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EP-4735645-A2 - METHODS FOR DETECTION AND TREATMENT OF CANCER

EP4735645A2EP 4735645 A2EP4735645 A2EP 4735645A2EP-4735645-A2

Abstract

In alternative embodiments, provided are methods for detecting a cancer, the method comprising: obtaining a sample comprising biological fluids or cells from a subject or human; isolating extracellular vesicles (EVs) having a selected diameter range; determining the presence and concentration of one or at least two proteins, Haptoglobin (HP) and Catalase (CAT), in the selected diameter range from the sample; and correlating the presence of a combination of the one or at least two proteins with a source of the sample, wherein if HP and CAT are individually detected, or if HP and CAT are both detected, then cancer has been positively detected. Also provided are methods for treating, lessoning the symptoms of or decreasing the chance of recurrence of, a cancer comprising administering to an individual in need thereof an antibody (Ab) or an antigen (Ag) binding fragment that specifically binds haptoglobin (HP) and/or a haptoglobin-hemoglobin complex.

Inventors

  • TANAKA, HIROAKI
  • WOJCIK, JEROME
  • ZUCAL, Chiara
  • ABDERRAHIM, HADI

Assignees

  • EVBiome

Dates

Publication Date
20260506
Application Date
20240628

Claims (20)

  1. 1. A method for detecting a cancer or a tumor, the method comprising: (a) obtaining a sample comprising biological fluids, cells or tissue from a subject, wherein optionally the subject is a human patient or an animal subject, wherein optionally the sample comprises or is derived from a biopsy or a subject tissue sample or a control tissue sample; (b) isolating extracellular vesicles (EVs) having a selected diameter range, wherein optionally the selected diameter range of the isolated EVs is between about 50 nm and 500 nm, or between about 100 nm and 400 nm, or between about 150 nm and 300 nm; (c) determining the presence of Haptoglobin (HP) and/or Catalase (CAT) in the isolated EVs; and (d) measuring the concentration and/or the amount of Haptoglobin (HP) and/or Catalase (CAT) in the sample, wherein optionally the concentration and/or the amount of Haptoglobin (HP) and/or Catalase (CAT) in the sample is measured by an ELISA (enzy me-linked immunosorbent assay) and/or HPLC (High Performance Liquid Chromatography), wherein if HP and CAT are individually detected, or if HP and CAT are both detected, then Colorectal and/or Lung cancer have been positively detected or diagnosed, and optionally if HP and CAT are detected using ELISA (optionally using an ABC AM™ kit) at a level at or above about 580 pg/mL for HP and 10 pg/mL for CAT, or are detected at a level over between about 560 pg/mL to 600 pg/mL for HP and over between about 8 pg/mL to 10 pg/mL for CAT, then the cancer (optionally, a colorectal and/or lung cancer) have been positively detected or diagnosed, and and optionally if HP alone is detected using an ELISA (optionally using a PROTEINTECH™ kit) at a level at or above about 29,700 pg/mL, or is detected at a level over between about 29,000 pg/mL to 30,000 pg/mL, then the cancer (optionally, a colorectal and/or lung cancer) have been positively detected or diagnosed.
  2. 2. The method of claim 1. wherein the cancer or tumor is colorectal and/or Lung cancer.
  3. 3. A method for treating a cancer, the method comprising: (a) first detecting whether an individual in need thereof has a cancer or a tumor using a method as set forth in claim 1 ; and (b) followed by treating the individual in need thereof with a drug or therapy to treat or ameliorate, or lesson the symptoms of or chance of recurrence of, the tumor or cancer.
  4. 4. The method of claim 3, wherein the cancer or tumor is colorectal cancer (CRC) or lung cancer, wherein optionally the lung cancer is non-small cell lung cancer (NSCLC).
