US20180264095A1 - Population-based immunogenic peptide identification platform - Google Patents

Population-based immunogenic peptide identification platform Download PDF

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Publication number
US20180264095A1
US20180264095A1 US15/910,965 US201815910965A US2018264095A1 US 20180264095 A1 US20180264095 A1 US 20180264095A1 US 201815910965 A US201815910965 A US 201815910965A US 2018264095 A1 US2018264095 A1 US 2018264095A1
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Prior art keywords
cell epitope
antigen
hla class
molecules
subjects
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US15/910,965
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Inventor
Julianna Lisziewicz
Levente Molnár
Enikõ R. TÖKE
József Toth
Orsolya Lorincz
Zsolt Csiszovszki
Eszter Somogyi
Katalin Pántya
Mónika Megyesi
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Treos Bio Ltd
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Treos Bio Zrt
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Priority claimed from EP17159243.9A external-priority patent/EP3370065A1/en
Priority claimed from EP17159242.1A external-priority patent/EP3369431A1/en
Priority claimed from GBGB1703809.2A external-priority patent/GB201703809D0/en
Application filed by Treos Bio Zrt filed Critical Treos Bio Zrt
Assigned to TREOS BIO ZRT. reassignment TREOS BIO ZRT. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: CSISZOVSZKI, ZSOLT, DR., LISZIEWICZ, JULIANNA, DR., LORINCZ, ORSOLYA, DR., MEGYESI, Mónika, MOLNÁR, Levente, PÁNTYA, Katalin, SOMOGYI, ESZTER, DR., TOKE, ENIKO R., DR., TOTH, József
Publication of US20180264095A1 publication Critical patent/US20180264095A1/en
Assigned to TREOS BIO LIMITED reassignment TREOS BIO LIMITED ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: TREOS BIO ZRT.
Priority to US17/454,225 priority Critical patent/US20220072114A1/en
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Definitions

  • the disclosure relates to methods of predicting whether a polypeptide is immunogenic for a specific human subject, methods of identifying fragments of a polypeptide that are immunogenic for a specific human subject, methods of preparing precision pharmaceutical compositions or kits comprising such polypeptide fragments, human subject-specific pharmaceutical compositions comprising such polypeptide fragments, and methods of treatment using such compositions.
  • peptides In antigen presenting cells (APC) protein antigens are processed into peptides. These peptides bind to human leukocyte antigen molecules (HLAs) and are presented on the cell surface as peptide-HLA complexes to T cells. Different individuals express different HLA molecules and different HLA molecules present different peptides. Therefore, according to the state of the art, a peptide, or a fragment of a larger polypeptide, is identified as immunogenic for a specific human subject if it is presented by a HLA molecule that is expressed by the subject. In other words, the state of the art describes immunogenic peptides as HLA-restricted epitopes.
  • HLA restricted epitopes induce T cell responses in only a fraction of individuals who express the HLA molecule. Peptides that activate a T cell response in one individual are inactive in others despite HLA allele matching. Therefore, it was unknown how an individual's HLA molecules present the antigen-derived epitopes that positively activate T cell responses.
  • the fragments of a polypeptide antigen that are immunogenic for a specific individual are those that can bind to multiple class I (activate cytotoxic T cells) or class II (activate helper T cells) HLAs expressed by that individual.
  • the disclosure provides a method of predicting the cytotoxic T cell response rate and/or the helper T cell response rate of a specific or target human population to administration of a polypeptide, or to administration of a pharmaceutical composition, kit or panel of polypeptides comprising one or more polypeptides as active ingredients, the method comprising
  • the disclosure further provides a method of predicting the clinical response rate of a specific or target human population to administration of a pharmaceutical composition, kit or panel of polypeptides comprising one or more polypeptides as active ingredients, the method comprising
  • the disclosure further provides methods of treatment of a human subject in need thereof, the method comprising administering to the subject a polypeptide, pharmaceutical composition or kit of the polypeptides of a panel of polypeptides that has been identified or selected based on the predicted immune or clinical response rate determined as described above; their use in a method of treatment of a relevant human subject; and their use in the manufacture of a medicament for treating a relevant subject.
  • the disclosure also provides a method of designing or preparing a polypeptide, or a polynucleic acid that encodes a polypeptide, for use in a method of inducing an immune response in a subject of a specific or target human population, the method comprising
  • the disclosure provides a method of inducing an immune response in a subject of a specific or target human population, the method comprising designing or preparing a polypeptide, a panel of polypeptides, a polynucleic acid encoding a polypeptide, or a pharmaceutical composition or kit for use in said specific or target human population as described above and administering the polypeptide(s), polynucleic acid, pharmaceutical composition or the active ingredient polypeptides of the kit to the subject.
  • the disclosure provides a polypeptide, panel of polypeptides, polynucleic acid, pharmaceutical composition or kit for use in a method of inducing an immune response in a subject of a specific or target human population, wherein the polypeptide, panel of polypeptides, polynucleic acid, pharmaceutical composition or kit is designed or prepared as described above for use in said specific or target human population, and wherein the composition or kit optionally comprises at least one pharmaceutically acceptable diluent, carrier, or preservative.
  • compositions, panel of polypeptides or kit for use in a method of inducing an immune response in a human subject
  • the pharmaceutical composition, panel of polypeptides or kit comprises as active ingredients a first and a second and optionally one or more additional peptides, wherein each peptide comprises an amino acid sequence that is a T cell epitope capable of binding to at least three HLA class I molecules of at least 10% of human subjects, wherein the T cell epitope of the first, second and optionally any additional regions are different from each other, and wherein the pharmaceutical composition or kit optionally comprises at least one pharmaceutically acceptable diluent, carrier, or preservative.
  • the disclosure provides a pharmaceutical composition, panel of polypeptides or kit for use in a method of inducing an immune response in a human subject, wherein the pharmaceutical composition, panel of polypeptides or kit comprises an active ingredient polypeptide comprising a first region and a second region and optionally one or more additional regions, wherein each region comprises an amino acid sequence that is a T cell epitope capable of binding to at least three HLA class I molecules of at least 10% of human subjects, wherein the T cell epitope of the first, second and optionally any additional regions are different from each other, and wherein the pharmaceutical composition or kit optionally comprises at least one pharmaceutically acceptable diluent, carrier, or preservative.
  • the disclosure provides a pharmaceutical composition, panel of polypeptides or kit for use in a method treating a cancer in a subject in need thereof, wherein the pharmaceutical composition, panel of polypeptides or kit comprises as active ingredients a first and a second peptide and optionally one or more additional peptides, wherein each peptide comprises an amino acid sequence that is an HLA class I-binding T cell epitope, and wherein for each said T cell epitope at least 10% of human subjects having cancer both
  • the disclosure provides a pharmaceutical composition, panel of polypeptides or kit for use in a method treating a cancer in a subject in need thereof, wherein the pharmaceutical composition, panel of polypeptides or kit comprises an active ingredient polypeptide comprising a first and a second region and optionally one or more additional regions, wherein each region comprises an amino acid sequence that is an HLA class I-binding T cell epitope, and wherein for each said T cell epitope at least 10% of human subjects having cancer both
  • the disclosure provides a pharmaceutical composition, panel of polypeptides or kit for use in a method treating a cancer selected from colorectal, breast, ovarian, melanoma, non-melanoma skin, lung, prostate, kidney, bladder, stomach, liver, cervix uteri, oesophagus, non-Hodgkin lymphoma, leukemia, pancreas, corpus uteri, lip, oral cavity, thyroid, brain, nervous system, gallbladder, larynx, pharynx, myeloma, nasopharynx, Hodgkin lymphoma, testis and Kaposi sarcoma in a subject in need thereof, wherein the pharmaceutical composition, panel of polypeptides or kit comprises as active ingredients a first and a second peptide and optionally one or more additional polypeptides, wherein each peptide comprises an amino acid sequence that is an HLA class I-binding T cell epitope, and wherein for each said T cell epi
  • the disclosure provides a pharmaceutical composition, panel of polypeptides or kit for use in a method treating a cancer selected from colorectal, breast, ovarian, melanoma, non-melanoma skin, lung, prostate, kidney, bladder, stomach, liver, cervix uteri, oesophagus, non-Hodgkin lymphoma, leukemia, pancreas, corpus uteri, lip, oral cavity, thyroid, brain, nervous system, gallbladder, larynx, pharynx, myeloma, nasopharynx, Hodgkin lymphoma, testis and Kaposi sarcoma in a subject in need thereof, wherein the pharmaceutical composition, panel of polypeptides or kit comprises an active ingredient polypeptide comprising a first and a second region and optionally one or more additional regions, wherein each region comprises an amino acid sequence that is an HLA class I-binding T cell epitope, and wherein for each said T cell epitope
  • the disclosure provides a method of treatment of a human subject in need thereof, the method comprising administering to the subject a polypeptide, a panel of polypeptides, a pharmaceutical composition or the active ingredient polypeptides of a kit described above, wherein the subject has been determined to express at least three HLA class I molecules and/or at least three HLA class II molecules capable of binding to the polypeptide or to one or more of the active ingredient polypeptides of the pharmaceutical composition or kit.
  • the invention provides a system comprising
  • compositions for treatment of a disease or disorder in a subject of a target human population comprising one or more polypeptides, each comprising at least a first region and a second region, (a) the first region being of 10-50 amino acids in length comprising a first amino acid sequence that is a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population; and (b) the second region being of 10-50 amino acids in length comprising a second amino acid sequence that is a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population; wherein the amino acid sequence of the T cell epitope of each of first and second regions comprise different sequences.
  • the composition comprises at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, or at least 12 different polypeptides. In some embodiments, the composition comprises 2-40 different polypeptides.
  • the T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population comprises 7 to 11 amino acids, and/or the T cell epitope that binds at least three HLA class II molecules of at least 10% of subjects in the target population comprises 13 to 17 amino acids.
  • the first region of 10-50 amino acids in length is from an antigen; and the second region of 10-50 amino acids in length is from a same or different antigen.
  • the epitopes of the first and second regions are from a single antigen. In some embodiments, the epitopes of the first and second regions are from two or more different antigens.
  • the antigen is a cancer-associated antigen, a tumor-associated antigen, or an antigen expressed by a target pathogenic organism, an antigen expressed by a virus, an antigen expressed by a bacterium, an antigen expressed by a fungus, an antigen associated with an autoimmune disorder, or is an allergen. In some embodiments, the antigen is selected from the antigens listed in Tables 2 to 7.
  • the two or more different antigens are selected from the antigens listed in Tables 2 to 7 and/or different cancer associated antigens.
  • one or more of the antigens are cancer testis antigens (CTAs).
  • the one or more polypeptides further comprise up to 10 amino acids flanking the T cell epitope that are not part of a consecutive sequence flanking the epitope in a corresponding antigen.
  • the one or more polypeptides have been screened to eliminate substantially all neoepitopes that span a junction between the first region and second region and that (i) corresponds to a fragment of a human polypeptide expressed in healthy cells; (ii) is a T cell epitope capable of binding to at least three HLA class I molecules of at least 10% of subjects in the target population; or (iii) meets both requirements (i) and (ii).
  • the target population is cancer patients and wherein each of the first region and second region comprises an amino acid sequence that is an HLA class I-binding T cell epitope, and wherein for each T cell epitope, at least 10% of subjects in the target population express a tumor associated antigen selected from the antigens listed in Table 2 that comprises the T cell epitope; and at least 10% of subjects in the target population have at least three HLA class I molecules capable of binding to the T cell epitope; wherein the T cell epitope of the first and second regions are different from each other.
  • the composition further comprises a pharmaceutically acceptable adjuvant, diluent, carrier, preservative, or combination thereof.
  • the adjuvant is selected from the group consisting of Montanide ISA-51, QS-21, GM-CSF, cyclophosamide, bacillus Calmette-Guerin (BCG), corynbacterium parvum , levamisole, azimezone, isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freunds adjuvant (complete), Freunds adjuvant (incomplete), mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions, oil emulsions, dinitrophenol, diphtheria toxin (DT), and combinations thereof.
  • kits comprising, one or more separate containers each container comprising: (i) one or more polypeptides comprising at least a first region and a second region, (a) the first region of 10-50 amino acids in length comprising a first amino acid sequence that is a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population; and (b) the second region of 10-50 amino acids in length comprising a second amino acid sequence that is a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population; wherein the amino acid sequence of the T cell epitope of each of first and second regions comprise different sequences and (ii) a pharmaceutically acceptable adjuvant, diluent, carrier, preservative, or combination thereof.
  • compositions comprising: one or more nucleic acid molecules expressing one or more polypeptides comprising at least a first region and a second region, (a) the first region of 10-50 amino acids in length comprising a first amino acid sequence that is a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population; and (b) the second region of 10-50 amino acids in length comprising a second amino acid sequence that is a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population; wherein the amino acid sequence of the T cell epitope of each of first and second regions comprise different sequences.
  • a polypeptide or a polynucleic acid that encodes a polypeptide, for use in a method of inducing an immune response in a subject of a target human population, the method comprising:
  • Disclosed herein in certain embodiments are methods of inducing an immune response in a subject of a target human population, the method comprising, administering to the subject a pharmaceutical composition comprising one or more polypeptides comprising at least a first region and a second region, (a) the first region being of 10-50 amino acids in length comprising a first amino acid sequence that is a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population; and (b) the second region being of 10-50 amino acids in length comprising a second amino acid sequence that is a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population; wherein the amino acid sequence of the T cell epitope of each of first and second regions comprise different sequences.
  • the method further comprises prior to the administering step, determining if the subject is likely to have an have a clinical response to administration of a pharmaceutical composition by (i) assaying a biological sample of the subject to determine HLA genotype of the subject; (ii) determining that the pharmaceutical composition comprises two or more sequences that are a T cell epitope capable of binding to at least three HLA class I molecules of the subject; and (iii) determining the probability that a tumor of the subject expresses one or more antigen corresponding to the T cell epitopes identified in step (ii) using population expression data for each antigen, to identify the likelihood of the subject to have a clinical response to administration of the pharmaceutical composition.
  • the first region of 10-50 amino acids in length is from an antigen; and the second region of 10-50 amino acids in length is from a same or different antigen.
  • the epitopes of the first and second regions are from two or more different antigens.
  • the antigen is a cancer-associated antigen, a tumor-associated antigen, or an antigen expressed by a target pathogenic organism, an antigen expressed by a virus, an antigen expressed by a bacterium, an antigen expressed by a fungus, an antigen associated with an autoimmune disorder, or is an allergen.
  • the T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population comprises 7 to 11 amino acids, and/or the T cell epitope that binds at least three HLA class II molecules of at least 10% of subjects in the target population comprises 13 to 17 amino acids.
  • compositions for treatment of a disease or disorder in a subject of a target human population comprising (a) at least two polypeptides, each of the at least two polypeptides being 10-50 amino acids in length comprising an amino acid sequence that is a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population, and/or at least three HLA class II molecules of at least 10% of subjects in the target population, wherein the amino acid sequence of the T cell epitope of each of the at least two polypeptides are different from each other; and (b) a pharmaceutically-acceptable adjuvant.
  • the composition comprises at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, or at least 12 different polypeptides. In some embodiments, the composition comprises 3-40 different polypeptides.
  • the T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population comprises 7 to 11 amino acids, and/or the T cell epitope that binds at least three HLA class II molecules of at least 10% of subjects in the target population comprises 13 to 17 amino acids.
  • the epitopes of the amino acid sequences of the at least two polypeptides are from a single antigen.
  • the epitopes of the amino acid sequences of the at least two polypeptides are from two or more different antigens.
  • the antigen is a cancer-associated antigen, a tumor-associated antigen, or an antigen expressed by a target pathogenic organism, an antigen expressed by a virus, an antigen expressed by a bacterium, an antigen expressed by a fungus, an antigen associated with an autoimmune disorder, or is an allergen.
  • the antigen is selected from the antigens listed in Tables 2 to 7.
  • the two or more different antigens are selected from the antigens listed in Tables 2 to 7 and/or different cancer associated antigens.
  • one or more of the antigens are cancer testis antigens (CTAs).
  • CTAs cancer testis antigens
  • each of the at least two polypeptides being 10-50 amino acids in length is from an antigen a same or different antigen.
  • the at least two different polypeptides further comprise up to 10 amino acids flanking the T cell epitope that are not part of a consecutive sequence flanking the epitope in a corresponding antigen.
  • two of the at least two polypeptides are arranged end to end or overlapping in a joined polypeptide.
  • two or more different joined polypeptides, wherein the two or more different joined polypeptides comprise different epitopes from each other.
  • the joined polypeptides have been screened to eliminate substantially all neoepitopes that span a junction between the two polypeptides and that (i) corresponds to a fragment of a human polypeptide expressed in healthy cells; (ii) is a T cell epitope capable of binding to at least three HLA class I molecules of at least 10% of subjects in the target population; or (iii) meets both requirements (i) and (ii).
  • the target population is cancer patients and wherein each polypeptide comprises an amino acid sequence that is an HLA class I-binding T cell epitope, and wherein for each T cell epitope, at least 10% of subjects in the target population express a tumor associated antigen selected from the antigens listed in Table 2 that comprises the T cell epitope; and at least 10% of subjects in the target population have at least three HLA class I molecules capable of binding to the T cell epitope; wherein the T cell epitope of the at least two polypeptides are different from each other.
  • the composition further comprises a pharmaceutically acceptable diluent, carrier, preservative, or combination thereof.
  • the adjuvant is selected from the group consisting of Montanide ISA-51, QS-21, GM-CSF, cyclophosamide, bacillus Calmette-Guerin (BCG), corynbacterium parvum , levamisole, azimezone, isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freunds adjuvant (complete), Freunds adjuvant (incomplete), mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions, oil emulsions, dinitrophenol, diphtheria toxin (DT), and combinations thereof.
  • compositions for treatment of a disease or disorder in a subject of a target human population comprising (a) a polypeptide of 10-50 amino acids in length and comprising a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population; and (b) a pharmaceutically-acceptable adjuvant.
  • the composition comprises at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, or at least 12 different polypeptides, each of the different polypeptides being 10-50 amino acids in length comprising a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population, wherein the amino acid sequence of the T cell epitope of each of the different polypeptides are different from each other.
  • the composition comprises 2-40 different polypeptides.
  • the T cell epitope that binds at least three HLA class I molecules of the subject comprises 7 to 11 amino acids, and/or the T cell epitope that binds at least three HLA class II molecules comprises 13 to 17 amino acids.
  • the composition comprises at least two different polypeptides, wherein the epitopes of the at least two different polypeptides are from a single antigen. In some embodiments, the composition comprises at least two different polypeptides, wherein the epitopes of the at least two different polypeptides are from two or more different antigens.
