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  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
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  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
  • A61K31/517—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with carbocyclic ring systems, e.g. quinazoline, perimidine
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  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
  • A61K39/39533—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals
  • A61K39/39558—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals against tumor tissues, cells, antigens
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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  • A61P35/00—Antineoplastic agents
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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
  • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K2300/00—Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00
• • C—CHEMISTRY; METALLURGY
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  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
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  • C12Q2600/00—Oligonucleotides characterized by their use
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  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/156—Polymorphic or mutational markers

Definitions

• the present invention relates generally to the fields of medicine and oncology. More particularly, it concerns methods for selecting cancer patients for treatment with poziotinib, alone or in combination with HER2/HER3 targeting antibodies, as well as methods of treating cancer patients so selected.
• NRG1 fusions occur in 0.3% of non-small cell lung cancer (NSCLC), and have been observed in several other cancer types including gallbladder (0.5%), breast (0.2%), ovarian (0.4%), and colorectal (0.1%) cancers (Jonna et al., 2019).
• NSCLC non-small cell lung cancer
• Common NRG1 fusions partners are CD74 (29% of NRG1 fusions), ATP1B1 (10% of NRG1 fusions), and SDC4 (7% of NRG1 fusions) (Jonna et al., 2019).
• NRG1 binds the HER3 receptor to cause preferential hetero-dimerization with HER2 (Shin et al., 2018; Jung et al., 2015; Femandez-Cuesta et al., 2014), one of the most potent forms of ERBB family signaling (Holbro et al., 2003).
• Previous reports have shown that targeting the HER2/HER3 signaling pathway can be effective in inhibiting NRG1 fusion-driven ErbB signaling (Shin et al., 2018; Femandez-Cuesta et al., 2014; Drilon et al., 2018).
• step (a) comprises (i) obtaining or having obtained a biological sample from the patient; and (ii) performing or having performed an assay on the biological sample to determine the patient’s cancer has an NRG1 fusion.
• provided herein are methods of treating a patient having a cancer, the methods comprising administering to the patient a therapeutically effective amount of poziotinib, wherein the cancer has an NRG1 fusion.
• compositions comprising a therapeutically effective amount of poziotinib, for use in the treatment of cancer in a patient, wherein the patient’s cancer has an NRG1 fusion.
• step (a) comprises (i) obtaining or having obtained a biological sample from the patient; and (ii) performing or having performed an assay on the biological sample to determine the patient’s cancer has an NRG1 fusion.
• the methods further comprise (c) administering or having administered to the selected patient a therapeutically effective amount of poziotinib.
• step (a) comprises (i) obtaining or having obtained a biological sample from the patient; and (ii) performing or having performed an assay on the biological sample to determine the patient’s cancer has an NRG1 fusion
• provided herein are methods of treating a patient having a cancer, the method comprising administering to the patient a combined therapeutically effective amount of poziotinib and a HER2/HER3 targeting antibody, wherein the cancer has an NRG1 fusion.
• compositions comprising a therapeutically effective amount of poziotinib and a HER2/HER3 targeting antibody, for use in the treatment of cancer in a patient, wherein the patient’s cancer has an NRG1 fusion.
• step (a) comprises (i) obtaining or having obtained a biological sample from the patient; and (ii) performing or having performed an assay on the biological sample to determine the patient’s cancer has an NRG1 fusion.
• the methods further comprise (c) administering or having administered to the selected patient a combined therapeutically effective amount of poziotinib and a HER2/HER3 targeting antibody.
• the NRG1 fusion is an NRG1- DOC4 fusion, an NRG1-VAMP2 fusion, an NRG1-CLU fusion, an NRG1-SLC3A2 fusion, anNRGl-CD74 fusion, an NRG1-ATP1B1 fusion, or anNRGl-SDC4 fusion.
• the methods further comprise administering to the patient an HER2/HER3 targeting antibody.
• the HER2/HER3 targeting antibody comprises trastuzumab, pertuzumab, or T-DM1.
• the methods further comprise administering a further anti-cancer therapy to the patient.
• the further anti cancer therapy is a surgical therapy, a chemotherapy, a radiation therapy, a cryotherapy, a hormonal therapy, a toxin therapy, an immunotherapy, or a cytokine therapy.
• the cancer is a breast cancer, a lung cancer, a colorectal cancer, a neuroblastoma, a pancreatic cancer, a brain cancer, a stomach cancer, a skin cancer, a testicular cancer, a prostate cancer, an ovarian cancer, a liver cancer, an esophageal cancer, a cervical cancer, a head and neck cancer, a melanoma, or a glioblastoma.
• the cancer is a breast cancer or a lung cancer.
• the patient has previously undergone at least one round of anti-cancer therapy.
• the methods further comprise reporting the presence of an NRG1 fusion in the patient’s cancer.
• reporting comprises preparing a written or electronic report.
• the methods further comprise providing the report to the subject, a doctor, a hospital, or an insurance company.
• essentially free in terms of a specified component, is used herein to mean that none of the specified component has been purposefully formulated into a composition and/or is present only as a contaminant or in trace amounts.
• the total amount of the specified component resulting from any unintended contamination of a composition is therefore well below 0.05%, preferably below 0.01%.
• Most preferred is a composition in which no amount of the specified component can be detected with standard analytical methods.
• FIG. 1 Bar graph of ICso values of MDA175-VII (NRG1-DOC4 fusion) treated with poziotinib for 72 hours.
• FIG. 2A Dose response curve of MDA175-VII (NRG1-DOC4 fusion) cell line treated with the indicated HER2/HER3 antibodies with and without low dose poziotinib (0.1 nM) for 72 hours.
• the lines represent, from top to bottom, T-DM1, Trastuzumab, Pertuzumab, Trastuzumab + Poziotinib O.lnM, T-DM1 + Poziotinib O.lnM, and Pertuzumab + Poziotinib O.lnM.
• FIG. 2B Bar graph of ICso values of MDA175-VII (NRG1-DOC4 fusion) cell line treated with the indicated HER2/HER3 antibodies with and without low dose poziotinib (0.1 nM) for 72 hours.
• the present methods comprise the administration of poziotinib (also known as HM781-36B), either alone or in combination with a HER2/HER3 targeting antibody, to cancer patients identified as having an NRG1 fusion.
• the present methods comprise the identification and selection of cancer patients likely to benefit from the administration of poziotinib, either alone or in combination with a HER2/HER3 targeting antibody, by determining whether the patient’s cancer has an NRG1 fusion.
• An NRG1 fusion gene comprises at least a portion of the NRGl-gene fused to a sequence from a different chromosomal location. “At least a portion” indicates that the entire NRG1 gene may be present in a fusion or a portion thereof. The fusion may have at least the coding sequence of exons 6, 7, and 8 of NRG1. Another way to define the NRG1 portion in the NRGl-fusion gene is that it comprises the EGF-like domain of NRG1. The EGF-like domain is encoded by the 3' end of the gene and is necessary for binding to ErbB-3. The NRG1 -fusions retain an in-frame coding region for the EGF-like domain. The portion of the NRG1 gene may be fused to a sequence from a different chromosomal location such that the said sequence is located 5' or 3' to the portion of the NRG1 gene.
• the 3' end of the NRGl-gene may be fused to a sequence from a different chromosomal location.
