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NZ776159B2 - Shared neoantigens - Google Patents
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NZ776159B2 - Shared neoantigens - Google Patents

Shared neoantigens

Info

Publication number
NZ776159B2
NZ776159B2 NZ776159A NZ77615916A NZ776159B2 NZ 776159 B2 NZ776159 B2 NZ 776159B2 NZ 776159 A NZ776159 A NZ 776159A NZ 77615916 A NZ77615916 A NZ 77615916A NZ 776159 B2 NZ776159 B2 NZ 776159B2
Authority
NZ
New Zealand
Prior art keywords
seq
composition
gene
neoantigenic peptide
cancer
Prior art date
Application number
NZ776159A
Other versions
NZ776159A (en
Inventor
Pavan Bachireddy
Edward F Fritsch
Nir Hacohen
Michael Steven Rooney
Sachet Ashok Shukla
Jing Sun
Catherine J Wu
Original Assignee
Dana Farber Cancer Institute Inc
The Broad Institute Inc
The General Hospital Corporation
Filing date
Publication date
Application filed by Dana Farber Cancer Institute Inc, The Broad Institute Inc, The General Hospital Corporation filed Critical Dana Farber Cancer Institute Inc
Publication of NZ776159A publication Critical patent/NZ776159A/en
Publication of NZ776159B2 publication Critical patent/NZ776159B2/en

Links

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/515—Animal cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/58—Medicinal preparations containing antigens or antibodies raising an immune response against a target which is not the antigen used for immunisation
    • A61K2039/585—Medicinal preparations containing antigens or antibodies raising an immune response against a target which is not the antigen used for immunisation wherein the target is cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/70—Multivalent vaccine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001102—Receptors, cell surface antigens or cell surface determinants
    • A61K39/001103—Receptors for growth factors
    • A61K39/001104—Epidermal growth factor receptors [EGFR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001102—Receptors, cell surface antigens or cell surface determinants
    • A61K39/001103—Receptors for growth factors
    • A61K39/001106—Her-2/neu/ErbB2, Her-3/ErbB3 or Her 4/ErbB4
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001148—Regulators of development
    • A61K39/00115—Apoptosis related proteins, e.g. survivin or livin
    • A61K39/001151—Apoptosis related proteins, e.g. survivin or livin p53
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001152—Transcription factors, e.g. SOX or c-MYC
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001154—Enzymes
    • A61K39/001162—Kinases, e.g. Raf or Src
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001154—Enzymes
    • A61K39/001164—GTPases, e.g. Ras or Rho
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001196—Fusion proteins originating from gene translocation in cancer cells
    • A61K39/001197—Breakpoint cluster region-abelson tyrosine kinase [BCR-ABL]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4748—Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/30—Special therapeutic applications
    • C12N2320/31—Combination therapy
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/30—Special therapeutic applications
    • C12N2320/34—Allele or polymorphism specific uses
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/56—Staging of a disease; Further complications associated with the disease
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/60—Complex ways of combining multiple protein biomarkers for diagnosis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/70—Mechanisms involved in disease identification
    • G01N2800/7023—(Hyper)proliferation
    • G01N2800/7028—Cancer
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Abstract

Disclosed herein is a pharmaceutical composition comprising a neoantigenic peptide wherein the neoantigenic peptide comprises a tumor-specific neoepitope consisting of 8-10 amino acids in length comprising an amino acid sequence encoded by a sequence downstream of a frameshift mutation in a gene, wherein the gene is UBR5.

