WO2022200478A1 - Tumor treatment with a 4-1bb/her2-bispecific agent and a her2-targeted tyrosine kinase inhibitor - Google Patents

Tumor treatment with a 4-1bb/her2-bispecific agent and a her2-targeted tyrosine kinase inhibitor Download PDF

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Publication number
WO2022200478A1
WO2022200478A1 PCT/EP2022/057721 EP2022057721W WO2022200478A1 WO 2022200478 A1 WO2022200478 A1 WO 2022200478A1 EP 2022057721 W EP2022057721 W EP 2022057721W WO 2022200478 A1 WO2022200478 A1 WO 2022200478A1
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her2
tumor
dose
tki
bispecific agent
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PCT/EP2022/057721
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French (fr)
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Thomas Jaquin
Rachida Bel Aiba
Markus Zettl
Shane Olwill
Luke Walker
Kristina HEINIG
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Pieris Pharmaceuticals Gmbh
Seagen Inc.
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Publication of WO2022200478A1 publication Critical patent/WO2022200478A1/en

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    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K16/00Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/32Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against translation products of oncogenes
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/33Heterocyclic compounds
    • A61K31/395Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/517Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with carbocyclic ring systems, e.g. quinazoline, perimidine
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K39/395Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
    • A61K39/39533Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals
    • A61K39/39558Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals against tumor tissues, cells, antigens
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00Antineoplastic agents
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K16/00Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2878Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K2317/00Immunoglobulins specific features
    • C07K2317/20Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/24Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K2317/00Immunoglobulins specific features
    • C07K2317/30Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/31Immunoglobulins specific features characterized by aspects of specificity or valency multispecific

Definitions

  • 4-1 BB is a co-stimulatory immune checkpoint and member of the tumor necrosis factor receptor (TNFR) family. It is primarily expressed on activated CD4+ and CD8+ T cells, activated B cells, and natural killer (NK) cells, and plays an important role in the regulation of the immune response.
  • TNFR tumor necrosis factor receptor
  • NK natural killer
  • TCR T cell receptor
  • MHC major histocompatibility complex
  • a monospecific 4-1BB-targeting agent such as an anti-4-1 BB antibody, may not be efficient by itself to cluster 4-1 BB and lead to efficient activation. Additionally, a monospecific 4-1 BB- targeting agent may lead to non-localized 4-1 BB clustering and activation, because the expression of 4-1 BB is not limited to tumor infiltrating lymphocytes (Makkouk et al., 2016, Alizadeh et al., 2011).
  • TNFR family members also illustrates the mechanisms of anti-TNFR antibodies, whereby the antibodies interact via their Fc regions with Fc-gamma receptors, engage activating Fc-gamma receptor-expressing immune cells, and facilitate the subsequent anti-tumor activity (Bulliard et al., 2014, Bulliard et al., 2013), suggesting an anti-4- 1BB antibody may trigger 4-1 BB clustering depending on the abundance of Fc-gamma receptor-positive cells but not restricted to a tumor microenvironment.
  • HER2 is a clinically-validated target across a broad spectrum of tumor types.
  • HER2 gene and overexpression of its product have been shown to play an important role in the development and progression of various types of cancer including breast, bladder, gastric, gastroesophageal, colorectal, and biliary tract cancer.
  • Anti-HER2 therapeutics such as trastuzumab, a monoclonal antibody specific for HER2, accrue significant clinical benefit in patients with early stage or metastatic HER2-positive (HER2+) breast cancer.
  • trastuzumab monotherapy in the metastatic setting results in response rates of 11-26% (clinical benefit rate: 48%), implying that many HER2+ tumors will not respond to monotherapy (Vogel et al. , 2002).
  • Cinrebafusp alfa (also known as PRS-343) is safe and clinically effective in the treatment of patients with advanced or metastatic HER2+ tumors (as described in PCT/EP2020/080892). Cinrebafusp alfa is designed to localize 4-1 BB/CD137 activation in the tumor in a HER2-dependent manner and promotes 4-1 BB clustering by bridging 4-1BB-positive T cells with HER2-expressing tumor cells, thereby providing a potent co-stimulatory signal to tumor antigen-specific T cells.
  • the present disclosure provides, among other things, methods for treating tumors, in particular HER2-expressing tumors, including HER2+ tumors and tumors that are characterized by a low expression of HER2.
  • the methods comprise the administration of a 4- 1 BB/HER2-bispecific agent and a HER2-targeted tyrosine kinase inhibitor (TKI).
  • TKI HER2-targeted tyrosine kinase inhibitor
  • 4-1 BB means human 4-1 BB (hu4-
  • Human 4-1 BB means a full-length protein defined by UniProt Q07011 , a fragment thereof, or a variant thereof, e.g., a naturally occurring variant, such as an alternatively spliced form or naturally-occurring allelic variant of hu4-1BB.
  • 4-1 BB is also known as CD137, tumor necrosis factor receptor superfamily member 9 (TNFRSF9) and induced by lymphocyte activation (ILA).
  • 4-1 BB of non-human species e.g., cynomolgus 4-1 BB and mouse 4-1 BB, is used.
  • HER2 means human HER2
  • Human HER2 means a full-length protein defined by UniProt P04626, a fragment thereof, or a variant thereof, e.g., a naturally occurring variant, such as an alternatively spliced form or naturally-occurring allelic variant of HER2.
  • HER2 is also known as human epidermal growth factor receptor 2, HER2/neu, receptor tyrosine-protein kinase erbB-2, cluster of differentiation 340 (CD340), proto-oncogene Neu, ERBB2 (human), Erbb2 (rodent), c-neu, or p185, and is a member of the ErbB family of receptor tyrosine kinases comprising HER1 (EGFR, ErbB1), HER2, HER3 (ErbB3) and HER4 (ErbB4).
  • Human HER2 is encoded by the ERBB2 gene.
  • HER2 of non-human species e.g., cynomolgus HER2 and mouse HER2, is used.
  • Cancer and “cancerous” refers to the physiological condition in mammals that is typically characterized by unregulated cell growth.
  • a “tumor” may comprise one or more cancerous cells.
  • a “lesion” is a localized change in a tissue or an organ. Tumors are types of lesions. “Target lesions” are lesions that have been specifically measured. “Non-target lesions” are lesions whose presences have been noted, but whose measurements have not been taken. The terms “cancer”, “tumor”, and “lesion” are used interchangeably herein.
  • the term “HER2-expressing tumor” or “HER2-expressing tumor cell” is meant to refer to a tumor/tumor cell with detectable expression of HER2, e.g., detectable by a quantitative assay, such as an mRNA-based qRT-PCR assay.
  • the term “HER2-expressing tumor” or “HER2-expressing tumor cell” refers to a HER2-positive (HER2+) tumor/tumor cell or to a tumor/tumor cell characterized by a low expression of HER2.
  • HER2-positive (HER2+) tumor is not particularly limited as long as it is recognized as such tumor by a person skilled in the art.
  • the term “HER2-positive (HER2+) tumor” is meant to refer to a tumor which is classified as a HER2+ tumor by immunohistochemistry (IHC) and/or (fluorescent) in situ hybridization ((F)ISH) analysis, e.g., according to the 2018 ASCO/CAP guidelines for HER2 testing in breast cancer (Wolff et al., 2018) or the 2016 CAP/ASCP/ASCO guidelines for HER2 testing in gastric or gastroesophageal adenocarcinoma (Bartley et al., 2016).
  • IHC immunohistochemistry
  • FISH fluorescent in situ hybridization
  • a HER2+ tumor is characterized by a HER2 status of IHC3+, IHC2+/(F)ISH+ or (F)ISH+, preferably IHC3+ or IHC2+/(F)ISH+.
  • a HER2+ tumor is characterized by HER2 gene amplification, e.g., as determined by (F)ISH or next generation sequencing (NGS) analysis.
  • HER2 low tumor is not particularly limited as long as it is recognized as such tumor by a person skilled in the art.
  • a “tumor characterized by a low expression of HER2” refers to a tumor which exhibits expression of HER2, albeit at a level which does not warrant its classification as a HER2+ tumor by IHC and (F)ISH.
  • a HER2 low tumor is a tumor which exhibits expression of HER2 at a level which is detectable by a quantitative assay, such as an mRNA-based qRT-PCR assay, but which is not classified as a HER2+ tumor by IHC and/or (F)ISH, e.g., according to the 2018 ASCO/CAP guidelines for HER2 testing in breast cancer (Wolff et al. , 2018) or the 2016 CAP/ASCP/ASCO guidelines for HER2 testing in gastric or gastroesophageal adenocarcinoma (Bartley et al., 2016).
  • a quantitative assay such as an mRNA-based qRT-PCR assay
  • a HER2 low tumor is characterized by a HER2 status of IHC1+ or IHC2+/(F)ISH- (i.e. , IHC2+ without HER2 gene amplification).
  • HER2 low tumors may also include tumors that are, for example, characterized by a HER2 status of IHC0 (and (F)ISH-), but that still exhibit expression of HER2, e.g., as determined in a quantitative assay, such as an mRNA-based qRT- PCR assay.
  • a HER2 low tumor does not exhibit HER2 gene amplification, e.g., as determined by (F)ISH or next generation sequencing (NGS) analysis.
  • metalstatic refers to a state of cancer where the cancer cells break away from where they first formed and form new tumors (metastatic tumors) in other parts of the body.
  • An "advanced” cancer may be locally advanced or metastatic. Locally advanced cancer refers to cancer that has grown outside the site or organ of origin but has not yet spread to distant parts of the body.
  • TME Tumor microenvironment
  • the tumor stroma comprises a compilation of cells, including fibroblasts/myofibroblasts, glial, epithelial, fat, immune, vascular, smooth muscle, and immune cells, blood vessels, signaling molecules, and the extracellular matrix (ECM), and serves a structural or connective role.
  • full tumor tissue consists of tumor cells and tumor stroma.
  • an “anti-tumor agent” or “anti-tumor drug” may act on a tumor, particularly a malignant tumor, and preferably has an anti-tumor effect or anti-tumor activity.
  • the “anti-tumor effect” or “anti-tumor activity” refers to actions of an anti-tumor agent on a tumor, particularly a malignant tumor, including stimulation of tumor-specific immune responses, reduction in target lesion, reduction in tumor size, suppression of the growth of tumor cells, suppression of metastasis, complete remission, partial remission, stabilization of disease, extension of the term before recurrence, extension of survival time of patients, or improvement of quality of life of patients.
  • An anti-tumor effect or anti-tumor activity may comprise or be associated with one or more of the following: (a) increased IL-2 secretion; (b) increased IL-2 secretion in a tumor microenvironment; (c) increased IFN-gamma secretion; (d) increased IFN- gamma secretion in a tumor microenvironment; (e) expansion of CD4 + T cells; (f) expansion of CD4 + T cells in a tumor microenvironment; (g) expansion of CD8 + T cells; (h) expansion of CD8 + T cells in a tumor microenvironment; (i) expansion of tumor-infiltrating lymphocytes; (j) activation of NK cells and increased antibody-dependent cell-mediated cytotoxicity (ADCC); (k) activation of NK cells and increased ADCC in a tumor microenvironment; and (I) increased secretion of soluble 4-1 BB (s4-1 BB).
  • treat refers to clinical intervention designed to alter the natural course of the subject being treated during the course of a physiological condition or disorder or clinical pathology.
  • a treatment may be a therapeutic treatment and/or a prophylactic or preventative measure, wherein the object is to prevent or slow down (lessen) an undesired physiological change or disorder, such as the growth, development or spread of a hyperproliferative condition, such as cancer.
  • Desired effects of treatment include, but are not limited to, decreasing the rate of disease progression, ameliorating or palliating the disease state, alleviating symptoms, stabilizing or not worsening the disease state, and remission of improved prognosis, whether detectable or undetectable. Desired effects of treatment also include prolonging survival as compared to expected survival if not receiving treatment.
  • a subject in need of treatment includes a subject already with the condition or disorder or prone to have the condition or disorder or a subject in which the condition or disorder is to be prevented.
  • a treatment given to a subject with tumor may lead to tumor response as described in Response Evaluation Criteria in Solid Tumors (RECIST) guideline (version 1.1) (Eisenhauer et al., 2009).
  • RECIST Response Evaluation Criteria in Solid Tumors
  • a treatment given to a subject with tumor may lead to complete response, partial response, stable disease, or progressive disease.
  • “Complete response (CR)” refers to the disappearance of all target lesions.
  • Partial response (PR)” refers to at least a 30% decrease in the sum of diameters of target lesions, taking as reference the baseline sum diameters.
  • Progressive disease refers to at least a 20% increase in the sum of diameters of target lesions, taking as reference the smallest sum on study (this includes the baseline sum if that is the smallest on study). In addition to the relative increase of 20%, the sum must also demonstrate an absolute increase of at least 5 mm.
  • Stable disease refers to neither sufficient shrinkage to qualify for PR nor sufficient increase to qualify for PD, taking as reference the smallest sum diameters while on study.
  • Duration of response (DoR) may be calculated as the time from the date of first documented response (CR or PR) to the date of documented progression or death after achieving response.
  • “combination”, “in combination with”, or “in conjunction with” relates to administration of one substance, drug, or other agent in addition to another substance, drug, or other agent.
  • the administration of substance, drug, or other agent may be before, during, or after administration of the other.
  • an “effective amount” of a drug or therapeutic agent is an amount sufficient to effect beneficial or desired effects of a treatment.
  • an effective amount an anti tumor agent may be one that is sufficient to enhance T cell activation to a desired level.
  • the effectiveness of a drug or therapeutic agent can be determined by suitable methods known in the art.
  • the effectiveness of an anti-tumor agent may be determined by Response Evaluation Criteria in Solid Tumors (RECIST).
  • An effective amount can be administered in one or more individual administrations or doses.
  • An effective amount can be administered alone with one agent or in combination with one or more additional agents.
  • T cell activation refers to a process leading to proliferation and/or differentiation of T cells. The activation of T cells may lead to the initiation and/or perpetuation of immune responses. As used herein, T cell activation may be used to assess the health of subjects with disease or disorders associated with dysregulated immune responses, such as cancer, autoimmune disease, and inflammatory disease. T cell proliferation refers to the expansion of a T cell population. “T cell proliferation” and “T cell expansion” are used interchangeably herein.
  • the terms “enhance T cell activity”, “activate T cells”, and “stimulate T cell response”, are used interchangeably herein and refer to inducing, causing, or stimulating T cells to have a sustained or amplified biological functions, or renew or reactivate exhausted or inactive T cells.
  • Exemplary signs of enhanced T cell activity include, but are not limited to: increased secretion of interleukin-2 (IL-2) from T cells, increased secretion of Interferon-gamma (IFN-gamma or IFN-y) from T cells, increased T cell proliferation, and/or increased antigen responsiveness (e.g., viral, pathogen, and tumor clearance). Methods of measuring such enhancement are known to the skilled in the art.
  • anti- or “targeting”, when used to describe a molecule in association with a protein target of interest means the molecule is capable of binding the protein target and/or modulating one or more biological functions of the protein target.
  • a protein target of interest e.g., 4-1 BB or HER2
  • an “anti-4-1 BB” molecule or a molecule “targeting 4-1 BB” as described herein is capable of binding 4-1 BB and/or modulating one or more biological functions of 4-1 BB.
  • Biological function of a protein target refers to the ability of the protein target to carry out its biological mission(s), e.g., binding to its binding partner(s) and mediating signaling pathway(s). Such molecule may, for example, act as an agonist of the protein target of interest.
  • antibody includes whole antibodies or any antigen binding fragment (i.e., “antigen-binding domain”) or single chain thereof.
  • a whole antibody refers to a glycoprotein comprising at least two heavy chains (HCs) and two light chains (LCs) inter connected by disulfide bonds.
  • Each heavy chain is comprised of a heavy chain variable domain (V H or HCVR) and a heavy chain constant region (C H ).
  • the heavy chain constant region is comprised of three domains, C Hi , C H 2 and C H 3.
  • Each light chain is comprised of a light chain variable domain (V L or LCVR) and a light chain constant region (C L ).
  • the light chain constant region is comprised of one domain, C L .
  • V H and V L regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDRs), interspersed with regions that are more conserved, termed framework regions (FRs).
  • CDRs complementarity determining regions
  • FRs framework regions
  • Each V H and V L is composed of three CDRs and four FRs, arranged in the following order from the amino-terminus to the carboxy-terminus: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
  • the variable regions of the heavy and light chains contain a binding domain that interacts with an antigen (for example, PD- L1).
  • the constant regions of the antibodies may optionally mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (C1q) of the classical complement system.
  • antigen-binding domain or “antigen-binding fragment” of an antibody refers to one or more fragments of an antibody that retain the ability to specifically bind to an antigen (e.g., HER2 or 4-1 BB). It has been shown that the antigen-binding function of an antibody can be performed by fragments of a full-length antibody.
  • binding fragments encompassed within the term “antigen-binding fragment” of an antibody include (i) a Fab fragment consisting of the V H , V L , C L and C Hi domains; (ii) a F(ab') 2 fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fab' fragment consisting of the V H , V L , C L and C Hi domains and the region between C Hi and C H 2 domains; (iv) an Fd fragment consisting of the V H and C Hi domains; (v) a single-chain Fv fragment consisting of the V H and V L domains of a single arm of an antibody, (vi) a dAb fragment (Ward et al.
  • V H domain consisting of a V H domain; and (vii) an isolated complementarity determining region (CDR) or a combination of two or more isolated CDRs which may optionally be joined by a synthetic linker; (viii) a “diabody” comprising the V H and V L connected in the same polypeptide chain using a short linker (see, e.g., patent documents EP 404,097; WO 93/11161; and Holliger et al., 1993); (ix) a “domain antibody fragment” containing only the V H or V L , where in some instances two or more V H regions are covalently joined.
  • CDR complementarity determining region
  • Antibodies may be polyclonal or monoclonal; xenogeneic, allogeneic, or syngeneic; or modified forms thereof (e.g., humanized, chimeric, or multispecific). Antibodies may also be fully human.
  • effector functions refer to those biological activities attributable to the Fc region of an antibody, which vary with the antibody isotype.
  • antibody effector functions include: C1q binding and complement dependent cytotoxicity (CDC), Fc receptor binding, antibody-dependent cell-mediated cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), cytokine secretion, immune complex-mediated antigen uptake by antigen presenting cells, down regulation of cell surface receptors (e.g. B cell receptor), and B cell activation.
  • the term “Npocalin” refers to a monomeric protein of approximately 18-20 kDa in weight, having a cylindrical b-pleated sheet supersecondary structural region comprising a plurality of b-strands (preferably eight b-strands designated A to H) connected pair-wise by a plurality of (preferably four) loops at one end to thereby comprise a ligand-binding pocket and define the entrance to the ligand-binding pocket.
  • the loops comprising the ligand-binding pocket used in the present invention are loops connecting the open ends of b-strands A and B, C and D, E and F, and G and H, and are designated loops AB, CD, EF, and GH.
  • Proteins falling in the definition of “Npocalin” as used herein include, but are not limited to, human lipocalins including tear Npocalin (Tic, Lcn1), Lipocalin-2 (Lcn2) or neutrophil gelatinase-associated Npocalin (NGAL), apolipoprotein D (ApoD), apolipoprotein M, a acid glycoprotein 1, a acid glycoprotein 2, armicroglobulin, complement component 8y, retinol-binding protein (RBP), the epididymal retinoic acid-binding protein, glycodelin, odorant binding protein I la, odorant-binding protein lib, lipocalin-15 (Lcn15), and prostaglandin D synthase.
  • Tic tear Npocalin
  • Lcn2 Lipocalin-2
  • NGAL neutrophil gelatinase-associated Npocalin
  • ApoD apolipoprotein D
  • apolipoprotein M a acid glyco
  • Lipocalin-2 or “neutrophil gelatinase-associated Npocalin” refers to human Lipocalin-2 (hLcn2) or human neutrophil gelatinase-associated Npocalin (hNGAL) and further refers to the mature human Lipocalin-2 or mature human neutrophil gelatinase- associated lipocalin.
  • the term “mature” when used to characterize a protein means a protein essentially free from the signal peptide.
  • a “mature hNGAL” of the instant disclosure refers to the mature form of human neutrophil gelatinase-associated lipocalin, which is free from the signal peptide.
  • Mature hNGAL is described by residues 21-198 of the sequence deposited with the SWISS-PROT Data Bank under Accession Number P80188, the amino acid sequence of which is indicated in SEQ ID NO: 1.
  • a “native sequence” refers to a protein or a polypeptide having a sequence that occurs in nature or having a wild-type sequence, regardless of its mode of preparation. Such native sequence protein or polypeptide can be isolated from nature or can be produced by other means, such as by recombinant or synthetic methods.
  • the “native sequence lipocalin” refers to a lipocalin having the same amino acid sequence as the corresponding polypeptide derived from nature.
  • a native sequence lipocalin can have the amino acid sequence of the respective naturally-occurring (wild-type) lipocalin from any organism, in particular, a mammal.
  • the term “native sequence”, when used in the context of a lipocalin specifically encompasses naturally-occurring truncated or secreted forms of the lipocalin, naturally-occurring variant forms such as alternatively spliced forms and naturally-occurring allelic variants of the lipocalin.
  • the terms “native sequence lipocalin” and “wild-type lipocalin” are used interchangeably herein.
  • a “mutein,” a “mutated” entity (whether protein or nucleic acid), or “mutant” refers to the exchange, deletion, or insertion of one or more amino acids or nucleotides, compared to the naturally-occurring (wild-type) protein or nucleic acid. Said term also includes fragments of a mutein as described herein.
  • the present disclosure explicitly encompasses lipocalin muteins, as described herein, having a cylindrical b-pleated sheet supersecondary structural region comprising eight b-strands connected pair-wise by four loops at one end to thereby comprise a ligand-binding pocket and define the entrance of the ligand binding pocket, wherein at least one amino acid of each of at least three of said four loops has been mutated as compared to the native sequence lipocalin.
  • Lipocalin muteins of the present disclosure preferably have the function of binding 4-1 BB as described herein.
  • fragment in connection with the lipocalin muteins of the disclosure, refers to proteins or polypeptides derived from full-length mature hNGAL or lipocalin muteins that are N-terminally and/or C-terminally truncated, i.e., lacking at least one of the N-terminal and/or C-terminal amino acids.
  • fragments may include at least 10 or more, such as 20 or 30 or more, consecutive amino acids of the primary sequence of mature hNGAL or the lipocalin mutein it is derived from and are usually detectable in an immunoassay of mature hNGAL.
  • Such a fragment may lack up to 2, up to 3, up to 4, up to 5, up to 10, up to 15, up to 20, up to 25, or up to 30 (including all numbers in between) of the N-terminal and/or C- terminal amino acids.
  • the fragment is preferably a functional fragment of mature hNGAL or the lipocalin mutein from which it is derived, which means that it preferably retains the binding specificity, preferably to 4-1 BB, of mature hNGAL or the lipocalin mutein it is derived from.
  • a functional fragment may comprise at least amino acids at positions 13-157, 15-150, 18-141 , 20-134, 25-134, or 28-134 corresponding to the linear polypeptide sequence of mature hNGAL.
  • a “fragment” with respect to 4-1 BB or HER2 refers to N-terminally and/or C- terminally truncated 4-1 BB or HER2 or protein domains of 4-1 BB or HER2. Fragments of 4-1 BB or HER2 as described herein retain the capability of the full-length 4-1 BB or HER2 to be recognized and/or bound by a 4-1BB/HER2-bispecific agent, in particular a lipocalin mutein, an antibody, and/or a fusion protein of the disclosure.
  • a “variant” of a protein described herein may generally refer to a variant protein having an amino acid sequence which is at least about 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98% or 99% identical to the amino acid sequence of said protein.
  • the variant may be a naturally occurring variant, such as an alternatively spliced form or naturally-occurring allelic variant of said protein.
  • the variant is a functional variant.
  • binding specificity relates to the ability of a biomolecule to discriminate between the desired target (for example, 4-1 BB or HER2) and one or more reference targets. It is understood that such specificity is not an absolute but a relative property and can be determined, for example, by means of SPR, western blots, ELISA, fluorescence activated cell sorting (FACS), radioimmunoassay (RIA), electrochemiluminescence (ECL), immunoradiometric assay (IRMA), ImmunoHistoChemistry (IHC), and peptide scans.
  • FACS fluorescence activated cell sorting
  • RIA radioimmunoassay
  • ECL electrochemiluminescence
  • IRMA immunoradiometric assay
  • IHC ImmunoHistoChemistry
  • the term “specific for,” “specific binding,” “specifically bind,” or “binding specificity” means that the agents or their antigen-targeting moieties bind to, react with, or are directed against 4-1 BB and/or HER2, as described herein, but do not essentially bind another protein.
  • the term “another protein” includes any proteins that are not 4-1 BB or HER2 or proteins closely related to or being homologous to 4-1 BB or HER2.
  • 4-1 BB or HER2 from species other than human and fragments and/or (naturally occurring) variants of 4-1 BB or HER2 are not excluded by the term “another protein.”
  • the term “does not essentially bind” means that the 4-1BB/HER2- bispecific agents described herein or their individual antigen-targeting moieties bind another protein with lower binding affinity than 4-1 BB and/or HER2, i.e., show a cross-reactivity of less than 30%, preferably 20%, more preferably 10%, particularly preferably less than 9, 8, 7, 6, or 5%.
  • bispecific refers to a molecule is able to specifically bind to at least two distinct targets.
  • a bispecific molecule comprises at least two target-binding sites, each of which is specific for a different target.
  • the bispecific molecule is capable of simultaneously binding two targets.
  • 4-1BB/HER2-bispecific agent is meant to refer to a bispecific molecule comprising at least one 4-1BB-targeting moiety and at least one HER2- targeting moiety.
