy chain transgenes comprising DNA encoding at least one variable (V) gene segment, one diversity (D) gene segment, one joining (J) gene segment, and at least one constant region gene segment. The immunoglobulin light chain transgene comprises DNA encoding at least one V gene segment, one J gene segment, and at least one constant region gene segment. The gene segments encoding the light and heavy chain gene segments are heterologous to the transgenic non-human animal in that they are derived from or correspond to DNA encoding immunoglobulin heavy and light chain gene segments of a species that is not comprised of the transgenic non-human animal. In one aspect of the invention, the transgene is constructed such that the individual gene segments are not rearranged, i.e., are not rearranged, thereby encoding a functional immunoglobulin light or heavy chain. This unrearranged transgene supports recombination (functional rearrangement) of V, D and the J gene segment, preferably supports integration of all or part of the D region gene segment in a rearranged immunoglobulin heavy chain produced in a transgenic non-human animal when exposed to the PD-1, PD-L1, or PD-L2 antigens.

In an alternative option, the transgene comprises an unrearranged "mini locus". Such transgenes generally include C, D and the major portion of the J segment and the subtype of the V gene segment. In such transgenic constructs, various RNA processing, recombination signals, and similar regulatory sequences, e.g., promoter, enhancer, species switching region, splice donor and splice acceptor sequences, include the corresponding sequences from heterologous DNA. Such regulatory sequences may be incorporated into a transgene in the same or related species of non-human animals used in the present invention. For example, human immunoglobulin gene fragments can be combined into transgenes with rodent immunoglobulin enhancer sequences used in transgenic mice. Alternatively, synthetic regulatory sequences may be incorporated into the transgene, wherein such synthetic regulatory sequences are not homologous to functional DNA sequences naturally occurring in the genome of a known mammal. According to a consensus rule-such as: for example, rules specifying allowed sequences for splice acceptor sites or promoter/enhancer motifs-design of synthetic regulatory sequences. For example, mini-loci include: a portion of a genomic immunoglobulin locus that has at least one internal (i.e., not terminal to) deletion of a non-essential DNA portion (e.g., intervening sequences; introns, or portions thereof) as compared to a naturally occurring germline Ig locus.

Transgenic and transchromosomal mice used in the present invention can exhibit immunoglobulin production with a major repertoire, ideally substantially similar to that of native mice. Thus, for example, in embodiments in which endogenous Ig genes are inactivated, the total immunoglobulin level may be in the range of about 0.1 to 10mg/ml, or about 0.5 to 5mg/ml, or at least about 1.0mg/ml of serum. When a transgene that effects IgM conversion to IgG is introduced into a transgenic mouse, the ratio of serum IgG to IgM in an adult mouse may be about 10: 1. The ratio of IgG to IgM will be greatly reduced in immature mice. Typically, greater than about 10%, preferably 40 to 80%, of spleen and lymph node B cells exclusively express human IgG proteins.

The repertoire will ideally approximate that exhibited by native mice, typically at least about 10% high, or 25 to 50% or more. Generally, at least about a thousand different immunoglobulins (ideally IgG) will be produced, e.g., preferably 10, depending primarily on the number of different V, J and D regions introduced into the mouse genome⁴To 10⁶Or more. These immunoglobulins will generally recognize about half or moreHighly antigenic proteins, e.g., staphylococcal protein a. Generally, the immunoglobulin will exhibit less than 10% of the preselected antigen^-7Affinity of M (K)_D) E.g. below 10^-8M、10^-9M or 10^-10M is even lower.

In some embodiments, it may be preferable to generate mice with a predetermined repertoire, thereby limiting the selection of V genes displayed in an antibody response to a predetermined antigen type. A heavy chain transgene with a predetermined repertoire can include: for example, human V is preferentially used in human antibody response to a predetermined antigen type_HA gene. Or, some V_HGenes can be excluded from a defined repertoire for a variety of reasons (e.g., low probability of encoding a high affinity V-region for a predetermined antigen; low propensity for somatic mutation and affinity stimulation (sharpening), or immunogenicity to a particular human). Thus, such gene fragments can be readily identified, for example, by hybridization or DNA sequencing, prior to rearrangement of the transgene comprising the different heavy or light chain gene fragments, as they are from a biological species that is not a transgenic animal.

Transgenic and transchromosomal mice as described above can be immunized with, for example, a purified or enriched preparation of PD-1, PD-L1, or PD-L2 antigen and/or cells expressing PD-1, PD-L1, or PD-L2. Alternatively, transgenic mice can be immunized with DNA encoding human PD-1, PD-L1, or PD-L2. The mice will then produce B cells that undergo species switching by intratransgenic recombination (cis switching) and express immunoglobulins that are reactive with PD-1, PD-L1, or PD-L2. The immunoglobulin may be a human antibody (also referred to as a "human sequence antibody"), in which human transgene sequences encoding heavy and light chain polypeptides, which may include sequences obtained by somatic mutation and V region recombination junctions and germline coding sequences; these human antibodies may be referred to as human V even though other non-germline sequences may be present due to somatic mutations and divergent V-J and V-D-J recombination junctions_LOr V_HGene fragment and human J_LOr D_HAnd J_HThe fragments encode polypeptide sequences that are substantially identical. Each antibodyThe variable region of the body chain is typically at least 80% encoded by human germline V, J and-in the case of the heavy chain-the D gene segment; often at least 85% of the variable region is encoded by human germline sequences present on the transgene; typically 90% or 95% or more of the variable region sequences are encoded by human germline sequences present on the transgene. However, since non-germline sequences are introduced by somatic mutation and VJ and VDJ ligation, human sequence antibodies will often have some variable region sequences (and less often constant region sequences) that are not encoded by human V, D or J gene segments found in the human transgene(s) of the mouse germline. Typically, such non-germline sequences (or respective nucleotide sites) will aggregate in or near the CDRs or in regions where somatic mutations are known to aggregate.

Human antibodies that bind a predetermined antigen can be produced by isotype switching, thereby generating human antibodies that include a human sequence gamma chain (e.g., gamma 1, gamma 2a, gamma 2B, or gamma 3) and a human sequence light chain (e.g., kappa). Such isotype-switched human antibodies often comprise one or more somatic mutations (one or more) that are generally located in the variable region and are usually within or within about 10 residues of the CDRs, resulting from affinity maturation and B cell selection of the antigen, particularly after secondary (or subsequent) antigen challenge. These high affinity human antibodies may have less than 10^-7Binding affinity (K) of M_D) E.g. below 10^-8M、10^-9M、10^-10M、10^-10M even lower binding affinity (K)_D)。

Another aspect of the invention includes B cells obtained from transgenic or transchromosomal mice as described herein. B cells can be used to generate hybridomas expressing human monoclonal antibodies with high affinity (e.g., less than 10)^-7M) binds to human PD-1, PD-L1 or PD-L2.

Development of high affinity human monoclonal antibodies to PD-1, PD-L1 or PD-L2 can be promoted by: the method is used to expand the repertoire of human variable region gene segments in transgenic mice having a genome comprising an integrated human immunoglobulin transgeneThe method comprises introducing into the genome a V gene transgene comprising a V region gene segment that is not present in said integrated human immunoglobulin transgene. Typically, the V region transgene is an artificial yeast chromosome comprising human V, e.g., as may occur naturally in the human genome or as may be spliced together separately by recombinant methods_HOr V_L(V_K) A portion of an array of gene segments, which may include disordered or missing V gene segments. Typically YACs contain at least five or more functional V gene segments thereon. In this variation, it is possible to generate transgenic mice by group V bank expansion, wherein the mice express immunoglobulin chains that: comprising the variable region sequence encoded by a V region gene segment present on a V region transgene and the C region encoded on a human Ig transgene. By means of V group bank expansion, transgenic mice with at least 5 different V genes can be generated; such as those generated by mice comprising at least about 24 or more V genes. Some V gene segments may not be functional (e.g., pseudogenes and the like); these fragments may be retained or, if desired, selectively removed by recombinant methods available to the skilled person.

Once a mouse germline is engineered to contain a functional YAC with an expanded V segment repertoire that is essentially absent from a human Ig transgene containing J and C gene segments, this property can be propagated and propagated into other genetic backgrounds, including such backgrounds: where functional YACs with expanded V-segment repertoires were propagated into mouse germline with different human Ig transgenes. Multifunctional YACs with expanded V segment repertoires can be propagated into the germ line, working in concert with the human Ig transgene(s). Although also referred to herein as YAC transgenes, such transgenes, when integrated into the genome, can be substantially devoid of yeast sequences, such as sequences required for autonomous replication of yeast; such sequences may optionally be removed by genetic engineering (e.g., restriction digestion and pulsed field gel electrophoresis or other suitable methods) after replication in yeast is no longer necessary (i.e., prior to fertilization of the egg prior to introduction into a mouse ES cell or mouse). Methods for transmitting human sequence immunoglobulin expression profiles include propagating a vector containing human Ig transgene(s) andand optionally also transgenic mice with functional YACs with expanded V-segment repertoires. V_HAnd V_LGene fragments may be present on YACs. Transgenic mice can be bred into any background desired by practitioners, including backgrounds with other human transgenes, including human Ig transgenes and/or transgenes encoding other human lymphocyte proteins. The invention also provides high affinity human sequence immunoglobulins generated from transgenic mice bearing an expanded V-block repertoire YAC transgene. While the foregoing describes preferred embodiments of the transgenic animals of the present invention, other embodiments are contemplated which have been classified into the following four categories:

(1) a transgenic animal comprising an unrearranged heavy chain and a rearranged light chain immunoglobulin transgene;

(2) a transgenic animal comprising an unrearranged heavy chain and an unrearranged light chain immunoglobulin transgene;

(3) a transgenic animal comprising rearranged heavy chain and unrearranged light chain immunoglobulin transgenes; and

(4) a transgenic animal comprising a rearranged heavy chain and a rearranged light chain immunoglobulin transgene.

VI.Antibody conjugates/immunotoxins

In another aspect, the invention features human PD-1, PD-L1, or PD-L2 antibodies that bind a therapeutic moiety, such as a cytotoxin, a drug (e.g., an immunosuppressant), or a radioisotope. When conjugated to a cytotoxin, these antibody conjugates are referred to as "immunotoxins". A cytotoxin or cytotoxic agent includes any agent that is harmful to (e.g., kills) a cell. Examples include paclitaxel, cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, doxorubicin, daunorubicin, dihydroxy anthrax dione, mitoxantrone, mithramycin, actinomycin D, 1-dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, and puromycin, and analogs or homologs thereof. Therapeutic agents include, but are not limited to, antimetabolites (e.g., methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil aminomidamide), alkylating agents (e.g., mechlorethamine, thiotepa, chlorambucil, melphalan, nitroso urea mustard (BSNU) and lomustine (CCNU), cyclophosphamide (cycloothoramide), busulfan, dibromomannitol, streptozotocin, mitomycin C and cis-dichlorodiammineplatinum (II) (DDP) cisplatin), anthracyclines (e.g., daunorubicin and doxorubicin), antibiotics (e.g., dactinomycin, bleomycin, mithramycin and anthranilic Acid (AMC)), and antimitotics (e.g., vincristine and vinblastine). The antibodies of the invention can bind radioisotopes, e.g., radioiodine, to produce cytotoxic radiopharmaceuticals useful for treating related diseases, such as cancer.

Bound human PD-1, PD-L1, or PD-L2 antibodies can be used diagnostically or prognostically to monitor polypeptide levels in tissues as part of a clinical testing procedure, e.g., to, e.g., determine the efficacy of a given treatment regimen. Coupling (i.e., physically linking) the antibody to a detectable substance can facilitate detection. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent substances, luminescent substances, bioluminescent substances, and radioactive substances. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, P-galactosidase or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent substances include umbelliferone, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; examples of luminescent substances include luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin; and examples of suitable radioactive materials include₁₂₅I、₁₃₁I、.₃₅S or₃H。

The antibody conjugates of the invention may be used to modulate a given biological response. The therapeutic moiety is not to be construed as limited to classical chemotherapeutic agents. For example, the drug moiety may be a protein or polypeptide having a desired biological activity. Such proteins may include: for example, enzymatically active toxins or active fragments thereof, such as abrin, ricin a, pseudomonas exotoxin, or diphtheria toxin; proteins, such as tumor necrosis factor or interferon gamma; or biological response modifiers, such as, for example, lymphokines, interleukin-1 ("IL-1"), interleukin-2 ("IL-2"), interleukin-6 ("IL-6"), granulocyte macrophage colony stimulating factor ("GM-CSF"), granulocyte colony stimulating factor ("G-CSF"), or other cytokines or growth factors.

