Cd80 variant immunomodulatory proteins and uses thereof

Abstract

Provided herein are variant CD80 polypeptides, immunomodulatory proteins comprising variant CD80 polypeptides, and nucleic acids encoding such proteins. The immunomodulatory proteins provide therapeutic utility for a variety of immunological and oncological conditions. Compositions and methods for making and using such proteins are provided.

1 . A CD80-Fc fusion immunomodulatory protein comprising a variant CD80 polypeptide and an Fc domain, wherein the variant CD80 polypeptide comprises the amino acid substitution A71G or A71D in:
 (i) the amino acid sequence set forth in SEQ ID NO:2 or   (ii) a portion of (i) comprising the IgV domain, wherein the IgV domain is amino acids 35-141 of SEQ ID NO:1.   
     
     
         2 - 7 . (canceled) 
     
     
         8 . The CD80-Fc fusion immunomodulatory protein of  claim 1  wherein the variant CD80 polypeptide comprises amino acid modifications selected from Q27H/T41S/A71D, T13R/C16R/L70Q/A71D, V22L/M38V/M47T/A71D/L85M, I30V/T57I/L70P/A71D/A91T, V22I/L70M/A71D, A71D, T41S/A71D/V84A, E35D/A71D, E35D/M47I, S44P/A71D, Q27H/M43I/A71D/R73S, E35D/T57I/L70Q/A71D, M42I/I61V/A71D, P51A/A71D, H18Y/M47I/T57I/A71G, V20I/M47V/A71D, A71D/L72V/E95K, V22L/E35G/A71D/L72P, E35D/A71D, E35D/I67L/A71D, Q27H/E35G/A71D/L72P/T79I, T13R/M42V/M47I/A71D, E35D/A71D/L72V, M47V/I69F/A71D/V83I, E35D/T57A/A71D/L85Q, H18Y/A26T/E35D/A71D/L85Q, V68M/L70M/A71D/E95K, E35D/M43I/A71D, H18Y/A71D/L72P/E88V, V20I/A71D, E23G/A26S/E35D/T62N/A71D/L72V/L85M, V22L/E35D/M43L/A71G/D76H, E35G/K54E/A71D/L72P, L70Q/A71D, D46E/A71D, V22A/E35D/V68E/A71D, Q33L/E35D/M47L/A71G/F92S, Q33L/E35D/M43V/M47I/A71G, E35D/M47L/A71G/L97Q, E35D/M47V/A71G/L85M/L97Q, H18Y/Y31H/E35D/M47V/A71G/L85Q, E35D/D46V/M47I/A71G/F92V, E35D/M47V/T62A/A71G/V83A/Y87H/L97M, Q33L/E35D/M47I/N48D/A71G, A26E/E35D/M47L/A71G, E35D/M47L/A71G/L85Q, E35D/M47V/A71G/E88D, E35D/A71G, E35D/M47V/A71G, I30V/E35D/M47V/A71G/A91V, I30V/Y31C/E35D/M47V/A71G/L85M, E35D/T41S/M47V/A71G/K89N, E35D/D46E/M47V/A71D/D90G, E35D/D46E/M47V/A71D, E35D/T41S/M43I/A71G/D90G, E35D/T41S/M43I/M47V/A71G, E35D/T41S/M43I/M47L/A71G, H18Y/V22A/E35D/M47V/T62S/A71G, H18Y/A26E/E35D/M47L/V68M/A71G/D90G, Q27H/E35D/D46V/M47L/A71G, V22L/Q27H/E35D/M47I/A71G, E35D/T41S/M43V/M47I/L70M/A71G, E35D/M47V/T62A/A71D/K93E, E35D/M47L/A71G/L85M/F92Y, E35D/Y53H/A71G/D90G/L97R, E35D/A71D/L72V/R73H/E81K, T28Y/Q33H/E35D/D46V/M47I/A71G, D46V/M47I/A71G, M47I/A71G, E35D/M43I/D46E/A71G/L85M, H18Y/E35D/M47L/A71G/A91S, M43I/M47L/A71G, E35D/M47L/A71G/L85M, V22A/E35D/M47L/A71G, E35D/M47L/A71G, S15T/H18Y/E35D/M47V/T62A/N64S/A71G/L85Q/D90N, E35D/M47L/V68M/A71G/L85Q/D90G, H18Y/E35D/M47I/V68M/A71G/R94L, Q33R/M47V/T62N/A71G, H18