  • the targeting moieties may be independently selected from the group consisting of antibodies and antigen-binding fragments thereof, antibody mimetics, small molecules and other antigen-binding molecules, such as aptamers.
  • Antibody mimetics are organic compounds (typically artificial peptides or proteins) that, like antibodies, can specifically bind antigens, but that are not structurally related to antibodies.
  • Exemplary antibody mimetics include, but are not limited to, Affibody molecules, Affilins, Affimers, Affitins, Alphabodies, lipocalin muteins, Avimers, DARPins, Fynomers, Kunitz domain peptides, Monobodies and nanoCLAMPs.
  • the 4-1BB/HER2-bispecific agent may be a conjugate or a fusion protein.
  • the 4-1BB/HER2-bispecific agent may be a bispecific antibody, e.g., having a format as described in Brinkmann and Kontermann, 2017.
  • conjugate As used interchangeably herein, the terms “conjugate,” “conjugation,” “fuse,”
  • fusion refers to the joining together of two or more subunits, through all forms of covalent or non-covalent linkage, by means including, but not limited to, genetic fusion, chemical conjugation, coupling through a linker or a cross-linking agent, and non-covalent association.
  • fusion polypeptide or “fusion protein” as used herein refers to a polypeptide or protein comprising two or more subunits.
  • a fusion protein as described herein comprises two or more subunits, at least one of these subunits being capable of specifically binding to 4-1 BB, and a further subunit capable of specifically binding to HER2.
  • these subunits may be linked by covalent or non-covalent linkage.
  • the fusion protein is a translational fusion between the two or more subunits.
  • the translational fusion may be generated by genetically engineering the coding sequence for one subunit in a reading frame with the coding sequence of a further subunit.
  • Both subunits may be interspersed by a nucleotide sequence encoding a linker.
  • the subunits of a fusion protein of the present disclosure may also be linked through chemical conjugation.
  • the subunits forming the fusion protein are typically linked to each other as follows: C-terminus of one subunit to N-terminus of another subunit, or C-terminus of one subunit to C- terminus of another subunit, or N-terminus of one subunit to N-terminus of another subunit, or N-terminus of one subunit to C-terminus of another subunit.
  • the subunits of the fusion protein can be linked in any order and may include more than one of any of the constituent subunits.
  • fusion protein may also refer to the protein comprising the fused sequences and all other polypeptide chain(s) of the protein (complex).
  • fusion protein may refer to the single polypeptide chain comprising the lipocalin mutein and the heavy or light chain of the immunoglobulin.
  • fusion protein may also refer to the entire immunoglobulin (both light and heavy chains) and the lipocalin mutein fused to one or both of its heavy and/or light chains.
  • a preferred subunit of a fusion protein disclosed herein refers to a single protein or a separate polypeptide chain, which may form a stable folded structure by itself and define a unique function of providing a binding motif towards a target.
  • a preferred subunit of the disclosure is a lipocalin mutein.
  • a preferred subunit of the disclosure is a full-length immunoglobulin or an antigen-binding domain thereof.
  • a “linker” that may be comprised by a fusion protein of the present disclosure joins together two or more subunits of a fusion protein as described herein.
  • the linkage can be covalent or non-covalent.
  • a preferred covalent linkage is via a peptide bond, such as a peptide bond between amino acids.
  • a preferred linker is a peptide linker. Accordingly, in a preferred embodiment, said linker comprises one or more amino acids, such as 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids.
  • Preferred peptide linkers are described herein, including glycine-serine (GS) linkers, glycosylated GS linkers, and proline- alanine-serine polymer (PAS) linkers.
  • GS glycine-serine
  • PAS proline- alanine-serine polymer
  • Exemplary linkers include, but are not limited to, the linkers with the amino acid sequences of SEQ ID NOs: 4-14.
  • Other preferred linkers include chemical linkers.
  • cinrebafusp alfa also known as PRS-343, refers to the 4-1BB/HER2- bispecific fusion protein having the amino acid sequences of SEQ ID NOs: 50 and 51.
  • the overall structure of cinrebafusp alfa is shown in Figure 9 D.
  • sequence identity or “identity” denotes a property of sequences that measures their similarity or relationship.
  • sequence identity means the percentage of pair-wise identical residues - following (homologous) alignment of a sequence of a protein or polypeptide of the disclosure with a sequence in question - with respect to the number of residues in the longer of these two sequences. Sequence identity is measured by dividing the number of identical amino acid residues by the total number of residues and multiplying the product by 100.
  • BLAST Altschul et al., 1997)
  • BLAST2 Altschul et al., 1990
  • FASTA Pearson and Lipman, 1988
  • GAP Needleman and Wunsch, 1970
  • Smith-Waterman Smith and Waterman, 1981
  • Wisconsin GCG Package for determining sequence identity using standard parameters.
  • the percentage of sequence identity can, for example, be determined herein using the program BLASTP, version 2.2.5, November 16, 2002 (Altschul et al., 1997), calculating the percentage of numbers of “positives” (homologous amino acids) from the total number of amino acids selected for the alignment.
  • Gaps are spaces in an alignment that are the result of additions or deletions of amino acids. Thus, two copies of exactly the same sequence have 100% identity, but sequences that are less highly conserved, and have deletions, additions, or replacements, may have a lower degree of sequence identity.
  • HER2-targeted TKI refers to tyrosine kinase inhibitors (TKIs) of HER2, preferably human HER2.
  • TKIs tyrosine kinase inhibitors
  • Suitable TKIs are known to a person skilled in the art and are described in, e.g., Arkin and Moasser, 2008, and Conlon et al., 2021.
  • the term is meant to include TKIs which exclusively or selectively target HER2 as well as TKIs which target HER2 and at least one other member of the ErbB family, e.g., epidermal growth factor receptor (EGFR).
  • EGFR epidermal growth factor receptor
  • Exemplary HER2-targeted TKIs include, but are not limited to, tucatinib, lapatinib, neratinib, pyrotinib, erlotinib and afatinib.
  • reversible TKI refers to a TKI which binds reversibly to its target tyrosine kinase (e.g., HER2) and slows down or inhibits its activity.
  • a reversible TKI does not bind covalently to its target tyrosine kinase.
  • exemplary reversible HER2-targeted TKIs include, but are not limited to, tucatinib, lapatinib and erlotinib.
  • small molecule generally refers to a low molecular weight (e.g., ⁇ 900 Daltons) organic compound.
  • Tucatinib also known as ONT-380 and ARRY-380, refers to the small molecule TKI that suppresses or blocks HER2 activation. Tucatinib is sold under the brand name “Tukysa ® ” and has the following structure:
  • lapatinib refers to the small molecule TKI targeting HER2 and EGFR.
  • Lapatinib is sold under the brand names “Tykerb ® ” and “Tyverb ® ”, and has the following structure:
  • Neratinib also known as HKI-272, refers to the small molecule TKI targeting HER2 and EGFR. Neratinib is sold under the brand name “Nerlynx ® ”, and has the following structure:
  • pyrotinib also known as SHR-1258, refers to the small molecule TKI targeting HER2 and EGFR and having the following structure:
  • erlotinib refers to the small molecule TKI targeting EGFR and HER2.
  • Erlotinib is sold under the brand name “Tarceva ® ” and has the following structure:
  • afatinib refers to the small molecule inhibitor of HER2 and EGFR.
  • Afatinib is sold under the brand names “Gilotrif ® ” and “Giotrif ® ” and has the following structure:
  • sample is defined as a biological sample taken from any subject.
  • Biological samples include, but are not limited to, blood, serum, urine, feces, semen, or tissue, including tumor tissue.
  • a “subject” is a vertebrate, preferably a mammal, more preferably a human.
  • the term “mammal” is used herein to refer to any animal classified as a mammal, including, without limitation, humans, domestic and farm animals, and zoo, sports, or pet animals, such as sheep, dogs, horses, cats, cows, rats, pigs, apes such as cynomolgus monkeys, to name only a few illustrative examples.
  • the “mammal” is human.
  • kit of parts refers to an article of manufacture comprising one or more containers and, optionally, a data carrier.
  • Said container(s) may be filled with the (re-)agents and compositions as described herein. Additional containers may be included in the kit that contain, e.g., diluents, buffers and/or further (re agents or compositions.
  • Said data carrier may be a non-electronic data carrier, e.g., a graphical data carrier such as an information leaflet, an information sheet, a bar code or an access code, or an electronic data carrier, such a CD, a DVD, a microchip or another semiconductor-based electronical data carrier.
  • the access code may allow access to a database.
  • Said data carrier may comprise instructions for the use of the (re-)agents and compositions as described herein.
  • the term “pharmaceutical composition” refers to a composition comprising the (re-)agents as described herein and, optionally, one or more pharmaceutically acceptable carriers and/or excipients.
  • pharmaceutically acceptable refers to the non-toxicity of a material, which, preferably, does not interfere with the activity of the active (re-)agent(s) of the pharmaceutical composition.
  • the term “about” or “approximately” means within 20%, preferably within 15%, preferably within 10%, and more preferably within 5% of a given value or range. It also includes the concrete number, i.e. “about 20” includes the number of 20. The term “at least about” as used herein includes the concrete number, i.e., “at least about 20” includes 20.
  • Figure 1 provides representative results of experiments in which the ability of the fusion protein of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses with or without addition of tucatinib was investigated, using tumor cell lines characterized by different expression levels of HER2.
  • Cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 1 A) as well as tumor cell lines expressing HER2 at a significantly lower level: ZR-75-1 (IHC2+/(F)ISH-; Figure 1 B), MKN-7 ( Figure 1 C) and HT-29 (IHC1+; Figure 1 D) (see also Table 1).
  • an anti-human CD3 antibody was coated on a plastic culture dish, and subsequently the cell line under study was cultured on the dish overnight (with or without addition of 50 nM tucatinib).
  • purified T cells were incubated on the coated surface for two days in the presence of various concentrations of (i) PRS-343 (with or without tucatinib), (ii) a modified lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without tucatinib) and (iii) the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without tucatinib).
  • Figure 2 provides a summary of the results of three independent IL-2 secretion experiments as shown in Figure 1, using PBMCs of four donors in total.
  • Figure 3 provides representative results of experiments in which the ability of the fusion protein of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses with or without addition of lapatinib was investigated, using tumor cell lines characterized by different expression levels of HER2.
  • Cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 3 A) as well as tumor cell lines expressing HER2 at a significantly lower level: ZR-75-1 (IHC2+/(F)ISH-; Figure 3 B), MKN-7 ( Figure 3 C) and HT-29 (IHC1+; Figure 3 D) (see also Table 1).
  • an anti-human CD3 antibody was coated on a plastic culture dish, and subsequently the cell line under study was cultured on the dish overnight (with or without addition of 50 nM lapatinib).
  • purified T cells were incubated on the coated surface for two days in the presence of various concentrations of (i) PRS-343 (with or without lapatinib), (ii) a modified lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without lapatinib) and (iii) the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without lapatinib).
  • Figure 4 provides representative results of experiments in which the ability of the fusion protein of SEQ ID NOs: 50 and 51 (PRS-343) to activate the 4-1 BB pathway in the presence of target tumor cell lines characterized by different expression levels of HER2, with or without addition of tucatinib, was investigated.
  • Cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 4 A) as well as tumor cell lines expressing HER2 at a significantly lower level: JIMT-1 ( Figure 4 A), ZR-75-1 (IHC2+/(F)ISH-; Figure 4 B), HT-29 (IHC1+; Figure 4 B) and MKN-7 ( Figure 4 C) (see also Table 1).
  • NF-KB- luc2P/4-1BB Jurkat reporter cells were added to the coated tumor cells in the presence of various concentrations of (i) PRS-343 (with or without tucatinib) and (ii) a modified lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without tucatinib).
  • the luminescence signal (RLU) represents a relative measurement of 4-1 BB pathway activation. Background depicted as mean (dotted line) ⁇ SEM (grey area).
  • Bg1 background of Jurkat:4-1BB + tumor cells in tucatinib
  • bg2 background of Jurkat: 4-1 BB + target cells in DMSO.
  • Figure 5 provides representative results of experiments in which the ability of the fusion protein of SEQ ID NOs: 50 and 51 (PRS-343) to activate the 4-1 BB pathway in the presence of target tumor cell lines characterized by different expression levels of HER2, with or without addition of tucatinib, was investigated.
  • Cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 5 A) as well as tumor cell lines expressing HER2 at a significantly lower level: JIMT-1 ( Figure 5 B), ZR-75-1 (IHC2+/(F)ISH-; Figure 5 B), HT-29 (IHC1+; Figure 5 C) and MKN-7 ( Figure 5 C) (see also Table 1).
  • NF-KB- luc2P/4-1BB Jurkat reporter cells were added to the coated tumor cells in the presence of various concentrations of (i) PRS-343 (with or without tucatinib) and (ii) a modified lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without tucatinib).
  • the luminescence signal (RLU) represents a relative measurement of 4-1 BB pathway activation. Background depicted as mean (dotted line) ⁇ SEM (grey area).
  • Bg1 background of Jurkat:4-1BB + tumor cells in tucatinib bg2: background of Jurkat: 4-1 BB + tumor cells in DMSO bg3: background of Jurkat: 4-1 BB + tumor cells in medium.
  • Figure 6 provides representative results of experiments in which the ability of the fusion protein of SEQ ID NOs: 50 and 51 (PRS-343) to activate the 4-1 BB pathway in the presence of target tumor cell lines characterized by different expression levels of HER2, with or without addition of lapatinib, was investigated.
  • Cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 6 A) as well as tumor cell lines expressing HER2 at a significantly lower level: ZR-75-1 (IHC2+/(F)ISH-; Figure 6 A), JIMT-1 (Figure 6 B), MKN-7 ( Figure 6 B) and HT-29 (IHC1+; Figure 6 C) (see also Table 1).
  • NF-KB- luc2P/4-1BB Jurkat reporter cells were added to the coated tumor cells in the presence of various concentrations of (i) PRS-343 (with or without lapatinib) and (ii) a modified lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without lapatinib).
  • the luminescence signal (RLU) represents a relative measurement of 4-1 BB pathway activation. Background depicted as mean (dotted line) ⁇ SEM (grey area).
  • Bg1 background of Jurkat:4-1BB + tumor cells in lapatinib
  • bg2 background of Jurkat: 4-1 BB + target cells in DMSO.
  • Figure 7 provides representative results of experiments in which the ability of the fusion polypeptide of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses in the presence of target tumor cell lines characterized by different expression levels of HER2, with or without addition of tucatinib, was investigated, using supernatant IFN-gamma levels as readout.
  • Tumor cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 7 A) as well as tumor cell lines expressing HER2 at a significantly lower level: ZR-75-1 (IHC2+/(F)ISH-; Figure 7 B), HT-29 (IHC1+; Figure 7 C) and MKN-7 ( Figure 7 D) (see also Table 1).
  • Top and bottom panels relate to two independent experiments using PBMCs from different volunteer donors. Tumor cells with or without addition of 50 nM tucatinib were mixed with T cells that were previously expanded for 12 days following stimulation with a pool of defined peptides from various known viral pathogens (CEF pool, JPT).
  • An lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without addition of tucatinib) and the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without addition of tucatinib) were used as controls.
  • Analysis and quantification were performed using Mesoscale Discovery software (MSD DISCOVERY WORKBENCH Software). Data were exported to GraphPad Prism for further analysis.
  • Figure 8 provides representative results of experiments in which the ability of the fusion polypeptide of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses in the presence of target tumor cell lines characterized by different expression levels of HER2, with or without addition of tucatinib, was investigated, using soluble 4-1 BB (s4-1BB) levels, a biomarker for target engagement of 4-1BB-agonistic agents, as readout.
  • s4-1BB soluble 4-1 BB
  • Tumor cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 8 A) as well as tumor cell lines expressing HER2 at a significantly lower level: ZR-75-1 (IHC2+/(F)ISH-; Figure 8 B), HT- 29 (IHC1+; Figure 8 C) and MKN-7 ( Figure 8 D) (see also Table 1).
  • Top and bottom panels relate to two independent experiments using PBMCs from different volunteer donors. Tumor cells with or without addition of 50 nM tucatinib were mixed with T cells that were previously expanded for 12 days following stimulation with a pool of defined peptides from various known viral pathogens (CEF pool, JPT).
  • An lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without addition of tucatinib) and the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without addition of tucatinib) were used as controls.
  • Analysis and quantification were performed using Mesoscale Discovery software (MSD DISCOVERY WORKBENCH Software). Data were exported to GraphPad Prism for further analysis.
  • Figure 9 provides an overview over the design of 4-1 BB/HER2-bispecific fusion proteins comprising an antibody specific for HER2 (e.g., an antibody shown in SEQ ID NOs: 50 and 48) and a lipocalin mutein specific for 4-1 BB (e.g., a lipocalin mutein shown in SEQ ID NO: 22).
  • an antibody specific for HER2 e.g., an antibody shown in SEQ ID NOs: 50 and 48
  • a lipocalin mutein specific for 4-1 BB e.g., a lipocalin mutein shown in SEQ ID NO: 22.
  • Representative 4-1BB/HER2-bispecific fusion proteins were made by genetically fusing one or more anti-4-1 BB lipocalin muteins, via a peptide linker, at the N-terminus or the C-terminus, to an anti-HER2 antibody at the C-terminus of the antibody heavy chain domain (HC) ( Figure 9 D), the N-terminus of the HC ( Figure 9 A), the C-terminus of the antibody light chain (LC) ( Figure 9 C), and/or the N-terminus of the LC ( Figure 9 B), resulting in the fusion proteins of SEQ ID NOs: 50 and 51, SEQ ID NOs: 50 and 53, SEQ ID NOs: 52 and 49, and SEQ ID NOs: 54 and 49.
  • An engineered lgG4 backbone with the mutations S228P, F234A, and L235A was used for the anti-HER2 antibody as included in the fusion proteins.
  • Figure 10 provides representative results of experiments in which the surface distribution of the fusion polypeptide of SEQ ID NOs: 50 and 51 (PRS-343) on tumor cells with or without addition of tucatinib was determined by pulse chase flow cytometry.
  • Tumor cells with different expression levels of HER2 were used, namely SK-BR-3 cells (IHC3+; Figure 10 A) and MKN-7 cells ( Figure 10 B) (see also Table 1).
  • DMSO was used as control.
  • the present disclosure provides new therapies including 4-1BB/HER2-bispecific agents and HER2-targeted TKIs.
  • the present disclosure also provides that a 4-1BB/HER2- bispecific agent and a HER2-targeted TKI act in a synergistic manner to provide an anti-tumor effect against tumor cells characterized by different expression levels of HER2, including HER2+ tumor cells and tumor cells characterized by a low expression of HER2.
  • the present disclosure provides a method of treating a tumor in a subject, comprising administering to the subject: (a) a 4-1BB/HER2-bispecific agent; and (b) a HER2-targeted tyrosine kinase inhibitor (TKI).
  • TKI HER2-targeted tyrosine kinase inhibitor
  • the present disclosure provides a method of treating a tumor in a subject, comprising: (a) administering to the subject a 4-1BB/HER2-bispecific agent, wherein the subject is also receiving a HER2- targeted tyrosine kinase inhibitor (TKI), so that the subject receives therapy with both; or (b) administering to the subject a HER2-targeted TKI, wherein the subject is also receiving a 4- 1 BB/HER2-bispecific agent, so that the subject receives therapy with both.
  • the tumor is a HER2-expressing tumor.
  • the tumor is characterized by a low expression of HER2.
  • the tumor is characterized by a HER2 status of IHC1+ or IHC2+/(F)ISH-. In some embodiments, the tumor does not exhibit HER2 gene amplification, e.g., as determined by (F)ISH or next generation sequencing (NGS) analysis.
  • F F
  • NGS next generation sequencing
  • the tumor is a HER2-positive (HER2+) tumor.
  • the tumor is characterized by a HER2 status of IHC3+, IHC2+/(F)ISH+ or (F)ISH+, preferably IHC3+ or IHC2+/(F)ISH+.
  • the tumor exhibits HER2 gene amplification, e.g., as determined by (F)ISH or next generation sequencing (NGS) analysis.
  • the 4-1BB/HER2-bispecific agent comprises at least one
  • the targeting moieties are independently selected from the group consisting of antibodies and antigen-binding fragments thereof, antibody mimetics, small molecules and other antigen-binding molecules, such as aptamers.
  • the antibody mimetics are selected from the group consisting of Affibody molecules, Affilins, Affimers, Affitins, Alphabodies, lipocalin muteins, Avimers, DARPins, Fynomers, Kunitz domain peptides, Monobodies and nanoCLAMPs.
  • HER2- targeting antibodies are known in the art and include, for example, trastuzumab and pertuzumab.
  • 4-1BB-targeting antibodies are also known in the art and include, for example, urelumab and utomilumab.
  • the 4-1BB/HER2-bispecific agent is a conjugate or a fusion protein.
  • the 4-1BB/HER2-bispecific agent is a bispecific antibody.
  • the 4-1BB/HER2-bispecific agent is a fusion protein comprising an antibody or an antigen-binding domain thereof specific for HER2 and at least one lipocalin mutein specific for 4-1 BB. More particularly, the fusion protein may comprise at least two subunits in any order: (1) a first subunit that comprises an antibody or an antigen-binding domain thereof specific for HER2, and (2) a second subunit that comprises a lipocalin mutein specific for 4-1 BB. In some embodiments, the fusion protein contains at least one additional subunit, for example, a third subunit. In some embodiments, the fusion protein contains a third subunit that comprises a lipocalin mutein specific for 4-1 BB.
  • At least one subunit of the fusion protein is fused at its N-terminus and/or its C-terminus to another subunit. In some embodiments, at least one subunit of the fusion protein is fused to another subunit via a linker.
  • a linker as described herein may be a peptide linker, for example, an unstructured glycine-serine (GS) linker, a glycosylated GS linker, or a proline-alanine-serine polymer (PAS) linker.
  • GS unstructured glycine-serine
  • PAS proline-alanine-serine polymer
  • a (Gly 4 Ser) 3 linker ((G 4 S) 3 ) as shown in SEQ ID NO: 4 is used.
  • Other exemplary linkers are shown in SEQ ID NOs: 5-14.
  • the second subunit of the fusion protein is linked via a linker, preferably a (G 4 S) 3 linker, at its N-terminus to each of the C-terminus of the heavy chain constant region (CH) of the antibody or an antigen binding domain thereof comprised in the first subunit.
  • a lipocalin mutein subunit is fused to an antibody subunit of the fusion protein via a peptide linker.
  • a lipocalin mutein subunit is fused, via a peptide linker, at its N-terminus or its C- terminus to an antibody subunit at the C-terminus of the antibody heavy chain (HC), the N- terminus of the HC, the C-terminus of the antibody light chain (LC), and/or the N-terminus of the LC (e.g., as shown in Figure 9).
  • the 4-1BB/HER2-bispecific agent is a fusion protein comprising an antibody specific for HER2 fused at the C-terminus of both heavy chains to the N-terminus of a lipocalin mutein specific for 4-1 BB, preferably via a peptide linker, e.g., a (G 4 S) 3 linker.
  • a peptide linker e.g., a (G 4 S) 3 linker.
  • the Fc function of the Fc region of the antibody or an antigen-binding domain thereof comprised in the fusion protein is preserved. Accordingly, the fusion protein may be capable of binding Fc receptor-positive cell at the same time while simultaneously engaging 4-1 BB and HER2. In some other embodiments, the Fc function of the Fc region of the antibody or an antigen-binding domain thereof comprised in the fusion protein is reduced or fully suppressed, while the fusion protein is simultaneously engaging 4-1 BB and HER2. In some embodiments, this may be achieved, for example, by switching from the lgG1 backbone to lgG4, as lgG4 is known to display reduced Fc-gamma receptor interactions compared to lgG1.
  • mutations may be introduced into the lgG4 backbone such as F234A and L235A.
  • an S228P mutation may also be introduced into the lgG4 backbone to minimize the exchange of lgG4 half-antibody (Silva et al. , 2015).
  • F234A and L235A mutations may be introduced for decreased ADCC and ADCP (Glaesner et al., 2010) and/or M428L and N434S mutations or M252Y, S254T, and T256E mutations for extended serum half-life (Dall'Acqua et al., 2006, Zalevsky et al., 2010).
  • an additional N297A mutation may be present in the antibody heavy chain of the fusion protein in order to remove the natural glycosylation motif.
  • the antibody or antigen-binding domain thereof comprised in the fusion protein comprises the three heavy chain complementarity-determining regions (CDRs) shown in SEQ ID NO: 40, SEQ ID NO: 41, and SEQ ID NO: 42, and/or the three light chain CDRs shown in SEQ ID NO: 43, SEQ ID NO: 44, and SEQ ID NO: 45.
  • the antibody or antigen-binding domain thereof comprised in the fusion protein comprises a heavy chain variable region (HCVR) shown in SEQ ID NO: 46, and/or a light chain variable region (LCVR) shown in SEQ ID NO: 47.
  • HCVR heavy chain variable region
  • LCVR light chain variable region
  • the antibody or antigen-binding domain thereof comprised in the fusion protein comprises a heavy chain shown in SEQ ID NO: 49, and/or a light chain shown in SEQ ID NO: 50.
  • the antibody or antigen-binding domain thereof comprised in the fusion protein has a HCVR with at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or even higher sequence identity to an amino acid sequence shown in SEQ ID NO: 46, and/or a LCVR with at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or even higher sequence identity to an amino acid sequence shown in SEQ ID NO: 47.
  • the antibody or antigen-binding domain thereof comprised in the fusion protein has a heavy chain with at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or even higher sequence identity to an amino acid sequence shown in SEQ ID NO: 49, and/or a light chain with at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or even higher sequence identity to the amino acid sequence shown in SEQ ID NO: 50.
