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WO2026015612A1 - Methods of treating smarcb1-deficient cancers - Google Patents

Methods of treating smarcb1-deficient cancers

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WO2026015612A1
WO2026015612A1 PCT/US2025/036939 US2025036939W WO2026015612A1 WO 2026015612 A1 WO2026015612 A1 WO 2026015612A1 US 2025036939 W US2025036939 W US 2025036939W WO 2026015612 A1 WO2026015612 A1 WO 2026015612A1
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antigen
inhibitor
seq
amino acid
antibody
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David Knorr
Thomas S. ULDRICK JR.
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Regeneron Pharmaceuticals Inc
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Regeneron Pharmaceuticals Inc
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    • 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
    • C07K16/2803Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C07K16/2809Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against the T-cell receptor (TcR)-CD3 complex
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • C07K16/28Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C07K16/2818Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against CD28 or CD152
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    • C07K16/2803Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C07K16/2827Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against B7 molecules, e.g. CD80, CD86
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    • C07K16/28Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/30Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
    • C07K16/3076Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells against structure-related tumour-associated moieties
    • C07K16/3092Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells against structure-related tumour-associated moieties against tumour-associated mucins
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    • C07K2317/31Immunoglobulins specific features characterized by aspects of specificity or valency multispecific

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Abstract

The present disclosure provides methods of treating a SMARCB1-deficient cancer. In certain embodiments, the methods comprise administering an anti-MUC16/anti-CD3 antibody or antigen-binding fragment thereof to a subject in need thereof. In certain embodiments, the methods further comprise administering a PD-1 inhibitor (e.g., an anti-PD-1 antibody) or a PD-L1 inhibitor (e.g., an anti-PD-L1 antibody) to the subject in need thereof.

Description

METHODS OF TREATING SMARCB1 -DEFICIENT CANCERS
REFERENCE TO A SEQUENCE LISTING
[0001] This application incorporates by reference a computer readable Sequence Listing in ST.26 XML format, titled 1 1893WO01 -Sequence, created on July 1 , 2025 and containing 28,540 bytes.
FIELD OF THE INVENTION
[0002] The present disclosure provides methods for treating SMARCB1 -deficient cancers. In certain embodiments, the present methods comprise administering to a subject in need thereof bispecific antibodies or antigen-binding fragments thereof that bind to MUC16 and CD3. In certain embodiments, a PD-1 inhibitor or PD-L1 inhibitor is also administered to the subject in need thereof in combination with the bispecific antibody. In certain embodiments, the subject has been previously treated with one or more anti-cancer therapies.
BACKGROUND
[0003] SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1 ) protein is part of a large complex involved in chromatin structure regulation. The expression of this gene is correlated with tumor suppression. Cancers deficient in SMARCB1 are particularly aggressive and associated with high mortality rates. Epitheliod sarcoma (ES) and renal medullary carcinoma (RMC), for example, are SMARCB1 -deficient cancers associated with very poor prognosis. For patients with SMARCB1 -deficient cancers, there is an urgent need for new and effective therapeutic strategies.
[0004] Mucin 16 (MUC16), also known as cancer antigen 125, carcinoma antigen 125, carbohydrate antigen 125, or CA-125, is a single transmembrane domain highly glycosylated integral membrane glycoprotein that is highly expressed in certain cancers. MUC16 consists of three major domains: an extracellular N-terminal domain, a large tandem repeat domain interspersed with sea urchin sperm, enterokinase, and agrin (SEA) domains, and a carboxyl terminal domain that comprises a segment of the transmembrane region and a short cytoplasmic tail. Proteolytic cleavage results in shedding of the extracellular portion of MUC16 into the bloodstream. Expression on cancer cells is shown to protect tumor cells from the immune system. [0005] CD3 is a homodimeric or heterodimeric antigen expressed on T cells in association with the T cell receptor complex (TCR) and is required for T cell activation. Functional CD3 is formed from the dimeric association of two of four different chains: epsilon, zeta, delta and gamma. The CD3 dimeric arrangements include gamma/epsilon, delta/epsilon and zeta/zeta. Antibodies against CD3 have been shown to cluster CD3 on T cells, thereby causing T cell activation in a manner similar to the engagement of the TCR by peptide-loaded MHC molecules. Thus, anti-CD3 antibodies have been proposed for therapeutic purposes involving the activation of T cells. In addition, bispecific antibodies that are capable of binding CD3 and a target antigen have been proposed for therapeutic uses involving targeting T cell immune responses to tissues and cells expressing the target antigen.
[0006] Programmed death receptor-1 (PD-1 ) signaling in the tumor microenvironment plays a key role in allowing tumor cells to escape immune surveillance by the host immune system.
Blockade of the PD-1 signaling pathway has demonstrated clinical activity in patients with multiple tumor types, and antibody therapeutics that block PD-1 (e.p., nivolumab and pembrolizumab) have been approved for the treatment of metastatic melanoma and metastatic squamous non-small cell lung cancer. Recent data has demonstrated the clinical activity of PD-1 blockade in patients with aggressive NHL and Hodgkin's lymphoma (Lesokhin, etal. 2014, Abstract 291 , 56th ASH Annual Meeting and Exposition, San Francisco, Calif.; Ansell et al. 2015, N. Engl. J. Med. 372(4):31 1 -9). [0007] Many SMARCB1 -deficient cancers have been found to develop resistance to known immunotherapy treatments. Therefore, for patients with SMARCB1 -deficient cancers, new therapeutics and methods of treatment are needed.
BRIEF SUMMARY OF THE DISCLOSURE
[0008] In one aspect, the present disclosure provides a method of treating SMARCB1 -deficient cancer in a subject in need thereof, comprising administering to the subject a bispecific antibody or antigen-binding fragment thereof comprising a first antigen-binding domain that specifically binds human mucin 16 (MUC16) and a second antigen-binding domain that specifically binds human CD3, as monotherapy, or in combination with a PD-1 inhibitor or PD-L1 inhibitor.
[0009] In one aspect, the present disclosure provides a method of treating a SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1 ) deficient cancer in a subject in need thereof, comprising administering to the subject a bispecific antibody or antigen-binding fragment thereof comprising a first antigen-binding domain that specifically binds mucin 16 (MUC16), and a second antigen-binding domain that specifically binds human CD3 in a dosing regimen comprising: (a) administering an initial dose of the bispecific antibody or antigen-binding fragment thereof in week 1 ; (b) administering an intermediate dose of the bispecific antibody or antigen-binding fragment thereof in week 2; and (c) administering a full dose of the bispecific antibody or antigen-binding fragment thereof in a subsequent week of the dosing regimen.
[0010] In some embodiments of the dosing regimen, the full dose is administered from week 3 or week 4 of the dosing regimen. In some embodiments, the intermediate dose is greater than the initial dose, and wherein the full dose is greater than the intermediate dose. In some embodiments, the initial dose is 0.1 mg to 10 mg. In some embodiments, the initial dose is about 1 mg. In some embodiments, the intermediate dose is 10 mg to 30 mg. In some embodiments, the intermediate dose is about 20 mg.
[0011] In some embodiments of the dosing regimen, the intermediate dose is administered to the subject in two dose fractions on consecutive days in week 2 of the dosing regimen. In some embodiments, each of the two dose fractions comprises about 10 mg of the bispecific antibody or antigen-binding fragment thereof. In some embodiments, the bispecific antibody is administered at a full dose once every three weeks (Q3W) from week 5 or week 6 of the dosing regimen.
[0012] In some embodiments, the methods include administering to the subject a PD-1 inhibitor or a PD-L1 inhibitor in combination with the bispecific antibody or antigen-binding fragment thereof. In some embodiments, a dose of the PD-1 inhibitor or the PD-L1 inhibitor is administered in combination with the bispecific antibody or antigen-binding fragment thereof after the subject has received at least three full doses of the bispecific antibody or antigen-binding fragment thereof. In some embodiments, the full dose of the bispecific antibody or antigen-binding fragment thereof is 150 mg to 350 mg. In some embodiments, the full dose is about 250 mg.
[0013] In any of the various embodiments, the dose of the PD-1 inhibitor or PD-L1 inhibitor is 250 mg to 800 mg. In some embodiments, the dose of the PD-1 inhibitor or PD-L1 inhibitor is about 200 mg. In some embodiments, the dose of the PD-1 inhibitor or PD-L1 inhibitor is about 350 mg. In some embodiments, the dose of the PD-1 inhibitor or PD-L1 inhibitor is about 600 mg. In some embodiments, the dose of the PD-1 inhibitor or PD-L1 inhibitor is about 700 mg.
[0014] In any of the various embodiments, the PD-1 inhibitor or PD-L1 inhibitor is administered once every three weeks, once every four weeks, once every five weeks, or once every six weeks. [0015] In some embodiments of the methods disclosed herein, the bispecific antibody or antigenbinding fragment thereof is administered intravenously or subcutaneously to the subject. In some embodiments, the PD-1 inhibitor or the PD-L1 inhibitor is administered intravenously or subcutaneously to the subject. In some embodiments, the bispecific antibody or antigen-binding fragment thereof, and the PD-1 inhibitor or the PD-L1 inhibitor are administered in separate formulations.
[0016] In some embodiments of the methods disclosed herein, the first antigen-binding domain of the bispecific antibody or antigen-binding fragment thereof comprises a heavy chain variable region (HCVR) comprising three heavy chain complementarity determining regions, HCDR1 , HCDR2 and HCDR3, comprising the amino acid sequences of SEQ ID NOs: 5, 6, and 7, respectively, and a light chain variable region (LCVR) comprising three light chain complementarity determining regions, LCDR1 , LCDR2 and LCDR3, comprising the amino acid sequences of SEQ ID NOs: 8, 9, and 10, respectively. In some embodiments, the HCVR of the first antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 1 , and the LCVR of the first antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 2.
[0017] In some embodiments of the methods disclosed herein, the second antigen-binding domain of the bispecific antibody or antigen-binding fragment thereof comprises a heavy chain variable region (HCVR) comprising three heavy chain complementarity determining regions, HCDR1 , HCDR2 and HCDR3, comprising the amino acid sequences of SEQ ID NOs: 11 , 12, and 13, respectively, and a light chain variable region (LCVR) comprising three light chain complementarity determining regions, LCDR1 , LCDR2 and LCDR3, comprising the amino acid sequences of SEQ ID NOs: 8, 9, and 10, respectively. In some embodiments, the HCVR of the second antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 3, and the LCVR of the second antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 2. [0018] In some embodiments of the methods disclosed herein, the second antigen-binding domain of the bispecific antibody or antigen-binding fragment thereof comprises a heavy chain variable region (HCVR) comprising three heavy chain complementarity determining regions, HCDR1 , HCDR2 and HCDR3, comprising the amino acid sequences of SEQ ID NOs: 14, 15, and 16, respectively, and a light chain variable region (LCVR) comprising three light chain complementarity determining regions, LCDR1 , LCDR2 and LCDR3, comprising the amino acid sequences of SEQ ID NOs: 8, 9, and 10, respectively. In some embodiments, the HCVR of the second antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 4, and the LCVR of the second antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 2. [0019] In some embodiments, the bispecific antibody comprises a human IgG heavy chain constant region. In some embodiments, the human IgG heavy chain constant region is isotype lgG1 . In some embodiments, the human IgG heavy chain constant region is isotype lgG4. In some embodiments, the bispecific antibody comprises a chimeric hinge that reduces Fey receptor binding relative to a wild-type hinge of the same isotype. In some embodiments, the bispecific antibody comprises a first heavy chain and a second heavy chain, and wherein the first heavy chain or the second heavy chain, but not both, comprises a CH3 domain comprising a H435R (EU numbering) modification and a Y436F (EU numbering) modification.
[0020] In some embodiments of the methods disclosed herein, the bispecific antibody comprises a first heavy chain comprising the amino acid sequence of SEQ ID NO: 17, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 19, and a common light chain paired with each of the first heavy chain and second heavy chain, respectively, comprising the amino acid sequence of SEQ ID NO: 18.
[0021] In some embodiments of the methods disclosed herein, the bispecific antibody comprises a first heavy chain comprising the amino acid sequence of SEQ ID NO: 17, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 20, and a common light chain paired with each of the first heavy chain and second heavy chain, respectively, comprising the amino acid sequence of SEQ ID NO: 18.
[0022] In some embodiments of the methods disclosed herein, the PD-1 inhibitor is an anti-PD-1 antibody or antigen-binding fragment thereof, or the PD-L1 inhibitor is an anti-PD-L1 antibody or antigen-binding fragment thereof.
[0023] In some embodiments, the anti-PD-1 antibody or antigen-binding fragment comprises a heavy chain variable region (HCVR) comprising three heavy chain complementarity determining regions, HCDR1 , HCDR2 and HCDR3, comprising the amino acid sequences of SEQ ID NOs: 23, 24, and 25, respectively, and a light chain variable region (LCVR) comprising three light chain complementarity determining regions, LCDR1 , LCDR2 and LCDR3, comprising the amino acid sequences of SEQ ID NOs: 26, 27, and 28, respectively. In some embodiments, the HCVR of the anti-PD-1 antibody or antigen-binding fragment thereof comprises the amino acid sequence of SEQ ID NO: 21 , and the LCVR of the anti-PD-1 antibody or antigen-binding fragment thereof comprises the amino acid sequence of SEQ ID NO: 22. In some embodiments, the anti-PD-1 antibody or antigen-binding fragment is an anti-PD-1 antibody comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 29, and a light chain comprising the amino acid sequence of SEQ ID NO: 30.
[0024] In some embodiments, the methods disclosed herein include administering an additional therapeutic agent or therapy. In some embodiments, the additional therapeutic agent is a chemotherapeutic drug, a DNA alkylator, an immunomodulator, radiotherapy, a different bispecific antibody that interacts with a different tumor cell surface antigen and a T cell or immune cell antigen, an antibody drug conjugate, an additional PD-1 inhibitor, an additional PD-L1 inhibitor, a CTLA-4 checkpoint inhibitor, or combinations thereof. In some embodiments, the additional therapy is surgery.
[0025] In some embodiments of the methods disclosed herein, the SMARCB1 -deficient cancer is synovial sarcoma, malignant rhabdoid tumors, atypical teratoid/rhabdoid tumors, epithelioid sarcoma, renal medullary carcinoma, a kidney cancer, renal cell carcinoma (RCC), collecting duct RCC, papillary RCC, renal leiomyoblastoma, epithelioid malignant perhpheral nerve sheath tumors, myoepithelial carcinoma, extraskeletal myxoid chondrosarcoma, chordoma, pediatric chordoma, pancreas undifferentiated rhabdoid carcinoma, sinonasal basaloid carcinoma, rhabdoid carcinoma of the gastrointestinal tract, schwannaomatosis, gastrointestinal stromal tumors, or ossifying fibromyxoid tumor. In some embodiments, the SMARCB1 -deficient cancer is renal medullary carcinoma. In some embodiuments, the SMARCB1 -deficient cancer is renal cell carcinoma, including, without limitation, collecting duct renal cell carcinoma and papillary renal cell carcinoma. In some embodiments, the SMARCB1 -deficient cancer is epithelioid sarcoma.
[0026] In some embodiments of the methods disclosed herein, the subject has progressed following at least one prior therapy to treat the SMARCB1 -deficient cancer. In some embodiments, the subject has a serum CA-125 level of > 70 units/mL prior to treatment with the bispecific antibody or antigen-binding fragment thereof, or a positive H score of >25 for CA-125 by IHC in tumor tissues prior to treatment with the bispecific antibody or antigen-binding fragment thereof. In some embodiments, the SMARCB1 -deficient cancer is locally advanced or metastatic.
[0027] In some embodiments of the methods disclosed herein, the PD-1 inhibitor is cemiplimab. In some embodiments, the bispecific antibody is ubamatamab.
[0028] Any of the various methods discussed above or herein can be reformatted as (i) a bispecific anti-MUC16 x CD3 antibody for use in a method for treating SMARCB1 -deficient cancer, or (ii) a bispecific anti-MUC16 x CD3 antibody for use in combination with a PD-1 or PD-L1 inhibitor (e.g., cemiplimab) in a method for treating SMARCB1 -deficient cancer, or (iii) a PD-1 or PD-L1 inhibitor (e.g., cemiplimab) for use in combination with a bispecific anti-MUC16 x CD3 antibody in a method for treating SMARCB1 -deficient cancer, or (iv) use of a bispecific anti-MUC16 x CD3 antibody in the manufacture of a medicament for treating SMARCB1 -deficient cancer, or (v) use of a bispecific anti-MUC16 x CD3 antibody in the manufacture of a medicament for treating
SMARCB1 -deficient cancer in combination with a PD-1 or PD-L1 inhibitor (e.g., cemiplimab), or (vi) use of a a PD-1 or PD-L1 inhibitor (e.g., cemiplimab) in the manufacture of a medicament for treating SMARCB1 -deficient cancer in combination with a bispecific anti-MUC16 x CD3 antibody, or (vii) use of a combination of a bispecific anti-MUC16 x CD3 antibody and a PD-1 or PD-L1 inhibitor (e.g., cemiplimab) in the manufacture of a medicament for treating SMARCB1 -deficient cancer (e.g., where the two agents are formulated for separate administration).