• the NRG1 fusion gene may be a fusion of the 3' end of the NRGl-gene with the 5' sequence of one of the genes selected from the group consisting of DOC4 (also known as Teneurin Transmembrane Protein 4 (TENM4); Protein Odd Oz/Ten-M Homolog 4; Tenascin-M4; Ten-M4; Ten-4; ODZ4; TNM4; Odz, Odd Oz/Ten-M Homolog 4 (Drosophila); Odz, Odd Oz A en-M Homolog 4; Teneurin-4; KIAA1302; Doc4; ETM5; HGNC: 29945; Entrez Gene: 26011; Ensembl: ENSG00000149256; OMIM: 610084; and UniProtKB: Q6N022); CD74
• DOC4 also known as
• Certain embodiments of the present disclosure concern determining if a subject has an NRGl fusion. Detection methods are known the art including PCR analyses, nucleic acid sequencing, fluorescence in situ hybridization (FISH), chromogenic in situ hybridization (CISH), and comparative genomic hybridization (CGH).
• Samples that are suitable for use in the methods described herein contain genetic material, e.g. , genomic DNA (gDNA). Genomic DNA is typically extracted from biological samples such as blood or mucosal scrapings of the lining of the mouth, but can be extracted from other biological samples including urine, tumor, or expectorant.
• the sample itself will typically include nucleated cells (e.g., blood or buccal cells) or tissue removed from the subject, including tumor tissue.
• nucleated cells e.g., blood or buccal cells
• tissue removed from the subject including tumor tissue.
• Methods and reagents are known in the art for obtaining, processing, and analyzing samples.
• the sample is obtained with the assistance of a health care provider, e.g, to draw blood or take a tumor biopsy.
• the sample is obtained without the assistance of a health care provider, e.g, where the sample is obtained non-invasively, such as a sample comprising buccal cells that is obtained using a buccal swab or brush, or a mouthwash sample.
• the patient sample can be any bodily tissue or fluid that includes nucleic acids from the cancer in the subject.
• the sample will be a blood sample comprising circulating tumor cells or cell-free DNA.
• the sample can be a tissue, such as a tumor tissue.
• the tumor tissue may be fresh frozen or formalin-fixed, paraffin-embedded (FFPE).
• a biological sample may be processed for DNA isolation.
• DNA in a cell or tissue sample can be separated from other components of the sample.
• Cells can be harvested from a biological sample using standard techniques known in the art. For example, cells can be harvested by centrifuging a cell sample and resuspending the pelleted cells. The cells can be resuspended in a buffered solution such as phosphate- buffered saline (PBS). After centrifuging the cell suspension to obtain a cell pellet, the cells can be lysed to extract DNA, e.g, gDNA. The sample can be concentrated and/or purified to isolate DNA.
• PBS phosphate- buffered saline
• genomic DNA can be extracted with kits such as the QIAamp® Tissue Kit (Qiagen, Chatsworth, Calif.) or the Wizard® Genomic DNA purification kit (Promega).
• Amplification of nucleic acids can be accomplished using methods known in the art, e.g, PCR.
• a sample e.g, a sample comprising genomic DNA
• the DNA in the sample is then examined to determine the identity of an NRG1 fusion as described herein.
• An NRG1 fusion can be detected by any method described herein, e.g ., by sequencing or by hybridization of the gene in the genomic DNA, RNA, or cDNA to a nucleic acid probe, e.g. , a DNA probe (which includes cDNA and oligonucleotide probes) or an RNA probe.
• the nucleic acid probe can be designed to specifically or preferentially hybridize with a particular NRGl fusion.
• a set of probes typically refers to a set of primers, usually primer pairs, and/or detectably-labeled probes that are used to detect the target genetic variations (e.g, NRGl fusions) used in the actionable treatment recommendations of the present disclosure.
• the primer pairs are used in an amplification reaction to define an amplicon that corresponds to an NRGl fusion.
• the set of amplicons are detected by a set of matched probes.
• the present methods may use TaqManTM (Roche Molecular Systems, Pleasanton, Calif.) assays that are used to detect a set of target genetic variations, such as NRGl fusions.
• the set of probes are a set of primers used to generate amplicons that are detected by a nucleic acid sequencing reaction, such as a next generation sequencing reaction.
• a nucleic acid sequencing reaction such as a next generation sequencing reaction.
• AmpliSEQTM Life Technologies/Ion Torrent, Carlsbad, Calif.
• TruSEQTM Illumina, San Diego, Calif.
• sequence analysis includes Maxam-Gilbert sequencing, Sanger sequencing, capillary array DNA sequencing, thermal cycle sequencing, solid-phase sequencing, sequencing with mass spectrometry such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS), and sequencing by hybridization.
• electrophoretic analysis include slab gel electrophoresis such as agarose or polyacrylamide gel electrophoresis, capillary electrophoresis, and denaturing gradient gel electrophoresis.
• next generation sequencing methods can be performed using commercially available kits and instruments from companies such as the Life Technologies/Ion Torrent PGM or Proton, the Illumina HiSEQ or MiSEQ, and the Roche/454 next generation sequencing system.
• nucleic acid analysis can include direct manual sequencing (U.S. Patent No. 5,288,644); automated fluorescent sequencing; single-stranded conformation polymorphism assays (SSCP); clamped denaturing gel electrophoresis (CDGE); two- dimensional gel electrophoresis (2DGE or TDGE); conformational sensitive gel electrophoresis (CSGE); denaturing gradient gel electrophoresis (DGGE); denaturing high performance liquid chromatography (DHPLC); infrared matrix-assisted laser desorption/ionization (IR-MALDI) mass spectrometry; mobility shift analysis; restriction enzyme analysis; quantitative real-time PCR; heteroduplex analysis; chemical mismatch cleavage (CMC); RNase protection assays; use of polypeptides that recognize nucleotide mismatches, e.g ., E. coli mutS protein; allele-specific PCR, and combinations of such methods. See, e.g. , U.S. Patent No. 5,28
• a method of identifying an NRG1 fusion in a sample comprises contacting a nucleic acid from said sample with a nucleic acid probe that is capable of specifically hybridizing to a nucleic acid encoding an NRGl fusion and detecting said hybridization.
• said probe is detectably labeled such as with a radioisotope (3 ⁇ 4, 32 P, or 33 P), a fluorescent agent (rhodamine, or fluorescein) or a chromogenic agent.
• the probe is an antisense oligomer, for example PNA, morpholino-phosphoramidates, LNA or 2'-alkoxyalkoxy.
• the probe may be from about 8 nucleotides to about 100 nucleotides, or about 10 to about 75, or about 15 to about 50, or about 20 to about 30.
• said probes of the present disclosure are provided in a kit for identifying NRGl fusions in a sample, said kit comprising oligonucleotides that specifically hybridize to specific NRGl fusions.
• the kit may further comprise instructions for treating patients having tumors that contain NRGl fusion with poziotinib, either alone or in combination with HER2/HER3 targeting antibodies, based on the result of a hybridization test using the kit.
• a “HER2/HER3 targeting antibody” as used herein includes any molecule that interferes with the function of HER2 and/or HER3.
• HER2/HER3 targeting antibody includes an anti-HER2 antibody (e.g., trastuzumab or pertuzumab), an anti-HER3 antibody, and an anti-HER2/HER3 bispecific antibody (e.g., the antibodies disclosed in WO20 18/ 182422 or MCLA-128).
