# US 6,861,234 B1 · Method of epitope discovery > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 6,861,234 B1 - Document ID: US6861234B1 - Status: Granted - Kind: B1 - Application number: 09/561,074 - Filed: 2000-04-28 - Granted: 2005-03-01 - Earliest claimed: 2000-04-28 - Assignees: MannKind Corporation - Inventors: John J. L. Simard; David C. Diamond - Web page: https://patentgrep.com/patent/US6861234B1 ## CPC - A61K 39/0011: {Cancer antigens} - A61K 39/001106: {Her-2/neu/ErbB2, Her-3/ErbB3 or Her 4/ErbB4} - A61K 39/001151: {p53} - A61K 39/001156: {Tyrosinase and tyrosinase related proteinases [TRP-1 or TRP-2]} - A61K 39/001164: {GTPases, e.g. Ras or Rho} - A61K 39/001182: {Carcinoembryonic antigen [CEA]} - A61K 39/001184: {Cancer testis antigens, e.g. SSX, BAGE, GAGE or SAGE} - A61K 39/001186: {MAGE} - A61K 39/001188: {NY-ESO} - A61K 39/001189: {PRAME} - A61K 39/001191: {Melan-A/MART} - A61K 39/001192: {Glycoprotein 100 [Gp100]} - A61K 39/001194: {Prostate specific antigen [PSA]} - A61K 2039/5158: {Antigen-pulsed cells, e.g. T-cells} - Y02A 50/30: Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change - A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D) - Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE ## Abstract A method of epitope discovery comprising the step of selecting an epitope from a population of peptide fragments of an antigen associated with a target cell, wherein the fragments have a known or predicted affinity for a major histocompatibility complex class I receptor peptide binding cleft, wherein the epitope selected corresponds to a proteasome cleavage product of the target cell. ## Claims ### Claim 1 A method of epitope discovery comprising the steps of: choosing a neoplastic target cell; identifying a proteasome activity of the target cell, wherein said proteasome is either a housekeeping proteasome or an immune proteasome; and selecting an epitope from a population of peptide fragments of an antigen associated with the target cell, wherein the antigen is selected from the group consisting of MelanA (MART-1), gp100 (Pmel 17), tyrosinase, RP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, CEA, RAGE, NY-ESO, SCP-1, Hom/Mel-40, PRAME, p53, H-Ras, HER-2/neu, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, Epstein Barr virus antigens, EBNA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, p185erbB2, p180crbB-3, c-met, nm-23H1, PSA, TAG-72-4, CAM 17.1, NuMa, K-ras, β-Catenin, CDK1, Mum-1, and p16, and wherein the fragments have a known or predicted affinity for a major histocompatibility complex class I receptor peptide binding cleft, wherein the epitope selected corresponds to a cleavage product associated with said proteasome activity of the target cell. ### Claim 2 A method of epitope discovery comprising the steps of: choosing a target cell that is infected by a virus; identifying a proteasome activity of the target cell, wherein said proteasome is either a housekeeping proteasome or an immune proteasome; and selecting an epitope from a population of peptide fragments of an antigen associated with the target cell, wherein the fragments have a known or predicted affinity for a major histocompatibility complex class I receptor peptide binding cleft, wherein the epitope selected corresponds to a cleavage product associated with said proteasome activity of the target cell. ### Claim 3 (depends on 2) The method of claim 2, wherein the virus is selected from the group consisting of: adenovirus, cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1, herpes simplex virus 2, human herpesvirus 6, varicella-zoster virus, hepatitis B virus, hepatitis D virus, papilloma virus, parvovirus B19, polyomavirus BK, polyomavirus IC, hepatitis C virus, measles virus, rubella virus, human immunodeficiency virus (Hr), human T cell leukemia virus I, and human T cell leukemia virus II. ### Claim 4 (depends on 2) The method of claim 2, wherein the antigen is selected from the group consisting of adenovirus, cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1, herpes simplex virus 2, human herpesvirus 6, varicella-zoster virus, hepatitis B virus, hepatitis D virus, papilloma virus, parvovirus B19, polyomavirus BK, polyomavirus JC, hepatitis C virus, measles virus, rubella virus, human immunodeficiency virus (HIV), human T cell leukemia virus I, and human T cell leukemia virus II. ### Claim 5 A method of epitope discovery comprising the steps of: choosing a target cell that is infected by an intracellular parasite, wherein the intracellular parasite is a bacterium, a protozoan, a fungus, or a prion; identifying a proteasome activity of the target cell, wherein said proteasome is either a housekeeping proteasome or an immune proteasome; and selecting an epitope from a population of peptide fragments of an antigen associated with the target cell, wherein the fragments have a known or predicted affinity for a major histocompatibility complex class I receptor peptide binding cleft, wherein the epitope selected corresponds to a cleavage product associated with said proteasome activity of the target cell. ### Claim 6 (depends on 5) The method of claim 5, wherein the intracellular parasite is selected from the group consisting of Chlamydia, Listeria, Salmonella, Legionella, Brucella, Coxiella, Rickettsia, Mycobacterium, Leishmania, Trypanasoma, Toxoplasma, and Plasmodium. ### Claim 7 (depends on 5) The method of claim 5, wherein the antigen is a parasite-associated antigen. ### Claim 8 (depends on 4) The method of claim 4, wherein the product is determined by in vitro analysis. ### Claim 9 (depends on 4) The method of claim 4, wherein the proteasome is a housekeeping proteasome. ### Claim 10 (depends on 4) The method of claim 4, wherein the proteasome is an immune proteasome. ### Claim 11 A method of discovering an epitope comprising the steps of: providing a sequence from a