  5. 5. The method of claim 4, wherein the cancer or tumor is a leukemic cell cancer, acute lymphoblastic leukemia (ALL), angioimmunoblastic T cell lymphoma, Burkitt lymphoma, chronic myelogenous leukemia in blast crisis, diffuse large B-cell lymphoma, hairy cell leukemia, myeloma, precursor B lymphoblastic leukemia or lymphoma, follicular lymphoma, diffuse large B- cell lymphoma, mantle cell lymphoma, precursor T lymphoblastic leukemia or lymphoma, non-hematolymphoid sarcoma, or a carcinoma such as a renal cell carcinoma or a metaplastic breast carcinoma.
  6. 6. The method of any of claims 3 to 5, wherein the treating the individual in need thereof with a drug or therapy to treat or ameliorate, or lesson the symptoms of or chance of recurrence of, the tumor or cancer, comprises administering to an individual in need thereof an antibody (Ab), an antigen (Ag) binding fragment thereof, or a monomeric or dimeric antigen binding protein (ABP) that specifically binds haptoglobin (HP) and/or a haptoglobin-hemoglobin complex.
  7. 7. The method of claim 5. wherein the antibody (Ab), antigen (Ag) binding fragment thereof, or monomeric or dimeric antigen binding protein (ABP) that specifically binds haptoglobin (HP) and/or a haptoglobin-hemoglobin complex, comprises or is fabricated as: an antigen-binding fragment (Fab, or an Ab fragment having just one constant and one variable domain of each of an Ab heavy and light chain). a F(ab')2 (or an Ab digested by pepsin yielding two fragments: a F(ab')2 fragment and a pFc' (pepsin cleavage Fc) fragment), a Fab' (a single chain of a F(ab')2 fragment). a single-chain variable fragment (scFv) (or a fusion protein of a variable region of an Ab heavy and light chain connected together with a linker peptide optionally of about ten to about 25 amino acids in length), a (scFv)2, or a di-scFv or a bi-scFv, or a single peptide chain having two variable heavy and two variable light regions yielding tandem scFv, a minibody (or a fusion protein of a variable region of an Ab heavy and light chain connected together with an alkyl group, optionally a methyl or an ethyl group) a diabody (or an scFv with a linker peptide too short (optionally about five amino acids) for the two variable regions to fold together forcing the scFvs to dimerize), a triabody or a tetrabody (or an scFv with a linker peptide too short (optionally about one or two amino acids) for the two variable regions to fold together forcing the scFvs to trimerize or tetramize), a single-domain antibody (dAB) (or a single variable region of an Ab heavy or Ab light chain), a plurality of complementarity determining region (CDR) fragments, a multispecific antibody formed from two or more antibody fragments, a monoclonal or a polyclonal antibody (Ab); and/or a humanized Ab having a non-human (optionally murine) antigen binding fragment or complement determining region (CDR) that specifically binds to human haptoglobulin implanted in a human antibody.
  8. 8. The method of claim 6 or 7, wherein the antibody (Ab), antigen (Ag) binding fragment thereof, or monomeric or dimeric antigen binding protein (ABP) that specifically binds the haptoglobin (HP) or the haptoglobin-hemoglobin complex is formulated as a pharmaceutical composition, or is formulated for administration in vivo; or is formulated for enteral or parenteral administration, or for oral, intravenous (IV) or intrathecal (IT) administration, or is administered orally, parenterally, by inhalation spray, nasally, topically, intrathecally, intrathecally, intracerebrally, epidurally, intracranially or rectally.
  9. 9. The method of claim 8, wherein the antibody (Ab), antigen (Ag) binding fragment thereof, or monomeric or dimeric antigen binding protein (ABP) that specifically binds the haptoglobin (HP) or the haptoglobin-hemoglobin complex is formulated as a nanoparticle, a particle, a micelle or a liposome or lipoplex, a polymersome, a polyplex or a dendrimer; or is formulated as, or contained in, a nanoparticle, a liposome, a tablet, a pill, a capsule, a gel, a geltab, a liquid, a powder, an emulsion, a lotion, an aerosol, a spray, a lozenge, an aqueous or a sterile or an injectable solution, or an implant.