• a HER2/HER3 targeting antibody may prevent the formation of HER2/HER2 dimers and/or HER2/HER3 dimers (e.g., trastuzumab or pertuzumab).
• a HER2/HER3 targeting antibody may be an antibody drug conjugate (e.g., T-DM1 or U3-1402).
• the HER2/HER3 targeting antibody is trastuzumab (Genentech and Roche), trastuzumab emtansine (T-DM1; Genentech and Roche), pertuzumab (Genentech), ertumaxomab (Fresenius), margetuximab (MacroGenics), MCLA- 128 (zenocutuzumab; Merus) MM-111 (Merrimack), MM-121 (Merrimack), CT-P06 (Celltrion), GSK2849330 (GlaxoSmithKline), PF-05280014 (Pfizer), MM-302 (Merrimack), SB3 (Merck & Co), CMAB302 (Shanghai CP Guojian), RG7116 (lemretuzumab; Genentech and Roche), trastuzumab
• Trastuzumab (CAS 180288-69-1, HERCEPTIN®, huMAb4D5-8, rhuMAb HER2, Genentech) is a humanized, IgGl kappa, monoclonal antibody that selectively binds with high affinity to the extracellular domain of the human epidermal growth factor receptor 2 protein, HER2 (ErbB2) (U.S. Pat. Nos. 5,677,171; 5,821,337; 6,054,297; 6,165,464; 6,339,142; 6,407,213; 6,639,055; 6,719,971; 6,800,738; 7,074,404).
• Trastuzumab contains human framework regions with the complementarity-determining regions of a murine antibody (4D5) that binds to HER2. Trastuzumab binds to the HER2 antigen and thus inhibits the growth of cancerous cells. Trastuzumab has been shown, in both in vitro assays and in animals, to inhibit the proliferation of human tumor cells that overexpress HER2. Trastuzumab is a mediator of antibody-dependent cellular cytotoxicity, ADCC.
• Trastuzumab emtansine also known as ado-trastuzumab emtansine and sold under the trade name KADCYLA®, is an antibody-drug conjugate consisting of the humanized monoclonal antibody trastuzumab covalently linked to the cytotoxic agent emtansine (DM1).
• trastuzumab alone stops growth of cancer cells by binding to the HER2 receptor, whereas trastuzumab emtansine undergoes receptor-mediated internalization into cells, is catabolized in lysosomes where DM1 -containing catabolites are released and subsequently bind tubulin to cause mitotic arrest and cell death.
• T-DM1 may be administered at a dose of 2-3 mg/kg, such as 3.6 mg/kg.
• the T-DM1 may be administered by intravenous infusion.
• Pertuzumab (CAS Reg. No. 380610-27-5, OMNITARG®, 2C4, Genentech) is a recombinant, humanized monoclonal antibody that inhibits dimerization of HER2 (U.S. Pat. Nos. 6,054,297; 6,407,213; 6,800,738; 6,627,196, 6,949,245; 7,041,292).
• Pertuzumab contains the human IgGl (x) framework sequences.
• Pertuzumab and trastuzumab target different extracellular regions of the HER2 tyrosine kinase receptor.
• Pertuzumab binds to an epitope within sub-domain 2 of HER2, while the epitope from trastuzumab is localized to sub-domain 4.
• Pertuzumab blocks the ability of the HER2 receptor to collaborate with other HER receptor family members, i.e., HER1/EGFR, HER3, and HER4 (U.S. Pat. No. 6,949,245).
• HER1/EGFR HER1/EGFR
• HER3 HER4
• HER4 U.S. Pat. No. 6,949,245
• Additional exemplary HER2/HER3 targeting antibodies include MM- 121/SAR256212, which is a fully human monoclonal antibody that targets the HER3 receptor and which has been reported to be useful in the treatment of non-small cell lung cancer (NSCLC), breast cancer and ovarian cancer.
• SAR256212 is an investigational fully human monoclonal antibody that targets the HER3 (ErbB3) receptor.
• Duligotuzmab (MEHD7945A, RG7597) is a humanized IgGl monoclonal antibody that targets HERl and HER3, and has been described as being useful in head and neck cancers.
• Margetuximab (MGAH22) is an Fc- optimized monoclonal antibody that targets HER2.
• Antibodies according to the present disclosure may be defined, in the first instance, by their binding specificity. Those of skill in the art, by assessing the binding specificity/affmity of a given antibody using techniques well known to those of skill in the art, can determine whether such antibodies fall within the scope of the instant claims. Various techniques known to persons of ordinary skill in the art can be used to determine whether an antibody interacts with a polypeptide or protein. Exemplary techniques include, for example, routine cross-blocking assays. Cross-blocking can be measured in various binding assays such as ELISA, biolayer interferometry, or surface plasmon resonance.
• the present disclosure includes antibodies that may bind to the same epitope, or a portion of the epitope. Likewise, the present disclosure also includes antibodies that compete for binding to a target or a fragment thereof with any of the specific exemplary antibodies described herein. One can easily determine whether an antibody binds to the same epitope as, or competes for binding with, a reference antibody by using routine methods known in the art.
• test antibody binds to the same epitope as a reference
• the reference antibody is allowed to bind to target under saturating conditions.
• the ability of a test antibody to bind to the target molecule is assessed. If the test antibody is able to bind to the target molecule following saturation binding with the reference antibody, it can be concluded that the test antibody binds to a different epitope than the reference antibody. On the other hand, if the test antibody is not able to bind to the target molecule following saturation binding with the reference antibody, then the test antibody may bind to the same epitope as the epitope bound by the reference antibody.
• Two antibodies bind to the same or overlapping epitope if each competitively inhibits (blocks) binding of the other to the antigen. That is, a 1-, 5-, 10-, 20- or 100-fold excess of one antibody inhibits binding of the other by at least 50% but preferably 75%, 90% or even 99% as measured in a competitive binding assay.
• two antibodies have the same epitope if essentially all amino acid mutations in the antigen that reduce or eliminate binding of one antibody reduce or eliminate binding of the other.
• Two antibodies have overlapping epitopes if some amino acid mutations that reduce or eliminate binding of one antibody reduce or eliminate binding of the other.
• Additional routine experimentation e.g ., peptide mutation and binding analyses
• peptide mutation and binding analyses can then be carried out to confirm whether the observed lack of binding of the test antibody is in fact due to binding to the same epitope as the reference antibody or if steric blocking (or another phenomenon) is responsible for the lack of observed binding.
• steric blocking or another phenomenon
• Structural studies with EM or crystallography also can demonstrate whether or not two antibodies that compete for binding recognize the same epitope.
• the antibodies may be defined by their variable sequence, which include additional “framework” regions.
• the antibodies sequences may vary from these sequences, optionally using methods discussed in greater detail below.
• nucleic acid sequences may vary from those set out above in that (a) the variable regions may be segregated away from the constant domains of the light and heavy chains, (b) the nucleic acids may vary from those set out above while not affecting the residues encoded thereby, (c) the nucleic acids may vary from those set out above by a given percentage, e.g ., 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% homology, (d) the nucleic acids may vary from those set out above by virtue of the ability to hybridize under high stringency conditions, as exemplified by low salt and/or high temperature conditions, such as provided by about 0.02 M to about 0.15 M NaCl at temperatures of about 50
• two sequences are said to be “identical” if the sequence of nucleotides or amino acids in the two sequences is the same when aligned for maximum correspondence, as described below. Comparisons between two sequences are typically performed by comparing the sequences over a comparison window to identify and compare local regions of sequence similarity.