  • the antibody comprises: (a) three heavy chain complementarity-determining regions (CDRs) shown in SEQ ID NO: 40, SEQ ID NO: 41, and SEQ ID NO: 42, and three light chain CDRs shown in SEQ ID NO: 43, SEQ ID NO: 44, and SEQ ID NO: 45; and (b) a heavy chain with at least 95% sequence identity to the amino acid sequence shown in SEQ ID NO: 49, and a light chain with at least 95% sequence identity to the amino acid sequence shown in SEQ ID NO: 50.
  • CDRs three heavy chain complementarity-determining regions
  • the antibody or antigen-binding domain thereof comprised in the fusion protein is an anti-HER2 antibody. In some embodiments, the antibody or antigen binding domain thereof comprised in the fusion protein is trastuzumab. In some embodiments, the antibody or antigen-binding domain thereof comprised in the fusion protein is trastuzumab with an lgG4 backbone.
  • the lipocalin mutein comprised in the fusion protein is a mutein of mature human neutrophil gelatinase-associated lipocalin (hNGAL) having binding specificity for 4-1 BB.
  • hNGAL human neutrophil gelatinase-associated lipocalin
  • a mutein of mature hNGAL may be designated herein as an “hNGAL mutein”.
  • the lipocalin mutein comprised in the fusion protein is capable of binding human 4-1 BB with high affinity and/or co-stimulating human T cells when immobilized on a plastic dish together with an anti-CD3 antibody.
  • the lipocalin mutein comprised in the fusion protein comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 21-39 or of a fragment or variant thereof.
  • the lipocalin mutein comprised in the fusion protein has the amino acid sequence shown in SEQ ID NO: 22.
  • the lipocalin mutein comprised in the fusion protein has an amino acid sequence with high sequence identity, such as at least 70%, at least 75%, at least 80%, at least 82%, at least 85%, at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or higher identity, to an amino acid sequence selected from the group consisting of SEQ ID NOs: 21-39.
  • the lipocalin mutein comprised in the fusion protein has an amino acid sequence with high sequence identity, such as at least 70%, at least 75%, at least 80%, at least 82%, at least 85%, at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or higher identity, to the amino acid sequence shown in SEQ ID NOs: 22.
  • Suitable lipocalin muteins that are specific for 4-1 BB are also described in WO 2016/177762 A1, which is incorporated herein by reference in its entirety.
  • the fusion protein is generated by genetic fusion of a 4-
  • 1BB-specific hNGAL mutein to a trastuzumab lgG4 variant, joined by a flexible, non- immunogenic peptide linker.
  • the fusion protein comprises the sets of amino acid sequences selected from the group consisting of SEQ ID NOs: 50 and 51, SEQ ID NOs: 50 and 53, SEQ ID NOs: 52 and 49, and SEQ ID NOs: 54 and 49.
  • the fusion protein comprises amino acid sequences having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or higher sequence identity to the amino acid sequences shown in SEQ ID NOs: 50 and 51, SEQ ID NOs: 50 and 53, SEQ ID NOs: 52 and 49, and SEQ ID NOs: 54 and 49.
  • a given value for the sequence identity means that a protein of interest comprises an amino acid sequence that has at least the given value of sequence identity to one chain of the bispecific fusion protein and comprises an amino acid sequence that has at least the given value of sequence identity to the other chain of the fusion protein.
  • the fusion protein comprises the amino acid sequences shown in SEQ ID NOs: 50 and 51.
  • the fusion protein comprises two chains having the amino acid sequence shown in SEQ ID NO: 50 and two chains having the amino acid sequence shown in SEQ ID NO: 51.
  • Suitable 4-1 BB/HER2-bispecifc fusion proteins comprising an antibody or an antigen-binding domain thereof specific for HER2 and a lipocalin mutein specific for 4-1 BB are also described in WO 2016/177802 A1, which is incorporated herein by reference in its entirety.
  • the 4-1BB/HER2-bispecific agent is capable of engaging
  • the 4-1BB/HER2-bispecific agent is capable of inducing 4-1 BB clustering and signaling in a HER2-dependent manner. In some embodiments, the 4-1BB/HER2-bispecific agent is capable of activating 4-1 BB signaling in a HER2-expressing tumor microenvironment. In some embodiments, the 4-1BB/HER2-bispecific agent is capable of co-stimulating T cell responses and/or enhancing T cell functions in a HER2-expressing tumor microenvironment.
  • the method comprises administering the 4-1BB/HER2- bispecific agent at an interval of about once every three weeks, about once every two weeks, or about once every week. In some embodiments, the method comprises administering the 4- 1BB/HER2-bispecific agent at an interval of about once every two weeks. In some embodiments, the method comprises administering the 4-1BB/HER2-bispecific agent at a dose of from about 2.5 mg/kg to about 27 mg/kg. In some embodiments, the method comprises administering the 4-1BB/HER2 bispecific agent at a dose of about 2.5 mg/kg, about 5 mg/kg, about 8 mg/kg, about 12 mg/kg or about 18 mg/kg.
  • the method comprises administering the 4-1BB/HER2-bispecific agent at a dose of about 8 mg/kg. In some embodiments, the method comprises administering the 4-1BB/HER2 bispecific agent at a dose of about 18 mg/kg.
  • Methods of treating tumors which comprise administering the specific 4- 1BB/HER2-bispecific agent cinrebafusp alfa are also described in PCT/EP2020/080892, which is incorporated herein by reference in its entirety.
  • the method comprises administering the 4-1BB/HER2- bispecific agent at a first dose and, subsequently, at a second dose, wherein the first dose exceeds the second dose.
  • the 4-1BB/HER2-bispecific agent is administered at the first dose up to five times, up to four times, up to three times or up to two times.
  • the 4-1BB/HER2-bispecific agent is administered two times at the first dose.
  • the first dose is from about 5 mg/kg to about 27 mg/kg.
  • the second dose is from about 2.5 mg/kg to about 18 mg/kg.
  • the first dose is about 18 mg/kg.
  • the second dose is about 8 mg/kg.
  • the method comprises administering the 4-1BB/HER2- bispecific agent two times at a dose of about 18 mg/kg and, subsequently, at a dose of about 8 mg/kg, wherein the 4-1BB/HER2-bispecific agent is administered at an interval of about once every two weeks.
  • the 4-1BB/HER2-bispecific agent is administered intravenously, e.g., by intravenous infusion.
  • the HER2-targeted TKI is a small molecule HER2- targeted TKI.
  • the HER2-targeted TKI is selected from the group consisting of tucatinib, lapatinib, neratinib, pyrotinib, erlotinib and afatinib.
  • the HER2-targeted TKI is a reversible HER2-targeted TKI.
  • the HER2-targeted TKI is tucatinib or lapatinib.
  • the HER2-targeted TKI is tucatinib.
  • the HER2-targeted TKI is administered at a daily dose of from about 20 mg to about 1500 mg. In some embodiments, the HER2-targeted TKI is administered once daily or twice daily. In some embodiments, the HER2-targeted TKI is tucatinib and is administered at a dose of about 150, 200, 250 or 300 mg (e.g., when administered twice daily). In some embodiments the HER2-targeted TKI is tucatinib and is administered at a dose of about 300 mg twice daily. In some embodiments, the HER2-targeted TKI is lapatinib and is administered at a dose of about 1250 mg once daily.
  • the HER2-targeted TKI is neratinib and is administered at a dose of about 240 mg once daily. In some embodiments, the HER2-targeted TKI is pyrotinib and is administered at a dose of about 400 mg once daily. In some embodiments, the HER2-targeted TKI is erlotinib and is administered at a dose of about 100 mg or about 150 mg once daily. In some embodiments, the HER2-targeted TKI is afatinib and is administered at a dose of about 20, 30, 40 or 50 mg once daily, in particular of about 40 mg or about 50 mg once daily.
  • the HER2-targeted TKI is administered orally, e.g., in the form of a tablet.
  • the subject is previously treated with an anti-HER2 therapy.
  • the anti-HER2 therapy comprises administration of one or more anti-HER2 antibodies, such as trastuzumab and/or pertuzumab, and/or of an HER2-targeted TKI.
  • the subject is previously treated with chemotherapy (e.g., with a platinum and fluoropyrimidine).
  • the subject is previously treated with a platinum, fluoropyrimidine and anti-HER2 therapy.
  • the subject is previously treated with at least one, and not more than two, prior treatment regimens for advanced disease.
  • the tumor is selected from the group consisting of gastric cancer, gastroesophageal cancer (e.g., gastroesophageal junction cancer), colon cancer and breast cancer (e.g., breast adenocarcinoma).
  • gastroesophageal cancer e.g., gastroesophageal junction cancer
  • colon cancer e.g., breast adenocarcinoma
  • breast cancer e.g., breast adenocarcinoma
  • the tumor is gastric cancer or gastroesophageal cancer.
  • the tumor is gastric or gastroesophageal junction adenocarcinoma.
  • the method provides an anti-tumor effect comprising one or more of the following: (a) increased IL-2 secretion; (b) increased IL-2 secretion in a tumor microenvironment; (c) increased IFN-gamma secretion; (d) increased IFN-gamma secretion in a tumor microenvironment; (e) expansion of CD4 + T cells; (f) expansion of CD4 + T cells in a tumor microenvironment; (g) expansion of CD8 + T cells; (h) expansion of CD8 + T cells in a tumor microenvironment; (i) expansion of tumor-infiltrating lymphocytes; (j) activation of NK cells and increased antibody-dependent cell-mediated cytotoxicity (ADCC); (k) activation of NK cells and increased ADCC in a tumor microenvironment; and (I) increased secretion of soluble 4-1 BB (s4- 1BB).
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • the method provides an enhanced anti-tumor effect as compared to the 4-1BB/HER2-bispecific agent or the HER2-targeted TKI alone.
  • the enhanced anti-tumor effect is additive or synergistic, preferably synergistic.
  • TKI induce enhanced IL-2 secretion in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the 4-1BB/HER2-bispecific agent or the HER2-targeted TKI alone, e.g., additively or synergistically, preferably synergistically.
  • IL-2 secretion may be measured, for example, in a functional T cell activation assay as essentially described in Example 1.
  • the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI induce enhanced 4-1 BB pathway activation and/or 4-1 BB signaling in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the 4-1BB/HER2-bispecific agent or the HER2-targeted TKI alone, e.g., additively or synergistically, preferably synergistically.
  • Activation of the 4-1 BB pathway and/or 4-1 BB signaling may be measured, for example, in a reporter cell assay as essentially described in Example 2.
  • the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI induce enhanced IFN-gamma secretion in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the 4-1BB/HER2- bispecific agent or the HER2-targeted TKI alone, e.g., additively or synergistically, preferably synergistically.
  • IFN-gamma secretion may be measured, for example, in a recall assay as essentially described in Example 3.
  • the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI induce enhanced secretion of soluble 4-1 BB (s4-1BB) in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the 4- 1BB/HER2-bispecific agent or the HER2-targeted TKI alone, e.g., additively or synergistically, preferably synergistically.
  • s4-1BB secretion may be measured, for example, in a recall assay as essentially described in Example 3.
  • the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI induce enhanced T cell activation and/or enhanced stimulation of T cell responses in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the 4-1BB/HER2-bispecific agent or the HER2-targeted TKI alone, e.g., additively or synergistically, preferably synergistically.
  • T cell activation and/or stimulation of T cell responses may be measured, for example, in one or more assays as essentially described in Examples 1-3.
  • the HER2-targeted TKI prolongs the presence of the 4- 1BB/HER2-bispecific agent on the surface of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors. In some embodiments, the HER2-targeted TKI prolongs the binding of the 4-1BB/HER2-bispecific agent to HER2-expressing tumor cells. In some embodiments, the prolonged presence/binding of the 4-1BB/HER-2-bispecific agent is shown by pulse chase flow cytometry, e.g., as essentially described in Example 5.
  • the treatment provides at least one effect selected from the group consisting of stimulation of tumor-specific immune responses, reduction in tumor size, suppression of the growth of tumor cells, suppression of metastasis, complete remission, partial remission, stable disease, extension of the term before recurrence, extension of survival time, complete response, and partial response.
  • the methods provided herein are prophylactic and/or therapeutic.
  • the methods provided herein may further comprise an additional therapy.
  • an additional therapy may be radiation therapy, surgery (e.g., lumpectomy and a mastectomy), chemotherapy, gene therapy, DNA therapy, viral therapy, RNA therapy, immunotherapy, bone marrow transplantation, nanotherapy, monoclonal antibody therapy, or a combination of the foregoing.
  • Such additional therapy may be in the form of adjuvant or neoadjuvant therapy.
  • an additional therapy is the administration of a small molecule enzymatic inhibitor or an anti-metastatic agent.
  • the additional therapy is the administration of side-effect limiting agents (e.g., agents intended to lessen the occurrence and/or severity of side effects of treatment, such as anti-nausea agents, etc.).
  • the present disclosure provides a method for inducing IL-2 secretion in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors, wherein the method comprises applying a 4-1BB/HER2-bispecific agent as described herein and a HER2-targeted TKI as described herein.
  • the present disclosure provides a method for inducing 4-1 BB pathway activation and/or 4-1 BB signaling in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors, wherein the method comprises applying a 4-1BB/HER2-bispecific agent as described herein and a HER2-targeted TKI as described herein.
  • the present disclosure provides a method for inducing IFN- gamma secretion in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors, wherein the method comprises applying a 4- 1BB/HER2-bispecific agent as described herein and a HER2-targeted TKI as described herein.
  • the present disclosure provides a method for inducing secretion of soluble 4-1 BB (s4-1BB) in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors, wherein the method comprises applying a 4- 1BB/HER2-bispecific agent as described herein and a HER2-targeted TKI as described herein.
  • s4-1BB soluble 4-1 BB
  • the present disclosure provides a method for inducing T cell activation and/or stimulation of T cell responses in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors, wherein the method comprises applying a 4-1BB/HER2-bispecific agent as described herein and a HER2-targeted TKI as described herein.
  • the present disclosure provides a 4-1BB/HER2-bispecific agent as described herein or a pharmaceutical composition comprising the same for use in a method as described herein, e.g., a method for treating a tumor in a subject as described herein.
  • the present disclosure provides a HER2-targeted tyrosine kinase inhibitor (TKI) as described herein or a pharmaceutical composition comprising the same for use in a method as described herein, e.g., a method for treating a tumor in a subject as described herein.
  • TKI HER2-targeted tyrosine kinase inhibitor
  • the present disclosure provides the use of a 4-1BB/HER2- bispecific agent as described herein or a pharmaceutical composition comprising the same in the manufacture of a medicament for treating a tumor in a subject, wherein the treatment comprises administering to the subject (a) the 4-1BB/HER2-bispecific agent or pharmaceutical composition comprising the same and (b) a HER2-targeted tyrosine kinase inhibitor (TKI) as described herein or a pharmaceutical composition comprising the same.
  • TKI HER2-targeted tyrosine kinase inhibitor
  • the present disclosure provides the use of a HER2-targeted TKI as described herein or a pharmaceutical composition comprising the same in the manufacture of a medicament for treating a tumor in a subject, wherein the treatment comprises administering to the subject (a) a 4-1BB/HER2-bispecific agent as described herein or a pharmaceutical composition comprising the same and (b) the HER2-targeted tyrosine kinase inhibitor (TKI) or pharmaceutical composition comprising the same.
  • TKI tyrosine kinase inhibitor
  • the present disclosure provides a combination comprising (a) a 4-1BB/HER2-bispecific agent; and (b) a HER2-targeted tyrosine kinase inhibitor (TKI), wherein the combination is suitable to be administered to a subject in at least one cycle.
  • the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI are administered concurrently or sequentially.
  • the combination comprises the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI each in an amount that, in combination with the other, may be able to induce an effect (e.g., anti-tumor effect) as described herein.
  • the combination is for use in a method as described herein.
  • kits of parts comprising (a) a pharmaceutical composition comprising a 4-1BB/HER2-bispecific agent as described herein; and (b) a pharmaceutical composition comprising a HER2-targeted tyrosine kinase inhibitor (TKI) as described herein.
  • TKI HER2-targeted tyrosine kinase inhibitor
  • the present disclosure provides that, in any one of the aspects and embodiments described herein and above, the 4-1BB/HER2-bispecific agent may be replaced with a bispecific agent targeting HER2 and a second target, wherein the second target is an immune response stimulating molecule other than 4-1 BB.
  • the immune response stimulating molecule is a co-stimulatory molecule other than 4-1 BB.
  • the co-stimulatory molecule is (i) a member of the TNFR family other than 4-1 BB, such as 0X40, GITR, CD40L, CD27 and CD30, (ii) a member of the T cell Ig and mucin (TIM) domain family, such as TIM-1, TIM2, and TIM-3, (iii) a member of the IgG superfamily, such as CD28 and CTLA-4, or (iv) a member of the toll-like receptor (TLR) family, such as TLR7 and TLR8.
  • the bispecific agent is, for example, an OX40/HER2- bispecific agent.
  • the immune response stimulating molecule is stimulator of interferon genes protein (STING).
  • the bispecific agent is a STING/HER2-bispecific agent, e.g., a conjugate comprising a small molecule STING agonist (e.g., as described in Le Naour et al., 2020) and an anti-HER2 antibody or antigen-binding fragment thereof.
  • STING/HER2-bispecific agent e.g., a conjugate comprising a small molecule STING agonist (e.g., as described in Le Naour et al., 2020) and an anti-HER2 antibody or antigen-binding fragment thereof.
  • such bispecific agent and a HER2-targeted TKI as described herein act synergistically to provide/induce one or more effects (e.g., one or more anti-tumor effects) as described herein.
  • such bispecific agent and a HER2-targeted TKI as described herein act synergistically to induce enhanced T cell activation and/or enhanced stimulation of T cell responses in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the bispecific agent or the HER2-targeted TKI alone.
  • Example 1 Functional T cell activation assay using tumor cells with different HER2 expression levels
  • a target-cell dependent T cell activation assay was employed to assess the ability of the fusion polypeptide of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses with or without addition of a HER2-targeted TKI, using supernatant interleukin 2 (IL- 2) levels as a readout.
  • PRS-343 fusion polypeptide of SEQ ID NOs: 50 and 51
  • IL- 2 supernatant interleukin 2
  • tumor cell lines characterized by different expression levels of HER2 were used (see below Table 1 for HER2 expression levels as determined by FACS).
  • PRS-343 Since the mechanism of action of PRS-343 is not based on inhibition of HER2 signaling but on using HER2 on the tumor cell surface to attract 4-1BB-positive T cells to the tumor environment, it is hypothesized that tumors which express HER2 but in amounts that do not meet the classic criteria for HER2 positivity might also benefit from treatment with 4-1 BB/HER2- bispecifc agents such as PRS-343.
  • Table 1 Relative expression of HER2 in selected tumor cell lines.
  • PBMC peripheral blood mononuclear cells
  • PBMC Human peripheral blood mononuclear cells
  • the T lymphocytes were isolated from the resulting PBMC using a Pan T cell purification Kit (Miltenyi Biotec GmbH) and the manufacturer ' s protocols.
  • Purified T cells were re-suspended in a buffer consisting of 90% FCS and 10% DMSO, immediately frozen down using liquid nitrogen and stored in liquid nitrogen until further use.
  • T cells were thawed for 16 h and cultivated in culture media (RPMI 1640, Life Technologies) supplemented with 10% FCS and 1% Penicillin- Streptomycin (Life Technologies).
  • Human IL-2 levels in the cell culture supernatants were quantified using the IL-2 DuoSet kit from R&D Systems.
  • a 384 well plate (MSD) was coated at room temperature for 1 h with 1 pg/mL “Human IL-2 Capture Antibody” (R&D System) diluted in PBS.
  • wells were washed 5 times with 80 pL PBS-T (PBS containing 0.05% Tween20) using a Biotek EL405 select CW washer (Biotek).
  • PRS-343 and a HER2-targeted TKI act synergistically to enhance T cell activation in the presence of tumor cells with different levels of HER2 expression, including cells characterized by a low expression of HER2.
  • Example 2 Investigating 4-1 BB pathway activation using NF-KB-IUC2P/4- 1 BB Jurkat reporter cells and tumor cells with high and low HER2 levels
  • a target-cell based reporter assay was employed to assess the ability of PRS-343 to activate the 4-1BB/CD137 pathway in target tumor cells characterized by different expression levels of HER2 (see Table 1) with or without addition of a HER2-targeted TKI.
  • various cancer cells were mixed with NF-KB-IUC2P/4-1 BB Jurkat cells (Promega, CS196004) engineered to overexpress 4-1 BB and carrying a NF-KB Luciferase reporter gene.
  • An lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without addition of an HER2-targeted TKI) and the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without addition of an HER2-targeted TKI) were used as controls.
  • the background signal measured in the presence of cancer cells alone was assessed in wells to which no NF-KB-IUC2P/4-1 BB Jurkat cells had been added. In the experiment, cancer cells were cultured on the dishes overnight with a fixed dose of TKI (50 or 500 nM).
  • NF-KB-IUC2P/4-1 BB Jurkat cells were incubated for four hours on the coated surface in the presence of various concentrations of PRS-343 or control antibodies.
  • the luminescence induced by the addition of Bio-GloTM buffer (Promega, G7940) on the Jurkat reporter cells was measured. In the following, the experiment is described in detail.
  • Bio-GloTM buffer Promega, G7940
  • luminescence was measured using a luminescence plate reader (Cytation 5, Biotek). Analysis, quantification and curve fitting were performed using Graphpad Prism software.
  • PRS-343 and a HER2-targeted TKI act synergistically to enhance 4-1 BB pathway activation/4-1 BB signaling in the presence of tumor cells with different levels of HER2 expression, including cells characterized by a low expression of HER2, thereby validating the data generated in the co-culture assay of
  • Example 3 T cell recall assay using tumor cells with different HER2 expression levels
  • a target-cell dependent T cell recall assay as previously described, for example, in Kowalewski et al. , 2015, was employed to assess the ability of the fusion polypeptide of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses with or without addition of a HER2-targeted TKI, using supernatant IFN-gamma or soluble 4-1 BB (s4-1 BB) levels as readouts.
  • tumor cell lines characterized by different expression levels of HER2 were mixed with T cells that were previously expanded for 12 days following stimulation with a pool of defined peptides from various known viral pathogens (CEF pool, JPT).
  • CEF pool, JPT a pool of defined peptides from various known viral pathogens
  • An lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without addition of an HER2-targeted TKI) and the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without addition of an HER2-targeted TKI) were used as controls.
  • the experiment is described in detail.
  • PBMCs Human peripheral blood mononuclear cells
  • PBMCs Human peripheral blood mononuclear cells
  • PBMCs were thawed and cultivated ON in a 6-well plate in a suitable thawing medium and then stimulated with 1 pg/mL of CEF peptide pool diluted in antigen recall medium containing IL-2 (final volume of 2.5 ml_).
  • IL-2 stimulation was regularly carried out (every 2 to 3 days). The cells were ready to be used in the recall assay 13 days after thawing.
  • Figures 8 A through D show the same synergistic effect of PRS-343 and tucatinib also for the secretion of s4-1 BB, a biomarker for target engagement of 4-1BB-agonistic agents (Segal et al. , 2018). No effect on s4-1 BB secretion was observed when tucatinib was combined with urelumab.
  • PRS-343 and a HER2-targeted TKI act synergistically to enhance IFN-gamma secretion in the presence of tumor cells with different levels of HER2 expression, including cells characterized by a low expression of HER2
  • results demonstrate a significantly increased 4-1 BB arm activity of PRS-343 in the presence of a HER2-targeted TKI.
  • Example 4 A phase 2, multi-center, open-label study of cinrebafusp alfa (PRS-343) in combination with tucatinib in patients with HER2 low gastric or gastroesophageal junction (GEJ) adenocarcinoma
  • PRS-343 cinrebafusp alfa
  • GEJ gastroesophageal junction
  • This example describes a phase 2 study of cinrebafusp alfa (PRS-343) in combination with the HER2-targeted TKI tucatinib in patients with gastric or GEJ adenocarcinoma that is characterized by IHC/(F)ISH as HER2 IHC1+ or HER2 IHC2+/(F)ISH- (i.e., IHC2+ without HER2 gene amplification) following guidelines established by the College of American Pathologists (CAP), American Society of Clinical Oncology (ASCO) and the American Society for Clinical Pathology (ASCP) in a current tissue specimen. Patients with histologically confirmed disease who have progressed on at least one prior treatment regimen will be eligible for study participation.
  • CAP College of American Pathologists
  • ASCO American Society of Clinical Oncology
  • ASCP American Society for Clinical Pathology
  • the primary objective is to determine the preliminary anti-tumor activity of the combination of cinrebafusp alfa and tucatinib as measured by objective response rate (ORR) according to standard criteria (RECIST 1.1) (Eisenhauer 2009).
  • the secondary objectives of the study are (i) to determine the safety and tolerability of the combination of cinrebafusp alfa and tucatinib, (ii) to evaluate the systemic pharmacokinetics (PK) of cinrebafusp alfa and tucatinib, (iii) to investigate the pharmacodynamics (PD) of cinrebafusp alfa 1 by measuring serum levels of s4- 1BB, and (iv) to determine preliminary clinical activity of cinrebafusp alfa and tucatinib combination [e.g., progression-free survival (PFS), duration of response (DOR), disease control rate (DCR) and overall survival (OS)].
  • PFS progression-free survival
  • DOR duration of response
  • DCR disease control rate
  • OS overall survival
  • Cinrebafusp alfa will be administered by intravenous (IV) infusion at 18 mg/kg on Days 1 and 15 of Cycle 1 (Loading Dose) and 8 mg/kg on Days 1 and 15 of subsequent cycles.
  • Tucatinib will be administered following standard prescribing guidelines of twice daily oral (PO) administration of 300 mg (approximately 12 hours apart, with or without food).
