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US-12624117-B2 - Antagonistic anti-tumor necrosis factor receptor superfamily polypeptides

US12624117B2US 12624117 B2US12624117 B2US 12624117B2US-12624117-B2

Abstract

Described are antagonistic TNFR2 polypeptides, such as antibodies and antigen-binding fragments thereof, and the use of these polypeptides to inhibit the proliferation of regulatory T cells (T-regs) and/or myeloid-derived suppressor cells (MDSCs), to expand T effector cell populations or function, and to reduce the proliferation of, or directly kill, tumor cells, such as tumor cells that express TNFR2 antigen. The polypeptides, such as antibodies and antigen-binding fragments thereof, are TNFR2 antagonists, such as dominant TNFR2 antagonists. The polypeptides can be used to suppress the T-reg- or MDSC-mediated deactivation of tumor reactive T lymphocytes, expand populations of tumor-reactive cytotoxic T cells, and/or to directly kill TNFR2+ tumor cells. The antagonistic TNFR2 polypeptides described herein can be used to treat a wide variety of cancers and infectious diseases.

Inventors

  • Denise L. Faustman

Assignees

  • THE GENERAL HOSPITAL CORPORATION

Dates

Publication Date
20260512
Application Date
20190820

Claims (20)

  1. 1 . A humanized antibody or antigen-binding fragment thereof that specifically binds human TNFR2, wherein the antibody or antigen-binding fragment thereof comprises: (a) a human IgG2 hinge region that lacks a cysteine residue at positions 232 and 233 of the amino acid sequence of the IgG2 hinge region, numbering according to Kabat; (b) a heavy chain comprising an amino acid sequence with at least 85% sequence identity to the amino acid sequence of any one of SEQ ID NOs: 302-306, wherein the heavy chain comprises the following CDRs: a CDR-H1 having the amino acid sequence of SEQ ID NO: 274, a CDR-H2 having the amino acid sequence of SEQ ID NO: 258, and a CDR-H3 having the amino acid sequence of SEQ ID NO: 259; and (c) a light chain comprising an amino acid sequence with at least 85% sequence identity to the amino acid sequence of any one of SEQ ID NOs: 297-301, wherein the light chain comprises the following CDRs: a CDR-L1 having the amino acid sequence of SEQ ID NO: 260, a CDR-L2 having the amino acid sequence YTS, and a CDR-L3 having the amino acid sequence of SEQ ID NO: 273.
  2. 2 . An antibody or antigen-binding fragment thereof that specifically binds human TNFR2, wherein the antibody or antigen-binding fragment thereof comprises: (a) a heavy chain comprising the amino acid sequence of SEQ ID NO: 302 and a light chain comprising the amino acid sequence of SEQ ID NO: 297; (b) a heavy chain comprising the amino acid sequence of SEQ ID NO: 302 and a light chain comprising the amino acid sequence of SEQ ID NO: 298; (c) a heavy chain comprising the amino acid sequence of SEQ ID NO: 302 and a light chain comprising the amino acid sequence of SEQ ID NO: 299; (d) a heavy chain comprising the amino acid sequence of SEQ ID NO: 302 and a light chain comprising the amino acid sequence of SEQ ID NO: 300; (e) a heavy chain comprising the amino acid sequence of SEQ ID NO: 302 and a light chain comprising the amino acid sequence of SEQ ID NO: 301; (f) a heavy chain comprising the amino acid sequence of SEQ ID NO: 303 and a light chain comprising the amino acid sequence of SEQ ID NO: 297; (g) a heavy chain comprising the amino acid sequence of SEQ ID NO: 303 and a light chain comprising the amino acid sequence of SEQ ID NO: 298; (h) a heavy chain comprising the amino acid sequence of SEQ ID NO: 303 and a light chain comprising the amino acid sequence of SEQ ID NO: 299; (i) a heavy chain comprising the amino acid sequence of SEQ ID NO: 303 and a light chain comprising the amino acid sequence of SEQ ID NO: 300; (j) a heavy chain comprising the amino acid sequence of SEQ ID NO: 303 and a light chain comprising the amino acid sequence of SEQ ID NO: 301; (k) a heavy chain comprising the amino acid sequence of SEQ ID NO: 304 and a light chain comprising the amino acid sequence of SEQ ID NO: 