[0029] In various embodiments, any of the features or components of embodiments discussed above or herein may be combined, and such combinations are encompassed within the scope of the present disclosure. Any specific value discussed above or herein may be combined with another related value discussed above or herein to recite a range with the values representing the upper and lower ends of the range, and such ranges are encompassed within the scope of the present disclosure. [0030] Other embodiments will become apparent from a review of the ensuing detailed description.
BRIEF DESCRIPTION OF THE DRAWINGS
[0031] Figure 1 illustrates an exemplary dosing schedule, as discussed in Example 2, for treatment of SMARCB1 -deficient cancer patients by administration of a bispecific anti-MUC16/anti- CD3 antibody, ubamatamab, as monotherapy, and in combination with an anti-PD1 inhibitor, cemiplimab.
[0032] Figure 2 illustrates an exemplary dosing schedule, as discussed in Example 2, for treating SMARCB1 -deficient cancer patients by administration of a bispecific anti-MUC16/anti-CD3 antibody, ubamatamab, as monotherapy
[0033] Figure 3 illustrates an exemplary dosing schedule, as discussed in Example 2, for treating SMARCB1 -deficient cancer patients by administration of a bispecific anti-MUC16/anti-CD3 antibody, ubamatamab, in combination with an anti-PD1 inhibitor, cemiplimab.
[0034] Figures 4A and 4B show flow cytometry results identifying the presence of MUC16 on ovarian carcinoma cells (OVCAR3) and SMARCB1 -deficient renal leiomyoblastoma cells (G402) (Fig. 4A), and the relative absence of MUC16 on SMARCB1 -deficient epithelioid sarcoma cells (VA- ES-BJ) and alveolar carcinoma cells (SW-1573) (Fig. 4B).
[0035] Figure 5 shows the cytotoxic activity and T-cell activation of REGN4018 (ubamatamab) in connection with ovarian carcinoma cells (OVCAR3) and SMARCB1 -deficient renal leiomyoblastoma cells (G402).
DETAILED DESCRIPTION
[0036] It is to be understood that this disclosure is not limited to particular methods and experimental conditions described, as such methods and conditions may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.
[0037] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. As used herein, the term "about," when used in reference to a particular recited numerical value, means that the value may vary from the recited value by no more than 1 %. For example, as used herein, the expression "about 100" includes 99 and 101 and all values in between (e.g., 99.1 , 99.2, 99.3, 99.4, etc.). [0038] Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the subject matter of the present disclosure, the preferred methods and materials are now described. All patents, applications and non-patent publications mentioned in this specification are incorporated herein by reference in their entireties.
[0039] Abbreviations
ADR Adverse Drug Reaction AE Adverse Event ALT/SGPT Alanine Aminotransferase/ Serum Glutamic Pyruvic Transaminase AST/SGOT Aspartate Aminotransferase/ Serum Glutamic Oxaloacetic Transaminase BCC Basal Cell Carcinoma BiTE Bispecific T-Cell Engager BNP Brain Natriuretic Peptide BP Blood Pressure BUN Blood Urea Nitrogen CARPA Complement Activation-Related Pseudoallergy CBC Complete Blood Count ccRCC Clear-Cell Renal Cell Carcinoma CHF Congestive Heart Failure chRCC Chromophobe Renal Cell Carcinoma Cl Confidence Intervals CK Creatinine Kinase CMP Comprehensive Metabolic Panel CNS Central Nervous System CR Complete Response CRF Case Report Form CRP C-Reactive Protein CRS Cytokine Release Syndrome CSCC Cutaneous Squamous Cell Carcinoma CT Computed Tomography CTCAE Common Terminology Criteria for Adverse Events CTLA-4 Cytotoxic T Lymphocyte Antigen-4 DCR Disease Control Rate DOR Duration of Response DSMP Data Safety Monitoring Plan ECG Electrocardiogram EMG Electromyography EMR Electronic Medical Record EOI End of Infusion EOT End of Treatment ES Epithelioid Sarcoma ESR Erythrocyte Sedimentation Rate FDA Food and Drug Administration FFPE Formalin-Fixed Paraffin-Embedded GCP Good Clinical Practice G-CSF Granulocyte Colony Stimulating Factor HBV Hepatitis B Virus HCV Hepatitis C Virus HepBsAg Hepatitis B Surface Antigen HHI Hedgehog Pathway Inhibitor
HIV Human Immunodeficiency Virus
IB Investigator’s Brochure
ICANS Immune Effector Cell-Associated Neurotoxicity Syndrome
ICF Informed Consent Form
ICH International Council on Harmonisation
IFE Immunofixation Electrophoresis
IFNy Interferon gamma
IHC Immunohistochemistry
IL-6 lnterleukin-6
INR International Normalized Ratio imAR Immune-Mediated Adverse Reaction irAE Immune-related Adverse Event
IRB Institutional Review Board irPD Immune-Related Progressive Disease
IRR Infusion-Related Reactions
IV (or iv) Intravenously
LAG-3 Lymphocyte Activation Gene-3
LES Lambert-Eaton Syndrome
LVEF Left Ventricular Ejection Fraction mAb Monoclonal Antibody
MG Myasthenia Gravis
MHC Major Histocompatibility Complex
MRI Magnetic Resonance Imaging mTOR Mechanistic Target of Rapamycin
MUGA Multigated Acquisition
MuSK Muscle-Specific Tyrosine Kinase
NCI National Cancer Institute
NSAID Nonsteroidal Anti-inflammatory Drug
NSCLC Non-Small Cell Lung Cancer
OR Objective Response
ORA Office of Research Administration
ORR Overall Response Rate or Objective Response Rate
OS Overall Survival
PBMC Peripheral Blood Mononuclear Cell
PCR Polymerase Chain Reaction
PD Progressive Disease
PD-1 Programmed Death Receptor-1
PD-L1 Programmed Death-ligand 1
PFS Progression Free Survival
PK Pharmacokinetic
PR Partial Response aPTT Activated Partial Thromboplastin Time
Q3W Once every 3 Weeks
QW Once Weekly
RCC Renal Cell Carcinoma
RECIST Response Evaluation Criteria in Solid Tumors irRECIST Immune-Related Response Evaluation Criteria in Solid Tumors
RMC Renal Medullary Carcinoma
RNA Ribonucleic Acid
RNI Reportable New Information RV Right Vehicle
SAE Serious Adverse Event
SAV Single Agent Vial scRNA-seq Single Cell Ribonucleic Acid Sequencing
SD Stable Disease
SDi Shortest Diameter of a lesion
SPEP Serum Protein Electrophoresis
TMTB Total Measured Tumor Burden
TOX Trial Limiting Toxicity
TPS Tumor Proportion Score
TSH Thyroid Stimulating Hormone
TTE Transthoracic Echocardiogram
ULN Upper Limit of Normal
WOCBP Women of Childbearing Potential
Definitions
[0040] The expression "CD3," as used herein, refers to an antigen which is expressed on T cells as part of the multimolecular T cell receptor (TCR) and which consists of a homodimer or heterodimer formed from the association of two of four receptor chains: CD3-epsilon, CD3-delta, CD3-zeta, and CD3-gamma. All references to proteins, polypeptides and protein fragments herein are intended to refer to the human version of the respective protein, polypeptide or protein fragment unless explicitly specified as being from a non-human species. Thus, the expression "CD3" means human CD3 unless specified as being from a non-human species, e.g., "mouse CD3," "monkey CD3," etc.
[0041] As used herein, "an antibody that binds CD3" or an "anti-CD3 antibody" includes antibodies and antigen-binding fragments thereof that specifically recognize a single CD3 subunit (e.g., epsilon, delta, gamma or zeta), as well as antibodies and antigen-binding fragments thereof that specifically recognize a dimeric complex of two CD3 subunits (e.g., gamma/epsilon, delta/epsilon, and zeta/zeta CD3 dimers). The antibodies and antigen-binding fragments of the present disclosure may bind soluble CD3 and/or cell surface expressed CD3. Soluble CD3 includes natural CD3 proteins as well as recombinant CD3 protein variants such as, e.g., monomeric and dimeric CD3 constructs, that lack a transmembrane domain or are otherwise unassociated with a cell membrane.
[0042] As used herein, the expression "cell surface-expressed CD3" means one or more CD3 protein(s) that is/are expressed on the surface of a cell in vitro or in vivo, such that at least a portion of a CD3 protein is exposed to the extracellular side of the cell membrane and is accessible to an antigen-binding portion of an antibody. "Cell surface-expressed CD3" includes CD3 proteins contained within the context of a functional T cell receptor in the membrane of a cell. The expression "cell surface-expressed CD3" includes CD3 protein expressed as part of a homodimer or heterodimer on the surface of a cell (e.g., gamma/epsilon, delta/epsilon, and zeta/zeta CD3 dimers). The expression, "cell surface-expressed CD3" also includes a CD3 chain (e.g., CD3- epsilon, CD3-delta or CD3-gamma) that is expressed by itself, without other CD3 chain types, on the surface of a cell. A "cell surface-expressed CD3" can comprise or consist of a CD3 protein expressed on the surface of a cell which normally expresses CD3 protein. Alternatively, "cell surface-expressed CD3" can comprise or consist of CD3 protein expressed on the surface of a cell that normally does not express human CD3 on its surface but has been artificially engineered to express CD3 on its surface.
[0043] As used herein, the expression “MUC16” refers to Mucin 16, a large integral membrane glycoprotein tht is highly expressed in certain cancers but only expressed at low levels in epithelial cells of normal tissue. In normal tissue, the protein is thought to function in barrier formation via formation of protective mucous barriers to prevent pathogens from entering cells. However, in cancer cells, higher epxression of this gene is associated with poorer clinical outcomes in patients. The amino acid sequences of human MUC16 isoforms can be found in GenBank accession numbers NP 001388430.1 , NP 001401615.1 , NP 001401616.1 , and NP 078966.2.
[0044] The expression “SMARCB1 ,” as used herein, refers to the SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 gene or protein. The gene or protein can also be referred to as RDT, CSS3, INI1 , SNF5, Snr1 , BAF47, MRD15, RTPS1 , Sfhl p, hSNFS, SNF5LA, SWNTS1 , or PPP1 R144. The protein functions in regulating chromatin structure to allow transcriptional machinery to access genomic DNA. The gene is considered a tumor suppressor. The amino acid sequences of human SMARCB1 isoforms can be found in GenBank accession numbers NP 001007469.1 , NP 001304875.1 , N P 001349806.1 , and NP 003064.2.
[0045] The expression “PD-1 ,” as used herein, refers to the programmed cell death 1 gene or protein and can also be referred to as PDCD1 , PD1 , CD279, or SLEB2. PD-1 is an immune- inhibitory receptor expressed in activated T cells and involved in the regulation of T cell function. The amino acid sequence of human PD-1 can be found in GenBank accession number NP 005009.2.
[0046] The expression “PD-L 1 ,” as used herein, refers to the programmed cell death ligand 1 gene or protein and can also be referred to as CD274, B7-H, B7H1 , PDL1 , PDCD1 L1 , or PDCD1 LG1 . PD-L1 is an immune inhibitory ligand expressed by hematopoietic and non- hematopoietic cells including T cells and B cells. The encoded protein is a type I transmembrane protein that has immunoglobulin V-like and C-like domains and interaction of this ligand with its receptor inhibits T-cell activation and cytokine production. The amino acid sequence of human PD- L1 can be found in GenBank accession numbers NP 001254635.1 and human PD-L1 isforms, for example, can be found in GenBank accession numbers NP 001300958.1 , NP 054862.1 , XP 054218785.1 , and XP_047279218.1 .
[0047] As used herein, “an antibody that binds MUC16” or an “anti-MUC16 antibody” includes antibodies and antigen-binding fragments thereof that specifically recognize MUC16.
[0048] The term "antigen-binding molecule" includes antibodies and antigen-binding fragments of antibodies, including, e.g., bispecific antibodies.
[0049] The term "antibody", as used herein, means any antigen-binding molecule or molecular complex comprising at least one complementarity determining region (CDR) that specifically binds to or interacts with a particular antigen (e.g., MUC16, CD3, PD-1 or PD-L1). The term "antibody" includes immunoglobulin molecules comprising four polypeptide chains, two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, as well as multimers thereof (e.g., IgM). The term “antibody” also includes immunoglobulin molecules consisting of four polypeptide chains, two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds. Each heavy chain comprises a heavy chain variable region (abbreviated herein as HCVR or VH) and a heavy chain constant region. The heavy chain constant region comprises three domains, CH1 , CH2 and CH3. Each light chain comprises a light chain variable region (abbreviated herein as LCVR or VL) and a light chain constant region. The light chain constant region comprises one domain (Ci_1 ). The V 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 (FR). Each VH and V is composed of three CDRs and four FRs, arranged from aminoterminus to carboxy-terminus in the following order: FR1 , CDR1 , FR2, CDR2, FR3, CDR3, FR4. In different embodiments of the disclosure, the FRs of the anti-MUC16 antibody or anti-CD3 antibody (or antigen-binding portion thereof) may be identical to the human germline sequences, or may be naturally or artificially modified. An amino acid consensus sequence may be defined based on a side-by-side analysis of two or more CDRs.
[0050] The term "antibody", as used herein, also includes antigen-binding fragments of full antibody molecules. The terms "antigen-binding portion" of an antibody, "antigen-binding fragment" of an antibody, and the like, as used herein, include any naturally occurring, enzymatically obtainable, synthetic, or genetically engineered polypeptide or glycoprotein that specifically binds an antigen to form a complex. Antigen-binding fragments of an antibody may be derived, e.g., from full antibody molecules using any suitable standard techniques such as proteolytic digestion or recombinant genetic engineering techniques involving the manipulation and expression of DNA encoding antibody variable and optionally constant domains. Such DNA is known and/or is readily available from, e.g., commercial sources, DNA libraries (including, e.g., phage-antibody libraries), or can be synthesized. The DNA may be sequenced and manipulated chemically or by using molecular biology techniques, for example, to arrange one or more variable and/or constant domains into a suitable configuration, or to introduce codons, create cysteine residues, modify, add or delete amino acids, etc.
[0051] Non-limiting examples of antigen-binding fragments include: (i) Fab fragments; (ii) F(ab')2 fragments; (iii) Fd fragments; (iv) Fv fragments; (v) single-chain Fv (scFv) molecules; (vi) dAb fragments; and (vii) minimal recognition units consisting of the amino acid residues that mimic the hypervariable region of an antibody (e.g., an isolated complementarity determining region (CDR) such as a CDR3 peptide), or a constrained FR3-CDR3-FR4 peptide. Other engineered molecules, such as domain-specific antibodies, single domain antibodies, domain-deleted antibodies, chimeric antibodies, CDR-grafted antibodies, diabodies, triabodies, tetrabodies, minibodies, nanobodies (e.g. monovalent nanobodies, bivalent nanobodies, etc.), small modular immunopharmaceuticals (SMIPs), and shark variable IgNAR domains, are also encompassed within the expression "antigenbinding fragment," as used herein.
[0052] In certain embodiments of the disclosure, the anti-MUC16 monospecific antibodies or anti- MUC16 x anti-CD3 bispecific antibodies of the disclosure are human antibodies. The term "human antibody", as used herein, is intended to include antibodies having variable and constant regions derived from human germline immunoglobulin sequences. The human antibodies of the disclosure may include amino acid residues not encoded by human germline immunoglobulin sequences (e.g., mutations introduced by random or site-specific mutagenesis in vitro or by somatic mutation in vivo), for example in the CDRs and in particular CDR3. However, the term "human antibody", as used herein, is not intended to include antibodies in which CDR sequences derived from the germline of another mammalian species, such as a mouse, have been grafted onto human framework sequences.
[0053] The antibodies of the disclosure may, in some embodiments, be recombinant human antibodies. The term "recombinant human antibody", as used herein, is intended to include all human antibodies that are prepared, expressed, created or isolated by recombinant means, such as antibodies expressed using a recombinant expression vector transfected into a host cell (described further below), antibodies isolated from a recombinant, combinatorial human antibody library (described further below), antibodies isolated from an animal (e.g., a mouse) that is transgenic for human immunoglobulin genes (see e.g., Taylor et al. (1992) Nucl. Acids Res. 20:6287-6295) or antibodies prepared, expressed, created or isolated by any other means that involves splicing of human immunoglobulin gene sequences to other DNA sequences. Such recombinant human antibodies have variable and constant regions derived from human germline immunoglobulin sequences. In certain embodiments, however, such recombinant human antibodies are subjected to in vitro mutagenesis (or, when an animal transgenic for human Ig sequences is used, in vivo somatic mutagenesis) and thus the amino acid sequences of the VH and VL regions of the recombinant antibodies are sequences that, while derived from and related to human germline V and V sequences, may not naturally exist within the human antibody germline repertoire in vivo.
[0054] Human antibodies can exist in two forms that are associated with hinge heterogeneity. In one form, an immunoglobulin molecule comprises a stable four chain construct of approximately 150-160 kDa in which the dimers are held together by an interchain heavy chain disulfide bond. In a second form, the dimers are not linked via inter-chain disulfide bonds and a molecule of about 75- 80 kDa is formed composed of a covalently coupled light and heavy chain (half-antibody). These forms have been extremely difficult to separate, even after affinity purification. The frequency of appearance of the second form in various intact IgG isotypes is due to, but not limited to, structural differences associated with the hinge region isotype of the antibody. A single amino acid substitution in the hinge region of the human lgG4 hinge can significantly reduce the appearance of the second form (Angal et al. (1993) Molecular Immunology 30:105) to levels typically observed using a human IgG 1 hinge. The instant disclosure encompasses antibodies having one or more mutations in the hinge, CH2 or CH3 region which may be desirable, for example, in production, to improve the yield of the desired antibody form.