  • Subjects are enrolled in the study based on the following criteria: 1. Signed written informed consent obtained prior to performing any study procedure, including screening procedures; 2. Men and women 318 years of age; 3. Eastern Cooperative Oncology Group (ECOG) Performance Status 0 or 1; 4. Histologically or cytologically confirmed gastric or GEJ adenocarcinoma; 5.
  • subjects who meet any of the following criteria are not enrolled: 1. Disease of squamous or undifferentiated histology; 2. History or evidence of known CNS metastases or carcinomatous meningitis; patients with brain metastases are eligible provided they have shown clinical and radiographic stable disease for at least 4 weeks after definitive therapy and have not used steroids (> 10 mg/day of prednisone or equivalent) for at least 2 weeks prior to the first dose of study treatment; 3. Intolerance to trastuzumab or other HER2- directed agent in prior treatment regimen(s); 4.
  • DVT deep vein thrombosis
  • PE pulmonary embolism
  • Exclusion Criterion 21 should consult with the Medical Monitor in the case of a history of these or similar events; 5.
  • NSAIDs nonsteroidal anti-inflammatory drugs
  • ibuprofen e.g., indomethacin, ibuprofen, naproxen or similar agents
  • antiplatelet agents e.g., clopidogrel, ticlopidine, dipyridamole, anagrelide
  • Uncontrolled or poorly controlled hypertension (arterial hypertension 3 150 mm Hg or diastolic 3 90 mmHg) for > four weeks despite standard medical management; 12. Any arterial thromboembolic event, including but not limited to myocardial infarction, transient ischemic attack, cerebrovascular accident or unstable angina, within six months prior to first dose of study treatment; 13. Serious or non-healing wound, ulcer or bone fracture within 28 days prior to first study-directed treatment (these events may be acceptable for patients after discussion with the Medical Monitor); 14. Bowel obstruction, history or presence of inflammatory enteropathy or extensive intestinal resection (hemicolectomy or extensive small intestine resection with chronic diarrhea), Crohn’s disease, ulcerative colitis or chronic diarrhea; 15.
  • Gastrointestinal perforation or fistula within 6 months prior to study entry or have risk factors for perforation (these events may be acceptable for patients after discussion with the Medical Monitor); 16. Grade 3 or Grade 4 Gl bleeding within 3 months prior to first study treatment (these events may be acceptable for patients after discussion with the Medical Monitor); 17. Inability to swallow pills or presence of any significant gastrointestinal disease which would preclude the adequate absorption of an oral medication; 18. Cirrhosis at a level of Child-Pugh B or worse OR cirrhosis of any degree and a history of hepatic encephalopathy or hepatorenal syndrome or clinically meaningful ascites resulting from cirrhosis.
  • Clinically meaningful cirrhosis is defined as ascites from cirrhosis requiring diuretics or paracentesis; 19. Any medical, psychiatric, cognitive or other condition that compromises the patient’s ability to understand information, to give informed consent or to comply with the study protocol; 20. Any severe concurrent disease or condition (including active infection, cardiac arrhythmia, interstitial lung disease) that in the judgment of the Investigator would make study participation inappropriate for the patient; 21. Prior anthracycline exposure (epirubicin > 720 mg/m 2 ); 22.
  • Patients on the strong CYP2C8 inhibitor gemfibrozil at screening must discontinue its use at least 24 hours before the first dose of study drug and if needed, substitute an alternate lipid-lowering agent; 23.
  • HIV active human immunodeficiency virus
  • Systemic steroid therapy (>10 mg daily prednisone or equivalent) or any other form of immunosuppressive therapy within 7 days prior to the first dose of study treatment; topical, inhaled, nasal and ophthalmic steroids are not prohibited; 29. History of autoimmune disease that has required systemic treatment with disease-modifying agents, corticosteroids, or immunosuppressive drugs unless in the opinion of the investigator the patient is in a complete and durable remission; physiologic replacement therapies, such as thyroxine, insulin, or physiologic corticosteroid replacement therapy for adrenal or pituitary insufficiency, is allowed; 30. Prior organ transplantation including allogeneic or autologous stem cell transplantation; 31.
  • HER2-directed and/or EGFR- directed tyrosine kinase inhibitor (TKI) agents Prior receipt of HER2-directed and/or EGFR- directed tyrosine kinase inhibitor (TKI) agents; 32. Concurrent or previous other malignancy within 3 years of study entry with the exception of cured basal or squamous cell skin cancer, superficial bladder cancer, prostate intra-epithelial neoplasm, carcinoma in situ of the cervix, or other non-invasive or indolent malignancy; 33. Receipt of an investigational agent, chemotherapy or other cancer-directed therapy within 4 weeks (6 weeks for nitrosoureas and mitomycin C) of initiation of study treatment; 34.
  • TKI tyrosine kinase inhibitor
  • Receipt of radiation therapy within 4 weeks of scheduled Day 1 dosing unless the radiation comprised a limited field to non-visceral structures; palliative radiotherapy is permitted; 35. Receipt of trastuzumab or adotrastuzumab emtansine or any other commercial or experimental drug that engages the same epitope as trastuzumab within 4 weeks of scheduled C1D1 dosing; 36. Concurrent enrollment in another therapeutic clinical study; 37.
  • Cinrebafusp alfa drug product is an aqueous solution for infusion. It is supplied in 20 ml_ glass vials containing 16 ml_ of cinrebafusp alfa drug product at a target protein concentration of 25 mg/ml_. Tucatinib is supplied as 50 mg and 150 mg film-coated tablets for oral use.
  • Cinrebafusp alfa and tucatinib will be administered by 2-hour intravenous infusion at 18 mg/kg on Days 1 and 15 in Cycle 1 (Loading Dose) and at 8 mg/kg on Days 1 and 15 in subsequent cycles. The dose should be calculated at the beginning of each cycle and used throughout the cycle unless a patient experiences a 10% or more variation in weight.
  • Tucatinib will be administered at 300 mg taken orally twice daily with or without a meal. Tucatinib will be administered in the clinic on Day 1 prior to administration of cinrebafusp alfa.
  • the primary endpoint of this study is the overall response rate (ORR) as defined by RECIST version 1.1.
  • the secondary endpoints are (i) progression-free survival (PFS), disease control rate (DCR, CR+PR+SD), duration of response (DOR), time to progression (TTP), overall survival (OS), and (ii) the overall safety profile as assessed by the type, frequency, severity, timing and causal relationship of any adverse events, changes in vital signs, ECGs, serum chemistry or other laboratory assessments, treatment delays or discontinuations, immunogenicity of cinrebafusp alfa and tucatinib.
  • Exploratory endpoints are (i) the status of genomic and immune biomarkers in blood and tissue and evaluation of treatment- associated changes from baseline; evaluation of soluble 4-1 BB (s4-1BB) levels and HER2 amplification in cell-free circulating tumor DNA (ctDNA) isolated from plasma; alterations in immune cell subsets from blood and/or PBMCs, and immunohistochemical analysis of HER2, PD-L1, CD8, Ki-67, GrzB and other relevant markers and molecules that may be found to be relevant during the course of this investigation in tumor tissue, (ii) C ma x and AUCo-tiast of cinrebafusp alfa in Cycles 1 and 2, (iii) evaluation of any correlations between cinrebafusp alfa drug concentration in serum and clinical activity, safety and PD observations, (iv) comparison of levels of HER2 and HER2 gene amplification in an archival tissue specimen and in a tumor biopsy specimen collected after completion of prior HER2-directed therapy
  • peripheral venous blood (4 ml_) will be collected from all patients during Cycles 1 - 6.
  • a sample will be collected before initiation of cinrebafusp alfa infusion and at 5 minutes, 1 hour, 2 hours and 4 hours after the end of cinrebafusp alfa infusion.
  • a sample will be collected on Day 8 of Cycles 1 and 2.
  • a sample will be collected on Day 15 of Cycles 1 and 2 and Day 1 of Cycles 3, 4, 5 and 6, a sample will be collected before initiation of cinrebafusp alfa infusion and at 5 minutes after the end of cinrebafusp alfa infusion.
  • C max and AUCo- tiast of cinrebafusp alfa will be assessed in samples collected during Cycles 1 and 2.
  • peripheral venous blood (4 ml_) will be collected from all patients during all Cycles on Day 1, Day 8 and Day 15 always before treatment with tucatinib and cinrebafusp alfa.
  • Plasma will be prepared with standard centrifugation protocols, and s4- 1BB levels will be measured by ELISA. Treatment induced changes over time will be assessed to determine target engagement of cinrebafusp alfa.
  • Example 5 Pulse chase flow cytometry
  • 5x10 4 SK-BR-3 cells (breast adenocarcinoma) or 5x10 4 MKN-7 cells (gastric adenocarcinoma) per well were seeded in triplicates into 96-well flat bottom assay plates (Greiner) and incubated for 24 hours with 50 nM tucatinib (SelleckChem) or DMSO in cell culture medium (RPMI, 10% FCS) at 37°C in a humified incubator.
  • ALTSCHUL S. F., GISH, W., MILLER, W., MYERS, E. W. & LIPMAN, D. J. 1990. Basic local alignment search tool. J Mol Biol, 215, 403-10.
  • ALTSCHUL S. F., MADDEN, T. L, SCHAFFER, A. A., ZHANG, J., ZHANG, Z., MILLER, W. & LIPMAN, D. J. 1997.
  • Gapped BLAST and PSI-BLAST a new generation of protein database search programs. Nucleic Acids Res, 25, 3389-402.
  • BULLIARD Y., JOLICOEUR, R., WINDMAN, M., RUE, S. M., ETTENBERG, S., KNEE, D.
  • EISENHAUER E. A., THERASSE, P., BOGAERTS, J., SCHWARTZ, L. H., SARGENT, D., FORD, R., DANCEY, J., ARBUCK, S., GWYTHER, S., MOONEY, M., RUBINSTEIN, L, SHANKAR, L., DODD, L, KAPLAN, R., LACOMBE, D. & VERWEIJ, J. 2009. New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1). Eur J Cancer,
  • GLAESNER W., VICK, A. M., MILLICAN, R., ELLIS, B., TSCHANG, S. H., TIAN, Y., BOKVIST, K., BRENNER, M., KOESTER, A., PORKSEN, N., ETGEN, G. & BUMOL, T.
  • HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL). Proc Natl Acad Sci U SA, 112, 166-75. LEE, H. W., PARK, S. J., CHOI, B. K., KIM, H. H., NAM, K. O. & KWON, B. S. 2002. 4-1 BB promotes the survival of CD8+ T lymphocytes by increasing expression of Bcl-xL and Bfl-1.
  • MAKKOUK A., CHESTER, C. & KOHRT, H. E. 2016. Rationale for anti-CD137 cancer immunotherapy. Eur J Cancer, 54, 112-119.
  • MASSARELLI E., SEGAL, N. H., RIBRAG, V., MELERO, I., GANGADHAR, T. C., URBA,
  • NEELY J., SURYAWANSHI, S., LEVY, R. & KHUSHALANI, N. Clinical safety and efficacy assessment of the CD137 agonist urelumab alone and in combination with nivolumab in patients with hematologic and solid tumor malignancies. 31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016), 2016 National Harbor, MD, USA. NEEDLEMAN, S. B. & WUNSCH, C. D. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol, 48, 443-53. PEARSON, W. R. & LIPMAN, D. J. 1988. Improved tools for biological sequence comparison.

Abstract

The disclosure provides methods and compositions for treating tumors, particularly HER2- expressing tumors, including tumors characterized by a low expression of HER2 and HER2- positive (HER2+) tumors. The method comprises administering a HER2/4-1BB-bispecific agent and a HER2-targeted tyrosine kinase inhibitor (TKI). The disclosure further provides combinations and kits of parts comprising a HER2/4-1 BB-bispecific agent and a HER2-targeted TKI.

Description

T umor treatment with a 4-1 BB/HER2-bispecific agent and a HER2-targeted tyrosine kinase inhibitor
I. BACKGROUND
[001] 4-1 BB is a co-stimulatory immune checkpoint and member of the tumor necrosis factor receptor (TNFR) family. It is primarily expressed on activated CD4+ and CD8+ T cells, activated B cells, and natural killer (NK) cells, and plays an important role in the regulation of the immune response. The clustering of 4-1 BB leads to activation of the receptor and downstream signaling (Yao et al., 2013, Snell et al. , 2011). In a T cell pre-stimulated by the T cell receptor (TCR) binding to a cognate major histocompatibility complex (MHC) target, co stimulation via 4-1 BB leads to enhanced activation, survival, and proliferation, as well as to the production of pro-inflammatory cytokines and an improved capacity to kill (Dawicki and Watts, 2004, Lee et al., 2002).
[002] In line with the mode of 4-1 BB activation, which requires receptor clustering, a monospecific 4-1BB-targeting agent, such as an anti-4-1 BB antibody, may not be efficient by itself to cluster 4-1 BB and lead to efficient activation. Additionally, a monospecific 4-1 BB- targeting agent may lead to non-localized 4-1 BB clustering and activation, because the expression of 4-1 BB is not limited to tumor infiltrating lymphocytes (Makkouk et al., 2016, Alizadeh et al., 2011). Recent work on TNFR family members also illustrates the mechanisms of anti-TNFR antibodies, whereby the antibodies interact via their Fc regions with Fc-gamma receptors, engage activating Fc-gamma receptor-expressing immune cells, and facilitate the subsequent anti-tumor activity (Bulliard et al., 2014, Bulliard et al., 2013), suggesting an anti-4- 1BB antibody may trigger 4-1 BB clustering depending on the abundance of Fc-gamma receptor-positive cells but not restricted to a tumor microenvironment.
[003] Accordingly, the efficacy and toxicity are in fact major concerns of an anti-4-1 BB monotherapy. Ongoing clinical trials of two agonist antibodies, urelumab and utomilumab, present significant challenges. Urelumab has substantial toxicity at doses above 1 mg/kg and is demonstrated safe at only 0.1 mg/kg (every 3 weeks). Clinical efficacy results with low-dose urelumab monotherapy, however, were largely ineffective and there has been limited clinical activity of urelumab at the tolerated dose (Massarelli et al., 2016, Segal et al., 2017). Utomilumab is tolerated at a higher dose (up to 10 mg/kg every 4 weeks) but is a less potent 4- 1BB agonist relative to urelumab and has potential efficacy challenges (Tolcher et al., 2017, Chester et al., 2018, Segal et al., 2018). [004] HER2 is a clinically-validated target across a broad spectrum of tumor types.
Amplification of the HER2 gene and overexpression of its product have been shown to play an important role in the development and progression of various types of cancer including breast, bladder, gastric, gastroesophageal, colorectal, and biliary tract cancer. Anti-HER2 therapeutics such as trastuzumab, a monoclonal antibody specific for HER2, accrue significant clinical benefit in patients with early stage or metastatic HER2-positive (HER2+) breast cancer. However, many patients with metastatic disease do not respond to therapy or develop refractory disease, and some patients suffer disease recurrence. For example, trastuzumab monotherapy in the metastatic setting results in response rates of 11-26% (clinical benefit rate: 48%), implying that many HER2+ tumors will not respond to monotherapy (Vogel et al. , 2002).
[005] It has previously been shown that a 4-1BB/HER2-bispecifc agent, cinrebafusp alfa (also known as PRS-343), is safe and clinically effective in the treatment of patients with advanced or metastatic HER2+ tumors (as described in PCT/EP2020/080892). Cinrebafusp alfa is designed to localize 4-1 BB/CD137 activation in the tumor in a HER2-dependent manner and promotes 4-1 BB clustering by bridging 4-1BB-positive T cells with HER2-expressing tumor cells, thereby providing a potent co-stimulatory signal to tumor antigen-specific T cells.
[006] However, despite these recent advances, there remains the need for further improved targeted therapy for patients with HER2-positive cancer. There also remains the need for targeted therapy for patients with cancer characterized by a low expression of HER2, i.e., cancers which express HER2, albeit at levels that do not meet the classic criteria for HER2 positivity.
II. SUMMARY
[007] The present disclosure provides, among other things, methods for treating tumors, in particular HER2-expressing tumors, including HER2+ tumors and tumors that are characterized by a low expression of HER2. The methods comprise the administration of a 4- 1 BB/HER2-bispecific agent and a HER2-targeted tyrosine kinase inhibitor (TKI).
III. DEFINITIONS
[008] The following list defines terms, phrases, and abbreviations used throughout the instant specification. All terms listed and defined herein are intended to encompass all grammatical forms.
[009] As used herein, unless otherwise specified, “4-1 BB” means human 4-1 BB (hu4-
1 BB). Human 4-1 BB means a full-length protein defined by UniProt Q07011 , a fragment thereof, or a variant thereof, e.g., a naturally occurring variant, such as an alternatively spliced form or naturally-occurring allelic variant of hu4-1BB. 4-1 BB is also known as CD137, tumor necrosis factor receptor superfamily member 9 (TNFRSF9) and induced by lymphocyte activation (ILA). In some particular embodiments, 4-1 BB of non-human species, e.g., cynomolgus 4-1 BB and mouse 4-1 BB, is used.
[0010] As used herein, unless otherwise specified, “HER2” means human HER2
(huHER2). Human HER2 means a full-length protein defined by UniProt P04626, a fragment thereof, or a variant thereof, e.g., a naturally occurring variant, such as an alternatively spliced form or naturally-occurring allelic variant of HER2. HER2 is also known as human epidermal growth factor receptor 2, HER2/neu, receptor tyrosine-protein kinase erbB-2, cluster of differentiation 340 (CD340), proto-oncogene Neu, ERBB2 (human), Erbb2 (rodent), c-neu, or p185, and is a member of the ErbB family of receptor tyrosine kinases comprising HER1 (EGFR, ErbB1), HER2, HER3 (ErbB3) and HER4 (ErbB4). Human HER2 is encoded by the ERBB2 gene. In some particular embodiments, HER2 of non-human species, e.g., cynomolgus HER2 and mouse HER2, is used.
[0011] “Cancer” and “cancerous” refers to the physiological condition in mammals that is typically characterized by unregulated cell growth. A “tumor” may comprise one or more cancerous cells. A “lesion” is a localized change in a tissue or an organ. Tumors are types of lesions. “Target lesions” are lesions that have been specifically measured. “Non-target lesions” are lesions whose presences have been noted, but whose measurements have not been taken. The terms “cancer”, “tumor”, and “lesion” are used interchangeably herein.
[0012] As used herein, the term “HER2-expressing tumor” or “HER2-expressing tumor cell” is meant to refer to a tumor/tumor cell with detectable expression of HER2, e.g., detectable by a quantitative assay, such as an mRNA-based qRT-PCR assay. In some embodiments, the term “HER2-expressing tumor” or “HER2-expressing tumor cell” refers to a HER2-positive (HER2+) tumor/tumor cell or to a tumor/tumor cell characterized by a low expression of HER2.
[0013] The term “HER2-positive (HER2+) tumor”, as used herein, is not particularly limited as long as it is recognized as such tumor by a person skilled in the art. In some embodiments, the term “HER2-positive (HER2+) tumor” is meant to refer to a tumor which is classified as a HER2+ tumor by immunohistochemistry (IHC) and/or (fluorescent) in situ hybridization ((F)ISH) analysis, e.g., according to the 2018 ASCO/CAP guidelines for HER2 testing in breast cancer (Wolff et al., 2018) or the 2016 CAP/ASCP/ASCO guidelines for HER2 testing in gastric or gastroesophageal adenocarcinoma (Bartley et al., 2016). In some particular embodiments, a HER2+ tumor is characterized by a HER2 status of IHC3+, IHC2+/(F)ISH+ or (F)ISH+, preferably IHC3+ or IHC2+/(F)ISH+. In some embodiments, a HER2+ tumor is characterized by HER2 gene amplification, e.g., as determined by (F)ISH or next generation sequencing (NGS) analysis.
[0014] As used herein, the term “tumor characterized by a low expression of HER2”
(also referred to herein as “HER2 low tumor”) is not particularly limited as long as it is recognized as such tumor by a person skilled in the art. In some embodiments, a “tumor characterized by a low expression of HER2” refers to a tumor which exhibits expression of HER2, albeit at a level which does not warrant its classification as a HER2+ tumor by IHC and (F)ISH. In some embodiments, a HER2 low tumor is a tumor which exhibits expression of HER2 at a level which is detectable by a quantitative assay, such as an mRNA-based qRT-PCR assay, but which is not classified as a HER2+ tumor by IHC and/or (F)ISH, e.g., according to the 2018 ASCO/CAP guidelines for HER2 testing in breast cancer (Wolff et al. , 2018) or the 2016 CAP/ASCP/ASCO guidelines for HER2 testing in gastric or gastroesophageal adenocarcinoma (Bartley et al., 2016). In some particular embodiments, a HER2 low tumor is characterized by a HER2 status of IHC1+ or IHC2+/(F)ISH- (i.e. , IHC2+ without HER2 gene amplification). However, for the avoidance of doubt, HER2 low tumors may also include tumors that are, for example, characterized by a HER2 status of IHC0 (and (F)ISH-), but that still exhibit expression of HER2, e.g., as determined in a quantitative assay, such as an mRNA-based qRT- PCR assay. In some embodiments, a HER2 low tumor does not exhibit HER2 gene amplification, e.g., as determined by (F)ISH or next generation sequencing (NGS) analysis.
[0015] The term “metastatic” refers to a state of cancer where the cancer cells break away from where they first formed and form new tumors (metastatic tumors) in other parts of the body. An "advanced" cancer may be locally advanced or metastatic. Locally advanced cancer refers to cancer that has grown outside the site or organ of origin but has not yet spread to distant parts of the body.
[0016] “Tumor microenvironment (TME)” refers to the environment around a tumor, composed of non-cancer cells and their stroma. The tumor stroma comprises a compilation of cells, including fibroblasts/myofibroblasts, glial, epithelial, fat, immune, vascular, smooth muscle, and immune cells, blood vessels, signaling molecules, and the extracellular matrix (ECM), and serves a structural or connective role. In this context, “full tumor tissue” consists of tumor cells and tumor stroma.
[0017] As used herein, an “anti-tumor agent” or “anti-tumor drug” may act on a tumor, particularly a malignant tumor, and preferably has an anti-tumor effect or anti-tumor activity. The “anti-tumor effect” or “anti-tumor activity” refers to actions of an anti-tumor agent on a tumor, particularly a malignant tumor, including stimulation of tumor-specific immune responses, reduction in target lesion, reduction in tumor size, suppression of the growth of tumor cells, suppression of metastasis, complete remission, partial remission, stabilization of disease, extension of the term before recurrence, extension of survival time of patients, or improvement of quality of life of patients. An anti-tumor effect or anti-tumor activity may comprise or be associated with one or more of the following: (a) increased IL-2 secretion; (b) increased IL-2 secretion in a tumor microenvironment; (c) increased IFN-gamma secretion; (d) increased IFN- gamma secretion in a tumor microenvironment; (e) expansion of CD4+ T cells; (f) expansion of CD4+ T cells in a tumor microenvironment; (g) expansion of CD8+ T cells; (h) expansion of CD8+ T cells in a tumor microenvironment; (i) expansion of tumor-infiltrating lymphocytes; (j) activation of NK cells and increased antibody-dependent cell-mediated cytotoxicity (ADCC); (k) activation of NK cells and increased ADCC in a tumor microenvironment; and (I) increased secretion of soluble 4-1 BB (s4-1 BB).
[0018] As used herein, “treat” or “treatment” refers to clinical intervention designed to alter the natural course of the subject being treated during the course of a physiological condition or disorder or clinical pathology. A treatment may be a therapeutic treatment and/or a prophylactic or preventative measure, wherein the object is to prevent or slow down (lessen) an undesired physiological change or disorder, such as the growth, development or spread of a hyperproliferative condition, such as cancer. Desired effects of treatment include, but are not limited to, decreasing the rate of disease progression, ameliorating or palliating the disease state, alleviating symptoms, stabilizing or not worsening the disease state, and remission of improved prognosis, whether detectable or undetectable. Desired effects of treatment also include prolonging survival as compared to expected survival if not receiving treatment. A subject in need of treatment includes a subject already with the condition or disorder or prone to have the condition or disorder or a subject in which the condition or disorder is to be prevented.
[0019] A treatment given to a subject with tumor may lead to tumor response as described in Response Evaluation Criteria in Solid Tumors (RECIST) guideline (version 1.1) (Eisenhauer et al., 2009). For example, a treatment given to a subject with tumor may lead to complete response, partial response, stable disease, or progressive disease. “Complete response (CR)” refers to the disappearance of all target lesions. “Partial response (PR)” refers to at least a 30% decrease in the sum of diameters of target lesions, taking as reference the baseline sum diameters. “Progressive disease (PD)” refers to at least a 20% increase in the sum of diameters of target lesions, taking as reference the smallest sum on study (this includes the baseline sum if that is the smallest on study). In addition to the relative increase of 20%, the sum must also demonstrate an absolute increase of at least 5 mm. “Stable disease (SD)” refers to neither sufficient shrinkage to qualify for PR nor sufficient increase to qualify for PD, taking as reference the smallest sum diameters while on study. “Duration of response (DoR)” may be calculated as the time from the date of first documented response (CR or PR) to the date of documented progression or death after achieving response.
[0020] As used herein, “combination”, “in combination with”, or “in conjunction with” relates to administration of one substance, drug, or other agent in addition to another substance, drug, or other agent. The administration of substance, drug, or other agent may be before, during, or after administration of the other.
[0021] An “effective amount” of a drug or therapeutic agent is an amount sufficient to effect beneficial or desired effects of a treatment. For example, an effective amount an anti tumor agent may be one that is sufficient to enhance T cell activation to a desired level. In some embodiments, the effectiveness of a drug or therapeutic agent can be determined by suitable methods known in the art. For example, the effectiveness of an anti-tumor agent may be determined by Response Evaluation Criteria in Solid Tumors (RECIST). An effective amount can be administered in one or more individual administrations or doses. An effective amount can be administered alone with one agent or in combination with one or more additional agents.