Techniques For binding such therapeutic moieties to Antibodies are well known, see, e.g., Arnon et al, "Monoclonal Antibodies For Immunotargeting Of Drugs In Cancer Therapy", Monoclonal Antibodies And Cancer Therapy, Reisfeld et al (eds.), pp.24356 (AlanR.Liss, Inc.1985); hellstrom et al, "Antibodies For Drug Delivery", Controlled Drug Delivery (2nd Ed.), Robinson et al (eds.), pp.62353 (Marcel Dekker, Inc.1987); thorpe, "Antibody Carriers Of Cytotoxin Agents In Cancer Therapy: a Review ", monoclonal antibodies' 84: biological And Clinical Applications, Pinchera et al (eds.), pp.475506 (1985); "Analysis, Results, And" Analysis, applied Of The Therapeutic Use Of radioactive amplified fluorescent In Cancer Therapy ", In Monoclonal Antibodies For Cancer Therapy, Baldwin et al (eds.), pp.30316 (Academic Press 1985) And Thorpe et al," The Preparation Of amplified Cytotoxic proteins Of Antibody-Toxin Conjugates ", Immunol.Rev., 62: 11958(1982).

VII.Pharmaceutical composition

In another aspect, the invention provides a composition, e.g., a pharmaceutical composition, comprising one or a combination of monoclonal antibodies or antigen-binding portion(s) thereof (e.g., antigen-binding fragment) of the invention, such as an antigen-binding fragment, formulated together with a pharmaceutically acceptable carrier. In one embodiment, the composition comprises a combination of a plurality (e.g., two or more) of the isolated human antibodies of the invention. Preferably, each antibody in the composition binds to a different preselected epitope of PD-1, PD-L1, and/or PD-L2.

The pharmaceutical compositions of the invention may also be administered in combination therapy, i.e. in combination with other agents. For example, a combination therapy may comprise a composition of the invention and at least one or more additional therapeutic agents, such as anti-inflammatory agents, DMARDs (disease modifying antirheumatic drugs), immunosuppressive agents, chemotherapeutic agents, and psoriasis agents. The pharmaceutical compositions of the present invention may also be administered in conjunction with radiation therapy. The invention also includes co-administration with other antibodies, e.g., antibodies specific for CD4 and antibodies specific for IL-2.

As used herein, "pharmaceutically acceptable carrier" includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. Preferably, the carrier is suitable for intravenous, intramuscular, subcutaneous, parenteral, spinal or epidermal administration (e.g., by injection or infusion). Depending on the route of administration, the active compounds, i.e., antibodies, bispecific and multispecific molecules, may be encapsulated in a material to protect the compound from acids and other natural conditions that inactivate the compound.

"pharmaceutically acceptable salt" refers to a salt that retains the desired biological activity of the parent compound and does not impart any undesirable toxicological effects (see, e.g., Berge, s.m., et al, (1977) j.pharm.sci.66: 119). Examples of such salts include acid addition salts and base addition salts. Acid addition salts include those derived from non-toxic inorganic acids such as hydrochloric, nitric, phosphoric, sulfuric, hydrobromic, hydroiodic, phosphorous and similar inorganic acids, and those derived from non-toxic organic acids such as aliphatic monocarboxylic and dicarboxylic acids, phenyl-substituted alkanoic acids, hydroxy alkanoic acids, aromatic acids, aliphatic and aromatic sulfonic acids and similar organic acids. Base addition salts include those derived from alkaline earth metals such as sodium, potassium, magnesium, calcium, and the like, and those derived from non-toxic organic amines such as N, N' -dibenzylethylenediamine, N-methylglucamine, chloroprocaine, choline, diethanolamine, ethylenediamine, procaine, and the like.

The compositions of the present invention can be administered by a variety of methods known in the art. As the skilled person will appreciate, the route and/or manner of administration will vary depending on the desired result. The active compounds can be formulated together with carriers that will prevent rapid release of the compound, such as controlled release formulations, including implants, transdermal patches, and microencapsulated delivery systems. Biodegradable, biocompatible polymers such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid may be used. Various methods of preparing such formulations are patented or are generally known to those skilled in the art. See, for example, Sustainated and coordinated Release Drug Delivery Systems, J.R. Robinson, ed., Marcel Dekker, Inc., New York, 1978.

In order to administer a compound of the present invention by some route of administration, it may be necessary to coat the compound with a material that prevents its inactivation, or to co-administer the compound therewith. For example, the compounds can be administered to an individual in a suitable carrier, e.g., a liposome or diluent. Pharmaceutically acceptable diluents include saline and buffered aqueous solutions. Liposomes include water-in-oil CGF emulsions in water and conventional liposomes (Strejan et al (1984) J. Neuropimunol.7: 27).

Pharmaceutically acceptable carriers include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. The use of such pharmaceutically active agent vehicles and agents is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, its use in the pharmaceutical compositions of the invention is contemplated. Supplementary active compounds may also be incorporated into the compositions.

Therapeutic compositions generally must be sterile and stable under the conditions of manufacture and storage. The compositions may be formulated as solutions, microemulsions, liposomes or other regular structures suitable for high drug concentrations. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. For example, suitable fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. In many cases, it will be preferred to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the compositions agents which delay absorption, for example, monostearate salts and gels.

Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by sterile microfiltration. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying (lyophilization) that yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

The dosage regimen is adjusted to provide the optimal desired response (e.g., therapeutic response). For example, a single bolus (bolus) may be administered, several divided doses may be administered over time, or the dose may be proportionally reduced or increased as indicated by the urgency of the treatment. For example, the human antibodies of the invention can be administered by subcutaneous injection once or twice a week or by subcutaneous injection once or twice a month. Parenteral compositions are formulated in unit dosage forms, and are particularly beneficial for ease of administration and uniformity of dosage. Unit dosage form as used herein refers to physically discrete units suitable as unitary dosages for the subjects to be treated; each unit contains a predetermined amount of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specifications for the unit dosage form of the present invention are dictated and directly determined by: (a) the unique characteristics of the active compound and the particular therapeutic effect to be achieved; and (b) limitations inherent in the art of synthesis of such active compounds that treat sensitivity in individuals.

In one embodiment, the agent of the invention is an antibody. As defined herein, a therapeutically effective amount of an antibody (i.e., an effective dose) ranges from about 0.001 to 30mg/kg body weight; or about 0.01 to 25mg/kg body weight; or about 0.1 to 20mg/kg body weight; or about 1 to 10mg/kg, 2 to 9mg/kg, 3 to 8mg/kg, 4 to 7mg/kg, or 5 to 6mg/kg body weight. The skilled artisan will appreciate that certain factors may affect the dosage required to effectively treat a subject, including, but not limited to, the severity of the disease or disorder, prior treatment, general health and/or age of the subject, and other diseases present. Furthermore, treatment of a subject with a therapeutically effective amount of an antibody may comprise a single treatment, or preferably a series of treatments. It will also be appreciated that the effective dose of antibody used in treatment may be increased or decreased over the course of a particular treatment. The variation in dosage can result from the results of the diagnostic assay.

Examples of pharmaceutically acceptable antioxidants include (1) water-soluble antioxidants such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite, and the like, (2) oil-soluble antioxidants such as ascorbyl palmitate, Butylated Hydroxyanisole (BHA), Butylated Hydroxytoluene (BHT), lecithin, propyl gallate, α -tocopherol, and the like, and (3) metal chelators such as citric acid, ethylenediaminetetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.

For therapeutic compositions, the formulations of the present invention include those suitable for oral, nasal, topical (including buccal and sublingual), rectal, vaginal and/or parenteral administration. The formulations may conveniently be presented in unit dosage form and may be prepared by any of the methods well known in the art of pharmacy. The amount of active ingredient that may be combined with the carrier materials to produce a single dosage form will vary depending upon the subject being treated and the particular mode of administration. The amount of active ingredient that can be combined with the carrier materials to produce a single dosage form will generally be that amount of the composition which produces a therapeutic effect. Generally, above 100%, the content will be in the following ranges: from about 0.001% to about 90% of active ingredient, alternatively from about 0.005% to about 70%, alternatively from about 0.01% to about 30%.

Formulations of the invention suitable for vaginal administration also include pessaries, tampons, creams, gels, pastes, foams or spray formulations containing such carriers as are known in the art to be suitable. Dosage forms for topical or transdermal administration of the compositions of the present invention include powders, sprays, ointments, pastes, ointments, lotions, gels, solutions, patches and inhalants. The active compound may be mixed under sterile conditions with a pharmaceutically acceptable carrier, with any preservatives, buffers, or propellants which may be required.

The phrases "parenteral administration" and "parenterally administered" as used herein mean modes of administration other than enteral and topical administration, typically by injection, including, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal, epidural, and intrasternal (intrasternal) injection and perfusion.

Examples of suitable aqueous and nonaqueous carriers that may be used in the pharmaceutical compositions of the invention include: water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol and the like) and suitable mixtures thereof; vegetable oils, such as olive oil; and injectable organic esters, such as ethyl oleate. Suitable fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.

These compositions may also contain adjuvants such as preserving, wetting, emulsifying, and dispersing agents. Prevention of the presence of microorganisms can be ensured by the above-described sterilization procedures and by inclusion of various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, for example, sugars, sodium chloride and the like in the compositions. In addition, prolonged absorption of the injectable pharmaceutical form can be brought about by the inclusion of agents which delay absorption, such as aluminum monostearate and gelatin.

When the compounds of the present invention are administered as a medicament to humans and animals, they may be administered alone or as a pharmaceutical composition comprising: for example, 0.001 to 90% (e.g., 0.005 to 70%, such as 0.01 to 30%) of the active ingredient is combined with a pharmaceutically acceptable carrier.

Regardless of the route of administration chosen, the compounds of the present invention and/or the pharmaceutical compositions of the present invention, which may be used in an appropriately hydrated form, may be formulated into pharmaceutically acceptable dosage forms by conventional methods known to those skilled in the art.

The actual dosage level of the active ingredient of the pharmaceutical compositions of this invention can be varied so as to obtain an amount of the active ingredient which is effective to achieve the desired therapeutic response for a particular patient, composition and form of administration, and which is non-toxic to the patient. The selected dosage level will depend upon a variety of pharmacokinetic factors including the activity of the particular composition of the invention or ester, salt or amide thereof employed, the route of administration, the time of administration, the rate of excretion of the particular compound employed, the duration of the treatment, other drugs, compounds and/or materials used in conjunction with the particular composition employed, the age, sex, body weight, condition, general health and prior medical history of the patient being treated, and like factors well known in the medical arts. A physician or veterinarian of ordinary skill in the art can readily determine and prescribe the effective amount of the pharmaceutical composition required. For example, a physician or veterinarian can start doses of a compound of the invention used in a pharmaceutical composition at a level below that required to achieve the desired therapeutic effect and gradually increase the dose until the desired effect is achieved. In general, a suitable daily dosage of a composition of the invention will be the amount of such compound: which is the lowest dose effective to produce a therapeutic effect. Such effective dosages will generally depend on the factors described above. Intravenous, intramuscular, intraperitoneal or subcutaneous administration is preferred, preferably close to the target site. If desired, an effective daily dose of the therapeutic composition can be administered, optionally in unit dosage form, in two, three, four, five, six or more separate doses administered at appropriate intervals throughout the day. Although the compound of the present invention may be administered alone, it is preferable to administer the compound in a pharmaceutical preparation (composition).

The therapeutic composition may be administered using medical devices known in the art. For example, in one embodiment, the therapeutic compositions of the present invention can be administered using a needleless hypodermic syringe, such as the device disclosed in U.S. Pat. No. 5,399,163, 5,383,851, 5,312,335, 5,064,413, 4,941,880, 4,790,824 or 4,596,556. Examples of known implants and components with which the invention may be used include: U.S. patent No. 4,487,603, which discloses an implantable micro-infusion pump for dispensing at a controlled rate; U.S. patent No. 4,486,194, which discloses a therapeutic device for transdermal drug delivery; U.S. Pat. No. 4,447,233, which discloses a medication infusion pump for delivering a drug at a precise infusion rate; U.S. Pat. No. 4,447,224, which discloses a variable flow implantable infusion device for continuous drug delivery; U.S. Pat. No. 4,439,196, which discloses an osmotic drug delivery system having multi-compartment spacing; and U.S. patent No. 4,475,196, which discloses osmotic drug delivery systems. Numerous other such implants, delivery systems and assemblies will be apparent to those skilled in the art.