  • the antigen is an antigen expressed by a cancer cell, a neoantigen expressed by a cancer cell, a cancer-associated antigen, a tumor-associated antigen, or an antigen expressed by a target pathogenic organism, an antigen expressed by a virus, an antigen expressed by a bacterium, an antigen expressed by a fungus, an antigen associated with an autoimmune disorder, or is an allergen.
  • the antigen is selected from the antigens listed in Tables 2 to 7.
  • the composition comprises at least two different polypeptides, wherein two of the polypeptides are arranged end to end or overlapping in a joined polypeptide.
  • the adjuvant is selected from the group consisting of Montanide ISA-51, QS-21, GM-CSF, cyclophosamide, bacillus Calmette-Guerin (BCG), corynbacterium parvum , levamisole, azimezone, isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freunds adjuvant (complete), Freunds adjuvant (incomplete), mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions, oil emulsions, dinitrophenol, diphtheria toxin (DT), and combinations thereof.
  • the composition comprises at least two different polypeptides, wherein two of the at least two polypeptides are arranged end to end or overlapping in a joined polypeptide. In some embodiments, the composition comprises two or more different joined polypeptides, wherein the two or more different joined polypeptides comprise different epitopes from each other.
  • the joined polypeptides have been screened to eliminate substantially all neoepitopes that span a junction between the two polypeptides and that (i) corresponds to a fragment of a human polypeptide expressed in healthy cells of the subject; (ii) is a T cell epitope capable of binding to at least two HLA class I molecules of the subject; or (iii) meets both requirements (i) and (ii).
  • the at least two polypeptides do not comprise any amino acid sequences that (i) correspond to a fragment of a human polypeptide expressed in healthy cells; or (ii) correspond to a fragment of a human polypeptide expressed in healthy cells and is a T cell epitope capable of binding to at least two HLA class I molecules of the subject.
  • Disclosed herein in certain embodiments are methods of identifying and treating a subject of a target population of cancer patients who will likely have a clinical response to administration of a pharmaceutical composition of the disclosure, the method comprising, (i) assaying a biological sample of the subject to determine HLA genotype of the subject; (ii) determining that the pharmaceutical composition comprises two or more sequences that are a T cell epitope capable of binding to at least three HLA class I molecules of the subject; (iii) determining the probability that a tumor of the subject expresses one or more antigen corresponding to the T cell epitopes identified in step (ii) using population expression data for each antigen, to identify the likelihood of the subject to have a clinical response to administration of the pharmaceutical composition; and (iv) administering the composition of the disclosure to the identified subject.
  • the method further comprises prior to the administering step, assaying a tumor sample from the subject to determine that the three or more peptides of the pharmaceutical composition comprise two or more different amino acid sequences each of which is a fragment of a cancer-associated antigen expressed by cancer cells of the subject as determined in step (i); and a T cell epitope capable of binding to at least three HLA class I molecules of the subject; and confirming the subject as likely to have a clinical response to the method of treatment.
  • the composition comprises at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, or at least 12 different polypeptides.
  • the composition comprises 2-40 different polypeptides.
  • the T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population comprises 7 to 11 amino acids, and/or the T cell epitope that binds at least three HLA class II molecules of at least 10% of subjects in the target population comprises 13 to 17 amino acids.
  • the first region of 10-50 amino acids in length is from an antigen; and the second region of 10-50 amino acids in length is from a same or different antigen.
  • the epitopes of the first and second regions are from a single antigen. In some embodiments, the epitopes of the first and second regions are from two or more different antigens.
  • the antigen is a cancer-associated antigen or a tumor-associated antigen. In some embodiments, the antigen is selected from the antigens listed in Table 2. In some embodiments, the two or more different antigens are selected from the antigens listed in Table 2 and/or different cancer associated antigens. In some embodiments, one or more of the antigens are cancer testis antigens (CTAs). In some embodiments, the one or more polypeptides further comprise up to 10 amino acids flanking the T cell epitope that are not part of a consecutive sequence flanking the epitope in a corresponding antigen.
  • CTAs cancer testis antigens
  • the one or more polypeptides have been screened to eliminate substantially all neoepitopes that span a junction between the first region and second region and that (i) corresponds to a fragment of a human polypeptide expressed in healthy cells; (ii) is a T cell epitope capable of binding to at least three HLA class I molecules of at least 10% of subjects in the target population; or (iii) meets both requirements (i) and (ii).
  • the target population is cancer patients and wherein each of the first region and second region comprises an amino acid sequence that is an HLA class I-binding T cell epitope, and wherein for each T cell epitope, at least 10% of subjects in the target population express a tumor associated antigen selected from the antigens listed in Table 2 that comprises the T cell epitope; and at least 10% of subjects in the target population have at least three HLA class I molecules capable of binding to the T cell epitope; wherein the T cell epitope of the first and second regions are different from each other.
  • the composition further comprises a pharmaceutically acceptable adjuvant, diluent, carrier, preservative, or combination thereof.
  • the adjuvant is selected from the group consisting of Montanide ISA-51, QS-21, GM-CSF, cyclophosamide, bacillus Calmette-Guerin (BCG), corynbacterium parvum , levamisole, azimezone, isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freunds adjuvant (complete), Freunds adjuvant (incomplete), mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions, oil emulsions, dinitrophenol, diphtheria toxin (DT), and combinations thereof.
  • kits comprising: a first composition comprising (i) a first polypeptide of 10-50 amino acids in length and comprising a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population; and (ii) a pharmaceutically-acceptable adjuvant; and a second composition comprising (i) a second polypeptide of 10-50 amino acids in length and comprising a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population; and (ii) a pharmaceutically-acceptable adjuvant, wherein the first and second polypeptides comprise different T cell epitopes.
  • the first composition and/or the second composition comprise one or more additional polypeptides, wherein each additional polypeptide being of 10-50 amino acids in length comprising an amino acid sequence that is a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population, wherein the amino acid sequences comprise different T cell epitopes.
  • Disclosed herein in certain embodiments are methods of identifying and treating a subject of a target population of cancer patients who will likely have an immune response to administration of a pharmaceutical composition of the disclosure, the method comprising, (i) assaying a biological sample of the subject to determine HLA genotype of the subject; (ii) determining that the pharmaceutical composition comprises two or more sequences that are a T cell epitope capable of binding to at least three HLA class I molecules of the subject; (iii) administering the composition of the disclosure to the identified subject.
  • compositions comprising: a nucleic acid molecule expressing two or more polypeptides, each polypeptide being 10-50 amino acids in length comprising a T cell epitope that binds at least three HLA class I molecules of at least 10% of subjects in the target population and/or at least three HLA class II molecules of at least 10% of subjects in the target population, wherein each of the two or more polypeptides comprises a different T cell epitope, wherein the polypeptides do not comprise amino acid sequences that are adjacent to each other in a corresponding antigen.
  • FIG. 1 ROC curve of HLA restricted PEPI biomarkers.
  • FIG. 2 ROC curve of ⁇ 1 PEPI3+ Test for the determination of the diagnostic accuracy.
  • FIGS. 3A-B Distribution of HLA class I PEPI3+ compared to CD8+ T cell responses measured by a state of art assay among peptide pools used in the CD8+ T cell response assays.
  • FIG. 3A HLA class I restricted PEPI3+s. The 90% Overall Percent of Agreement (OPA) among the T cell responses and PEPI3+ peptides demonstrate the utility of the disclosed peptides for prediction of vaccine induced T cell response set of individuals.
  • FIG. 3B Class I HLA restricted epitopes (PEPI1+). The OPA between predicted epitopes and CD8+ T cell responses was 28% (not statistically significant).
  • FIGS. 4A-B Distribution of HLA class II PEPIs compared to CD4+ T cell responses measured by a state of art assay among peptide pools used in the assays.
  • FIG. 4B The class II HLA restricted epitopes. OPA between class II HLA restricted epitopes and CD4+ T cell responses was 66% (not statistically significant).
  • FIGS. 5A-D Multiple HLA binding peptides that define the HPV-16 LPV vaccine specific T cell response set of 18 VIN-3 and 5 cervical cancer patients.
  • HLA class I restricted PEPI3 counts FIGS. 5A and 5B
  • HLA class II restricted PEPI3 counts FIGS. 5C and 5D
  • Light grey immune responders measured after vaccination in the clinical trial
  • Dark grey Immune non-responders measured after vaccination in the clinical trial.
  • Results show that ⁇ 3 HLA class I binding peptides predict the CD8+ T cell reactivity and ⁇ 4 HLA class II binding peptides predict the CD4+ T cell reactivity.
  • FIG. 6 The multiple HLA class I binding peptides that define the HPV vaccine specific T cell response set of 2 patients.
  • Panel A Four HPV antigens in the HPV vaccine. Boxes represent the length of the amino acid sequences from the N terminus to the C terminus.
  • Panel B Process to identify the multiple HLA binding peptides of two patients: HLA sequences of the patients labelled as 4-digit HLA genotype right from the patient's ID. The location of the 1 st amino acid of the 54 and 91 epitopes that can bind to the patient 12-11 and patient 14-5 HLAs (PEPI1+) respectively are depicted with lines.
  • PEPI2 represents the peptides selected from PEPI1+s that can bind to multiple HLAs of a patient (PEPI2+).
  • PEPI3 represent peptides that can bind to ⁇ 3 HLAs of a patient (PEPI3+).
  • PEPI4 represent peptides that can bind to ⁇ 4 HLAs of a patient (PEPI4+).
  • PEPI5 represent peptides that can bind to ⁇ 5 HLAs of a patient (PEPI5+).
  • PEPI6 represent peptides that can bind to 6 HLAs of a patient (PEPI6).
  • Panel C The DNA vaccine specific PEPI3+ set of two patients characterizes their vaccine specific T cell responses.
  • FIG. 7 Correlation between the ⁇ 1 PEPI3+ Score and CTL response rates of peptide targets determined in clinical trials.
  • FIG. 8 Correlation between the ⁇ 1 PEPI3+ Score and the clinical Immune Response Rate (IRR) of immunotherapy vaccines. Dashed lines: 95% confidence band.
  • FIG. 9 Correlation between the ⁇ 2 PEPI3+ Score and Disease Control Rate (DCR) of immunotherapy vaccines. Dashed lines: 95% confidence band.
  • FIG. 10 HLA map of the Rindopepimut on the HLA alleles of the subjects in the Model Population.
  • FIGS. 11A-B Provides of vaccine antigen expression in the XYZ patient's tumor cells.
  • FIG. 12 MRI findings of patient XYZ treated with personalised (PIT) vaccine. This late stage, heavily pretreated ovarian cancer patient had an unexpected objective response after the PIT vaccine treatment. These MRI findings suggest that PIT vaccine in combination with chemotherapy significantly reduced her tumor burden. The patient now continues the PIT vaccine treatment.
  • FIG. 15 CTA Expression Curve calculated by analyzing expression frequency data of tumor specific antigens (CTAs) in human breast cancer tissues. (No cell line data were included.)
  • FIGS. 16A-B Antigen expression distribution for breast cancer based on the calculation of multi-antigen responses from expression frequencies of the selected 10 different CTAs.
  • FIG. 16A non-cumulative distribution to calculate the expected value for the number of expressed antigens (AG50). This value shows that probably 6.14 vaccine antigens will be expressed by breast tumor cells.
  • FIG. 16B cumulative distribution curve of the minimum number of expressed antigens (CTA expression curve). This shows that minimum 4 vaccine antigens will be expressed with 95% probability in breast cancer cell (AG95).
  • AGP50 is a measure of the effectiveness of the disclosed breast cancer vaccine in attacking breast tumor in an unselected patient population.
  • AGP50 is a measure of the effectiveness of the disclosed breast cancer vaccine in attacking breast tumor in an unselected patient population.
  • FIG. 19 CTA Expression Curve calculated by analyzing expression frequency data of tumor specific antigens (CTAs) in human colorectal cancer tissues. (No cell line data were included.)
  • FIGS. 20A-B Antigen expression distribution for colorectal cancer based on the calculation of multi-antigen responses from expression frequencies of the selected 7 different CTAs.
  • FIG. 20A non-cumulative distribution to calculate the expected vale for the number of expressed vaccine antigens in colorectal cancers (AG50). This value shows that probably 4.96 vaccine antigens will be expressed by colorectal tumor cells.
  • FIG. 20B cumulative distribution curve of the minimum number of expressed antigens (CTA expression curve). This shows that minimum 3 antigens will be expressed with 95% probability in the colorectal cancer cell (AG95).
  • AGP50 is a measure of the effectiveness of the disclosed colorectal cancer vaccine in attacking colorectal tumors in an unselected patient population.
  • FIG. 23 Schot al. showing exemplary positions of amino acids in overlapping HLA class I- and HLA class-II binding epitopes in a 30-mer peptide.
  • FIGS. 24A-B Antigenicity of PolyPEPI1018 CRC Vaccine in a general population.
  • the antigenicity of PolyPEPI1018 in a subject is determined by the AP count, which indicates the number of vaccine antigens that induce T cell responses in a subject.
  • the AP count of PolyPEPI1018 was determined in each of the 433 subjects in the Model Population using the PEPI Test, and the AP50 count was then calculated for the Model Population.
  • the AP50 of PolyPEPI1018 in the Model Population is 4.73.
  • the mean number of immunogenic antigens (i.e., antigens with ⁇ 1 PEPI) in PolyPEPI1018 in a general population is 4.73.
  • Abbreviations: AP antigens with ⁇ 1 PEPI.
  • Left Panel Cumulative distribution curve.
  • Right Panel Distinct distribution curve.
  • FIGS. 25A-B Effectiveness of PolyPEPI1018 CRC Vaccine in a general population.
  • Vaccine induced T cells can recognize and kill tumor cells if a PEPI in the vaccine is presented by the tumor cell.
  • the number of AGPs (expressed antigens with PEPI) is an indicator of vaccine effectiveness in an individual, and is dependent on both the potency and antigenicity of PolyPEPI1018.
  • the mean number of immunogenic CTAs (i.e., AP [expressed antigens with ⁇ 1 PEPI]) in PolyPEPI1018 is 2.54 in the Model Population.
  • the likelihood that PolyPEPI1018 induces T cell responses against multiple antigens in a subject (i.e., mAGP) in the Model Population is 77%.
  • SEQ ID NOs: 1 to 20 set forth 9 mer T cell epitopes described in Table 30.
  • SEQ ID NOs: 21 to 40 set forth 9 mer T cell epitopes described in Table 33.
  • SEQ ID NOs: 41-71 (81 to 111) set forth the breast cancer vaccine peptides set forth in Table 31.
  • SEQ ID NOs 72-102 (112 to 142) set forth the colorectal cancer vaccine peptides set forth in Table 34.
  • SEQ ID Nos: 103-115 (159 to 171) set forth the additional peptide sequences described in Table 17.
  • SEQ ID NOs: 116-128 (362 to 374) set forth personalised vaccine peptides designed for patient XYZ described in Table 26.
  • SEQ ID NOs: 129-140 (375 to 386) set forth personalised vaccine peptides designed for patient ABC described in Table 29.
  • SEQ ID NOs: 141-188 (387 to 434) set forth further 9 mer T cell epitopes described in Table 41.
  • HLAs are encoded by the most polymorphic genes of the human genome. Each person has a maternal and a paternal allele for the three HLA class I molecules (HLA-A*, HLA-B*, HLA-C*) and four HLA class II molecules (HLA-DP*, HLA-DQ*, HLA-DRB1*, HLA-DRB3*/4*/5*). Practically, each person expresses a different combination of 6 HLA class I and 8 HLA class II molecules that present different epitopes from the same protein antigen. The function of HLA molecules is to regulate T cell responses. However up to date it was unknown how the HLAs of a person regulate T cell activation.
  • HLA-A*02:25 The nomenclature used to designate the amino acid sequence of the HLA molecule is as follows: gene name*allele:protein number, which, for instance, can look like: HLA-A*02:25.
  • “02” refers to the allele.
  • alleles are defined by serotypes—meaning that the proteins of a given allele will not react with each other in serological assays.
  • Protein numbers (“25” in the example above) are assigned consecutively as the protein is discovered. A new protein number is assigned for any protein with a different amino acid sequence (e.g. even a one amino acid change in sequence is considered a different protein number). Further information on the nucleic acid sequence of a given locus may be appended to the HLA nomenclature, but such information is not required for the methods described herein.
  • the HLA class I genotype or HLA class II genotype of an individual may refer to the actual amino acid sequence of each class I or class II HLA of an individual, or may refer to the nomenclature, as described above, that designates, minimally, the allele and protein number of each HLA gene.
  • An HLA genotype may be obtained or determined using any suitable method. For example, the sequence may be determined via sequencing the HLA gene loci using methods and protocols known in the art. Alternatively, the HLA set of an individual may be stored in a database and accessed using methods known in the art.
  • a given HLA of a subject will only present to T cells a limited number of different peptides produced by the processing of protein antigens in an APC.
  • display or “present”, when used in relation to HLA, references the binding between a peptide (epitope) and an HLA.
  • to “display” or “present” a peptide is synonymous with “binding” a peptide.
  • epitope refers to a sequence of contiguous amino acids contained within a protein antigen that possess a binding affinity for (is capable of binding to) one or more HLAs.
  • An epitope is HLA- and antigen-specific (HLA-epitope pairs, predicted with known methods), but not subject specific.
  • An epitope, a T cell epitope, a polypeptide, a fragment of a polypeptide or a composition comprising a polypeptide or a fragment thereof is “immunogenic” for a specific human subject if it is capable of inducing a T cell response (a cytotoxic T cell response or a helper T cell response) in that subject.
  • the helper T cell response is a Th1-type helper T cell response.
  • an epitope, a T cell epitope, a polypeptide, a fragment of a polypeptide or a composition comprising a polypeptide or a fragment thereof is “immunogenic” for a specific human subject if it is more likely to induce a T cell response or immune response in the subject than a different T cell epitope (or in some cases two different T cell epitopes each) capable of binding to just one HLA molecule of the subject.
  • T cell response and “immune response” are used herein interchangeably, and refer to the activation of T cells and/or the induction of one or more effector functions following recognition of one or more HLA-epitope binding pairs.
  • an “immune response” includes an antibody response, because HLA class II molecules stimulate helper responses that are involved in inducing both long lasting CTL responses and antibody responses. Effector functions include cytotoxicity, cytokine production and proliferation.
  • an epitope, a T cell epitope, or a fragment of a polypeptide is immunogenic for a specific subject if it is capable of binding to at least two, or in some cases at least three, class I or at least two, or in some cases at least three or at least four class II HLAs of the subject.
  • PEPI personal epitope
  • a “PEPI” is a fragment of a polypeptide consisting of a sequence of contiguous amino acids of the polypeptide that is a T cell epitope capable of binding to one or more HLA class I molecules of a specific human subject.
  • a “PEPI” is a fragment of a polypeptide consisting of a sequence of contiguous amino acids of the polypeptide that is a T cell epitope capable of binding to one or more HLA class II molecules of a specific human subject.