[0055] The antibodies of the disclosure may be isolated antibodies. An "isolated antibody," as used herein, means an antibody that has been identified and separated and/or recovered from at least one component of its natural environment. For example, an antibody that has been separated or removed from at least one component of an organism, or from a tissue or cell in which the antibody naturally exists or is naturally produced, is an "isolated antibody" for purposes of the present disclosure. An isolated antibody also includes an antibody in situ within a recombinant cell. Isolated antibodies are antibodies that have been subjected to at least one purification or isolation step. According to certain embodiments, an isolated antibody may be substantially free of other cellular material and/or chemicals.
[0056] The anti-MUC16 x anti-CD3 antibodies, and the anti-PD-1 or anti-PD-L1 antibodies disclosed herein may comprise one or more amino acid substitutions, insertions and/or deletions in the framework and/or CDR regions of the heavy and light chain variable domains as compared to the corresponding germline sequences from which the antibodies were derived. Such mutations can be readily ascertained by comparing the amino acid sequences disclosed herein to germline sequences available from, for example, public antibody sequence databases. The present disclosure also includes anti-MUC16 x anti-CD3 antibodies and anti-PD1 or anti-PD-L1 antibodies comprising variants of any of the HCVR, LCVR, and/or CDR amino acid sequences disclosed herein having one or more conservative substitutions. For example, the present disclosure includes anti-MUC16 x anti-CD3 antibodies having HCVR, LCVR, and/or CDR amino acid sequences with, e.g., 10 or fewer, 8 or fewer, 6 or fewer, 4 or fewer, etc. conservative amino acid substitutions relative to any of the HCVR, LCVR, and/or CDR amino acid sequences set forth herein. In some cases, the antibodies share 95%, 96%, 97%, 98% or 99% amino acid sequence identity with the HCVR(s) and/or LCVR or heavy chain(s) and/or light chain discussed herein.
[0057] As used herein, the term "binding" in the context of the binding of an antibody, immunoglobulin, antibody-binding fragment, or Fc-containing protein to either, e.g., a predetermined antigen, such as a cell surface protein or fragment thereof, typically refers to an interaction or association between a minimum of two entities or molecular structures, such as an antibody-antigen interaction. For instance, binding affinity typically corresponds to a KD value of about 107 M or less, such as about 10-8 M or less, such as about 10‘9 M or less when determined by, for instance, surface plasmon resonance (SPR) technology in a BIAcore 3000 instrument using the antigen as the ligand and the antibody, Ig, antibody-binding fragment, or Fc-containing protein as the analyte (or antiligand). Cell-based binding strategies, such as fluorescent-activated cell sorting (FACS) binding assays, are also routinely used, and FACS data correlates well with other methods such as radioligand competition binding and SPR (Benedict, CA, J Immunol Methods. 1997, 201 (2):223-31 ; Geuijen, CA, et al. J Immunol Methods. 2005, 302(1 -2):68-77). Accordingly, the antibody or antigen-binding protein of the disclosure binds to the predetermined antigen or cell surface molecule (receptor) having an affinity corresponding to a KD value that is at least ten-fold lower than its affinity for binding to a non-specific antigen (e.g., BSA, casein). According to the present disclosure, the affinity of an antibody corresponding to a KD value that is equal to or less than tenfold lower than a non-specific antigen may be considered non-detectable binding, however such an antibody may be paired with a second antigen binding arm for the production of a bispecific antibody of the disclosure.
Methods of Treating SMARCB1 -Deficient Cancers
[0058] The present disclosure includes methods for treating SMARCB1 -deficient cancers in subjects. The methods according to this aspect of the disclosure comprise administering a therapeutically-effective amount of a bispecific antibody against MUC16 and CD3, as monotherapy, or in combination with a PD-1 inhibitor or PD-L1 inhibitor, to a subject in need thereof. As used herein, the terms "treat", "treating", or the like, mean to alleviate symptoms, eliminate the causation of symptoms either on a temporary or permanent basis, to delay or inhibit the proliferation of cancer cells. As used herein, the expression "a subject in need thereof" means a human or non-human animal that exhibits one or more indicia of symptomic SMARCB1 -deficient cancers as discussed herein.
[0059] SMARCB1 -deficient cancers refer to cancers that have decreased or complete loss of SMARCB1 expression compared to normal tissues/cells. Some examples of cancers associated with a SMARCB1 deficiency include synovial sarcoma, malignant rhabdoid tumors, atypical teratoid/rhabdoid tumors, epothelioid sarcoma (ES), renal medullary carcinoma (RMC), epithelioid malignant perhpheral nerve sheath tumors, myoepithelial carcinoma, extraskeletal myxoid chondrosarcoma, chordoma, pediatric chordoma, pancreas undifferentiated rhabdoid carcinoma, sinonasal basaloid carcinoma, rhabdoid carcinoma of the gastrointestinal tract, schwannaomatosis, gastrointestinal stromal tumors, and ossifying fibromyxoid tumors.
[0060] ES and RMC are characterized by complete loss of expression by immunohistochemistry (IHC) of the SMARCB1 protein. ES is generally associated with poor prognosis with overall 5- and 10-year survival rates of 60% and 49%, respectively. Metastatic disease is noted in approximately 42% of patients. RMC is the most aggressive renal cell carcinoma in adolescents and young adults with close to universal fatality despite therapy. Although rare, RMC is the third most common kidney cancer among adolescents and young adults, and comprises the vast majority of SMARCB1 -deficient renal malignancies. RMC predominantly afflicts young individuals of African descent who harbor the sickle cell trait. The increased regional ischemia induced by red blood cell sickling in the medullary vasa recta of individuals with sickle hemoglobinopathies predisposes renal inner medulla cells to SMARCB1 loss resulting in RMC. Similarly to other renal malignancies such as clear cell renal cell carcinoma and collecting duct carcinoma, men are twice as likely to be affected by RMC than women. Afflicted patients have a median age of 28 years (range 9-48 years) and most patients (-67%) will present with metastatic disease, primarily to the lymph nodes (85% of cases), lungs (46%), liver (15%), and bone (15%). Approximately 27% of patients with metastatic disease will have 1 -2 metastatic sites, whereas 73% of patients will have more than 2 sites of metastatic involvement. Sickle hemoglobinopathies such as sickle cell trait can induce a decrease in SMARCB1 expression to protect renal medullary cells from hypoxic stress. RMC is resistant to currently approved immune checkpoint therapies such as the anti-PD-1 inhibitor pembrolizumab, highlighting the need to develop the next generation of immunotherapy strategies. There is also extremely high upregulation of MUC16 gene expression in RMC compared to normal tissue.
[0061] Serum biomarkers (e.g., circulating CA125) have been previously identified to be increased in patients with epitheliod sarcoma, a cancer associated with loss of SMARCB1 . CA125 is the circulating form of MUC16, and is elevated in other cancers where MUC16 is overexpressed on the cell surface (e.g., ovarian cancer). We propose that mRNA levels of MUC16 will serve as a surrogate for surface MUC16 expression, in particular in cancers where circulating CA125 is not significantly elevated as it is in ovarian cancer. Specifically, we hypothesize that SMARCB1 deficient cancers will demonstrate upregulation of MUC16 mRNA transcript. Additionally, upregulation of MUC16 mRNA transcripts in SMARCB1 deficient cancers will correlate with surface expression of MLIC16 by IHC analysis. Publicly available datasets for SMARCB1 deficient cancers exist supporting this hypothesis.
[0062] Bispecific anti-MUC16 x anti-CD3 antibodies have been shown to activate T cells and such activated T cells deplete target cells with EC50s in the picomolar range (US Patent No. 10,738,130). Experiments are underway to test depletion of SMARCB1 -deficient MUC16- expressing cell lines by bispecific anti-MUC16 x anti-CD3 antibodies.
[0063] Accordingly, the methods of the present disclosure, according to certain embodiments, comprise administering to a subject in need thereof a therapeutically effective amount of a bispecific anti-MUC16/anti-CD3 antibody or antigen-binding fragment thereof, as monotherapy, or in combination with a PD-1 inhibitor or a PD-L1 inhibitor. In certain embodiments, the combination may be administered in further combination with an additional therapy including a chemotherapeutic agent, radiation, and/or surgery. As used herein, the phrase “in combination with" means that the bispecific antibody, and optionally the PD-1 inhibitor or PD-L1 inhibitor or other agent or therapy, are administered to the subject in a time frame in which the combination can exert an overlapping effect. In certain embodiments, the bispecific antibody and the PD-1 inhibitor or PD-L1 inhibitor are administered in separate formulations. In certain embodiments, the antibody and the PD-1 inhibitor or PD-L1 inhibitor are administered in the same formulation.
[0064] In certain embodiments, the methods of the present disclosure are used in a subject with an SMARCB1 deficient cancer. The terms "tumor", "cancer", “lesions” and "malignancy" are interchangeably used herein. Treatment results can be measured by the objective response (OR) and disease control rate (DCR) as efficacy assessments based on the RECIST 1 .1 criteria. Treatment results can be also be measured by progression-free survival (PFS), and duration of response (DOR) based on the RECIST 1 .1 criteria. Measurable disease means the presence of at least one measurable lesion.
[0065] Target lesions can be evaluated by the following standards:
Complete Response (CR): Disappearance of all target lesions. Any pathological lymph nodes (whether target or non-target) must have reduction in short axis to <10 mm (<1 cm). Partial Response (PR): At least a 30% decrease in the sum of the diameters of target lesions, taking as reference the baseline sum diameters.
Progressive Disease (PD): At least a 20% increase in the sum of the 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 (0.5 cm). (Note: the appearance of one or more new lesions is also considered progression).
Stable Disease (SD): Neither sufficient shrinkage to qualify for PR nor sufficient increase to qualify for PD, taking as reference the smallest sum diameters while on study.
[0066] In certain embodiments, the administration of the bispecific antibody or antigen-binding fragment thereof, as monotherapy, or in combination with a PD-1 inhibitor or PD-L1 inhibitor provides for a complete response or partial response to treatment for the disease. The methods disclosed herein include methods for reducing the sum of the diameters of target lesions by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% in a subject. According to certain embodiments, the present disclosure includes methods for treating, or delaying or inhibiting the growth of a tumor. In certain embodiments, the present disclosure includes methods to promote tumor regression. In certain embodiments, the present disclosure includes methods to reduce tumor cell load or to reduce tumor burden.
[0067] In certain embodiments, the administration of the bispecific antibody or antigen-binding fragment thereof, as monotherapy, or in combination with a PD-1 inhibitor or PD-L1 inhibitor increases duration of survival of the subject, e.g., increases duration of survival by more than 1 month, more than 3 months, more than 6 months, more than 12 months, more than 18 months, more than 24 months, more than 36 months, more than 48 months, more than 5 years, more than 6 years, more than 7 years, more than 8 years, more than 9 years, or more than 10 years, relative to an untreated subject. In certain embodiments, administration of the bispecific antibody or antigenbinding fragment, as monotherapy, or in combination with a PD-1 inhibitor or PD-L1 inhibitor increases progression-free survival or overall survival. In certain embodiments, administration of the bispecific antibody or antigen-binding fragment thereor, as monotherapy, or in combination with a PD-1 inhibitor or PD-L1 inhibitor increases response and duration of response in a subject, e.g., by more than 2%, more than 3%, more than 4%, more than 5%, more than 6%, more than 7%, more than 8%, more than 9%, more than 10%, more than 20%, more than 30%, more than 40% or more than 50% over an untreated subject.
Bispecific Anti-MUC16 x Anti-CD3 Antibodies
[0068] According to certain exemplary embodiments of the present disclosure, the methods comprise administering a therapeutically effective amount of a bispecific antibody that specifically binds MUC16 and CD3 or an antigen-binding fragment thereof, as monotherapy, or in combination with administration of a PD-1 inhibitor or PD-L1 inhibitor. The antibodies and fragments may be referred to herein as, e.g., "anti-MUC16/anti-CD3," or "anti-MUC16 x CD3," or "anti-MUC16 x anti- CD3," or "MUC16 x CD3" bispecific antibodies or antigen-binding fragments thereof, or other similar terminology. One example of an anti-MUC16 x CD3 bispecific antibody is REGN4018 (ubamatamab). In certain embodiments, the anti-tumor activity of the bispecific anti-MUC16/anti- CD3 antibodies or antigen-binding fragments thereof of the present invention is not substantially impeded by the presence of high levels (e.g., up to 10,000 U/ml) of circulating CA125.
[0069] As used herein, the expression "bispecific antibody" refers to an immunoglobulin protein comprising at least a first antigen-binding domain and a second antigen-binding domain. In the context of the present disclosure, the first antigen-binding domain specifically binds a first antigen (e.g., MUC16), and the second antigen-binding domain specifically binds a second, distinct antigen (e.g., CD3). Each antigen-binding domain of a bispecific antibody comprises a heavy chain variable domain (HCVR) and a light chain variable domain (LCVR), each comprising three complementarity determining regions (CDRs). In the context of a bispecific antibody, the CDRs of the first antigenbinding domain may be designated with the prefix "A" and the CDRs of the second antigen-binding domain may be designated with the prefix "B". Thus, the CDRs of the first antigen-binding domain may be referred to herein as A-HCDR1 , A-HCDR2, and A-HCDR3; and the CDRs of the second antigen-binding domain may be referred to herein as B-HCDR1 , B-HCDR2, and B-HCDR3.
[0070] The first antigen-binding domain and the second antigen-binding domain are each connected to a separate multimerizing domain. As used herein, a "multimerizing domain" is any macromolecule, protein, polypeptide, peptide, or amino acid that has the ability to associate with a second multimerizing domain of the same or similar structure or constitution. In the context of the present disclosure, the multimerizing component is an Fc portion of an immunoglobulin (comprising a CH2-CHS domain), e.g., an Fc domain of an IgG selected from the isotypes lgG1 , lgG2, lgG3, and lgG4, as well as any allotype within each isotype group.
[0071] Bispecific antibodies of the present disclosure typically comprise two multimerizing domains, e.g., two Fc domains that are each individually part of a separate antibody heavy chain. The first and second multimerizing domains may be of the same IgG isotype such as, e.g., IgG 1 /IgG 1 , lgG2/lgG2, lgG4/lgG4. Alternatively, the first and second multimerizing domains may be of different IgG isotypes such as, e.g., lgG1/lgG2, lgG1/lgG4, lgG2/lgG4, etc.
[0072] Any bispecific antibody format or technology may be used to make the bispecific antibodies of the present disclosure. For example, an antibody or fragment thereof having a first antigen binding specificity can be functionally linked (e.g., by chemical coupling, genetic fusion, noncovalent association or otherwise) to one or more other molecular entities, such as another antibody or antibody fragment having a second antigen-binding specificity to produce a bispecific antibody. Specific exemplary bispecific formats that can be used in the context of the present disclosure include, without limitation, e.g., scFv-based or diabody bispecific formats, IgG-scFv fusions, dual variable domain (DVD)-lg, Quadroma, knobs-into-holes, common light chain (e.g., common light chain with knobs-into-holes, etc.), CrossMab, CrossFab, (SEED)body, leucine zipper, Duobody, IgG 1 /lgG2, dual acting Fab (DAF)-lgG, and Mab2 bispecific formats (see, e.g., Klein et al. 2012, mAbs 4:6, 1 -11 , and references cited therein, for a review of the foregoing formats).
[0073] In the context of bispecific antibodies of the present disclosure, Fc domains may comprise one or more amino acid changes (e.g., insertions, deletions or substitutions) as compared to the wild-type, naturally occurring version of the Fc domain. For example, the disclosure includes bispecific antibodies comprising one or more modifications in the Fc domain that results in a modified Fc domain having a modified binding interaction (e.g., enhanced or diminished) between Fc and FcRn. In one embodiment, the bispecific antibody comprises a modification in a CHZ or a CH3 region, wherein the modification increases the affinity of the Fc domain to FcRn in an acidic environment (e.g., in an endosome where pH ranges from about 5.5 to about 6.0). Non-limiting examples of such Fc modifications are disclosed in US Patent Publication No. 20150266966, incorporated herein in its entirety.