297; (l) a heavy chain comprising the amino acid sequence of SEQ ID NO: 304 and a light chain comprising the amino acid sequence of SEQ ID NO: 298; (m) a heavy chain comprising the amino acid sequence of SEQ ID NO: 304 and a light chain comprising the amino acid sequence of SEQ ID NO: 299; (n) a heavy chain comprising the amino acid sequence of SEQ ID NO: 304 and a light chain comprising the amino acid sequence of SEQ ID NO: 300; (o) a heavy chain comprising the amino acid sequence of SEQ ID NO: 304 and a light chain comprising the amino acid sequence of SEQ ID NO: 301; (p) a heavy chain comprising the amino acid sequence of SEQ ID NO: 305 and a light chain comprising the amino acid sequence of SEQ ID NO: 297; (q) a heavy chain comprising the amino acid sequence of SEQ ID NO: 305 and a light chain comprising the amino acid sequence of SEQ ID NO: 298; (r) a heavy chain comprising the amino acid sequence of SEQ ID NO: 305 and a light chain comprising the amino acid sequence of SEQ ID NO: 299; (s) a heavy chain comprising the amino acid sequence of SEQ ID NO: 305 and a light chain comprising the amino acid sequence of SEQ ID NO: 300; (t) a heavy chain comprising the amino acid sequence of SEQ ID NO: 305 and a light chain comprising the amino acid sequence of SEQ ID NO: 301; (u) a heavy chain comprising the amino acid sequence of SEQ ID NO: 306 and a light chain comprising the amino acid sequence of SEQ ID NO: 297; (v) a heavy chain comprising the amino acid sequence of SEQ ID NO: 306 and a light chain comprising the amino acid sequence of SEQ ID NO: 298; (w) a heavy chain comprising the amino acid sequence of SEQ ID NO: 306 and a light chain comprising the amino acid sequence of SEQ ID NO: 299; (x) a heavy chain comprising the amino acid sequence of SEQ ID NO: 306 and a light chain comprising the amino acid sequence of SEQ ID NO: 300; or (y) a heavy chain comprising the amino acid sequence of SEQ ID NO: 306 and a light chain comprising the amino acid sequence of SEQ ID NO: 301.
  3. 3 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 302 and the light chain comprises SEQ ID NO: 297.
  4. 4 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 302 and the light chain comprises SEQ ID NO: 298.
  5. 5 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 302 and the light chain comprises SEQ ID NO: 299.
  6. 6 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 302 and the light chain comprises SEQ ID NO: 300.
  7. 7 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 302 and the light chain comprises SEQ ID NO: 301.
  8. 8 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 303 and the light chain comprises SEQ ID NO: 297.
  9. 9 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 303 and the light chain comprises SEQ ID NO: 298.
  10. 10 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 303 and the light chain comprises SEQ ID NO: 299.
  11. 11 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 303 and the light chain comprises SEQ ID NO: 300.
  12. 12 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 303 and the light chain comprises SEQ ID NO: 301.
  13. 13 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 304 and the light chain comprises SEQ ID NO: 297.
  14. 14 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 304 and the light chain comprises SEQ ID NO: 298.
  15. 15 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 304 and the light chain comprises SEQ ID NO: 299.
  16. 16 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 304 and the light chain comprises SEQ ID NO: 300.
  17. 17 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 304 and the light chain comprises SEQ ID NO: 301.
  18. 18 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 305 and the light chain comprises SEQ ID NO: 297.
  19. 19 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 305 and the light chain comprises SEQ ID NO: 298.
  20. 20 . The humanized antibody or antigen-binding fragment thereof of claim 1 , wherein the heavy chain comprises SEQ ID NO: 305 and the light chain comprises SEQ ID NO: 299.