  10. 10. The method of any of claim 8 or 9, wherein the antibody (Ab), antigen (Ag) binding fragment thereof, or monomeric or dimeric antigen binding protein (ABP) that specifically binds the haptoglobin (HP) or the haptoglobin-hemoglobin complex is administered: (a) once a day. 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 seven weeks or once every eight weeks; or (b) at a dosage of between about 1 and 40 mg/Kg, or between about 5 and 20 mg/Kg.
  11. 11. A method for treating, ameliorating, lessoning the symptoms of or decreasing the chance of recurrence of, a tumor or a cancer, comprising administering to an individual in need thereof an antibody (Ab), an antigen (Ag) binding fragment thereof, or a monomeric or dimeric antigen binding protein (ABP) that specifically binds haptoglobin (HP) and/or a haptoglobin-hemoglobin complex.
  12. 12. The method of claim 11, wherein the antibody (Ab), antigen (Ag) binding fragment thereof, or monomeric or dimeric antigen binding protein (ABP) that specifically binds haptoglobin (HP) and/or a haptoglobin-hemoglobin complex, comprises or is fabricated as: an antigen-binding fragment (Fab, or an Ab fragment having just one constant and one variable domain of each of an Ab heavy and light chain). a F(ab')2 (or an Ab digested by pepsin yielding two fragments: a F(ab')2 fragment and a pFc' (pepsin cleavage Fc) fragment), a Fab' (a single chain of a F(ab')2 fragment). a single-chain variable fragment (scFv) (or a fusion protein of a variable region of an Ab heavy and light chain connected together with a linker peptide optionally of about ten to about 25 amino acids in length), a (scFv)2, or a di-scFv or a bi-scFv, or a single peptide chain having two variable heavy and two variable light regions yielding tandem scFv, a minibody (or a fusion protein of a variable region of an Ab heavy and light chain connected together with an alkyl group, optionally a methyl or an ethyl group) a diabody (or an scFv with a linker peptide too short (optionally about five amino acids) for the two variable regions to fold together forcing the scFvs to dimerize), a triabody or a tetrabody (or an scFv with a linker peptide too short (optionally about one or two amino acids) for the two variable regions to fold together forcing the scFvs to trimerize or tetramize), a single-domain antibody (dAB) (or a single variable region of an Ab heavy or Ab light chain), a plurality of complementarity determining region (CDR) fragments, a multispecific antibody formed from two or more antibody fragments, a monoclonal and/or a polyclonal antibody (Ab); and/or a humanized Ab having a non-human (optionally murine) antigen binding fragment or complement determining region (CDR) that specifically binds to human haptoglobulin implanted in a human antibody.
  13. 13. The method of claim 11 or 12, wherein the antibody (Ab), antigen (Ag) binding fragment thereof, or monomeric or dimeric antigen binding protein (ABP) that specifically binds the haptoglobin (HP) or the haptoglobin-hemoglobin complex: (a) comprises a murine complement determining region (CDR) that specifically binds to the haptoglobin (HP) or the haptoglobin-hemoglobin complex; or (b) is a humanized antibody comprising a murine complement determining region (CDR) that specifically binds to the haptoglobin (HP) or the haptoglobin- hemoglobin complex, wherein optionally the CDR has a sequence comprising SEQ ID NO: 1.
  14. 14. The method of any of claims 11 to 13, wherein the antibody (Ab), antigen (Ag) binding fragment thereof, or monomeric or dimeric antigen binding protein (ABP) that specifically binds the haptoglobin (HP) or the haptoglobin- hemoglobin complex is formulated as a pharmaceutical composition, or is formulated for administration in vivo; or is formulated for enteral or parenteral administration, or for oral, intravenous (IV) or intrathecal (IT) administration, or is administered orally, parenterally, by inhalation spray, nasally, topically, intrathecally, intrathecally, intracerebrally, epidurally, intracranially or rectally.
