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EA-053293-B1 - NEW CANCER ANTIGENS AND RELATED METHODS

EA053293B1EA 053293 B1EA053293 B1EA 053293B1EA-053293-B1

Abstract

Among other things, polypeptides and nucleic acids encoding said polypeptides are described, which are useful in the treatment, prevention and diagnosis of malignant neoplasms, in particular melanoma, especially cutaneous melanoma and uveal melanoma.

Inventors

  • Кассиотис Джордж
  • Янг Джордж
  • Аттиг Ян
  • Марино Фабио

Assignees

  • ДЗЕ ФРЭНСИЗ КРИК ИНСТИТЬЮТ ЛИМИТЕД
  • ЭНАРА БИО ЛИМИТЕД

Dates

Publication Date
20260504
Application Date
20200703
Priority Date
20190705

Claims (20)

  1. GTTCATCACCACACAAATTAGGAGCAACGTAA SEQ ID NO: 32 (cDNA sequence encoding CLT antigen 2) ATGTGGAACTCTCTGGAGGCCAGAAGTCCAAAATCAAGATGTTGCAGCACTG GTCCCTGGGAGGCTGTGCAGGAGAATCTGCTCTGGGCGTCTCTCCTGGCTCCTGGTG GTGCCACAATCTTCCCTGATCCTTGGCTTTTGAAGGCATCCCCCAGCTCTCTGCCTCA TCTTCACAGGACTTCTCCCTGTGCCTGTCTGTGCCCAAATTTCCCCTTCTATAAGGAC ACAGTCCTACTGCATCAGGGCCCCACGCTAA SEQ ID NO: 33 (cDNA sequence encoding CLT antigen 3) ATGGCCATGGGACAAAGAACCCCGTCTTTAGCTGAATTAAGGAAAAGTTCTG CAACATTTTTGACGTGCAACTTGGGGGCTCAAGCGGAGAAGCGAAGCAGAGCCCCT GGAAAACTCACATATGTGTCAACAATAGTCCTTGATGCCCCTGTAACAAAACTTGAG CAAGGCCTGGTGATGAAGAGATACAAGATTGTCACCCAAGGATTTGATTATACCCTCT GTTGAAAGTTAA SEQ ID NO: 34 (cDNA sequence encoding CLT antigen 4) ATGATTGTGAGGCCTCCCCAGCCATGTGGAACTAAATGCCTAAGAATTACAT CAGGAGTAAAAGTGAAGAAAAAGACTGTAAACTGCGTGCTAACTGCTTTGAAGAAT GAGAAGTCATGCCAAGCAAAATAG SEQ ID NO: 35 (cDNA sequence encoding CLT antigen 5) ATGAGCCCACCGGGAGGAAGGAACAACTCCAGACATGCTGCCTTAAGAGCT GTAACACTCACTGCGAAGGTCTGCAGCTTCACTCCTGAGCCAGTGAGACCACGAAC CCGCCACAAGGAAGAAACTCTGAACACATCATCTGAACATCAGAAGGAACAAACTC CAGACGCGCCACCTTAA SEQ ID NO: 36 (cDNA sequence encoding CLT antigen 6) ATGTGTGCACTGCAGGGACGGGGAGCTTCTCCTGCCGGAGCTGGTTTGTTCC ACTGGACAATGAGCCCTTTTCTGCTTGGCTCTCTGTATGGGCACATACACAATGAGG CGGTTTAG SEQ ID NO: 37 (cDNA sequence encoding CLT antigen 7) ATGAGGTTTGGAGATCTGAGTAGTTTACTGAAGGCACTCACATTGAAAGATT TTATGAAGCTGAAATTCAAATCTAGATGTGCCCCATCCAAAGACCACCCTCTTTATA CAGCAACATGCTGCTTCCCCTGGATCAAGAAACACAAGGAGCCTTCATCTACCACAT AA SEQ ID NO: 38 (cDNA sequence encoding CLT antigen 8) ATGAACAGCCCTGTTAAGAAGTGGGCAAAAAACATGAACAGGCTCTTCTCAG AAGACATACATGTCGCCAACAAACATATGAAAAACTACTCAAAATCACAAGTCAGG AAAGAAATGCGAATGAAAGCCATAATGAAGTACCATCACACACCAGTCAGAATGGC TACTATTAAAAAGTAA SEQ ID NO: 39 (peptide sequence derived from CLT antigen 6) SLYGHIHNEA CLAUSES OF THE INVENTION 1. An isolated polypeptide comprising a sequence selected from: (a) the sequence of SEQ ID NO: 2; and (b) an immunogenic variant of the sequence of (a) that is at least 95% identical to SEQ ID NO: 2; and (c) an immunogenic fragment of the sequence of (a) comprising at least 9 contiguous amino acids of SEQ ID NO: 2, wherein the fragment consists of a sequence selected from any of SEQ ID NOs: 11-14. - 50 053293
  2. 2. The isolated polypeptide according to claim 1, comprising or consisting of the sequence SEQ ID NO: 2.
  3. 3. A fusion protein comprising the isolated polypeptide of claim 1 or 2 fused to a second or additional polypeptide selected from (i) one or more other polypeptides selected from (x) polypeptides having the sequences of SEQ ID NOs: 1 and 3-8, and immunogenic variants of the polypeptides of (x) that are at least 95% identical thereto, and immunogenic fragments of the polypeptides of (x) that comprise at least 9 contiguous amino acids of the sequence of said polypeptide, wherein the fragment consists of a sequence selected from any of SEQ ID NOs: 11-14, and (y) polypeptides having the sequences of SEQ ID NOs: 9, 10, 15-22, and 39 (ii) other polypeptides that are melanoma-associated antigens, (iii) polypeptide sequences that are capable of enhancing the immune response, and (iv) polypeptide sequences that are capable of providing potent CD4+ help in enhancing CD8+ T cell responses to antigen epitopes.
  4. 4. An isolated nucleic acid encoding a polypeptide according to claim 1 or 2.
  5. 5. An isolated nucleic acid encoding the fusion protein according to paragraph 3.
  6. 6. The nucleic acid according to claim 4 or 5, which is DNA.
  7. 7. The nucleic acid of claim 6, comprising or consisting of a sequence selected from any of SEQ ID NOs: 24 and 32.
  8. 8. A vector containing a nucleic acid according to any one of claims 4 to 7.
  9. 9. The vector of claim 8, which contains DNA encoding regulatory elements suitable for ensuring transcription of a translationally active RNA molecule in a human host cell.