Y/V22A/E35D/T41S/M47V/T62N/A71G/A91G, E35D/D46E/M47L/V68M/A71G/Y87C/K93R, E35D/M47L/Y53F/V68M/A71G/K93R/E95V, E35D/M47V/N48K/V68M/A71G/L85M, H18Y/E35D/M47L/V68M/A71G/L85M, H18Y/E35D/M47L/Y53F/V68M/A71G, H18Y/E35D/M47L/Y53F/V68M/A71G/K93R/E95V, H18Y/E35D/V68M/A71G/R94Q/E95V, R29C/E35D/M47L/V68M/A71G/L85M, A26E/E35D/M47L/V68M/A71G/D90G, H18Y/E35D/M47L/V68M/A71G/D90G, H18Y/A26E/M47L/V68M/A71G/D90G, H18Y/A26E/E35D/V68M/A71G/D90G, H18Y/A26E/E35D/M47L/A71G/D90G, H18Y/A26E/E35D/M47L/V68M/A71G, E35D/M47L/V68M/A71G/D90G, H18Y/M47L/V68M/A71G/D90G, H18Y/A26E/V68M/A71G/D90G, H18Y/A26E/E35D/A71G/D90G, A26E/M47L/V68M/A71G/D90G, A26E/E35D/V68M/A71G/D90G, A26E/E35D/M47L/A71G/D90G, A26E/E35D/M47L/V68M/A71G, H18Y/E35D/V68M/A71G/D90G, H18Y/E35D/M47L/A71G/D90G, H18Y/E35D/M47L/V68M/A71G, H18Y/A26E/M47L/A71G/D90G, H18Y/A26E/M47L/V68M/A71G, H18Y/A26E/E35D/V68M/A71G, H18Y/A26E/E35D/M47L/A71G, M47L/V68M/A71G/D90G, H18Y/V68M/A71G/D90G, H18Y/A26E/A71G/D90G, E35D/V68M/A71G/D90G, E35D/M47L/A71G/D90G, E35D/M47L/V68M/A71G, A26E/V68M/A71G/D90G, A26E/M47L/A71G/D90G, A26E/M47L/V68M/A71G, A26E/E35D/A71G/D90G, A26E/E35D/V68M/A71G, H18Y/M47L/A71G/D90G, H18Y/M47L/V68M/A71G, H18Y/E35D/A71G/D90G, H18Y/E35D/V68M/A71G, H18Y/E35D/M47L/A71G, H18Y/A26E/V68M/A71G, H18Y/A26E/M47L/A71G, H18Y/A26E/E35D/A71G, H18Y/E35D/M47V/V68M/A71G, H18C/A26P/E35D/M47L/V68M/A71G, H181/A26P/E35D/M47V/V68M/A71G, H18L/A26N/D46E/V68M/A71G/D90G, H18L/E35D/M47V/V68M/A71G/D90G, H18T/A26N/E35D/M47L/V68M/A71G, H18V/A26K/E35D/M47L/V68M/A71G, H18V/A26N/E35D/M47V/V68M/A71G, H18V/A26P/E35D/M47V/V68L/A71G, H18V/A26P/E35D/M47L/V68M/A71G, H18V/E35D/M47V/V68M/A71G/D90G, H18Y/A26P/E35D/M47I/V68M/A71G, H18Y/A26P/E35D/M47V/V68M/A71G, H18Y/E35D/M47V/V68L/A71G/D90G, H18Y/E35D/M47V/V68M/A71G/D90G, A26P/E35D/M47I/V68M/A71G/D90G, H18V/A26G/E35D/M47V/V68M/A71G/D90G, H18V/A26S/E35D/M47L/V68M/A71G/D90G, H18V/A26R/E35D/M47L/V68M/A71G/D90G, H18V/A26D/E35D/M47V/V68M/A71G/D90G, H18V/A26Q/E35D/M47V/V68L/A71G/D90G, H18A/A26P/E35D/M47L/V68M/A71G/D90G, H18A/A26N/E35D/M47L/V68M/A71G/D90G, H18F/A26P/E35D/M47I/V68M/A71G/D90G, H18F/A26H/E35D/M47L/V68M/A71G/D90G, H18F/A26N/E35D/M47V/V68M/A71G/D90K, H18Y/A26N/E35D/M47F/V68M/A71G/D90G, H18Y/A26P/E35D/M47Y/V68I/A71G/D90G, H18Y/A26Q/E35D/M47T/V68M/A71G/D90G, H18R/A26P/E35D/D46N/M47V/V68M/A71G/D90P, and H18F/A26D/E35D/D46E/M47T/V68M/A71G/D90G, with reference to the numbering of positions set forth in SEQ ID NO: 2. 
     
     
         9 - 11 . (canceled) 
     
     
         12 . The CD80-Fc fusion immunomodulatory protein of  claim 1 , wherein the variant CD80 polypeptide exhibits increased binding affinity to the ectodomain of human PD-L1 compared to the binding affinity of an unmodified CD80 for the ectodomain of human PD-L1. 
     