[0074] The present disclosure also includes bispecific antibodies comprising a first CH3 domain and a second Ig CH3 domain, wherein the first and second Ig CH3 domains differ from one another by at least one amino acid, and wherein at least one amino acid difference reduces binding of the bispecific antibody to Protein A as compared to a bi-specific antibody lacking the amino acid difference. In one embodiment, the first Ig CH3 domain binds Protein A and the second Ig CH3 domain contains a mutation that reduces or abolishes Protein A binding such as an H95R modification (by IMGT exon numbering; H435R by EU numbering). The second CH3 may further comprise a Y96F modification (by IMGT ; Y436F by EU). See, for example, US Patent No. 8,586,713. Further modifications that may be found within the second CH3 include: D16E, L18M, N44S, K52N, V57M, and V82I (by IMGT; D356E, L358M, N384S, K392N, V397M, and V422I by EU) in the case of lgG1 antibodies; N44S, K52N, and V82I (IMGT; N384S, K392N, and V422I by EU) in the case of lgG2 antibodies; and Q15R, N44S, K52N, V57M, R69K, E79Q, and V82I (by IMGT; Q355R, N384S, K392N, V397M, R409K, E419Q, and V422I by EU) in the case of lgG4 antibodies. [0075] In certain embodiments, the Fc domain may be chimeric, combining Fc sequences derived from more than one immunoglobulin isotype. For example, a chimeric Fc domain can comprise part or all of a CH2 sequence derived from a human lgG1 , human lgG2 or human lgG4 CH2 region, and part or all of a CH3 sequence derived from a human IgG 1 , human lgG2 or human lgG4. A chimeric Fc domain can also contain a chimeric hinge region. For example, a chimeric hinge may comprise an "upper hinge" sequence, derived from a human IgG 1 , a human lgG2 or a human lgG4 hinge region, combined with a "lower hinge" sequence, derived from a human IgG 1 , a human lgG2 or a human lgG4 hinge region. A particular example of a chimeric Fc domain that can be included in any of the antibodies set forth herein comprises, from N- to C-terminus: [lgG4 CHl]-[lgG4 upper hinge]- [lgG2 lower hinge]-[lgG4 CH2]-[lgG4 CH3]. Another example of a chimeric Fc domain that can be included in any of the antibodies set forth herein comprises, from N- to C-terminus: [IgG 1 CH1]- [IgG 1 upper hinge]-[lgG2 lower hinge]-[lgG4 CH2]-[lgG1 CH3]. These and other examples of chimeric Fc domains or chimeric heavy chain constant regions that can be included in any of the antibodies of the present disclosure are described in US Patent Publication No. 20140243504, which is herein incorporated in its entirety. Chimeric Fc domains and chimeric heavy chain constant regions having these general structural arrangements, and variants thereof, can have altered Fc receptor binding, which in turn affects Fc effector function.
[0076] According to certain exemplary embodiments of the present invention, the bispecific anti- MUC16/anti-CD3 antibody, or antigen-binding fragment thereof comprises heavy chain variable regions (A-HCVR and B-HCVR), light chain variable regions (A-LCVR and B-LCVR), and/or complementarity determining regions (CDRs) comprising any of the amino acid sequences of the bispecific anti-MUC16/anti-CD3 antibodies as set forth in WO 2018/067331 . In certain exemplary embodiments, the bispecific anti-MUC16/anti-CD3 antibody or antigen-binding fragment thereof that can be used in the context of the methods of the present disclosure comprises: (a) a first antigenbinding arm comprising the heavy chain complementarity determining regions (A-HCDR1 , A- HCDR2 and A-HCDR3) of a heavy chain variable region (A-HCVR) comprising the amino acid sequence of SEQ ID NO: 1 and the light chain complementarity determining regions (A-LCDR1 , A- LCDR2 and A-LCDR3) of a light chain variable region (A-LCVR) comprising the amino acid sequence of SEQ ID NO: 2; and (b) a second antigen-binding arm comprising the heavy chain CDRs (B-HCDR1 , B-HCDR2 and B-HCDR3) of a HCVR (B-HCVR) comprising an amino acid sequence of SEQ ID NO: 3 or SEQ ID NO: 4, and the light chain CDRs (B-LCDR1 , B-LCDR2 and B-LCDR3) of a LCVR (B-LCVR) comprising the amino acid sequence of SEQ ID NO: 2. According to certain embodiments, the A-HCDR1 comprises the amino acid sequence of SEQ ID NO: 5; the A-HCDR2 comprises the amino acid sequence of SEQ ID NO: 6; the A-HCDR3 comprises the amino acid sequence of SEQ ID NO: 7; the A-LCDR1 comprises the amino acid sequence of SEQ ID NO: 8; the A-LCDR2 comprises the amino acid sequence of SEQ ID NO: 9; the A-LCDR3 comprises the amino acid sequence of SEQ ID NO: 10; the B-HCDR1 comprises the amino acid sequence of SEQ ID NO: 1 1 ; the B-HCDR2 comprises the amino acid sequence of SEQ ID NO: 12; and the B-HCDR3 comprises the amino acid sequence of SEQ ID NO: 13; and the B-LCDR1 comprises the amino acid sequence of SEQ ID NO: 8; the B-LCDR2 comprises the amino acid sequence of SEQ ID NO: 9; the B-LCDR3 comprises the amino acid sequence of SEQ ID NO: 10. According to certain embodiments, the A-HCDR1 comprises the amino acid sequence of SEQ ID NO: 5; the A-HCDR2 comprises the amino acid sequence of SEQ ID NO: 6; the A-HCDR3 comprises the amino acid sequence of SEQ ID NO: 7; the A-LCDR1 comprises the amino acid sequence of SEQ ID NO: 8; the A-LCDR2 comprises the amino acid sequence of SEQ ID NO: 9; the A-LCDR3 comprises the amino acid sequence of SEQ ID NO: 10; the B-HCDR1 comprises the amino acid sequence of SEQ ID NO: 14; the B-HCDR2 comprises the amino acid sequence of SEQ ID NO: 15; and the B-HCDR3 comprises the amino acid sequence of SEQ ID NO: 16; and the B- LCDR1 comprises the amino acid sequence of SEQ ID NO: 8; the B-LCDR2 comprises the amino acid sequence of SEQ ID NO: 9; the B-LCDR3 comprises the amino acid sequence of SEQ ID NO: 10. In yet other embodiments, the bispecific anti-MUC16/anti-CD3 antibody or antigen-binding fragment thereof comprises: (a) a first antigen-binding arm comprising a HCVR (A-HCVR) comprising SEQ ID NO: 1 and a LCVR (A-LCVR) comprising SEQ ID NO: 2; and (b) a second antigen-binding arm comprising a HCVR (B-HCVR) comprising SEQ ID NO: 3, and a LCVR (B- LCVR) comprising SEQ ID NO: 2. In yet other embodiments, the bispecific anti-MUC16/anti-CD3 antibody or antigen-binding fragment thereof comprises: (a) a first antigen-binding arm comprising a HCVR (A-HCVR) comprising SEQ ID NO: 1 and a LCVR (A-LCVR) comprising SEQ ID NO: 2; and (b) a second antigen-binding arm comprising a HCVR (B-HCVR) comprising SEQ ID NO: 4, and a LCVR (B-LCVR) comprising SEQ ID NO: 2. In certain exemplary embodiments, the bispecific anti- CD3xMUC16 antibody comprises a MUC16-binding arm comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 17 and a light chain comprising the amino acid sequence of SEQ ID NO: 18, and a CD3-binding arm comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 19, and a light chain comprising the amino acid sequence of SEQ ID NO: 18. In certain exemplary embodiments, the bispecific anti-CD3xMUC16 antibody comprises a MUC16-binding arm comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 17 and a light chain comprising the amino acid sequence of SEQ ID NO: 18, and a CD3-binding arm comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 20, and a light chain comprising the amino acid sequence of SEQ ID NO: 18. [0077] The methods of the present disclosure also encompass use of a bioequivalent to the bispecific antibodies discussed herein. The term "bioequivalent", as used herein, refers to antibodies or fragments thereof that are pharmaceutical equivalents or pharmaceutical alternatives whose rate and/or extent of absorption do not show a significant difference with that of the bispecific antibodies discussed above when administered at the same molar dose under similar experimental conditions, either single dose or multiple dose. In the context of the disclosure, the term refers to antigen-binding proteins that bind to MUC16 and CD3, which do not have clinically meaningful differences to the bispecific antibodies discussed herein in their safety, purity and/or potency.
PD-1 and PD-L1 Inhibitors
[0078] Exemplary methods of the present disclosure comprise administering a therapeutically effective amount of a bispecific antibody that specifically binds MLIC16 and CD3 or an antigenbinding fragment thereof, as monotherapy, or in combination with a PD-1 inhibitor or a PD-L1 inhibitor. PD-1 inhibitors are a type of immune checkpoint inhibitor. PD-1 inhibitors can include anti- PD-1 antibodies or antigen-binding fragments thereof that specifically bind PD-1. PD-L1 inhibitors can include anti-PD-L1 antibodies or antigen-binding fragments thereof that specifically bind PD-L1 . [0079] In some embodiments, the anti-PD-1 antibody or antigen-binding fragment comprises: (a) three heavy chain complementarity determining regions (HCDR1 , HCDR2 and HCDR3) contained within a heavy chain variable region (HCVR) comprising the amino acid sequence of SEQ ID NO: 21 ; and (b) three light chain complementarity determining regions (LCDR1 , LCDR2 and LCDR3) contained within a light chain variable region (LCVR) comprising the amino acid sequence of SEQ ID NO: 22. In some cases, the anti-PD-1 antibody or antigen-binding fragment comprises a HCDR1 comprising the amino acid sequence of SEQ ID NO: 23, a HCDR2 comprising the amino acid sequence of SEQ ID NO: 24, and a HCDR3 comprising the amino acid sequence of SEQ ID NO: 25. In some cases, the anti-PD-1 antibody or antigen-binding fragment comprises a LCDR1 comprising the amino acid sequence of SEQ ID NO: 26, a LCDR2 comprising the amino acid sequence of SEQ ID NO: 27, and a LCDR3 comprising the amino acid sequence of SEQ ID NO: 28. In some cases, the anti-PD-1 antibody or antigen-binding fragment comprises a HCVR comprising the amino acid sequence of SEQ ID NO: 21 , and a LCVR comprising the amino acid sequence of SEQ ID NO: 22. In some cases, the anti-PD-1 antibody or antigen-binding fragment is an anti-PD-1 antibody comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 29 and a light chain comprising the amino acid sequence of SEQ ID NO: 30. An exemplary anti-PD-1 antibody comprising a HCVR of SEQ ID NO: 21 and a LCVR of SEQ ID NO: 22 is cemiplimab (LIBTAYO®). [0080] According to certain exemplary embodiments, the methods of the present disclosure comprise the use of cemiplimab, or a bioequivalent thereof. The term "bioequivalent", as used herein, refers to anti-PD-1 antibodies that are pharmaceutical equivalents or pharmaceutical alternatives whose rate and/or extent of absorption do not show a significant difference with that of cemiplimab when administered at the same molar dose under similar experimental conditions, either single dose or multiple dose. In the context of the disclosure, the term refers to antigenbinding proteins that bind to PD-1 , and which do not have clinically meaningful differences with cemiplimab in their safety, purity and/or potency.
[0081] Other anti-PD-1 antibodies that can be used in the context of the methods of the present disclosure include, e.g., the antibodies referred to and known in the art as nivolumab (U.S. Pat. No. 8,008,449), pembrolizumab (U.S. Pat. No. 8,354,509), MEDI0608 (U.S. Pat. No. 8,609,089), pidilizumab (U.S. Pat. No. 8,686,1 19), or any of the anti-PD-1 antibodies as set forth in U.S. Pat. Nos. 6,808,710, 7,488,802, 8,168,757, 8,354,509, 8,779,105, or 8,900,587. Anti-PD-L1 antibodies include those set forth in WO 2013/079174, WO 2018/222949, and WO 2010/077634. Specific anti-PD-L1 antibodies include REGN3504, atezolizumab, avelumab, and durvalumab.
Efficacy and Monitoring
[0082] The methods discussed in the present disclosure may further comprise monitoring efficacy parameters associated with effects of the bispecific antibody or antigen-binding fragment thereof, as monotherapy, or in combination with a PD-1 inhibitor or PD-L1 inhibitor, measured by objective response (OR), disease control rate (DCR), progression-free survival (PFS), and duration of response (DOR). Samples of peripheral blood can be taken for identifying changes in specific immune cell subsets (e.g., ICOS+ CD4/CD8 T cells) by flow cytometry. Samples of tumor tissues can be taken to conduct spatial transcriptomics analyses to elucidate the dynamic evolution of tumor and immune cell compartments and their spatial relationships following treatment(s). The methods may further include cytokine release syndrome (CRS) monitoring and management to evaluate efficacy and safety within individual subjects or populations of subjects.
[0083] CRS has been observed in connection with the administration of anti-MUC16 x CD3 antibodies. Corticosteroids or anti-IL-6 pathway therapies (e.g., sarilumab or tocilizumab) may be utilized in the management of CRS as discussed herein. Dexamethasone or other predmedications may also be utilized in the management of CRS. In some embodiments, an anti-l L-6R inhibitor, such as an anti- 1 L-6R antibody (e.g., sarilumab) is administered prophylactically prior to a dose (e.g., an initial dose, or an initial dose and an intermediate dose) of the anti-MUC16 x CD3 antibody (e.g., ubamatamab).
[0084] The efficacy analysis can include measuring any of the following: (1 ) Evaluation of Target Lesions
(a) Complete Response (CR): Disappearance of all target lesions. Any pathological lymph nodes (whether target or non-target) must have reduction in short axis to <10 mm (<1 cm).
(b) Partial Response (PR): At least a 30% decrease in the sum of the diameters of target lesions, taking as reference the baseline sum diameters.
(c) Progressive Disease (PD): At least a 20% increase in the sum of the 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 (0.5 cm). (Note: the appearance of one or more new lesions is also considered progressions).
(d) Stable Disease (SD): Neither sufficient shrinkage to qualify for PR nor sufficient increase to qualify for PD, taking as reference the smallest sum diameters while on study.
(2) Evaluation of Non-target Lesions
(a) Complete Response (CR): The disappearance of all non-target lesions.
(b) Incomplete Response/Stable Disease: The persistence of one or more non-target lesion(s).
(c) Progressive Disease: The appearance of one or more new lesions and/or unequivocal progression of existing non-target lesions
(3) Evaluation of Target Lesions per irRECIST
(a) Complete Response (CR): Complete disappearance of all measurable and non- measurable lesions. Lymph nodes must decrease to < 10 mm in short axis
(b) Partial Response (PR): At least a 30% decrease in TMTB relative to baseline.
(c) Progressive Disease (PD): At least a 20% increase, and minimum 5 mm absolute increase, in TMTB compared to the smallest TMTB recorded since the treatment started. Confirmation of progression is recommended at a minimum of 4 weeks after the first PD assessment, and especially in patients with a minimal TMTB %-increase over 20% during the flare time-window of the first 12 weeks of treatment, to account for expected delayed response.
(d) Stable Disease (SD): Insufficient shrinkage to qualify for PR (or CR), or insufficient increase to qualify for PD, taking as reference the smallest TMTB recorded since the treatment started. (4) Evaluation of Non-target Lesions per irRECIST
(a) Complete Response (CR): Disappearance of all non-target lesions. All lymph nodes must be non-pathological in size (< 10 mm short axis).
(b) Immune-related Non-CR/Non-PD: Persistence of one or more non-target lesion(s) and/or maintenance of tumor marker level above the normal limits. This also includes non-target lesions that demonstrated unequivocal progression at the initial demonstration of PD but then stabilized or regressed on subsequent scans.
(c) Immune-related Progressive Disease (irPD): Unequivocal progression of existing non- target lesions on a disease assessment subsequent to initial demonstration of PD. Therefore, irPD by non-target lesions requires one of the following on a disease assessment >4 weeks after the initial demonstration of PD:
• New unequivocal progression OR
• Further unequivocal progression (if unequivocal progression present at initial PD) irRECIST Terms
• Measurable Lesions:
Lesions that can be accurately measured in at least one dimension: o >10 mm in the longest diameter by CT or MRI scan (or no less than double the slice thickness) for non-nodal lesions o >15 mm in short axis for nodal lesions o >10 mm caliper measurement by clinical exam o >20 mm by chest X-ray
• Non-measurable Lesions:
All other lesions, including: o Small lesions with longest diameter < 10 mm with conventional techniques, < 10 mm with spiral CT scan (or < 2 x the axial slice thickness) o Pathological lymph nodes with > 10 to <15 mm short axis o Other types of lesions that are confidently felt to represent neoplastic tissue, but are difficult to measure in a reproducible manner, such as bone lesions, ascites, pleural/pericardial effusion, leptomeningeal metastases, cystic lesions, ill-defined abdominal masses, inflammatory breast disease, and lymphangitis cutis/pulmonis,
• Measurable Disease: The presence of at least one measurable lesion.
• Target Lesions: All measurable lesions up to a maximum of 2 lesions per organ and 5 lesions in total, representative of all involved organs, should be identified as target lesions and recorded and measured at baseline. Target lesions should be selected on the basis of their size (those with the longest diameter) and their suitability for accurate repeated measurements (either by imaging techniques or clinically).
• Non-target Lesions: All other lesions (or sites of disease) should be identified as non-target lesions and should also be recorded at baseline. There is no limit to the number of non-target lesions that can be recorded at baseline. Measurements of these lesions are not required, but the presence or absence of each should be noted throughout follow-up.
• Measurable New Lesions: Measurable new lesions are defined as all new lesions (up to a maximum of 2 lesions per organ, and 5 lesions in total, per timepoint) representative of all involved organs, meeting criteria as defined for baseline target lesion selection and meet the same minimum size requirements of 10 mm in long diameter and minimum 15 mm in short axis for new measurable lymph nodes. New measurable lesions are prioritized according to size, and the largest lesions are selected as new measured lesions.