  • PEPI is a T cell epitope that is recognised by the HLA set of a specific individual.
  • PEPIs are specific to an individual because different individuals have different HLA molecules which each bind to different T cell epitopes.
  • PEPI1 refers to a peptide, or a fragment of a polypeptide, that can bind to one HLA class I molecule (or, in specific contexts, HLA class II molecule) of an individual.
  • PEPI1+ refers to a peptide, or a fragment of a polypeptide, that can bind to one or more HLA class I molecule of an individual.
  • PEPI2 refers to a peptide, or a fragment of a polypeptide, that can bind to two HLA class I (or II) molecules of an individual.
  • PEPI2+ refers to a peptide, or a fragment of a polypeptide, that can bind to two or more HLA class I (or II) molecules of an individual, i.e. a fragment identified according to a method of the disclosure.
  • PEPI3 refers to a peptide, or a fragment of a polypeptide, that can bind to three HLA class I (or II) molecules of an individual.
  • PEPI3+ refers to a peptide, or a fragment of a polypeptide, that can bind to three or more HLA class I (or II) molecules of an individual.
  • PEPI4 refers to a peptide, or a fragment of a polypeptide, that can bind to four HLA class I (or II) molecules of an individual.
  • PEPI4+ refers to a peptide, or a fragment of a polypeptide, that can bind to four or more HLA class I (or II) molecules of an individual.
  • PEPI5 refers to a peptide, or a fragment of a polypeptide, that can bind to five HLA class I (or II) molecules of an individual.
  • PEPI5+ refers to a peptide, or a fragment of a polypeptide, that can bind to five or more HLA class I (or II) molecules of an individual.
  • PEPI6 refers to a peptide, or a fragment of a polypeptide, that can bind to all six HLA class I (or six HLA class II) molecules of an individual.
  • epitopes presented by HLA class I molecules are about nine amino acids long and epitopes presented by HLA class II molecules are about fifteen amino acids long.
  • an epitope may be more or less than nine (for HLA Class I) or more or less than fifteen (for HLA Class II) amino acids long, as long as the epitope is capable of binding HLA.
  • an epitope that is capable of binding to class I HLA may be between 7, or 8 or 9 and 9 or 10 or 11 amino acids long.
  • An epitope that is capable of binding to a class II HLA may be between 13, or 14 or 15 and 15 or 16 or 17 amino acids long.
  • the disclosure herein includes, for example, a method of predicting whether a polypeptide is immunogenic for a relevant population or cohort of human subjects (e.g., in a model human population) or identifying a fragment of a polypeptide as immunogenic for a relevant population or cohort of human subjects (e.g., in a model human population), the method comprising the steps of
  • a T cell epitope is capable of binding to a given HLA if it has an IC50 or predicted IC50 of less than 5000 nM, less than 2000 nM, less than 1000 nM, or less than 500 nM.
  • T cell epitope presentation by multiple HLAs of an individual is generally needed to trigger a T cell response.
  • the methods of the disclosure comprise determining whether a polypeptide has a sequence that is a T cell epitope capable of binding to at least two HLA class I molecules or at least two HLA class II (PEPI2+) molecules of a human subject (e.g., in a model human population).
  • the best predictor of a cytotoxic T cell response to a given polypeptide is the presence of at least one T cell epitope that is presented by three or more HLA class I molecules of an individual ( ⁇ 1 PEPI3+). Accordingly, in some cases the method comprises determining whether a polypeptide has a sequence that is a T cell epitope capable of binding to at least three HLA class I molecules of a specific human subject. In some cases the method comprises determining whether a polypeptide has a sequence that is a T cell epitope capable of binding to just three HLA class I of a human subject (e.g., in a model human population).
  • a helper T cell response may be predicted by the presence of at least one T cell epitope that is presented by three or more ( ⁇ 1 PEPI3+) or 4 or more ( ⁇ 1 PEPI4+) HLA class II of an individual. Therefore in some cases, the method comprises determining whether a polypeptide has a sequence that is a T cell epitope capable of binding to at least three HLA class II of a human subject (e.g., in a model human population). In other cases, the method comprises determining whether a polypeptide has a sequence that is a T cell epitope capable of binding to at least four HLA class II of a human subject. In other cases, the method comprises determining whether a polypeptide has a sequence that is a T cell epitope capable of binding to at just three and/or just four HLA class II of a human subject.
  • the disclosed methods and compositions may be used to predict whether a polypeptide/fragment will induce both a cytotoxic T cell response and a helper T cell response in a human subject.
  • the polypeptide/fragment comprises both an amino acid sequence that is a T cell epitope capable of binding to multiple HLA class I molecules of the subject and an amino acid sequence that is a T cell epitope capable of binding to multiple HLA class II molecules of the subject.
  • the HLA class I-binding and HLA class II-binding epitopes may fully or partially overlap.
  • such fragments of a polypeptide may be identified by selecting an amino acid sequence that is a T cell epitope capable of binding to multiple (e.g.
  • HLA class I molecules of the subject at least two or at least three
  • HLA class II molecules of the subject screening one or more longer fragments of the polypeptide that are extended at the N- and/or C-terminus for binding to one or more or the most possible (i.e. when no suitable HLA class II-binding PEPI3+s are available) HLA class II molecules of the subject or of a high percentage of subjects in a population.
  • Some subjects may have two HLA alleles that encode the same HLA molecule (for example, two copies for HLA-A*02:25 in case of homozygosity).
  • the HLA molecules encoded by these alleles bind all of the same T cell epitopes.
  • binding to at least two HLA molecules of the subject includes binding to the HLA molecules encoded by two identical HLA alleles in a single subject. In other words, “binding to at least two HLA molecules of the subject” and the like could otherwise be expressed as “binding to the HLA molecules encoded by at least two HLA alleles of the subject”.
  • polypeptide refers to a full-length protein, a portion of a protein, or a peptide characterized as a string of amino acids.
  • peptide refers to a short polypeptide comprising between 2, or 3, or 4, or 5, or 6, or 7, or 8, or 9, or 10, or 11, or 12, or 13, or 14, or 15 and 10, or 11, or 12, or 13, or 14, or 15, or 20, or 25, or 30, or 35, or 40, or 45, or 50 amino acids.
  • fragment or “fragment of a polypeptide” as used herein refer to a string of amino acids or an amino acid sequence typically of reduced length relative to the or a reference polypeptide and comprising, over the common portion, an amino acid sequence identical to the reference polypeptide.
  • a fragment according to the disclosure may be, where appropriate, included in a larger polypeptide of which it is a constituent.
  • the fragment may comprise the full length of the polypeptide, for example where the whole polypeptide, such as a 9 amino acid peptide, is a single T cell epitope.
  • the polypeptide is, or the polypeptide consists of all or part of an antigen that is, expressed by a pathogenic organism (for example, a bacteria or a parasite), a virus, or a cancer cell, that is associated with an autoimmune disorder or response or a disease-associated cell, or that is an allergen, or an ingredient of a medicine or pharmaceutical composition such as a vaccine or immunotherapy composition.
  • a pathogenic organism for example, a bacteria or a parasite
  • virus for example, a virus, or a cancer cell, that is associated with an autoimmune disorder or response or a disease-associated cell, or that is an allergen, or an ingredient of a medicine or pharmaceutical composition such as a vaccine or immunotherapy composition.
  • the method of the disclosure comprises an initial step of identifying or selecting a suitable polypeptide, for example a polypeptide as further described below.
  • the polypeptide or antigen may be expressed in the cells or specifically in diseased cells of the specific or target human population (e.g. a tumor-associated antigen, a polypeptide expressed by a virus, intracellular bacteria or parasite, or the in vivo product of a vaccine or immunotherapy composition) or acquired from the environment (e.g. a food, an allergen or a drug).
  • the polypeptide or antigen may be present in a sample taken from a subject of the specific or target human population.
  • Both polypeptide antigens and HLAs can be exactly defined by amino acid or nucleotide sequences and sequenced using methods known in the art.
  • the polypeptide or antigen may be a cancer- or tumor-associated antigen (TAA).
  • TAAs are proteins expressed in cancer or tumor cells.
  • the cancer or tumour cell may be present in a sample obtained from a subject of the specific or target human population.
  • TAAs include new antigens (neoantigens) expressed during tumorigenesis, products of oncogenes and tumor suppressor genes, overexpressed or aberrantly expressed cellular proteins (e.g. HER2, MUC1), antigens produced by oncogenic viruses (e.g. EBV, HPV, HCV, HBV, HTLV), cancer testis antigens (CTA)(e.g. MAGE family, NY-ESO) and cell-type-specific differentiation antigens (e.g.
  • TAA sequences may be found experimentally, or in published scientific papers, or through publicly available databases, such as the database of the Ludwig Institute for Cancer Research (www.cta.lncc.br/), Cancer Immunity database (cancerimmunity.org/peptide/) and the TANTIGEN Tumor T cell antigen database (cvc.dfci.harvard.edu/tadb/).
  • the polypeptide or antigen is not expressed or is minimally expressed in normal healthy cells or tissues, but is expressed (in those cells or tissues) in a high proportion of (with a high frequency in) subjects having a particular disease or condition, such as a type of cancer or a cancer derived from a particular cell type or tissue, for example breast cancer, ovarian cancer or melanoma.
  • a particular disease or condition such as a type of cancer or a cancer derived from a particular cell type or tissue, for example breast cancer, ovarian cancer or melanoma.
  • a further example is colorectal cancer.
  • non-limiting cancer examples include non-melanoma skin, lung, prostate, kidney, bladder, stomach, liver, cervix uteri, oesophagus, non-Hodgkin lymphoma, leukemia, pancreas, corpus uteri, lip, oral cavity, thyroid, brain, nervous system, gallbladder, larynx, pharynx, myeloma, nasopharynx, Hodgkin lymphoma, testis and Kaposi sarcoma.
  • the polypeptide may be expressed at low levels in normal healthy cells, but at high levels (overexpressed) in diseased (e.g. cancer) cells or in subjects having the disease or condition.
  • the polypeptide is expressed in, or expressed at a high level relative to normal healthy cells or subjects in, at least 2%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more of such individuals, or of a subject-matched human subpopulation or model or target population.
  • the population may be matched to the subject by ethnicity, geographical location, gender, age, disease, disease type or stage, genotype, or expression of one or more biomarkers.
  • the expression frequencies can be determined from published figures and scientific publications.
  • the method of the disclosure comprises a step of identifying or selecting such a polypeptide.
  • the polypeptide is associated with or highly (over-) expressed in cancer cells, or in solid tumors.
  • cancers include carcinomas, sarcomas, lymphomas, leukemias, germ cell tumors, or blastomas.
  • the cancer may or may not be a hormone related or dependent cancer (e.g., an estrogen or androgen related cancer).
  • the tumor may be malignant or benign.
  • the cancer may or may not be metastatic.
  • the polypeptide is a cancer testis antigens (CTA).
  • CTA cancer testis antigens
  • CTA are not typically expressed beyond embryonic development in healthy cells. In healthy adults, CTA expression is limited to male germ cells that do not express HLAs and cannot present antigens to T cells. Therefore, CTAs are considered expressional neoantigens when expressed in cancer cells.
  • CTA expression is (i) specific for tumor cells, (ii) more frequent in metastases than in primary tumors and (iii) conserved among metastases of the same patient (Gajewski ed. Targeted Therapeutics in Melanoma. Springer New York. 2012).
  • the polypeptide may be a mutational neoantigen, which is expressed by a cell, for example a cancer cell, of the individual, but altered from the analogous protein in a normal or healthy cell.
  • the methods of the disclosure comprise the step of identifying a polypeptide that is a mutational neoantigen, or that is a mutational neoantigen in the specific human subject, or of identifying a neoepitope.
  • the neoantigen may be present in a sample obtained from the subject.
  • Mutational neoantigens or neoepitopes can be used to target disease-associated cells, such as cancer cells, that express the neoantigen or a neoantigen comprising the neoepitope. Mutations in a polypeptide expressed by a cell, for example a cell in a sample taken from a subject, can be detected by, for example, sequencing, but the majority do not induce an immune response against the neoantigen-expressing cells.
  • the identification of mutational neoantigens that do induce an immune response is based on prediction of mutational HLA restricted epitopes and further in vitro testing of the immunogenicity of predicted epitopes in individual's blood specimen. This process is inaccurate, long and expensive.
  • the polypeptide is a mutational neoantigen
  • the immunogenic fragment of the polypeptide comprises a neoantigen specific mutation (or consists of a neoepitope).
  • the polypeptide may be a viral protein that is expressed intracellularly. Examples include HPV16 E6, E7; HIV Tat, Rev, Gag, Pol, Env; HTLV-Tax, Rex, Gag, Env, Human herpes virus proteins, Dengue virus proteins.
  • the polypeptide may be a parasite protein that is expressed intracellularly, for example malaria proteins.
  • the polypeptide may be an active ingredient of a pharmaceutical composition, such as a vaccine or immunotherapy composition, optionally a candidate active ingredient for a new pharmaceutical composition.
  • active ingredient refers to a polypeptide that is intended to induce an immune response and may include a polypeptide product of a vaccine or immunotherapy composition that is produced in vivo after administration to a subject.
  • the polypeptide may be produced in vivo by the cells of a subject to whom the composition is administered.
  • the polypeptide may be processed and/or presented by cells of the composition, for example autologous dendritic cells or antigen presenting cells pulsed with the polypeptide or comprising an expression construct encoding the polypeptide.
  • the pharmaceutical composition may comprise a polynucleotide or cell encoding one or more active ingredient polypeptides.
  • the polypeptide may be a target polypeptide antigen of a pharmaceutical, vaccine or immunotherapy composition.
  • a polypeptide is a target polypeptide antigen if the composition is intended or designed to induce an immune response (e.g. a cytotoxic T cell response) that targets or is directed at the polypeptide.
  • a target polypeptide antigen is typically a polypeptide that is expressed by a pathogenic organism, a virus or a diseased cell such as a cancer cell.
  • a target polypeptide antigens may be a TAA or a CTA. Presently, >200 clinical trials are investigating cancer vaccines with tumor antigens.
  • the polypeptide may be an allergen that enters the body of an individual through, for example, the skin, lung or oral routes.
  • Non-limiting examples of suitable polypeptides include those listed in one or more of Tables 2 to 6.
  • Genetic sequences may be obtained from the sequencing of biological materials. Sequencing can be done by any suitable method that determines DNA and/or RNA and/or amino acid sequences.
  • the disclosure utilizes both the HLA genotypes and amino acid sequences. However, methods to identify HLA genotype from genetic sequences of an individual and methods of obtaining amino acid sequences derived from DNA or RNA sequence data are not the subject of the disclosure.
  • AAA62707.1 AAA30429.1 AAA30478.1 NP_851372.1 ABW98943.1 ABW98945.1 ABW98953.1 NP_776953.1 AAA30430.1 AAA30431.1 AAB29137.1 AAA30433.1 NP_776719.1 Q28133.1 Q28050.1 CAA29664.1 AAA30615.1 CAA32835.1 AAA30413.1 P02754.3 ACG59280.1 AAA51411.1 CAA76847.1 NP_776945.1 NP_851341.1 P80207.1 P80208.1 S65144 S65145 AAN86249.1 XP_013623213.1 S65143 CAA46782.1 BAA09634.1 P69199.1 P81729.1 CAA57342.1 AAN11300.1 P30575.1 AAC48794.1 CAD82911.1 CAD82912.1 AAC48795.1 AAB30434.1 CAA76841.1 BAC10663.1 ACY38525.1 AHY24648.1 CAA68720.1 CCF72371.1 CCK33472.1 CAC
  • polypeptide antigens induce immune responses in only a fraction of human subjects.
  • diagnostic test that can predict whether a polypeptide antigen would likely induce an immune response in an individual.
  • a test that can predict whether a person is an immune responder to a vaccine or immunotherapy composition.
  • the polypeptide antigen-specific T cell response of an individual is defined by the presence within the polypeptide of one or more fragments that may be presented by multiple HLA class I or multiple HLA class II molecules of the individual.
  • the disclosure involves a method of predicting whether a subject will have an immune response to administration of a polypeptide, wherein an immune response is predicted if the polypeptide is immunogenic according to any method described herein.
  • a cytotoxic T cell response is predicted if the polypeptide comprises at least one amino acid sequence that is a T cell epitope capable of binding to at least two HLA class I molecules of the subject.
  • a helper T cell response is predicted if the polypeptide comprises at least one amino acid sequence that is a T cell epitope capable of binding to at least two HLA class II molecules of the subject.
  • No cytotoxic T cell response is predicted if the polypeptide does not comprise any amino acid sequence that is a T cell epitope capable of binding to at least two HLA class I molecules of the subject.
  • No helper T cell response is predicted if the polypeptide does not comprise any amino acid sequence that is a T cell epitope capable of binding to at least two HLA class II molecules of the subject.
  • the polypeptide is an active component of a pharmaceutical composition
  • the method comprises predicting the development or production of anti-drug antibodies (ADA) to the polypeptide.
  • the pharmaceutical composition may be a drug selected from those listed in Table 8.
  • ADA development will occur if, or to the extent that, an active component polypeptide is recognised by multiple HLA class II molecules of the subject, resulting in a helper T cell response to support an antibody response to the active component.
  • the presence of such epitopes (PEPIs) may predict the development of ADA in the subject.
  • the method may further comprise selecting or recommending for treatment of the human subject administration to the subject of a pharmaceutical composition that is predicted to induce low or no ADA, and optionally further administering the composition to the subject.
  • the method predicts that the pharmaceutical composition will induce unacceptable ADA and the method further comprises selecting or recommending or treating the subject with a different treatment or therapy.
  • the polypeptide may be a checkpoint inhibitor.
  • the method may comprise predicting whether the subject will respond to treatment with the checkpoint inhibitor.
  • Example drugs associated with ADA-related adverse events Drug ADA-related adverse event Abciximab anaphylaxis Adalimumab anti-drug antibodies and treatment failure Basiliximab anaphylaxis Cetuximab IgE, anaphlyaxis Epoetin Antibody-mediated pure red cell aplasia Erythropoietin pure red cell aplasia Etanercept no apparent effect on safety Factor-IX anaphylaxis Infliximab anaphylaxis OKT3 anaphylaxis Pegloticase anti-dug antibody, treatment failure rIFN-beta anaphylaxis recombinant factor VIII anaphylaxis Thrombopoietin thrombocitopenia Ustekinumab anti-ustekinumab antibodies, affected treatment efficacy
  • ⁇ 2 PEPI3+ The presence in a vaccine or immunotherapy composition of at least two polypeptide fragments (epitopes) that can bind to at least three HLA class I of an individual ( ⁇ 2 PEPI3+) is predictive for a clinical response. In other words, if ⁇ 2 PEPI3+ can be identified within the active ingredient polypeptide(s) of a vaccine or immunotherapy composition, then an individual is a likely clinical responder.