[0022] As used herein, “T cell activation” refers to a process leading to proliferation and/or differentiation of T cells. The activation of T cells may lead to the initiation and/or perpetuation of immune responses. As used herein, T cell activation may be used to assess the health of subjects with disease or disorders associated with dysregulated immune responses, such as cancer, autoimmune disease, and inflammatory disease. T cell proliferation refers to the expansion of a T cell population. “T cell proliferation” and “T cell expansion” are used interchangeably herein.
[0023] The terms “enhance T cell activity”, “activate T cells”, and “stimulate T cell response”, are used interchangeably herein and refer to inducing, causing, or stimulating T cells to have a sustained or amplified biological functions, or renew or reactivate exhausted or inactive T cells. Exemplary signs of enhanced T cell activity include, but are not limited to: increased secretion of interleukin-2 (IL-2) from T cells, increased secretion of Interferon-gamma (IFN-gamma or IFN-y) from T cells, increased T cell proliferation, and/or increased antigen responsiveness (e.g., viral, pathogen, and tumor clearance). Methods of measuring such enhancement are known to the skilled in the art.
[0024] The term “anti-” or “targeting”, when used to describe a molecule in association with a protein target of interest (e.g., 4-1 BB or HER2), means the molecule is capable of binding the protein target and/or modulating one or more biological functions of the protein target. For example, an “anti-4-1 BB” molecule or a molecule “targeting 4-1 BB” as described herein, is capable of binding 4-1 BB and/or modulating one or more biological functions of 4-1 BB. “Biological function” of a protein target refers to the ability of the protein target to carry out its biological mission(s), e.g., binding to its binding partner(s) and mediating signaling pathway(s). Such molecule may, for example, act as an agonist of the protein target of interest.
[0025] As used herein, “antibody” includes whole antibodies or any antigen binding fragment (i.e., “antigen-binding domain”) or single chain thereof. A whole antibody refers to a glycoprotein comprising at least two heavy chains (HCs) and two light chains (LCs) inter connected by disulfide bonds. Each heavy chain is comprised of a heavy chain variable domain (VH or HCVR) and a heavy chain constant region (CH). The heavy chain constant region is comprised of three domains, CHi , CH2 and CH3. Each light chain is comprised of a light chain variable domain (VL or LCVR) and a light chain constant region (CL). The light chain constant region is comprised of one domain, CL. The VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDRs), interspersed with regions that are more conserved, termed framework regions (FRs). Each VH and VL is composed of three CDRs and four FRs, arranged in the following order from the amino-terminus to the carboxy-terminus: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen (for example, PD- L1). The constant regions of the antibodies may optionally mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (C1q) of the classical complement system.
[0026] As used herein, “antigen-binding domain” or “antigen-binding fragment” of an antibody refers to one or more fragments of an antibody that retain the ability to specifically bind to an antigen (e.g., HER2 or 4-1 BB). 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 fragment” of an antibody include (i) a Fab fragment consisting of the VH, VL, CL and CHi domains; (ii) a F(ab')2 fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fab' fragment consisting of the VH, VL, CL and CHi domains and the region between CHi and CH2 domains; (iv) an Fd fragment consisting of the VH and CHi domains; (v) a single-chain Fv fragment consisting of the VH and VL domains of a single arm of an antibody, (vi) a dAb fragment (Ward et al. , 1989) consisting of a VH domain; and (vii) an isolated complementarity determining region (CDR) or a combination of two or more isolated CDRs which may optionally be joined by a synthetic linker; (viii) a “diabody” comprising the VH and VL connected in the same polypeptide chain using a short linker (see, e.g., patent documents EP 404,097; WO 93/11161; and Holliger et al., 1993); (ix) a “domain antibody fragment” containing only the VH or VL, where in some instances two or more VH regions are covalently joined. [0027] Antibodies may be polyclonal or monoclonal; xenogeneic, allogeneic, or syngeneic; or modified forms thereof (e.g., humanized, chimeric, or multispecific). Antibodies may also be fully human.
[0028] The term “effector functions” as used herein with respect to antibodies refer to those biological activities attributable to the Fc region of an antibody, which vary with the antibody isotype. Examples of antibody effector functions include: C1q binding and complement dependent cytotoxicity (CDC), Fc receptor binding, antibody-dependent cell-mediated cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), cytokine secretion, immune complex-mediated antigen uptake by antigen presenting cells, down regulation of cell surface receptors (e.g. B cell receptor), and B cell activation.
[0029] As used herein, the term “Npocalin” refers to a monomeric protein of approximately 18-20 kDa in weight, having a cylindrical b-pleated sheet supersecondary structural region comprising a plurality of b-strands (preferably eight b-strands designated A to H) connected pair-wise by a plurality of (preferably four) loops at one end to thereby comprise a ligand-binding pocket and define the entrance to the ligand-binding pocket. Preferably, the loops comprising the ligand-binding pocket used in the present invention are loops connecting the open ends of b-strands A and B, C and D, E and F, and G and H, and are designated loops AB, CD, EF, and GH. It is well-established that the diversity of the said loops in the otherwise rigid Npocalin scaffold gives rise to a variety of different binding modes among the Npocalin family members, each capable of accommodating targets of different sizes, shape, and chemical character (reviewed, e.g. in Skerra, 2000, Flower et al. , 2000, Flower, 1996). It is understood that the Npocalin family of proteins has naturally evolved to bind a wide spectrum of ligands, sharing unusually low levels of overall sequence conservation (often with sequence identities of less than 20%) yet retaining a highly conserved overall folding pattern. The correspondence between positions in various lipocalins is also well-known to one of skill in the art (see, e.g., U.S. Patent No. 7,250,297). Proteins falling in the definition of “Npocalin” as used herein include, but are not limited to, human lipocalins including tear Npocalin (Tic, Lcn1), Lipocalin-2 (Lcn2) or neutrophil gelatinase-associated Npocalin (NGAL), apolipoprotein D (ApoD), apolipoprotein M, a acid glycoprotein 1, a acid glycoprotein 2, armicroglobulin, complement component 8y, retinol-binding protein (RBP), the epididymal retinoic acid-binding protein, glycodelin, odorant binding protein I la, odorant-binding protein lib, lipocalin-15 (Lcn15), and prostaglandin D synthase.
[0030] As used herein, “Lipocalin-2” or “neutrophil gelatinase-associated Npocalin” refers to human Lipocalin-2 (hLcn2) or human neutrophil gelatinase-associated Npocalin (hNGAL) and further refers to the mature human Lipocalin-2 or mature human neutrophil gelatinase- associated lipocalin. The term “mature” when used to characterize a protein means a protein essentially free from the signal peptide. A “mature hNGAL” of the instant disclosure refers to the mature form of human neutrophil gelatinase-associated lipocalin, which is free from the signal peptide. Mature hNGAL is described by residues 21-198 of the sequence deposited with the SWISS-PROT Data Bank under Accession Number P80188, the amino acid sequence of which is indicated in SEQ ID NO: 1.
[0031] As used herein, a “native sequence” refers to a protein or a polypeptide having a sequence that occurs in nature or having a wild-type sequence, regardless of its mode of preparation. Such native sequence protein or polypeptide can be isolated from nature or can be produced by other means, such as by recombinant or synthetic methods.
[0032] The “native sequence lipocalin” refers to a lipocalin having the same amino acid sequence as the corresponding polypeptide derived from nature. Thus, a native sequence lipocalin can have the amino acid sequence of the respective naturally-occurring (wild-type) lipocalin from any organism, in particular, a mammal. The term “native sequence”, when used in the context of a lipocalin specifically encompasses naturally-occurring truncated or secreted forms of the lipocalin, naturally-occurring variant forms such as alternatively spliced forms and naturally-occurring allelic variants of the lipocalin. The terms “native sequence lipocalin” and “wild-type lipocalin” are used interchangeably herein.
[0033] As used herein, a “mutein,” a “mutated” entity (whether protein or nucleic acid), or “mutant” refers to the exchange, deletion, or insertion of one or more amino acids or nucleotides, compared to the naturally-occurring (wild-type) protein or nucleic acid. Said term also includes fragments of a mutein as described herein. The present disclosure explicitly encompasses lipocalin muteins, as described herein, having a cylindrical b-pleated sheet supersecondary structural region comprising eight b-strands connected pair-wise by four loops at one end to thereby comprise a ligand-binding pocket and define the entrance of the ligand binding pocket, wherein at least one amino acid of each of at least three of said four loops has been mutated as compared to the native sequence lipocalin. Lipocalin muteins of the present disclosure preferably have the function of binding 4-1 BB as described herein.
[0034] As used herein, the term “fragment,” in connection with the lipocalin muteins of the disclosure, refers to proteins or polypeptides derived from full-length mature hNGAL or lipocalin muteins that are N-terminally and/or C-terminally truncated, i.e., lacking at least one of the N-terminal and/or C-terminal amino acids. Such fragments may include at least 10 or more, such as 20 or 30 or more, consecutive amino acids of the primary sequence of mature hNGAL or the lipocalin mutein it is derived from and are usually detectable in an immunoassay of mature hNGAL. Such a fragment may lack up to 2, up to 3, up to 4, up to 5, up to 10, up to 15, up to 20, up to 25, or up to 30 (including all numbers in between) of the N-terminal and/or C- terminal amino acids. It is understood that the fragment is preferably a functional fragment of mature hNGAL or the lipocalin mutein from which it is derived, which means that it preferably retains the binding specificity, preferably to 4-1 BB, of mature hNGAL or the lipocalin mutein it is derived from. As an illustrative example, such a functional fragment may comprise at least amino acids at positions 13-157, 15-150, 18-141 , 20-134, 25-134, or 28-134 corresponding to the linear polypeptide sequence of mature hNGAL.
[0035] A “fragment” with respect to 4-1 BB or HER2 refers to N-terminally and/or C- terminally truncated 4-1 BB or HER2 or protein domains of 4-1 BB or HER2. Fragments of 4-1 BB or HER2 as described herein retain the capability of the full-length 4-1 BB or HER2 to be recognized and/or bound by a 4-1BB/HER2-bispecific agent, in particular a lipocalin mutein, an antibody, and/or a fusion protein of the disclosure.
[0036] As used herein, a “variant” of a protein described herein may generally refer to a variant protein having an amino acid sequence which is at least about 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98% or 99% identical to the amino acid sequence of said protein. In some embodiments, the variant may be a naturally occurring variant, such as an alternatively spliced form or naturally-occurring allelic variant of said protein. In some embodiments, the variant is a functional variant.
[0037] As used herein, “specific for,” “specific binding,” “specifically bind,” or “binding specificity” relates to the ability of a biomolecule to discriminate between the desired target (for example, 4-1 BB or HER2) and one or more reference targets. It is understood that such specificity is not an absolute but a relative property and can be determined, for example, by means of SPR, western blots, ELISA, fluorescence activated cell sorting (FACS), radioimmunoassay (RIA), electrochemiluminescence (ECL), immunoradiometric assay (IRMA), ImmunoHistoChemistry (IHC), and peptide scans. When used herein in the context of the 4- 1 BB/HER2-bispecific agents described herein or their individual antigen-targeting moieties, the term “specific for,” “specific binding,” “specifically bind,” or “binding specificity” means that the agents or their antigen-targeting moieties bind to, react with, or are directed against 4-1 BB and/or HER2, as described herein, but do not essentially bind another protein. The term “another protein” includes any proteins that are not 4-1 BB or HER2 or proteins closely related to or being homologous to 4-1 BB or HER2. However, 4-1 BB or HER2 from species other than human and fragments and/or (naturally occurring) variants of 4-1 BB or HER2 are not excluded by the term “another protein.” The term “does not essentially bind” means that the 4-1BB/HER2- bispecific agents described herein or their individual antigen-targeting moieties bind another protein with lower binding affinity than 4-1 BB and/or HER2, i.e., show a cross-reactivity of less than 30%, preferably 20%, more preferably 10%, particularly preferably less than 9, 8, 7, 6, or 5%. Whether the 4-1BB/HER2-bispecific agents described herein or their individual antigen targeting moieties react as defined herein above can easily be tested, inter alia, by comparing the reaction the 4-1BB/HER2-bispecific agents described herein or their individual antigen targeting moieties with 4-1 BB and/or HER2 and the reaction of the 4-1BB/HER2-bispecific agents described herein or their individual antigen-targeting moieties with (an)other protein(s).
[0038] As used herein, “bispecific” refers to a molecule is able to specifically bind to at least two distinct targets. Typically, a bispecific molecule comprises at least two target-binding sites, each of which is specific for a different target. In some embodiments, the bispecific molecule is capable of simultaneously binding two targets.
[0039] The term “4-1BB/HER2-bispecific agent”, as used herein, is meant to refer to a bispecific molecule comprising at least one 4-1BB-targeting moiety and at least one HER2- targeting moiety. The targeting moieties may be independently selected from the group consisting of antibodies and antigen-binding fragments thereof, antibody mimetics, small molecules and other antigen-binding molecules, such as aptamers. “Antibody mimetics” are organic compounds (typically artificial peptides or proteins) that, like antibodies, can specifically bind antigens, but that are not structurally related to antibodies. Exemplary antibody mimetics include, but are not limited to, Affibody molecules, Affilins, Affimers, Affitins, Alphabodies, lipocalin muteins, Avimers, DARPins, Fynomers, Kunitz domain peptides, Monobodies and nanoCLAMPs. In some embodiments, the 4-1BB/HER2-bispecific agent may be a conjugate or a fusion protein. In some embodiments, the 4-1BB/HER2-bispecific agent may be a bispecific antibody, e.g., having a format as described in Brinkmann and Kontermann, 2017.
[0040] As used interchangeably herein, the terms “conjugate,” “conjugation,” “fuse,”
“fusion,” or “linked” refer to the joining together of two or more subunits, through all forms of covalent or non-covalent linkage, by means including, but not limited to, genetic fusion, chemical conjugation, coupling through a linker or a cross-linking agent, and non-covalent association.
[0041] The term “fusion polypeptide” or “fusion protein” as used herein refers to a polypeptide or protein comprising two or more subunits. In some embodiments, a fusion protein as described herein comprises two or more subunits, at least one of these subunits being capable of specifically binding to 4-1 BB, and a further subunit capable of specifically binding to HER2. Within the fusion protein, these subunits may be linked by covalent or non-covalent linkage. Preferably, the fusion protein is a translational fusion between the two or more subunits. The translational fusion may be generated by genetically engineering the coding sequence for one subunit in a reading frame with the coding sequence of a further subunit. Both subunits may be interspersed by a nucleotide sequence encoding a linker. However, the subunits of a fusion protein of the present disclosure may also be linked through chemical conjugation. The subunits forming the fusion protein are typically linked to each other as follows: C-terminus of one subunit to N-terminus of another subunit, or C-terminus of one subunit to C- terminus of another subunit, or N-terminus of one subunit to N-terminus of another subunit, or N-terminus of one subunit to C-terminus of another subunit. The subunits of the fusion protein can be linked in any order and may include more than one of any of the constituent subunits. If one or more of the subunits is part of a protein (complex) that consists of more than one polypeptide chain, the term “fusion protein” may also refer to the protein comprising the fused sequences and all other polypeptide chain(s) of the protein (complex). As an illustrative example, where a full-length immunoglobulin is fused to a lipocalin mutein via a heavy or light chain of the immunoglobulin, the term “fusion protein” may refer to the single polypeptide chain comprising the lipocalin mutein and the heavy or light chain of the immunoglobulin. The term “fusion protein” may also refer to the entire immunoglobulin (both light and heavy chains) and the lipocalin mutein fused to one or both of its heavy and/or light chains.
[0042] As used herein, the term “subunit” of a fusion protein disclosed herein refers to a single protein or a separate polypeptide chain, which may form a stable folded structure by itself and define a unique function of providing a binding motif towards a target. In some embodiments, a preferred subunit of the disclosure is a lipocalin mutein. In some other embodiments, a preferred subunit of the disclosure is a full-length immunoglobulin or an antigen-binding domain thereof.
[0043] A “linker” that may be comprised by a fusion protein of the present disclosure joins together two or more subunits of a fusion protein as described herein. The linkage can be covalent or non-covalent. A preferred covalent linkage is via a peptide bond, such as a peptide bond between amino acids. A preferred linker is a peptide linker. Accordingly, in a preferred embodiment, said linker comprises one or more amino acids, such as 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids. Preferred peptide linkers are described herein, including glycine-serine (GS) linkers, glycosylated GS linkers, and proline- alanine-serine polymer (PAS) linkers. Exemplary linkers include, but are not limited to, the linkers with the amino acid sequences of SEQ ID NOs: 4-14. Other preferred linkers include chemical linkers.
[0044] The term “cinrebafusp alfa”, also known as PRS-343, refers to the 4-1BB/HER2- bispecific fusion protein having the amino acid sequences of SEQ ID NOs: 50 and 51. The overall structure of cinrebafusp alfa is shown in Figure 9 D. [0045] As used herein, the term “sequence identity” or “identity” denotes a property of sequences that measures their similarity or relationship. The term “sequence identity” or “identity” as used in the present disclosure means the percentage of pair-wise identical residues - following (homologous) alignment of a sequence of a protein or polypeptide of the disclosure with a sequence in question - with respect to the number of residues in the longer of these two sequences. Sequence identity is measured by dividing the number of identical amino acid residues by the total number of residues and multiplying the product by 100. A skilled artisan will recognize available computer programs, for example BLAST (Altschul et al., 1997), BLAST2 (Altschul et al., 1990), FASTA (Pearson and Lipman, 1988), GAP (Needleman and Wunsch, 1970), Smith-Waterman (Smith and Waterman, 1981), and Wisconsin GCG Package, for determining sequence identity using standard parameters. The percentage of sequence identity can, for example, be determined herein using the program BLASTP, version 2.2.5, November 16, 2002 (Altschul et al., 1997), calculating the percentage of numbers of “positives” (homologous amino acids) from the total number of amino acids selected for the alignment.
[0046] “Gaps” are spaces in an alignment that are the result of additions or deletions of amino acids. Thus, two copies of exactly the same sequence have 100% identity, but sequences that are less highly conserved, and have deletions, additions, or replacements, may have a lower degree of sequence identity.
[0047] The term “HER2-targeted TKI” (or “HER2-targeting TKI”), as used herein, refers to tyrosine kinase inhibitors (TKIs) of HER2, preferably human HER2. Suitable TKIs are known to a person skilled in the art and are described in, e.g., Arkin and Moasser, 2008, and Conlon et al., 2021. The term is meant to include TKIs which exclusively or selectively target HER2 as well as TKIs which target HER2 and at least one other member of the ErbB family, e.g., epidermal growth factor receptor (EGFR). Exemplary HER2-targeted TKIs include, but are not limited to, tucatinib, lapatinib, neratinib, pyrotinib, erlotinib and afatinib.
[0048] The term “reversible TKI”, as used herein, refers to a TKI which binds reversibly to its target tyrosine kinase (e.g., HER2) and slows down or inhibits its activity. In contrast to an “irreversible TKI”, a reversible TKI does not bind covalently to its target tyrosine kinase. Exemplary reversible HER2-targeted TKIs include, but are not limited to, tucatinib, lapatinib and erlotinib.
[0049] The term “small molecule”, as used herein, generally refers to a low molecular weight (e.g., < 900 Daltons) organic compound.
[0050] The term "tucatinib," also known as ONT-380 and ARRY-380, refers to the small molecule TKI that suppresses or blocks HER2 activation. Tucatinib is sold under the brand name “Tukysa®” and has the following structure:
Figure imgf000015_0001
[0051] The term “lapatinib” refers to the small molecule TKI targeting HER2 and EGFR.
Lapatinib is sold under the brand names “Tykerb®” and “Tyverb®”, and has the following structure:
Figure imgf000015_0002
[0052] The term “neratinib”, also known as HKI-272, refers to the small molecule TKI targeting HER2 and EGFR. Neratinib is sold under the brand name “Nerlynx®”, and has the following structure:
Figure imgf000015_0003
[0053] The term “pyrotinib”, also known as SHR-1258, refers to the small molecule TKI targeting HER2 and EGFR and having the following structure:
Figure imgf000016_0001
[0054] The term “erlotinib” refers to the small molecule TKI targeting EGFR and HER2.
Erlotinib is sold under the brand name “Tarceva®” and has the following structure:
Figure imgf000016_0002
[0055] The term “afatinib” refers to the small molecule inhibitor of HER2 and EGFR.
Afatinib is sold under the brand names “Gilotrif®” and “Giotrif®” and has the following structure:
Figure imgf000016_0003
[0056] A “sample” is defined as a biological sample taken from any subject. Biological samples include, but are not limited to, blood, serum, urine, feces, semen, or tissue, including tumor tissue.
[0057] A “subject” is a vertebrate, preferably a mammal, more preferably a human. The term “mammal” is used herein to refer to any animal classified as a mammal, including, without limitation, humans, domestic and farm animals, and zoo, sports, or pet animals, such as sheep, dogs, horses, cats, cows, rats, pigs, apes such as cynomolgus monkeys, to name only a few illustrative examples. Preferably, the “mammal” is human. [0058] As used herein, the term “kit of parts” (in short: “kit”) refers to an article of manufacture comprising one or more containers and, optionally, a data carrier. Said container(s) may be filled with the (re-)agents and compositions as described herein. Additional containers may be included in the kit that contain, e.g., diluents, buffers and/or further (re agents or compositions. Said data carrier may be a non-electronic data carrier, e.g., a graphical data carrier such as an information leaflet, an information sheet, a bar code or an access code, or an electronic data carrier, such a CD, a DVD, a microchip or another semiconductor-based electronical data carrier. The access code may allow access to a database. Said data carrier may comprise instructions for the use of the (re-)agents and compositions as described herein.
[0059] As used herein, the term “pharmaceutical composition” refers to a composition comprising the (re-)agents as described herein and, optionally, one or more pharmaceutically acceptable carriers and/or excipients. The term “pharmaceutically acceptable”, as used herein, refers to the non-toxicity of a material, which, preferably, does not interfere with the activity of the active (re-)agent(s) of the pharmaceutical composition.
[0060] As used herein, the term “about” or “approximately” means within 20%, preferably within 15%, preferably within 10%, and more preferably within 5% of a given value or range. It also includes the concrete number, i.e. “about 20” includes the number of 20. The term “at least about” as used herein includes the concrete number, i.e., “at least about 20” includes 20.
[0061] As used herein, the term “and/or” includes the meaning of “and,” “or,” and “all or any other combination of the elements connected by said term.”
[0062] As used herein, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise.
IV. DESCRIPTIONS OF FIGURES
[0063] Figure 1 : provides representative results of experiments in which the ability of the fusion protein of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses with or without addition of tucatinib was investigated, using tumor cell lines characterized by different expression levels of HER2. Cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 1 A) as well as tumor cell lines expressing HER2 at a significantly lower level: ZR-75-1 (IHC2+/(F)ISH-; Figure 1 B), MKN-7 (Figure 1 C) and HT-29 (IHC1+; Figure 1 D) (see also Table 1). In the experiment, an anti-human CD3 antibody was coated on a plastic culture dish, and subsequently the cell line under study was cultured on the dish overnight (with or without addition of 50 nM tucatinib). The next day, purified T cells were incubated on the coated surface for two days in the presence of various concentrations of (i) PRS-343 (with or without tucatinib), (ii) a modified lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without tucatinib) and (iii) the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without tucatinib). Supernatant interleukin 2 levels were determined by an electrochemoluminescence-based assay. Background depicted as mean (dotted line) ± SEM (grey area). Bg1: average level of IL-2 secretion in the presence of target cells, T cells and tucatinib; bg2: average level of IL-2 secretion in the presence of target cells, T cells an DMSO.
[0064] Figure 2: provides a summary of the results of three independent IL-2 secretion experiments as shown in Figure 1, using PBMCs of four donors in total. X-values were transformed using X=log(X), signals were normalized to the respective background using Y = - (Y = signal, K = respective background). The Shapiro-Wilk test was used for testing for normality (27/30 data sets passed normality test
Figure imgf000018_0001
assumed normal distribution; parametric ANOVA). Significance was tested by Area Under Curve (baseline = 1) of each individual curve and pairwise 1-way ANOVA of Total Area, followed by Bonferroni post-hoc test to correct for multiple comparison. P=0.08.
[0065] Figure 3: provides representative results of experiments in which the ability of the fusion protein of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses with or without addition of lapatinib was investigated, using tumor cell lines characterized by different expression levels of HER2. Cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 3 A) as well as tumor cell lines expressing HER2 at a significantly lower level: ZR-75-1 (IHC2+/(F)ISH-; Figure 3 B), MKN-7 (Figure 3 C) and HT-29 (IHC1+; Figure 3 D) (see also Table 1). In the experiment, an anti-human CD3 antibody was coated on a plastic culture dish, and subsequently the cell line under study was cultured on the dish overnight (with or without addition of 50 nM lapatinib). The next day, purified T cells were incubated on the coated surface for two days in the presence of various concentrations of (i) PRS-343 (with or without lapatinib), (ii) a modified lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without lapatinib) and (iii) the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without lapatinib). Supernatant interleukin 2 levels were determined by an electrochemoluminescence-based assay. Background depicted as mean (dotted line) ± SEM (grey area). Bg1: average level of IL-2 secretion in the presence of target cells, T cells and lapatinib; bg2: average level of IL-2 secretion in the presence of target cells, T cells an DMSO; bg: average level of IL-2 secretion in the presence of target cells and T cells.