• Total Measured Tumor Burden (TMTB): The TMTB is calculated as the sum of the longest diameter for all non-nodal target lesions, new non-nodal measurable lesions, and of the short axes of nodal target lesions and new nodal measurable lesions. The TMTB will be used as the reference from which to characterize the objective tumor response. In irRECIST, new measurable lesions (maximum 5, maximum 2 in one organ) are added to the TMTB at each follow-up and percent increase of TMTB over baseline will determine stable disease (SD) or progressive disease (PD).
[0085] T reatment with the bispecific anti-MUC16 x anti-CD3 antibody or antigen-binding fragment thereof (e.g., ubamatamab), as monotherapy, or in combination with PD1 or PD-L1 inhibition (e.g., cemiplimab) will meet one or more of the following endpoints during treatment as set forth in Example 2.
[0086] Primary Endpoints:
• Objective response. Objective response is defined as a best response of CR or PR by RECIST 1 .1 at any time during trial. This will be reported separately for Stage I and Stage 11. The latest imaging performed within 4 weeks prior to Stage II treatment initiation will serve as the new baseline for Stage II objective response assessment. Patients who receive treatment on either stage will count towards that stage. Treated patients who do not have assessment will count as not having an objective response.
• Disease control. Disease control is defined as CR, PR, or SD by RECIST 1.1 through 18 weeks in either stage I or stage IL This will be reported separately for Stage I and Stage II. The latest imaging performed within 4 weeks prior to Stage II treatment initiation will serve as the new baseline for Stage II disease control assessment. Patients who receive treatment on either stage will count towards that stage. Treated patients who do not have assessment will count as not having disease control at 18 weeks.
[0087] Secondary Endpoints:
• Overall Survival (OS) will be calculated as the time from start of protocol treatment until death or last contact. Patients who are alive at the time of data lock will be censored on their date of last contact. OS will similarly be calculated starting at stage II among patients who start treatment on stage II. If stage I is found futile and some patients start directly on stage II, then an additional subgroup analysis among patients who started on stage I and those who started on stage II may be presented.
• Progression-Free Survival (PFS). PFS is the time from starting protocol treatment until progression by RECIST 1.1 or death from any cause, whichever comes first. Patients who are alive and free of progression at their last disease assessment will be censored on that date. PFS for stage II will also be presented among patients who start treatment on stage II. If stage I is found futile and some patients start directly on stage II, then an additional subgroup analysis among patients who started on stage I and those who initially started on stage II may be presented.
• Duration of Response (DOR). DOR is the time from CR or PR is first noted on stage I until progression by RECIST 1 .1 or death from disease, whichever comes first. Patients who are alive and free of progression at their last disease assessment will be censored on that date. Patients who die without progression will be censored on their date of death. Patients with unknown cause of death will be assumed to have died from disease. DOR for stage II will also be similarly presented among patients who start treatment on Stage II and have response on stage II.
• Adverse Events. Adverse events will be recorded in Prometheus according to NCI CTCAE version 5.0 along with date and attribution to study drug.
• Trial limiting toxicity (TOX) is defined as: o Any grade 3 or higher adverse event that is possibly, probably, or definitely related to protocol therapy and occurs within the first 6 weeks of therapy with two exceptions:
■ Any grade 3 adverse event that is potentially treatable with steroids or drugs such as tocilizumab targeting the IL-6 pathway will only count as an extreme toxicity if it does not improve to grade 1 or better within 2 weeks.
■ Clinically nonsignificant, transient, and reversible laboratory grade >1 abnormalities, such as CRS-associated increases in liver enzymes/total bilirubin, uric acid, triglycerides, alkaline phosphatase, BUN, creatinine, and inorganic phosphorus; decreases in albumin, globulin, and total cholesterol; or changes in neutrophil, lymphocytes, monocyte, eosinophil, and basophil counts. o A delay of >3 months from anticipated nephrectomy date in patients in the RMC cohort due to adverse events possibly, probably, or definitely related to protocol therapy.
[0088] Exploratory Endpoints:
• Objective response at any point in the regimen. Objective response is defined as a best response of CR or PR by RECIST 1 .1 at any time during trial. This will be reported as the best response in either Stage I or Stage II. The latest imaging performed within 4 weeks prior to Stage II treatment initiation will serve as the new baseline for Stage II objective response assessment. Patients who receive treatment on either stage will count towards that stage. Treated patients who do not have assessment will count as not having an objective response.
• Disease control at any point in the regimen. Disease control is defined as CR, PR, or SD by RECIST 1.1 through 18 weeks in either stage I or stage II. This will be reported as occurring in either Stage I and Stage II. The latest imaging performed within 4 weeks prior to Stage II treatment initiation will serve as the new baseline for Stage II disease control assessment. Patients who receive treatment on either stage will count towards that stage. Treated patients who do not have assessment will count as not having disease control at 18 weeks.
• Baseline serum CA-125
• Baseline MLIC16 expression levels by IHC
Pharmaceutical Compositions and Administration
[0089] The present disclosure includes methods which comprise administering a bispecific anti- MUC16/anti-CD3 antibody or antigen-binding fragment thereof, as monotherapy, or in combination with administration of a PD-1 inhibitor or PD-L1 inhibitor to a subject wherein the antibody (or fragment) and/or optionally the PD-1 inhibitor or PD-L1 inhibitor is contained within a pharmaceutical composition. The bispecific antibody, and optionally the PD-1 inhibitor or PD-L1 inhibitor can be formulated together or separately. Preferably, the bispecific antibody, and optionally the PD-1 inhibitor or PD-L1 inhibitor are formulated for separate administration to a subject. The pharmaceutical compositions of the disclosure may be formulated with suitable carriers, excipients, and other agents that provide suitable transfer, delivery, tolerance, and the like. A multitude of appropriate formulations can be found in the formulary known to all pharmaceutical chemists: Remington's Pharmaceutical Sciences, Mack Publishing Company, Easton, Pa. These formulations include, for example, powders, pastes, ointments, jellies, waxes, oils, lipids, lipid (cationic or anionic) containing vesicles (such as LIPOFECTIN™), DNA conjugates, anhydrous absorption pastes, oil-in-water and water-in-oil emulsions, emulsions carbowax (polyethylene glycols of various molecular weights), semi-solid gels, and semi-solid mixtures containing carbowax. See also Powell et al. "Compendium of excipients for parenteral formulations" PDA (1998) J Pharm Sci Technol 52:238-31 1 .
[0090] Various delivery systems are known and can be used to administer the pharmaceutical composition of the disclosure, e.g., encapsulation in liposomes, microparticles, microcapsules, recombinant cells capable of expressing the mutant viruses, receptor mediated endocytosis (see, e.g., Wu et al., 1987, J. Biol. Chem. 262: 4429-4432). Methods of administration include, but are not limited to, intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, and oral routes. The composition may be administered by any convenient route, for example by infusion or bolus injection, or by injection, and may be administered together with other biologically active agents. In some cases, the antibodies are administered subcutaneously, or subcutaneously and intravenously.
[0091] A pharmaceutical composition of the present disclosure can be delivered subcutaneously or intravenously with a standard needle and syringe. In addition, with respect to subcutaneous delivery, a pen delivery device readily has applications in delivering a pharmaceutical composition of the present disclosure. Such a pen delivery device can be reusable or disposable. A reusable pen delivery device generally utilizes a replaceable cartridge that contains a pharmaceutical composition. Once all of the pharmaceutical composition within the cartridge has been administered and the cartridge is empty, the empty cartridge can readily be discarded and replaced with a new cartridge that contains the pharmaceutical composition. The pen delivery device can then be reused. In a disposable pen delivery device, there is no replaceable cartridge. Rather, the disposable pen delivery device comes prefilled with the pharmaceutical composition held in a reservoir within the device. Once the reservoir is emptied of the pharmaceutical composition, the entire device is discarded.
[0092] Numerous reusable pen and autoinjector delivery devices have applications in the subcutaneous delivery of a pharmaceutical composition of the present disclosure. Examples include, but are not limited to AUTOPEN™ (Owen Mumford, Inc., Woodstock, UK), DISETRONIC™ pen (Disetronic Medical Systems, Bergdorf, Switzerland), HUMALOG MIX 75/25™ pen, HUMALOG™ pen, HUMALIN 70/30™ pen (Eli Lilly and Co., Indianapolis, IN), NOVOPEN™ I, II and III (Novo Nordisk, Copenhagen, Denmark), NOVOPEN JUNIOR™ (Novo Nordisk, Copenhagen, Denmark), BD™ pen (Becton Dickinson, Franklin Lakes, NJ), OPTIPEN™, OPTIPEN PRO™, OPTIPEN STARLET™, and OPTICLIK™ (sanofi-aventis, Frankfurt, Germany), to name only a few. Examples of disposable pen delivery devices having applications in subcutaneous delivery of a pharmaceutical composition of the present disclosure include, but are not limited to the SOLOSTAR™ pen (sanofi-aventis), the FLEXPEN™ (Novo Nordisk), and the KWIKPEN™ (Eli Lilly), the SURECLICK™ Autoinjector (Amgen, Thousand Oaks, CA), the PENLET™ (Haselmeier, Stuttgart, Germany), the EPIPEN (Dey, L.P.), and the HUMIRA™ Pen (Abbott Labs, Abbott Park IL), to name only a few.
[0093] In certain situations, the pharmaceutical composition can be delivered in a controlled release system. In one embodiment, a pump may be used. In another embodiment, polymeric materials can be used; see, Medical Applications of Controlled Release, Langer and Wise (eds.), 1974, CRC Pres., Boca Raton, Fla. In yet another embodiment, a controlled release system can be placed in proximity of the composition's target, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, 1984, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115- 138). Other controlled release systems are discussed in the review by Langer, 1990, Science 249:1527-1533.
[0094] The injectable preparations may include dosage forms for intravenous, subcutaneous, intracutaneous and intramuscular injections, drip infusions, etc. These injectable preparations may be prepared by known methods. For example, the injectable preparations may be prepared, e.g., by dissolving, suspending or emulsifying the antibody or its salt in a sterile aqueous medium or an oily medium conventionally used for injections. As the aqueous medium for injections, there are, for example, physiological saline, an isotonic solution containing glucose and other auxiliary agents, etc., which may be used in combination with an appropriate solubilizing agent. The injection thus prepared is preferably filled in an appropriate ampoule.
[0095] Advantageously, the pharmaceutical compositions for use described above are prepared into dosage forms in a unit dose suited to fit a dose of the active ingredients. Such dosage forms in a unit dose include, for example, a vial or a prefilled syringe. In some embodiments, a vial can contain a single dose of a therapeutic agent, or multiple doses of a single therapeutic agent or multiple therapeutic agents.
Additional Combination Therapies
[0096] The present disclosure provides methods which comprise administering a bispecific anti- MUC16/anti-CD3 antibody or antigen-binding fragment thereof described herein, as monotherapy, or in combination with a PD-1 inhibitor or PD-L1 inhibitor. The present disclosure also provides methods which comprise administering a bispecific anti-MUC16/anti-CD3 antibody or antigenbinding fragment thereof, as monotherapy, or in combination with a PD-1 inhibitor or PD-L1 inhibitor, further in combination with an additional therapeutic agent. Exemplary additional therapeutic agents that may be combined with or administered in combination with a bispecific antibody or antigen-binding fragment, and optionally a PD-1 inhibitor or PD-L1 inhibitor, include, e.g., an anti-tumor agent {e.g. chemotherapeutic agents such as gemcitbine or docetaxel), an EZH2 inhibitor such as tazemetostat, radiotherapy, or any other agent or therapy {e.g., surgery) known to be effective in treating a SMARCB1 -deficient cancer in a subject. In certain embodiments, the additional therapeutic agent may be a monoclonal antibody, an antibody drug conjugate, an additional (or second) checkpoint inhibitor, or combinations thereof. Other agents that may be beneficially administered in combination with the bispecific antibodies or antigen-binding fragments and PD-1 or PD-L1 inhibitors of the disclosure include cytokine inhibitors, including small-molecule cytokine inhibitors and antibodies that bind to cytokines such as IL-1 , IL-2, IL-3, IL-4, IL-5, IL-6, IL-8, IL-9, IL-1 1 , IL-12, IL-13, IL-17, IL-18, or to their respective receptors. The combination of anti- MUC16 x anti-CD3 bispecific antibodies or antigen-binding fragments and optionally a PD-1 or PD- L1 inhibitor may also be administered as part of a therapeutic regimen comprising one or more therapeutic combinations selected from a monoclonal antibody other than those described herein, which may interact with a different antigen on the tumor cell surface, a bispecific antibody, which has one arm that binds to an antigen on the tumor cell surface and the other arm binds to an antigen on a T cell, an antibody drug conjugate, an additional checkpoint inhibitor, for example, one that targets CTLA-4, or combinations thereof. In certain embodiments, the additional checkpoint inhibitors may be selected from other PD-1 inhibitors or PD-L1 inhibitors, such as pembrolizumab (Keytruda) or nivolumab (Opdivo). In certain embodiments, the additional checkpoint inhibitors may be selected from PD-L1 inhibitors, such as atezolizumab (Tecentriq), avelumab (Bavencio), or durvalumab (Imfinzi). In certain embodiments, the additional checkpoint inhibitors may be selected from CTLA-4 inhibitors, such as ipilimumab (Yervoy).
[0097] The additional therapeutically active component(s) may be administered just prior to, concurrent with, or shortly after the administration of a bispecific antibodies or antigen-binding fragments and optionally a PD-1 inhibitor/PD-L 1 inhibitor. In some cases, the combination of agents are formulated separately {e.g., in different pharmaceutical compositions). In some cases, the combination of agents are formulated together {e.g., in the same pharmaceutical composition). The present disclosure also includes pharmaceutical compositions in which a bispecific anti- MUC16/anti-CD3 antibody or antigen-binding fragment of the present disclosure is co-formulated with a PD-1 inhibitor or PD-L1 inhibitor, and with one or more of the additional therapeutically active component(s) as described elsewhere herein. Administration Regimens
[0098] The present disclosure includes methods comprising administering to a subject a bispecific anti-MUC16 x CD3 antibody or antigen-binding fragment thereof, as monotherapy, or in combination with a PD-1 inhibitor or PD-L1 inhibitor.
[0099] The bispecific antibody or antigen-binding domain may be administered at a dosing frequency of about four times a week, twice a week, once a week, once every two weeks, once every three weeks, once every four weeks, once every five weeks, once every six weeks, once every eight weeks, once every twelve weeks, or less frequently so long as a therapeutic response is achieved. In some embodiments, administration of the bispecific antibody or antigen-binding fragment is once weekly (QW). In some embodiments, administration of the bispecific antibody or antigen-binding fragment is twice weekly (2QW). In some embodiments, administration of the bispecific antibody or antigen-binding fragment is thrice weekly (3QW). In some embodiments, administration of the bispecific antibody or antigen-binding fragment is once every two weeks (Q2W). In some embodiments, administration of the bispecific antibody or antigen-binding fragment is once every three weeks (Q3W). In some embodiments, administration of the bispecific antibody or antigen-binding fragment is once every four weeks (Q4W).
[0100] The PD-1 inhibitor or PD-L1 inhibitor may be administered at a dosing frequency of about four times a week, three times a week, twice a week, once a week, once every two weeks, once every three weeks, once every four weeks, once every five weeks, once every six weeks, once every eight weeks, once every twelve weeks, or less frequently so long as a therapeutic response is achieved. In some embodiments, administration of the PD-1 inhibitor or PD-L1 inhibitor is once weekly (QW). In some embodiments, administration of the PD-1 inhibitor or PD-L1 inhibitor is twice weekly (2QW). In some embodiments, administration of the PD-1 inhibitor or PD-L1 inhibitor is thrice weekly (3QW). In some embodiments, administration of the PD-1 inhibitor or PD-L1 inhibitor is once every two weeks (Q2W). In some embodiments, administration of the PD-1 inhibitor or PD- L1 inhibitor is once every three weeks (Q3W). In some embodiments, administration of the PD-1 inhibitor or PD-L1 inhibitor is once every four weeks (Q4W). In some embodiments, administration of the PD-1 inhibitor or PD-L1 inhibitor is once every five weeks (Q5W). In some embodiments, administration of the PD-1 inhibitor or PD-L1 inhibitor is once every six weeks (Q6W).
[0101] According to certain embodiments of the present disclosure, multiple doses of a bispecific anti-MUC16/anti-CD3 antibody or antigen-binding fragment thereof, and optionally mulitple doses of a PD-1 inhibitor or PD-L1 inhibitor, may be administered to a subject over a defined time course. The methods according to this aspect of the disclosure comprise administering to a subject one or more doses of a bispecific anti-MUC16/anti-CD3 antibody or antigen-binding fragment thereof, as monotherapy, or in combination with one or more doses of a PD-1 inhibitor or PD-L1 inhibitor. As used herein, "sequential administering" means that each dose of the antibody is administered to the subject at a different point in time, e.g., on different days separated by a predetermined interval {e.g., hours, days, weeks or months). The present disclosure includes methods which comprise sequential administration to the patient a single initial dose of a bispecific antibody (or fragment), followed by one or more secondary doses of the bispecific antibody (or fragment), and optionally followed by one or more tertiary doses of the bispecific antibody (or fragment). The present disclosure includes methods which comprise sequential administration to the patient of a single initial dose of the PD-1 inhibitor or PD-L1 inhibitor, followed by one or more secondary doses of the PD-1 inhibitor or PD-L1 inhibitor, and optionally followed by one or more tertiary doses of the PD-1 inhibitor or PD-L1 inhibitor.
