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US-12624087-B2 - CD155 variant immunomodulatory proteins and uses thereof

US12624087B2US 12624087 B2US12624087 B2US 12624087B2US-12624087-B2

Abstract

Provided herein are immunomodulatory proteins comprising variant CD155 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.

Inventors

  • Ryan Swanson
  • Michael Kornacker
  • Daniel William DEMONTE
  • Mark F. Maurer

Assignees

  • ALPINE IMMUNE SCIENCES, INC.

Dates

Publication Date
20260512
Application Date
20221014

Claims (20)

  1. 1 . A variant CD155 polypeptide comprising an amino acid sequence that exhibits at least 90% sequence identity to SEQ ID NO: 47 or amino acid residues 4-199 of SEQ ID NO: 47, wherein the variant CD155 polypeptide comprises the amino acid substitution L104Q with reference to positions set forth in SEQ ID NO:47 of unmodified CD155; wherein the variant CD155 polypeptide specifically binds to the ectodomain of TIGIT with increased affinity compared to that of the unmodified CD155.
  2. 2 . The variant CD155 polypeptide of claim 1 , further comprising one or more amino acid substitutions selected from G7E, D8G, V9A, V9D, V9I, V9L, V10F, V10G, V10I, V11A, V11E, V11M, Q12H, Q12K, Q12L, A13E, A13R, T15I, T15S, Q16H, P18C, P18F, P18H, P18L, P18S, P18T, P18Y, G19D, F201, F20S, F20Y, L21S, L21M, G22S, D23A, D23G, D23N, D23Y, S24A, S24P, V25A, V25E, T26M, C29R, Y30C, Y30F, Y30H, Q32L, Q32R, V33M, P34S, N35D, N35F, N35S, M36I, M36R, M36T, E37G, E37P, E37S, E37V, V38A, V38G, T39A, T39S, H40Q, H40R, H40T, V41A, V41M, S42A, S42C, S42G, S42L, S42N, S42P, S42Q, S42T, S42V, S42W, L44P, L44V, T45A, T45G, T45I, T45S, T45Q, T45V, W46C, W46R, A47E, A47G, A47V, R48Q, H49L, H49Q, H49R, G50S, E51G, E51K, E51V, S52A, S52E, S52G, S52K, S52L, S52M, S52P, S52Q, S52R, S52T, S52W, G53R, S54C, S54G, S54H, S54N, S54R, M55I, M55L, M55V, A56V, V57A, V57L, V57T, F58L, F58Y, H59E, H59N, N59R, Q60H, Q60K, Q60P, Q60R, T61A, T61G, T61K, T61M, T61R, T61S, Q62F, Q62H, Q62K, Q62L, Q62M, Q62R, Q62Y, P64S, S65A, S65C, S65G, S65D, S65T, S65Y, S65H, S65N, S65T, S65W, S67A, S67E, S67G, S67H, S67L, S67T, S67V, S67W, E68D, E68G, S69L, S69P, K70E, K70R, K70Q, L72Q, E73D, E73G, E73R, V75A, V75L, A76E, A76G, A76T, A77T, A77V, R78G, R78K, R78S, L79P, L79Q, L79V, G80D, G80S, A81E, A81P, A81T, A81V, E82D, E82G, L83P, L83Q, R84W, N85D, N85Y, N87T, L88P, R89K, M90I, M90L, M90V, F91S, F91T, F91P, G92A, G92E, G92W, R94H, V95A, E96D, D97G, E98D, E98S, G99D, G99Y, N100Y, T102S, V106A, V106I, V106L, T107A, T107L, T107M, T107S, T107V, F108H, F108L, F108Y, Q110R, G111D, G111R, S112I, S112N, S112V, R113G, R113W, S114N, S114T, V115A, V115M, D116G, or D116N, or a conservative amino acid substitution thereof.
  3. 3 . The variant CD155 polypeptide of claim 1 , comprising amino acid substitutions selected from S42A/L104Q/G111R, S42A/S52Q/L104Q/G111R, S52M/L104Q, S42L/S52L/Q62F/L104Q, S42N/L104Q/G111R, L104Q, S42W/S52R/Q62Y/L104Q, S52R/Q62F/L104Q/G111R, S42G/S52L/Q62F/L104Q, T45Q/S52K/Q62F/L104Q/G111R, T45Q/S52Q/Q62Y/L104Q/G111R, P18S/S65W/S67A/M90V/V95A/L104Q/G111R, or P18S/S65W/S67A/L104Q/G111R.