     
         13 - 23 . (canceled) 
     
     
         24 . The CD80-Fc fusion immunomodulatory protein of  claim 1 , wherein the variant CD80 polypeptides comprises:
 the sequence of amino acids set forth in any of SEQ ID NOs:5, 7, 10-12, 22-23, 27-28, 34-37, 39-41, 43-49, 52, 57-59, 62, 64, 66-68, 70-72, 74, 2043-2044, 2049-2052, 2054-2055, 2059, 2064, 2068-2073, 2076, 2078-2084, 2086-2087, 2089, 2091, 2094, 2098-2099, 2104, 2299-2300, 2302-2303, 2306, 2308-2310, 2327-2329, 2331-2332, 2346, 2353-2354, 2362, 2364-2365, 2367, 2374, 2446-2450, 2452-2456, 2459-2461, 2463-2465, 2467-2468, 2470, 2472-2476, 2479-2480, 2482-2484, 2486-2487, 2489, 2492, 2494-2495, 2497, 2499, 2502, 2504, 2506, or 2930-2960 or a specific binding fragment thereof, or a sequence of amino acids that exhibits at least 95% sequence identity to any of SEQ ID NOs:5, 7, 10-12, 22-23, 27-28, 34-37, 39-41, 43-49, 52, 57-59, 62, 64, 66-68, 70-72, 74, 2043-2044, 2049-2052, 2054-2055, 2059, 2064, 2068-2073, 2076, 2078-2084, 2086-2087, 2089, 2091, 2094, 2098-2099, 2104, 2299-2300, 2302-2303, 2306, 2308-2310, 2327-2329, 2331-2332, 2346, 2353-2354, 2362, 2364-2365, 2367, 2374, 2446-2450, 2452-2456, 2459-2461, 2463-2465, 2467-2468, 2470, 2472-2476, 2479-2480, 2482-2484, 2486-2487, 2489, 2492, 2494-2495, 2497, 2499, 2502, 2504, 2506, or 2930-2960; or   the sequence of amino acids set forth in any of SEQ ID NOs:79, 81, 84-86, 96-97, 101-102, 108-111, 113-115, 117-123, 126, 131-133, 136, 138, 140-142, 144-146, 148, 153, 155, 158-160, 170-171, 175-176, 182-185, 187-189, 191-197, 200, 205-207, 210, 212, 214-216, 218-220, 222, 2139-2140, 2145-2148, 2150-2151, 2155, 2160, 2164-2169, 2172, 2174-2180, 2182-2183, 2185, 2187, 2190, 2194-2195, 2200, 2235-2236, 2241-2244, 2246-2247, 2251, 2256, 2260-2265, 2268, 2270-2276, 2278-2279, 2281, 2283, 2286, 2290-2291, 2296, 2510-2511, 2513-2514, 2517, 2519-2521, 2538-2540, 2542-2543, 2557, 2564-2565, 2573, 2575-2576, 2578, 2585, 2657-2661, 2663-2667, 2670-2672, 2674-2676, 2678-2679, 2681, 2683-2687, 2690-2691, 2693-2695, 2697-2698, 2700, 2703, 2705-2706, 2708, 2710, 2713, 2715, 2717, 2721-2722, 2724-2725, 2728, 2730-2732, 2749-2751, 2753-2754, 2768, 2775-2776, 2784, 2786-2787, 2789, 2796, 2868-2872, 2874-2878, 2881-2883, 2885-2887, 2889-2890, 2892, 2894-2898, 2901-2902, 2904-2906, 2908-2909, 2911, 2914, 2916-2917, 2919, 2921, 2924, 2926, 2928, or 2961-3022 or a specific binding fragment thereof, or a sequence of amino acids that exhibits at least 95% sequence identity to any of SEQ ID NOs:79, 81, 84-86, 96-97, 101-102, 108-111, 113-115, 117-123, 126, 131-133, 136, 138, 140-142, 144-146, 148, 153, 155, 158-160, 170-171, 175-176, 182-185, 187-189, 191-197, 200, 205-207, 210, 212, 214-216, 218-220, 222, 2139-2140, 2145-2148, 2150-2151, 2155, 2160, 2164-2169, 2172, 2174-2180, 2182-2183, 2185, 2187, 2190, 2194-2195, 2200, 2235-2236, 2241-2244, 2246-2247, 2251, 2256, 2260-2265, 2268, 2270-2276, 2278-2279, 2281, 2283, 2286, 2290-2291, 2296, 2510-2511, 2513-2514, 2517, 2519-2521, 2538-2540, 2542-2543, 2557, 2564-2565, 2573, 2575-2576, 2578, 2585, 2657-2661, 2663-2667, 2670-2672, 2674-2676, 2678-2679, 2681, 2683-2687, 2690-2691, 2693-2695, 2697-2698, 2700, 2703, 2705-2706, 2708, 2710, 2713, 2715, 2717, 2721-2722, 2724-2725, 2728, 2730-2732, 2749-2751, 2753-2754, 2768, 2775-2776, 2784, 2786-2787, 2789, 2796, 2868-2872, 2874-2878, 2881-2883, 2885-2887, 2889-2890, 2892, 2894-2898, 2901-2902, 2904-2906, 2908-2909, 2911, 2914, 2916-2917, 2919, 2921, 2924, 2926, 2928, or 2961-3022.   
     