[0102] The terms "initial dose," "secondary doses," and "tertiary doses," refer to the temporal sequence of administration. Thus, the "initial dose" is the dose which is administered at the beginning of the treatment regimen (also referred to as the "baseline dose"); the "secondary doses" are the doses which are administered after the initial dose (also referred to as the “intermediate dose”; and the "tertiary doses" are the doses which are administered after the secondary doses (also referred to as the “full dose”). The initial, secondary, and tertiary doses may all contain the same amount of the antibody or antigen-binding fragment thereof {e.g., the bispecific antibody) or the same amount of the PD-1 inhibitor or PD-L1 inhibitor. In certain embodiments, however, the amount contained in the initial, secondary and/or tertiary doses varies from one another e.g., adjusted up or down as appropriate) during the course of treatment. In certain embodiments, one or more {e.g., 1 , 2, 3, 4, or 5) doses are administered at the beginning of the treatment regimen as "loading doses," of either the bispecific antibody or the PD-1 inhibitor or PD-L1 inhibitor, followed by subsequent doses that are administered on a less frequent basis {e.g., "maintenance doses").
[0103] In one exemplary embodiment of the present disclosure, each secondary and/or tertiary dose is administered 1 to 10 {e.g., 1 , 1.5, 2, 2.5, 3, 3.5, or 4, or more) days after the immediately preceding dose. The phrase "the immediately preceding dose," as used herein, means, in a sequence of multiple administrations, the dose of a bispecific anti-MUC16/anti-CD3 or antigenbinding fragment thereof and/or the dose of a PD-1 inhibitor or PD-L1 inhibitor to a patient prior to the administration of the very next dose in the sequence with no intervening doses.
[0104] The methods according to this aspect of the disclosure may comprise administering to a patient any number of secondary and/or tertiary doses of bispecific anti-MUC16/anti-CD3 antibody or antigen-binding fragment thereof, with (optionally) any number of secondary and/or tertiary doses of a PD-1 inhibitor od PD-L1 inhibitor. For example, in certain embodiments, only a single secondary dose of the bispecific anitbody or antigen-binding fragment, and/or only a single secondary dose of the PD-1 inhibitor or PD-L1 inhibitor, is administered to the patient. In other embodiments, two or more (e.g., 2, 3, 4, 5, 6, 7, 8, or more) secondary doses of either agent, or both agents, are administered to the patient. Likewise, in certain embodiments, only a single tertiary dose of either agent, or both agents, is administered to the patient. In other embodiments, two or more (e.g., 2, 3, 4, 5, 6, 7, 8, or more) tertiary doses of either agent, or both agents, are administered to the patient.
[0105] In embodiments involving multiple secondary doses of both agents, each secondary dose may be administered at the same frequency as the other secondary doses. For example, each secondary dose of either the bispecific antibody, or optionally the PD-1 inhibitor or PD-L1 inhibitor may be administered to the patient 1 , 2, 3, or 4 weeks (e.g., 1 week or 3 weeks) after the immediately preceding dose. Similarly, in embodiments involving multiple tertiary doses, each tertiary dose may be administered at the same frequency as the other tertiary doses. For example, each tertiary dose may be administered to the patient 1 to 4 weeks (e.g., 1 week, 2 weeks, or 4 weeks) after the immediately preceding dose. Alternatively, the frequency at which the secondary and/or tertiary doses are administered to a patient can vary over the course of the treatment regimen (e.g., the tertiary or “full” doses may begin with weekly administration, and then be modified to once every two weeks (Q2W), once every three weeks (Q3W), and/or once every four weeks (Q4W) administration.
[0106] In embodiments of the methods discussed herein, the bispecific antibody or antigenbinding fragment thereof, and/or optionally the PD-1 inhibitor or PD-L1 inhibitor, may be administered for up to 99 weeks or more (e.g., once weekly, once every other week, once every three weeks, once every four weeks, once every five weeks, or once every six weeks). In some cases, the bispecific antibody or antigen-binding fragment and/or optionally the PD-1 inhibitor or PD-L1 inhibitor may be administered for 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 or more weeks at one or more doses as discussed herein.
[0107] In embodiments of the methods discussed herein, the bispecific antibody or antigenbinding fragment thereof, and optionally the PD-1 inhibitor or PD-L1 inhibitor are administered in exemplary dosing regimens as shown in Figures 1 , 2, or 3.
[0108] In some embodiments of the methods discussed herein, a premedication is used prior to administration of the combination of a bispecific anti-MUC16/anti-CD3 antibody, and optionally a PD-1 inhibitor or PD-L1 inhibitor. For example, premedication such as an antihistamine, acetaminophen, and/or dexamethosone may be used prior to administration of the bispecific antibody and/or optionally the PD-1 inhibitor or PD-L1 inhibitor. In an embodiment, premedication is administered with the administration of the bispecific anti-MUC16/CD3 antibody during a step-up cycle prior to monotherapy or combination therapy.
Dosage
[0109] The amount of bispecific anti-MUC16/anti-CD3 antibody or antigen-binding fragment thereof, or optionally the amount of a PD-1 inhibitor or PD-L1 inhibitor administered to a subject according to the methods of the present disclosure is, generally, a therapeutically effective amount. As used herein, the phrase "therapeutically effective amount" means an amount of antibody (a bispecific anti-MUC16/anti-CD3 antibody or antigen-binding fragment thereof) or optionally an amount of a PD-1 inhibitor or PD-L1 inhibitor, that results in one or more of: (a) treatment of a SMARCB1 -deficient cancer in a subject; and/or (b) enhanced survival of a SMARCB1 -deficient cancer patient, as compared to an untreated control (or control population), or a control (or control population) treated with other standard of care agents.
[0110] In the case of a bispecific anti-MUC16/anti-CD3 antibody (e.g., ubamatamab) or antigenbinding fragment thereof, a therapeutically effective amount can be from about 0.1 milligram (mg) to about 1000 mg, e.g., about 0.1 mg, about 0.2 mg, about 0.3 mg, about 0.4 mg, about 0.5 mg, about 0.6 mg, about 0.7 mg, about 0.8 mg, about 0.9 mg, about 1 mg, about 2 mg, about 3 mg, about 4 mg, about 5 mg, about 6 mg, about 7 mg, about 8 mg, about 9 mg, about 10 mg, about 11 mg, about 12 mg, about 13 mg, about 14 mg, about 15 mg, about 16 mg, about 17 mg, about 18 mg, about 19 mg, about 20 mg, about 21 mg, about 22 mg, about 23 mg, about 24 mg, about 25 mg, about 26 mg, about 27 mg, about 28 mg, about 29 mg, about 30 mg, about 35 mg, about 36 mg, about 37 mg, about 38 mg, about 39 mg, about 40 mg, about 41 mg, about 42 mg, about 43 mg, about 44 mg, about 45 mg, about 46 mg, about 47 mg, about 48 mg, about 49 mg, about 50 mg, about 51 mg, about 52 mg, about 53 mg, about 54 mg, about 55 mg, about 56 mg, about 57 mg, about 58 mg, about 59 mg, about 60 mg, about 61 mg, about 62 mg, about 63 mg, about 64 mg, about 65 mg, about 66 mg, about 67 mg, about 68 mg, about 69 mg, about 70 mg, about 71 mg, about 72 mg, about 73 mg, about 74 mg, about 75 mg, about 76 mg, about 77 mg, about 78 mg, about 79 mg, about 80 mg, about 81 mg, about 82 mg, about 83 mg, about 84 mg, about 85 mg, about 86 mg, about 87 mg, about 88 mg, about 89 mg, about 90 mg, about 91 mg, about 92 mg, about 93 mg, about 94 mg, about 95 mg, about 96 mg, about 97 mg, about 98 mg, about 99 mg, about 100 mg, about 101 mg, about 102 mg, about 103 mg, about 104 mg, about 105 mg, about 106 mg, about 107 mg, about 108 mg, about 109 mg, about 110 mg, about 115 mg, about 120 mg, about 125 mg, about 130 mg, about 135 mg, about 140 mg, about 145 mg, about 150 mg, about 155 mg, about 160 mg, about 165 mg, about 170 mg, about 175 mg, about 180 mg, about 185 mg, about 190 mg, about 195 mg, about 200 mg, about 205 mg, about 210 mg, about 215 mg, about 220 mg, about 225 mg, about 230 mg, about 235 mg, about 240 mg, about 245 mg, about 250 mg, about 255 mg, about 260 mg, about 265 mg, about 270 mg, about 275 mg, about 280 mg, about 285 mg, about 290 mg, about 295 mg, about 300 mg, about 310 mg, about 320 mg, about 330 mg, about 340 mg, about 350 mg, about 400 mg, about 450 mg, about 500 mg, about 550 mg, about 600 mg, about 650 mg, about 700 mg, about 750 mg, about 800 mg, about 850 mg, about 900 mg, about 950 mg, or about 1000 mg of the bispecific anti-MUC16/anti-CD3 antibody or antigen-binding fragment thereof. In certain embodiments, the bispecific antibodies or antigen-binding fragments are administered at doses of 1 mg, 20 mg, and/or 250 mg in a dosing regimen to the subject to treat SMARCB1 -deficient cancer. In certain embodiments, the bispecific antibodies or antigen-binding fragments are administered to the subject at an initial dose of about 1 mg, an intermediate dose of about 20 mg, and a full dose of about 250 mg in a dosing regimen to treat a SMARCB1 -deficient cancer. In any embodiments, the doses of the bispecific antibody or antigen-binding fragment thereof may be split into dose fractions (e.g., two dose fractions of equal or unequal amounts). For example, in an embodiment, the transitional dose is administered in two equal dose fractions on two consecutive days (e.g., the 20 mg dose is split into two 10 mg dose fractions for administration on consecutive days). In an embodiment, the initial dose may be split into two equal dose fractions (e.g., 0.5 mg and 0.5 mg) or two unequal dose fractions (e.g., 0.3 mg and 0.7 mg) for administration on two days (e.g., consecutive days).
[0111] In the case of a PD-1 inhibitor (e.g., cemiplimab) or a PD-L1 inhibitor, a therapeutically effective amount can be from about 1 milligram (mg) to about 1000 mg, e.g., about 1 mg, about 10 mg, about 20 mg, about 30 mg, about 40 mg, about 50 mg, about 60 mg, about 70 mg, about 80 mg, about 90 mg, about 100 mg, about 1 10 mg, about 115 mg, about 120 mg, about 125 mg, about 130 mg, about 135 mg, about 140 mg, about 145 mg, about 150 mg, about 155 mg, about 160 mg, about 165 mg, about 170 mg, about 175 mg, about 180 mg, about 185 mg, about 190 mg, about 191 mg, about 192 mg, about 193 mg, about 194 mg, about 195 mg, about 196 mg, about 197 mg, about 198 mg, about 199 mg, about 200 mg, about 201 mg, about 202 mg, about 203 mg, about 204 mg, about 205 mg, about 206 mg, about 207 mg, about 208 mg, about 209 mg, about 210 mg, about 215 mg, about 220 mg, about 225 mg, about 230 mg, about 235 mg, about 240 mg, about 245 mg, about 250 mg, about 255 mg, about 260 mg, about 265 mg, about 270 mg, about 275 mg, about 280 mg, about 285 mg, about 290 mg, about 295 mg, about 300 mg, about 305 mg, about 310 mg, about 315 mg, about 320 mg, about 325 mg, about 330 mg, about 335 mg, about 340 mg, about 341 mg, about 342 mg, about 343 mg, about 344 mg, about 345 mg, about 346 mg, about 347 mg, about 348 mg, about 349 mg, about 350 mg, about 351 mg, about 352 mg, about 353 mg, about 354 mg, about 355 mg, about 356 mg, about 357 mg, about 358 mg, about 359 mg, about 360 mg, about 365 mg, about 370 mg, about 375 mg, about 380 mg, about 385 mg, about 390 mg, about 395 mg, about 400 mg, about 425 mg, about 450 mg, about 475 mg, about 500 mg, about 550 mg, about 560 mg, about 570 mg, about 580 mg, about 590 mg, about 591 mg, about 592 mg, about 593 mg, about 594 mg, about 595 mg, about 596 mg, about 597 mg, about 598 mg, about 599 mg, about 600 mg, about 601 mg, about 602 mg, about 603 mg, about 604 mg, about 605 mg, about 606 mg, about 607 mg, about 608 mg, about 609 mg, about 610 mg, about 620 mg, about 630 mg, about 640 mg, about 650 mg, about 660 mg, about 670 mg, about 680 mg, about 690 mg, about 691 mg, about 692 mg, about 693 mg, about 694 mg, about 695 mg, about 696 mg, about 697 mg, about 698 mg, about 699 mg, about 700 mg, about 701 mg, about 702 mg, about 703 mg, about 704 mg, about 705 mg, about 706 mg, about 707 mg, about 708 mg, about 709 mg, about 710 mg, about 720 mg, about 730 mg, about 740 mg, about 750 mg, about 760 mg, about 770 mg, about 780 mg, about 790 mg, about 800 mg, about 850 mg, about 900 mg, about 950 mg, or about 1000 mg of the PD-1 inhibitor or PD-L1 inhibitor. In certain embodiments, the PD-1 inhibitor (e.g., cemiplimab) or the PD-L1 inhibitor is administered in a dosing regimen at a dose of about 200 mg to the subject to treat a SMARCB1 -deficient cancer. In certain embodiments, the PD-1 inhibitor (e.g., cemiplimab) or the PD-L1 inhibitor is administered in a dosing regimen at a dose of about 350 mg to the subject to treat a SMARCB1 -deficient cancer. In certain embodiments, the PD-1 inhibitor (e.g., cemiplimab) or the PD-L1 inhibitor is administered in a dosing regimen at a dose of about 600 mg to the subject to treat a SMARCB1 -deficient cancer. In certain embodiments, the PD-1 inhibitor (e.g., cemiplimab) or the PD-L1 inhibitor is administered in a dosing regimen at a dose of about 700 mg to the subject to treat a SMARCB1 -deficient cancer.
[0112] Exemplary dosage regimens and dosing schedules for a bispecific anti-MUC16/anti-CD3 antibody (ubamatamab), as monotherapy, or in combination with a PD-1 inhibitor (cemiplimab) are shown in Figures 1 -3.
[0113] A summary of the sequences and the corresponding SEQ ID NOs referenced herein is shown in Table 1 , below.
Table 1 : Summary of Sequences
EXAMPLES
[0114] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the methods and compositions of the disclosure, and are not intended to limit the scope of what the inventors regard as their invention. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.
Example 1 : Generation of Bispecific Antibodies that Bind Mucin 16 (MUC16) and CD3
[0115] Bispecific antibodies comprising an anti-MUC16-specific binding domain and an anti-CD3- specific binding domain were constructed using standard methodologies, wherein the anti-MUC16 antigen binding domain and the anti-CD3 antigen binding domain each comprise different, distinct HCVRs paired with a common LCVR. In some instances the bispecific antibodies were constructed utilizing a heavy chain from an anti-CD3 antibody, a heavy chain from an anti-MUC16 antibody, and a common light chain (see Table 2).
[0116] The bispecific antibodies created in accordance with the present Example comprise two separate antigen-binding domains (/.e., binding arms). The first antigen-binding domain comprises a heavy chain variable region derived from an anti-MUC16 antibody ("MUC16-VH"), and the second antigen-binding domain comprises a heavy chain variable region derived from an anti-CD3 antibody ("CD3-VH"). Both the anti-MUC16 and the anti-CD3 binding domains share a common light chain. The MUC16-VH/CD3-VH pairing creates antigen-binding domains that specifically recognize CD3 on T cells and MUC16 on tumor cells.
[0117] A summary of the component parts of the antigen-binding domains of the various anti- MUC16 x CD3 bispecific antibodies constructed is set forth in Table 2. The corresponding CDR sequences and full-length heavy and light chain sequences are identified in Table 1 .
Table 2: Summary of Component Parts of Anti-MUC16 x Anti-CD3 Bispecific Antibodies
Example 2: Methods of Treating MUC16-Expressing SMARCB1 -Deficient Malignancies with Anti-MUC16 x Anti-CD3 Bispecific Antibodies as Monotherapy, or in Combination with a PD-1 Inhibitor (Cemiplimab)
[0118] This study will evaluate the safety and efficacy of ubamatamab alone or in combination with cemiplimab in patients with MUC16-expressing SMARCB1 -deficient malignancies such as renal medulary carcinoma (RMC) or epithelioid sarcoma (ES) who have progressed on at least one prior line of therapy.
[0119] Objectives: Both primary and secondary objectives will be explored.
[0120] The primary objective of this study is to determine the objective response rate (ORR) and disease control rate (DCR), per RECIST 1.1 , of ubamatamb alone and in combination with cemiplimab in pateints with locally advanced or metastatic MUC16-expressing SMARCB1 -deficient malignancies, RMC or ES, who have progressed on at least one prior line of therapy.
[0121] The secondary objectives of the study are to determine the efficacy and safety of ubamatamab alone or in combination with cemiplimab in patients with locally advanced or metastatic MUC16-expressing SMARCB1 -deficient malignancies such as RMC or ES who have progressed on at least one prior line of therapy. Efficacy will be measured by overall survival (OS), progression-free survival (PFS), and duration of response (DOR).