In certain embodiments, the human monoclonal antibodies of the invention can be prepared to ensure proper distribution in vivo. For example, the Blood Brain Barrier (BBB) excludes many highly hydrophilic compounds. To ensure that the therapeutic compounds of the invention cross the BBB (if desired), they can be formulated, for example, in liposomes. For a method of preparing liposomes, see: for example, U.S. Pat. nos. 4,522,811; 5,374,548, respectively; and 5,399,331. Liposomes can include one or more moieties that are selectively delivered to specific cells or organs, thereby enhancing targeted drug delivery (see, e.g., v.v. ranade (1989) j.clin.pharmacol.29: 685). Exemplary targeting moieties include folate or biotin (see, e.g., Low et al, U.S. Pat. No. 5,416,016); mannoside (Umezawa et al, (1988) biochem. Biophys. Res. Commun.153: 1038); antibodies (P.G.Bloeman et al. (1995) FEBS Lett.357: 140; M.Owais et al (1995) antibodies.Agents Chemother.39: 180); the surfactant protein A receptor (Briscoe et al, (1995) am.J. physiol.1233: 134), different species of which may constitute components of the formulations and molecules of the invention; p120(Schreier et al, (1994) J.biol.chem.269: 9090); see also k.keinanen; m.l. laukkanen (1994) FEBS lett.346: 123; j.j.killion; fidler (1994) Immunomethods 4: 273. in one embodiment of the invention, the therapeutic compounds of the invention are formulated in liposomes; in another embodiment, the liposome comprises a targeting moiety. In yet another embodiment, the therapeutic compound in the liposome is delivered to the site proximal to the tumor or infection by bolus injection. The composition must have fluidity to the extent that it is easy to inject. It must be stable under the conditions of preparation and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.

The composition must be sterile and fluid to the extent that the composition can be delivered by syringe. In addition to water, the carrier can be an isotonic buffered saline solution, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol (polyethylene glycol), and the like), and suitable mixtures thereof. For example, by using a coating such as lecithin, proper fluidity can be maintained by maintaining the desired particle size in the case of dispersion and by using a surfactant. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as mannitol or sorbitol, and sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by the inclusion in the composition of an agent that delays absorption, for example, aluminum monostearate or gelatin.

When the active compound is suitably protected, the compound may be administered orally, e.g., with an inert diluent or with an assimilable edible carrier, as described above.

VIII.Applications and methods of the invention

The antibodies (including derivatives and conjugates of the antibodies) and compositions comprising the antibodies described herein are useful for a variety of in vitro and in vivo diagnostic and therapeutic applications (e.g., by up-regulating or down-regulating immune responses). For example, a PD-1 ligand bound to PD-1 or B7-1 signals inhibition. Thus, modulation of the interaction between PD-1 and PD-1 ligand or between PD-1 ligand and B7 polypeptide results in modulation of the immune response. PD-1 ligands can also co-stimulate T cells. Thus, in one embodiment, an antibody that blocks the interaction between PD-1 ligand and PD-1 or B7 may prevent inhibitory signaling. In one embodiment, an antibody that blocks the co-stimulatory signal of the PD-1 ligand blocks the co-stimulatory signal to immune cells. In addition, the ligation of PD-L2 induced cytokine secretion and dendritic cell survival. Thus, antibodies that block PD-L2 linkage can inhibit dendritic cell survival and reduce cytokine expression by dendritic cells, and through these mechanisms suppress immune responses. In particular, the antibodies described herein are useful in diagnostic, prognostic, prophylactic and therapeutic applications relating to specific disorders mediated by PD-1, PD-L1 and/or PD-L2, as described, for example, in Keir et al (2008) annu, rev, immunol.26: 677; sharp et al, (2007) nat. immunol.8: 239; freeman et al, (2007) J.Exp.Med.10: 2223, and (c); each of which is incorporated herein by reference in its entirety.

In one embodiment, the antibodies and antigen binding fragments of the invention are useful for diagnostic, prognostic, prophylactic and therapeutic applications relating to neurodegenerative diseases (senile psychosis, alzheimer's disease, down's syndrome, parkinson's disease, creutzfeldt-jakob disease, diabetic neuropathy, parkinsonism, huntington's disease, machado-joseph disease, amyotrophic lateral sclerosis, diabetic neuropathy and creutzfeldt-jakob disease).

In another embodiment, the antibodies and antigen-binding fragments of the invention may be used for diagnostic, prognostic, prophylactic and therapeutic applications (e.g., treatment and delay of onset or progression of disease) of diseases that promote immune response, such as asthma, autoimmune diseases (glomerulonephritis, arthritis, dilated cardiomyopathy, ulcerative colitis (ulcerous colitis), sjogren's syndrome, crohn's disease, systemic erythema (sythetales), chronic rheumatoid arthritis, multiple sclerosis, psoriasis, allergic contact dermatitis, polymyositis (polymyosis), thickening of the skin, nodular adventititis, rheumatic fever, vitiligo vulgaris, insulin-dependent diabetes mellitus, behcet's disease, hashimoto's disease, addison's disease, dermatomyositis, myasthenia gravis, reiter's syndrome, graves disease, pernicious anemia (anaemia persica), goodpasture syndrome, goodpasture's syndrome, morbid syndrome, and delayed onset or progression of disease, Infertility, chronic active hepatitis, pemphigus, autoimmune thrombocytopenic purpura, and autoimmune hemolytic anemia, active chronic hepatitis, addison's disease, antiphospholipid syndrome, atopic allergy, autoimmune atrophic gastritis, autoimmune achlorhydria autoimmunee, abdominal diseases, cushing's syndrome, dermatomyositis, discoid lupus, lupus erythematosus, goodpasture's syndrome, hashimoto's thyroiditis, idiopathic adrenal atrophy, idiopathic thrombocytopenia, insulin dependent diabetes mellitus, lang-yidi's syndrome, lupus-like hepatitis, lymphopenia in some cases, mixed connective tissue disease, pemphigoid, pemphigus vulgaris, pernicious anemia (pernicious aea), phacogenic uveitis, polyarteritis nodosa, polyglandular self-syndrome, primary biliary cirrhosis, chronic active hepatitis, atopic dermatitis, and autoimmune hemolytic anemia, Primary sclerosing cholangitis, raynaud's syndrome, recurrent polychondritis, schmitt's syndrome, localized scleroderma (or apical ridge syndrome), sympathetic ophthalmia, systemic lupus erythematosus, takayasu's arteritis, temporal arteritis, thyrotoxicosis, type B insulin resistance, ulcerative colitis, and wegener's granulomatosis).

In yet another embodiment, the antibodies and antigen-binding fragments of the invention may be used in diagnostic, prognostic, prophylactic and therapeutic applications (e.g., treatment and delay of the onset or course of disease) for the treatment and/or prevention of persistent infectious diseases (e.g., viral infectious diseases including HPV, HBV, Hepatitis C Virus (HCV), retroviruses such as human immunodeficiency virus (HIV-1 and HIV-2), herpesviruses such as EB virus (EBV), Cytomegalovirus (CMV), HSV-1 and HSV-2, and influenza viruses.) other antigens associated with pathogens are antigens of various parasites including peptide malaria, preferably, NANOP repeat-based malaria, also bacteria, fungi and other pathogenic diseases including, e.g., Aspergillus (Aspergillus), Brucella (Brucella), Clostridium (Salmonella), bovine spongiella (Streptococcus), bovine spongiella (Salmonella), bovine spongiella (serohilus), bovine spongitis (serohilus), bovine spongiella (serohilus), bovine spongiensis), bovine spongiella (serohilus), bovine spongitis (serohilus), bovine spongiella), bovine spongitis (seroidea (serous), bovine spongiella), bovine spongitis (serous), bovine spongitis (seroidea (serous), bovine spongitis (bovine spongiella), bovine spongitis (serous), bovine spongiella), bovine spongitis (serous), and other (serous), bovine spongitis (serous), and other infectious diseases (serous), other infectious diseases (serous), and other infectious diseases (serous), other infectious diseases (serous), bovine spongitis (serous), other infectious diseases (serous), other strains of the other infectious diseases (serous), other strains of the other strains (serous), and other strains of the like serous), and other strains of the like the serous), and other strains of the like the strains of the like the strains of the serous), and serous (serous), and other strains of the like the serous malassens (serous), and serous malassens (serous malassens), and serous malassens (serous), and serous (serous), and other strains of the like the strains of the strains.

In yet another embodiment, the antibodies or antigen binding fragments of the invention can be used for diagnostic, prognostic, prophylactic and therapeutic applications as follows: organ transplant rejection, Graft Versus Host Disease (GVHD), allergic diseases, and diseases caused by attenuation of immune response in which PD-1, PD-L1, and/or PD-L2 are involved-for example, cancer and infectious diseases.

The antibodies or antigen-binding fragments described herein are administered to an individual according to known methods as follows: such as intravenous (e.g., in a bolus or by continuous infusion over a period of time), subcutaneous, intramuscular, intraperitoneal, intracerobrospinal, intraarticular, intrasynovial, intrathecal, or inhalation routes.

An individual is treated if one or more beneficial or expected results, including a desired clinical result, are obtained. For purposes of the present invention, beneficial or desired clinical results include, but are not limited to, one or more of the following: reducing one or more symptoms caused by the disease, improving the quality of life of an individual suffering from the disease, reducing the dosage of other medications required to treat the disease, delaying the progression of the disease, and/or prolonging survival of the individual.

1.Screening method

One aspect of the invention relates to methods of modulating immune responses (e.g., antibodies that modulate the function of PD-1, PD-L1, or PD-L2) by modulating co-stimulation using the antibodies. Such methods employ screening assays, including cell-based and non-cell-based assays. In one embodiment, the assay provides a method for identifying antibodies that modulate the interaction between a PD-1 ligand and PD-1. In another embodiment, the assay provides a method for identifying antibodies that modulate the interaction between a PD-1 ligand and a B7 polypeptide.

In one embodiment, the invention relates to assays for screening such candidates or testing for such antibodies: which binds or modulates the activity of PD-1, PD-L1, or PD-L2, e.g., modulates the ability of a polypeptide to interact with (e.g., bind to) its cognate binding partner. In one embodiment, the method of identifying an antibody that modulates an immune response involves determining the ability of the antibody to modulate, e.g., enhance or inhibit, the interaction between PD-1 and a PD-1 ligand and further determining the ability of the antibody to modulate the interaction between the PD-1 ligand and a B7 polypeptide. In one embodiment, an antibody is selected that modulates the interaction between the PD-1 ligand and PD-1 (e.g., does not modulate the interaction between the PD-1 ligand and the B7 polypeptide). In another embodiment, antibodies are selected that modulate the interaction between the PD-1 ligand and the B7 polypeptide (e.g., do not modulate the interaction between the PD-1 ligand and PD-1).

In another embodiment, a method of identifying an antibody that reduces an immune response involves: determining the ability of the candidate antibody to enhance the interaction between the PD-1 ligand and the B7 polypeptide; and selecting an antibody that inhibits the interaction between the PD-1 ligand and the B7 polypeptide. In another embodiment, a method of identifying an antibody that reduces an immune response involves: determining the ability of the candidate antibody to enhance the interaction between the PD-1 ligand and PD-1; and selecting an antibody that enhances the interaction between the PD-1 ligand and PD-1.

In one embodiment, the assay is a cell-based assay comprising contacting a cell expressing PD-1, PD-L1, or PD-L2 with a test antibody and determining the ability of the test antibody to modulate (e.g., stimulate or inhibit) the binding of PD-1 or a PD-1 ligand target to its binding partner. For example, determining the ability of PD-1, PD-1 ligand, or B7 polypeptide to bind to or interact with its binding partner can be accomplished by measuring direct binding or by measuring a parameter of immune cell activation.