  • a “clinical response” or “clinical benefit” as used herein may be the prevention of or a delay in the onset of a disease or condition, the amelioration of one or more symptoms, the induction or prolonging of remission, or the delay of a relapse or recurrence or deterioration, or any other improvement or stabilisation in the disease status of a subject.
  • a “clinical response” may correlate to “disease control” or an “objective response” as defined by the Response Evaluation Criteria In Solid Tumors (RECIST) guidelines.
  • the disclosure involves a method of predicting whether the subject will have a clinical response to administration of a pharmaceutical composition such as a vaccine or immunotherapy composition comprising one or more polypeptides as active ingredients.
  • the method may comprise determining whether the one or more polypeptides together comprise at least two different sequences each of which is a T cell epitope capable of binding to at least two, or in some cases at least three HLA class I molecules of the subject; and predicting that the subject will have a clinical response to administration of the pharmaceutical composition if the one or more polypeptides together comprise at least two different sequences each of which is a T cell epitope capable of binding to at least two, or in some cases at least three HLA class I molecules of the subject; or that the subject will not have a clinical response to administration of the pharmaceutical composition if the one or more polypeptides together comprise no more that one sequence that is a T cell epitope capable of binding to at least two, or in some cases at least three HLA class I molecules of the subject.
  • two T cell epitopes are “different” from each other if they have different sequences, and in some cases also if they have the same sequence that is repeated in a target polypeptide antigen. In some cases the different T cell epitopes in a target polypeptide antigen do not overlap with one another.
  • all of the fragments of one or more polypeptides or active ingredient polypeptides that are immunogenic for a human subject are identified using the methods described herein.
  • the identification of at least one fragment of the polypeptide(s) that is a T cell epitope capable of binding to at least two, or at least three HLA class I molecules of the subject predicts that the polypeptide(s) will elicit or is likely to elicit a cytotoxic T cell response in the subject.
  • the identification of at least one fragment of the polypeptide(s) that is a T cell epitope capable of binding to at least two, or at least three, or at least four HLA class II molecules of the subject predicts that the polypeptide(s) will elicit or is likely to elicit a helper T cell response in the subject.
  • the identification of no fragments of the polypeptide(s) that are T cell epitopes capable of binding to at least two, or at least three HLA class I molecules of the subject predicts that the polypeptide(s) will not elicit or is not likely to elicit a cytotoxic T cell response in the subject.
  • the identification of no fragments of the polypeptide(s) that are T cell epitopes capable of binding to at least two, or at least three, or at least four HLA class II molecules of the subject predicts that the polypeptide(s) will not elicit or is not likely to elicit a helper T cell response in the subject.
  • the identification of at least two fragments of one or more active ingredient polypeptides of a vaccine or immunotherapy composition, wherein each fragment is a T cell epitope capable of binding to at least two, or at least three HLA class I molecules of the subject predicts that the subject is more likely to have, or will have a clinical response to the composition.
  • the identification of less than two fragments of the one or more polypeptides that are T cell epitopes capable of binding to at least two, or at least three HLA class I molecules of the subject predicts that the subject is less likely to have, or will not have, a clinical response to the composition.
  • one reason for the increased likelihood of deriving clinical benefit from a vaccine/immunotherapy comprising at least two multiple-HLA binding PEPIs is that diseased cell populations, such as cancer or tumor cells or cells infected by viruses or pathogens such as HIV, are often heterogenous both within and between affected subjects.
  • a specific cancer patient for example, may or may not express or overexpress a particular cancer associated target polypeptide antigen of a vaccine, or their cancer may comprise heterogeneous cell populations, some of which (over-)express the antigen and some of which do not.
  • the likelihood of developing resistance is decreased when more multiple HLA-binding PEPIs are included or targeted by a vaccine/immunotherapy because a patient is less likely to develop resistance to the composition through mutation of the target PEPI(s).
  • the likelihood that a subject will respond to treatment is therefore increased by (i) the presence of more multiple HLA-binding PEPIs in the active ingredient polypeptides; (ii) the presence of PEPIs in more target polypeptide antigens; and (iii) (over-)expression of the target polypeptide antigens in the subject or in diseased cells of the subject.
  • expression of the target polypeptide antigens in the subject may be known, for example if target polypeptide antigens are in a sample obtained from the subject.
  • the probability that a specific subject, or diseased cells of a specific subject, (over-)express a specific or any combination of target polypeptide antigens may be determined using population expression frequency data.
  • the population expression frequency data may relate to a subject- and/or disease-matched population or the intent-to-treat population.
  • the frequency or probability of expression of a particular cancer-associated antigen in a particular cancer or subject having a particular cancer, for example breast cancer can be determined by detecting the antigen in tumor, e.g. breast cancer tumor samples.
  • such expression frequencies may be determined from published figures and scientific publications.
  • a method of the invention comprises a step of determining the expression frequency of a relevant target polypeptide antigen in a relevant population.
  • biomarkers Disclosed is a range of pharmacodynamic biomarkers to predict the activity/effect of vaccines in individual human subjects as well as in populations of human subjects.
  • the biomarkers have been developed specifically for cancer vaccines, but similar biomarkers could be used for other vaccines or immunotherapy compositions. These biomarkers expedite more effective vaccine development and also decrease the development cost and may be used to assess and compare different compositions.
  • Exemplary biomarkers are as follows.
  • the results of a prediction as set out above may be used to inform a physician's decisions concerning treatment of the subject.
  • the polypeptide is an active ingredient, for example of a vaccine or immunotherapy composition
  • the method of the disclosure predicts that the subject will have, is likely to have, or has above a threshold minimum likelihood of having an immune response and/or a clinical response to a treatment comprising administering the active ingredient polypeptide to the subject, and the method further comprises selecting the treatment for or selecting the vaccine or immunotherapy composition for treatment of the specific human subject.
  • kits or panel of polypeptides comprising one or more polypeptides as active ingredients, wherein the pharmaceutical composition, kit or panel of polypeptides has been determined to have a threshold minimum likelihood of inducing a clinical response in the subject, wherein the likelihood of response has been determined using a method described herein.
  • a minimum PEPI3+ count for example 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 or more PEPI3+
  • a subject is selected for treatment if their likelihood of a response targeted at a predefined number of target polypeptide antigens, optionally wherein the target polypeptide antigens are (predicted to be) expressed, is above a predetermined threshold (e.g. 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 or more).
  • a predetermined threshold e.g. 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 or more.
  • the method may predict that the one or more polypeptide(s) of the composition will not elicit a T cell response and/or a clinical response in the subject and further comprise selecting a different treatment for the subject.
  • the differences among HLAs may influence the probability that a subject will experience immune-toxicity from a drug or polypeptide administered to the subject.
  • There may be a toxic immune response if a polypeptide administered to the subject comprises a fragment that corresponds to a fragment of an antigen expressed in normal healthy cells of the subject and that comprises an amino acid that is a T cell epitope capable of binding to multiple HLA class I molecules of the subject. Therefore, some cases in accordance with the disclosure, involve identifying a toxic immunogenic region or fragment of a polypeptide or identifying subjects who are likely to experience immune-toxicity in response to administration of one or more polypeptides or a fragments thereof.
  • the polypeptide may be an active ingredient of a vaccine or immunotherapy composition as described herein.
  • the method may comprise determining whether the polypeptide(s) comprises a sequence that is a T cell epitope capable of binding to at least two, or in other cases to at least three HLA class I molecules of the subject. In some cases the method comprises determining that the polypeptide comprises a sequence that is a T cell epitope capable of binding to at least four, or at least five HLA class I molecules of the subject; or an amino acid sequence that is a T cell epitope capable of binding to at least four, or at least five, or at least six or at least seven HLA class II of the subject. The method may further comprise identifying said sequence as toxic immunogenic for the subject or predicting a toxic immune response in the subject.
  • the method further comprises predicting no toxic immune response in the subject.
  • the method may further comprise selecting or recommending for treatment of the subject administration of one or more polypeptides or a pharmaceutical composition that is predicted to induce no or low immune-toxicity, and optionally further treating the subject by administering the polypeptide.
  • the disclosure also provides a method of treating a subject in need thereof by administrating to the subject such a polypeptide or composition.
  • a method described herein further comprises mutating a polypeptide that is predicted to be immunogenic for a subject, or that is predicted to be immunogenic in a proportion of subjects in a human population. Also provided is a method of reducing the immunogenicity of a polypeptide that has been identified as immunogenic in a subject or in a proportion of a human population as described herein.
  • the polypeptide may be mutated to reduce the number of PEPIs in the polypeptide or to reduce the number of HLA class I or class II molecules of the subject or of said population that bind to the fragment of the polypeptide that is identified as immunogenic in the subject or in a proportion of said population.
  • the mutation may reduce or prevent a toxic immune response or may increase the efficacy by preventing the ADA development in the subject or in a proportion of said population.
  • the mutated polypeptide may be further selected or recommended for treatment of the subject or of a subject of said population.
  • the subject may further be treated by administration of the mutated polypeptide.
  • the disclosure also provides a method of treating a subject in need thereof by administrating to the subject such a mutated polypeptide.
  • the methods described herein may be used to predict the response or response rate of a wider human population to administration of one or more polypeptides or compositions comprising one or more polypeptides.
  • a method of the disclosure may be repeated for a plurality of human subjects to predict the response or response rate in those subjects.
  • the method of the disclosure may be repeated for each subject in a relevant sample or model population of subjects and the results used to predict or define the response or response rate in a broader human population represented by the sample or model population.
  • the sample/model population may be relevant to the intent-to-treat population for a pharmaceutical composition.
  • a relevant population is one that is representative or similar to the population for whom or amongst whom treatment with the pharmaceutical composition is intended.
  • the sample/model population is representative for the whole human race.
  • the sample/model population may be disease- or subject-matched to the broader population (subpopulation), for example by ethnicity, geographical location, gender, age, disease or cancer, disease or cancer type or stage, genotype, expression of one or more biomarkers, partially by HLA genotype (for example subjects have one or more particular HLA alleles).
  • the sample/model population may have HLA class I and/or class II genomes that are representative of those found in the world population, or in subjects having a particular disease or condition, or ethnic background, from a particular geographical location, or having a particular disease-associated biomarker (for example, women having the BRCA mutation for a breast cancer vaccine).
  • the sample/model population is representative for at least 70%, or 75% or 80% or 84% or 85% or 86% or 90% or 95% of the broader population by HLA diversity and/or HLA frequency.
  • the method may comprise the step of selecting or defining a relevant sample or model population.
  • Each subject in the sample/model population is minimally defined by their HLA class I or class II genotype, e.g. complete 4-digit HLA class I genotype.
  • Data concerning the HLA genotype of the sample/model population may be stored or recorded in or retrieved from a database or be an in silico model human population.
  • the methods described herein may be used to conduct an in silico clinical trial that predicts the proportion of immune-responders or the proportion of clinical responders in a population for a given drug, such as a vaccine or immunotherapy composition. This is useful for pre-selecting drugs that are likely to have high rates of efficacy to undergo clinical testing.
  • a population of individuals or a subpopulation of individuals can comprise the study cohort of an in silico clinical trial conducted with a drug. Each individual in the study cohort is characterized by its HLA genotype.
  • the proportion of individuals in the study cohort having ⁇ 1 PEPI2+, or ⁇ 1 PEPI3+, or ⁇ 1 PEPI4+, or ⁇ 1 PEPI5+, derived from the polypeptides of the drug may be calculated.
  • the “PEPI Score” refers specifically to the ⁇ 1 PEPI3+ Score. This PEPI Score predicts the proportion of subjects with T cell responses in a clinical trial conducted with the same drug in a relevant cohort of subjects.
  • the disclosure provides a method of conducting an in silico trial for a vaccine or immunotherapy composition having one or more polypeptide active ingredients.
  • the in silico trial may predict the cytotoxic T cell response rate of a human population.
  • the method may comprise: (i) selecting or defining an in silico model human population comprising a plurality of subjects each defined by HLA class I genotype, wherein the in silico model human population may correspond to or be representative of, or relevant to the intend-to-treat, said human population in which the cytotoxic T cell response rate is to be predicted; (ii) determining for each subject in the in silico model human population whether the one or more active ingredient polypeptides comprise at least one sequence that is PEPI2+, PEPI3+, PEPI4+ or PEPI5+(depending the size, administration route and adjuvants of the polypeptide composition); and (iii) predicting the cytotoxic T cell response rate (of said human population), wherein a higher proportion of the in silico model human
  • the in silico trial may predict the clinical response rate of a human population.
  • the method may comprise (i) selecting or defining an in silico model human population comprising a plurality of subjects defined by HLA class I genotype, wherein the in silico model human population may correspond to or be representative of said human population (relevant to the intend-to-treat population) in which the clinical response rate is to be predicted; (ii) determining for each subject in the in silico model human population whether the one or more active ingredient polypeptides comprise at least two different sequences each of which is a T cell epitope capable of binding to at least three, or at least four, or at least five HLA class I of the subject; and (iii) predicting the clinical response rate (of said human population), wherein a higher proportion of the in silico model human population that meet the requirements of step (ii) predicts a higher clinical response rate
  • An equivalent method may be used to predict, for example, the immune toxicity rate, checkpoint inhibitor response rate, ADA development rate, or helper T cell response rate of a human population (or subpopulation) to administration of a polypeptide or pharmaceutical composition comprising one or more polypeptides as active ingredients.
  • the method may be repeated for one or more further polypeptides or fragments thereof or vaccine or pharmaceutical or immunotherapy compositions.
  • the polypeptides, fragments or compositions may be ranked according to their predicted response rates in said human population. This method is useful for selecting the most effective or most safe polypeptide drugs for the intent-to-treat population.
  • the disclosure provides a method of designing or preparing a polypeptide, or a polynucleic acid that encodes a polypeptide, for inducing an immune response, a cytotoxic T cell response or a helper T cell response in a human subject (e.g. in a target or intent-to-treat population).
  • the disclosure also provides an immunogenic composition, or pharmaceutical composition, kit or panel of peptides, methods of designing or preparing the same, compositions that may be obtained by those methods, and their use in a method of inducing an immune response, a cytotoxic T cell response, or a helper T cell response in the subject, or a method of treating, vaccinating or providing immunotherapy to a subject.
  • the methods involve identifying and/or selecting a T cell epitope that binds to multiple, e.g. at least three HLA class I molecules of individual subjects across the target population with a high frequency, and designing or/or preparing a polypeptide that comprises one or more such epitopes (PEPI3+s).
  • PEPI3+s Such high frequency population PEPI3+s may be referred to herein as “bestEPIs”.
  • BestEPIs induce immune responses in a high proportion of human subjects in the specific or target human population.
  • the polypeptide may be an active ingredient in a pharmaceutical composition or kit or panel of polypeptides for use in a method of treatment of a subject of the specific or target human population.
  • composition/kit may optionally further comprise at least one pharmaceutically acceptable diluent, carrier, or preservative and/or additional polypeptides that do not comprise any bestEPIs.
  • the polypeptides may be engineered or non-naturally occurring.
  • the kit may comprise one or more separate containers each containing one or more of the active ingredient peptides.
  • the composition/kit may be a personalised medicine to prevent, diagnose, alleviate, treat, or cure a disease of an individual, such as a cancer.
  • the bestEPI is capable of binding to multiple, for example to at least three HLA class I and/or to at least three HLA class II molecules of a high percentage of the subjects in a sample or model population, such as described herein.
  • a “high” percentage may be at least or more than 1%, 2%, 5%, 10%, 12%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49% or 50% of the relevant population or subpopulation of human subjects.
  • a “high” percentage is relative to the percentage of subjects in the population having other PEPI3+s.
  • the PEPI3+ may be the most frequent in the population, or more frequent than 50%, or 55% or 60% or 65% or 70% or 75% or 80% or 85% or 90% or 95% or 97% or 99% of all PEPI3+ and/or PEPI4+ and/or PEPI4+ in one or more reference target polypeptide antigens.
  • the probability that the target polypeptide antigen is expressed in a subject of the specific or target population is taken into account to determine the overall likelihood that the bestEPI will induce an immune response that targets a polypeptide antigen that is expressed by a subject of the specific or target human population.
  • the bestEPI is predicted to express both the relevant target polypeptide antigen and multiple, for example at least three HLA class I or at least three HLA class II molecules capable of binding to the bestEPI in at least or more than 1%, 2%, 5%, 10%, 12%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49% or 50% of the relevant population of human subjects.
  • multiple T cell epitopes/PEPI3+s optionally from one or more target polypeptide antigens may be ranked by the percentage of subjects in the model or intend-to-treat population having multiple, for example at least three HLA class I or at least three HLA class II molecules capable of binding to each fragment; or by the percentage of subjects in the model or intend-to-treat population that are predicted to express both the target polypeptide antigen comprising the fragment and multiple, for example at least three HLA class I or at least three HLA class II molecules capable of binding to the fragments.
  • the peptide or composition may be designed to comprise one or more PEPI3+s that are selected based on their ranking.
  • each bestEPI is a fragment of a target polypeptide antigen and polypeptides that comprise one or more of the bestEPIs are the target polypeptide antigens for the treatment, vaccination or immunotherapy.
  • the method may comprise the step of identifying one or more suitable target polypeptide antigens.
  • each target polypeptide antigen will be associated with the same disease or condition, pathogenic organism or group of pathogenic organisms or virus, or type of cancer.
  • composition, kit or panel may comprise, or the method may comprise selecting, for each bestEPI a sequence of up to 50, 45, 40, 35, 30, 25, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10 or 9 consecutive amino acids of the target polypeptide antigen, such as a polypeptide described herein, which consecutive amino acids comprise the amino acid sequence of the bestEPI.
  • amino acid sequence is flanked at the N and/or C terminus by additional amino acids that are not part of the consecutive sequence of the target polypeptide antigen. In some cases the sequence is flanked by up to 41 or 35 or 30 or 25 or 20 or 15 or 10, or 9 or 8 or 7 or 6 or 5 or 4 or 3 or 2 or 1 additional amino acid at the N and/or C terminus or between target polypeptide fragments.
  • each polypeptide either consists of a fragment of a target polypeptide antigen, or consists of two or more such fragments arranged end to end (arranged sequentially in the peptide end to end) or overlapping in a single peptide (where two or more of the fragments comprise partially overlapping sequences, for example where two bestEPIs in the same polypeptide are within 50 amino acids of each other).
  • neoepitopes When fragments of different polypeptides or from different regions of the same polypeptide are joined together in an engineered peptide there is the potential for neoepitopes to be generated around the join or junction.
  • Such neoepitopes encompass at least one amino acid from each fragment on either side of the join or junction, and may be referred to herein as junctional amino acid sequences.
  • the neoepitopes may induce undesired T cell responses against healthy cells (autoimmunity).