  10. 10. The vector according to claim 8 or 9, which is a viral vector.
  11. 11. The vector according to claim 10, which is an adenovirus vector, a vector based on an adeno-associated virus (AAV), an alphavirus, a herpes virus, an arenavirus, a measles virus, a poxvirus, a paramyxovirus, a lentivirus, or a rhabdovirus.
  12. 12. An immunogenic pharmaceutical composition comprising a polypeptide, nucleic acid, fusion protein or vector according to any one of claims 1 to 11 together with a pharmaceutically acceptable carrier.
  13. 13. A vaccine composition comprising a polypeptide, nucleic acid or vector according to any one of claims 1 to 11 together with a pharmaceutically acceptable carrier.
  14. 14. The composition according to claim 12 or 13, which contains one or more immunostimulants.
  15. 15. A method for generating an immune response in a human, which comprises administering to said human a polypeptide, nucleic acid, vector or composition according to any one of claims 1-14.
  16. 16. The method according to claim 15, wherein an immune response is generated against a malignant tumor expressing a sequence selected from SEQ ID NO: 2, an immunogenic variant of SEQ ID NO: 2 that is at least 95% identical to SEQ ID NO: 2, and an immunogenic fragment of SEQ ID NO: 2 containing at least 9 contiguous amino acids of SEQ ID NO: 2, wherein the fragment consists of a sequence selected from any of SEQ ID NOs: 11-14.
  17. 17. A method for treating a human suffering from a malignant neoplasm, wherein the cancer cells express a sequence selected from SEQ ID NO: 2 or an immunogenic fragment of SEQ ID NO: 2 comprising at least 9 contiguous amino acids of SEQ ID NO: 2, wherein the fragment consists of a sequence selected from any of SEQ ID NOs: 11-14 and an immunogenic variant of SEQ ID NO: 2 that is at least 95% identical to SEQ ID NO: 2, or preventing a malignant neoplasm in a human, wherein the malignant neoplasm will express a sequence selected from SEQ ID NO: 2, an immunogenic fragment of SEQ ID NO: 2 comprising at least 9 contiguous amino acids of SEQ ID NO: 2, wherein the fragment consists of a sequence selected from any of SEQ ID NOs: 11-14 and an immunogenic variant of SEQ ID NO: 2 that is at least 95% identical to SEQ ID NO: 2, wherein the method comprises administering to said human a polypeptide, a nucleic acid encoding said polypeptide, a fusion protein, a nucleic acid, a vector or a composition according to any one of claims 1-14.
  18. 18. A method for treating a malignant neoplasm in a human, wherein the cancer cells express a sequence selected from SEQ ID NO: 2, an immunogenic variant of SEQ ID NO: 2 that is at least 95% identical to SEQ ID NO: 2, and an immunogenic fragment of SEQ ID NO: 2 comprising at least 9 contiguous amino acids of SEQ ID NO: 2, wherein the fragment consists of a sequence selected from any of SEQ ID NOs: 11-14, which comprises collecting from said human a population of leukocytes comprising at least T cells, stimulating and/or amplifying said T cells in the presence of a polypeptide, a nucleic acid encoding said polypeptide, a fusion protein, a nucleic acid, a vector or a composition according to any one of claims 1-14, and reintroducing to the human some or all of said leukocytes, at least stimulated and/or amplified T cells.
  19. 19. A method for producing a population of T cells that are cytotoxic to cancer cells expressing a sequence selected from SEQ ID NO: 2, or an immunogenic fragment of SEQ ID NO: 2 comprising at least 9 contiguous amino acids of SEQ ID NO: 2, wherein the fragment consists of a sequence selected from any of SEQ ID NOs: 11-14, and an immunogenic variant of SEQ ID NO: 2, - 51 053293 at least 95% identical to SEQ ID NO: 2, which comprises (a) obtaining T cells from a patient with a malignant neoplasm and (ii) stimulating and amplifying the T cell population ex vivo using the polypeptide, nucleic acid, fusion protein, vector or composition of any one of claims 1-14.
  20. 20. A population of T cells obtained using a method that includes (a) obtaining T cells from a patient with a malignant neoplasm and (b) stimulating and amplifying the population of T cells ex vivo using a polypeptide having the sequence of SEQ ID NO: 2, or an immunogenic fragment of SEQ ID NO: 2 containing at least 9 contiguous amino acids of SEQ ID NO: 2, wherein the fragment consists of a sequence selected from any of SEQ ID NOs: 11-14.

