Tumor-specific neoantigens and methods of using the same

Patent metadata

Field	Value
Publication number	US-12528848-B2
Application number	US-201917058999-A
Country	US
Kind code	B2
Filing date	May 28, 2019
Priority date	May 25, 2018
Publication date	Jan 20, 2026
Grant date	Jan 20, 2026

Abstract

The disclosure relates to methods of manufacturing individualized vaccines that comprise nucleic acid molecules that encode one or more neoantigens specific for antigens that are expressed by a tumor in a subject. Compositions comprising coding regions encoding neoantigens organized in a pattern of nucleic acid sequences are also disclosed as well as methods of immunizing a subject using the same.

First claim

We claim:

1 . A method of treating cancer in a subject having cancer, the method comprising administering to the subject a nucleic acid molecule, wherein the nucleic acid molecule comprises:
(i) a DNA backbone region, and (ii) an expressible nucleic acid sequence operably linked to a regulatory sequence;
wherein the expressible nucleic acid sequence is a DNA comprising Formula I that encodes a chimeric polypeptide comprising a concatemer of a linked series of neoantigens or antigenic determinants thereof from the cancer, Formula I comprising independently selected, non-repetitive antigen expression domains (AED):
(AED 1 )-(linker) 1 -(AED 2 )-(linker) 2 -(AED 3 )-(linker) 3 . . . (AED n )-(linker) n -[AED n+1 ],

wherein each AED encodes one of the neoantigens or antigenic determinants thereof, each linker has a length independently selectable from about 15 to about 300 nucleotides and encodes a furin cleavage site, the length of each AED is independently selectable from about 90 to about 250 nucleotides, n is any positive integer from about 19 to about 58, and the DNA backbone region comprises SEQ ID NO:68 or a functional fragment thereof comprising about 90% sequence identity to SEQ ID NO:68, and wherein the sequence of SEQ ID NO: 68 or the functional fragment thereof comprises the regulatory sequence and a multiple cloning site, and the expressible nucleic acid sequence is positioned within the multiple cloning site.

2 . The method of claim 1 , wherein the administering comprises administering a therapeutically effective amount of the nucleic acid molecule that is effective to achieve:
(i) a clinical outcome selected from the group consisting of tumor regression, tumor shrinkage, tumor necrosis, anti-tumor response by the immune system, prevention or delay of tumor recurrence, prevention of tumor growth, prevention of tumor spread and/or induce tumor elimination, or a combination thereof; (ii) an increase, enhancement or prolongation of anti-tumor activity by T cells; (iii) an increase in the number of anti-tumor T cells or activated T cells as compared with the number prior to treatment; or (iv) a combination thereof.

3 . The method of claim 1 , wherein the administering comprises electroporation.

4 . The method of claim 1 , wherein the length of each AED is independently selectable from about 90 to about 100 nucleotides.

5 . The method of claim 1 , wherein each linker has a length independently selectable from about 18 to about 30 natural or non-natural nucleotides.

6 . The method of claim 1 , wherein the length of each AED is independently selectable from about 90 to about 100 nucleotides, each linker has a length independently selectable from about 18 to about 30 nucleotides, and the backbone region comprises the sequence of SEQ ID NO:68 or a functional fragment thereof comprising 95% sequence identity to SEQ ID NO:68.

7 . The method of claim 1 further comprising administering to the subject one or more immunostimulatory agent, wherein the one or more immunostimulatory agent comprises a nucleic acid sequence encoding IL-12.

8 . The method of claim 1 further comprising administering to the subject an inhibitor of the programmed death-I (PD-I) pathway.

9 . The method of claim 1 , wherein the administering comprises intradermal injection.

10 . The method of claim 1 , wherein the administering comprises administering a dose of about 1 mg of the nucleic acid molecule.

11 . The method of claim 1 , wherein the administering comprises administering a dose of from about 0.1 mg to about 10 mg of the nucleic acid molecule.

12 . The method of claim 1 , wherein the DNA that encodes the chimeric polypeptide consists of the concatemer of linked series of AEDs.

13 . The method of claim 1 , wherein the DNA backbone region comprises SEQ ID NO: 68.