• a “comparison window” as used herein refers to a segment of at least about 20 contiguous positions, usually 30 to about 75, 40 to about 50, in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
• Optimal alignment of sequences for comparison may be conducted using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters.
• This program embodies several alignment schemes described in the following references: Dayhoff, M. O. (1978) A model of evolutionary change in proteins— Matrices for detecting distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogeny pp. 626-645 Methods in Enzymology vol.
• optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman (1981) Add. APL. Math 2:482, by the identity alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity methods of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85: 2444, by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.
• BLAST and BLAST 2.0 are described in Altschul et al. (1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively.
• BLAST and BLAST 2.0 can be used, for example with the parameters described herein, to determine percent sequence identity for the polynucleotides and polypeptides of the disclosure.
• Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. The rearranged nature of an antibody sequence and the variable length of each gene requires multiple rounds of BLAST searches for a single antibody sequence.
• IgBLAST (world- wide-web at ncbi.nlm.nih.gov/igblast/) identifies matches to the germline V, D and J genes, details at rearrangement junctions, the delineation of Ig V domain framework regions and complementarity determining regions.
• IgBLAST can analyze nucleotide or protein sequences and can process sequences in batches and allows searches against the germline gene databases and other sequence databases simultaneously to minimize the chance of missing possibly the best matching germline V gene.
• cumulative scores can be calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always ⁇ 0). Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
• the BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
• a scoring matrix can be used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative scoring residue alignments; or the end of either sequence is reached.
• the BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
• the “percentage of sequence identity” is determined by comparing two optimally aligned sequences over a window of comparison of at least 20 positions, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less, usually 5 to 15 percent, or 10 to 12 percent, as compared to the reference sequences (which does not comprise additions or deletions) for optimal alignment of the two sequences.
• the percentage is calculated by determining the number of positions at which the identical nucleic acid bases or amino acid residues occur in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the reference sequence (i.e., the window size) and multiplying the results by 100 to yield the percentage of sequence identity.
• an antibody is as a “derivative” of any of the described antibodies and their antigen-binding fragments.
• the term “derivative” refers to an antibody or antigen-binding fragment thereof that immunospecifically binds to an antigen but which comprises, one, two, three, four, five or more amino acid substitutions, additions, deletions or modifications relative to a “parental” (or wild-type) molecule.
• Such amino acid substitutions or additions may introduce naturally occurring (i.e., DNA-encoded) or non- naturally occurring amino acid residues.
• derivative encompasses, for example, as variants having altered CHI, hinge, CH2, CH3 or CH4 regions, so as to form, for example antibodies, etc., having variant Fc regions that exhibit enhanced or impaired effector or binding characteristics.
• derivative additionally encompasses non-amino acid modifications, for example, amino acids that may be glycosylated ( e.g ., have altered mannose, 2-N-acetylglucosamine, galactose, fucose, glucose, sialic acid, 5-N- acetylneuraminic acid, 5-glycolneuraminic acid, etc.
• the altered carbohydrate modifications modulate one or more of the following: solubilization of the antibody, facilitation of subcellular transport and secretion of the antibody, promotion of antibody assembly, conformational integrity, and antibody-mediated effector function.
• the altered carbohydrate modifications enhance antibody mediated effector function relative to the antibody lacking the carbohydrate modification. Carbohydrate modifications that lead to altered antibody mediated effector function are well known in the art.
• a derivative antibody or antibody fragment can be generated with an engineered sequence or glycosylation state to confer preferred levels of activity in antibody dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), antibody-dependent neutrophil phagocytosis (ADNP), or antibody-dependent complement deposition (ADCD) functions as measured by bead-based or cell-based assays or in vivo studies in animal models.
• ADCC antibody dependent cellular cytotoxicity
• ADCP antibody-dependent cellular phagocytosis
• ADNP antibody-dependent neutrophil phagocytosis
• ADCD antibody-dependent complement deposition
• a derivative antibody or antibody fragment may be modified by chemical modifications using techniques known to those of skill in the art, including, but not limited to, specific chemical cleavage, acetylation, formulation, metabolic synthesis of tunicamycin, etc.
• an antibody derivative will possess a similar or identical function as the parental antibody.
• an antibody derivative will exhibit an altered activity relative to the parental antibody.
• a derivative antibody (or fragment thereof) can bind to its epitope more tightly or be more resistant to proteolysis than the parental antibody.
• the present invention provides methods of treating a cancer patient with poziotinib, either alone or in combination with a HER2/HER3 targeting antibody. Such treatment may also be in combination with another therapeutic regime, such as chemotherapy or immunotherapy. Certain aspects of the present invention can be used to select a cancer patient for treatment based on the presence of an NRG1 fusion in the patient’s cancer cells. In various aspects, about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% of the cells that comprise the cancer may harbor an NRG1 fusion, which indicates that the patient is a candidate for treatment. In some aspects, the patient’s cancer cells lack a mutation at EGFR T790 and/or at EGFR C797. In some aspects, the patient’s cancer cells lack a mutation at HER2 T798 and/or at HER2 C805.
• the subject was determined to have an NRG1 fusion by analyzing a genomic sample from the subject.
• the genomic sample is isolated from saliva, blood, urine, or tumor tissue.
• the presence of an NRG1 fusion is determined by nucleic acid sequencing (e.g, DNA sequencing of tumor tissue or circulating free DNA from plasma) or PCR analyses.
• Certain embodiments concern the administration of poziotinib (also known as HM781-36B, HM781-36, and l-[4-[4-(3,4-dichloro-2-fluoroanilino)-7-methoxyquinazolin-6- yl]oxypiperidin-l-yl]prop-2-en-l-one) to a subject determined to have an NRGl fusion.
• Poziotinib is a quinazoline-based pan-HER inhibitor that irreversibly blocks signaling through the HER family of tyrosine-kinase receptors including HER1, HER2, and HER4.
• Poziotinib or structurally similar compounds may be used in the present methods.
• the poziotinib is further defined as poziotinib hydrochloride salt.
• the poziotinib hydrochloride salt is formulated as a tablet.
• the poziotinib may be administered orally, such as in a tablet.
• the poziotinib may be administered in a dose of 4-25 mg, such as at a dose of 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 mg.
• the poziotinib is administered at a dose of 6 mg, 8 mg, 12 mg, or 16 mg.
• the dosing may be twice per day, daily, every other day, every 3 days or weekly.
• the dosing may be on a continuous schedule, such as on 28 days cycles.
• the poziotinib and/or HER2/HER3 targeting antibody are administered intravenously, subcutaneously, intraosseously, orally, transdermally, in sustained release, in controlled release, in delayed release, as a suppository, or sublingually.
• administering the poziotinib and/or HER2/HER3 targeting antibody comprises local, regional or systemic administration.
• the poziotinib and/or HER2/HER3 targeting antibody are administered two or more times, such as daily, every other day, or weekly.
• the poziotinib is administered prior to or after the HER2/HER3 targeting antibody, such as 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 2 weeks, 3 weeks, 1 month or more apart. In some aspects, the poziotinib is administered simultaneously with the HER2/HER3 targeting antibody.
• subject or “patient” as used herein refers to any individual to which the subject methods are performed.
• patient is human, although as will be appreciated by those in the art, the patient may be an animal.