  15. 15. The method of claim 14, wherein the antibody (Ab), antigen (Ag) binding fragment thereof, or monomeric or dimeric antigen binding protein (ABP) that specifically binds the haptoglobin (HP) or the haptoglobin-hemoglobin complex is formulated as a nanoparticle, a particle, a micelle or a liposome or lipoplex, a polymersome, a polyplex or a dendrimer; or is formulated as, or contained in, a nanoparticle, a liposome, a tablet, a pill, a capsule, a gel, a geltab, a liquid, a powder, an emulsion, a lotion, an aerosol, a spray, a lozenge, an aqueous or a sterile or an injectable solution, or an implant.
  16. 16. The method of any of claim 14 or 15, wherein the antibody (Ab), antigen (Ag) binding fragment thereof, or monomeric or dimeric antigen binding protein (ABP) that specifically binds the haptoglobin (HP) or the haptoglobin- hemoglobin complex is administered: (a) once a day, once a week, once every two weeks, once every three weeks, once even 7 four weeks, once every five weeks, once every six weeks, once every seven weeks or once every eight weeks; or (b) at a dosage of between about 1 and 40 mg/Kg. or between about 5 and 20 mg/Kg.
  17. 17. The method of claim 11, wherein the cancer or tumor is colorectal cancer (CRC) or lung cancer, wherein optionally the lung cancer is non-small cell lung cancer (NSCLC).
  18. 18. The method of claim 11 , wherein the cancer or tumor is a leukemic cell cancer, acute lymphoblastic leukemia (ALL), angioimmunoblastic T cell lymphoma, Burkitt lymphoma, chronic myelogenous leukemia in blast crisis, diffuse large B-cell lymphoma, hairy cell leukemia, myeloma, precursor B lymphoblastic leukemia or lymphoma, follicular lymphoma, diffuse large B- cell lymphoma, mantle cell lymphoma, precursor T lymphoblastic leukemia or lymphoma, non-hematolymphoid sarcoma, or a carcinoma such as a renal cell carcinoma or a metaplastic breast carcinoma, an acute lymphocytic cancer, acute myeloid leukemia, alveolar rhabdomyosarcoma, bladder cancer, bone cancer, brain cancer, breast cancer, cancer of the anus, anal canal, rectum, cancer of the eye, cancer of the intrahepatic bile duct, cancer of the joints, cancer of the neck, gallbladder, or pleura, cancer of the nose, nasal cavity, or middle ear, cancer of the oral cavity, cancer of the vulva, chronic lymphocytic leukemia, chronic myeloid cancer, colon cancer, esophageal cancer, cervical cancer, fibrosarcoma, gastrointestinal cancer, Hodgkin lymphoma, hypopharynx cancer, kidney cancer, larynx cancer, leukemia, liquid tumors, liver cancer, lung cancer, lymphoma, malignant mesothelioma, mastocytoma, melanoma, multiple myeloma, nasopharynx cancer, non-Hodgkin lymphoma, ovarian cancer, pancreatic cancer, peritoneum, omentum, and mesentery cancer, pharynx cancer, prostate cancer, colorectal cancer, renal cancer, skin cancer, small intestine cancer, soft tissue cancer, solid tumors, stomach cancer, testicular cancer, thyroid cancer, ureter cancer, and/or urinary bladder cancer.
  19. 19. A method for determining the efficacy of a cancer or tumor treatment or therapy, comprising measuring the level of haptoglobin (HP) and/or haptoglobin- hemoglobin complexes in a sample from (or derived from) an individual or subject before beginning the cancer or tumor treatment or therapy, and at least once again after commencing the cancer or tumor treatment or therapy, wherein lower levels of the haptoglobin (HP) and/or haptoglobin-hemoglobin complexes in the individual or subject after commencing the cancer or tumor treatment or therapy as compared to before beginning the cancer or tumor treatment or therapy determines or indicates that the cancer treatment or therapy is effective against the cancer or tumor.
  20. 20. The method of claim 19, wherein the subject is a human patient or an animal subject, and optionally the sample comprises or is derived from a biopsy or a subject tissue sample or a control tissue sample.