  4. 4 . The variant CD155 polypeptide of claim 1 , comprising the sequence of amino acids set forth in any of SEQ ID NOS: 183-184, 188-189, 199, 204, 207, 209, 222, 242-243, 274 and 1269 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: 183-184, 188-189, 199, 204, 207, 209, 222, 242-243, 274 and 1269 or a specific binding fragment thereof and that contains the one or more of the amino acid modifications thereof, or the sequence of amino acids set forth in any of SEQ ID NOS: 280, 281, 285-286, 296, 301, 304, 306, 319, 339-340, 371, 377-378, 382-383, 393, 398, 401, 403, 416, 436-437, 468, 1270, and 1271 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: 280, 281, 285-286, 296, 301, 304, 306, 319, 339-340, 371, 377-378, 382-383, 393, 398, 401, 403, 416, 436-437, 468, 1270, and 1271 or a specific binding fragment thereof and that contains the one or more of the amino acid modifications thereof.
  5. 5 . The variant CD155 polypeptide of claim 1 , wherein the variant CD155 polypeptide specifically binds to the ectodomain of CD226 or CD96 with increased affinity compared to the binding of the unmodified CD155 to the same ectodomain of, CD226 or CD96.
  6. 6 . A fusion protein comprising the variant CD155 polypeptide of claim 1 , wherein the variant CD155 polypeptide is linked to a multimerization domain.
  7. 7 . The fusion protein of claim 6 , wherein the multimerization domain is an Fc domain or a variant Fc domain with reduced effector function.
  8. 8 . A homodimer comprising two copies of the fusion protein of claim 6 .
  9. 9 . The fusion protein of claim 6 , wherein the variant CD155 polypeptide comprises the amino acid substitutions P18S/S65W/S67A/L104Q/G111R.
  10. 10 . The fusion protein of claim 6 , wherein the variant CD155 polypeptide comprises the sequence of amino acids set forth in SEQ ID NO: 1271.
  11. 11 . The variant CD155 polypeptide of claim 1 wherein the variant CD155 polypeptide is a transmembrane immunomodulatory protein further comprising a transmembrane domain.
  12. 12 . An immunomodulatory protein, comprising the variant CD155 of claim 1 linked to a second polypeptide comprising an immunoglobulin superfamily (IgSF) domain.
  13. 13 . A conjugate, comprising a variant CD155 polypeptide of claim 1 linked to a targeting moiety that specifically binds to a molecule on the surface of a cell.
  14. 14 . A nucleic acid molecule, encoding the variant CD155 polypeptide of claim 1 .
  15. 15 . A method of producing a variant CD155 polypeptide, 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 polypeptide in the host cell.
  16. 16 . A method of engineering a cell expressing a variant CD155 polypeptide, comprising introducing a nucleic acid molecule encoding the variant CD155 polypeptide of claim 1 into a host cell under conditions in which the polypeptide is expressed in the host cell.
  17. 17 . An engineered cell, comprising the variant CD155 polypeptide of claim 1 or a nucleic acid molecule encoding a sequence of amino acids comprising the variant CD155 polypeptide of claim 1 .
  18. 18 . The engineered cell of claim 17 , wherein the cell further comprises a chimeric antigen receptor (CAR) or an engineered T-cell receptor (TCR).
  19. 19 . An infectious agent, comprising a variant CD155 polypeptide of claim 1 or a nucleic acid molecule encoding the variant CD155 polypeptide of claim 1 .
  20. 20 . A pharmaceutical composition, the variant CD155 polypeptide of claim 1 ; an immunomodulatory protein or conjugate the variant CD155 polypeptide of claim 1 ; an engineered cell or infectious agent the variant CD155 polypeptide of claim 1 ; or a nucleic acid molecule encoding the variant CD155 polypeptide of claim 1 .