• animals including mammals such as rodents (including mice, rats, hamsters and guinea pigs), cats, dogs, rabbits, farm animals including cows, horses, goats, sheep, pigs, etc., and primates (including monkeys, chimpanzees, orangutans and gorillas) are included within the definition of patient.
• rodents including mice, rats, hamsters and guinea pigs
• cats dogs, rabbits, farm animals including cows, horses, goats, sheep, pigs, etc.
• primates including monkeys, chimpanzees, orangutans and gorillas
• Treatment refers to administration or application of a therapeutic agent to a subject or performance of a procedure or modality on a subject for the purpose of obtaining a therapeutic benefit of a disease or health-related condition.
• a treatment may include administration chemotherapy, immunotherapy, radiotherapy, performance of surgery, or any combination thereof.
• cancer e.g., tumor cells
• proliferative disease e.g., cancer, psoriasis
• pathogenic infection e.g., cancer, psoriasis
• cancers that are treated in connection with the methods provided herein include, but are not limited to, solid tumors, metastatic cancers, or non-metastatic cancers.
• the cancer may originate in the lung, kidney, bladder, blood, bone, bone marrow, brain, breast, colon, esophagus, duodenum, small intestine, large intestine, colon, rectum, anus, gum, head, liver, nasopharynx, neck, ovary, pancreas, prostate, skin, stomach, testis, tongue, or uterus.
• the cancer may specifically be of the following histological type, though it is not limited to these: neoplasm, malignant; carcinoma; non-small cell lung cancer; renal cancer; renal cell carcinoma; clear cell renal cell carcinoma; lymphoma; blastoma; sarcoma; carcinoma, undifferentiated; meningioma; brain cancer; oropharyngeal cancer; nasopharyngeal cancer; biliary cancer; pheochromocytoma; pancreatic islet cell cancer; Li- Fraumeni tumor; thyroid cancer; parathyroid cancer; pituitary tumor; adrenal gland tumor; osteogenic sarcoma tumor; neuroendocrine tumor; breast cancer; lung cancer; head and neck cancer; prostate cancer; esophageal cancer; tracheal cancer; liver cancer; bladder cancer; stomach cancer; pancreatic cancer; ovarian cancer; uterine cancer; cervical cancer; testicular cancer; colon cancer; rectal cancer; skin cancer; giant and spindle cell carcinoma; small cell carcinoma; small cell carcinoma;
• therapeutic benefit refers to anything that promotes or enhances the well-being of the subject with respect to the medical treatment of this condition. This includes, but is not limited to, a reduction in the frequency or severity of the signs or symptoms of a disease.
• treatment of cancer may involve, for example, a reduction in the invasiveness of a tumor, reduction in the growth rate of the cancer, or prevention of metastasis. Treatment of cancer may also refer to prolonging survival of a subject with cancer.
• an effective response of a patient or a patient refers to the clinical or therapeutic benefit imparted to a patient at risk for, or suffering from, a disease or disorder.
• Such benefit may include cellular or biological responses, a complete response, a partial response, a stable disease (without progression or relapse), or a response with a later relapse.
• an effective response can be reduced tumor size or progression-free survival in a patient diagnosed with cancer.
• neoplastic condition treatment involves one or a combination of the following therapies: surgery to remove the neoplastic tissue, radiation therapy, and chemotherapy.
• Other therapeutic regimens may be combined with the administration of the anticancer agents, e.g., therapeutic compositions and chemotherapeutic agents.
• the patient to be treated with such anti-cancer agents may also receive radiation therapy and/or may undergo surgery.
• the appropriate dosage of a therapeutic composition will depend on the type of disease to be treated, as defined above, the severity and course of the disease, previous therapy, the patient’s clinical history and response to the agent, and the discretion of the physician.
• the agent may be suitably administered to the patient at one time or over a series of treatments.
• compositions including combination therapies, enhance the therapeutic or protective effect, and/or increase the therapeutic effect of another anti-cancer or anti-hyperproliferative therapy.
• Therapeutic and prophylactic methods and compositions can be provided in a combined amount effective to achieve the desired effect, such as the killing of a cancer cell and/or the inhibition of cellular hyperproliferation.
• a tissue, tumor, or cell can be contacted with one or more compositions or pharmacological formulation(s) comprising one or more of the agents or by contacting the tissue, tumor, and/or cell with two or more distinct compositions or formulations.
• a combination therapy can be used in conjunction with radiotherapy, surgical therapy, or immunotherapy.
• Administration in combination can include simultaneous administration of two or more agents in the same dosage form, simultaneous administration in separate dosage forms, and separate administration. That is, the subject therapeutic composition and another therapeutic agent can be formulated together in the same dosage form and administered simultaneously. Alternatively, subject therapeutic composition and another therapeutic agent can be simultaneously administered, wherein both the agents are present in separate formulations. In another alternative, the therapeutic agent can be administered just followed by the other therapeutic agent or vice versa. In the separate administration protocol, the subject therapeutic composition and another therapeutic agent may be administered a few minutes apart, or a few hours apart, or a few days apart.
• An anti-cancer first treatment may be administered before, during, after, or in various combinations relative to a second anti-cancer treatment.
• the administrations may be in intervals ranging from concurrently to minutes to days to weeks.
• the first treatment is provided to a patient separately from the second treatment, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the two compounds would still be able to exert an advantageously combined effect on the patient.
• a course of treatment will last 1-90 days or more (this such range includes intervening days). It is contemplated that one agent may be given on any day of day 1 to day 90 (this such range includes intervening days) or any combination thereof, and another agent is given on any day of day 1 to day 90 (this such range includes intervening days) or any combination thereof. Within a single day (24-hour period), the patient may be given one or multiple administrations of the agent(s). Moreover, after a course of treatment, it is contemplated that there is a period of time at which no anti cancer treatment is administered.
• This time period may last 1-7 days, and/or 1-5 weeks, and/or 1-12 months or more (this such range includes intervening days), depending on the condition of the patient, such as their prognosis, strength, health, etc. It is expected that the treatment cycles would be repeated as necessary. [0075] Various combinations may be employed. For the example below, either
• poziotinib is “A” and a HER2/HER3 targeting antibody is “B” or (b) poziotinib, either alone or in combination with a HER2/HER3 targeting antibody, is “A” and another anti cancer therapy is “B”:
• Administration of any compound or therapy of the present invention to a patient will follow general protocols for the administration of such compounds, taking into account the toxicity, if any, of the agents. Therefore, in some embodiments there is a step of monitoring toxicity that is attributable to combination therapy.
• chemotherapeutic agents may be used in accordance with the present invention.
• the term “chemotherapy” refers to the use of drugs to treat cancer.
• a “chemotherapeutic agent” is used to connote a compound or composition that is administered in the treatment of cancer. These agents or drugs are categorized by their mode of activity within a cell, for example, whether and at what stage they affect the cell cycle. Alternatively, an agent may be characterized based on its ability to directly cross-link DNA, to intercalate into DNA, or to induce chromosomal and mitotic aberrations by affecting nucleic acid synthesis.
• chemotherapeutic agents include alkylating agents, such as thiotepa and cyclosphosphamide; alkyl sulfonates, such as busulfan, improsulfan, and piposulfan; aziridines, such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines, including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide, and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; cally statin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); cryptophycins (particularly cryptophycin 1 and cryptophycin 8); do
• DNA damaging factors include what are commonly known as g-rays, X-rays, and/or the directed delivery of radioisotopes to tumor cells.