target cell, wherein the sequence encodes or comprises a protein expressed in the target cell, wherein the target cell is a neoplastic cell; identifying a population of peptide fragments of the protein, wherein the protein is selected from the group consisting of MelanA (MART-I), gp100 (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, CEA, RAGE, NY-ESO, SCP-1, Hom/Mel-40, PRAME, p53, H-Ras, HER-2/neu, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, Epstein Barr virus antigens EBNA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, p185erbB2, p180erbB-3, c-met, nm-23H1, PSA, TAG-72-4, CAM 17.1, NuMa, K-ras, β-Catenin, CDK4, Mum-1, and p16, wherein members of the population of peptide fragments have a known or predicted affinity for a major histocompatibility complex class I receptor peptide binding cleft; and selecting either a housekeeping epitope or an immune epitope from the population of peptide fragments, based thin a proteasome that is active in the target cell, wherein the proteasome is a housekeeping proteasome or an in immune proteasome. ### Claim 12 A method of discovering an epitope comprising the steps of: providing a sequence from a target cell, wherein the sequence encodes or comprises a protein expressed in the target cell, wherein the target cell is infected by a virus; identifying a population of peptide fragments of the protein, wherein members of the population of peptide fragments have a known or predicted affinity for a major histocompatibility complex class I receptor peptide binding cleft; and selecting either a housekeeping epitope or an immune epitope from the population of peptide fragments, based upon a proteasome that is active in the target cell, wherein the proteasome is a housekeeping proteasome or an immune proteasome. ### Claim 13 (depends on 12) The method of claim 12, wherein the virus is selected from the group consisting of: adenovirus, cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1, herpes simplex virus 2, human herpesvirus 6, varicella-zoster virus, hepatitis B virus, hepatitis D virus, papilloma virus, parvovirus B19, polyomavirus BK, polyomavirus JC, hepatitis C virus, measles virus, rubella virus, human immunodeficiency virus (HIV), human T cell leukemia virus I, and human T cell leukemia virus II. ### Claim 14 (depends on 12) The method of claim 12, wherein the antigen is selected from the group consisting of adenovirus, cytomegalovirus, Epstein-Bar virus, herpes simplex virus 1, herpes simplex virus 2, human herpesvirus 6, varicella-zoster virus, hepatitis B virus, hepatitis D virus, papilloma virus, parvovirus B19, polyomavirus BK polyomavirus JC, hepatitis C virus, measles virus, rubella virus, human immunodeficiency virus (HIV), human T cell leukemia virus I, and human T cell leukemia virus II. ### Claim 15 A method of discovering an epitope comprising the steps of: providing a sequence from a target cell, wherein the sequence encodes or comprises a protein expressed in the target call, wherein the target cell is infected by an intracellular parasite, and wherein the intracellular parasite is a bacterium, a protozoan, a fungus, or a prion; identifying a population of peptide fragments of the protein, wherein members of the population of peptide fragments have a known or predicted affinity for a major histocompatibility complex class I receptor peptide binding cleft; and selecting either a housekeeping epitope or an immune epitope from the population of peptide fragments, based upon a proteasome that is active in the target cell, wherein the proteasome is a housekeeping proteasome or an immune proteasome. ### Claim 16 (depends on 15) The method of claim 15, wherein the intracellular parasite is selected from the group consisting of Chlamydia, Listeria, Salmonella, Legionella, Brucella, Coxiella, Rickettsia, Mycobacterium, Leishmania, Trypanasoma, Toxoplasma, and Plasmodium. ### Claim 17 (depends on 15) The method of claim 15 wherein the antigen is a parasite-associated antigen. ### Claim 18 A method of discoing an epitope comprising the steps of: providing a sequence from a target cell, wherein the sequence encodes or comprises a protein expressed in the target cell, wherein the target cell is an intracellular parasite; identifying a population of peptide fragments of the protein, wherein members of the population of peptide fragments have a known or predicted affinity for a major histocompatibility complex class I receptor peptide binding cleft, wherein the affinity is determined by an algorithm; and selecting either a housekeeping epitope or an immune epitope from the population of peptide fragments, based upon a proteasome that is active in the target cell, wherein the proteasome is a housekeeping proteasome or an immune proteasome. ### Claim 19 A method of epitope discovery comprising the steps of: providing a neoplastic cell and a sequence, wherein the sequence comprises or encodes an antigen associated with the neoplastic cell, wherein the antigen is selected from the group consisting of MelanA (MART-I), gp100 (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, CEA, RAGE, NY-ESO, SCP-1, Hom/Mel-40, PRAME, p53, H-Ras, HER-2/neu, BCR-ABL, EZA-PRL, H4-RET, IGH-IGK, MYL-RAR, Epstein Barr virus antigens, EBNA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, p185erbB2, p180erbB-3, c-met, nm-23H1, PSA, TAG-72-4, CAM 17.1, NuMa, K-ras, β-Catenin, CDK4, Mum-1, and p16; identifying a population of peptide fragments of the antigen, wherein the population of peptide fragments is predicted to have an affinity for a major histocompatibility complex class I receptor peptide binding cleft; and selecting an epitope from the population of peptide fragments, wherein the epitope is determined by in vitro analysis to be a proteasome cleavage reaction product of a housekeeping proteasome or an immune proteasome active in the neoplastic cell.