For example, in a direct binding assay, PD-1 or PD-1 ligand protein (or its respective target polypeptide) may be bound to a radioisotope or enzymatic label, such that by detecting the labeled protein in the complex, the binding of PD-1 ligand to PD-1 or to the B7 polypeptide can be determined. For example, PD-1 or PD-1 may be used¹²⁵I、³⁵S、¹⁴C or³H is directly or indirectly labelled, and the radioisotope is detected by direct counting by radiation (radiology) or by scintillation counting. Alternatively, the PD-1 or PD-1 ligand may be labeled with an enzyme such as: e.g., horseradish peroxidase, alkaline phosphatase or luciferase, and the detection of the enzyme label can be determined by determining the conversion of the appropriate substrate to product。

It is also within the scope of the invention to determine the ability of a compound to modulate the interaction between PD-1 and PD-1 ligand or between PD-1 ligand and B7 polypeptide without labeling any interactors therein. For example, the interaction between PD-1 and PD-1 ligand or between PD-1 ligand and B7 polypeptide can be detected with its target polypeptide using a microphysiometer (microphysiometer) without labeling PD-1, PD-1 ligand, B7 polypeptide or the target polypeptide (McConnell, H.M. et al (1992) Science 257: 1906-. As used herein, a "microphysiological recorder" (e.g., Cytosensor) is an analytical instrument that utilizes light-addressable potentiometric sensors (LAPSs) to measure the rate at which cells acidify their environment. This change in acidification rate can be used as an indicator of the interaction between the compound and the receptor.

In another embodiment, determining the ability of an antibody to interact with a given set of polypeptides can be accomplished by determining the activity of one or more members of the set of polypeptides. For example, the activity of PD-1 or PD-1 ligands can be determined by: detecting induction of a second messenger (e.g., tyrosine kinase activity) by the cell, detecting catalytic/enzymatic activity of an appropriate substrate, detecting induction of a reporter gene comprising a target response regulatory element operably linked to a nucleic acid encoding a detectable marker, chloramphenicol acetyltransferase, or detecting a cellular response modulated by PD-1 or a PD-1 ligand. Determining the ability of an antibody to bind to or interact with the polypeptide can be accomplished, for example, by measuring the ability of a compound in a proliferation assay to modulate co-stimulation or inhibition of immune cells, or by interfering with the ability of the polypeptide to bind to an antibody that recognizes a portion thereof.

When added to an in vitro assay, antibodies that block or inhibit the interaction of PD-1 ligand with a co-stimulatory receptor, as well as antibodies that promote PD-1 ligand-mediated inhibitory signals, may be identified by their ability to inhibit immune cell proliferation and/or effector function or induce anergy. For example, the cells can be cultured in the presence of an agent that stimulates signal transduction by activating the receptor. A variety of accepted cell activation readers can be used to measure cell proliferation or effector functions (e.g., antibody production, cytokine production, phagocytosis) in the presence of an activator. The ability of the test antibody to block this activation can be readily determined by measuring the ability of the antibody to achieve the measured reduction in proliferation or effector function using techniques known in the art.

For example, antibodies of the invention can be tested in T cell assays for their ability to inhibit or enhance co-stimulation, such as Freeman et al, (2000) j.exp.med.192: 1027 and Latchman et al (2001) nat. Immunol.2: 261. CD4+ T cells can be isolated from human PBMCs and stimulated with activated anti-CD 3 antibodies. By passing³H thymidine binding can measure T cell proliferation. Analysis was performed with or without CD28 co-stimulation. Similar assays can be performed with Jurkat T cells and PHA blasts from PBMC.

In yet another embodiment, the assay of the invention is a cell-free assay in which PD-1 or a PD-1 ligand, or a biologically active portion thereof, is contacted with a test antibody and the ability of the test antibody to bind to the polypeptide, or biologically active portion thereof, is determined. Binding of the test antibody to PD-1 or a PD-1 ligand polypeptide can be determined directly or indirectly as described above. In yet another embodiment, the analyzing comprises: contacting a polypeptide or biologically active portion thereof with a binding partner thereof to form an assay mixture, contacting the assay mixture with a test antibody, and determining the ability of the test antibody to interact with the polypeptide in the assay mixture, wherein determining the ability of the test antibody to interact with the polypeptide comprises: determining the ability of the test antibody to preferentially bind to the polypeptide or biologically active portion thereof relative to the binding partner.

For example, the ability of the test antibody to block this interaction can be tested by forming an assay mixture with the PD-1 ligand and the PD-1 polypeptide, and determining the ability of PD-1 to bind the PD-1 ligand and determining the ability of the PD-1 ligand to bind the PD-1 polypeptide by one of the methods described above for determining binding. Determination of the ability of a PD-1 polypeptide to bind a PD-1 ligand and determination of the ability of a PD-1 ligand to bind a B7 polypeptide can also be accomplished using techniques such as the real-time Biomolecule Interaction Assay (BIA) (Sjolander, S.and Urbaniczky, C. (1991) anal. chem.63: 2338-. As used herein, "BIA" is a technique to study biospecific interactions in real time without labeling any interactors (e.g., BIA nuclei). Changes in the optical phenomena of Surface Plasmon Resonance (SPR) can be used as an indicator of real-time reactions between biological polypeptides. PD-1, PD-1 ligand and B7 polypeptide can be immobilized on a BIA core plate, and binding of the antibody to PD-1, PD-1 ligand and B7 polypeptide can be examined. An example of using the BIA technique is described by Fitz et al (1997) Oncogene 15: 613, to (i).

The cell-free assays of the invention are suitable for soluble proteins and/or membrane-bound forms of proteins (e.g., PD-1 ligand or PD-1 protein or a biologically active portion thereof, or PD-1 ligand or a binding partner to which PD-1 binds). In the case of cell-free assays using membrane-bound forms of the protein (e.g., cell surface PD-1 ligand or PD-1 receptor), it may be desirable to use a solubilizing agent to keep the membrane-bound form of the protein solubilized. Examples of such solubilizing agents include: nonionic detergents, e.g. N-octyl glucoside, N-dodecyl maltoside, octanoyl-N-methylglucamide, decanoyl-N-methylglucamide, TritonX-100、TritonX-114、ThesitIsotridecylpoly (glycol ether)_n3- [ (3-Cholamidopropyl) dimethylamino (aminominio)]-1-propanesulfonate (CHAPS), 3- [ (3-cholamidopropyl) dimethylamino]-2-hydroxy-1-propanesulfonate (CHAPSO) or N-dodecyl ═ N, N-dimethyl-3-amino-1-propanesulfonate.

In one or more embodiments of the above assay methods, it may be desirable to immobilize the PD-1, PD-1 ligand, and B7 polypeptide or appropriate target polypeptide, to help separate one or both of the proteins in complexed form from uncomplexed form, and to thereby accommodate automation of the assay. Binding of the test antibody to PD-1 or the PD-1 ligand can be achieved in any vessel suitable for holding the reactants. Examples of such containers include: microtiter plates, test tubes, and microcentrifuge tubes. In one embodiment, a fusion protein may be provided that: it adds a domain that binds one or both of the proteins to the matrix. For example, glutathione-S-transferase/PD-1, PD-1 ligand or B7 polypeptide fusion protein or glutathione-S-transferase/target fusion protein can be adsorbed onto glutathione agarose beads (Sigma Chemical, St. Louis, Mo.) or glutathione-derivatized microtiter plates, which are then conjugated to test compounds, and the mixture incubated under conditions conducive to complex formation (e.g., physiological conditions of salt and pH). After incubation, the beads, in the case of beads in which the matrix is immobilized, or the wells of the microtiter plate, are washed to remove any unbound components, and the complexes are determined, either directly or indirectly, e.g., as described above. Alternatively, the complex can be dissociated from the matrix and the level of binding or activity of PD-1, PD-1 ligand, or B7 polypeptide determined using standard techniques.

In an alternative embodiment, determining the ability of a test compound to modulate the activity of PD-1 or a PD-1 ligand can be accomplished by: determining the ability of the test antibody to modulate the activity of a polypeptide acting downstream of PD-1 or a PD-1 ligand, e.g., a polypeptide that interacts with a PD-1 ligand or a polypeptide that acts downstream of PD-1, e.g., by interacting with the cytoplasmic domain of PD-1. For example, the level of the second messenger can be determined, the activity of the reactant polypeptide on the appropriate target can be determined, or the binding of the reactant to the appropriate target can be determined as described above.

The invention further relates to novel antibodies identified by the screening assays described above. Thus, it is within the scope of the invention to further employ antibodies identified as described herein in appropriate animal models. For example, an antibody identified as described herein can be used in animal models to determine the efficacy, toxicity, or side effects of treatment with the antibody. Alternatively, antibodies identified as described herein can be used in animal models to determine the mechanism of action of the antibody. Furthermore, the invention relates to the use of novel antibodies identified by the above screening assays for the treatments described herein.

2.Prophylactic method

In one aspect, the invention relates to methods for preventing a disease or disorder associated with a deleterious or less than ideal immune response in an individual. For example, an individual at risk of disease can be identified that would benefit from treatment with the claimed antibodies or methods by any diagnostic or prognostic assay known in the art or a combination of diagnostic or prognostic assays known in the art. Prophylactic antibody administration can be performed prior to manifestation of a condition associated with a deleterious or less than ideal immune response. Appropriate antibodies for treatment can be determined based on clinical signs, and can be identified for treatment, for example, using the screening assays described herein.

3.Method of treatment

Another aspect of the invention relates to therapeutic methods for modulating an immune response, e.g., by modulating the interaction between PD-1 and a PD-1 ligand and/or between a PD-1 ligand and a B7 polypeptide. For example, modulation of the interaction between PD-1 and PD-1 ligand or between PD-1 ligand and B7 polypeptide results in modulation of the immune response. Thus, in one embodiment, an antibody that blocks the interaction between PD-1 and a PD-1 ligand may prevent inhibitory signaling. PD-1 ligands may also enhance the costimulatory signal of T cells. Thus, in another embodiment, an antibody that prevents the PD-1 ligand from providing a costimulatory signal can inhibit T cell costimulation.

These modulatory antibodies can be administered in vitro (e.g., by contacting a cell with the antibody), or alternatively in vivo (e.g., by administering the agent to a subject). The invention therefore relates to a process as follows: for example, by modulating the interaction between a PD-1 ligand and a PD-1 or B7 polypeptide, individuals suffering from a disease or disorder that would benefit from modulation of the immune response are treated.

4.Immune responseIs adjusted to fall

Various embodiments of the invention relate to up-regulating the inhibitory function of a PD-1 ligand or down-regulating the co-stimulatory function of a PD-1 ligand to down-regulate an immune response. Downregulation may be in the form of suppressing or blocking an ongoing immune response, or may include preventing induction of an immune response. The function of activated immune cells may be inhibited by down-regulating immune cell responses or by inducing specific anergy of immune cells, or both.

For example, the immune response can be down-regulated using: an anti-PD-1 ligand antibody that blocks co-stimulation (e.g., while not causing or increasing the interaction between PD-L1 and PD-1) by the PD-1 ligand, or an anti-PD-1 ligand antibody that promotes binding of PD-1 ligand to PD-1 (e.g., while not causing or while inhibiting co-stimulation by the PD-1 ligand).

In one embodiment of the invention, tolerance is induced against a particular antigen by co-administering the antigen and an antibody that blocks co-stimulation with the PD-1 ligand. For example, tolerance may be induced for a particular protein. In one embodiment, an immune response to an allergen or foreign protein that does not require an immune response can be suppressed. For example, patients who frequently receive factor VIII develop antibodies against the coagulation factor. Co-administration of an antibody that blocks PD-1 ligand-mediated co-stimulatory signals or an antibody that stimulates PD-1-mediated inhibitory signals in conjunction with (or through physical linkage with, e.g., cross-linking) recombinant factor VIII can result in down regulation.

In one embodiment, two separate agents that down-regulate the immune response may be combined into a single composition or administered separately (simultaneously or sequentially), thereby more effectively down-regulating the immune cell-mediated immune response in an individual. In addition, a therapeutically active amount of one or more of the subject antibodies can be used in conjunction with other down-regulators to affect an immune response. Examples of other immunomodulators include, without limitation: antibodies that block co-stimulatory signals (e.g., anti-CD 28 or ICOS), antibodies that are agonists of CTLA4 and/or antibodies against other immune cell markers (e.g., anti-CD 40, anti-CD 40 ligand, or anti-cytokine), fusion proteins (e.g., CTLA4-Fc), and immunosuppressive drugs (e.g., rapamycin, cyclosporine a, or FK 506).