• Other forms of DNA damaging factors are also contemplated, such as microwaves, proton beam irradiation (U.S. Patents 5,760,395 and 4,870,287), and UV-irradiation. It is most likely that all of these factors affect a broad range of damage on DNA, on the precursors of DNA, on the replication and repair of DNA, and on the assembly and maintenance of chromosomes.
• Dosage ranges for X-rays range from daily doses of 50 to 200 roentgens for prolonged periods of time (3 to 4 wk), to single doses of 2000 to 6000 roentgens.
• Dosage ranges for radioisotopes vary widely, and depend on the half-life of the isotope, the strength and type of radiation emitted, and the uptake by the neoplastic cells.
• immunotherapeutics generally, rely on the use of immune effector cells and molecules to target and destroy cancer cells.
• Rituximab (Rituxan®) is such an example.
• the immune effector may be, for example, an antibody specific for some marker on the surface of a tumor cell.
• the antibody alone may serve as an effector of therapy or it may recruit other cells to actually affect cell killing.
• the antibody also may be conjugated to a drug or toxin (chemotherapeutic, radionuclide, ricin A chain, cholera toxin, pertussis toxin, etc.) and serve merely as a targeting agent.
• the effector may be a lymphocyte carrying a surface molecule that interacts, either directly or indirectly, with a tumor cell target.
• Various effector cells include cytotoxic T cells and NK cells.
• the tumor cell must bear some marker that is amenable to targeting, i.e., is not present on the majority of other cells.
• Common tumor markers include CD20, carcinoembryonic antigen, tyrosinase (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, MucB, PLAP, laminin receptor, erb B, and pi 55.
• An alternative aspect of immunotherapy is to combine anticancer effects with immune stimulatory effects.
• Immune stimulating molecules also exist including: cytokines, such as IL-2, IL-4, IL-12, GM-CSF, gamma-IFN, chemokines, such as MIP-1, MCP-1, IL-8, and growth factors, such as FLT3 ligand.
• cytokines such as IL-2, IL-4, IL-12, GM-CSF, gamma-IFN
• chemokines such as MIP-1, MCP-1, IL-8
• growth factors such as FLT3 ligand.
• immunotherapies currently under investigation or in use are immune adjuvants, e.g ., Mycobacterium bovis, Plasmodium falciparum, dinitrochlorobenzene, and aromatic compounds (U.S. Patents 5,801,005 and 5,739,169; Hui and Hashimoto, Infection Immun., 66(11):5329-5336, 1998; Christodoulides et ak, Microbiology, 144(Pt 11):3027-3037, 1998); cytokine therapy, e.g, interferons a, b, and g, IL-1, GM-CSF, and TNF (Bukowski et ak, Clinical Cancer Res., 4(10):2337-2347, 1998; Davidson et ak, J.
• immune adjuvants e.g ., Mycobacterium bovis, Plasmodium falciparum, dinitrochlorobenzene, and aromatic compounds
• the immune therapy could be adoptive immunotherapy, which involves the transfer of autologous antigen- specific T cells generated ex vivo.
• the T cells used for adoptive immunotherapy can be generated either by expansion of antigen- specific T cells or redirection of T cells through genetic engineering. Isolation and transfer of tumor specific T cells has been shown to be successful in treating melanoma. Novel specificities in T cells have been successfully generated through the genetic transfer of transgenic T cell receptors or chimeric antigen receptors (CARs).
• CARs are synthetic receptors consisting of a targeting moiety that is associated with one or more signaling domains in a single fusion molecule.
• the binding moiety of a CAR consists of an antigen-binding domain of a single-chain antibody (scFv), comprising the light and variable fragments of a monoclonal antibody joined by a flexible linker. Binding moieties based on receptor or ligand domains have also been used successfully.
• the signaling domains for first generation CARs are derived from the cytoplasmic region of the CD3zeta or the Fc receptor gamma chains. CARs have successfully allowed T cells to be redirected against antigens expressed at the surface of tumor cells from various malignancies including lymphomas and solid tumors.
• the present application provides for a combination therapy for the treatment of cancer wherein the combination therapy comprises adoptive T cell therapy and a checkpoint inhibitor.
• the adoptive T cell therapy comprises autologous and/or allogenic T-cells.
• the autologous and/or allogenic T-cells are targeted against tumor antigens.
• Immunomodulatory agents include immune checkpoint inhibitors, agonists of co-stimulatory molecules, and antagonists of immune inhibitory molecules.
• the immunomodulatory agents may be drugs, such as small molecules, recombinant forms of ligand or receptors, or antibodies, such as human antibodies (e.g ., International Patent Publication W02015/016718; Pardoll, Nat Rev Cancer , 12(4): 252-264, 2012; both incorporated herein by reference).
• Known inhibitors of immune checkpoint proteins or analogs thereof may be used, in particular chimerized, humanized, or human forms of antibodies may be used.
• alternative and/or equivalent names may be in use for certain antibodies mentioned in the present disclosure. Such alternative and/or equivalent names are interchangeable in the context of the present disclosure. For example, it is known that lambrolizumab is also known under the alternative and equivalent names MK-3475 and pembrolizumab.
• Co-stimulatory molecules are ligands that interact with receptors on the surface of the immune cells, e.g., CD28, 4-1BB, 0X40 (also known as CD134), ICOS, and GITR.
• the complete protein sequence of human 0X40 has Genbank accession number NP 003318.
• the immunomodulatory agent is an anti-OX40 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
• Anti-human-OX40 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-OX40 antibodies can be used.
• An exemplary anti-OX40 antibody is PF- 04518600 (see, e.g, WO 2017/130076).
• ATOR-1015 is a bispecific antibody targeting CTLA4 and 0X40 (see, e.g., WO 2017/182672, WO 2018/091740, WO 2018/202649, WO 2018/002339).
• ICOS co-stimulatory molecule that can be targeted in the methods provided herein
• the complete protein sequence of human ICOS has Genbank accession number NP 036224.
• the immune checkpoint inhibitor is an anti-ICOS antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
• Anti-human-ICOS antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-ICOS antibodies can be used.
• Exemplary anti-ICOS antibodies include JTX-2011 (see, e.g, WO 2016/154177, WO 2018/187191) and GSK3359609 (see, e.g, WO 2016/059602).
• GITR glucocorticoid-induced tumour necrosis factor receptor-related protein
• AITR glucocorticoid-induced tumour necrosis factor receptor-related protein
• the complete protein sequence of human GITR has Genbank accession number NP 004186.
• the immunomodulatory agent is an anti-GITR antibody (e.g, a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
• Anti-human-GITR antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-GITR antibodies can be used.
• An exemplary anti-GITR antibody is TRX518 (see, e.g, WO 2006/105021).
• Immune checkpoint proteins that may be targeted by immune checkpoint blockade include adenosine A2A receptor (A2AR), B7-H3 (also known as CD276), B and T lymphocyte attenuator (BTLA), CCL5, CD27, CD38, CD8A, CMKLR1, cytotoxic T- lymphocyte-associated protein 4 (CTLA-4, also known as CD 152), CXCL9, CXCR5, HLA- DRBl, HLA-DQA1, HLA-E, killer-cell immunoglobulin (KIR), lymphocyte activation gene- 3 (LAG-3, also known as CD223), Mer tyrosine kinase (MerTK), NKG7, programmed death 1 (PD-1), programmed death-ligand 1 (PD-L1, also known as CD274), PDCD1LG2, PSMB10, STAT1, T cell immunoreceptor with Ig and ITIM domains (TIGIT), T-cell immunoglobulin domain and mucin domain 3 (TIM), TIM
• a PD-1 binding antagonist is a molecule that inhibits the binding of PD-1 to its ligand binding partners.