  • the peptides may be designed, or the polypeptides may be screened, to avoid, eliminate or minimise neoepitopes that correspond to a fragment of a protein expressed in normal healthy human cells and/or neoepitopes that are capable of binding to at least two, or in some cases at least three, or at least four HLA class I molecules of the subject, or in some cases at least two, or at least three or four or five HLA class II molecules of the subject.
  • the peptide is designed, or the polypeptide screened, to eliminate polypeptides having a junctional neoepitope that is capable of binding in more than a threshold percentage of human subjects in a specific, target or model population, to at least two HLA class I molecules expressed by individual subjects of the population.
  • the threshold is 30%, or 20%, or 15%, or 10%, or 5%, or 2%, or 1%, or 0.5% of said population.
  • the methods of the disclosure may be used to identify or screen for such neoepitopes as described herein. Alignment may be determined using known methods such as BLAST algorithms. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/).
  • the at least two bestEPIs of the composition polypeptides may both target a single antigen (e.g a polypeptide vaccine comprising two multiple HLA-binding PEPIs derived from a single antigen, for example a tumor associated antigen, targeted by the vaccine/immunotherapy) or may target different antigens (e.g. a polypeptide vaccine comprising one multiple HLA-binding PEPI derived from one antigen, e.g. a tumor associated antigen, and a second multiple HLA-binding PEPI derived from a different antigen, e.g. a different tumor associated antigen, both targeted by the vaccine/immunotherapy).
  • a single antigen e.g a polypeptide vaccine comprising two multiple HLA-binding PEPIs derived from a single antigen, for example a tumor associated antigen, targeted by the vaccine/immunotherapy
  • different antigens e.g. a polypeptide vaccine comprising one multiple HLA-binding PEPI
  • the active ingredient polypeptide(s) together comprise, or the method comprises selecting, a total of or at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 or more different bestEPIs.
  • the bestEPIs may be fragments of one or more different target polypeptide antigens.
  • each target polypeptide antigen that are immunogenic for a high proportion of subjects in a target population it is possible to incorporate multiple such fragments, optionally from multiple different target polypeptide antigens, in a single active ingredient polypeptide or multiple active ingredient polypeptides intended for use in combination or to maximise the number of T cell clones that can be activated by one or more polypeptides of a certain length.
  • exemplary CTA expression probabilities in breast cancer are as follows: MAGE C2: 21%; MAGE A1: 37%; SPC1: 38%; MAGE A9: 44%.
  • Treatment of patient ABC with a vaccine comprising PEPIs in only MAGE C2: 21% and MAGE A1 has a mAGP probability of 7%.
  • Treatment of patient ABC with a vaccine comprising PEPIs in only SPC1: 38%; MAGE A9 has a mAGP probability of 11%.
  • Treatment of patient ABC with a vaccine comprising PEPIs in MAGE C2: 21%; MAGE A1: 37%; SPC1: 38%; MAGE A9 has a mAGP probability of 44% (44>7+11).
  • Patient ABC's PIT vaccine described in Example 16 contains a further 8 PEPIs, and thus, the probability of having a mAGP is over 99.93%.
  • the bestEPIs of the active ingredient polypeptides are from two or more different target polypeptide antigens, for example different antigens associated with a specific disease or condition, for example different cancer- or tumor-associated antigens or antigens expressed by a target pathogen.
  • the PEPIs are from a total of or at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 or more different target polypeptide antigens.
  • the different target polypeptide antigens may be any different polypeptides that it is useful to target or that can be selectively targeted with different PEPI3+s.
  • different target polypeptide antigens are non-homologues or non-paralogues or have less than 95%, or 90%, or 85% or 80% or 75% or 70% or 60% or 50% sequence identity across the full length of each polypeptide.
  • different polypeptides are those that do not share any PEPI3+s.
  • the PEPI3+s are from different target polypeptide antigens when they are not shared with other polypeptide antigens targeted by the active ingredient polypeptides.
  • one or more or each of the immunogenic polypeptide fragments is from a polypeptide that is present in a sample taken from a human subject (e.g., of the target population). This indicates that the polypeptide is expressed in the subject, for example a cancer- or tumor-associated antigen or a cancer testis antigen expressed by cancer cells of the subject.
  • one or more or each of the polypeptides is a mutational neoantigen, or an expressional neoantigen of the subject.
  • One or more or each fragment may comprise a neoantigen specific mutation.
  • one or more or each of the immunogenic polypeptide fragments is from a target polypeptide antigen that is not generally expressed or is minimally expressed in normal healthy cells or tissue, but is expressed in a high proportion of (with a high frequency in) subjects or in the diseased cells of a subject having a particular disease or condition, as described above.
  • the method my comprise identifying or selecting such a target polypeptide antigen.
  • two or more or each of the immunogenic polypeptide fragments/bestEPIs are from different cancer- or tumor-associated antigens that are each (over-)expressed with a high frequency in subjects having a type of cancer or a cancer derived from a particular cell type or tissue.
  • the immunogenic polypeptide fragments are from a total of or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 different cancer- or tumor-associated polypeptides.
  • one or more or each or at least one, at least two, at least three, at least four, at least five or at least six or at least seven of the polypeptides are selected from the antigens listed in any one of Tables 2 to 7.
  • one or more or each of the target polypeptide antigens is a cancer testis antigen (CTA).
  • CTA cancer testis antigen
  • the immunogenic polypeptide fragments/bestEPIs are from at least 1, or at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 CTAs, or from a total of 3 or more different target polypeptide antigens, optionally wherein 1, 2, or all three or at least three are CTAs, or from 4 or more different polypeptide antigens, optionally wherein 1, 2, 3 or all four or at least 1, 2, 3 or 4 are CTAs, or from 5 or more different polypeptide antigens, optionally wherein 1, 2, 3, 4 or all five or at least 1, 2, 3, 4, or 5 are CTAs, or from 6 or more different polypeptide antigens, optionally wherein 1, 2, 3, 4, 5 or all six or at least 1, 2, 3, 4, 5, or 6 are CTAs, or from 7 or more different polypeptide antigens, optionally wherein
  • one or more of the polypeptide fragments comprises an amino acid sequence that is a T cell epitope capable of binding to at least two, or at least three HLA class I of a high percentage of subjects in the population subject and one or more of the polypeptide fragments comprises an amino acid sequence that is a T cell epitope capable of binding to at least two, or at least three, or at least four HLA class II of the subject of a high percentage of subjects in the population, wherein the HLA class I and HLA class II binding fragments may optionally overlap.
  • a composition prepared by such a method may elicit both a cytotoxic T cell response and a helper T cell response in the subject.
  • the disclosure relates to a pharmaceutical composition, kit, or panels of polypeptides as described above having one or more polypeptides as active ingredient(s). These may be for use in a method of inducing an immune response, treating, vaccinating or providing immunotherapy to a subject, and the pharmaceutical composition may be a vaccine or immunotherapy composition.
  • a treatment comprises administering one or more polypeptides or pharmaceutical compositions that together comprise all of the active ingredient polypeptides of the treatment to the subject.
  • Multiple polypeptides or pharmaceutical compositions may be administered together or sequentially, for example all of the pharmaceutical compositions or polypeptides may be administered to the subject within a period of 1 year, or 6 months, or 3 months, or 60 or 50 or 40 or 30 days.
  • the immunogenic or pharmaceutical compositions or kits described herein may comprise, in addition to one or more immunogenic peptides, a pharmaceutically acceptable excipient, carrier, diluent, buffer, stabiliser, preservative, adjuvant or other materials well known to those skilled in the art. Such materials are preferably non-toxic and preferably do not interfere with the pharmaceutical activity of the active ingredient(s).
  • the pharmaceutical carrier or diluent may be, for example, water containing solutions. The precise nature of the carrier or other material may depend on the route of administration, e.g. oral, intravenous, cutaneous or subcutaneous, nasal, intramuscular, intradermal, and intraperitoneal routes.
  • the pharmaceutical compositions of the disclosure may comprise one or more “pharmaceutically acceptable carriers”. These are typically large, slowly metabolized macromolecules such as proteins, saccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, sucrose (Paoletti et al., 2001, Vaccine, 19:2118), trehalose (WO 00/56365), lactose and lipid aggregates (such as oil droplets or liposomes). Such carriers are well known to those of ordinary skill in the art.
  • the pharmaceutical compositions may also contain diluents, such as water, saline, glycerol, etc.
  • auxiliary substances such as wetting or emulsifying agents, pH buffering substances, and the like, may be present.
  • Sterile pyrogen-free, phosphate buffered physiologic saline is a typical carrier (Gennaro, 2000, Remington: The Science and Practice of Pharmacy, 20th edition, ISBN:0683306472).
  • compositions of the disclosure may be lyophilized or in aqueous form, i.e. solutions or suspensions. Liquid formulations of this type allow the compositions to be administered direct from their packaged form, without the need for reconstitution in an aqueous medium, and are thus ideal for injection.
  • the pharmaceutical compositions may be presented in vials, or they may be presented in ready filled syringes. The syringes may be supplied with or without needles. A syringe will include a single dose, whereas a vial may include a single dose or multiple doses.
  • Liquid formulations of the disclosure are also suitable for reconstituting other medicaments from a lyophilized form.
  • the disclosure provides a kit, which may comprise two vials, or may comprise one ready-filled syringe and one vial, with the contents of the syringe being used to reconstitute the contents of the vial prior to injection.
  • compositions of the disclosure may include an antimicrobial, particularly when packaged in a multiple dose format.
  • Antimicrobials may be used, such as 2-phenoxyethanol or parabens (methyl, ethyl, propyl parabens).
  • Any preservative is preferably present at low levels.
  • Preservative may be added exogenously and/or may be a component of the bulk antigens which are mixed to form the composition (e.g. present as a preservative in pertussis antigens).
  • compositions of the disclosure may comprise detergent e.g. Tween (polysorbate), DMSO (dimethyl sulfoxide), DMF (dimethylformamide).
  • Detergents are generally present at low levels, e.g. ⁇ 0.01%, but may also be used at higher levels, e.g. 0.01-50%.
  • compositions of the disclosure may include sodium salts (e.g. sodium chloride) and free phosphate ions in solution (e.g. by the use of a phosphate buffer).
  • sodium salts e.g. sodium chloride
  • free phosphate ions e.g. by the use of a phosphate buffer.
  • the pharmaceutical composition may be encapsulated in a suitable vehicle either to deliver the peptides into antigen presenting cells or to increase the stability.
  • a suitable vehicle is suitable for delivering a pharmaceutical composition of the disclosure.
  • suitable structured fluid delivery systems may include nanoparticles, liposomes, microemulsions, micelles, dendrimers and other phospholipid-containing systems. Methods of incorporating pharmaceutical compositions into delivery vehicles are known in the art.
  • the pharmacological compositions may comprise one or more adjuvants and/or cytokines.
  • Suitable adjuvants include an aluminum salt such as aluminum hydroxide or aluminum phosphate, but may also be a salt of calcium, iron or zinc, or may be an insoluble suspension of acylated tyrosine, or acylated sugars, or may be cationically or anionically derivatised saccharides, polyphosphazenes, biodegradable microspheres, monophosphoryl lipid A (MPL), lipid A derivatives (e.g.
  • 3-O-deacylated MPL [3D-MPL], quil A, Saponin, QS21, Freund's Incomplete Adjuvant (Difco Laboratories, Detroit, Mich.), Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.), AS-2 (Smith-Kline Beecham, Philadelphia, Pa.), CpG oligonucleotides, bioadhesives and mucoadhesives, microparticles, liposomes, polyoxyethylene ether formulations, polyoxyethylene ester formulations, muramyl peptides or imidazoquinolone compounds (e.g. imiquamod and its homologues).
  • Human immunomodulators suitable for use as adjuvants in the disclosure include cytokines such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc), macrophage colony stimulating factor (M-CSF), tumour necrosis factor (TNF), granulocyte, macrophage colony stimulating factor (GM-CSF) may also be used as adjuvants.
  • cytokines such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc)
  • M-CSF macrophage colony stimulating factor
  • TNF tumour necrosis factor
  • GM-CSF macrophage colony stimulating factor
  • the compositions comprise an adjuvant selected from the group consisting of Montanide ISA-51 (Seppic, Inc., Fairfield, N.J., United States of America), QS-21 (Aquila Biopharmaceuticals, Inc., Lexington, Mass., United States of America), GM-CSF, cyclophosamide, bacillus Calmette-Guerin (BCG), corynbacterium parvum , levamisole, azimezone, isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freunds adjuvant (complete and incomplete), mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions, oil emulsions, dinitrophenol, diphtheria toxin (DT).
  • Montanide ISA-51 Seppic, Inc., Fairfield, N.J., United States of America
  • QS-21 Amla Biopharmaceuticals, Inc.
  • the cytokine may be selected from the group consisting of a transforming growth factor (TGF) such as but not limited to TGF- ⁇ and TGF- ⁇ ; insulin-like growth factor-I and/or insulin-like growth factor-II; erythropoietin (EPO); an osteoinductive factor; an interferon such as but not limited to interferon-. ⁇ , - ⁇ , and - ⁇ ; a colony stimulating factor (CSF) such as but not limited to macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF).
  • TGF transforming growth factor
  • TGF- ⁇ and TGF- ⁇ insulin-like growth factor-I and/or insulin-like growth factor-II
  • EPO erythropoietin
  • an osteoinductive factor such as but not limited to interferon-. ⁇ , - ⁇ , and - ⁇
  • CSF colony stimulating factor
  • the cytokine is selected from the group consisting of nerve growth factors such as NGF- ⁇ ; platelet-growth factor; a transforming growth factor (TGF) such as but not limited to TGF- ⁇ . and TGF- ⁇ ; insulin-like growth factor-I and insulin-like growth factor-II; erythropoietin (EPO); an osteoinductive factor; an interferon (IFN) such as but not limited to IFN- ⁇ , IFN- ⁇ , and IFN- ⁇ ; a colony stimulating factor (CSF) such as macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF); an interleukin (II) such as but not limited to IL-1, IL-1.alpha., IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12;
  • TGF
  • an adjuvant or cytokine can be added in an amount of about 0.01 mg to about 10 mg per dose, preferably in an amount of about 0.2 mg to about 5 mg per dose.
  • the adjuvant or cytokine may be at a concentration of about 0.01 to 50%, preferably at a concentration of about 2% to 30%.
  • compositions of the disclosure are prepared by physically mixing the adjuvant and/or cytokine with the PEPIs under appropriate sterile conditions in accordance with known techniques to produce the final product.
  • Vaccine and immunotherapy composition preparation is generally described in Vaccine Design (“The subunit and adjuvant approach” (eds Powell M. F. & Newman M. J. (1995) Plenum Press New York). Encapsulation within liposomes, which is also envisaged, is described by Fullerton, U.S. Pat. No. 4,235,877.
  • the compositions disclosed herein are prepared as a nucleic acid vaccine.
  • the nucleic acid vaccine is a DNA vaccine.
  • DNA vaccines, or gene vaccines comprise a plasmid with a promoter and appropriate transcription and translation control elements and a nucleic acid sequence encoding one or more polypeptides of the disclosure.
  • the plasmids also include sequences to enhance, for example, expression levels, intracellular targeting, or proteasomal processing.
  • DNA vaccines comprise a viral vector containing a nucleic acid sequence encoding one or more polypeptides of the disclosure.
  • compositions disclosed herein comprise one or more nucleic acids encoding peptides determined to have immunoreactivity with a biological sample.
  • the compositions comprise one or more nucleotide sequences encoding 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more peptides comprising a fragment that is a T cell epitope capable of binding to at least three HLA class I molecules and/or at least three HLA class II molecules of a patient.
  • the peptides are derived from an antigen that is expressed in cancer.
  • the DNA or gene vaccine also encodes immunomodulatory molecules to manipulate the resulting immune responses, such as enhancing the potency of the vaccine, stimulating the immune system or reducing immunosuppression.
  • Immunomodulatory molecules to manipulate the resulting immune responses, such as enhancing the potency of the vaccine, stimulating the immune system or reducing immunosuppression.
  • Strategies for enhancing the immunogenicity of DNA or gene vaccines include encoding of xenogeneic versions of antigens, fusion of antigens to molecules that activate T cells or trigger associative recognition, priming with DNA vectors followed by boosting with viral vector, and utilization of immunomodulatory molecules.
  • the DNA vaccine is introduced by a needle, a gene gun, an aerosol injector, with patches, via microneedles, by abrasion, among other forms. In some forms the DNA vaccine is incorporated into liposomes or other forms of nanobodies.
  • the DNA vaccine includes a delivery system selected from the group consisting of a transfection agent; protamine; a protamine liposome; a polysaccharide particle; a cationic nanoemulsion; a cationic polymer; a cationic polymer liposome; a cationic nanoparticle; a cationic lipid and cholesterol nanoparticle; a cationic lipid, cholesterol, and PEG nanoparticle; a dendrimer nanoparticle.
  • the DNA vaccines is administered by inhalation or ingestion.
  • the DNA vaccine is introduced into the blood, the thymus, the pancreas, the skin, the muscle, a tumor, or other sites.
  • the compositions disclosed herein are prepared as an RNA vaccine.
  • the RNA is non-replicating mRNA or virally derived, self-amplifying RNA.
  • the non-replicating mRNA encodes the peptides disclosed herein and contains 5′ and 3′ untranslated regions (UTRs).
  • the virally derived, self-amplifying RNA encodes not only the peptides disclosed herein but also the viral replication machinery that enables intracellular RNA amplification and abundant protein expression.
  • the RNA is directly introduced into the individual.
  • the RNA is chemically synthesized or transcribed in vitro.
  • the mRNA is produced from a linear DNA template using a T7, a T3, or an Sp6 phage RNA polymerase, and the resulting product contains an open reading frame that encodes the peptides disclosed herein, flanking UTRs, a 5′ cap, and a poly(A) tail.
  • various versions of 5′ caps are added during or after the transcription reaction using a vaccinia virus capping enzyme or by incorporating synthetic cap or anti-reverse cap analogues.
  • an optimal length of the poly(A) tail is added to mRNA either directly from the encoding DNA template or by using poly(A) polymerase.
  • the RNA encodes one or more peptides comprising a fragment that is a T cell epitope capable of binding to at least three HLA class I and/or at least three HLA class II molecules of a patient.
  • the fragments are derived from an antigen that is expressed in cancer.
  • the RNA includes signals to enhance stability and translation.
  • the RNA also includes unnatural nucleotides to increase the half-life or modified nucleosides to change the immunostimulatory profile.
  • the RNAs is introduced by a needle, a gene gun, an aerosol injector, with patches, via microneedles, by abrasion, among other forms.
  • the RNA vaccine is incorporated into liposomes or other forms of nanobodies that facilitate cellular uptake of RNA and protect it from degradation.