Downregulation or prevention of PD-1 ligand co-stimulation, or promotion of the interaction between PD-1 ligand and PD-1 may be used to downregulate the immune response as follows: for example, in the case of transplantation of tissues, skin and organs, in Graft Versus Host Disease (GVHD) or in inflammatory diseases such as systemic lupus erythematosus and multiple sclerosis. For example, blockade of immune cell function results in reduced tissue destruction in tissue transplantation. Generally, in tissue transplantation, rejection of the graft is initiated by recognition of the graft as foreign by immune cells, followed by an immune response that destroys the graft. Administration of an antibody that inhibits co-stimulation by PD-1 ligand, either alone or in conjunction with another down-regulator, prior to or simultaneously with transplantation, may promote inhibition of signal production. In addition, inhibition of the co-stimulatory signal of the PD-1 ligand or promotion of the inhibitory signal of the PD-1 ligand or PD-1 may also be sufficient to render the immune cells anergic (anergize), thereby inducing tolerance in the individual. The necessity of repeated administration of these blockers can be avoided by blocking the PD-1 ligand-mediated costimulatory signals to induce long-term tolerance.

Blocking the co-stimulatory function of other polypeptides may also be desirable in order to achieve sufficient immunosuppression or tolerance in an individual. For example, it may be desirable to block the function of B7-1, B7-2, or B7-1 and B7-2 by administering (separately or together in a single composition) a combination of soluble forms prior to or concurrently with transplantation: a peptide having the activity of each of these antigens, a blocking antibody against these antigens, or a blocking small molecule. Alternatively, it may be desirable to promote the inhibitory activity of PD-1 ligand or PD-1 and to inhibit the co-stimulatory activity of B7-1 and/or B7-2. Other downregulators that can be used in connection with the downregulation methods of the present invention include: for example, down-regulators of inhibitory signals conducted by CTLA4, soluble forms of CTLA4, antibodies that activate inhibitory signals by CTLA4, blocking antibodies against other immune cell markers or other receptor ligand pairs in soluble form (e.g., agents that disrupt the interaction between CD40 and CD40 ligands (e.g., anti-CD 40 ligand antibodies)), anti-cytokine antibodies, or immunosuppressive drugs.

Modulation of the decline in immune response may also be useful in the treatment of autoimmune diseases. Many autoimmune diseases result from inappropriate immune cell activation, which is reactive against self tissues, and which promotes the production of cytokines and autoantibodies involved in the pathology of the disease. Preventing the activation of autoreactive immune cells can reduce or eliminate disease symptoms. Administration of the following reagents can be used to inhibit immune cell activation and prevent autoantibodies or cytokine production that may be involved in the disease process: it blocks co-stimulation of immune cells by disrupting the interaction between PD-1 ligand and B7 polypeptide, or by promoting the interaction between PD-1 ligand and PD-1, without modulating the interaction between PD-1 ligand and B7 polypeptide or while downregulating the interaction between PD-1 ligand and B7 polypeptide. Furthermore, agents that promote the inhibitory function of PD-1 ligands or PD-1 may induce antigen-specific tolerance of autoreactive immune cells, which may lead to long-term remission of the disease. The efficacy of an agent to prevent or alleviate an autoimmune disease can be determined using a number of well-characterized animal models of human autoimmune disease. Examples include systemic lupus erythematosus in murine experimental autoimmune encephalitis, MRL/lpr/lpr mice or NZB-hybrid mice, murine autoimmune collagenous arthritis, NOD and BB rat diabetes, and murine experimental myasthenia gravis (see, e.g., Paul ed., Fundamental Immunology, Raven Press, New York, Third Edition 1993, Chapter 30).

Inhibition of immune cell activation, e.g., by inhibiting IgE production, is therapeutically applicable in the treatment of allergy and allergic reactions. Antibodies that promote PD-1 ligand or PD-1 inhibitory function can be administered to allergic subjects to inhibit immune cell-mediated allergic reactions in the individual. By exposure to an allergen in combination with an appropriate MHC polypeptide, inhibition of immune cell PD-1 ligand co-stimulation or stimulation of PD-1 ligand or PD-1 inhibitory pathway can be accompanied. The allergic reaction itself may be systemic or local depending on the allergen entry pathway and the pattern of IgE deposition on mast cells or basophils. Thus, inhibition of immune cell-mediated allergic reactions can be achieved by local or systemic administration of inhibitory forms of agents that inhibit the interaction of PD-1 ligand with co-stimulatory receptors or antibodies that promote the inhibitory function of PD-1 ligand or PD-1.

Inhibition of immune cell activation by blocking PD-1 ligand co-stimulation or by promoting the interaction between PD-1 ligand and PD-1 may also be of central importance in the treatment of immune cell viral infections. For example, in Acquired Immune Deficiency Syndrome (AIDS), immune cell activation stimulates viral replication. Modulation of these interactions can lead to inhibition of viral replication, thereby ameliorating the AIDS process. Modulation of these interactions may also be used to promote maintenance of pregnancy. PD-1 ligands are typically highly expressed in placental trophoblasts, i.e., layers of cells that form the interface between the mother and fetus and can act to prevent maternal rejection of the fetus. Women at risk of spontaneous abortion due to immunological rejection of the embryo or fetus (e.g., women who have had spontaneous abortion or women who have difficulty in conception) may be treated with agents that modulate these interactions.

Modulation of the decline in immune response by modulation of PD-1 ligand co-stimulation or by modulation of PD-1 ligand/PD-1 binding may also be useful in treating autoimmune attack in autologous tissues. For example, PD-1 ligand is often highly expressed in the heart and can protect the heart from autoimmune attack. It is demonstrated by the fact that: balb/c PD-1 knockout mice present a large autoimmune challenge to the heart as a thrombus formation. Thus, by modulating these interactions, conditions caused or exacerbated by autoimmune attack (e.g., heart disease, myocardial infarction, or atherosclerosis in this example) may be ameliorated or improved. Thus, it is within the scope of the present invention to modulate conditions exacerbated by autoimmune attack, such as autoimmune diseases (as well as conditions such as heart disease, myocardial infarction and atherosclerosis).

5.Up-regulation of immune response

Also therapeutically useful are means of blocking the interaction of PD-1 ligand with PD-1 or B7-1 as a means of up-regulating the immune response. The up-regulation of the immune response may be in the form of: enhance an existing immune response or elicit an initial immune response. For example, enhancing an immune response using the subject compositions and methods can be useful in the context of microbial (e.g., bacterial, viral, or parasitic) infection. In one embodiment, an antibody that blocks the interaction of a PD-1 ligand with PD-1 is used to enhance the immune response. Such antibodies (e.g., non-activating antibodies that block PD-L1 binding to PD-1) are therapeutically useful in situations where up-regulation of antibody and cell-mediated responses would be beneficial. Exemplary conditions include viral skin diseases such as herpes or herpes zoster, in which case such agents may be provided topically to the skin. In addition, systemic viral diseases, such as influenza, common cold and encephalitis, are alleviated by systemic administration of such agents.

Alternatively, the immune response of an infected patient can be enhanced by ex vivo methods, e.g., by removing immune cells from the patient, contacting immune cells with an antibody that blocks the interaction of PD-1 ligand with PD-1 in vitro, and reintroducing stimulated immune cells into the patient in vitro.

In certain instances, it may be desirable to further administer other agents that upregulate the immune response, e.g., other forms of members of B7 family that transduce signals through costimulatory receptors, to further enhance the immune response.

Antibodies that block the interaction of PD-1 ligand with PD-1 or B7-1 can be used prophylactically in vaccines directed against a variety of polypeptides (e.g., polypeptides derived from pathogens). Immunity to a pathogen (e.g., a virus) can be induced by vaccination with viral proteins in an appropriate adjuvant and antibodies that block the interaction of PD-1 ligand with PD-1 or B7-1.

In another embodiment, up-regulation or enhancement of immune response function can be used to induce tumor immunity, as described herein.

In another embodiment, an immune response can be stimulated by the methods described herein to overcome preexisting tolerance. For example, by administering an antibody that blocks the interaction of a PD-1 ligand with PD-1, an immune response can be induced against an antigen to which a subject is unable to administer a significant immune response, e.g., to a self-antigen, such as a tumor-specific antigen. In one embodiment, autoantigens, such as tumor specific antigens, may be co-administered. In another embodiment, an immune response can be stimulated against an antigen (e.g., a self-antigen) to thereby treat a neurological disease. In another embodiment, the subject agents may be used as adjuvants to facilitate the response to foreign antigens during an automated immunization process.

In one embodiment, the immune cells are obtained from a subject and cultured ex vivo in the presence of an antibody described herein, thereby expanding the immune cell population and/or promoting immune cell activation. In further embodiments, the immune cells are then administered to the subject. As is known in the art, immune cells can be stimulated in vitro, for example, by providing an initial activation signal and a co-stimulation signal to the immune cells. Multiple agents may also be used to co-stimulate immune cell proliferation. In one embodiment, the immune cells are cultured ex vivo according to the method described in PCT application No. WO 94/29436. The co-stimulatory polypeptide may be soluble, attached to a cell membrane or attached to a solid surface such as a bead.

Further embodiments of the invention are mentioned in the examples below. The invention is further illustrated by the following examples, which should not be construed as further limiting. The contents of all references, patents, and published patent applications cited throughout the sequence listing, figures, and this application are expressly incorporated herein by reference.

Examples

The following examples describe the generation of monoclonal antibodies suitable for therapeutic purposes targeting human PD-1, PD-L1 and PD-L2. Complex human anti-human PD-1, PD-L1, and PD-L2 antibodies were generated from murine anti-human EH12.2H7, 29E.2A3, and 24F.10C12 antibodies, respectively. Fragments of human V region sequences are derived from unrelated human antibody (germline and non-germline) sequence databases. Each selected sequence fragment (and the junction between fragments) was tested for its potential to bind MHC class II using a binding prediction algorithm. All final composite human antibody sequence variants were designed to avoid T cell epitopes. The synthetic oligonucleotides encoding combinations of human sequence fragments are used to generate the V region genes of the composite human antibodies. It is then cloned into a vector containing human constant regions, and antibodies are generated and tested for binding to the antigen of interest by competition ELISA.

Example 1: design of composite human antibody variable region sequence

Structural models of mouse EH12.2H7, 29e.2a3, and 24 f.10c12V regions were generated using Swiss Pdb, and analyzed to identify important "limiting" amino acids in the mouse V region, which may be necessary for the binding properties of the antibody. Only the residues contained in the CDRs are considered important, including the CDR residues defined under the Kabat and Chothia definitions.

From the above analysis, it was thought that a composite human form of EH12.2H7, 29e.2a3, and 24f.10c12 could be generated with a wide range of sequences outside the CDRs, but with a narrow range of possible alternative residues within the CDR sequences. Preliminary analysis shows that corresponding sequence fragments from several human antibodies can be combined to generate CDRs similar or identical to mouse sequences. For the CDR-out and flanking regions, a broad selection of human sequence fragments was identified as a possible component of the variable regions of novel composite human antibodies.

Based on the above analysis, a large panel of preliminary sequence fragments useful for generating EH12.2H7, 29e.2a3, and 24f.10c12 composite human antibody variants was selected and analyzed by MHC class II binding prediction algorithms and BLAST, which searches a proprietary database of T cell epitopes associated with known antibody sequences. Discarding such sequence fragments: where potential MHC class II binding peptides are identified or evaluated against a database of known T cell epitopes as significant hits (hit). This resulted in a reduction in fragment sets, which were again analyzed as above for combinations of these fragment sets, thereby ensuring that the junctions between fragments were free of potential T cell epitopes. The selected fragments are then combined to generate heavy and light chain variable region sequences for synthesis. For all three antibodies, five heavy chains and four light chains were constructed with the sequences detailed below;

antigen composite VH sequence composite VK sequence

PD-1 FIG. 2(A-E) FIG. 3(A-D)

PD-L1 FIG. 4(A-E) FIG. 5(A-D)

PD-L2 FIG. 6(A-E) FIG. 7(A-D)

The sequence fragments of these composite human antibody sequences used to generate antibodies against PD-1, PD-L1, and PD-L2, respectively, are detailed in tables 1, 2, and 3.

