CTLA-4 variant immunomodulatory proteins and uses thereof
Provided herein are variant CTLA-4 polypeptides and immunomodulatory proteins and nucleic acids encoding such proteins. The immunomodulatory proteins provide therapeutic utility for a variety of disease applications, including for treatment of autoimmune or inflammatory conditions. Compositions and methods for making and using such proteins are provided.
1. A variant CTLA-4 polypeptide, comprising an IgV domain or a specific binding fragment thereof, wherein the variant CTLA-4 polypeptide comprises one or more amino acid modifications in an unmodified CTLA-4 polypeptide or a specific binding fragment thereof corresponding to position(s) selected from among 29, 53, 56, 58, 82, 87, and 98, with reference to positions set forth in SEQ ID NO:2 and wherein the sequence includes L63P and Y105L.
2. The variant CTLA-4 polypeptide of claim 1 , wherein the unmodified CTLA-4 polypeptide comprises (i) the sequence of amino acids set forth in SEQ ID NO:2, (ii) a sequence of amino acids that has at least 95% sequence identity to SEQ ID NO:2; or (iii) a portion of (i) or (ii) comprising an IgV domain or specific binding fragment of the IgV domain.
3. The variant CTLA-4 polypeptide of claim 1 , wherein the variant CTLA-4 polypeptide specifically binds to the ectodomain of human ICOSL, human CD80 and/or human CD86 with increased affinity compared to the binding of the unmodified CTLA-4 polypeptide for the same ectodomain(s).
4. The variant CTLA-4 polypeptide of claim 1 , wherein the one or more amino acid modifications are selected from G29W, T53 S, M56K, N58S, Q82R, M87V, and L98Q.
5. The variant CTLA-4 polypeptide of claim 1 , consisting of one or more amino acid modifications selected from among
G29W/N58S/L63P/Q82R/L98Q/Y105L,
T53S/L63P/Y105L, and
M56KN58S/L63P/M87V/L98Q/Y105L.
6. The variant CTLA-4 polypeptide of claim 1 , wherein the variant CTLA-4 polypeptide specifically binds to the ectodomain of human ICOSL with increased affinity and specifically binds to the ectodomain of one or more of the other of human CD80 or human CD86 with decreased affinity compared to the binding of the unmodified CTLA-4 for the same ectodomains.
7. The variant CTLA-4 polypeptide of claim 1 , comprising the sequence of amino acids of the extracellular domain set forth in any of SEQ ID NOS: 93, 579, and 586, or a specific binding fragment thereof.
8. The variant CTLA-4 polypeptide of claim 1 that is a soluble protein; wherein the variant CTLA-4 polypeptide lacks the CTLA-4 transmembrane domain and intracellular signaling domain; and/or the variant CTLA-4 polypeptide is not capable of being expressed on the surface of a cell.
9. The variant CTLA-4 polypeptide of claim 1 that is linked to a multimerization domain.
10. A variant CTLA-4-Fc fusion protein, comprising the variant CTLA-4 polypeptide of claim 3 .
11. The variant CTLA-4 Fc fusion protein of claim 10 , wherein the Fc domain is a variant Fc domain with reduced effector function.
12. An immunomodulatory polypeptide, comprising the variant CTLA-4 of claim 3 linked to a second polypeptide comprising an immunoglobulin superfamily (IgSF) domain.
13. A conjugate, comprising the variant CTLA-4 of claim 1 linked to a moiety that specifically binds to a molecule on the surface of a cell.
14. A nucleic acid molecule, encoding the variant CTLA-4 polypeptide of claim 3 .
15. A vector, comprising the nucleic acid molecule of claim 14 .
16. A cell, comprising the nucleic acid of claim 14 or a vector comprising the nucleic acid molecule of claim 14 .
17. A method of producing a variant CTLA-4 polypeptide or an immunomodulatory protein, comprising introducing the nucleic acid molecule of claim 14 or a vector comprising the nucleic acid molecule of claim 14 into a host cell under conditions to express the protein in the cell.
18. A method of engineering a cell expressing a variant CTLA-4 polypeptide, comprising introducing a nucleic acid molecule encoding the variant CTLA-4 polypeptide of claim 1 into a host cell under conditions in which the polypeptide is expressed in the cell.
19. An engineered cell, expressing the variant CTLA-4 polypeptide of claim 3 or a nucleic acid molecule encoding a sequence of amino acids comprising the variant CTLA-4 polypeptide of claim 3 .
20. A pharmaceutical composition, comprising the variant CTLA-4 polypeptide of claim 1 and a pharmaceutically acceptable excipient.
21. An article of manufacture comprising the pharmaceutical composition of claim 20 in a vial or container.
22. A kit comprising the pharmaceutical composition of claim 20 , and instructions for use.
23. A method of modulating an immune response in a subject, comprising administering the pharmaceutical composition of claim 20 to the subject.
24. A method of treatment, comprising administering to a subject that has a disease or condition the pharmaceutical composition of claim 20 .
25. The variant CTLA-4 polypeptide of claim 1 , comprising SEQ ID NO: 93.
26. The variant CTLA-4 polypeptide of claim 1 , comprising SEQ ID NO: 579.
27. The variant CTLA-4 polypeptide of claim 1 , comprising SEQ ID NO: 586.
28. The variant CTLA-4 polypeptide of claim 1 , comprising SEQ ID NO: 238.
29. The variant CTLA-4 polypeptide of claim 1 , comprising SEQ ID NO: 375.
30. The variant CTLA-4 polypeptide of claim 1 , comprising SEQ ID NO: 612.
31. The variant CTLA-4 polypeptide of claim 1 , comprising SEQ ID NO: 619.