Description

METHODS FOR DETECTION AND TREATMENT OF CANCER RELATED APPLICATIONS This Patent Convention Treaty (PCT) International Application claims the benefit of priority to U.S. Provisional Patent Application Serial No. (USSN) 63/523.872, filed June 28, 2023. The aforementioned application is expressly incorporated herein by reference in their entirety and for all purposes. REFERENCE TO ELECTRONIC SEQUENCE LISTING The application contains a Sequence Listing which has been submitted electronically in .XML format and is hereby incorporated by reference in its entirety. Said .XML copy, created on June 28, 2024, is named “7226. 152961. xml” and is 2,429 bytes in size. The sequence listing contained in this .XML file is part of the specification and is hereby incorporated by reference herein in its entirety. TECHNICAL FIELD This invention generally relates to biology and cancer diagnosis. In alternative embodiments, provided are methods for detecting Colorectal and/or Lung cancer, the method comprising: obtaining a sample comprising biological fluids or cells from a subject, wherein optionally the subject is a human patient; isolating extracellular vesicles (EVs) having a selected diameter range; determining the presence and concentration of one or at least two proteins, Haptoglobin (HP) and Catalase (CAT), in the selected diameter range from the sample; and optionally correlating the presence of a combination of the at least two proteins with a source of the sample, wherein optionally the source comprises a cancer biopsy or a tissue sample or a control tissue sample, wherein if HP and CAT are individually detected, or if HP and CAT are both detected, then Colorectal and/or Lung cancer have been positively detected. BACKGROUND Currently, colonoscopy is considered the best and most reliable method for the detection of neoplastic lesions that are at risk of progression to colorectal cancer (CRC). It is recommended as a primary first-line screening test in average and high- risk populations. However, colonoscopy has important and potentially consequential limitations. Importantly, polyps are occasionally missed during the procedure due to challenges with the procedure. Detection rate is highly dependent on quality standards including the colonoscopist skills, technology, and several patient-related factors. There is also a risk of perforation and bleeding. Quintero, E., Gastroenterol Res Pract. 2012 Apr 4; 2012: 846985 doi: 10.1155/2012/846985. Accordingly, there is an unmet need for methods of testing and diagnosing patients as having colorectal cancer (CRC). There is also an unmet need for better early-stage detection of CRC. There is a need for more accurate, faster, and more simple diagnostic screening of CRC in patients. The inventions described herein meet these unsolved challenges and needs. Lung cancer is highly treatable when detected at an early stage. Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, accounting for approximately 85% to 90% of all lung cancer cases. The remaining 10% to 15% of lung cancers are classified as small cell lung cancer (SCLC). NSCLC is a broad term that encompasses different subtypes of lung cancer, including adenocarcinoma, squamous cell carcinoma, and large cell carcinoma. Each subtype has distinct characteristics and treatment approaches. Among the NSCLC subtypes, adenocarcinoma is the most prevalent, followed by squamous cell carcinoma. Currently, CT (Computed Tomography) scan is considered one of the best methods for early detection of lung cancer. The high sensitivity of CT scans enables the detection of even tiny nodules or lesions, which can be indicative of lung cancer. The level of imaging resolution provided by the cross sectional images can help in differentiating between benign and malignant nodules or tumours. Therefore, CT scan-based lung cancer screening programs have been established for high-risk individuals, such as heavy smokers or those with a history of lung cancer. It's important to note that while CT scans are highly effective in detecting lung cancer, false-positive results can occur, potentially leading to unnecessary' invasive procedures. Additionally, radiation exposure from CT scans should be considered and balanced with the potential benefits. Just like in the case of colorectal cancer. The inventions described herein can help meet these unsolved challenges and needs. Extracellular vesicles (EVs) are membranous vesicles secreted from the cells into biological fluids (blood, urine, saliva, CSF, milk, etc). EVs can have different cellular biogenesis, including vesicles generated from the multivesicular body recycling or from plasma membrane budding. In the first case, EVs are referred to as exosomes, while in the second case they are referred to as microvesicles or ectosomes. EVs are heterogeneous in size, with a diameter ranging from a few nanometers to micrometres. Given the impossibility of distinguishing exosomes from micro ves