TABLE 1 sources (derivations) of human sequence fragments constituting anti-PD-1 composite human antibodies

Table 1 continues:

TABLE 2 sources of human sequence fragments constituting anti-PD-L1 composite human antibodies

Table 2 continues:

table 2 continues:

TABLE 3 sources of human sequence fragments constituting anti-PD-L2 composite human antibodies

Table 3 continues:

example 2: generation and testing of composite human antibodies

The composite human antibody VH and VK region genes for EH12.2H7, 29e.2a3, and 24f.10c12 initial variant 1 were synthesized using a series of overlapping oligonucleotides annealed, ligated, and PCR amplified to give full-length synthetic V regions (fig. 2A, 3A, 4A, 5A, 6A, and 7A). For each of the composite human antibodies, the initial variant 1 was used as a template, and subsequent sequence variants were constructed using long overlapping oligonucleotides and PCR. The assembled variants were then cloned directly into an expression vector (FIG. 1) and their sequence verified.

All combinations of chimeric and complex heavy and light chains (i.e., 20 pairs of each antibody) were stably transfected into NS0 cells by electroporation and selected in medium containing 200nM methotrexate (high glucose DMEM with L-glutamine and sodium pyruvate, 5% ultra-low IgG FCS, pen/strep, all from Invitrogen). Expression levels of several anti-drug colonies for each construct were examined and the best expression line was selected and frozen under liquid nitrogen.

Supernatants from each of the combinatorial best expressing lines were quantitated relative to IgG 1/kappa standard using Fc capture type K light chain detection ELISA. The quantitative supernatants were then tested in a competitive ELISABinding to its target antigen. Human Fc-PD-1, Fc-PD-L1 or Fc-PD-L2 (R) in carbonate buffer pH 9.6 at 50. mu.l/well 1. mu.g/ml at 4 ℃&D system) coating 96-well Maxisorb^TMPlates (Nunc) were left overnight. Repeated titrations (ranging from 0.0078 μ g/ml to 8 μ g/ml) of mouse reference antibody and pooled with biotinylated mouse reference antibody at constant concentration (40ng/ml) in PBS pH 7.4/2% BSA. A100. mu.l/well titration was added to wash (4X in PBS pH 7.4/0.05% Tween 20) the assay plates and incubated for 1 hour at room temperature. Plates were washed as above and streptavidin HRP (Sigma) diluted in 1/1000 in PBS pH 7.4/2% BSA was added at 100. mu.l/well and incubated for an additional 1 hour at room temperature. After washing again, bound biotinylated reference antibody was detected with 100 μ l/well OPD substrate. The absorbance was measured at 490nm and the binding curve of the test antibody was compared to a murine reference standard. Absorbance was plotted against sample concentration and a straight line was fitted through each data set. The equation of this line was used to calculate the concentration (IC) required to inhibit 50% of biotin-EH12.2H7 binding to PD-1, biotin-29 E.2A3 binding to PD-L1, and biotin-24 F.10C12 binding to human PD-L2₅₀)。

Selecting the best IC₅₀The antibody of (3), all of these variant cell lines of the EH12.2H7, 29e.2a3, and 24f.10c12 antibodies were increased to 100ml and grown to saturation. The antibodies were purified from each culture by protein a affinity chromatography. Briefly, the supernatant pH was adjusted with 0.1 volume of 10 XPBS pH 7.4 and passed through a 1ml Mab Select Sure protein A column (GE Healthcare). The column was washed with 10 volumes of PBS pH 7.4 before elution with 50mM citrate buffer pH 3.0. 1ml fractions were collected and immediately neutralized with 0.1ml of 1m Tris-HCl pH 9.0. Protein containing fractions (determined by absorbance at 280 nm) were collected, buffer exchanged in PBS pH 7.4, and purified antibody was stored at +4 ℃. FIGS. 8A-C show SDS-PAGE gels of 1. mu.g of each antibody stained with Coomassie blue. Antibody concentration was calculated by UV absorption based on calculated molar extinction coefficient, e.g. E of EH12.2H7 at 280nm _0.1％1.61E, 29E.2A3 at 280nm_0.1％1.46, and E at 280nm of 24F.10C12_0.1％＝1.57。

Binding of the purified antibody to human Fc-PD-1, Fc-PD-L1 or Fc-PD-L2 was tested by competition ELISA as described above. The test antibody was titrated repeatedly from 0.0625. mu.g/ml to 8.0. mu.g/ml. The absorbance at 490nm was measured and plotted against the concentration of test antibody (FIGS. 9A-C, 10A-C).

Table 4 summarizes the results of the combination of complex VH and VK variant sequences for anti-PD-1, PD-L1, and PD-L2 antibodies. For EH12.2H7, all humanized antibodies had increased IC50 relative to the mouse reference, in particular a two-fold increase in VH4/VK3 binding. In the case of 29e.2a3, variants VH2/VK1 and VH2/VK4 had equivalent binding to the mouse reference, while the binding of variants VH2/VK2 and VH4/VK2 was reduced by 1.75 and 1.36 fold, respectively. For 24f.10c12, all selected variants had similar but slightly reduced binding relative to the mouse reference (1.13 fold).

Table 4: IC50 value of PD-1, PD-L1 and PD-L2 composite human antibody sequence variants

As a result of these experiments, a composite human antibody specific to human PD-1, PD-L1 and PD-L2 was constructed from amino acid sequence fragments completely derived from the variable regions of an unrelated human antibody. All CDRs and framework regions in the composite human antibody variants include more than one unrelated human sequence fragment (derived from the human sequence database), and all composite human antibodies are specifically designed to avoid T-cell epitopes. Four primary Candidate antibodies (Candidate) were initially selected to bind to human PD-1, PD-L1 or PD-L2, demonstrating binding within twice that of mouse antibodies based on subsequent analysis.

Example 5: enhanced stimulation of T cell activation by inhibition of PD-1: PD ligand interaction

The PD-1 signaling pathway inhibits moderate TCR/CD28 costimulatory signaling, with a first reduction in cytokine production without concomitant reduction in T cell proliferation. As TCR/CD28 costimulatory signals are diminished, the PD-1 pathway predominates, with a dramatic decrease in cytokine production, accompanied by a decrease in proliferation. Therefore, in order to confirm that inhibition of the PD-1 pathway by inhibiting the interaction with PD-L1 or PD-L2 using the composite human antibody of the present invention enhances T cell activation, Mixed Lymphocyte Reaction (MLR) was performed.

Immature bone marrow dendritic cells are isolated by culturing human peripheral blood mononuclear cells in IL-4 and GM-CSF, exposing the immature dendritic cells to IL-1 β, TNF- α, IL-6, and PGE₂The inflammatory mixture of (a), causing the development of mature dendritic cells with APC function. However, addition of IL-10 to inflammatory cytokines during the maturation phase also functions only with APC from 1/6 to 1/3.

T cell activation assay (MLR) was performed using IL-10 treated dendritic cells as APC in the presence of a composite human antibody of PD-1, PD-L1 and/or PD-L2 or a control antibody. The addition of anti-PD-1, anti-PD-L1, and/or PD-L2 mAb to cultures of IL-10 treated dendritic cells and allogeneic T cells was expected to result in increased T cell proliferation and cytokine expression relative to IgG treated culture controls. The combination of anti-PD-1 antibodies with anti-PD-L1 antibodies, anti-PD-L2 antibodies, also resulted in a greater increase in stimulation than was seen with either antibody alone.

Example 6: inhibition of the PD-1 pathway in Chronically Infected Mice (Chronically-Infected Mice)

The effect of chronic viral infection on CD8T cell function was studied using mice infected with various lymphocytic choriomeningitis virus (LCMV) strains. LCMV Armstrong strain causes such acute infections: cleared within 8 days, leaving a population of highly functional, quiescent memory CD8T cells that survived for long periods of time. In contrast, LCMV Cl-13 strain establishes persistent infection in the host, manifested as viremia that persists for up to 3 months.

To determine that blocking PD-1 signaling restores T cell function and enhances viral control during chronic LCMV infection, PD-1 signaling during chronic LCMV infection was disrupted using a combination human anti-PD-1, anti-PD-L1, and/or anti-PD-L2 antibody of the invention. Antibodies were administered to mice infected with LCMV Cl-13 every 3 days from day 23 to day 37 post-infection. Several fold increases of LCMV-specific CD8T cells were expected in treated mice on day 37 relative to untreated controls. It is also expected that later induction of proliferation will be specific for CD8T cells, and the number of CD4T cells in the spleen of treated and untreated mice will likely be approximately the same.

In addition to increased proliferation of CD8T cells, inhibition of PD-1 signaling is expected to also result in increased production of antiviral cytokines in virus-specific CD8T cells the production of IFN- γ and TNF- α by CD8T cells in treated mice will likely be several-fold higher than in untreated mice.

CD4T cells play a key role in the generation and maintenance of CD8T cell responses. In this regard, CD8T cells, which displace CD4T cells, are unable to confer a normal immune response and are therefore often referred to as "useless T cells". In addition, chronic LCMV infection is more severe with CD4T cell depletion. Therefore, useless T cells generated during LCMV-Cl-13 infection showed even more severe functional impairment than T cells generated in the presence of CD4T cells.

CD4T cells were depleted upon LCMV-Cl-13 infection, and mice were treated with the composite human anti-PD-1, anti-PD-L1 and/or anti-PD-L1 antibodies of the present invention on days 46 to 60 post-infection. It is expected that treated mice will likely have several times more LCMV-specific CD8T cells in the spleen after treatment than untreated control mice. Growth of this virus-specific CD8T cell in treated mice may result in increased proliferation as measured by the BrdU incorporation method. BrdU analysis was performed by adding 1mg/ml BrdU to the drinking water during treatment and staining according to the manufacturer's protocol (BD Biosciences, san diego, Calif.).

To determine that inhibition of PD-1 signaling increases the lytic activity of unwanted, depleted, virus-specific CD8T cells, post-treatment utilization⁵¹The Cr release assay (Wherry et al, 2003. J.Virol.77: 4911-27) detects the in vitro lytic activity of virus-specific CD8T cells. Viral titers in spleen, liver, lung and serum were expected to decrease several fold after 2 weeks of treatment relative to untreated mice.

Example 7: administration of PD-1 signaling inhibitor vaccines

One approach to promoting T cell responses during persistent infection is therapeutic vaccination. The principle of the method is as follows: during chronic viral infection, endogenous antigens may not be present in an optimal or immunogenic manner; and providing the antigen in the form of a vaccine may provide more effective stimulation of virus-specific T cells and B cells. Using a chronic LCMV model, mice were given a recombinant vaccinia virus expressing LCMV GP33 epitope as a therapeutic vaccine (VVGP33), which resulted in a modest increase in CD8T cell responses in some chronically infected mice. The therapeutic vaccine is inoculated with the compound human anti-PD-1 antibody, anti-PD-L1 antibody and/or anti-PD-L2 antibody. It is expected that LCMV-specific T cell responses will be promoted to higher levels than either treatment alone, and that the effect of the combination treatment will likely be better than additive.

Example 8: chimpanzees as model for persistent HCV infection immunotherapy

Chimpanzees provide a model for persistence of human HCV. Defects in T cell immunity that lead to persistence of the lifetime virus include a deficiency in HCV-specific CD4 helper T cells and a diminished or altered activity of CD8 effector T cells. Persistent infection chimpanzees are treated with a combination human anti-PD-1 antibody, anti-PD-L1 antibody, and/or anti-PD-L2 antibody of the invention. The efficacy of blocking the inhibitory pathway was determined in conjunction with vaccination with recombinant structural and non-structural HCV proteins, and whether this strategy could increase the frequency and longevity of virus-specific memory T cells. T cell immune deficiency has unique HCV specificity in persistently infected humans and chimpanzees. Antiviral activity can then be restored by administering to the chimpanzees humanized monoclonal antibodies that block signaling by these molecules.

Persistent infection chimpanzees are treated with a combination human anti-PD-1 antibody, anti-PD-L1 antibody, and/or anti-PD-L2 antibody of the invention. Following treatment with the antibody, the humoral and cellular immune responses and HCV RNA load were determined. Samples were then collected at monthly intervals on weeks 1, 2, 3, 5, and 8. The sample includes: 1) sera for transaminase, autoantibody, HCV neutralizing antibody and cytokine response analysis, 2) plasma for viral load and genome evolution, 3) PBMC for immunity, co-stimulatory/inhibitory receptor expression and functional in vitro assays, 4) fresh (unfixed) liver for intrahepatic lymphocyte and RNA isolation, and 5) fixed (formalin/paraffin embedded) liver for histological and immunohistochemical analysis. Regional lymph nodes were also collected at 2 or 3 time points and evaluated for expression of co-inhibitory molecules and splice variants by immunohistochemistry and molecular techniques.