[0066] Figure 4: provides representative results of experiments in which the ability of the fusion protein of SEQ ID NOs: 50 and 51 (PRS-343) to activate the 4-1 BB pathway in the presence of target tumor cell lines characterized by different expression levels of HER2, with or without addition of tucatinib, was investigated. Cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 4 A) as well as tumor cell lines expressing HER2 at a significantly lower level: JIMT-1 (Figure 4 A), ZR-75-1 (IHC2+/(F)ISH-; Figure 4 B), HT-29 (IHC1+; Figure 4 B) and MKN-7 (Figure 4 C) (see also Table 1). In the experiment, tumor cells were cultured on the dish overnight (with or without 50 nM tucatinib). The following day, NF-KB- luc2P/4-1BB Jurkat reporter cells were added to the coated tumor cells in the presence of various concentrations of (i) PRS-343 (with or without tucatinib) and (ii) a modified lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without tucatinib). The luminescence signal (RLU) represents a relative measurement of 4-1 BB pathway activation. Background depicted as mean (dotted line) ± SEM (grey area). Bg1: background of Jurkat:4-1BB + tumor cells in tucatinib; bg2: background of Jurkat: 4-1 BB + target cells in DMSO.
[0067] Figure 5: provides representative results of experiments in which the ability of the fusion protein of SEQ ID NOs: 50 and 51 (PRS-343) to activate the 4-1 BB pathway in the presence of target tumor cell lines characterized by different expression levels of HER2, with or without addition of tucatinib, was investigated. Cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 5 A) as well as tumor cell lines expressing HER2 at a significantly lower level: JIMT-1 (Figure 5 B), ZR-75-1 (IHC2+/(F)ISH-; Figure 5 B), HT-29 (IHC1+; Figure 5 C) and MKN-7 (Figure 5 C) (see also Table 1). In the experiment, tumor cells were cultured on the dish overnight (with or without 500 nM tucatinib). The following day, NF-KB- luc2P/4-1BB Jurkat reporter cells were added to the coated tumor cells in the presence of various concentrations of (i) PRS-343 (with or without tucatinib) and (ii) a modified lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without tucatinib). The luminescence signal (RLU) represents a relative measurement of 4-1 BB pathway activation. Background depicted as mean (dotted line) ± SEM (grey area). Bg1: background of Jurkat:4-1BB + tumor cells in tucatinib bg2: background of Jurkat: 4-1 BB + tumor cells in DMSO bg3: background of Jurkat: 4-1 BB + tumor cells in medium.
[0068] Figure 6: provides representative results of experiments in which the ability of the fusion protein of SEQ ID NOs: 50 and 51 (PRS-343) to activate the 4-1 BB pathway in the presence of target tumor cell lines characterized by different expression levels of HER2, with or without addition of lapatinib, was investigated. Cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 6 A) as well as tumor cell lines expressing HER2 at a significantly lower level: ZR-75-1 (IHC2+/(F)ISH-; Figure 6 A), JIMT-1 (Figure 6 B), MKN-7 (Figure 6 B) and HT-29 (IHC1+; Figure 6 C) (see also Table 1). In the experiment, tumor cells were cultured on the dish overnight (with or without 50 nM lapatinib). The following day, NF-KB- luc2P/4-1BB Jurkat reporter cells were added to the coated tumor cells in the presence of various concentrations of (i) PRS-343 (with or without lapatinib) and (ii) a modified lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without lapatinib). The luminescence signal (RLU) represents a relative measurement of 4-1 BB pathway activation. Background depicted as mean (dotted line) ± SEM (grey area). Bg1: background of Jurkat:4-1BB + tumor cells in lapatinib; bg2: background of Jurkat: 4-1 BB + target cells in DMSO.
[0069] Figure 7: provides representative results of experiments in which the ability of the fusion polypeptide of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses in the presence of target tumor cell lines characterized by different expression levels of HER2, with or without addition of tucatinib, was investigated, using supernatant IFN-gamma levels as readout. Tumor cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 7 A) as well as tumor cell lines expressing HER2 at a significantly lower level: ZR-75-1 (IHC2+/(F)ISH-; Figure 7 B), HT-29 (IHC1+; Figure 7 C) and MKN-7 (Figure 7 D) (see also Table 1). Top and bottom panels relate to two independent experiments using PBMCs from different volunteer donors. Tumor cells with or without addition of 50 nM tucatinib were mixed with T cells that were previously expanded for 12 days following stimulation with a pool of defined peptides from various known viral pathogens (CEF pool, JPT). An lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without addition of tucatinib) and the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without addition of tucatinib) were used as controls. Analysis and quantification were performed using Mesoscale Discovery software (MSD DISCOVERY WORKBENCH Software). Data were exported to GraphPad Prism for further analysis.
[0070] Figure 8: provides representative results of experiments in which the ability of the fusion polypeptide of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses in the presence of target tumor cell lines characterized by different expression levels of HER2, with or without addition of tucatinib, was investigated, using soluble 4-1 BB (s4-1BB) levels, a biomarker for target engagement of 4-1BB-agonistic agents, as readout. Tumor cell lines utilized were the highly HER2-positive cells SK-BR-3 (IHC3+; Figure 8 A) as well as tumor cell lines expressing HER2 at a significantly lower level: ZR-75-1 (IHC2+/(F)ISH-; Figure 8 B), HT- 29 (IHC1+; Figure 8 C) and MKN-7 (Figure 8 D) (see also Table 1). Top and bottom panels relate to two independent experiments using PBMCs from different volunteer donors. Tumor cells with or without addition of 50 nM tucatinib were mixed with T cells that were previously expanded for 12 days following stimulation with a pool of defined peptides from various known viral pathogens (CEF pool, JPT). An lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without addition of tucatinib) and the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without addition of tucatinib) were used as controls. Analysis and quantification were performed using Mesoscale Discovery software (MSD DISCOVERY WORKBENCH Software). Data were exported to GraphPad Prism for further analysis.
[0071] Figure 9: provides an overview over the design of 4-1 BB/HER2-bispecific fusion proteins comprising an antibody specific for HER2 (e.g., an antibody shown in SEQ ID NOs: 50 and 48) and a lipocalin mutein specific for 4-1 BB (e.g., a lipocalin mutein shown in SEQ ID NO: 22). Representative 4-1BB/HER2-bispecific fusion proteins were made by genetically fusing one or more anti-4-1 BB lipocalin muteins, via a peptide linker, at the N-terminus or the C-terminus, to an anti-HER2 antibody at the C-terminus of the antibody heavy chain domain (HC) (Figure 9 D), the N-terminus of the HC (Figure 9 A), the C-terminus of the antibody light chain (LC) (Figure 9 C), and/or the N-terminus of the LC (Figure 9 B), resulting in the fusion proteins of SEQ ID NOs: 50 and 51, SEQ ID NOs: 50 and 53, SEQ ID NOs: 52 and 49, and SEQ ID NOs: 54 and 49. An engineered lgG4 backbone with the mutations S228P, F234A, and L235A was used for the anti-HER2 antibody as included in the fusion proteins.
[0072] Figure 10: provides representative results of experiments in which the surface distribution of the fusion polypeptide of SEQ ID NOs: 50 and 51 (PRS-343) on tumor cells with or without addition of tucatinib was determined by pulse chase flow cytometry. Tumor cells with different expression levels of HER2 were used, namely SK-BR-3 cells (IHC3+; Figure 10 A) and MKN-7 cells (Figure 10 B) (see also Table 1). DMSO was used as control.
V. DETAILED DESCRIPTION OF THE DISCLOSURE
[0073] The present disclosure provides new therapies including 4-1BB/HER2-bispecific agents and HER2-targeted TKIs. The present disclosure also provides that a 4-1BB/HER2- bispecific agent and a HER2-targeted TKI act in a synergistic manner to provide an anti-tumor effect against tumor cells characterized by different expression levels of HER2, including HER2+ tumor cells and tumor cells characterized by a low expression of HER2.
[0074] Accordingly, in one aspect, the present disclosure provides a method of treating a tumor in a subject, comprising administering to the subject: (a) a 4-1BB/HER2-bispecific agent; and (b) a HER2-targeted tyrosine kinase inhibitor (TKI). In another aspect, the present disclosure provides a method of treating a tumor in a subject, comprising: (a) administering to the subject a 4-1BB/HER2-bispecific agent, wherein the subject is also receiving a HER2- targeted tyrosine kinase inhibitor (TKI), so that the subject receives therapy with both; or (b) administering to the subject a HER2-targeted TKI, wherein the subject is also receiving a 4- 1 BB/HER2-bispecific agent, so that the subject receives therapy with both. [0075] In some embodiments, the tumor is a HER2-expressing tumor.
[0076] In some embodiments, the tumor is characterized by a low expression of HER2.
In some embodiments, the tumor is characterized by a HER2 status of IHC1+ or IHC2+/(F)ISH-. In some embodiments, the tumor does not exhibit HER2 gene amplification, e.g., as determined by (F)ISH or next generation sequencing (NGS) analysis.
[0077] In some embodiments, the tumor is a HER2-positive (HER2+) tumor. In some embodiments, the tumor is characterized by a HER2 status of IHC3+, IHC2+/(F)ISH+ or (F)ISH+, preferably IHC3+ or IHC2+/(F)ISH+. In some embodiments, the tumor exhibits HER2 gene amplification, e.g., as determined by (F)ISH or next generation sequencing (NGS) analysis.
[0078] In some embodiments, the 4-1BB/HER2-bispecific agent comprises at least one
4-1BB-targeting moiety and at least one HER2-targeting moiety, wherein the targeting moieties are independently selected from the group consisting of antibodies and antigen-binding fragments thereof, antibody mimetics, small molecules and other antigen-binding molecules, such as aptamers. In some embodiments, the antibody mimetics are selected from the group consisting of Affibody molecules, Affilins, Affimers, Affitins, Alphabodies, lipocalin muteins, Avimers, DARPins, Fynomers, Kunitz domain peptides, Monobodies and nanoCLAMPs. HER2- targeting antibodies are known in the art and include, for example, trastuzumab and pertuzumab. 4-1BB-targeting antibodies are also known in the art and include, for example, urelumab and utomilumab. In some embodiments, the 4-1BB/HER2-bispecific agent is a conjugate or a fusion protein. In some embodiments, the 4-1BB/HER2-bispecific agent is a bispecific antibody.
[0079] In some embodiments, the 4-1BB/HER2-bispecific agent is a fusion protein comprising an antibody or an antigen-binding domain thereof specific for HER2 and at least one lipocalin mutein specific for 4-1 BB. More particularly, the fusion protein may comprise at least two subunits in any order: (1) a first subunit that comprises an antibody or an antigen-binding domain thereof specific for HER2, and (2) a second subunit that comprises a lipocalin mutein specific for 4-1 BB. In some embodiments, the fusion protein contains at least one additional subunit, for example, a third subunit. In some embodiments, the fusion protein contains a third subunit that comprises a lipocalin mutein specific for 4-1 BB. In some embodiments, at least one subunit of the fusion protein is fused at its N-terminus and/or its C-terminus to another subunit. In some embodiments, at least one subunit of the fusion protein is fused to another subunit via a linker. A linker as described herein may be a peptide linker, for example, an unstructured glycine-serine (GS) linker, a glycosylated GS linker, or a proline-alanine-serine polymer (PAS) linker. In some embodiments, a (Gly4Ser)3 linker ((G4S)3) as shown in SEQ ID NO: 4 is used. Other exemplary linkers are shown in SEQ ID NOs: 5-14. In some embodiments, the second subunit of the fusion protein is linked via a linker, preferably a (G4S)3 linker, at its N-terminus to each of the C-terminus of the heavy chain constant region (CH) of the antibody or an antigen binding domain thereof comprised in the first subunit. In some embodiments, a lipocalin mutein subunit is fused to an antibody subunit of the fusion protein via a peptide linker. In some embodiments, a lipocalin mutein subunit is fused, via a peptide linker, at its N-terminus or its C- terminus to an antibody subunit at the C-terminus of the antibody heavy chain (HC), the N- terminus of the HC, the C-terminus of the antibody light chain (LC), and/or the N-terminus of the LC (e.g., as shown in Figure 9). In some particular embodiments, the 4-1BB/HER2-bispecific agent is a fusion protein comprising an antibody specific for HER2 fused at the C-terminus of both heavy chains to the N-terminus of a lipocalin mutein specific for 4-1 BB, preferably via a peptide linker, e.g., a (G4S)3 linker.
[0080] In some embodiments, the Fc function of the Fc region of the antibody or an antigen-binding domain thereof comprised in the fusion protein is preserved. Accordingly, the fusion protein may be capable of binding Fc receptor-positive cell at the same time while simultaneously engaging 4-1 BB and HER2. In some other embodiments, the Fc function of the Fc region of the antibody or an antigen-binding domain thereof comprised in the fusion protein is reduced or fully suppressed, while the fusion protein is simultaneously engaging 4-1 BB and HER2. In some embodiments, this may be achieved, for example, by switching from the lgG1 backbone to lgG4, as lgG4 is known to display reduced Fc-gamma receptor interactions compared to lgG1. In some embodiments, to further reduce the residual binding to Fc-gamma receptors, mutations may be introduced into the lgG4 backbone such as F234A and L235A. In some embodiments, an S228P mutation may also be introduced into the lgG4 backbone to minimize the exchange of lgG4 half-antibody (Silva et al. , 2015). In some embodiments, F234A and L235A mutations may be introduced for decreased ADCC and ADCP (Glaesner et al., 2010) and/or M428L and N434S mutations or M252Y, S254T, and T256E mutations for extended serum half-life (Dall'Acqua et al., 2006, Zalevsky et al., 2010). In some embodiments, an additional N297A mutation may be present in the antibody heavy chain of the fusion protein in order to remove the natural glycosylation motif.
[0081] In some embodiments, the antibody or antigen-binding domain thereof comprised in the fusion protein comprises the three heavy chain complementarity-determining regions (CDRs) shown in SEQ ID NO: 40, SEQ ID NO: 41, and SEQ ID NO: 42, and/or the three light chain CDRs shown in SEQ ID NO: 43, SEQ ID NO: 44, and SEQ ID NO: 45. In some embodiments, the antibody or antigen-binding domain thereof comprised in the fusion protein comprises a heavy chain variable region (HCVR) shown in SEQ ID NO: 46, and/or a light chain variable region (LCVR) shown in SEQ ID NO: 47. In some embodiments, the antibody or antigen-binding domain thereof comprised in the fusion protein comprises a heavy chain shown in SEQ ID NO: 49, and/or a light chain shown in SEQ ID NO: 50. In some embodiments, the antibody or antigen-binding domain thereof comprised in the fusion protein has a HCVR with at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or even higher sequence identity to an amino acid sequence shown in SEQ ID NO: 46, and/or a LCVR with at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or even higher sequence identity to an amino acid sequence shown in SEQ ID NO: 47. In other embodiments, the antibody or antigen-binding domain thereof comprised in the fusion protein has a heavy chain with at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or even higher sequence identity to an amino acid sequence shown in SEQ ID NO: 49, and/or a light chain with at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or even higher sequence identity to the amino acid sequence shown in SEQ ID NO: 50.
[0082] In some embodiments, the antibody comprises: (a) three heavy chain complementarity-determining regions (CDRs) shown in SEQ ID NO: 40, SEQ ID NO: 41, and SEQ ID NO: 42, and three light chain CDRs shown in SEQ ID NO: 43, SEQ ID NO: 44, and SEQ ID NO: 45; and (b) a heavy chain with at least 95% sequence identity to the amino acid sequence shown in SEQ ID NO: 49, and a light chain with at least 95% sequence identity to the amino acid sequence shown in SEQ ID NO: 50.
[0083] In some embodiments, the antibody or antigen-binding domain thereof comprised in the fusion protein is an anti-HER2 antibody. In some embodiments, the antibody or antigen binding domain thereof comprised in the fusion protein is trastuzumab. In some embodiments, the antibody or antigen-binding domain thereof comprised in the fusion protein is trastuzumab with an lgG4 backbone.
[0084] In some embodiments, the lipocalin mutein comprised in the fusion protein is a mutein of mature human neutrophil gelatinase-associated lipocalin (hNGAL) having binding specificity for 4-1 BB. A mutein of mature hNGAL may be designated herein as an “hNGAL mutein”.
[0085] In some embodiments, the lipocalin mutein comprised in the fusion protein is capable of binding human 4-1 BB with high affinity and/or co-stimulating human T cells when immobilized on a plastic dish together with an anti-CD3 antibody. In some embodiments, the lipocalin mutein comprised in the fusion protein comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 21-39 or of a fragment or variant thereof. In some embodiments, the lipocalin mutein comprised in the fusion protein has the amino acid sequence shown in SEQ ID NO: 22. In some embodiments, the lipocalin mutein comprised in the fusion protein has an amino acid sequence with high sequence identity, such as at least 70%, at least 75%, at least 80%, at least 82%, at least 85%, at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or higher identity, to an amino acid sequence selected from the group consisting of SEQ ID NOs: 21-39. In some embodiments the lipocalin mutein comprised in the fusion protein has an amino acid sequence with high sequence identity, such as at least 70%, at least 75%, at least 80%, at least 82%, at least 85%, at least 87%, at least 90%, at least 95%, at least 98%, at least 99%, or higher identity, to the amino acid sequence shown in SEQ ID NOs: 22. Suitable lipocalin muteins that are specific for 4-1 BB are also described in WO 2016/177762 A1, which is incorporated herein by reference in its entirety.
[0086] In some embodiments, the fusion protein is generated by genetic fusion of a 4-
1BB-specific hNGAL mutein to a trastuzumab lgG4 variant, joined by a flexible, non- immunogenic peptide linker.
[0087] In some embodiments, the fusion protein comprises the sets of amino acid sequences selected from the group consisting of SEQ ID NOs: 50 and 51, SEQ ID NOs: 50 and 53, SEQ ID NOs: 52 and 49, and SEQ ID NOs: 54 and 49. In some embodiments, the fusion protein comprises amino acid sequences having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98%, at least 99%, or higher sequence identity to the amino acid sequences shown in SEQ ID NOs: 50 and 51, SEQ ID NOs: 50 and 53, SEQ ID NOs: 52 and 49, and SEQ ID NOs: 54 and 49. In some embodiments, where the fusion protein comprises more than one amino acid chain, a given value for the sequence identity relates to the average sequence identity normalized by the number of amino acid residues in both amino acid chains. For example, if a fusion protein consists of amino acid chain A having 100 amino acids and amino acid chain B having 50 amino acids, and another fusion protein consists of amino acid chain A’ having 100 amino acids 80 % sequence identity to amino acid chain A and amino acid chain B’ having 50 amino acids and 95% sequence identity to amino acid chain B’, the average sequence identity between both fusion proteins will be (100/(100+50)) x 80 % + (50/(100+50)) x 95 % = 85 % sequence identity. In some preferred embodiments, where a fusion protein comprises more than one amino acid chain, a given value for the sequence identity means that a protein of interest comprises an amino acid sequence that has at least the given value of sequence identity to one chain of the bispecific fusion protein and comprises an amino acid sequence that has at least the given value of sequence identity to the other chain of the fusion protein. [0088] In some embodiments, the fusion protein comprises the amino acid sequences shown in SEQ ID NOs: 50 and 51. In some embodiments, the fusion protein comprises two chains having the amino acid sequence shown in SEQ ID NO: 50 and two chains having the amino acid sequence shown in SEQ ID NO: 51. Suitable 4-1 BB/HER2-bispecifc fusion proteins comprising an antibody or an antigen-binding domain thereof specific for HER2 and a lipocalin mutein specific for 4-1 BB are also described in WO 2016/177802 A1, which is incorporated herein by reference in its entirety.
[0089] In some embodiments, the 4-1BB/HER2-bispecific agent is capable of engaging
HER2 and 4-1 BB simultaneously. In some embodiments, the 4-1BB/HER2-bispecific agent is capable of inducing 4-1 BB clustering and signaling in a HER2-dependent manner. In some embodiments, the 4-1BB/HER2-bispecific agent is capable of activating 4-1 BB signaling in a HER2-expressing tumor microenvironment. In some embodiments, the 4-1BB/HER2-bispecific agent is capable of co-stimulating T cell responses and/or enhancing T cell functions in a HER2-expressing tumor microenvironment.
[0090] In some embodiments, the method comprises administering the 4-1BB/HER2- bispecific agent at an interval of about once every three weeks, about once every two weeks, or about once every week. In some embodiments, the method comprises administering the 4- 1BB/HER2-bispecific agent at an interval of about once every two weeks. In some embodiments, the method comprises administering the 4-1BB/HER2-bispecific agent at a dose of from about 2.5 mg/kg to about 27 mg/kg. In some embodiments, the method comprises administering the 4-1BB/HER2 bispecific agent at a dose of about 2.5 mg/kg, about 5 mg/kg, about 8 mg/kg, about 12 mg/kg or about 18 mg/kg. In some embodiments, the method comprises administering the 4-1BB/HER2-bispecific agent at a dose of about 8 mg/kg. In some embodiments, the method comprises administering the 4-1BB/HER2 bispecific agent at a dose of about 18 mg/kg. Methods of treating tumors which comprise administering the specific 4- 1BB/HER2-bispecific agent cinrebafusp alfa are also described in PCT/EP2020/080892, which is incorporated herein by reference in its entirety.
[0091] In some embodiments, the method comprises administering the 4-1BB/HER2- bispecific agent at a first dose and, subsequently, at a second dose, wherein the first dose exceeds the second dose. In some embodiments, the 4-1BB/HER2-bispecific agent is administered at the first dose up to five times, up to four times, up to three times or up to two times. In some embodiments, the 4-1BB/HER2-bispecific agent is administered two times at the first dose. In some embodiments, the first dose is from about 5 mg/kg to about 27 mg/kg. In some embodiments, the second dose is from about 2.5 mg/kg to about 18 mg/kg. In some embodiments, the first dose is about 18 mg/kg. In some embodiments, the second dose is about 8 mg/kg. In some embodiments, the method comprises administering the 4-1BB/HER2- bispecific agent two times at a dose of about 18 mg/kg and, subsequently, at a dose of about 8 mg/kg, wherein the 4-1BB/HER2-bispecific agent is administered at an interval of about once every two weeks.
[0092] In some embodiments, the 4-1BB/HER2-bispecific agent is administered intravenously, e.g., by intravenous infusion.
[0093] In some embodiments, the HER2-targeted TKI is a small molecule HER2- targeted TKI. In some embodiments, the HER2-targeted TKI is selected from the group consisting of tucatinib, lapatinib, neratinib, pyrotinib, erlotinib and afatinib. In some embodiments, the HER2-targeted TKI is a reversible HER2-targeted TKI. In some embodiments, the HER2-targeted TKI is tucatinib or lapatinib. In some embodiments, the HER2-targeted TKI is tucatinib.
[0094] In some embodiments, the HER2-targeted TKI is administered at a daily dose of from about 20 mg to about 1500 mg. In some embodiments, the HER2-targeted TKI is administered once daily or twice daily. In some embodiments, the HER2-targeted TKI is tucatinib and is administered at a dose of about 150, 200, 250 or 300 mg (e.g., when administered twice daily). In some embodiments the HER2-targeted TKI is tucatinib and is administered at a dose of about 300 mg twice daily. In some embodiments, the HER2-targeted TKI is lapatinib and is administered at a dose of about 1250 mg once daily. In some embodiments, the HER2-targeted TKI is neratinib and is administered at a dose of about 240 mg once daily. In some embodiments, the HER2-targeted TKI is pyrotinib and is administered at a dose of about 400 mg once daily. In some embodiments, the HER2-targeted TKI is erlotinib and is administered at a dose of about 100 mg or about 150 mg once daily. In some embodiments, the HER2-targeted TKI is afatinib and is administered at a dose of about 20, 30, 40 or 50 mg once daily, in particular of about 40 mg or about 50 mg once daily.
[0095] In some embodiments, the HER2-targeted TKI is administered orally, e.g., in the form of a tablet.
[0096] In some embodiments, the subject is previously treated with an anti-HER2 therapy. In some embodiments, the anti-HER2 therapy comprises administration of one or more anti-HER2 antibodies, such as trastuzumab and/or pertuzumab, and/or of an HER2-targeted TKI. In some embodiments, the subject is previously treated with chemotherapy (e.g., with a platinum and fluoropyrimidine). In some embodiments, the subject is previously treated with a platinum, fluoropyrimidine and anti-HER2 therapy. In some embodiments, the subject is previously treated with at least one, and not more than two, prior treatment regimens for advanced disease.
[0097] In some embodiments, the tumor is selected from the group consisting of gastric cancer, gastroesophageal cancer (e.g., gastroesophageal junction cancer), colon cancer and breast cancer (e.g., breast adenocarcinoma). In some embodiments, the tumor is gastric cancer or gastroesophageal cancer. In some embodiments, the tumor is gastric or gastroesophageal junction adenocarcinoma.
[0098] In some embodiments, the method provides an anti-tumor effect comprising one or more of the following: (a) increased IL-2 secretion; (b) increased IL-2 secretion in a tumor microenvironment; (c) increased IFN-gamma secretion; (d) increased IFN-gamma secretion in a tumor microenvironment; (e) expansion of CD4+ T cells; (f) expansion of CD4+ T cells in a tumor microenvironment; (g) expansion of CD8+ T cells; (h) expansion of CD8+ T cells in a tumor microenvironment; (i) expansion of tumor-infiltrating lymphocytes; (j) activation of NK cells and increased antibody-dependent cell-mediated cytotoxicity (ADCC); (k) activation of NK cells and increased ADCC in a tumor microenvironment; and (I) increased secretion of soluble 4-1 BB (s4- 1BB). In some embodiments, the method provides an enhanced anti-tumor effect as compared to the 4-1BB/HER2-bispecific agent or the HER2-targeted TKI alone. In some embodiments, the enhanced anti-tumor effect is additive or synergistic, preferably synergistic.