14 . The method of claim 1 , wherein the length of each AED is about 100 nucleotides, each linker is about 21 nucleotides, the DNA backbone region comprises SEQ ID NO: 68, and the method further comprises administering to the subject a nucleic acid sequence encoding IL-12.

15 . The method of claim 1 , wherein the cancer is hepatocellular cancer.

16 . A method of enhancing an immune response against a plurality of heterogeneous hyperproliferative cells expressing neoantigens or antigen determinants thereof in a subject having the plurality of heterogenous hyperproliferative cells, the method comprising administering to the subject a therapeutically effective amount of a nucleic acid molecule; wherein the therapeutically effective amount is effective to enhance the immune response of the subject to the plurality of heterogeneous hyperproliferative cells relative to an immune response elicited by administration of a control nucleic acid molecule free of a nucleic acid sequence encoding a neoantigen to the subject, and wherein the nucleic acid molecule comprises:
(i) a DNA backbone region, and (ii) an expressible nucleic acid sequence operably linked to a regulatory sequence; wherein the expressible nucleic acid sequence is a DNA that encodes a chimeric polypeptide comprising a concatemer of a linked series of the neoantigens or antigenic determinants thereof, and comprises Formula I, comprising independently selected non-repetitive antigen expression domains (AED):
(AED 1 )-(linker) 1 -(AED 2 )-(linker)] 2 -(AED 3 )-(linker) 3 . . . (AED n )-(linker) n -[AED n+1 ],

wherein
each AED independently encodes one of the neoantigens or antigenic determinants thereof,
wherein each linker has a length independently selectable from about 15 to about 300 nucleotides and encodes a furin protease cleavage site;
wherein the length of each AED is independently selectable from about 90 to about 250 nucleotides,
wherein n is any positive integer from about 19 to about 100,
wherein the DNA backbone region comprises the sequence of SEQ ID NO:68 or a functional fragment thereof comprising about 90% sequence identity to SEQ ID NO: 68, and
wherein the sequence of SEQ ID NO: 68 or the functional fragment thereof comprises the regulatory sequence and a multiple cloning site, and the expressible nucleic acid sequence is positioned within the multiple cloning site, and the neoantigen or antigenic determinant thereof expressed by the heterogeneous hyperproliferative cells is one of the neoantigens or antigenic determinants of the chimeric polypeptide.

17 . The method of claim 16 , wherein the subject has a tumor, and wherein the administering comprises administering a therapeutically effective amount of the nucleic acid sufficient to induce an immune response of a sufficient magnitude or efficacy to inhibit or retard tumor growth, induce tumor cell death, induce tumor regression, prevent or delay tumor recurrence, prevent tumor growth, prevent tumor spread and/or induce tumor elimination.

18 . The method of claim 16 , further comprising administration of one or more therapeutic agents.

19 . The method of claim 18 , wherein the therapeutic agent is a biologic therapeutic or a small molecule.

20 . The method of claim 19 , wherein the therapeutic agent is:
(i) a checkpoint inhibitor or functional fragment thereof or a nucleic acid molecule encoding a checkpoint inhibitor or a functional fragment thereof; (ii) an adjuvant; (iii) an immunostimulatory agent; or (iv) a chemotherapeutic agent.

21 . The method of claim 20 , wherein:
the checkpoint inhibitor inhibits a checkpoint protein selected from the group con

Assignees

• The Wistar Inst Of Anatomy & Biology
• Inovio Pharmaceuticals Inc
• Geneos Therapeutics Inc
• Wistar Inst
• Geneos Therapeutica Inc

Inventors

• Duperret Elizabeth Kennedy
• Puchalt Alfredo Perales
• Weiner David
• Sardesai Niranjan Y

Classifications

• A61K40/4271

  Melanoma antigens · CPC title

• A61K40/4201

  Neoantigens · CPC title

• A61K40/11

  T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells · CPC title

• A61K39/00119

  Melanoma antigens · CPC title

• A61K39/00

  Medicinal preparations containing antigens or antibodies (materials for immunoassay G01N33/53) · CPC title