To determine whether HCV antigen vaccination potentiated antibody therapeutic effects, chimpanzees were treated as follows: 1) intramuscular immunizations of recombinant envelope glycoproteins E1 and E2 (in MF59 adjuvant) and other proteins (nuclear and NS3, 4 and 5 made with ISCOMS) were performed at weeks 0, 4 and 24; 2) intramuscular immunization of vaccines for use with the antibodies of the invention, but co-administered with a combination human anti-PD-1 antibody, anti-PD-L1 antibody and/or anti-PD-L2 antibody of the antibodies of the invention, is performed. Following immunization, HCV-specific T and B cell responses were monitored at monthly intervals for a period of 1 year.

Markers detected on HCV tetramer positive T cells and total T cells in this assay include differentiation markers (e.g., CD45RA/RO, CD62L, CCR7, and CD27), activation markers (e.g., CD25, CD69, CD38, and HLA-DR), survival/proliferation markers (e.g., bcl-2 and Ki67), cytotoxic potential markers (e.g., granzyme and perforin), and cytokine receptor markers (CD122 and CD 127). The correlation of interest lies between the pre-treatment levels of chemokine IP-10 and the response to PEG IFN-. gamma./ribavirin. IP-10 levels were measured to investigate the potential correlation between negative regulatory pathways or HCV-specific T cell responses and IP-10 levels. PBMC inhibit the expression of receptors and ligands by flow cytometry.

Example 9: enhancement of SIV-specific immunity in vivo by PD-1 blockade

The immune recovery potential of PD-1 blockade during chronic Simian Immunodeficiency Virus (SIV) infection was examined in rhesus monkeys. A study was performed on 14 Indian rhesus macaques (rhesus macaque) infected with SIV. 8 macaques were used in the chronic early phase with 20050% SIV251 Tissue Culture Infectious Dose (TCID)₅₀) An intravenous infection was performed. 6 macaques were used for chronic advanced stage, 3 with SIV251 for intrarectal infection and 3 with SIV239 for intravenous infection. All macaques, except RDb11, were negative for the Mamu B08 and Mamu B17 alleles. RDb11 are positive for the Mamu B17 allele.

In vivo antibody therapy: a partially humanized murine anti-human PD-1 antibody (clone EH12-1540) (Dorfman et al, am. J. Surg. Pathol.30: 802-810, 2006) or a control antibody (SYNAGIS) was input to the cynomolgus monkey. The anti-PD-1 antibody has a mouse variable heavy domain (mutated to reduce FcR, complementary binding) linked to human IgG1, and a mouse variable light domain linked to human kappa. Clone EH12 was bound to cynomolgus monkey PD-1 in vitro and blocked the interaction between PD-1 and its ligand. SYNAGIS is a humanized mouse monoclonal antibody (IgG1 κ) specific for the F protein of respiratory syncytial virus. On days 0, 3, 7 and 10, the antibody was administered intravenously at 3mg per kg body weight.

Immune response: peripheral blood mononuclear cells from blood and lymphocytes from a rectal pinch (ping) biopsy were isolated as described previously (Velu et al, J.Virol.81: 5819-. Tetramer staining, intracellular cytokine production and determination of anti-SIV Env binding antibodies were performed as described previously (Amara et al, Science 292: 69-74, 2001; Kannanagnat et al, J.Virol.81: 8468-8476, 2007; Lai et al, Virology 369: 153-167, 2007).

PD-1 blockade was performed early (10 weeks) and late (about 90 weeks) in chronic SIV infection. 9 macaques (5 in the early stage, 4 in the late stage) received anti-PD-1 antibodies, 5 macaques (3 in the early stage, 2 in the late stage) received isotype control antibodies (Synagis, specific for anti-Respiratory Syncytial Virus (RSV)).

PD-1 blockade during chronic SIV infection caused SIV-specific CD8T cells to expand rapidly in the blood of whole macaques. Responses of CD8T cells to two immune major epitopes, Gag CM9(Allen et al, J. Immunol.160: 6062-. Most (> 98%) Gag-CM9 tetramer-specific CD8T cells expressed PD-1 before blocking. Gag-CM9 tetramer-specific CD8T cells expanded rapidly following PD-1 blockade and peaked on days 7-21. At peak response, these levels were approximately 2.5 to 11 fold higher than their respective levels on day 0 (P ═ 0.007) and remained elevated until days 28-45. Similar results were observed in blockade both early and late in chronic SIV infection. A 3-4 fold increase in the frequency of Gag-specific Interferon (IFN) -y positive CD8T cells was also observed in two Mamu a 01 negative animals (RTd11 and RDb11) 14 days after blocking, demonstrating that PD-1 blocking can increase the frequency of virus-specific CD8T cells restricted by non-Mamu a 01 alleles. No SIV-specific CD8T cell expansion was observed in the control antibody-treated macaques.

PD-1 blockade is also associated with active cell division in vivo with a significant increase in the frequency of virus-specific CD8T cells with increased functional properties. Consistent with the rapid expansion of SIV-specific CD8T cells, the frequency of Gag-CM9 tetramer-specific CD8 cells co-expressing Ki67, a marker for proliferating cells, also increased as early as 7 days after block (P ═ 0.01). Likewise, we observed an increased frequency of Gag-CM9 tetramer-specific CD8T cells co-expressing perforin and granzyme B (cytolytic potential; P ═ 0.001 and P ═ 0.03, respectively), CD28 (costimulatory potential; P ═ 0.001), CD127 (proliferative potential; P ═ 0.0003) and CCR7 (lymph node homing potential; 0.001). A 1.5 to 2-fold transient increase in the frequency of Ki67 positive CD8T cells was observed after blocking, which was tetramer negative. This may be due to expansion of CD8T cells and other chronic viral infections of these animals that are specific for other epitopes of Gag and other proteins of SIV. No significant increase in these markers was observed in 3 macaques treated with the control antibody.

No expansion of Tat-TL 8-specific CD8T cells was observed after blocking. This may be due to the fact that the virus is not recognized by Tat-TL 8-specific CD8T cells, since PD-1 blockade is known to cause T cell expansion only when it is simultaneously signaled through a T cell receptor. To test this possibility, the following viral genomes were sequenced: the viral genomes from all 3 Mamu a x 01 positive macaques infected with SIV251 and receiving blocking antibodies early in infection were present in plasma just before the onset of blocking. In fact, mutations in the viral genome corresponding to the epitope region of Tat TL8 were found. All these mutations have been shown or predicted to decrease the binding of Tat SL8/TL8 peptide to Mamu a × 01 MHC molecules and to be not recognized by Tat-SL8/TL8 specific CD8T cells. These results suggest that PD-1 blockade in vivo may not result in T cell expansion specifically off of the viral epitope mutants.

PD-1 blockade also caused expansion of Gag-CM 9-specific CD8T cells at colorectal mucosal tissue (gut), the preferential site of SIV/HIV replication. Although the expansion was significant in 1 of the blood, no expansion was observed in 2 of 7 macaques. In contrast to blood, dilation in the digestive tract peaked later to day 42 and levels ranged from 2 to 3 times relative to their respective day 0 (P0.003). Similar to blood, Gag-CM9 tetramer-specific cells co-expressing Ki67(P ═ 0.01), perforin (P ═ 0.03), granzyme B (P ═ 0.01), and CD28(P ═ 0.01) also increased in the gut after disruption.

More importantly, PD-1 blockade also increased the functional quality of antiviral CD8T cells and resulted in multifunctional cell production that was able to co-produce the cytokines IFN-y, Tumor Necrosis Factor (TNF) - α and Interleukin (IL) -2 during the late phase of infection, Gag-specific IFN- γ positive cells were less frequent the day that PD-1 blockade began in the chronic phase of infection, and were unable to co-express TNF- α and IL-2, however, after blockade, the frequency of IFN- γ positive cells was all increased in 4 cynomolgus macaques treated with PD-1 antibody (P0.03), and they acquired the ability to co-express TNF- α and IL-2, expansion of IFN- γ positive cells peaked at days 14-21, peak levels 2-10 times higher than their respective day 0 levels on day 21, about 16% of total Gag-specific cells co-express all three cytokines, about 30% co-express IFN- γ and TNF- α, which compared to the day 0.1% of total Gag specific cells at day 0, and about 0.01 to about 14% of total IFN- β - α.

To examine the effect of PD-1 on modulating B cell function during chronic immunodeficiency virus infection, the B cell response of SIV infected macaques after PD-1 blockade was characterized. Analysis of PD-1 expression by different B cell subsets before PD-1 blockade showed memory B cells (CD 20)⁺CD27⁺CD21^-) Relative to native B cells (CD 20)⁺CD27^-CD21⁺(ii) a P < 0.001) preferentially expresses PD-1. PD-1 blockade in vivo resulted in a 2 to 8 fold increase in titer of SIV-specific binding antibody by day 28 after blockade (P < 0.001). To further understand this, experiments were conducted on the proliferation of memory B cells from SIV-infected macaques treated simultaneously with anti-PD-1 antibodies and anti-retroviral therapy, and a significant increase in Ki67+ (proliferating) memory B cells was observed as early as day 3, whereas native B cells did not. These results demonstrate that PD-1-PDL is present during chronic SIV infectionPathways may have an effect on regulating B cell dysfunction.

Neutralization analysis showed a two-fold increase in titer against easy-to-neutralize, laboratory-adapted SIV251, no increase in titer against hard-to-neutralize, wild-type SIV251 or SIV 239. Of 2 of 9 animals treated with anti-PD-1 antibody, only minimal (< 2-fold) SIV-specific antibody expansion was observed after blocking. Significantly, the total memory B cell frequency of these 2 animals before blocking (-40% of total B cells) compared to the remaining 7 animals (-60-90% of total B cells), suggesting that the level of SIV-specific memory B cells before blocking may determine the level of expansion of SIV-specific antibodies after blocking.

PD-1 blockade caused a significant reduction in plasma viremia (P0.03) and also prolonged survival of SW infected macaques (P0.001). In 2 of 5 macaques treated with anti-PD-1 antibody early in the chronic phase, viral load declined by day 10 and remained at or below this level until day 90. In 1 macaque, viral load decreased transiently, while in the remaining 2 macaques, viral load increased transiently and returned to pre-blocking levels. In contrast to the early chronic phase, all 4 macaques treated with anti-PD-1 antibody in the late chronic phase showed a transient increase in viremia by day 7, but by day 21 viral load rapidly decreased to levels lower than their respective day 0 levels. However, viral RNA levels returned to pre-blocking levels by day 43. As expected, no significant reduction in plasma viral load was observed in any of the 5 macaques treated with the control antibody. By day 21-28 post-blocking, anti-PD-1-antibody treated animals had levels of viral RNA that were 2-10 fold lower than their respective day 0 levels (P ═ 0.03). By day 150 after blocking, 4 of 5 macaques in the control group died due to AIDS-related symptoms (e.g., loss of appetite, diarrhea, weight loss), while 9 animals in the anti-PD-1-antibody treated group were all alive (P ═ 0.001).

The initial increase in plasma viremia levels observed in all late-treated animals and some early-treated animals may be due to an increased frequency of activated CD4T cells. To determine this, the percentage of Ki67 positive total CD4T cells after blocking and the frequency of CD4T cells producing SIV Gag specific IFN-y (the preferential target of viral replication) were determined. These analyses showed that the percentage of Ki67 positive CD4T cells increased transiently by 7-14 days post-blocking (P ═ 0.002) and the increase in animals treated late in infection was higher than in animals treated early in infection (P ═ 0.015). Also, an increased frequency of Gag-specific CD4T cells was observed, but only in animals treated late in infection. No significant increase in these activated CD4T cells was observed in cynomolgus monkeys treated with the control antibody. These results indicate that activated CD4T cells may contribute to the observed initial rise in plasma viremia levels following blockade.