[0099] In some embodiments, the 4-1BB/HER2-bispecific agent and the HER2-targeted
TKI induce enhanced IL-2 secretion in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the 4-1BB/HER2-bispecific agent or the HER2-targeted TKI alone, e.g., additively or synergistically, preferably synergistically. IL-2 secretion may be measured, for example, in a functional T cell activation assay as essentially described in Example 1.
[00100] In some embodiments, the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI induce enhanced 4-1 BB pathway activation and/or 4-1 BB signaling in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the 4-1BB/HER2-bispecific agent or the HER2-targeted TKI alone, e.g., additively or synergistically, preferably synergistically. Activation of the 4-1 BB pathway and/or 4-1 BB signaling may be measured, for example, in a reporter cell assay as essentially described in Example 2.
[00101] In some embodiments, the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI induce enhanced IFN-gamma secretion in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the 4-1BB/HER2- bispecific agent or the HER2-targeted TKI alone, e.g., additively or synergistically, preferably synergistically. IFN-gamma secretion may be measured, for example, in a recall assay as essentially described in Example 3.
[00102] In some embodiments, the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI induce enhanced secretion of soluble 4-1 BB (s4-1BB) in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the 4- 1BB/HER2-bispecific agent or the HER2-targeted TKI alone, e.g., additively or synergistically, preferably synergistically. s4-1BB secretion may be measured, for example, in a recall assay as essentially described in Example 3.
[00103] In some embodiments, the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI induce enhanced T cell activation and/or enhanced stimulation of T cell responses in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the 4-1BB/HER2-bispecific agent or the HER2-targeted TKI alone, e.g., additively or synergistically, preferably synergistically. T cell activation and/or stimulation of T cell responses may be measured, for example, in one or more assays as essentially described in Examples 1-3.
[00104] In some embodiments, the HER2-targeted TKI prolongs the presence of the 4- 1BB/HER2-bispecific agent on the surface of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors. In some embodiments, the HER2-targeted TKI prolongs the binding of the 4-1BB/HER2-bispecific agent to HER2-expressing tumor cells. In some embodiments, the prolonged presence/binding of the 4-1BB/HER-2-bispecific agent is shown by pulse chase flow cytometry, e.g., as essentially described in Example 5.
[00105] In some embodiments, the treatment provides at least one effect selected from the group consisting of stimulation of tumor-specific immune responses, reduction in tumor size, suppression of the growth of tumor cells, suppression of metastasis, complete remission, partial remission, stable disease, extension of the term before recurrence, extension of survival time, complete response, and partial response.
[00106] In some embodiments, the methods provided herein are prophylactic and/or therapeutic. In some embodiments, the methods provided herein may further comprise an additional therapy. In some embodiments, an additional therapy may be radiation therapy, surgery (e.g., lumpectomy and a mastectomy), chemotherapy, gene therapy, DNA therapy, viral therapy, RNA therapy, immunotherapy, bone marrow transplantation, nanotherapy, monoclonal antibody therapy, or a combination of the foregoing. Such additional therapy may be in the form of adjuvant or neoadjuvant therapy. In some embodiments, an additional therapy is the administration of a small molecule enzymatic inhibitor or an anti-metastatic agent. In some embodiments, the additional therapy is the administration of side-effect limiting agents (e.g., agents intended to lessen the occurrence and/or severity of side effects of treatment, such as anti-nausea agents, etc.).
[00107] In a further aspect, the present disclosure provides a method for inducing IL-2 secretion in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors, wherein the method comprises applying a 4-1BB/HER2-bispecific agent as described herein and a HER2-targeted TKI as described herein.
[00108] In a further aspect, the present disclosure provides a method for inducing 4-1 BB pathway activation and/or 4-1 BB signaling in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors, wherein the method comprises applying a 4-1BB/HER2-bispecific agent as described herein and a HER2-targeted TKI as described herein.
[00109] In a further aspect, the present disclosure provides a method for inducing IFN- gamma secretion in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors, wherein the method comprises applying a 4- 1BB/HER2-bispecific agent as described herein and a HER2-targeted TKI as described herein.
[00110] In a further aspect, the present disclosure provides a method for inducing secretion of soluble 4-1 BB (s4-1BB) in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors, wherein the method comprises applying a 4- 1BB/HER2-bispecific agent as described herein and a HER2-targeted TKI as described herein.
[00111] In a further aspect, the present disclosure provides a method for inducing T cell activation and/or stimulation of T cell responses in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors, wherein the method comprises applying a 4-1BB/HER2-bispecific agent as described herein and a HER2-targeted TKI as described herein.
[00112] In a further aspect, the present disclosure provides a 4-1BB/HER2-bispecific agent as described herein or a pharmaceutical composition comprising the same for use in a method as described herein, e.g., a method for treating a tumor in a subject as described herein.
[00113] In a further aspect, the present disclosure provides a HER2-targeted tyrosine kinase inhibitor (TKI) as described herein or a pharmaceutical composition comprising the same for use in a method as described herein, e.g., a method for treating a tumor in a subject as described herein.
[00114] In a further aspect, the present disclosure provides the use of a 4-1BB/HER2- bispecific agent as described herein or a pharmaceutical composition comprising the same in the manufacture of a medicament for treating a tumor in a subject, wherein the treatment comprises administering to the subject (a) the 4-1BB/HER2-bispecific agent or pharmaceutical composition comprising the same and (b) a HER2-targeted tyrosine kinase inhibitor (TKI) as described herein or a pharmaceutical composition comprising the same.
[00115] In a further aspect, the present disclosure provides the use of a HER2-targeted TKI as described herein or a pharmaceutical composition comprising the same in the manufacture of a medicament for treating a tumor in a subject, wherein the treatment comprises administering to the subject (a) a 4-1BB/HER2-bispecific agent as described herein or a pharmaceutical composition comprising the same and (b) the HER2-targeted tyrosine kinase inhibitor (TKI) or pharmaceutical composition comprising the same.
[00116] In a further aspect, the present disclosure provides a combination comprising (a) a 4-1BB/HER2-bispecific agent; and (b) a HER2-targeted tyrosine kinase inhibitor (TKI), wherein the combination is suitable to be administered to a subject in at least one cycle. In some embodiments, the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI are administered concurrently or sequentially. In some embodiments, the combination comprises the 4-1BB/HER2-bispecific agent and the HER2-targeted TKI each in an amount that, in combination with the other, may be able to induce an effect (e.g., anti-tumor effect) as described herein. In some embodiments, the combination is for use in a method as described herein.
[00117] In a further aspect, the present disclosure provides a kit of parts comprising (a) a pharmaceutical composition comprising a 4-1BB/HER2-bispecific agent as described herein; and (b) a pharmaceutical composition comprising a HER2-targeted tyrosine kinase inhibitor (TKI) as described herein.
[00118] In yet a further aspect, the present disclosure provides that, in any one of the aspects and embodiments described herein and above, the 4-1BB/HER2-bispecific agent may be replaced with a bispecific agent targeting HER2 and a second target, wherein the second target is an immune response stimulating molecule other than 4-1 BB. In some embodiments, the immune response stimulating molecule is a co-stimulatory molecule other than 4-1 BB. In some embodiments, the co-stimulatory molecule is (i) a member of the TNFR family other than 4-1 BB, such as 0X40, GITR, CD40L, CD27 and CD30, (ii) a member of the T cell Ig and mucin (TIM) domain family, such as TIM-1, TIM2, and TIM-3, (iii) a member of the IgG superfamily, such as CD28 and CTLA-4, or (iv) a member of the toll-like receptor (TLR) family, such as TLR7 and TLR8. Thus, in some embodiments, the bispecific agent is, for example, an OX40/HER2- bispecific agent. In some embodiments, the immune response stimulating molecule is stimulator of interferon genes protein (STING). Thus, in some embodiments, the bispecific agent is a STING/HER2-bispecific agent, e.g., a conjugate comprising a small molecule STING agonist (e.g., as described in Le Naour et al., 2020) and an anti-HER2 antibody or antigen-binding fragment thereof. In some embodiments, such bispecific agent and a HER2-targeted TKI as described herein act synergistically to provide/induce one or more effects (e.g., one or more anti-tumor effects) as described herein. In some embodiments, such bispecific agent and a HER2-targeted TKI as described herein act synergistically to induce enhanced T cell activation and/or enhanced stimulation of T cell responses in the presence of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors as compared to the bispecific agent or the HER2-targeted TKI alone.
VI. EXAMPLES
[00119] Example 1: Functional T cell activation assay using tumor cells with different HER2 expression levels
[00120] A target-cell dependent T cell activation assay was employed to assess the ability of the fusion polypeptide of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses with or without addition of a HER2-targeted TKI, using supernatant interleukin 2 (IL- 2) levels as a readout. For that purpose, tumor cell lines characterized by different expression levels of HER2 were used (see below Table 1 for HER2 expression levels as determined by FACS). Since the mechanism of action of PRS-343 is not based on inhibition of HER2 signaling but on using HER2 on the tumor cell surface to attract 4-1BB-positive T cells to the tumor environment, it is hypothesized that tumors which express HER2 but in amounts that do not meet the classic criteria for HER2 positivity might also benefit from treatment with 4-1 BB/HER2- bispecifc agents such as PRS-343.
Table 1. Relative expression of HER2 in selected tumor cell lines.
Figure imgf000032_0001
An lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without addition of an HER2-targeted TKI) and the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without addition of an HER2-targeted TKI) were used as controls. In the following, the experiment is described in detail.
[00121] Human peripheral blood mononuclear cells (PBMC) from healthy volunteer donors were isolated from buffy coats by centrifugation through a Polysucrose density gradient (Biocoll 1.077 g/mL from Biochrom), following Biochrom's protocols. The T lymphocytes were isolated from the resulting PBMC using a Pan T cell purification Kit (Miltenyi Biotec GmbH) and the manufacturer's protocols. Purified T cells were re-suspended in a buffer consisting of 90% FCS and 10% DMSO, immediately frozen down using liquid nitrogen and stored in liquid nitrogen until further use. For the assay, T cells were thawed for 16 h and cultivated in culture media (RPMI 1640, Life Technologies) supplemented with 10% FCS and 1% Penicillin- Streptomycin (Life Technologies).
[00122] The following procedure was performed using triplicates for each experimental condition: flat-bottom tissue culture plates were pre-coated for 2 h at 37°C using 25 pL of 0.25 pg/mL anti-CD3 antibody. The plates were subsequently washed twice with PBS. 8.3 x 103 target tumor cells per well were plated and allowed to adhere overnight at 37°C in a humidified 5% C02 atmosphere. A fixed dose of HER2-targeted TKI (50 nM) was also added to the cells to pre-treat the cells overnight, as indicated. The target cells had before been grown in culture under standard conditions, detached using Accutase and re-suspended in culture media.
[00123] On the next day, 50 mI of the T cell suspension (corresponding to 2.5 x 104 T cells) and PRS-343 or control antibodies, at concentrations ranging from 0.00042 nM to 25 nM, were added to each well. Plates were covered with a gas permeable seal (4titude) and incubated at 37°C in a humidified 5% C02 atmosphere for 2 days. Subsequently, the IL-2 concentration in the supernatant was assessed as described below.
[00124] Human IL-2 levels in the cell culture supernatants were quantified using the IL-2 DuoSet kit from R&D Systems. In the first step, a 384 well plate (MSD) was coated at room temperature for 1 h with 1 pg/mL “Human IL-2 Capture Antibody” (R&D System) diluted in PBS. Subsequently, wells were washed 5 times with 80 pL PBS-T (PBS containing 0.05% Tween20) using a Biotek EL405 select CW washer (Biotek). After 1 h blocking in PBS-T additionally containing 1% casein (w/w), pooled supernatant and a concentration series of an IL-2 standard diluted in culture medium were incubated in the 384-well plate overnight at 4°C. To allow for detection and quantification of captured IL-2, a mixture of 100 ng/mL biotinylated goat anti-hlL- 2-Bio detection antibody (R&D System) and 1 pg/mL Sulfotag-labelled streptavidin (Mesoscale Discovery) were added in PBS-T containing 0.5% casein and incubated at room temperature for 1 h. After washing, 25 pL reading buffer was added to each well and the electrochemiluminescence (ECL) signal of every well was read using a Mesoscale Discovery reader (MSD Sector Imager S600). Analysis and quantification were performed using Mesoscale Discovery software (MSD DISCOVERY WORKBENCH Software). Data were exported to GraphPad Prism for further analysis.
[00125] The results of representative experiments are depicted in Figures 1 to 3. As shown in Figures 1 A through D, treatment of HER2-expressing tumor cells with PRS-343 and the HER2-targeted TKI tucatinib significantly enhanced IL-2 secretion from T cells, and, thus, T cell activation, as compared to treatment with PRS-343 alone. The clear synergistic effect was observed with all tested tumor cell lines. No such effect was observed when tucatinib was combined with the anti-4-1 BB antibody urelumab. The results of all experiments with PMBCs of four different donors in total are summarized in Figure 2. As shown in Figures 3 A through D, the same synergistic effect was observed with another HER2-targeted TKI, lapatinib, and, again, the effect was absent when tucatinib was combined with urelumab.
[00126] The results show that PRS-343 and a HER2-targeted TKI, such as tucatinib or lapatinib, act synergistically to enhance T cell activation in the presence of tumor cells with different levels of HER2 expression, including cells characterized by a low expression of HER2.
[00127] Example 2: Investigating 4-1 BB pathway activation using NF-KB-IUC2P/4- 1 BB Jurkat reporter cells and tumor cells with high and low HER2 levels
[00128] A target-cell based reporter assay was employed to assess the ability of PRS-343 to activate the 4-1BB/CD137 pathway in target tumor cells characterized by different expression levels of HER2 (see Table 1) with or without addition of a HER2-targeted TKI. For that purpose, various cancer cells were mixed with NF-KB-IUC2P/4-1 BB Jurkat cells (Promega, CS196004) engineered to overexpress 4-1 BB and carrying a NF-KB Luciferase reporter gene. An lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without addition of an HER2-targeted TKI) and the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without addition of an HER2-targeted TKI) were used as controls. The background signal measured in the presence of cancer cells alone was assessed in wells to which no NF-KB-IUC2P/4-1 BB Jurkat cells had been added. In the experiment, cancer cells were cultured on the dishes overnight with a fixed dose of TKI (50 or 500 nM). The next day, NF-KB-IUC2P/4-1 BB Jurkat cells were incubated for four hours on the coated surface in the presence of various concentrations of PRS-343 or control antibodies. As readout, the luminescence induced by the addition of Bio-Glo™ buffer (Promega, G7940) on the Jurkat reporter cells was measured. In the following, the experiment is described in detail.
[00129] The following procedure was performed using triplicates for each experimental condition: flat-bottom tissue culture plates were used to coat 6250 target tumor cells per well, with some wells remaining without target cancer cells as control wells. The cells were allowed to adhere overnight at 37°C in a humidified 5% C02 atmosphere. The target cells had before been grown in culture under standard conditions, detached using Accutase and resuspended in culture media.
[00130] On the next day, plates were washed twice with PBS, and 20 pl_ of the NF-KB- IUC2P/4-1BB Jurkat cells suspension (corresponding to 37500 cells) and 10 pL of PRS-343 at concentrations ranging from 0.001 nM to 25 nM or control antibodies at concentrations ranging from 0.001 nM to 25 nM. Plates were covered with a gas permeable seal (4titude) and incubated at 37°C in a humidified 5% C02 atmosphere for 4 hours. Subsequently, 30 pl_ of Bio-Glo™ buffer (Promega, G7940) was added to each well containing cells (1:1 v/v) and luminescence was measured using a luminescence plate reader (Cytation 5, Biotek). Analysis, quantification and curve fitting were performed using Graphpad Prism software.
[00131] The results of representative experiments are shown in Figures 4 to 6. As shown in Figures 4 and 5, treatment of HER2-expressing tumor cells with PRS-343 and the HER2- targeted TKI tucatinib (Figures 4 A through C: 50 mM tucatinib; Figures 5 A through C: 500 nM tucatinib) resulted in a strong increase in 4-1 BB signaling of 4-1 BB expressing reporter cells, as compared to treatment with PRS-343 alone. The clear synergistic effect was observed with all tested tumor cell lines. As shown in Figures 6 A through C, the same synergistic effect was observed with another HER2-targeted TKI, lapatinib.
[00132] The results show that PRS-343 and a HER2-targeted TKI, such as tucatinib or lapatinib, act synergistically to enhance 4-1 BB pathway activation/4-1 BB signaling in the presence of tumor cells with different levels of HER2 expression, including cells characterized by a low expression of HER2, thereby validating the data generated in the co-culture assay of
Example 1.
[00133] Example 3: T cell recall assay using tumor cells with different HER2 expression levels
[00134] A target-cell dependent T cell recall assay, as previously described, for example, in Kowalewski et al. , 2015, was employed to assess the ability of the fusion polypeptide of SEQ ID NOs: 50 and 51 (PRS-343) to co-stimulate T cell responses with or without addition of a HER2-targeted TKI, using supernatant IFN-gamma or soluble 4-1 BB (s4-1 BB) levels as readouts. For that purpose, tumor cell lines characterized by different expression levels of HER2 (see Table 1) with or without addition of a HER2-targeted TKI were mixed with T cells that were previously expanded for 12 days following stimulation with a pool of defined peptides from various known viral pathogens (CEF pool, JPT). An lgG4 version of the anti-HER2 monoclonal antibody trastuzumab (SEQ ID NOs: 50 and 57; with or without addition of an HER2-targeted TKI) and the anti-4-1 BB monoclonal antibody urelumab (SEQ ID NOs: 58 and 59; with or without addition of an HER2-targeted TKI) were used as controls. In the following, the experiment is described in detail.
[00135] Human peripheral blood mononuclear cells (PBMCs) from healthy volunteer donors were isolated from buffy coats by centrifugation through a polysucrose density gradient (Biocoll 1.077 g/mL from Biochrom), following Biochrom's protocols. Isolated PBMCs were re suspended in a buffer consisting of 90% FCS and 10% DMSO, immediately frozen down using liquid nitrogen and stored in liquid nitrogen until further use. For the T cell expansion phase of the assay, PBMCs were thawed and cultivated ON in a 6-well plate in a suitable thawing medium and then stimulated with 1 pg/mL of CEF peptide pool diluted in antigen recall medium containing IL-2 (final volume of 2.5 ml_). To expand the antigen specific T cells, IL-2 stimulation was regularly carried out (every 2 to 3 days). The cells were ready to be used in the recall assay 13 days after thawing.
[00136] The following procedure was performed using triplicates for each experimental condition. At D13 of the T cell stimulation, flat-bottom tissue culture plates were used to coat 8.3 x 103 target tumor cells per well, and the cells were allowed to adhere overnight at 37°C in a humidified 5% C02 atmosphere. A fixed dose of HER2-targeted TKI (50 nM or DMSO control) was also added to the cells to pre-treat the cells overnight, as indicated. The target cells had before been grown in culture under standard conditions, detached using Accutase and re suspended in culture medium.
[00137] On the next day, 40 mI of the T cell suspension (corresponding to 105 T cells), CEF peptide mix (0.25 pg/mL) and PRS-343 or control antibodies, at concentrations ranging from 0.025 nM to 25 nM, were added to each well. Plates were covered with a gas permeable seal (4titude) and incubated at 37°C in a humidified 5% C02 atmosphere for 2 days (final volumes 60 pL). Subsequently, the IFN-gamma and s4-1BB concentrations in the supernatant were assessed as described below.
[00138] Human IFN-gamma levels in the cell culture supernatants were quantified using the IFN-gamma DuoSet-kit from R&D Systems. In the first step, a 384-well plate (MSD) was coated at room temperature for 1 h with 1 pg/mL “Human IFN-g Capture Antibody” (R&D System) diluted in PBS. Subsequently, wells were washed 5 times with 80 pL PBS-T (PBS containing 0.05% Tween20) using a Biotek EL405 select CW washer (Biotek). After 1 h blocking in PBS-T additionally containing 1% casein (w/w), pooled supernatant and a concentration series of an IFN-gamma standard diluted in culture medium were incubated in the 384-well plate overnight at 4°C. To allow for detection and quantification of captured IFN-gamma, a mixture of 100 ng/mL biotinylated goat anti-hlL-2-Bio detection antibody (R&D System) and 1 pg/mL Sulfotag-labelled streptavidin (Mesoscale Discovery) were added in PBS-T containing 0.5% casein and incubated at room temperature for 1 h. After washing, 25 pl_ reading buffer was added to each well and the electrochemiluminescence (ECL) signal of every well was read using a Mesoscale Discovery reader (MSD Sector Imager S600). s4-1 BB levels were assessed by means of a proprietary enzyme-linked immunosorbent assay (ELISA). Analysis and quantification were performed using Mesoscale Discovery software (MSD DISCOVERY WORKBENCH Software). Data were exported to GraphPad Prism for further analysis.
[00139] The results of representative experiments are shown in Figures 7 and 8. As shown in Figures 7 A through D, treatment of HER2-expressing tumor cells with PRS-343 and the HER2-targeted TKI tucatinib lead to a clear increase in IFN-gamma secretion from T cells as compared to treatment with PRS-343 alone. The clear synergistic effect was observed with all tested tumor cell lines. No such effect was observed when tucatinib was combined with urelumab or an lgG4 version of trastuzumab. Figures 8 A through D show the same synergistic effect of PRS-343 and tucatinib also for the secretion of s4-1 BB, a biomarker for target engagement of 4-1BB-agonistic agents (Segal et al. , 2018). No effect on s4-1 BB secretion was observed when tucatinib was combined with urelumab.
[00140] The results show that PRS-343 and a HER2-targeted TKI, such as tucatinib, act synergistically to enhance IFN-gamma secretion in the presence of tumor cells with different levels of HER2 expression, including cells characterized by a low expression of HER2 Furthermore, the results demonstrate a significantly increased 4-1 BB arm activity of PRS-343 in the presence of a HER2-targeted TKI.
[00141] Example 4: A phase 2, multi-center, open-label study of cinrebafusp alfa (PRS-343) in combination with tucatinib in patients with HER2 low gastric or gastroesophageal junction (GEJ) adenocarcinoma
A. Study Objectives and Overview
[00142] This example describes a phase 2 study of cinrebafusp alfa (PRS-343) in combination with the HER2-targeted TKI tucatinib in patients with gastric or GEJ adenocarcinoma that is characterized by IHC/(F)ISH as HER2 IHC1+ or HER2 IHC2+/(F)ISH- (i.e., IHC2+ without HER2 gene amplification) following guidelines established by the College of American Pathologists (CAP), American Society of Clinical Oncology (ASCO) and the American Society for Clinical Pathology (ASCP) in a current tissue specimen. Patients with histologically confirmed disease who have progressed on at least one prior treatment regimen will be eligible for study participation. The primary objective is to determine the preliminary anti-tumor activity of the combination of cinrebafusp alfa and tucatinib as measured by objective response rate (ORR) according to standard criteria (RECIST 1.1) (Eisenhauer 2009). The secondary objectives of the study are (i) to determine the safety and tolerability of the combination of cinrebafusp alfa and tucatinib, (ii) to evaluate the systemic pharmacokinetics (PK) of cinrebafusp alfa and tucatinib, (iii) to investigate the pharmacodynamics (PD) of cinrebafusp alfa 1 by measuring serum levels of s4- 1BB, and (iv) to determine preliminary clinical activity of cinrebafusp alfa and tucatinib combination [e.g., progression-free survival (PFS), duration of response (DOR), disease control rate (DCR) and overall survival (OS)].
[00143] The study will consist of a 28-day screening period, a treatment period in which patients will receive cinrebafusp alfa in combination with tucatinib in 28-day cycles until documentation of objective disease progression per RECIST v1.1 or development of unacceptable toxicity, and a long-term follow-up period. Cinrebafusp alfa will be administered by intravenous (IV) infusion at 18 mg/kg on Days 1 and 15 of Cycle 1 (Loading Dose) and 8 mg/kg on Days 1 and 15 of subsequent cycles. Tucatinib will be administered following standard prescribing guidelines of twice daily oral (PO) administration of 300 mg (approximately 12 hours apart, with or without food). Full enrollment will be preceded by a three-patient safety run-in to confirm the safety of combining cinrebafusp with tucatinib. In the absence of prohibitive acute toxicity in the first cycle, additional patients, up to a maximum of 20, may then be enrolled to the single arm, open label study as they present to the study. Objective disease status will be assessed every eight (8) weeks for the first six (6) months and then every 12 weeks thereafter. Patients who withdraw from the study without evidence of disease progression will be followed until documentation of disease progression. All patients will be followed for survival. RECIST v1.1 will be used to assess anti-tumor activity and safety will be assessed using NCI CTCAE criteria, v5.0.