Description

CROSS-REFERENCE TO RELATED APPLICATIONS This application is a divisional of U.S. application Ser. No. 16/320,981 filed on Jan. 25, 2019 which is a National Stage application under 35 U.S.C. § 371 of International Application No. PCT/US2017/044261, filed on Jul. 27, 2017, which claims priority from U.S. provisional application No. 62/367,822, filed Jul. 28, 2016, U.S. provisional application No. 62/394,696, filed Sep. 14, 2016, U.S. provisional application No. 62/410,839, filed Oct. 20, 2016, U.S. provisional application No. 62/472,558, filed Mar. 16, 2017, and U.S. provisional application No. 62/475,196, filed Mar. 22, 2017, the contents of each of which are hereby incorporated by reference in their entirety. INCORPORATION BY REFERENCE OF SEQUENCE LISTING The present application is being filed along with a Sequence Listing in XML format. The Sequence Listing is provided as a file entitled 761612000510SEQLIST.xml, created Oct. 13, 2022 which is 2,910,218 bytes in size. The information in the electronic format of the Sequence Listing is incorporated by reference in its entirety. FIELD The present disclosure relates to therapeutic compositions for modulating immune response in the treatment of cancer and immunological diseases. In some aspects, the present disclosure relates to particular variants of CD155 that exhibit improved binding, such as improved binding affinity or selectivity, for one or more of the cognate binding partner proteins TIGIT, CD226 or CD96. BACKGROUND Modulation of the immune response by intervening in the processes that occur in the immunological synapse (IS) formed by and between antigen-presenting cells (APCs) or target cells and lymphocytes is of increasing medical interest. Mechanistically, cell surface proteins in the IS can involve the coordinated and often simultaneous interaction of multiple protein targets with a single protein to which they bind. IS interactions occur in close association with the junction of two cells, and a single protein in this structure can interact with both a protein on the same cell (cis) as well as a protein on the associated cell (trans), likely at the same time. Although therapeutics are known that can modulate the IS, improved therapeutics are needed. Provided are immunomodulatory proteins, including soluble proteins or transmembrane immunomodulatory proteins capable of being expressed on cells, that meet such needs. SUMMARY Provided herein are variant CD155 polypeptides. In some embodiments, the variant CD155 polypeptides comprise an IgV domain or a specific binding fragment thereof, an IgC domain or a specific binding fragment thereof, or both, wherein the variant CD155 polypeptide comprises one or more amino acid modifications in an unmodified CD155 or a specific binding fragment thereof corresponding to position(s) selected from 7, 8, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 67, 68, 69, 70, 72, 73, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 94, 95, 96, 97, 98, 99, 100, 102, 104, 106, 107, 108, 110, 111, 112, 113, 114, 115, or 116 with reference to positions set forth in SEQ ID NO: 47. In some embodiments, the amino acid modifications comprise amino acid substitutions, deletions or insertions. In some embodiments, the unmodified CD155 is a mammalian CD155 or a specific binding fragment thereof. In some embodiments, the unmodified CD155 is a human CD155 or a specific binding fragment thereof. In some embodiments, the unmodified CD155 comprises (i) the sequence of amino acids set forth in SEQ ID NO: 47, (ii) a sequence of amino acids that has at least 95% sequence identity to SEQ ID NO: 47; or (iii) a portion thereof comprising an IgV domain or specific binding fragment thereof. In some embodiments of any one of the variant CD155 polypeptides, the specific binding fragment of the IgV domain has a length of at least 50, 60, 70, 80, 90, 100, 110 or more amino acids; or the specific binding fragment of the IgV domain comprises a length that is at least 80% of the length of the IgV domain set forth as amino acids 24-139 of SEQ ID NO: 20. In some embodiments, the variant CD155 polypeptide comprises up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acid modifications, optionally amino acid substitutions, insertions and/or deletions. In some embodiments, the variant CD155 comprises a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NO: 47 or a specific binding fragment thereof. In some embodiments, the variant CD155 polypeptide exhibits altered binding to the ectodomain of TIGIT, CD226 or CD96 compared to the unmodified CD155. In some embodiments, the variant CD155 polypeptide exhibits altered binding to the ectodomain of TIGIT or CD226 compa