The viral load set point in plasma and total CD4T cells in blood and gut were similar between the anti-PD-1-antibody treated group and the control antibody treated group before PD-1 blockade began. However, the frequency of Gag CM9+ cells and Gag CM9+ cells co-expressing perforin, granzyme B or CD28 was not similar between the two treatment groups before blocking in vivo. This increases the likelihood of: these differences may contribute to Gag CM9+ cell expansion following PD-1 blockade. To investigate the effect of the frequency of Gag CM9+ cells before blocking on their post-blocking expansion, the anti-PD-1-antibody treatment group was divided into two subgroups based on the frequency of Gag CM9+ cells before the onset of blocking, so that one group had similar levels of Gag CM9+ cells as the control antibody treatment group and the other group had higher levels of Gag CM9+ cells relative to the control antibody treatment group. These subsets were then analyzed for Gag CM9+ cell expansion after blocking. Regardless of whether it was at low or high levels prior to blocking, Gag CM9+ cell expansion was evident in both animal subgroups after PD-1 blocking. Similar results were also observed for subset analyses based on the frequency of Gag CM9+ cells, which co-expressed molecules associated with better T cell function, such as perforin, granzyme B, CCR7, CD127 or CD 28. However, such a trend is observed: animals with higher levels of Gag CM9+ CD28+ cells before blocking expanded better Gag CM9+ CD28+ cells, indicating that expression of CD28 could be a biomarker predictive of PD-1 blocking outcome in vivo.

The above experiments demonstrate that PD-1 blockade with antibodies to PD-1 results in rapid expansion of virus-specific CD8T cells with improved functional quality. This enhanced T cell immunity is also seen in the blood, the main SIV infected pool, in the digestive tract. PD-1 blockade also causes memory B cell proliferation and SIV envelope-specific antibodies to increase. This improved immune response is associated with a significant reduction in plasma viral load and also prolongs the survival of SIV infected macaques. Blockade was effective both early (week 10) and late (week 90) in chronic infection, even with severe lymphopenia. These results demonstrate that cellular and humoral immune responses are enhanced during infection by pathogenic immunodeficiency viruses by blocking a single inhibitory pathway, and identify novel therapeutic approaches to control human immunodeficiency virus infection.

Example 10: in vitro PD-1: PDL pathway blockade by humanized PD-1 antibodies and humanized PD-L1 antibodies Increased proliferation of post-SIV-specific CD8T cells

The effect of humanized anti-PD-1 antibody from EH-12.2H7 and humanized anti-PD-L1 antibody from 29E.2A3 on the proliferative capacity of SIV Gag-specific CD8T cells was examined in vitro. The humanized anti-PD-1 antibody has the amino acid sequence of SEQ ID NO: 28 and SEQ ID NO: 32, and a light chain variable region sequence. The humanized anti-PD-L1 antibody has the amino acid sequence of SEQ ID NO: 35 and the heavy chain variable region sequence of SEQ ID NO: 42, light chain variable region sequence. The heavy chain constant region of the humanized antibody was derived from human IgG4 with a Ser 228 to Pro mutation (from CPSCP to CPPCP) -so that the antibody forms a dimer, and the light chain constant region was a human kappa light chain constant region. The amino acid numbering of Ser 228 is according to the EU numbering system. See Aalberse et al, Immunology 105: 9-19, 2002. PBMCs obtained from SIV-infected macaques (between 3 months and 1.5 years post-infection) were stained with carboxyfluorescein diacetate succinimidyl ester (CFSE) and stimulated with SIV Gag peptide pool (pool) or culture medium in the presence or absence of blocking antibodies for 6 days. At the end of stimulation, cell surface CD3 and CD8 and intracellular Ki-67 were stained. Cells were then obtained on a FACSCalibur and analyzed using Flowjo software. Lymphocytes were identified based on scatter, and CD8T cells (CD3+, CD8+) were then analyzed for Ki-67 and CFSE co-staining. Cells with low Ki-67+, CFSE were identified as proliferating cells.

As shown in fig. 14A, in vitro PD-1: PD-1 ligand pathway blockade with anti-PD-1 Ab resulted in a significant increase in proliferation of SIV-specific CD8T cell responses. In vitro blockade with anti-PD-L1 Ab resulted in a modest increase in proliferation of SIV-specific CD8T cell responses (fig. 14B).

Example 11: recovery of HCV-specific T cell proliferation by persistently infected intrahepatic monocytes of chimpanzees

CFSE-labeled intrahepatic lymphocytes (2X 10) were isolated from chimpanzee 1564 chronically infected with HCV genotype 1a H77 strain for more than 10 years⁶). Intrahepatic lymphocytes are as follows 4X 10⁶Irradiated PBMC depleted of self CD8 either untreated or pulsed with overlapping peptides comprising the entire HCV polyprotein (genotype 1aH77 strain) were cultured for 6 days. Cells were cultured in RPMI medium supplemented with L-glutamine and 10% FCS, with and without anti-PD-L1 blocking antibody (10 μ g/ml, added at day 0 and day 2). The humanized anti-PD-L1 antibody has the amino acid sequence of SEQ ID NO: 35 and seq id NO: 42, light chain variable region sequence. The heavy chain constant region of the humanized antibody was derived from human IgG4 with Ser 228 to Pro mutations (CPSCP to CPPCP) -so that the antibody forms a dimer, and the light chain constant region was a human kappa light chain constant region. The amino acid numbering of Ser 228 is according to the EU numbering system. See Aalberse et al, Immunology 105: 9-19, 2002. On day 6, cells were stained with CD8-PerCP, A0701/P7(758) -PE tetramer, PD-1-Alexa 647, CD4-Alexa 700, CD14-Alexa700, CD16-Alexa 700, CD19-Alexa 700, and Live/Dead Blue. Samples were obtained on a BD LSR II flow cytometer and data analyzed using FlowJo software.

As shown in figure 15, anti-PD-L1 antibody treatment restored HCV-specific T cell proliferation by persistent infection of intrahepatic monocytes in chimpanzees.

Is incorporated by reference

All publications, patents, and patent applications mentioned herein are incorporated by reference in their entirety to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.

Any polynucleotide and polypeptide sequences referred to in connection with accession numbers into the public databases, such as accession numbers maintained by the national institute of genetics (TIGR) on the world wide web and/or the National Center for Biotechnology Information (NCBI) on the world wide web, are also incorporated by reference in their entirety.

Equivalents of

Those skilled in the art will understand, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalent embodiments are intended to be encompassed by the appended claims.

Claims (39)

1. An isolated antibody, wherein the isolated antibody comprises:

a) a heavy chain variable region sequence selected from SEQ ID NOs: 34-38; and

b) a light chain variable region sequence selected from SEQ ID NOs:39-42,

wherein the isolated antibody binds to PD-L1 protein having the amino acid sequence of SEQ ID NO. 4.

2. The isolated antibody of claim 1, wherein the isolated antibody comprises:

a) a heavy chain variable region sequence selected from SEQ ID NOS 35 and 37; and

b) a light chain variable region sequence selected from the group consisting of SEQ ID NOs 39, 40 and 42.

3. The isolated antibody of claim 1, wherein the isolated antibody inhibits the binding of the 29E2a3 antibody to Fc-PD-L1.

4. The isolated antibody of claim 1, wherein the isolated antibody inhibits PD-L1-mediated signaling.

5. The isolated antibody of claim 2, wherein the isolated antibody inhibits the binding of the 29E2a3 antibody to Fc-PD-L1.

6. The isolated antibody of claim 2, wherein the isolated antibody inhibits PD-L1-mediated signaling.

7. The isolated antibody of claim 1, wherein the antibody is selected from the group consisting of Fab, Fab '-SH, Fv, scFv, and F (ab')₂An antigen-binding fragment of a fragment.

8. The isolated antibody of claim 2, wherein the antibody is selected from the group consisting of Fab, Fab '-SH, Fv, scFv, and F (ab')₂An antigen-binding fragment of a fragment.

9. An isolated nucleic acid encoding the antibody of any one of claims 1-8.

10. A vector comprising the isolated nucleic acid of claim 9.

11. A host cell comprising the nucleic acid of claim 9.

12. The host cell of claim 11, which produces an antibody encoded by the nucleic acid.

13. Use of the nucleic acid of claim 9 in the preparation of a non-human transgenic animal.

14. A pharmaceutical composition comprising the isolated antibody of any one of claims 1-8 and a pharmaceutically acceptable carrier.

15. Use of the antibody of any one of claims 1-8 in the preparation of a medicament for reactivating depleted T cells, wherein the reactivating depleted T cells comprises contacting a population of T cells with an effective amount thereof of the antibody, wherein at least some of the T cells express PD-L1.

16. The use of claim 15, wherein the contacting step is performed in vitro.

17. The use of claim 15, wherein the contacting step is performed ex vivo.

18. The use of claim 15, wherein the contacting step is performed in vivo.

19. Use of the isolated antibody of any one of claims 1-8 in the manufacture of a medicament for treating an individual suffering from a persistent infection.

20. Use of the isolated antibody of any one of claims 1-8 in the manufacture of a medicament for treating an individual suffering from a viral infection.

21. The use of claim 20, wherein the viral infection is selected from cytomegalovirus, epstein-barr virus, hepatitis b virus, hepatitis c virus, herpes virus, human immunodeficiency virus, human T-lymphotropic virus, lymphocytic choriomeningitis virus, respiratory syncytial virus, and/or rhinovirus.

22. Use of the isolated antibody of any one of claims 1-8 in the manufacture of a medicament for treating an individual suffering from a bacterial infection.

23. The use of claim 22, wherein the bacterial infection is selected from the group consisting of Helicobacter (Helicobacter), Mycobacterium (Mycobacterium), Porphyromonas (Porphyromonas), and Chlamydia (Chlamydia).

24. Use of the isolated antibody of any one of claims 1-8 in the manufacture of a medicament for treating an individual suffering from a helminth infection.

25. The use of claim 24, wherein the helminths are selected from the group consisting of Schistosoma (Schistosoma) and tapeworm (Taenia).

26. Use of the isolated antibody of any one of claims 1-8 in the manufacture of a medicament for treating an individual suffering from a protozoan infection.

27. The use of claim 26, wherein the protozoan infection is selected from the group consisting of Leishmania mexicana (Leishmania mexicana) and proteosome (Plasmodium).

28. Use of the isolated antibody of any one of claims 1-8 in the manufacture of a medicament for treating an individual having cancer.

29. The use of claim 28, wherein the cancer is selected from the group consisting of solid tumors, blood cancer, bladder cancer, brain cancer, breast cancer, colon cancer, stomach cancer, glioma, head cancer, liver cancer, lung cancer, lymphoma, myeloma, neck cancer, ovarian cancer, melanoma, pancreatic cancer, kidney cancer, salivary gland cancer, thymic epithelial cancer, and thyroid cancer.

30. The use of claim 28, wherein the cancer is leukemia or gastric cancer.

31. Use of the isolated antibody of any one of claims 1-8 in the manufacture of a medicament for treating an individual having a cancer that overexpresses PD-L1.

32. The use of claim 31, wherein the isolated antibody induces antibody-mediated cytotoxicity.

33. The use of claim 32, wherein the antibody is modified to increase antibody-induced cytotoxicity.

34. The use of claim 33, wherein the antibody is conjugated to an agent selected from the group consisting of a toxin and an imaging agent.

35. Use of the isolated antibody of any one of claims 1-8 in the manufacture of a medicament for treating an individual having an inflammatory disease.

36. The use of claim 35, wherein the inflammatory disease is selected from the group consisting of acute disseminated encephalomyelitis, addison's disease, ankylosing spondylitis, antiphospholipid antibody syndrome, autoimmune hemolytic anemia, autoimmune hepatitis, arthritis, becker's disease, bullous pemphigoid, coeliac disease, chagas disease, crohn's disease, dermatomyositis, type 1 diabetes, goodpasture's syndrome, graft-versus-host disease, graves 'disease, guillain-barre syndrome, hashimoto's disease, hyper IgE syndrome, idiopathic thrombocytopenic purpura, lupus erythematosus, multiple sclerosis, myasthenia gravis, pemphigus, pernicious anemia, polymyositis, primary biliary cirrhosis, psoriasis, rheumatoid arthritis, sjogren's syndrome, temporal arteritis, vasculitis, and wegener's granulomatosis.

37. Use of the isolated antibody of any one of claims 1-8 in the manufacture of a medicament for treating an individual suffering from transplant rejection.

38. The use of claim 37, wherein the transplant rejection is selected from organ rejection, bone marrow transplant rejection, and/or non-myeloablative bone marrow transplant rejection.

39. A method of producing the antibody of any one of claims 1-8, comprising: culturing cells that produce the antibody; and collecting the antibody produced by the cells.