  • the RNA vaccine includes a delivery system selected from the group consisting of a transfection agent; protamine; a protamine liposome; a polysaccharide particle; a cationic nanoemulsion; a cationic polymer; a cationic polymer liposome; a cationic nanoparticle; a cationic lipid and cholesterol nanoparticle; a cationic lipid, cholesterol, and PEG nanoparticle; a dendrimer nanoparticle; and/or naked mRNA; naked mRNA with in vivo electroporation; protamine-complexed mRNA; mRNA associated with a positively charged oil-in-water cationic nanoemulsion; mRNA associated with a chemically modified dendrimer and complexed with polyethylene glycol (PEG)-lipid; protamine-com
  • PEG poly
  • the RNA vaccine is administered by inhalation or ingestion.
  • the RNA is introduced into the blood, the thymus, the pancreas, the skin, the muscle, a tumor, or other sites, and/or by an intradermal, intramuscular, subcutaneous, intranasal, intranodal, intravenous, intrasplenic, intratumoral or other delivery route.
  • Polynucleotide or oligonucleotide components may be naked nucleotide sequences or be in combination with cationic lipids, polymers or targeting systems. They may be delivered by any available technique.
  • the polynucleotide or oligonucleotide may be introduced by needle injection, preferably intradermally, subcutaneously or intramuscularly.
  • the polynucleotide or oligonucleotide may be delivered directly across the skin using a delivery device such as particle-mediated gene delivery.
  • the polynucleotide or oligonucleotide may be administered topically to the skin, or to mucosal surfaces for example by intranasal, oral, or intrarectal administration.
  • Uptake of polynucleotide or oligonucleotide constructs may be enhanced by several known transfection techniques, for example those including the use of transfection agents.
  • transfection agents include cationic agents, for example, calcium phosphate and DEAE-Dextran and lipofectants, for example, lipofectam and transfectam.
  • the dosage of the polynucleotide or oligonucleotide to be administered can be altered.
  • Administration is typically in a “prophylactically effective amount” or a “therapeutically effective amount” (as the case may be, although prophylaxis may be considered therapy), this being sufficient to result in a clinical response or to show clinical benefit to the individual, e.g. an effective amount to prevent or delay onset of the disease or condition, to ameliorate one or more symptoms, to induce or prolong remission, or to delay relapse or recurrence.
  • the dose may be determined according to various parameters, especially according to the substance used; the age, weight and condition of the individual to be treated; the route of administration; and the required regimen.
  • the amount of antigen in each dose is selected as an amount which induces an immune response.
  • a physician will be able to determine the required route of administration and dosage for any particular individual.
  • the dose may be provided as a single dose or may be provided as multiple doses, for example taken at regular intervals, for example 2, 3 or 4 doses administered hourly.
  • peptides, polynucleotides or oligonucleotides are typically administered in the range of 1 pg to 1 mg, more typically 1 pg to 10 ⁇ g for particle mediated delivery and 1 ⁇ g to 1 mg, more typically 1-100 ⁇ g, more typically 5-50 ⁇ g for other routes.
  • each dose will comprise 0.01-3 mg of antigen.
  • An optimal amount for a particular vaccine can be ascertained by studies involving observation of immune responses in subjects.
  • more than one peptide or composition of peptides is administered.
  • Two or more pharmaceutical compositions may be administered together/simultaneously and/or at different times or sequentially.
  • the disclosure includes sets of pharmaceutical compositions and uses thereof.
  • the use of combination of different peptides, optionally targeting different antigens, is important to overcome the challenges of genetic heterogeneity of tumors and HLA heterogeneity of individuals.
  • the use of peptides of the disclosure in combination expands the group of individuals who can experience clinical benefit from vaccination.
  • Multiple pharmaceutical compositions of PEPIs, manufactured for use in one regimen, may define a drug product.
  • Routes of administration include but are not limited to intranasal, oral, subcutaneous, intradermal, and intramuscular.
  • the subcutaneous administration is particularly preferred.
  • Subcutaneous administration may for example be by injection into the abdomen, lateral and anterior aspects of upper arm or thigh, scapular area of back, or upper ventrodorsal gluteal area.
  • compositions of the disclosure may also be administered in one, or more doses, as well as, by other routes of administration.
  • routes of administration include, intracutaneously, intravenously, intravascularly, intraarterially, intraperitnoeally, intrathecally, intratracheally, intracardially, intralobally, intramedullarly, intrapulmonarily, and intravaginally.
  • the compositions according to the disclosure may be administered once or several times, also intermittently, for instance on a monthly basis for several months or years and in different dosages.
  • Solid dosage forms for oral administration include capsules, tablets, caplets, pills, powders, pellets, and granules.
  • the active ingredient is ordinarily combined with one or more pharmaceutically acceptable excipients, examples of which are detailed above.
  • Oral preparations may also be administered as aqueous suspensions, elixirs, or syrups.
  • the active ingredient may be combined with various sweetening or flavoring agents, coloring agents, and, if so desired, emulsifying and/or suspending agents, as well as diluents such as water, ethanol, glycerin, and combinations thereof.
  • compositions of the disclosure may be administered, or the methods and uses for treatment according to the disclosure may be performed, alone or in combination with other pharmacological compositions or treatments, for example chemotherapy and/or immunotherapy and/or vaccine.
  • the other therapeutic compositions or treatments may for example be one or more of those discussed herein, and may be administered either simultaneously or sequentially with (before or after) the composition or treatment of the disclosure.
  • the treatment may be administered in combination with checkpoint blockade therapy/checkpoint inhibitors, co-stimulatory antibodies, cytotoxic or non-cytotoxic chemotherapy and/or radiotherapy, targeted therapy or monoclonal antibody therapy. It has been demonstrated that chemotherapy sensitizes tumors to be killed by tumor specific cytotoxic T cells induced by vaccination (Ramakrishnan et al. J Clin Invest. 2010; 120(4):1111-1124).
  • chemotherapy agents include alkylating agents including nitrogen mustards such as mechlorethamine (HN2), cyclophosphamide, ifosfamide, melphalan (L-sarcolysin) and chlorambucil; anthracyclines; epothilones; nitrosoureas such as carmustine (BCNU), lomustine (CCNU), semustine (methyl-CCNU) and streptozocin (streptozotocin); triazenes such as decarbazine (DTIC; dimethyltriazenoimidazole-carboxamide; ethylenimines/methylmelamines such as hexamethylmelamine, thiotepa; alkyl sulfonates such as busulfan; Antimetabolites including folic acid analogues such as methotrexate (amethopterin); alkylating agents, antimetabolites, pyrimidine analogs such as fluorouracil (5-fluor
  • the method of treatment is a method of vaccination or a method of providing immunotherapy.
  • immunotherapy is the treatment of a disease or condition by inducing or enhancing an immune response in an individual.
  • immunotherapy refers to a therapy that comprises the administration of one or more drugs to an individual to elicit T cell responses.
  • immunotherapy refers to a therapy that comprises the administration or expression of polypeptides that contain one or more PEPIs to an individual to elicit a T cell response to recognize and kill cells that display the one or more PEPIs on their cell surface in conjunction with a class I HLA.
  • immunotherapy comprises the administration of one or more PEPIs to an individual to elicit a cytotoxic T cell response against cells that display tumor associated antigens (TAAs) or cancer testis antigens (CTAs) comprising the one or more PEPIs on their cell surface.
  • TAAs tumor associated antigens
  • CTAs cancer testis antigens
  • immunotherapy refers to a therapy that comprises the administration or expression of polypeptides that contain one or more PEPIs presented by class II HLAs to an individual to elicit a T helper response to provide co-stimulation to cytotoxic T cells that recognize and kill diseased cells that display the one or more PEPIs on their cell surface in conjunction with a class I HLAs.
  • immunotherapy refers to a therapy that comprises administration of one or more drugs to an individual that re-activate existing T cells to kill target cells.
  • the theory is that the cytotoxic T cell response will eliminate the cells displaying the one or more PEPIs, thereby improving the clinical condition of the individual.
  • immunotherapy may be used to treat tumors. In other instances, immunotherapy may be used to treat intracellular pathogen-based diseases or disorders.
  • the disclosure relates to the treatment of cancer or the treatment of solid tumors.
  • the treatment may be of cancers or malignant or benign tumors of any cell, tissue, or organ type.
  • the cancer may or may not be metastatic.
  • Exemplary cancers include carcinomas, sarcomas, lymphomas, leukemias, germ cell tumors, or blastomas.
  • the cancer may or may not be a hormone related or dependent cancer (e.g., an estrogen or androgen related cancer).
  • the disclosure relates to the treatment of a viral, bacterial, fungal or parasitic infection, or any other disease or condition that may be treated by immunotherapy.
  • the disclosure provides a system comprising a storage module configured to store data comprising the class I and/or class II HLA genotypes of each subject of a model population of human subjects; and the amino acid sequence of one or more test polypeptides; wherein the model population is representative of a test target human population; and a computation module configured to identify and/or quantify the amino acid sequences in the one or more test polypeptides that are capable of binding to multiple class I HLA molecules of each subject in the model population and/or the amino acid sequences in the one or more test polypeptides that are capable of binding to multiple class II HLA molecules of each subject in the model population.
  • the system may further comprise an output module configured to display any output prediction or treatment selection or recommendation described herein or the value of any pharmodynamic biomarker described herein.
  • the method of item 1 or item 2 further comprising repeating the method for one or more further polypeptides, pharmaceutical compositions, kits or panels of polypeptides, and ranking the polypeptides, pharmaceutical compositions, kits or panels of polypeptides according to their predicted cytotoxic T cell, helper T cell and/or or clinical response rates in said specific or target human population.
  • any one of items 1 to 3 further comprising selecting or recommending treatment of a subject in need thereof by administration of one or more polypeptides or pharmaceutical compositions or the polypeptides of one or more kits or panels of polypeptides, based on their predicted response rate or response rate ranking.
  • the method of item 4 or item 5 further comprising administering one or more of the selected or recommended polypeptides or pharmaceutical compositions or the polypeptides of one or more kits or panels of polypeptides to the subject.
  • a method of treatment of a human subject in need thereof comprising administering to the subject one or more polypeptides or pharmaceutical compositions that have been selected or recommended for treatment of the subject using a method according to item 4 or item 5.
  • each polypeptide fragment is a T cell epitope capable of binding to at least three HLA class I molecules or at least three HLA class II molecules of at least one subject in the model population; and ranking the fragments by
  • the method of item 9 which comprises selecting one or more of the polypeptide fragments based on their ranking, and designing or preparing the polypeptide to comprise or the polynucleic acid to encode the one of more selected polypeptide fragments.
  • any one of items 8 to 10 further comprising designing or preparing a polypeptide, a panel of polypeptides, or a pharmaceutical composition or kit comprising one or more polypeptides as active ingredients for use in a method of inducing an immune response in a subject of the specific or target human population, wherein the polypeptide(s) or active ingredient polypeptides comprises at least two polypeptide fragments, optionally between 2 and 15 polypeptide fragments, selected according to the method of item 8 or item 10.
  • a method of inducing an immune response in a subject of a specific or target human population comprising designing or preparing a polypeptide, a panel of polypeptides, a polynucleic acid encoding a polypeptide, or a pharmaceutical composition or kit for use in said specific or target human population according to the method of any one of items 8 to 15 and administering the polypeptide(s), polynucleic acid, pharmaceutical composition or the active ingredient polypeptides of the kit to the subject.
  • a polypeptide, panel of polypeptides, polynucleic acid, pharmaceutical composition or kit for use in a method of inducing an immune response in a subject of a specific or target human population wherein the polypeptide, panel of polypeptides, polynucleic acid, pharmaceutical composition or kit is designed or prepared according to the method of any one of items 8 to 16 for use in said specific or target human population, and wherein the composition or kit optionally comprises at least one pharmaceutically acceptable diluent, carrier, or preservative.
  • a pharmaceutical composition, panel of polypeptides or kit for use in a method of inducing an immune response in a subject of a specific or target human population wherein the pharmaceutical composition, panel of polypeptides or kit comprises as active ingredients a first and a second and optionally one or more additional polypeptides, wherein each polypeptide comprises an amino acid sequence that is a T cell epitope capable of binding to at least three HLA class I molecules of at least 10% of subjects in the specific or target population, wherein the T cell epitope of the first, second and optionally any additional regions are different from each other, and wherein the pharmaceutical composition or kit optionally comprises at least one pharmaceutically acceptable diluent, carrier, or preservative.
  • a pharmaceutical composition, panel of polypeptides or kit for use in a method of inducing an immune response in a human subject wherein the pharmaceutical composition, panel of polypeptides or kit comprises an active ingredient polypeptide comprising a first region and a second region and optionally one or more additional regions, wherein each region comprises an amino acid sequence that is a T cell epitope capable of binding to at least three HLA class I molecules of at least 10% of subjects in the specific or target population, wherein the T cell epitope of the first, second and optionally any additional regions are different from each other, and wherein the pharmaceutical composition or kit optionally comprises at least one pharmaceutically acceptable diluent, carrier, or preservative.
  • a pharmaceutical composition, panel of polypeptides or kit for use in a method treating a cancer in a subject in need thereof wherein the pharmaceutical composition, panel of polypeptides or kit comprises as active ingredients a first and a second peptide and optionally one or more additional peptides, wherein each peptide comprises an amino acid sequence that is an HLA class I-binding T cell epitope wherein at least 10% of human subjects having cancer both
  • a pharmaceutical composition, panel of polypeptides or kit for use in a method treating a cancer in a subject in need thereof wherein the pharmaceutical composition, panel of polypeptides or kit comprises an active ingredient polypeptide comprising a first and a second region and optionally one or more additional regions, wherein each region comprises an amino acid sequence that is an HLA class I-binding T cell epitope wherein at least 10% of human subjects having cancer both
  • a method of treatment of a human subject in need thereof comprising administering to the subject a polypeptide, a panel of polypeptides, a pharmaceutical composition or the active ingredient polypeptides of a kit according to any one of items 17 to 25, wherein the subject has been determined to express at least three HLA class I molecules and/or at least three HLA class II molecules capable of binding to the polypeptide or to one or more of the active ingredient polypeptides of the pharmaceutical composition or kit.
  • a system comprising
  • HLA I-epitope binding prediction process was validated by comparison with HLA I-epitope pairs determined by laboratory experiments. A dataset was compiled of HLA I-epitope pairs reported in peer reviewed publications or public immunological databases.
  • the probability of multiple HLA binding to an epitope shows the relationship between the number of HLAs binding an epitope and the expected minimum number of real binding. Per PEPI definition three is the expected minimum number of HLA to bind an epitope (bold).
  • the validated HLA-epitope binding prediction process was used to determine all HLA-epitope binding pairs described in the Examples below.
  • the presentation of one or more epitopes of a polypeptide antigen by one or more HLA I of an individual is predictive for a CTL response was determined.
  • All of these clinical trials measured antigen specific CD8+ CTL responses (immunogenicity) in the study subjects after vaccination. In some cases, correlation between CTL responses and clinical responses were reported.
  • the 157 patient datasets (Table 11) were randomized with a standard random number generator to create two independent cohorts for training and evaluation studies. In some cases the cohorts contained multiple datasets from the same patient, resulting in a training cohort of 76 datasets from 48 patients and a test/validation cohort of 81 datasets from 51 patients.
  • **Immunoassays are based on T cell stimulation with antigen-specific peptide pools and quantify the released cytokines by different techniques.
  • CT Clinical trial
  • SBT Sequence Based Typing
  • SSO Sequence-Specific Oligonucleotide
  • ICS Intracellular cytokine staining
  • SSP Sequence-specific priming
  • the reported CTL responses of the training dataset were compared with the HLA I restriction profile of epitopes (9 mers) of the vaccine antigens.
  • the antigen sequences and the HLA I genotype of each patient were obtained from publicly available protein sequence databases or peer reviewed publications and the HLA I-epitope binding prediction process was blinded to patients' clinical CTL response data.
  • the number of epitopes from each antigen predicted to bind to at least 1 (PEPI1+), or at least 2 (PEPI2+), or at least 3 (PEPI3+), or at least 4 (PEPI4+), or at least 5 (PEPI5+), or all 6 (PEPI6) HLA class I molecules of each patient was determined and the number of HLA bound were used as classifiers for the reported CTL responses.
  • the true positive rate (sensitivity) and true negative rate (specificity) were determined from the training dataset for each classifier (number of HLA bound) separately.
  • ROC analysis was performed for each classifier.
  • the true positive rate (Sensitivity) was plotted in function of the false positive rate (1-Specificity) for different cut-off points ( FIG. 1 ).
  • Each point on the ROC curve represents a sensitivity/specificity pair corresponding to a particular decision threshold (epitope (PEPI) count).
  • the area under the ROC curve (AUC) is a measure of how well the classifier can distinguish between two diagnostic groups (CTL responder or non-responder).
  • the threshold count of PEPI3+(number of antigen-specific epitopes presented by 3 or more HLA of an individual) that best predicted a positive CTL response was 1 (Table 13).
  • at least one antigen-derived epitope is presented by at least 3 HLA class I of a subject ( ⁇ 1 PEPI3+)
  • the antigen can trigger at least one CTL clone, and the subject is a likely CTL responder.
  • ⁇ 1 PEPI3+ Test to predict likely CTL responders (“ ⁇ 1 PEPI3+ Test”) provided 76% diagnostic sensitivity (Table 13).
  • the test cohort of 81 datasets from 51 patients was used to validate the ⁇ 1 PEPI3+ threshold to predict an antigen-specific CTL response. For each dataset in the test cohort it was determined whether the ⁇ 1 PEPI3+ threshold was met (at least one antigen-derived epitope presented by at least three class I HLA of the individual). This was compared with the experimentally determined CTL responses reported from the clinical trials (Table 14).
  • Performance characteristic Description Result Positive 100%[A/(A + B)] The likelihood that an individual that 84% predictive meets the ⁇ 1 PEPI3+ threshold has value (PPV) antigen-specific CTL responses after treatment with immunotherapy. Sensitivity 100%[A/(A + C)] The proportion of subjects with antigen- 75% specific CTL responses after treatment with immunotherapy who meet the ⁇ 1 PEPI3+ threshold. Specificity 100%[D/(B + D)] The proportion of subjects without antigen- 55% specific CTL responses after treatment with immunotherapy who do not meet the ⁇ 1 PEPI3+ threshold.
  • Negative 100%[D/(C + D)] The likelihood that an individual who does 42% predictive not meet the ⁇ 1 PEPI3+ threshold does not value (NPV) have antigen-specific CTL responses after treatment with immunotherapy.
  • Overall 100%[(A + D)/N] The percentage of predictions based on 70% percent the ⁇ 1 PEPI3+ threshold that match agreement the experimentally determined result, (OPA) whether positive or negative. Fisher's exact (p) 0.01
  • ROC analysis determined the diagnostic accuracy, using the PEPI3+ count as cut-off values ( FIG. 2 ).