[0122] Study Design: This is a phase II trial to determine the efficacy of ubamatamab alone or in combination with cemiplimab in patients with MUC16-expressing SMARCB1 -deficient malignancies such as RMC or ES who have progressed on at least one prior line of therapy. Patients with RMC will be enrolled in a separate disease cohort than those with ES, with each cohort having distinct efficacy and futility thresholds. Each enrolled patient will first be treated with ubamatamab monotherapy (Stage I) administered as outlined in Figures 1 and 2. Patients with disease progression at any timepoint after a minimum of 6 weeks of ubamatamab monotherapy will proceed to Stage II which will evaluate the efficacy of adding cemiplimab to ubamatamab with doses administered as outlined in Figures 1 and 3. Only patients who are already receiving a full dose of ubamatamab 250 mg IV Q3W monotherapy during stage I will be eligible to proceed to the addition of cemiplimab 350 mg IV Q3W (Stage II). Treatment will continue until disease progression, intolerable treatment-related toxicity, withdrawal of consent, or end of therapy is approved based on clinical context.
[0123] Patients with RMC who have not had cytoreductive nephrectomy will be evaluated by a surgeon after at least 18 weeks of either ubamatamab monotherapy (Stage I) or ubamatamab + cemiplimab combination (Stage II) to determine if they are good candidates for cytoreductive nephrectomy. Patients who are deemed to be appropriate candidates for cytoreductive nephrectomy will undergo this surgery, and then, at 4-6 weeks postoperatively, will repeat ubamatamab monotherapy step-up dosing and either continue full dose monotherapy Q3W (if nephrectomy occurred during Stage I) or add cemiplimab after step-up dosing in combination with the first dose of ubamatamab 250 mg IV Q3W (if nephrectomy occurred during Stage II). [0124] The screening period is up to 28 days for all patients. In the monotherapy stage (Stage I) cycle 1 will be 6 or 7 weeks (42 or 49 days) long depending on whether the last ubamatamab weekly full dose is given on day 22 or is delayed to day 29 due to toxicity after the initial (day 1), transitional (days 8/9), or first full ubamatamab dose at day 15. All cycles from cycle 2 onwards will be 6 weeks (42 days). During cycle 1 , individual patients will receive escalating doses of ubamatamab to reach the full dose.
[0125] In the combination therapy stage (Stage II) all cycles from cycle 2 onwards will again be 6 weeks (42 days), similarly to Stage I. Patients who are already on ubamatamab 250 mg IV Q3W monotherapy will omit the step-up dose escalation of cycle 1 and immediately proceed to cycle 2. However, patients entering Stage II without having received ubamatamab 250 mg IV monotherapy for >28 days will repeat the step-up dose escalation of cycle 1 shown in Figure 3. Cycle 1 of Stage II will be 3 or 4 weeks (21 or 28 days) long depending on whether the last ubamatamab weekly full dose is given on day 22 or is delayed to day 29 due to toxicity after the initial (day 1), transitional (days 8/9), or first full ubamatamab dose at day 15.
[0126] Study Duration: In the absence of treatment delays due to adverse event(s), treatment may continue for until one of the following criteria applies:
• Patient decides to withdraw from the study for any reason
• Termination of the study by IND/IDE sponsor
• Patient non-compliance
• Pregnancy
All women of childbearing potential should be instructed to contact the investigator immediately if they suspect they might be pregnant (e.g., missed or late menstrual period) at any time during study participation.
• The drug manufacturer can no longer provide the study agent.
[0127] Patients must be discontinued from study therapy but will remain on study follow-up for the following reasons:
• Any clinical adverse event, laboratory abnormality or intercurrent illness which, in the opinion of the Investigator, indicates that continued treatment with study therapies is not in the best interest of the patient
• Imprisonment or the compulsory detention for treatment of either a psychiatric or physical (e.g., infectious disease) illness.
[0128] Patients whose treatment is interrupted or permanently discontinued due to an AE or abnormal laboratory value suspected to be related to study drug must be followed at least weekly until the adverse event or abnormal laboratory resolves or returns to grade 1 . This may be done by telephone correspondence. If a patient requires, due to treatment-related toxicity, a dose delay of > 28 days from the intended day of the next scheduled dose, then the patient must be discontinued from the study treatment but will remain on study for follow-up.
[0129] Study Population: The study population includes patients with RMC or ES. Up to twenty patients will be enrolled for each cohort.
[0130] Inclusion Criteria - A patient must meet the following criteria to be eligible for inclusion in the study:
1 . Patients with locally advanced or metastatic RMC (RMC cohort) or ES (ES cohort) histologically confirmed by expert pathology review and loss of SMARCB1 staining by IHC. Patients with advanced or metastatic unclassified renal cell carcinoma with medullary phenotype (a rare SMARCB1 negative RMC variant occurring in individuals without sickle hemoglobinopathies) are also eligible for the RMC cohort.
2. Eligible patients should either demonstrate serum CA-125 levels > 70 units/mL during screening or positive H score of >25 for MUC16 (CA-125) by IHC in tumor tissues collected within 12 months from screening as noted in patient EMR: a. The H score is calculated using the standard formula commonly used in IHC: H score = [(0 x % negative cells) + (1 x % weak positive cells) + (2 x % moderate positive cells) + (3 x % strong positive cells). For instance, if 50% of tumor cells show weak staining, 30% of tumor cells show moderate staining, and 20% of cells show strong staining, the H-score would be: (50x1 )+(30x2)+(20x3)=50+60+60=170. b. If serum CA-125 > 70 units/mL then patients will be enrolled without delay. IHC for MUC16 will be used as a correlative biomarker but not for trial eligibility. c. If serum CA-125 < 70 units/mL then for trial eligibility, MUC16 expression should be checked by IHC in tumor tissues collected within 12 months from screening: i. If H score is < 25 then the patient will not be eligible for the trial ii. If H score > 25 then the patient will be eligible for the trial
3. Patients will be eligible in the RMC cohort regardless of whether they have had prior nephrectomy or still have their primary tumor in-situ.
4. Patients must have at least one measurable site of disease, defined as a lesion that can be accurately measured in at least one dimension (longest diameter to be recorded) and measures > 15 mm with conventional techniques or > 10 mm with more sensitive techniques such as MRI or CT scan. If the patient has had previous radiation to the marker lesion(s), there must be evidence of progression since the radiation.
5. Patients must have progressed on at least one line of prior therapy. 6. There must be evidence of progression on or after last treatment regimen received.
7. ECOG performance status 0-1 a. NOTE: If patient is unable to walk due to paralysis, but is mobile in a wheelchair, patient is considered to be ambulatory for the purpose of assessing their performance status.
8. Age (at the time of consent/assent): > 18 years
9. Consent to applicable laboratory protocol
10. Patients must have adequate organ and marrow function as defined below:
Hemoglobin3 > 9 g/dl (treatment allowed)
Absolute neutrophil countb > 1 ,000/piL
Platelets > 75,000/pL
Total bilirubin < 1 .5 mg/dl
AST(SGOT) or ALT (SGPT) < 2.5 X institutional ULN, except in known hepatic metastasis, wherein may be < 5 x ULN
Serum Creatinine0 < 1 .5 x ULN by gender (as long as patient does not require dialysis) a May receive transfusion within the screening period bWithout growth factor support (filgrastim or pegfilgrastim) for at least 14 days clf creatinine is not <1 ,5xllLN, then calculate by Cockcroft-Gault methods or local institutional standard and CrCI must be >30 mL/kg/1 .73 m2
11 . Patients with controlled brain metastases are allowed on protocol if the brain metastases were surgically resected or treated with radiosurgery or Gamma knife, without recurrence or edema for 1 month (4 weeks). Patients actively requiring glucocorticoids for uncontrolled brain or leptomeningeal metastases are not eligible.
12. Women of childbearing potential (WOCBP) must have a negative serum or urine pregnancy test (minimum sensitivity 25 I U/L or equivalent units of HCG) within 24 hours prior to the start of the study drug.
13. Women must not be breastfeeding.
14. WOCBP must agree to follow instructions for method(s) of contraception from the time of registration for treatment for the duration of treatment with study drug (s) plus 5 half-lives of study drug (s) plus 30 days (duration of ovulatory cycle) for a total of 5 months post treatment completion. Men must agree to effective contraception from the time of registration for treatment to 7 months post last protocol treatment.
[0131] Exclusion Criteria - A patient who meets any of the following criteria will be excluded from the study: Patients must not have any other malignancies within the past 2 years except for in situ carcinoma of any site, or adequately treated (without recurrence post-resection or postradiotherapy) carcinoma of the cervix or basal or squamous cell carcinomas of the skin, ductal carcinoma in situ of the breast or low-risk early stage prostate adenocarcinoma with negligible risk of metastasis or death Patients previously treated with T-cell-redirecting bispecific antibodies or MUC16-targeted therapies (including vaccines) are excluded. Patients who received CAR-T therapies within 30 days of first dose of study drug are also excluded. However, patients previously treated with immune checkpoint therapies such as anti-PD-1 , anti-PD-L1 , anti-CTLA-4, or anti-LAG-3 immune checkpoint inhibitors are eligible, as long as they have been off these therapies for at least 60 days (~3 half-lives) prior to initiation of study treatment with ubamatamab. Patients currently receiving anticancer therapies or who have received anticancer therapies (including chemotherapy and targeted therapies such as tazemetostat) within 2 weeks (14 days) prior to study Day 1 are excluded. Patients who have completed palliative radiation therapy more than 14 days prior to the first dose of the combination immunotherapy are eligible. Patients with persistent grade >2 adverse events from prior systemic therapies that would confound timely detection of immune-related adverse events due to ubamatamab and/or cemiplimab or otherwise hinder patient participation in the clinical trial. Patients, who have had a major surgery or significant traumatic injury (injury requiring > 4 weeks (28 days) to heal) within 4 weeks (28 days) of start of study drug, patients who have not recovered from the side effects of any major surgery (defined as requiring general anesthesia). Patients who have organ allografts. Known or suspected autoimmune disease. Patients with a history of inflammatory bowel disease (including Crohn’s disease and ulcerative colitis) and autoimmune disorders such as rheumatoid arthritis, systemic progressive sclerosis [scleroderma], Systemic Lupus Erythematosus or autoimmune vasculitis [e.g. , Wegener’s Granulomatosis] are excluded from this study. Patients with a history of Hashimoto’s thyroiditis only requiring hormone replacement, Type I diabetes, or psoriasis not requiring systemic treatment, or conditions not expected to recur in the absence of an external trigger are allowed to participate. Uncontrolled infection with human immunodeficiency virus, hepatitis B or hepatitis C infection; or diagnosis of immunodeficiency. a. Patients with HIV who have controlled infection (undetectable viral load with the exception of clinically insignificant blips and CD4 count above 350 either spontaneously or on a stable antiviral regimen) are permitted. b. Patients with hepatitis B surface antigen positive (HepBsAg+) who have controlled infection (serum hepatitis B virus DNA PCR that is below the limit of detection AND receiving antiviral therapy for hepatitis B) are permitted. c. Participants with HBsAg negative but total HBV core antibody positive (HBc Ab+) are permitted with the following requirements: Serum HBV DNA PCR should be tested and if it is above the limit of detection at screening then antiviral therapy for HBV must be initiated prior to study entry. If serum HBV DNA PCR is below the limit of detection periodic monitoring of HBsAg must be performed every 12 months +/- 3 months. d. Patients who are Hepatitis C virus antibody positive (HCV Ab +) who have controlled infection (undetectable HCV RNA by PCR either spontaneously or in response to a successful prior course of anti-HCV therapy) are permitted. Any underlying medical condition, which in the opinion of the Investigator, will make the administration of study drug hazardous or obscure the interpretation of adverse events, such as a condition associated with frequent diarrhea, uncontrolled nausea or vomiting. Patients with active COVID-19 disease as indicated by a positive polymerase reaction (PCR) test are excluded. Patients with previous COVID-19 disease are allowed if >30 days from last positive test, and COVID-19 symptoms have resolved and/or PCR test is now negative. Patients must not be scheduled to receive another experimental drug while on this study. Patients who are on high dose steroid (e.g., > 10 mg prednisone daily or equivalent) or other more potent immune suppression medications (e.g., infliximab). Topical, inhaled, intra-articular, ocular, or intranasal corticosteroids (with minimal systemic absorption) are allowed. A brief course (<48 hours) of systemic corticosteroids for prophylaxis (e.g., from contrast dye allergy) is permitted. Physiological corticosteroid replacement therapy for adrenal insufficiency (up to hydrocortisone 30 mg / daily or equivalent) is also permitted. Left ventricular ejection fraction (LVEF) assessment with documented LVEF < 50% by transthoracic echocardiogram (TTE) within 6 months prior to start of study treatment. In cases of LVEF 45-50% in absence of clinical symptoms, after review and clearance by cardiologist, the patient may be enrolled. Active myocarditis, regardless of etiology. Moderate to large pericardial effusion (e.g., > approximately 100 mL) as measured by echocardiogram at baseline. Multigated acquisition (MUGA) is not sufficient for evaluating pericardial effusion. Has a history of any clinically significant arrhythmia including atrial fibrillation or implantation of a pacemaker or defibrillator. 16. Patients who have any severe and/or uncontrolled medical conditions or other conditions that could affect their participation in the study such as: a. Symptomatic congestive heart failure of New York heart Association Class III or IV b. Unstable angina pectoris, symptomatic congestive heart failure, myocardial infarction within 6 months of start of study drug, serious uncontrolled cardiac arrhythmia or any other clinically significant cardiac disease c. Systemic fungal, bacterial, viral, or other infection that is not controlled (defined as exhibiting ongoing signs/symptoms related to the infection and without improvement) despite appropriate antibiotics or other treatment. d. Patients with a history of major psychiatric illness judged unable to fully understand the investigational nature of the study and the risks associated with the therapy.
17. Patients must not have history of other diseases, metabolic dysfunction, physical examination finding, or clinical laboratory finding giving reasonable suspicion of a disease or condition that contraindicates the use of ubamatamab or cemiplimab or that might affect the interpretation of the results of the study or render the patient at high risk from treatment complications.
18. Patients should not receive immunization with attenuated live vaccines within 30 days of planned start of study medication. a. Note: Seasonal influenza vaccines for injection are generally inactivated flu vaccines and are allowed; however intranasal influenza vaccines (e.g., Flu-Mist®) are live attenuated vaccines, and are not allowed.
19. Female patients who are pregnant or breast feeding, or adults of reproductive potential who are not willing to use effective birth control methods as defined above.
20. Any patients who cannot be compliant with the appointments required in this protocol must not be enrolled in this study.
21 . History of allergic reactions attributed to compounds of similar chemical or biologic composition to ubamatamab or cemiplimab.
22. Patients with psychiatric illness/social situations that would limit compliance with study requirements.
[0132] Treatment(s): Ubamatamab will be administered IV weekly or Q3W depending on treatment cycle. In Stage I, ubamatamab step-up monotherapy will be administered at the initial dose of 1 mg intravenously (IV) on week 1 , followed by the transitional dose of 20 mg IV on week 2 (the dose can be split as 10 mg on Day 8 and Day 9), then the full dose of ubamatamab 250 mg IV on weeks 3 and 4, and then 250 mg IV every 3 weeks (Q3W) thereafter (Figure 2). Patients experiencing progressive disease (PD) on ubamatamab monotherapy can enter the Stage II combination treatment of ubamatamab plus cemiplimab and will receive ubamatamab 250 mg IV Q3W in combination with cemiplimab 350 mg IV Q3W (Figure 3). Cemiplimab will be administered IV once every 3 weeks (Q3W) at a dose of 350 mg.
[0133] Preliminary Results: Preliminary results in patients with SMARCB1 -deficient epitheliod sarcoma show partial responses to treatment with ubamatamab. Patients with renal medullary carcinoma have not yet been treated.
Example 3: Evaluation of MUC16 Levels in SMARCB1 -Deficient Cell Lines
[0134] SMARCB1 -deficient cell lines, including G402 (renal leiomyoblastoma), VA-ES-BJ (epithelioid sarcoma), and SW-1573 (alveolar carcinoma) were analyzed by flow cytometry and RNA sequencing to evaluate MUC16 expression. OVCAR3 (ovarian carcinoma), known to express MUC16, was used as a positive control in the flow cytometry experiment.
[0135] RNA sequencing showed little MUC16 mRNA in the VA-ES-BJ and SW-1573 cell lines, but confirmed MUC16 RNA in the G402 cell line. Similarly, flow cytometry (using MUC16-binding antibodies and isotype controls) showed little MLIC16 expression on VA-ES-BJ and SW-1573 cell lines, whereas MUC16 was present on the G402 cell line (and the OVCAR3 positive control cell line), as shown in Figures 4A and 4B.