• the PD-1 ligand binding partners are PD-L1 and/or PD-L2.
• a PD-L1 binding antagonist is a molecule that inhibits the binding of PD-L1 to its binding partners.
• PD-L1 binding partners are PD-1 and/or B7-1.
• a PD- L2 binding antagonist is a molecule that inhibits the binding of PD-L2 to its binding partners.
• a PD-L2 binding partner is PD-1.
• the antagonist may be an antibody, an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or an oligopeptide.
• Exemplary antibodies are described in U.S. Patent Nos. 8,735,553, 8,354,509, and 8,008,449, all of which are incorporated herein by reference.
• Other PD-1 axis antagonists for use in the methods provided herein are known in the art, such as described in U.S. Patent Application Publication Nos. 2014/0294898, 2014/022021, and 2011/0008369, all of which are incorporated herein by reference.
• a PD-1 binding antagonist is an anti -PD-1 antibody (e.g ., a human antibody, a humanized antibody, or a chimeric antibody).
• the anti-PD-1 antibody is selected from the group consisting of nivolumab, pembrolizumab, and CT-011.
• the PD-1 binding antagonist is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PD-L1 or PD-L2 fused to a constant region (e.g, an Fc region of an immunoglobulin sequence)).
• the PD-1 binding antagonist is AMP- 224.
• Nivolumab also known as MDX-1106-04, MDX-1106, ONO-4538, BMS-936558, and OPDIVO ® , is an anti-PD-1 antibody described in W02006/121168.
• Pembrolizumab also known as MK-3475, Merck 3475, lambrolizumab, KEYTRUDA ® , and SCH-900475, is an anti-PD-1 antibody described in W02009/114335.
• CT-011 also known as hBAT or hBAT-1, is an anti-PD-1 antibody described in W02009/101611.
• AMP-224 also known as B7-DCIg, is a PD-L2-Fc fusion soluble receptor described in W02010/027827 and WO2011/066342.
• CTLA-4 cytotoxic T-lymphocyte-associated protein 4
• CD 152 cytotoxic T-lymphocyte-associated protein 4
• the complete cDNA sequence of human CTLA-4 has the Genbank accession number L15006.
• CTLA-4 is found on the surface of T cells and acts as an “off’ switch when bound to CD80 or CD86 on the surface of antigen-presenting cells.
• CTLA-4 is similar to the T-cell co-stimulatory protein, CD28, and both molecules bind to CD80 and CD86, also called B7-1 and B7-2 respectively, on antigen-presenting cells.
• CTLA-4 transmits an inhibitory signal to T cells, whereas CD28 transmits a stimulatory signal.
• Intracellular CTLA-4 is also found in regulatory T cells and may be important to their function. T cell activation through the T cell receptor and CD28 leads to increased expression of CTLA-4, an inhibitory receptor for B7 molecules.
• the immune checkpoint inhibitor is an anti-CTLA-4 antibody (e.g ., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
• Anti-human- CTLA-4 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-CTLA-4 antibodies can be used. For example, the anti-CTLA-4 antibodies disclosed in US Patent No. 8,119,129; PCT Publn. Nos.
• WO 01/14424, WO 98/42752, WO 00/37504 (CP675,206, also known as tremelimumab; formerly ticilimumab); U.S. Patent No. 6,207,156; Hurwitz et al. (1998) Proc Natl Acad Sci USA , 95(17): 10067-10071; Camacho et al. (2004) J Clin Oncology , 22(145): Abstract No. 2505 (antibody CP-675206); and Mokyr et al. (1998) Cancer Res , 58:5301-5304 can be used in the methods disclosed herein.
• the teachings of each of the aforementioned publications are hereby incorporated by reference.
• Antibodies that compete with any of these art-recognized antibodies for binding to CTLA-4 also can be used.
• a humanized CTLA-4 antibody is described in International Patent Application No. W02001/014424, W02000/037504, and U.S. Patent No. 8,017,114; all incorporated herein by reference.
• An exemplary anti-CTLA-4 antibody is ipilimumab (also known as 10D1, MDX- 010, MDX- 101, and Yervoy®) or antigen binding fragments and variants thereof (see, e.g. , WO 01/14424).
• the antibody comprises the heavy and light chain CDRs or VRs of ipilimumab. Accordingly, in one embodiment, the antibody comprises the CDR1, CDR2, and CDR3 domains of the VH region of ipilimumab, and the CDR1, CDR2, and CDR3 domains of the VL region of ipilimumab.
• the antibody competes for binding with and/or binds to the same epitope on CTLA-4 as the above-mentioned antibodies.
• the antibody has an at least about 90% variable region amino acid sequence identity with the above-mentioned antibodies (e.g, at least about 90%, 95%, or 99% variable region identity with ipilimumab).
• Other molecules for modulating CTLA-4 include CTLA-4 ligands and receptors such as described in U.S. Patent Nos. 5844905, 5885796 and International Patent Application Nos. WO1995001994 and WO1998042752; all incorporated herein by reference, and immunoadhesins such as described in U.S. Patent No. 8329867, incorporated herein by reference.
• lymphocyte-activation gene 3 also known as CD223.
• the complete protein sequence of human LAG-3 has the Genbank accession number NP-002277.
• LAG-3 is found on the surface of activated T cells, natural killer cells, B cells, and plasmacytoid dendritic cells.
• LAG-3 acts as an “off’ switch when bound to MHC class II on the surface of antigen-presenting cells. Inhibition of LAG-3 both activates effector T cells and inhibitor regulatory T cells.
• the immune checkpoint inhibitor is an anti -LAG-3 antibody (e.g ., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
• Anti-human-LAG-3 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-LAG-3 antibodies can be used.
• An exemplary anti-LAG-3 antibody is relatlimab (also known as BMS-986016) or antigen binding fragments and variants thereof (see, e.g., WO 2015/116539).
• anti-LAG-3 antibodies include TSR-033 (see, e.g, WO 2018/201096), MK-4280, and REGN3767.
• MGD013 is an anti-LAG-3/PD-l bispecific antibody described in WO 2017/019846.
• FS118 is an anti-LAG- 3/PD-L1 bispecific antibody described in WO 2017/220569.
• V-domain Ig suppressor of T cell activation (VISTA), also known as C10orf54.
• the complete protein sequence of human VISTA has the Genbank accession number NP 071436.
• VISTA is found on white blood cells and inhibits T cell effector function.
• the immune checkpoint inhibitor is an anti-VISTA3 antibody (e.g, a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
• Anti-human- VISTA antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art.
• art recognized anti-VISTA antibodies can be used.
• An exemplary anti-VISTA antibody is JNJ- 61610588 (also known as onvatilimab) (see, e.g., WO 2015/097536, WO 2016/207717, WO 2017/137830, WO 2017/175058).
• VISTA can also be inhibited with the small molecule CA- 170, which selectively targets both PD-L1 and VISTA (see, e.g., WO 2015/033299, WO 2015/033301).