  • the AUC value 0.73.
  • an AUC of 0.7 to 0.8 is generally considered as fair diagnostic.
  • the ⁇ 1 PEPI3+ Test was compared with a previously reported method for predicting a specific human subject's CTL response to peptide antigens.
  • the HLA genotypes of 28 cervical cancer and VIN-3 patients that received the HPV-16 synthetic long peptide vaccine (LPV) in two different clinical trials were determined from DNA samples 8 9 10 .
  • the LPV consists of long peptides covering the HPV-16 viral oncoproteins E6 and E7.
  • the amino acid sequence of the LPV was obtained from these publications.
  • the publications also report the T cell responses of each vaccinated patient to pools of overlapping peptides of the vaccine.
  • PEPI3+s patient class I HLA
  • Peptides that comprised at least one PEPI3+( ⁇ 1 PEPI3+) were predicted to induce a CTL response.
  • Peptides that comprised no PEPI3+ were predicted not to induce a CTL response.
  • the ⁇ 1 PEPI3+ Test correctly predicted 489 out of 512 negative CTL responses and 8 out of 40 positive CTL responses measured after vaccination ( FIG. 3A ). Overall, the agreement between the ⁇ 1 PEPI3+ Test and experimentally determined CD8+ T cell reactivity was 90% (p ⁇ 0.001).
  • the sensitivity of the prediction of HLA class II restricted epitopes was 78%, since the State of Art tool predicted 84 positive responses (positive CD4+ T cell reactivity to a peptide pool for a person's DP alleles) out of 107 (sensitivity 78%).
  • the specificity was 22% since it could rule out 7 negative responses out of 31.
  • Example 6 the ⁇ 1 PEPI3+ Test Predicts T Cell Responses to Full Length LPV Polypeptides
  • the ⁇ 1 PEPI3+ Test was used to predict patient CD8+ and CD4+ T cell responses to the full length E6 and E7 polypeptide antigens of the LPV vaccine. Results were compared to the experimentally determined responses were reported.
  • the Test correctly predicted the CD8+ T cell reactivity (PEPI3+) of 11 out of 15 VIN-3 patients with positive CD8+ T cell reactivity test results (sensitivity 73%, PPV 85%) and of 2 out of 5 cervical cancer patients (sensitivity 40%, PPV 100%).
  • the CD4+ T cell reactivities (PEPI4+) were correctly predicted 100% both of VIN-3 and cervical cancer patients ( FIGS. 5A-D ).
  • pGX3001 is an HPV16 based DNA vaccine containing full length E6 and E7 antigens with a linker in between.
  • pGX3002 is an HPV18 based DNA vaccine containing full length E6 and E7 antigens with a linker in between.
  • a Phase II clinical trial investigated the T cell responses of 17 HPV-infected patients with cervical cancer who were vaccinated with both pGX3001 and pGX3002 (VGX-3100 vaccination) 1 .
  • FIGS. 5A-D and FIG. 6 shows for two illustrative patients (patient 12-11 and patient 14-5) the position of each epitope (9 mer) presented by at least 1 (PEPI1+), at least 2 (PEPI2+), at least 3 (PEPI3+), at least 4 (PEPI4+), at least 5 (PEPI5+), or all 6 (PEPI6) class I HLA of these patients within the full length sequence of the two HPV-16 and two HPV-18 antigens.
  • PEPI1+ PEPI1+
  • PEPI2+ at least 3
  • PEPI4+ at least 4
  • PEPI5+ at least 5
  • PEPI6 all 6
  • Patient 12-11 had an overall PEPI1+ count of 54 for the combined vaccines (54 epitopes presented by one or more class I HLA).
  • Patient 14-5 had a PEPI1+ count of 91. Therefore patient 14-5 has a higher PEPI1+ count than patient 12-11 with respect to the four HPV antigens.
  • the PEPI1+s represent the distinct vaccine antigen specific HLA restricted epitope sets of patients 12-11 and 14-5. Only 27 PEPI1+s were common between these two patients.
  • PEPI3+ counts (number of epitopes presented by three or more patient class I HLA)
  • the results for patients 12-11 and 14-5 were reversed.
  • Patient 12-11 had a PEPI3+ count of 8, including at least one PEPI3+ in each of the four HPV16/18 antigens.
  • Patient 14-5 had a PEPI3+ count of 0.
  • the diversity of the patient's PEPI3+ set resembled the diversity of T cell responses generally found in cancer vaccine trials.
  • Patients 12-3 and 12-6 similar to patient 14-5, did not have PEPI3+s predicting that the HPV vaccine could not trigger T cell immunity. All other patients had at least one PEPI3 predicting the likelihood that the HPV vaccine can trigger T cell immunity. 11 patients had multiple PEPI3+ predicting that the HPV vaccine likely triggers polyclonal T cell responses.
  • Patients 15-2 and 15-3 could mount high magnitude T cell immunity to E6 of both HPV, but poor immunity to E7.
  • Other patients 15-1 and 12-11 had the same magnitude response to E7 of HPV18 and HPV16, respectively.
  • Example 8 Design of a Model Population for Conducting in Silico Trials and Identifying Candidate Precision Vaccine Targets for Large Population
  • a database of a “Big Population” containing 7,189 subjects characterized with 4-digit HLA genotype and demographic information was also established.
  • the Big Population has 328 different HLA class I alleles.
  • the HLA allele distribution of the Model Population significantly correlated with the Big Population (Table 16) (Pearson p ⁇ 0.001). Therefore the 433 patient Model Population is representative for a 16 times larger population.
  • the Model Population is representative for 85% of the human race as given by HLA diversity as well as HLA frequency.
  • the objective of this study was to determine whether a model population, such as the one described in Example 8, may be used to predict CTL reactivity rates of vaccines, i.e. used in an in silico efficacy trials.
  • peptide vaccines derived from cancer antigens that induced T cell responses in a subpopulation of subjects were identified from peer reviewed publications. These peptides have been investigated in clinical trials enrolling a total of 172 patients (4 ethnicities). T cell responses induced by the vaccine peptides have been determined from blood specimens and reported. The immune response rate as the percentage of study subjects with positive T cell responses measured in the clinical trials was determined ( FIG. 7 ).
  • the 12 peptides were investigated with the ⁇ 1 PEPI3+ Test in each of the 433 subjects of the Model Population described in Example 8.
  • the “ ⁇ 1 PEPI3+ Score” for each peptide was calculated as the proportion of subjects in the Model Population having at least one vaccine derived epitope that could bind to at least three subject-specific HLA class I ( ⁇ 1 PEPI3+). If the corresponding clinical trial stratified patients for HLA allele selected population, the Model Population was also filtered for subjects with the respective allele(s) (Example: WT1, HLA-A*0201).
  • Each vaccine peptide of the 19 clinical trials was investigated with the ⁇ 1 PEPI3+ Test in each subject of the Model Population.
  • the ⁇ 1 PEPI3+ Score for each peptide was calculated as the proportion of subjects in the Model Population having at least one vaccine derived PEPI3+.
  • the experimentally determined response rates reported from the trials were compared with the PEPI Scores, as in Example 9 (Table 20).
  • Example 11 in Silico Trial Based on the Identification of Multiple HLA Binding Epitopes in a Multi-Peptide Vaccine Predict the Reported Clinical Trial Immune Response Rate
  • IMA901 is a therapeutic vaccine for renal cell cancer (RCC) comprising 9 peptides derived from tumor-associated peptides (TUMAPs) that are naturally presented in human cancer tissue.
  • RCC renal cell cancer
  • TUMAPs tumor-associated peptides
  • a total of 96 HLA-A*02+ subjects with advanced RCC were treated with IMA901 in two independent clinical studies (phase I and phase II).
  • Each of the 9 peptides of IMA901 have been identified in the prior art as HLA-A2-restricted epitopes. Based on currently accepted standards, they are all strong candidate peptides to boost T cell responses against renal cancer in the trial subjects, because their presence has been detected in renal cancer patients, and because the trial patients were specifically selected to have at least one HLA molecule capable of presenting each of the peptides.
  • phase I and phase II study results show the variability of the immune responses to the same vaccine in different trial cohorts. Overall, however, there was a good agreement between response rates predicted by the ⁇ 2 PEPI3+ Test and the reported clinical response rates.
  • Example 12 in Silico Trial Based on the Identification of Vaccine-Derived Multiple HLA Binding Epitopes Predict Reported Experimental Clinical Response Rates
  • DCRs Disease Control Rates
  • ORR objective response rate
  • MultiPEPI Score Overall Percentage Immunotherapy DCR (Predicted DCR) of Agreement IMA901 phase I 43% 27% 61% IMA901 phase II 22% 27% 81% Ipilimumab 60% 65% 92% HPV-SLP 60% 70% 86% HPV-SLP 62% 70% 89% gp100-2 peptides 15% 11% 73% Immucin 73% 59% 81% StimuVax 0% 0% 100% VGX-3100 50% 56% 89% TSPP peptide vaccine 48% 31% 65% KIF20A-66 peptide 26% 7% 27% vaccine Peptide vaccine 27% 10% 37% 7-peptide cocktail 10% 9% 90% vaccine GVX301 29% 7% 24% MAGE-A3 Trojan 35% 10% 29% PepCan 52% 26% 50% Melanoma peptide 12% 6% 50% vaccine
  • Example 13 in Silico Trials Based on the Identification of Multiple HLA Binding Epitopes Predict the Reported Cellular Immune Response Rates to a Vaccine Targeting a Mutational Antigen
  • the epidermal growth factor receptor variant III is a tumor-specific mutation broadly expressed in glioblastoma multiforme (GBM) and other neoplasms.
  • the mutation comprises an in-frame deletion of 801 bp from the extracellular domain of the EGFR that splits a codon and yields a novel glycine at the fusion junction.
  • 1, 2 This mutation encodes a constitutively active tyrosine kinase that increases tumor formation and tumor cell migration and enhances resistance against radiation and chemotherapy.
  • 3, 4, 5, 6, 7, 8, 9 This insertion results in a tumor-specific epitope which is not found in normal adult tissues making EGFRvIII a suitable target candidate for antitumor immunotherapy.
  • Rindopepimut is a 13-amino-acid peptide vaccine (LEEKKGNYVVTDHC) spanning the EGFRvIII mutation with an additional C-terminal cysteine residue.
  • the peptide conjugated to keyhole limpet hemocyanin (KLH) was administered to newly diagnosed EGFRvIII-expressing GBM patients.
  • the first three vaccinations were given biweekly, starting 4 weeks after the completion of radiation.
  • Subsequent vaccines were given monthly until radiographic evidence of tumor progression or death. All vaccines were given intradermally in the inguinal region. Immunologic evaluation showed only 3 out of 18 patients developing cellular immune response assessed by DTH reaction test.
  • FIG. 10 An HLA map of the Rindopepimut on the HLA alleles of the subjects in the Model Population ( FIG. 10 ) illustrates that very few HLA-A and HLA-C alleles can bind the vaccine epitopes which explains the lack of PEPI3+ in the in silico cohort.
  • TPO Thrombopoietin
  • EpiVax/Genentech used State of Art technology to identify class II HLA restricted epitopes and found that the most immunogenic region of the TPO is located in the C-terminal end of TPO (US20040209324 A1).
  • PEPI3+s multiple class II HLA binding epitopes from TPO in 400 HLA class II genotyped US subjects were determined. Most of the PEPI3+ peptides of these individuals located within the N terminal region of the TPO between 1-165 amino acids. PEPI3+ were sporadically identified in some subjects also in the C terminal region. However, our results were different from the State of Art.
  • This example describes the treatment of an ovarian cancer patient with a personalised immunotherapy composition, wherein the composition was specifically designed for the patient based on her HLA genotype based on the disclosure described herein.
  • This Example and Example 16 below provide clinical data to support the principals regarding binding of epitopes by multiple HLA of a subject to induce a cytotoxic T cell response on which the present disclosure is based.
  • the HLA class I and class II genotype of metastatic ovarian adenocarcinoma cancer patient XYZ was determined from a saliva sample.
  • each peptide was selected, each of which met the following two criteria: (i) derived from an antigen that is expressed in ovarian cancers, as reported in peer reviewed scientific publications; and (ii) comprises a fragment that is a T cell epitope capable of binding to at least three HLA class I of patient XYZ (Table 26).
  • each peptide is optimized to bind the maximum number of HLA class II of the patient.
  • PEPI3 peptides in this immunotherapy composition can induce T cell responses in XYZ with 84% probability and the two PEPI4 peptides (POC01-P2 and POC01-P5) with 98% probability, according to the validation of the PEPI Test shown in Table 10.
  • T cell responses target 13 antigens expressed in ovarian cancers. Expression of these cancer antigens in patient XYZ was not tested. Instead the probability of successful killing of cancer cells was determined based on the probability of antigen expression in the patient's cancer cells and the positive predictive value of the ⁇ 1 PEPI3+ Test (AGP count).
  • AGP count predicts the effectiveness of a vaccine in a subject: Number of vaccine antigens expressed in the patient's tumor (ovarian adenocarcinoma) with PEPI.
  • the AGP count indicates the number of tumor antigens that vaccine recognizes and induces a T cell response against the patient's tumor (hit the target).
  • the AGP count depends on the vaccine-antigen expression rate in the subject's tumor and the HLA genotype of the subject. The correct value must be between 0 (no PEPI presented by expressed antigen) and maximum number of antigens (all antigens are expressed and present a PEPI).
  • FIGS. 11A-B The probability that patient XYZ will express one or more of the 12 antigens is shown in FIGS. 11A-B .
  • a pharmaceutical composition for patient XYZ may be comprised of at least 2 from the 13 peptides (Table 26), because the presence in a vaccine or immunotherapy composition of at least two polypeptide fragments (epitopes) that can bind to at least three HLA of an individual ( ⁇ 2 PEPI3+) was determined to be predictive for a clinical response.
  • the peptides are synthetized, solved in a pharmaceutically acceptable solvent and mixed with an adjuvant prior to injection. It is desirable for the patient to receive personalized immunotherapy with at least two peptide vaccines, but preferable more to increase the probability of killing cancer cells and decrease the chance of relapse.
  • the 12 peptides were formulated as 4 ⁇ 3 ⁇ 4 peptide (POC01/1, POC01/2, POC01/3, POC01/4).
  • One treatment cycle is defined as administration of all 13 peptides within 30 days.
  • the HLA class I and class II genotype of metastatic breast cancer patient ABC was determined from a saliva sample.
  • twelve peptides were selected, each of which met the following two criteria: (i) derived from an antigen that is expressed in breast cancers, as reported in peer reviewed scientific publications; and (ii) comprises a fragment that is a T cell epitope capable of binding to at least three HLA class I of patient ABC (Table 29).
  • each peptide is optimized to bind the maximum number of HLA class II of the patient.
  • the twelve peptides target twelve breast cancer antigens. The probability that patient ABC will express one or more of the 12 antigens is shown in FIG. 13 .
  • the 12 peptides were formulated as 4 ⁇ 3 peptide (PBR01/1, PBR01/2, PBR01/3, PBR01/4).
  • One treatment cycle is defined as administration of all 12 different peptide vaccines within 30 days.
  • Diagnosis bilateral metastatic breast carcinoma: Right breast is ER positive, PR negative, Her2 negative; Left Breast is ER, PR and Her2 negative.
  • BRC-09 was treated with 5 cycles of PIT vaccine. She was feeling very well and she refused a PET CT examination in September 2017. In November she had symptoms, PET CT scan showed progressive disease, but she refused all treatments. In addition, her oncologist found out that she did not take Palbocyclib since spring/summer. Patient ABC passed away in January 2018.
  • the combination of pablocyclib and the personalised vaccine was likely to have been responsible for the remarkable early response observed following administration of the vaccine.
  • Palbocyclib has been shown to improve the activity of immunotherapies by increases CTA presentation by HLAs and decreasing the proliferation of Tregs: (Goel et al. Nature. 2017:471-475).
  • the PIT vaccine may be used as add-on to the state-of-art therapy to obtain maximal efficacy.
  • PEPI3+ Test and the Model Population described in Example 8 For select CTAs we used the PEPI3+ Test and the Model Population described in Example 8 to identify the 9 mer epitopes (PEPI3+s) that are most frequently presented by at least 3HLAs of the individuals in the Model Population. We refer to these epitopes herein as “bestEPIs”.
  • BestEPIs An illustrative example of the “PEPI3+ hotspot” analysis and bestEPI identification is shown in FIG. 14 for the PRAME antigen.
  • Ntotal number of samples analyzed for the expression of the certain antigen
  • N+ number of individuals expressing the certain antigen
  • N% expression frequency of the certain antigen
  • B% bestEPI frequency, ie. the percentage of individuals having the bestEPI within the model population
  • N%*B% expression frequency multiplied by the bestEPI frequency.
  • Tumor heterogeneity can be addressed by including peptide sequences that target multiple CTAs in a vaccine or immunotherapy regime.
  • the AG values described above characterize a vaccine independently from the target patient population. They can be used to predict the likelihood that a specific cancer (e.g. breast cancer) expresses antigens targeted by a specific vaccine or immunotherapy composition. AG values are based on known tumor heterogeneity, but do not take HLA heterogeneity into account.
  • HLA heterogeneity of a certain population can be characterised from the viewpoint of an immunotherapy or vaccine composition by the number of antigens representing PEPI3+. These are the vaccine-specific CTA antigens for which ⁇ 1 PEPI3+ is predicted, referred to herein as the “AP”.
  • the average number of antigens with PEPI3+(AP50) shows how the vaccine can induce immune response against the antigens targeted by the composition (breast cancer vaccine specific immune response).
  • Vaccines can be further characterized by AGP values that refers to antigens with PEPIs”.
  • This parameter is the combination of the previous two parameters: (1) AG is depending on the antigen expression frequencies in the specific tumor type but not on the HLA genotype of individuals in the population, and (2) AP is depending on the HLA genotype of individuals in a population without taking account the expression frequencies of the antigen.
  • the AGP is depending on both, the expression frequencies of vaccine antigens in the disease and the HLA genotype of individuals in a population.
  • the likelihood that a specific patient will have an immune response or a clinical response to treatment with one or more cancer vaccine peptides can be determined based on (i) the identification of PEPI3+ within the vaccine peptide(s) (9 mer epitopes capable of binding at least three HLA of the patient); and/or (ii) a determination of target antigen expression in cancer cells of the patient, for example as measured in a tumour biopsy. In some cases both parameters are ideally determined and the optimal combination of vaccine peptides is selected for use in treatment of the patient.
  • PEPI3+ analysis alone may be used if a determination of the expressed tumour antigens, for example by biopsy, is not possible, not advised, or unreliable due to biopsy error (i.e. biopsy tissue samples taken from a small portion of the tumor or metastasised tumors do not represent the complete repertoire of CTAs expressed in the patient).