Claims (12)

WE CLAIM:
1. A composition comprising: a. a recombinant or synthetic neoantigenic peptide that binds to an HLA, b. a polynucleotide encoding the recombinant neoantigenic peptide, c. antigen presenting cells (APCs) comprising (a) or (b), d. T cells specific for the neoantigenic peptide stimulated with APCs comprising (a) or (b), e. a T cell receptor (TCR) that binds to an MHC: peptide complex comprising a tumor- specific neoepitope of the recombinant or synthetic neoantigenic peptide in (a) ; wherein the neoantigenic peptide comprises a tumor-specific neoepitope consisting of 8- 10 amino acids in length comprising an amino acid sequence encoded by a sequence downstream of a frameshift mutation in a gene, wherein the gene is UBR5 and the tumor-specific neoepitope consists of 8-10 contiguous amino acids of EVLPTKMSYAANLKNVMNMQNRQKKKGKNSPCCQKKLRVQNQGHLLMILLHN (SEQ ID NO: 3466).
2. The composition of claim 1, wherein the gene is UBR5 and the frameshift is a K2120fs.
3. The composition of claim 1, wherein the gene is UBR5 and the gene comprises a c.6360delA mutation.
4. The composition of claim 1, wherein the gene is UBR5, and wherein the neoantigenic peptide comprises KNSPCCQKK (SEQ ID NO: 30664), KLRVQNQGH (SEQ ID NO: 30665), RVQNQGHLL (SEQ ID NO: 30666), VQNQGHLLM (SEQ ID NO: 30667), LRVQNQGHL (SEQ ID NO: 30668), NQGHLLMIL (SEQ ID NO: 30669), MQNRQKKKGK (SEQ ID NO: 30670), KGKNSPCCQK (SEQ ID NO: 30671), KLRVQNQGHL (SEQ ID NO: 30672), RVQNQGHLLM (SEQ ID NO: 30673), LRVQNQGHLL (SEQ ID NO: 30674), VQNQGHLLMI (SEQ ID NO: 30675), or NQGHLLMILL (SEQ ID NO: 30676).
5. The composition of claim 1, wherein the gene is UBR5, and wherein the tumor-specific neoepitope is KNSPCCQKK (SEQ ID NO: 30664), KLRVQNQGH (SEQ ID NO: 30665), RVQNQGHLL (SEQ ID NO: 30666), VQNQGHLLM (SEQ ID NO: 30667), LRVQNQGHL (SEQ ID NO: 30668), NQGHLLMIL (SEQ ID NO: 30669), MQNRQKKKGK (SEQ ID NO: 30670), KGKNSPCCQK (SEQ ID NO: 30671), KLRVQNQGHL (SEQ ID NO: 30672), RVQNQGHLLM (SEQ ID NO: 30673), LRVQNQGHLL (SEQ ID NO: 30674), VQNQGHLLMI (SEQ ID NO: 30675), or NQGHLLMILL (SEQ ID NO: 30676).
6. The composition of claim 1, wherein the composition is a vaccine.
7. The composition of claim 1, wherein the polynucleotide encoding the recombinant neoantigenic peptide is DNA.
8. The composition of claim 1, wherein the polynucleotide encoding the recombinant neoantigenic peptide is a messenger RNA (mRNA).
9. A pharmaceutical composition comprising the composition of claim 1 and a pharmaceutically acceptable carrier, excipient or diluent.
10. The pharmaceutical composition of claim 9, wherein the pharmaceutical composition further comprises an adjuvant.
11. Use of the composition of any one of claims 1-8, or the pharmaceutical composition of claim 9 or 10, in the manufacture of a medicament for treating cancer in a human subject, wherein the cancer is colorectal cancer, cervical cancer, uterine cancer, endometrium cancer, or gastric cancer.
12. A composition of any one of claims 1-8; a pharmaceutical composition of claim 9 or 10; or a use as claimed in claim 11, substantially as described herein and with reference to any example thereof.
NZ776159A 2016-05-20 Shared neoantigens NZ776159B2 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201562179877P 2015-05-20 2015-05-20
US201662389377P 2016-02-23 2016-02-23
NZ737891A NZ737891B2 (en) 2016-05-20 Shared neoantigens

Publications (2)

Publication Number Publication Date
NZ776159A NZ776159A (en) 2025-03-28
NZ776159B2 true NZ776159B2 (en) 2025-07-01

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