Description

SEQUENCE LISTING This application contains a Sequence Listing which has been submitted electronically in ASCII file format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jan. 23, 2024, is named 00786-583002_Sequence_Listing_1_23_24_ST25 and is 195,185 bytes in size. BACKGROUND OF THE INVENTION The use of naturally-occurring and genetically engineered T lymphocytes is a prominent paradigm for ameliorating various human pathologies. For instance, while traditional therapeutic platforms for the treatment of cancer include surgical removal of tumor mass, radiation therapy, and administration of chemotherapeutics (Shewach, Chem. Rev., 109:2859-2861, 2009), the last decade has witnessed a resurgence in the application of adoptive immunotherapy to cancer treatment regimens. With the advent of chimeric antigen receptor (CAR-T) therapy, new methods have emerged for the infusion of autologous and allogeneic tumor-reactive T cells to patients (June, J. Clin. Invest., 117:1466-1476, 2007). CAR-T therapies harness the resources of the adaptive immune response in order to promote cancer cell cytotoxicity and eradicate tumor material. A common motif in adoptive immunotherapy is the use of T cells that exhibit the ability to selectively potentiate cytotoxicity in cells that display distinct tumor antigens. Examples of this technique include the administration of tumor-infiltrating lymphocytes (Dudley et al., J. Immunother., 26:332-342, 2003), as well as autologous or allogeneic T cells that have been genetically re-engineered so as to exhibit reactivity with a tumor-specific antigen (Yee et al., PNAS., 99:16168-16173, 2002). Despite the promise of T lymphocyte-based cancer immunotherapy, the development of this therapeutic platform has been hindered by the natural propensity of the immune system to suppress immune attacks mounted on self cells. Cancer cells express class I major histocompatibility complex (MHC) proteins that distinguish these cells from foreign cells. In order to prevent cell fratricide, regulatory T cells (T-reg cells) have evolved that suppress the activity of T cells that exhibit reactivity against “self” MHC antigens. T-reg cells represent a heterogeneous class of T cells that can be distinguished based on their unique surface protein presentation. The most well-understood populations of T-reg cells include CD4+, CD25+, FoxP3+ T-reg cells and CD17+ T-reg cells. The precise mechanisms by which these cells suppress autoreactive T cells is the subject of ongoing investigations, though it has been shown that certain classes of T-reg cells inhibit production of the proliferation-inducing cytokine IL-2 in target T cells and may additionally sequester IL-2 from autoreactive cells by virtue of the affinity of CD25 (a subdomain of the IL-2 receptor) for IL-2 (Josefowicz et al., Ann. Rev. Immun., 30:531-564, 2012). Although T-reg cells play an important role in maintaining peripheral tolerance, the same biochemical features that underlie the ability of these cells to modulate autoreactive T cell activity also serve to undermine adoptive immunotherapy and the natural immune response by suppressing the activity of tumor-reactive T lymphocytes. The development of chemical modulators of T-reg cell activity has been the subject of many pharmacological investigations, as access to an agent capable of inhibiting T-reg-mediated T cell suppression could vastly improve the scope and efficacy of adoptive cancer immunotherapy, as well as improve the ability of the immune system to eradicate pathogenic organisms that give rise to infectious diseases. There is a need for improved therapies for treating cell proliferation disorders, such as cancer, and a wide array of infectious diseases. SUMMARY OF THE INVENTION Described herein are antagonistic tumor necrosis factor receptor superfamily polypeptides, such as single-chain polypeptides, antibodies, antigen-binding fragments thereof, and constructs. For instance, featured are antagonistic tumor necrosis factor receptor 2 (TNFR2)-binding polypeptides, such as single-chain polypeptides, antibodies, antigen-binding fragments thereof, and constructs. Human TNFR2 contains four cysteine-rich domains (CRDs): CRD1 (amino acid residues 48-76 of SEQ ID NO: 7), CRD2 (amino acid residues 78-120 of SEQ ID NO: 7), CRD3 (amino acid residues 121-162 of SEQ ID NO: 7), and CRD4 (amino acid residues 162-202 of SEQ ID NO: 7). Antagonistic TNFR2 polypeptides described herein include those that bind one or more epitopes within CRD3 of TNFR2 and/or one or more epitopes within CRD4 of TNFR2, such as those that bind TNFR2 exclusively within one or more epitopes of CRD3 and/or one or more epitopes of CRD4 without binding TNFR2 within CRD1 and/or CRD2. The antagonistic TNFR2 polypeptides described herein include IgG2 isotype antibodies and antigen-binding fragments thereof that specifically bind TNFR2 at one or more of the epitopes detailed above. The present disclos