     
         25 - 28 . (canceled) 
     
     
         29 . The CD80-Fc fusion immunomodulatory protein of  claim 1 , wherein the Fc is a variant human IgG1 Fc with reduced effector function. 
     
     
         30 - 31 . (canceled) 
     
     
         32 . The CD80-Fc fusion immunomodulatory protein of  claim 1  that is a homodimer comprising two CD80-Fc fusions. 
     
     
         33 - 37 . (canceled) 
     
     
         38 . The CD80-Fc fusion immunomodulatory protein of  claim 1 , wherein the Fc region is a variant Fc region comprising one or more amino acid substitutions in a wildtype Fc region, said variant Fc region exhibiting one or more effector function that is reduced compared to the wildtype Fc region. 
     
     
         39 - 44 . (canceled) 
     
     
         45 . The CD80-Fc fusion immunomodulatory protein of  claim 1 , wherein the immunomodulatory protein exhibits PD-L1-dependent CD28 costimulation. 
     
     
         46 - 48 . (canceled) 
     
     
         49 . A conjugate, comprising the CD80-Fc fusion immunomodulatory protein of  claim 1  linked to a targeting moiety that specifically binds to a molecule on the surface of a cell. 
     
     
         50 - 53 . (canceled) 
     
     
         54 . A nucleic acid molecule(s), encoding the CD80-Fc fusion immunomodulatory protein of  claim 1 . 
     
     
         55 . A vector, comprising the nucleic acid molecule(s) of  claim 54 . 
     
     
         56 - 57 . (canceled) 
     
     
         58 . A method of producing a CD80-Fc fusion immunomodulatory protein comprising introducing the nucleic acid molecule(s) of  claim 54  or a vector comprising the nucleic acid molecule(s) of  claim 54  into a host cell under conditions to express the protein in the cell. 
     
     
         59 - 60 . (canceled) 
     
     
         61 . An engineered cell, comprising the CD80-Fc fusion immunomodulatory protein of  claim 1 , a conjugate comprising the CD80-Fc fusion immunomodulatory protein of  claim 1  linked to a targeting moiety that specifically binds to a molecule on the surface of a cell, or a nucleic acid molecule(s) encoding the CD80-Fc immunomodulatory protein of  claim 1 . 
     
     
         62 - 65 . (canceled) 
     
     
         66 . An infectious agent, comprising a nucleic acid molecule(s) encoding the CD80-Fc fusion immunomodulatory protein of  claim 1  or a conjugate comprising the CD80-Fc fusion immunomodulatory protein of  claim 1  linked to a targeting moiety that specifically binds to a molecule on the surface of a cell. 
     
     
         67 - 68 . (canceled) 
     
     
         69 . A pharmaceutical composition, comprising the CD80-Fc fusion immunomodulatory protein of  claim 1 , a conjugate comprising the CD80-Fc fusion immunomodulatory protein of  claim 1 , an engineered cell comprising the CD80-Fc fusion immunomodulatory protein of  claim 1 , or an infectious agent comprising a nucleic acid molecule(s) encoding the CD80-Fc fusion immunomodulatory protein of  claim 1 . 
     
     
         70 - 73 . (canceled) 
     
     
         74 . A kit comprising the pharmaceutical composition of  claim 69  and instructions for use. 
     
     
         75 . A method of modulating an immune response in a subject, comprising administering the pharmaceutical composition of  claim 69 . 
     
     
         76 - 146 . (canceled) 
     
     
         147 . The CD80-Fc fusion immunomodulatory protein of  claim 1 , wherein the variant CD80 polypeptide is linked via a linker to the Fc domain, wherein the linker has 1-20 amino acid residues. 
     
     
         148 . The CD80-Fc fusion immunomodulatory protein of  claim 1 , wherein the Fc is set forth in SEQ ID NO:1712. 
     
     
         149 . The CD80-Fc fusion immunomodulatory protein of  claim 1 , wherein the Fc is set forth in SEQ ID NO:1713. 
     
     
         150 . The CD80-Fc fusion immunomodulatory protein of  claim 1 , wherein the Fc is set forth in SEQ ID NO:1714. 
     
     
         151 . The CD80-Fc fusion immunomodulatory protein of  claim 1 , wherein the Fc is set forth in SEQ ID NO:1715.