  • the single peptide vaccines were immunogenic in 3%-23% of individuals.
  • the 30 mer peptides described in Example 18 above were each immunogenic in from 44% to 73% of individuals in the same cohorts. This result represents substantial improvement in immunogenicity of each peptide in PolyPEPI915.
  • Competing combination peptide products immune response rates were between 10-62%.
  • the invented PolyPEPI915 combination product were 96% in the Model Population and 93% in a breast cancer patient population, representing improvement in immunogenicity.
  • PolyPEPI915 vaccine Another improvement of using the PolyPEPI915 vaccine is the lower chance of tumor escape.
  • Each 30 mer peptide in PolyPEPI915 targets 2 tumor antigens. CTLs against more tumor antigens are more effective against heterologous tumor cells that CTLs against a single tumor antigen.
  • PolyPEPI915 vaccine is that individuals who likely respond to vaccination can be identified based on their HLA genotypes (sequence) and optionally antigen expression in their tumor using the methods described here. Pharmaceutical compositions with PolyPEPI vaccines will not be administered to individuals whose HLA cannot present any PEPI3 from the vaccines. During clinical trials correlation will be made between the mAGP or number of AGP in the PolyPEPI915 regimen and the duration of individual's responses. A vaccine combination with ⁇ 1 AGP is most likely required to destroy heterologous tumor cells.
  • Colorectal cancer CTAs were identified and ranked based on the overall expression frequencies of antigens found in colorectal cancer tumor samples as reported in peer reviewed publications ( FIG. 19 ) (Choi J, Chang H. The expression of MAGE and SSX, and correlation of COX2, VEGF, and survivin in colorectal cancer. Anticancer Res 2012. 32(2):559-564; Goossens-Beumer I J, Zeestraten E C, Benard A, Christen T, Reimers M S, Keijzer R, Sier C F, Morriss G J, Morreau H, Putter H, Vahrmeijer A L, van de Velde C J, Kuppen P J.
  • Ntotal number of biopsy samples (tumor specific antigen expression in human colorectal cancer tissues) analyzed for the expression of the certain antigen; N+: number of individuals expressing the certain antigen; N%: expression frequency of the certain antigen; B%: bestEPI frequency, ie. the percentage of induviduals having the bestEPI within the model population; N%*B%: expression frequency multiplied by the bestEPI frequency.
  • the PolyPEPI1018 Colorectal Cancer (CRC) Vaccine (PolyPEPI1018) composition is a peptide vaccine intended to be used as an add-on immunotherapy to standard-of-care CRC treatment options in patients identified as likely responders using a companion in vitro diagnostic test (CDx). Clinical trials are ongoing in the US and Italy to evaluate PolyPEPI1018 in metastatic colorectal cancer patients.
  • the product contains 6 peptides (6 of the 30 mer peptides PolyPEPI1015 described in examples 18 to 20 mixed with the adjuvant Montanide. The 6 peptides were selected to induce T cell responses against 12 epitopes from 7 cancer testis antigens (CTAs) that are most frequently expressed in CRC.
  • CTAs cancer testis antigens
  • the 6 peptides were optimized to induce long lasting CRC specific T cell responses.
  • Likely responder patients with T cell responses against multiple CTAs expressed in the tumor can be selected with a companion diagnostic (CDx).
  • CDx companion diagnostic
  • This example sets out the precision process used to design PolyPEPI1018. This process can be applied to design vaccines against other cancers and diseases.
  • tumor antigens are essential for the safety and efficacy of cancer vaccines.
  • the feature of a good antigen is to have restricted expression in normal tissues so that autoimmunity is prevented.
  • Several categories of antigen meet this requirement, including uniquely mutated antigens (e.g. p53), viral antigens (e.g. human papillomavirus antigens in cervical cancer), and differentiation antigens (e.g. CD20 in B-cell lymphoma).
  • CTAs cancer testis antigens
  • CTA expression knowledgebase contains CTAs that are expressed in CRC ranked in order by expression rate. Correlation studies conducted by the inventors (see Example 11) suggest that vaccines which induce CTL responses against multiple antigens that are expressed in tumor cells can benefit patients. Therefore, seven CTAs with high expression rates in CRC were selected for inclusion in PolyPEPI1018 development. Details are set out in Table 36.
  • Testis-Specific Protease-Like Protein 50 is an oncogene which induces cell proliferation, cell invasion, and tumor growth. It is frequently expressed in gastric-, breast-, cervical- and colorectal cancer samples; and rarely expressed in normal human tissues, except in spermatocytes of testes.
  • EpCAM 88.35% Epithelial Cell Adhesion Molecule is a tumor associated antigen, which is expressed in colon cancers and over-expressed in various human carcinomas. The high expression of EpCAM in cancer-initiating stem cells makes it a valuable target for cancer vaccines.
  • EpCAM is also expressed in at low or negligible levels in normal epithelial cells, with the exception of squamous epithelium, hepatocytes and keratinocytes.
  • Survivin 87.28% Survivin (Baculoviral IAP repeat-containing protein 5) is a multi-tasking protein that promotes cell proliferation and inhibits apoptosis. Though it is strongly expressed in fetal tissues and necessary for normal development, it is not expressed in most adult tissues. Survivin is expressed in various cancers including carcinomas. Normal tissues that express low level survivin include thymus, CD34 + bone-marrow-derived stem cells, and basal colonic epithelium.
  • CAGE1 74.47% Cancer-associated gene 1 protein is a typical CTA, which might play a role in cell proliferation and tumorigenesis.
  • CAGE1 is highly expressed in colorectal cancer tissues and weakly expressed in adjacent normal colorectal mucosa.
  • CAGE1 is expressed in melanoma, hepatoma, and breast tumors.
  • SPAG9 74.36% sperm-associated antigen 9 is involved in c-Jun N-terminal kinase-signaling and functions as a scaffold protein, thus playing an important role in cell survival, proliferation, apoptosis and tumor development.
  • SPAG9 expression was detected in epithelial ovarian cancer (90%), breast cancer (88%), cervical cancer (82%), renal cell cancer (88%) and colorectal cancer (74%) patients. None of the adjacent noncancerous tissues showed antigen expression. SPAG9 expression is restricted to testis.
  • FBXO39 38.60% FBXO39 (BCP-20) is a testis specific protein and is an important part of the E3 ubiquitin ligase complex. It participates in ubiquitination and has a role in regulating the cell cycle, immune responses, signaling, and proteasomal degradation of proteins.
  • FBXO39 is expressed in colon and breast cancers. FBXO39 expression has also been detected in ovary, placenta, and lung. FBXO39 expression is 100-fold higher in testis and 1,000- fold higher in colorectal cancers compared with normal tissue.
  • MAGEA8 43.75% Melanoma-associated antigen 8 function is not known, though it may play a role in embryonal development and tumor transformation or aspects of tumor progression.
  • MAGE-A8 gene is expressed in CRC and hepatocellular carcinoma. MAGE-A8 expression in normal tissues is restricted to the testis and the placenta.
  • the PEPI3+ biomarker predicts a subject's vaccine induced T cell responses.
  • the inventors developed and validated a test to accurately identify the PEPIs from antigen sequences and HLA genotypes (Examples 1, 2, 3).
  • the PEPI Test algorithm was used to identify the dominant PEPIs (besEPIs) from the 7 target CTAs to be included in PolyPEPI1018 CRC vaccine.
  • the dominant PEPIs identified with the process described here can induce CTL responses in the highest proportion of subjects:
  • the 12 dominant PEPIs that are derived from the 7 CTAs in PolyPEPI1018 are presented in the following table.
  • the PEPI % in Model Population indicates the proportion of 433 subjects with the indicated PEPI, i.e. the proportion of subjects where the indicated PEPI can induce CTL responses. There is very high variability (18%-78%) in the dominant PEPIs to induce CTL responses despite the optimization steps used in the identification process.
  • the inventors optimized each dominant PEPI to bind to most HLA class II alleles of most subjects. This should enhance efficacy, because it will induce CD4+T helper cells that can augment CD8 + CTL responses and contribute to long lasting T cell responses.
  • the example presented in FIG. 4 demonstrates that PEPIs that bind to 23 HLA class II alleles most likely activate T helper cells.
  • the 15-mer peptides selected with the process described here contain both HLA class I and class II binding dominant PEPIs. Therefore, these peptides can induce both CTL and T helper responses in the highest proportion of subjects.
  • the 12 optimized 15-mer peptides derived from the 7 CTAs in PolyPEPI1018 are presented in the Table 38. These peptides have different HLA class II binding characteristics. There is a high variability (0%-100%) in PEPI generation capacity ( ⁇ 3 HLA binding) among these peptides despite such an optimized personalized vaccine design.
  • CRC antigens alleles binding binding binding binding binding binding binding binding binding binding CRC-P1 TSP50 (83-97) 0 0% 0% 0% 0% 0% TSP50 (190-204) 4 100% 99% 88% 53% CRC-P2 EPCAM(139-153) 5 100% 100% 100% 98% SURVIVIN(127- 2 84% 58% 26% 11% 141) CRC-P3 EPCAM(251-265) 0 0% 0% 0% 0% MAGE-A8(113- 4 100% 100% 95% 72% 127) CRC-P6 CAGE(613-627) 5 100% 100% 99% 35% SURVIVIN(15-29) 3 100% 97% 83% 45% CRC-P7 CAGE(759-773) 3 100% 98% 87% 56% SPAG9(16-30) 1 66% 35% 9% 2% CRC-P8 FBXO39(95-109) 3 100% 94% 43% 13% FBXO39(284-298) 5 100% 100% 100% 100% 98% 98%
  • the 30-mer vaccine peptides have the following advantages compared to shorter peptides:
  • Each 30-mer peptide in PolyPEPI1018 consists of 2 HLA class I binding dominant PEPIs and at least one strong HLA class II binding PEPI. Strong binding PEPIs bind to 4 HLA class II alleles in ⁇ 50% of individuals. Therefore, the vaccine peptides are tailored to both HLA class I and class II alleles of individual subjects in a general population (which is a relevant population for CRC vaccine design).
  • Selected peptides for the PolyPEPI1018 composition are as shown in Table 39.
  • the inventors used the PEPI3+ Test to characterized the immunogenicity of PolyPEPI1018 in a cohort of 37 CRC patients with complete HLA genotype data. T cell responses were predicted in each patient against the same 9 mer peptides that will be used in clinical trials. These peptides represent the 12 dominant PEPI3+ within the PolyPEP11018 peptides. The 9 mers are shown in Table 39.
  • PEPI3+ prediction depends on the actual number of HLAs predicted to bind a particular epitope. Specifically, the inventors have determined that the probability that one HLA-restricted epitope induces a T cell response in a subject is typically 4%, which explains the poor sensitivity of the state-of-art prediction methods based on HLA restricted epitope prediction. Applying the PEPI3+ methodology, the inventors determined the probability that T cell response to each of the dominant PEPI3+-specific would be induced by PolyPEPI1018 in the 37 CRC patients. The results from this analysis are summarized in the Table 40.
  • a method was developed that can be performed on any antigen to determine its potential to induce toxic immune reaction, like autoimmunity.
  • the method is referred to herein as immunoBLAST.
  • PolyPEPI1018 contains six 30-mer polypeptides. Each polypeptide consists of two 15-mer peptide fragments derived from antigens expressed in CRC. Neoepitopes might be generated in the joint region of the two 15-mer peptides and could induce undesired T cell responses against healthy cells (autoimmunity). This was assesses using the inventors applied the immunoBLAST methodology.
  • a 16-mer peptide for each of the 30-mer components of PolyPEP1018 was designed. Each 16-mer contains 8 amino acids from the end of the first 15 residues of the 30-mer and 8 amino acids from the beginning of the second 15 residues of the 30-mer—thus precisely spanning the joint region of the two 15-mers. These 16-mers are then analysed to identify cross-reactive regions of local similarity with human sequences using BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi), which compares protein sequences to sequence databases and calculates the statistical significance of matches. 8-mers within the 16-mers were selected as the examination length since that length represents the minimum length needed for a peptide to form an epitope, and is the distance between the anchor points during HLA binding.
  • the positions of amino acids in a polypeptide are numbered.
  • the start positions of potential 9-mer peptides that can bind to HLAs and form neoepitopes are the 8 amino acids in positions 8-15.
  • the ratio of possible neoepitope generating peptides is 36.4% (8/22).
  • the PEPI3+ Test was used to identify neoepitopes and neoPEPI among the 9-mer epitopes in the joint region.
  • the risk of PolyPEPI1018 inducing unwanted T cell responses was assessed in the 433 subjects in the Model Population by determining the proportion of subjects with PEPI3+ among the 9-mers in the joint region.
  • the result of neoepitope/neoPEPI analysis is summarized in table 41.
  • the average predicted epitope number that could be generated by intracellular processing was 40.12.
  • Neoepitopes were frequently generated; 11.61 out of 40.12 (28.9%) epitopes are neoepitopes.
  • Most of the peptides were able to be identified as a neoepitope, but the number of subjects that present neoepitopes varied.
  • Epitopes harbored by PolyPEPI1018 create an average of 5.21 PEPI3+. These PEPIs can activate T cells in a subject. The amount of potential neoPEPIs was much lower than neoepitopes (3.7%). There is a marginal possibility that these neoPEPIs compete on T cell activation with PEPIs in some subjects. Importantly, the activated neoPEPI specific T cells had no targets on healthy tissue.
  • Neoepitopes of PolyPEPI1018 Epitope & PEPI3+ binding in 433 Subjects of the Model Population Poly- Epitope Binding (1 x HLA) PEPI3+ binding (3 x HLA) PEPI1018 Neo- Neo- Peptide Potential EPI EPI ID: Neoepitope Sub# Sub% NeoEPI count Sub# Sub% NeoEPI count CRC-P1 QFPVSEGKS 0 0.0% 7 0 0.0% 3 FPVSEGKSR 160 37.0% X 1 0.2% X PVSEGKSRY 150 34.6% X 0 0.0% VSEGKSRYR 194 44.8% X 1 0.2% X SEGKSRYRA 113 26.1% X 0 0.0% EGKSRYRAQ 77 17.8% X 0 0.0% GKSRYRAQR 37 8.5% X 0 0.0% KSRYRAQRF 337 77.8% X 33 7.6% X CRC-P2 IELKHKART 32 7.4% X 7 0
  • the inventors have developed pharmacodynamic biomarkers to predict the activity/effect of vaccines in individual human subjects as well as in populations of human subjects. These biomarkers expedite more effective vaccine development and also decrease the development cost.
  • the inventors have the following tools:
  • Antigen expression knowledgebase The inventors have collected data from experiments published in peer reviewed scientific journals regarding the tumor antigens expressed by tumor cells and organized by tumor type to create a database of CTA expression levels—CTA database (CTADB). As of April 2017, the CTADB contained data from 145 CTAs from 41,132 tumor specimens, and was organized by the CTA expression frequencies in different types of cancer.
  • CTADB CTA database
  • silico trial populations The inventors have also collected data on the HLA genotypes of several different model populations. Each individual in the populations has complete 4-digit HLA genotype and ethnicity data. The populations are summarized in Table 42.
  • Table 43 shows the antigenicity and effectiveness of PolyPEPI1018 in 37 CRC patients using AP and AGP50, respectively.
  • the AP and AGP50 have high variability.
  • the most immunogenic antigen in PolyPEPI1018 was FOX039; each patient had a PEPI3+.
  • FOX039 is expressed only 39% of CRC tumors, suggesting that 61% of patients will have FOX039 specific T cell responses that do not recognize the tumor.
  • the least immunogenic antigen was MAGE-A8; none of the 37 CRC patients had a PEPI3+ despite the antigen being expressed in 44% of CRC tumors.
  • AGP50 indicates the mean number of expressed antigens in CRC tumor with PEPIs. Patients with higher AGP50 values are more likely to respond to PolyPEPI1018 since higher AGP50 values indicate that the vaccine can induce T cell responses against more antigens expressed in CRC cells.
  • the last column in the Table 43 shows the probability of mAGP (multiple AGP; i.e., at least 2 AGPs) in each of the 37 CRC patients.
  • the average mAGP in patients with CRC is 66%, suggesting that there is a 66% likelihood that a CRC patient will induce T cell responses against multiple antigens expressed in the tumor.
  • Antigen expression data can be obtained from achieved tumor specimen and organized in databases. 4-digit HLA genotyping can be done from a saliva specimen. It is a validated test performed by certified laboratories worldwide for transplantation and paternity testing. These assessments will allow drug developers and physicians to gain deeper insights into the immunogenicity and activity of tumor response and the possible emergence of resistance.
  • the antigenicity of PolyPEPI1018 in a subject is determined by the AP count, which indicates the number of vaccine antigens that induce T cell responses in a subject.
  • the AP count of PolyPEPI1018 was determined in each of the 433 subjects in the Model Population using the PEPI Test, and the AP50 count was then calculated for the Model Population.
  • the AP50 of PolyPEPI1018 in the Model Population is 3.62. Therefore, the mean number of immunogenic antigens (i.e., antigens with ⁇ 1 PEPI) in PolyPEPI1018 in a general population is 3.62.
  • Vaccine induced T cells can recognize and kill tumor cells if a PEPI in the vaccine is presented by the tumor cell.
  • the number of AGPs (expressed antigens with PEPI) is an indicator of vaccine effectiveness in an individual, and is dependent on both the potency and antigenicity of PolyPEPI1018.
  • the mean number of immunogenic CTAs i.e., AP [expressed antigens with ⁇ 1 PEPI]) in PolyPEPI1018 is 2.54 in the Model Population.
  • Table 44 shows the comparison of the immunogenicity, antigenicity, and effectiveness of PolyPEPI1018 in different populations.
  • Example 24 Personalised Immunotherapy Composition for Treatment of Patient with Late Stage Metastatic Breast Cancer
  • IBC Inflammatory breast cancer
  • inflammatory breast cancer is a rare, but aggressive form of locally advanced breast cancer. It's called inflammatory breast cancer because its main symptoms are swelling and redness (the breast often looks inflamed).
  • Most inflammatory breast cancers are invasive ductal carcinomas (begin in the milk ducts). This type of breast cancer is associated with the expression of oncoproteins of high risk Human Papilloma Virus. Indeed, HPV16 DNA was diagnosed in the tumor of this patient.
  • T4 Tumor of any size with direct extension to the chest wall and/or to the skin (ulceration or skin nodules)
  • pN3a Metastases in ⁇ 10 axillary lymph nodes (at least 1 tumor deposit ⁇ 2.0 mm); or metastases to the infraclavicular (level III axillary lymph) nodes.
  • T cell responses were measured cells in peripheral mononuclear cells 2 weeks after the 1 st vaccination with the mix of peptides PBRC05_P1, PBRC05_P2, PBRC05_P3, PBRC05_P4, PBRC05_P5, PBRC05_P6, PBRC05_P7.

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