• the immune checkpoint inhibitor is an anti-CD38 antibody (e.g. , a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
• Anti-human-CD38 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-CD38 antibodies can be used.
• An exemplary anti-CD38 antibody is daratumumab (see, e.g, U.S. Pat. No. 7,829,673).
• T cell immunoreceptor with Ig and ITIM domains T cell immunoreceptor with Ig and ITIM domains (TIGIT).
• TIGIT T cell immunoreceptor with Ig and ITIM domains
• the complete protein sequence of human TIGIT has Genbank accession number NP 776160.
• the immune checkpoint inhibitor is an anti-TIGIT antibody (e.g, a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
• Anti-human-TIGIT antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-TIGIT antibodies can be used.
• An exemplary anti-TIGIT antibody is MK-7684 (see, e.g, WO 2017/030823, WO 2016/028656).
• IDO indoleamine 2,3-dioxygenase
• the complete protein sequence of human IDO has Genbank accession number NP 002155.
• the immunomodulatory agent is a small molecule IDO inhibitor.
• Exemplary small molecules include BMS-986205, epacadostat (INCB24360), and navoximod (GDC-0919). 4. Surgery
• Curative surgery includes resection in which all or part of cancerous tissue is physically removed, excised, and/or destroyed and may be used in conjunction with other therapies, such as the treatment of the present invention, chemotherapy, radiotherapy, hormonal therapy, gene therapy, immunotherapy, and/or alternative therapies.
• Tumor resection refers to physical removal of at least part of a tumor.
• treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and microscopically-controlled surgery (Mohs’ surgery).
• a cavity may be formed in the body.
• Treatment may be accomplished by perfusion, direct injection, or local application of the area with an additional anti-cancer therapy. Such treatment may be repeated, for example, every 1, 2, 3, 4, 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months. These treatments may be of varying dosages as well.
• agents may be used in combination with certain aspects of the present invention to improve the therapeutic efficacy of treatment.
• additional agents include agents that affect the upregulation of cell surface receptors and GAP junctions, cytostatic and differentiation agents, inhibitors of cell adhesion, agents that increase the sensitivity of the hyperproliferative cells to apoptotic inducers, or other biological agents. Increases in intercellular signaling by elevating the number of GAP junctions would increase the anti-hyperproliferative effects on the neighboring hyperproliferative cell population.
• cytostatic or differentiation agents can be used in combination with certain aspects of the present invention to improve the anti- hyperproliferative efficacy of the treatments.
• Inhibitors of cell adhesion are contemplated to improve the efficacy of the present invention.
• Examples of cell adhesion inhibitors are focal adhesion kinase (FAKs) inhibitors and Lovastatin. It is further contemplated that other agents that increase the sensitivity of a hyperproliferative cell to apoptosis, such as the antibody c225, could be used in combination with certain aspects of the present invention to improve the treatment efficacy.
• FAKs focal adhesion kinase
• Lovastatin Lovastatin
• kits are envisioned containing, diagnostic agents, therapeutic agents and/or delivery agents.
• the present invention contemplates a kit for detecting an NRG1 fusion in a patient’s tumor cells.
• the present invention contemplates a kit for preparing and/or administering a therapy of the invention.
• the kit may comprise reagents capable of use in administering an active or effective agent(s) of the invention.
• Reagents of the kit may include one or more anti-cancer components of a combination therapy, as well as reagents to prepare, formulate, and/or administer the components of the invention or perform one or more steps of the inventive methods.
• the kit may also comprise a suitable container means, which is a container that will not react with components of the kit, such as an eppendorf tube, an assay plate, a syringe, a bottle, or a tube.
• the container may be made from sterilizable materials such as plastic or glass.
• the kit may further include an instruction sheet that outlines the procedural steps of the methods, and will follow substantially the same procedures as described herein or are known to those of ordinary skill.
• NRG1-DOC4 fusion breast cancer cell line MDA175-VII
• ADCs antibody drug conjugates
• Cell viability was determined by the Cell Titer Glo assay.
• Poziotinib potently inhibited MDA175- VII cells with an average IC50 value of 0.287 nM (FIG. 1).
• HER2 targeting antibodies trastuzumab, T- DM1, and pertuzumab had IC50 values of >10000 ng/mL, 634.5 ng/mL, and 53.7 ng/mL, respectively (FIG. 2A).
• HER2 antibodies with low dose poziotinib lead to increased sensitivity to trastuzumab, pertuzumab and T-DM1, reducing IC50 values to 1.37 nM, 1.23 nM, and 1.32 nM, respectively (FIG. 2B).
• Ba/F3 cells generation Ba/F3 cells stably co-expressing WT ErbB2 and WT ErbB3 or WT ErbB3 and WT ErbB4 are generated as previously described. Briefly, retroviral or lentiviral constructs are transfected into Phoenix 293 T cells to produce virus which is incubated with Ba/F3 cell lines over night. Virus is removed and cells are cultured in puromycin for 10 days to select for Ba/F3 cell lines stably expressing retrovirus constructs. After selection, cells are sorted using anti-HER2, anti-HER3, and anti-HER4 antibodies (Biolegend). Cell lines are then transduced again with lentivirus containing NRG-fusion plasmids in Table 1 A. Cells are then sorted by FACS for NRG1 expression. Stable cell lines are then deprived of IL-3. Resulting stable cell lines are used in downstream analyses including drug screening.
• Drug screening and IC50 determination Drug screening is performed as previously described. Briefly, cells are plated in 384-well plates (Greiner Bio-One) at 2000-3000 cells per well in technical triplicate. Seven different concentrations of TKIs or DMSO vehicle are added to reach a final volume of 40 pL per well. After 72 hours, 11 pL of Cell Titer Glo (Promega) is added to each well. Plates are incubated for a minimum of 10 minutes, and bioluminescence is determined using a FLUOstar OPTIMA plate reader (BMG LABTECH). Raw bioluminescence values are normalized to DMSO control treated cells, and values are plotted in GraphPad Prism.
• Non-linear regressions are used to fit the normalized data with a variable slope, and IC50 values are determined by GraphPad prism by interpolation of concentrations at 50% inhibition. Drug screens are performed in technical triplicate on each plate and either duplicate or triplicate biological replicates.
• Overexpression models are generated by lentiviral transduction of NRGl fusions in Table 1A.
• Lentiviruses are generated using Lenti- X cells Lenti-X single shot kit (Takarabio). Lenti viruses are generated as described by the manufacturer. Lentiviruses are then added to the cell lines in Table IB. After 24 hours of viral transduction, virus is removed and cells are placed into 2 pg/ml puromycin for selection. After 10 days of selection, protein and RNA are harvested from cell lines and expression of NRGl-fusions are determined by western blotting and RT-PCR, respectively. Stable cell lines with NRG1 -fusion expression are used for downstream analyses including western blotting and ELISAs.
• HER signaling by western blotting and ELISA in over expressing cell lines.
• Parental and overexpressing (OE) cell lines are plated in 10 cm dishes and treated with poziotinib in increasing doses from 1 nm to 100 nm. Cells are incubated with inhibitor for 4 hrs, 1 day and 3 days, and protein is harvested using lysis buffer (Cell Signaling).
• Expression of NRGl-fusions, phospho- and total -EGFR, HER2, HER3, and HER4 are determined by western blotting and blots are exposed using BioRad Chemidoc imager.

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