Example 4: Cytotoxicity and T-Cell Activation in SMARCB1 -Deficient Cells
[0136] In order to quantify the cytotoxic efficacy of REGN4018 (MUC16xCD3) against G402 cells expressing Mucin-16 (MUC16), a 72-hour killing assay was performed. MUC16-expressing OVCAR-3 cells were used as a positive control, which are known to be killed by REGN4018. The G402 and OVCAR-3 cells were labeled with 1 uM of the fluorescent tracking dye Violet Cell Tracker. After labeling, cells were plated overnight at 37°C. Separately, human PBMCs were plated in supplemented RPMI media at 1 x106 cells/mL and incubated overnight at 37°C in order to enrich for lymphocytes by depleting adherent macrophages, dendritic cells, and some monocytes. The next day, target cancer cells were co-incubated with adherent cell-depleted naive PBMC (Effector/Target cell 5:1 ratio) and a serial dilution of REGN4018 (concentration range: 20 nM to 1.28 pM) or a control non-targetingxCD3 bispecific antibody for 72 hours at 37°C.
[0137] Cells were removed from cell culture plates using TrypLE dissociation buffer and analyzed by Flow Cytometry on a BD LSRFortessa X-20. For viability analysis, cells were stained with a live/dead Near IR Reactive dye (Invitrogen). For the assessment of specificity of killing, cancer cells were gated on Violet labeled populations. Cancer cell viability was calculated as the percent of live population and normalized by cells without antibody treatment. [0138] T cell activation was assessed by incubating cells with directly conjugated antibodies to CD2, CD4, CD8, CD25, and by reporting the percent of activated T cells (CD25+) out of total T cells (CD2+) or CD8+ T cells.
[0139] The EC50 values of the antibodies were determined from a four-parameter logistic equation over a dose-response curve using Graph Pad Prism software.
[0140] The MUC16xCD3 bispecific antibody REGN4018 exhibited cytotoxicity to both G402 and OVCAR-3 cells in a dose-dependent manner. The T cell activation induced by REGN4018 was shown as the increased CD25+ population of CD8+ T cells. The control non-targetingxCD3 bispecific antibody did not induce T cell activation or target cell cytotoxicity. Results are shown in Figure 5.
[0141] The present disclosure is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the disclosure in addition to those described herein will become apparent to those skilled in the art from the foregoing description. Such modifications are intended to fall within the scope of the appended claims.
Sequences
SEQ ID NO: 1
QVQLVESGGGLVKPGGSLRLSCAASGFTFSNYYMSWVRQAPGKGLEWISYISGRGSTIFYADSVKGRITISR
DNAKNSLFLQMNSLRAEDTAVYFCVKDRGGYSPYWGQGTLVTVSS
SEQ ID NO: 2
DIQMTQSPSSLSASVGDRVTITCRASQSISTYLNWYQQKPGKAPKLLIYTASSLQSGVPSRFSGSGSGTDFTL
TISSLQPEDFATYYCQQSYSTPPITFGQGTRLEIK
SEQ ID NO: 3
EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYSMHWVRQAPGKGLEWVSGISWNSGSKGYADSVKGRFTI
SRDNAKNSLYLQMNSLRAEDTALYYCAKYGSGYGKFYHYGLDVWGQGTTVTVSS
SEQ ID NO: 4
EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYSMHWVRQAPGKGLEWVSGISWNSGSIGYADSVKGRFTIS
RDNAKNSLYLQMNSLRAEDTALYYCAKYGSGYGKFYYYGMDVWGQGTTVTVSS
SEQ ID NO: 5
GFTFSNYY
SEQ ID NO: 6
ISGRGSTI
SEQ ID NO: 7
VKDRGGYSPY
SEQ ID NO: 8
QSISTY
SEQ ID NO: 9
TAS SEQ ID NO: 10
QQSYSTPPIT
SEQ ID NO: 11
GFTFDDYS
SEQ ID NO: 12
ISWNSGSK
SEQ ID NO: 13
AKYGSGYGKFYHYGLDV
SEQ ID NO: 14
GFTFDDYS
SEQ ID NO: 15
ISWNSGSI
SEQ ID NO: 16
AKYGSGYGKFYYYGMDV
SEQ ID NO: 17
QVQLVESGGGLVKPGGSLRLSCAASGFTFSNYYMSWVRQAPGKGLEWISYISGRGSTIFYADSVKGRITISR
DNAKNSLFLQMNSLRAEDTAVYFCVKDRGGYSPYWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALG
CLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRV
ESKYGPPCPPCPAPPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTK
PREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKNQ
VSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEALH
NHYTQKSLSLSLGK
SEQ ID NO: 18
DIQMTQSPSSLSASVGDRVTITCRASQSISTYLNWYQQKPGKAPKLLIYTASSLQSGVPSRFSGSGSGTDFTL
TISSLQPEDFATYYCQQSYSTPPITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKV
QWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
SEQ ID NO: 19
EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYSMHWVRQAPGKGLEWVSGISWNSGSKGYADSVKGRFTI
SRDNAKNSLYLQMNSLRAEDTALYYCAKYGSGYGKFYHYGLDVWGQGTTVTVSSASTKGPSVFPLAPCSRS
TSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKP
SNTKVDKRVESKYGPPCPPCPAPPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDG
VEVHNAKTKPREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPP
SQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFS
CSVMHEALHNRFTQKSLSLSPGK
SEQ ID NO: 20
EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYSMHWVRQAPGKGLEWVSGISWNSGSIGYADSVKGRFTIS
RDNAKNSLYLQMNSLRAEDTALYYCAKYGSGYGKFYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPCSRST
SESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPS
NTKVDKRVESKYGPPCPPCPAPPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGV
EVHNAKTKPREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPS
QEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSC
SVMHEALHNRFTQKSLSLSPGK
SEQ ID NO: 21
EVQLLESGGVLVQPGGSLRLSCAASGFTFSNFGMTWVRQAPGKGLEWVSGISGGGRDTYFADSVKGRFTIS
RDNSKNTLYLQMNSLKGEDTAVYYCVKWGNIYFDYWGQGTLVTVSS SEQ ID NO: 22
DIQMTQSPSSLSASVGDSITITCRASLSINTFLNWYQQKPGKAPNLLIYAASSLHGGVPSRFSGSGSGTDFTLTI
RTLQPEDFATYYCQQSSNTPFTFGPGTVVDFR
SEQ ID NO: 23
GFTFSNFG
SEQ ID NO: 24
ISGGGRDT
SEQ ID NO: 25
VKWGNIYFDY
SEQ ID NO: 26
LSINTF
SEQ ID NO: 27
AAS
SEQ ID NO: 28
QQSSNTPFT
SEQ ID NO: 29
EVQLLESGGVLVQPGGSLRLSCAASGFTFSNFGMTWVRQAPGKGLEWVSGISGGGRDTYFADSVKGRFTIS
RDNSKNTLYLQMNSLKGEDTAVYYCVKWGNIYFDYWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAAL
GCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKR
VESKYGPPCPPCPAPEFLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKT
KPREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEMTKN
QVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRLTVDKSRWQEGNVFSCSVMHEAL
HNHYTQKSLSLSLGK
SEQ ID NO: 30
DIQMTQSPSSLSASVGDSITITCRASLSINTFLNWYQQKPGKAPNLLIYAASSLHGGVPSRFSGSGS
GTDFTLTIRTLQPEDFATYYCQQSSNTPFTFGPGTVVDFRRTVAAPSVFIFPPSDEQLKSGTASVVC
LLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQ
GLSSPVTKSFNRGEC
*******

Claims

What is claimed is:
1 . A method of treating a SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1 ) deficient cancer in a subject in need thereof, comprising administering to the subject a bispecific antibody or antigen-binding fragment thereof comprising a first antigen-binding domain that specifically binds mucin 16 (MUC16), and a second antigen-binding domain that specifically binds human CD3 in a dosing regimen comprising:
(a) administering an initial dose of the bispecific antibody or antigen-binding fragment thereof in week 1 ;
(b) administering an intermediate dose of the bispecific antibody or antigen-binding fragment thereof in week 2; and
(c) administering a full dose of the bispecific antibody or antigen-binding fragment thereof in a subsequent week of the dosing regimen.
2. The method of claim 1 , wherein the full dose is administered from week 3 or week 4 of the dosing regimen.
3. The method of claim 1 or 2, wherein the intermediate dose is greater than the initial dose, and wherein the full dose is greater than the intermediate dose.
4. The method of any one of claims 1 -3, wherein the initial dose is 0.1 mg to 10 mg.
5. The method of any one of claims 1 -4, wherein the initial dose is about 1 mg.
6. The method of any one of claims 1 -5, wherein the intermediate dose is 10 mg to
30 mg.
7. The method of any one of claims 1 -6, wherein the intermediate dose is about 20 mg.
8. The method of any one of claims 1 -7, wherein the intermediate dose is administered to the subject in two dose fractions on consecutive days in week 2 of the dosing regimen.
9. The method of claim 8, wherein each of the two dose fractions comprises about
10. The method of any one of claims 1 -9, wherein the bispecific antibody is administered at a full dose once every three weeks (Q3W) from week 5 or week 6 of the dosing regimen.
11 . The method of any one of claims 1 -10 further comprising administering to the subject a PD-1 inhibitor or a PD-L1 inhibitor in combination with the bispecific antibody or antigenbinding fragment thereof.
12. The method of claim 1 1 , wherein a dose of the PD-1 inhibitor or the PD-L1 inhibitor is administered in combination with the bispecific antibody or antigen-binding fragment thereof after the subject has received at least three full doses of the bispecific antibody or antigenbinding fragment thereof.
13. The method of any one of claims 1 -12, wherein the full dose is 150 mg to 350 mg.
14. The method of any one of claims 1 -13, wherein the full dose is about 250 mg.
15. The method of any one of claims 11 -14, wherein the dose of the PD-1 inhibitor or PD-L1 inhibitor is 250 mg to 800 mg.
16. The method of any one of claims 11 -15, wherein the dose of the PD-1 inhibitor or PD-L1 inhibitor is about 200 mg, about 350 mg, about 600 mg, or about 700 mg.
17. The method of any one of claims 11 -16, wherein the PD-1 inhibitor or PD-L1 inhibitor is administered once every three weeks, once every four weeks, once every five weeks, or once every six weeks.
18. The method of any one of claims 1 -17, wherein the bispecific antibody or antigen-binding fragment thereof is administered intravenously or subcutaneously to the subject.
19. The method of any one of claims 11 -18, wherein the PD-1 inhibitor or the PD- L1 inhibitor is administered intravenously or subcutaneously to the subject.
20. The method of any one of claims 11 -19, wherein the bispecific antibody or antigen-binding fragment thereof, and the PD-1 inhibitor or the PD-L1 inhibitor are administered in separate formulations.
21 . The method of any one of claims 1 -20, wherein the first antigen-binding domain comprises a heavy chain variable region (HCVR) comprising three heavy chain complementarity determining regions, HCDR1 , HCDR2 and HCDR3, comprising the amino acid sequences of SEQ ID NOs: 5, 6, and 7, respectively, and a light chain variable region (LCVR) comprising three light chain complementarity determining regions, LCDR1 , LCDR2 and LCDR3, comprising the amino acid sequences of SEQ ID NOs: 8, 9, and 10, respectively.
22. The method of claim 21 , wherein the HCVR of the first antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 1 , and the LCVR of the first antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 2.
23. The method of any one of claims 1 -22, wherein the second antigen-binding domain comprises a heavy chain variable region (HCVR) comprising three heavy chain complementarity determining regions, HCDR1 , HCDR2 and HCDR3, comprising the amino acid sequences of SEQ ID NOs: 11 , 12, and 13, respectively, and a light chain variable region (LCVR) comprising three light chain complementarity determining regions, LCDR1 , LCDR2 and LCDR3, comprising the amino acid sequences of SEQ ID NOs: 8, 9, and 10, respectively.
24. The method of claim 23, wherein the HCVR of the second antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 3, and the LCVR of the second antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 2.
25. The method of any one of claims 1 -22, wherein the second antigen-binding domain comprises a heavy chain variable region (HCVR) comprising three heavy chain complementarity determining regions, HCDR1 , HCDR2 and HCDR3, comprising the amino acid sequences of SEQ ID NOs: 14, 15, and 16, respectively, and a light chain variable region (LCVR) comprising three light chain complementarity determining regions, LCDR1 , LCDR2 and LCDR3, comprising the amino acid sequences of SEQ ID NOs: 8, 9, and 10, respectively.
26. The method of claim 25, wherein the HCVR of the second antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 4, and the LCVR of the second antigen-binding domain comprises the amino acid sequence of SEQ ID NO: 2.
27. The method of any one of claims 1 -26, wherein the bispecific antibody comprises a human IgG heavy chain constant region.
28. The method of claim 27, wherein the human IgG heavy chain constant region is isotype lgG1.
29. The method of claim 27, wherein the human IgG heavy chain constant region is isotype lgG4.
30. The method of any one of claims 27-29, wherein the bispecific antibody comprises a chimeric hinge that reduces Fey receptor binding relative to a wild-type hinge of the same isotype.
31 . The method of any one of claims 27-30, wherein the bispecific antibody comprises a first heavy chain and a second heavy chain, and wherein the first heavy chain or the second heavy chain, but not both, comprises a CH3 domain comprising a H435R (EU numbering) modification and a Y436F (EU numbering) modification.
32. The method of any one of claims 1 -31 , wherein the bispecific antibody comprises a first heavy chain comprising the amino acid sequence of SEQ ID NO: 17, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 19, and a common light chain paired with each of the first heavy chain and second heavy chain, respectively, comprising the amino acid sequence of SEQ ID NO: 18.
33. The method of any one of claims 1 -31 , wherein the bispecific antibody comprises a first heavy chain comprising the amino acid sequence of SEQ ID NO: 17, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 20, and a common light chain paired with each of the first heavy chain and second heavy chain, respectively, comprising the amino acid sequence of SEQ ID NO: 18.
34. The method of any one of claims 11 -33, wherein the PD-1 inhibitor is an anti-PD- 1 antibody or antigen-binding fragment thereof, or the PD-L1 inhibitor is an anti-PD-L1 antibody or antigen-binding fragment thereof.
35. The method of claim 34, wherein the anti-PD-1 antibody or antigen-binding fragment comprises a heavy chain variable region (HCVR) comprising three heavy chain complementarity determining regions, HCDR1 , HCDR2 and HCDR3, comprising the amino acid sequences of SEQ ID NOs: 23, 24, and 25, respectively, and a light chain variable region (LCVR) comprising three light chain complementarity determining regions, LCDR1 , LCDR2 and LCDR3, comprising the amino acid sequences of SEQ ID NOs: 26, 27, and 28, respectively.
36. The method of claim 35, wherein the HCVR of the anti-PD-1 antibody or antigen-binding fragment thereof comprises the amino acid sequence of SEQ ID NO: 21 , and the LCVR of the anti-PD-1 antibody or antigen-binding fragment thereof comprises the amino acid sequence of SEQ ID NO: 22.
37. The method of claim 35 or 36, wherein the anti-PD-1 antibody or antigen-binding fragment is an anti-PD-1 antibody comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 29, and a light chain comprising the amino acid sequence of SEQ ID NO: 30.
38. The method of any one of claims 1 -37, further comprising administering an additional therapeutic agent or therapy.
39. The method of claim 38, wherein the additional therapeutic agent is a chemotherapeutic drug, a DNA alkylator, an immunomodulator, radiotherapy, a different bispecific antibody that interacts with a different tumor cell surface antigen and a T cell or immune cell antigen, an antibody drug conjugate, an additional PD-1 inhibitor, an additional PD-L1 inhibitor, a CTLA-4 checkpoint inhibitor, or combinations thereof.
40. The method of claim 38, wherein the additional therapy is surgery.
41 . The method of any one of claims 1 -40, wherein the SMARCB1 -deficient cancer is synovial sarcoma, malignant rhabdoid tumors, atypical teratoid/rhabdoid tumors, epithelioid sarcoma, renal medullary carcinoma, a kidney cancer, renal cell carcinoma (RCC), collecting duct RCC, papillary RCC, renal leiomyoblastoma, epithelioid malignant perhpheral nerve sheath tumors, myoepithelial carcinoma, extraskeletal myxoid chondrosarcoma, chordoma, pediatric chordoma, pancreas undifferentiated rhabdoid carcinoma, sinonasal basaloid carcinoma, rhabdoid carcinoma of the gastrointestinal tract, schwannaomatosis, gastrointestinal stromal tumors, or ossifying fibromyxoid tumor.
42. The method of any one of claims 1 -41 , wherein the SMARCB1 -deficient cancer is renal medullary carcinoma.
43. The method of any one of claims 1 -41 , wherein the SMARCB1 -deficient cancer is renal cell carcinoma, collecting duct renal cell carcinoma, or papillary renal cell carcinoma.
44. The method of any one of claims 1 -41 , wherein the SMARCB1 -deficient cancer is epithelioid sarcoma.
45. The method of any one of claims 1 -44, wherein the subject has progressed following at least one prior therapy to treat the SMARCB1 -deficient cancer.
46. The method of any one of claims 1 -45, wherein the subject has a serum CA-125 level of > 70 units/mL prior to treatment with the bispecific antibody or antigen-binding fragment thereof, or a positive H score of >25 for CA-125 by IHC in tumor tissues prior to treatment with the bispecific antibody or antigen-binding fragment thereof.
47. The method of any one of claims 1 -46, wherein the SMARCB1 -deficient cancer is locally advanced or metastatic.
48. The method of any one of claims 11 -47, wherein the PD-1 inhibitor is cemiplimab.
49. The method of any one of claims 1 -48, wherein the bispecific antibody is ubamatamab.
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