[00144] Subjects are enrolled in the study based on the following criteria: 1. Signed written informed consent obtained prior to performing any study procedure, including screening procedures; 2. Men and women ³18 years of age; 3. Eastern Cooperative Oncology Group (ECOG) Performance Status 0 or 1; 4. Histologically or cytologically confirmed gastric or GEJ adenocarcinoma; 5. Demonstration of HER2 IHC1+ or IHC2+/(F)ISH-, assessed in a central laboratory in a current tissue specimen and following guidelines for assessment of HER2 in gastric or GEJ adenocarcinoma established by the College of American Pathologists (CAP), American Society of Clinical Oncology (ASCO) and the American Society for Clinical Pathology (ASCP) (Bartley et al., 2016); 6. Received at least one prior treatment regimen for advanced disease; 7. Measurable disease according to Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 ; 8. Adequate organ and hematologic function as defined below: a) Serum AST and ALT £ 2.5 c upper limit of normal (ULN) or £ 5 c ULN in the presence of liver metastases, b) Total serum bilirubin < 1.5 c ULN, c) Serum creatinine < 1.5 c ULN or creatinine clearance measured via 24-hour urine collection ³ 40 mL/min if serum creatinine is > 1.5X ULN, d) Hemoglobin ³ 9 g/dL; packed red blood cell transfusions are not allowed in the week preceding screening evaluation, e) ANC ³ 1500/mm3, f) Platelet count ³ 100,000/mm3, g) INR £1.5 and PT £1.5 x ULN and PTT £1.5 c ULN; patients receiving oral anti-coagulants must be switched to low molecular weight heparin and have achieved stable coagulation profile prior to first dose of protocol therapy, h) Left ventricular ejection fraction (LVEF) determined by echocardiogram or multi-gated acquisition scan ³ 50%; 9. Resolution to Grade £ 1 by NCI CTCAE v5.0 of all clinically significant toxicities associated with prior therapy or procedures; 10. If sexually active, the patient must be post-menopausal, surgically sterile or using highly effective contraception. Highly effective contraception for women of child-bearing potential and males with female partners of child-bearing potential is defined as 1 barrier method (e.g., condom) and 1 additional method (e.g., hormonal) of contraception during the study and for at least three months from the last study treatment; 13. Women of child-bearing potential may not be breastfeeding and must have a negative serum pregnancy test within 96 hours prior to start of study treatment.
[00145] Additionally, subjects who meet any of the following criteria are not enrolled: 1. Disease of squamous or undifferentiated histology; 2. History or evidence of known CNS metastases or carcinomatous meningitis; patients with brain metastases are eligible provided they have shown clinical and radiographic stable disease for at least 4 weeks after definitive therapy and have not used steroids (> 10 mg/day of prednisone or equivalent) for at least 2 weeks prior to the first dose of study treatment; 3. Intolerance to trastuzumab or other HER2- directed agent in prior treatment regimen(s); 4. History of deep vein thrombosis (DVT), pulmonary embolism (PE) or any other significant thromboembolism during the three months prior to first dose of study treatment; the investigator is referred to Exclusion Criterion 21 and should consult with the Medical Monitor in the case of a history of these or similar events; 5. Chronic therapy with nonsteroidal anti-inflammatory drugs (NSAIDs; e.g., indomethacin, ibuprofen, naproxen or similar agents) or other antiplatelet agents (e.g., clopidogrel, ticlopidine, dipyridamole, anagrelide); aspirin up to 325 mg per day is permitted; 6. Significant bleeding disorders, vasculitis or a significant bleeding episode from the Gl tract within 3 months prior to study entry; 7. Arterial thromboembolic event within 6 months prior to study entry; 8. History of acute coronary syndromes, including myocardial infarction, coronary artery bypass graft, unstable angina, coronary angioplasty or stenting within past 24 weeks; 9. History of or current Class II, III or IV heart failure as defined by the New York Heart Association (NYHA) functional classification system or symptomatic or poorly controlled cardiac arrhythmia; 10. History of ejection fraction drop below the lower limit of normal with trastuzumab or other HER2-directed therapy; 11. Uncontrolled or poorly controlled hypertension (arterial hypertension ³ 150 mm Hg or diastolic ³ 90 mmHg) for > four weeks despite standard medical management; 12. Any arterial thromboembolic event, including but not limited to myocardial infarction, transient ischemic attack, cerebrovascular accident or unstable angina, within six months prior to first dose of study treatment; 13. Serious or non-healing wound, ulcer or bone fracture within 28 days prior to first study-directed treatment (these events may be acceptable for patients after discussion with the Medical Monitor); 14. Bowel obstruction, history or presence of inflammatory enteropathy or extensive intestinal resection (hemicolectomy or extensive small intestine resection with chronic diarrhea), Crohn’s disease, ulcerative colitis or chronic diarrhea; 15. Gastrointestinal perforation or fistula within 6 months prior to study entry or have risk factors for perforation (these events may be acceptable for patients after discussion with the Medical Monitor); 16. Grade 3 or Grade 4 Gl bleeding within 3 months prior to first study treatment (these events may be acceptable for patients after discussion with the Medical Monitor); 17. Inability to swallow pills or presence of any significant gastrointestinal disease which would preclude the adequate absorption of an oral medication; 18. Cirrhosis at a level of Child-Pugh B or worse OR cirrhosis of any degree and a history of hepatic encephalopathy or hepatorenal syndrome or clinically meaningful ascites resulting from cirrhosis. Clinically meaningful cirrhosis is defined as ascites from cirrhosis requiring diuretics or paracentesis; 19. Any medical, psychiatric, cognitive or other condition that compromises the patient’s ability to understand information, to give informed consent or to comply with the study protocol; 20. Any severe concurrent disease or condition (including active infection, cardiac arrhythmia, interstitial lung disease) that in the judgment of the Investigator would make study participation inappropriate for the patient; 21. Prior anthracycline exposure (epirubicin > 720 mg/m2); 22. Having used a strong cytochrome P450 CYP2C8 inhibitor within three elimination half-lives of the inhibitor or have used a strong CYP3A4 or moderate/strong CYP2C8 inducer within five days prior to first dose of study treatment. Patients on the strong CYP2C8 inhibitor gemfibrozil at screening must discontinue its use at least 24 hours before the first dose of study drug and if needed, substitute an alternate lipid-lowering agent; 23. Known active human immunodeficiency virus (HIV) disease, hepatitis B, or hepatitis C; 24. Any severe infection within 28 days prior to study start or requirement for oral or intravenous antibiotics within 14 days prior to study start; 25. Administration of live, attenuated vaccines within 28 days prior to start of treatment or anticipated need for vaccination with live attenuated vaccine during the study; vaccination for SARS-CoV-2 is permitted; 26. History of infusion reactions to any component/excipient of cinrebafusp alfa; history of allergic reactions to tucatinib or compounds chemically or biologically similar to tucatinib, or known allergy to any of the excipients in tucatinib; 27. History of severe hypersensitivity reactions to monoclonal antibodies or Grade ³3 immune-mediated adverse reaction to immune checkpoint inhibitor agents; 28. Systemic steroid therapy (>10 mg daily prednisone or equivalent) or any other form of immunosuppressive therapy within 7 days prior to the first dose of study treatment; topical, inhaled, nasal and ophthalmic steroids are not prohibited; 29. History of autoimmune disease that has required systemic treatment with disease-modifying agents, corticosteroids, or immunosuppressive drugs unless in the opinion of the investigator the patient is in a complete and durable remission; physiologic replacement therapies, such as thyroxine, insulin, or physiologic corticosteroid replacement therapy for adrenal or pituitary insufficiency, is allowed; 30. Prior organ transplantation including allogeneic or autologous stem cell transplantation; 31. Prior receipt of HER2-directed and/or EGFR- directed tyrosine kinase inhibitor (TKI) agents; 32. Concurrent or previous other malignancy within 3 years of study entry with the exception of cured basal or squamous cell skin cancer, superficial bladder cancer, prostate intra-epithelial neoplasm, carcinoma in situ of the cervix, or other non-invasive or indolent malignancy; 33. Receipt of an investigational agent, chemotherapy or other cancer-directed therapy within 4 weeks (6 weeks for nitrosoureas and mitomycin C) of initiation of study treatment; 34. Receipt of radiation therapy within 4 weeks of scheduled Day 1 dosing, unless the radiation comprised a limited field to non-visceral structures; palliative radiotherapy is permitted; 35. Receipt of trastuzumab or adotrastuzumab emtansine or any other commercial or experimental drug that engages the same epitope as trastuzumab within 4 weeks of scheduled C1D1 dosing; 36. Concurrent enrollment in another therapeutic clinical study; 37. Major surgery within 28 days of scheduled C1D1 dosing or minor surgery or subcutaneous venous access device placement within 7 days prior to initiation of study treatment or elective or planned major surgery to be performed during the course of the clinical trial (these events may be acceptable for patients after discussion with the Medical Monitor).
B. Study Procedures
[00146] Cinrebafusp alfa drug product is an aqueous solution for infusion. It is supplied in 20 ml_ glass vials containing 16 ml_ of cinrebafusp alfa drug product at a target protein concentration of 25 mg/ml_. Tucatinib is supplied as 50 mg and 150 mg film-coated tablets for oral use.
[00147] Eligible patients will receive cinrebafusp alfa and tucatinib in 28-day cycles. Cinrebafusp alfa will be administered by 2-hour intravenous infusion at 18 mg/kg on Days 1 and 15 in Cycle 1 (Loading Dose) and at 8 mg/kg on Days 1 and 15 in subsequent cycles. The dose should be calculated at the beginning of each cycle and used throughout the cycle unless a patient experiences a 10% or more variation in weight. Tucatinib will be administered at 300 mg taken orally twice daily with or without a meal. Tucatinib will be administered in the clinic on Day 1 prior to administration of cinrebafusp alfa. [00148] One hour prior to initiation of cinrebafusp alfa on each treatment day, prophylaxis with acetaminophen, ibuprofen, an H1 histamine antagonist, and an H2 antagonist will be initiated. The steroid-free regimen is preferred in order not to blunt a cinrebafusp alfa-mediated anti-tumor immune response. At the investigator’s discretion, the rate of infusions can be reduced by up to 50% to ameliorate hypersensitivity or infusion-related reactions.
[00149] After a one-month screening period, patients will be allowed to initiate and continue treatment with cinrebafusp alfa in combination with tucatinib in 28-day cycles as long as they continue to derive benefit from treatment, until documentation of objective disease progression or development of unacceptable or unmanageable treatment-related toxicity. It is anticipated that individual patients will participate in the treatment portion of the study for up to 12 months and in the long-term follow-up portion of the study for non-interventional assessment of survival for up to 24 additional months. Thus, the maximum anticipated duration of participation for an individual patient is up to 37 months.
C. Endpoints and Assessments
[00150] The primary endpoint of this study is the overall response rate (ORR) as defined by RECIST version 1.1. The secondary endpoints are (i) progression-free survival (PFS), disease control rate (DCR, CR+PR+SD), duration of response (DOR), time to progression (TTP), overall survival (OS), and (ii) the overall safety profile as assessed by the type, frequency, severity, timing and causal relationship of any adverse events, changes in vital signs, ECGs, serum chemistry or other laboratory assessments, treatment delays or discontinuations, immunogenicity of cinrebafusp alfa and tucatinib. Exploratory endpoints are (i) the status of genomic and immune biomarkers in blood and tissue and evaluation of treatment- associated changes from baseline; evaluation of soluble 4-1 BB (s4-1BB) levels and HER2 amplification in cell-free circulating tumor DNA (ctDNA) isolated from plasma; alterations in immune cell subsets from blood and/or PBMCs, and immunohistochemical analysis of HER2, PD-L1, CD8, Ki-67, GrzB and other relevant markers and molecules that may be found to be relevant during the course of this investigation in tumor tissue, (ii) Cmax and AUCo-tiast of cinrebafusp alfa in Cycles 1 and 2, (iii) evaluation of any correlations between cinrebafusp alfa drug concentration in serum and clinical activity, safety and PD observations, (iv) comparison of levels of HER2 and HER2 gene amplification in an archival tissue specimen and in a tumor biopsy specimen collected after completion of prior HER2-directed therapy, (v) comparison of levels of HER2 protein expression and/or gene amplification and HER2 gene amplification in ctDNA isolated before treatment initiation with clinical benefit derived from study treatment.
[00151] For PK analysis, peripheral venous blood (4 ml_) will be collected from all patients during Cycles 1 - 6. On Day 1 of Cycles 1 and 2, a sample will be collected before initiation of cinrebafusp alfa infusion and at 5 minutes, 1 hour, 2 hours and 4 hours after the end of cinrebafusp alfa infusion. On Day 8 of Cycles 1 and 2, a sample will be collected. On Day 15 of Cycles 1 and 2 and Day 1 of Cycles 3, 4, 5 and 6, a sample will be collected before initiation of cinrebafusp alfa infusion and at 5 minutes after the end of cinrebafusp alfa infusion. Cmaxand AUCo-tiast of cinrebafusp alfa will be assessed in samples collected during Cycles 1 and 2.
[00152] For analysis of s4-1BB, peripheral venous blood (4 ml_) will be collected from all patients during all Cycles on Day 1, Day 8 and Day 15 always before treatment with tucatinib and cinrebafusp alfa. Plasma will be prepared with standard centrifugation protocols, and s4- 1BB levels will be measured by ELISA. Treatment induced changes over time will be assessed to determine target engagement of cinrebafusp alfa.
[00153] The safety and tolerability of cinrebafusp alfa in combination with tucatinib will be evaluated based on the incidence and severity of adverse events, performance status, physical examinations, ECGs, laboratory safety evaluations and immunogenicity of cinrebafusp alfa. Laboratory abnormalities and adverse events will be graded according to NCI CTCAE version 5.0. The immunogenicity of cinrebafusp alfa in this patient population will be assessed on the basis of development of anti-drug antibodies and their titers in blood samples collected during the course of the study.
[00154] Example 5: Pulse chase flow cytometry
[00155] Distribution of the fusion polypeptide of SEC ID NOs: 50 and 51 (PRS-343) on the surface of HER2-expressing tumor cells in the presence or absence of the HER2-targeted TKI tucatinib was analyzed by pulse chase flow cytometry.
[00156] 5x104 SK-BR-3 cells (breast adenocarcinoma) or 5x104 MKN-7 cells (gastric adenocarcinoma) per well were seeded in triplicates into 96-well flat bottom assay plates (Greiner) and incubated for 24 hours with 50 nM tucatinib (SelleckChem) or DMSO in cell culture medium (RPMI, 10% FCS) at 37°C in a humified incubator. Medium was aspirated, and cells were pulsed with 10 nM PRS-343 for 10 min in cell culture medium in a humified incubator, washed 3 times and chased for 0 hours, 4 hours and 22 hours at 37°C in cell culture medium containing 50 nM tucatinib or DMSO, respectively. The cells were harvested and stained with a fixable Live-Dead dye (LIVE/DEAD Violet, Live Technologies) for 20 min at 4°C. Cells were fixed with 2% paraformaldehyde for 20 min at 4°C, followed by detection of extracellular PRS- 343 by goat-anti human IgG labeled with Alexa-Fluor 488 for 30 min on ice. The cells were analyzed with an IntelliCyt iQue Screener PLUS to measure the fluorescent signal corresponding to cell surface PRS-343 levels. The fluorescence signal of all time points was normalized to the 0 hours chase time point and expressed as a percentage. [00157] As shown in Figure 10 and below Tables 2 and 3, the combination of PRS-343 with tucatinib resulted in a prolonged presence of PRS-343 on the surface of tumor cells having different expression levels of HER2, as compared to the control (combination of PRS-343 with DMSO). Similar results were obtained with another HER2-targeted TKI, lapatinib (data not shown).
Table 2. Distribution of PRS-343 on the surface of SK-BR-3 tumor cells.
Figure imgf000044_0001
Table 3. Distribution of PRS-343 on the surface of MKN-7 tumor cells.
Figure imgf000044_0002
[00158] These results demonstrate that the HER2-targeted TKI prolongs the presence of PRS-343 on the surface of HER2-expressing tumor cells.
[00159] Embodiments illustratively described herein may suitably be practiced in the absence of any element or elements, limitation or limitations, not specifically disclosed herein. Thus, for example, the terms "comprising," "including," "containing," etc. shall be read expansively and without limitation. Additionally, the terms and expressions employed herein have been used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present embodiments have been specifically disclosed by preferred embodiments and optional features, modification and variations thereof may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention. All patents, patent applications, textbooks and peer-reviewed publications described herein are hereby incorporated by reference in their entirety. Furthermore, where a definition or use of a term in a reference, which is incorporated by reference herein is inconsistent or contrary to the definition of that term provided herein, the definition of that term provided herein applies and the definition of that term in the reference does not apply. Each of the narrower species and subgeneric groupings falling within the generic disclosure also forms part of the invention. This includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein. In addition, where features are described in terms of Markush groups, those skilled in the art will recognize that the disclosure is also thereby described in terms of any individual member or subgroup of members of the Markush group. Further embodiments will become apparent from the following claims.
[00160] Equivalents: Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims. All publications, patents and patent applications mentioned in this specification are herein incorporated by reference into the specification to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference.
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Claims

1. A method of treating a tumor in a subject, comprising administering to the subject:
(a) a 4-1BB/HER2-bispecific agent; and
(b) a HER2-targeted tyrosine kinase inhibitor (TKI).
2. A method of treating a tumor in a subject, comprising:
(a) administering to the subject a 4-1BB/HER2-bispecific agent, wherein the subject is also receiving a HER2-targeted tyrosine kinase inhibitor (TKI), so that the subject receives therapy with both; or
(b) administering to the subject a HER2-targeted TKI, wherein the subject is also receiving a 4-1BB/HER2-bispecific agent, so that the subject receives therapy with both.
3. The method of claim 1 or 2, wherein the tumor is characterized by a low expression of HER2.
4. The method of any one of claims 1-3, wherein the tumor is characterized by a HER2 status of IHC1+ or IHC2+/(F)ISH-.
5. The method of any one of claims 1-4, wherein the tumor does not exhibit HER2 gene amplification.
6. The method of claim 1 or 2, wherein the tumor is a HER2-positive (HER2+) tumor.
7. The method of any one of claims 1 , 2 and 6, wherein the tumor is characterized by a HER2 status of IHC3+, IHC2+/(F)ISH+ or (F)ISH+, preferably IHC3+ or IHC2+/(F)ISH+.
8. The method of any one of claims 1, 2, 6 and 7, wherein the tumor exhibits HER2 gene amplification.
9. The method of any one of claims 1-8, wherein the 4-1BB/HER2-bispecific agent is a fusion protein comprising an antibody specific for HER2 fused at the C-terminus of both heavy chains to the N-terminus of a lipocalin mutein specific for 4-1 BB.
10. The method of claim 9, wherein the antibody comprises:
(a) three heavy chain complementarity-determining regions (CDRs) shown in SEQ ID NO: 40, SEQ ID NO: 41 , and SEQ ID NO: 42, and three light chain CDRs shown in SEQ ID NO: 43, SEQ ID NO: 44, and SEQ ID NO: 45; and
(b) a heavy chain with at least 95% sequence identity to the amino acid sequence shown in SEQ ID NO: 49, and a light chain with at least 95% sequence identity to the amino acid sequence shown in SEQ ID NO: 50.
11. The method of claim 9 or 10, wherein the lipocalin mutein has at least 95% sequence identity to the amino acid sequence shown in SEQ ID NO: 22.
12. The method of any one of claims 9-11, wherein the fusion protein has at least 95% sequence identity to the amino acid sequences shown in SEQ ID NOs: 50 and 51.
13. The method of any one of claims 9-12, wherein the fusion protein comprises the amino acid sequences shown in SEQ ID NO: 50 and 51.
14. The method of any one of claims 9-13, wherein the fusion protein comprises two chains having the amino acid sequence shown in SEQ ID NO: 50 and two chains having the amino acid sequence shown in SEQ ID NO: 51.
15. The method of any one of claims 1-14, wherein the HER2-targeted TKI is selected from the group consisting of tucatinib, lapatinib, neratinib, pyrotinib, erlotinib and afatinib.
16. The method of any one of claims 1-15, wherein the HER2-targeted TKI is tucatinib.
17. The method of any one of claims 1-16, comprising administering the 4-1BB/HER2 bispecific agent at an interval of about once every three weeks, about once every two weeks, or about once every week.
18. The method of any one of claims 1-17, comprising administering the 4-1BB/HER2 bispecific agent at an interval of about once every two weeks.
19. The method of any one of claims 1-18, comprising administering the 4-1BB/HER2 bispecific agent at a dose of from about 2.5 mg/kg to about 27 mg/kg.
20. The method of any one of claims 1-19, comprising administering the 4-1BB/HER2 bispecific agent at a dose of about 2.5 mg/kg, about 5 mg/kg, about 8 mg/kg, about 12 mg/kg or about 18 mg/kg.
21. The method of any one of claims 1-20, comprising administering the 4-1BB/HER2 bispecific agent at a dose of about 8 mg/kg.
22. The method of any one of claims 1-21, comprising administering the 4-1BB/HER2 bispecific agent at a dose of about 18 mg/kg.
23. The method of any one of claims 1-22, comprising administering the 4-1BB/HER2- bispecific agent at a first dose and, subsequently, at a second dose, wherein the first dose exceeds the second dose.
24. The method of claim 23, wherein the 4-1 BB/HER2-bispecific agent is administered at the first dose up to five times, up to four times, up to three times or up to two times.
25. The method of claim 23 or 24, wherein the 4-1 BB/HER2-bispecific agent is administered two times at the first dose.
26. The method of any one of claims 23-25, wherein the first dose is from about 5 mg/kg to about 27 mg/kg.
27. The method of any one of claims 23-26, wherein the second dose is from about 2.5 mg/kg to about 18 mg/kg.
28. The method of any one of claims 23-27, wherein the first dose is about 18 mg/kg.
29. The method of any one of claims 23-28, wherein the second dose is about 8 mg/kg.
30. The method of any one of claims 23-29, comprising administering the 4-1BB/HER2- bispecific agent two times at a dose of about 18 mg/kg and, subsequently, at a dose of about
8 mg/kg, wherein the 4-1BB/HER2-bispecific agent is administered at an interval of about once every two weeks.
31. The method of any one of claims 1-30, wherein the 4-1 BB/HER2-bispecific agent is administered intravenously.
32. The method of any one of claims 1-31 , wherein the HER2-targeted TKI is administered at a daily dose of from about 20 mg to about 1500 mg.
33. The method of any one of claims 1-32, wherein the HER2-targeted TKI is administered once daily or twice daily.
34. The method of any one of claims 1-33, wherein the HER2-targeted TKI is tucatinib and is administered at a dose of about 300 mg twice daily.
35. The method of any one of claims 1-33, wherein the HER2-targeted TKI is lapatinib and is administered at a dose of about 1250 mg once daily.
36. The method of any one of claims 1-33, wherein the HER2-targeted TKI is neratinib and is administered at a dose of about 240 mg once daily.
37. The method of any one of claims 1-33, wherein the HER2-targeted TKI is pyrotinib and is administered at a dose of about 400 mg once daily.
38. The method of any one of claims 1-33, wherein the HER2-targeted TKI is erlotinib and is administered at a dose of about 100 mg or about 150 mg once daily.
39. The method of any one of claims 1-33, wherein the HER2-targeted TKI is afatinib and is administered at a dose of about 20, 30, 40 or 50 mg once daily.
40. The method of any one of claims 1-39, wherein the HER2-targeted TKI is administered orally.
41. The method of any one of claims 1-40, wherein the subject is previously treated.
42. The method of any one of claims 1-41 , wherein the subject is previously treated with an anti-HER2 therapy.
43. The method of any one of claims 1-42, wherein the tumor is selected from the group consisting of gastric cancer, gastroesophageal cancer (e.g., gastroesophageal junction cancer), colon cancer and breast cancer.
44. The method of any one of claims 1-43, wherein the tumor is gastric or gastroesophageal junction adenocarcinoma
45. The method of any one of claims 1-44, wherein the method provides an anti-tumor effect comprising one or more of the following:
(a) increased IL-2 secretion;
(b) increased IL-2 secretion in a tumor microenvironment;
(c) increased IFN-gamma secretion;
(d) increased IFN-gamma secretion in a tumor microenvironment;
(e) expansion of CD4+ T cells;
(f) expansion of CD4+ T cells in a tumor microenvironment;
(g) expansion of CD8+ T cells;
(h) expansion of CD8+ T cells in a tumor microenvironment;
(i) expansion of tumor-infiltrating lymphocytes;
0 activation of NK cells and increased antibody-dependent cell-mediated cytotoxicity (ADCC); and
(k) activation of NK cells and increased ADCC in a tumor microenvironment.
46. The method of any one of claims 1-45, wherein the method provides an enhanced anti tumor effect as compared to the 4-1BB/HER2-bispecific agent or the HER2-targeted TKI alone.
47. The method of claim 46, wherein the enhanced anti-tumor effect is synergistic.
48. The method of any one of claims 1-47, wherein the treatment provides at least one effect selected from the group consisting of stimulation of tumor-specific immune responses, reduction in tumor size, suppression of the growth of tumor cells, suppression of metastasis, complete remission, partial remission, stable disease, extension of the term before recurrence, extension of survival time, complete response, and partial response.
49. The method of any one of claims 1-48, wherein the HER2-targeted TKI prolongs the presence of the 4-1BB/HER2-bispecific agent on the surface of HER2-expressing tumor cells and/or in the microenvironment of HER2-expressing tumors.
50. A 4-1 BB/HER2-bispecific agent or a pharmaceutical composition comprising the same for use in a method of treating a tumor in a subject, wherein the method is as defined in any one of claims 1-49.
51. A HER2-targeted tyrosine kinase inhibitor (TKI) or a pharmaceutical composition comprising the same for use in a method of treating a tumor in a subject, wherein the method is as defined in any one of claims 1-49.
52. A combination comprising
(a) a 4-1BB/HER2-bispecific agent; and
(b) a HER2-targeted tyrosine kinase inhibitor (TKI), wherein the combination is suitable to be administered to a subject in at least one cycle.
53. The combination of claim 52, wherein the 4-1 BB/HER2-bispecific agent and the HER2 targeted TKI are administered concurrently or sequentially.
54. A kit of parts comprising
(a) a pharmaceutical composition comprising a 4-1BB/HER2-bispecific agent; and
(b) a pharmaceutical composition comprising a HER2-targeted tyrosine kinase inhibitor
(TKI).
55. The combination of claim 52 or 53, or the kit of parts of claim 54, wherein the 4- 1BB/HER2-bispecific agent is as defined in any one of claims 9-14.
56. The combination of any one of claims 52, 53 and 55, or the kit of parts of claim 54 or 55, wherein the HER2-targeted TKI is as defined in claim 15 or 16.
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