Description

Field of technology The present invention relates to antigenic polypeptides and corresponding polynucleotides for use in the treatment or prevention of malignant neoplasms, in particular for use in the treatment or prevention of melanoma (e.g., cutaneous melanoma or uveal melanoma). The present invention also relates, inter alia, to pharmaceutical and immunogenic compositions comprising said nucleic acids and polypeptides, immune cells loaded with said polypeptides and polynucleotides and/or stimulated by said polypeptides and polynucleotides, antibodies specific for said polypeptides, and cells (autologous or otherwise) obtained by genetic engineering using molecules that recognize said polypeptides. State of the art During normal immune surveillance of pathogenic microbes, intracellular proteins are degraded by all cells to form peptides that are loaded onto major histocompatibility complex (MHC) class I molecules, which are expressed on the surface of all cells. Most of these host-derived peptides are recognized as self and remain invisible to the adaptive immune system. However, foreign (non-self) peptides can stimulate the expansion of naive CD8+ T cells, which encode a T cell receptor (TCR) that tightly binds the MHC I-peptide complex. This expanded T cell population can produce effector CD8+ T cells (including cytotoxic T lymphocytes - CTLs) that can eliminate foreign antigen-labeled cells, as well as memory CD8+ T cells that can be re-amplified when foreign antigen-labeled cells appear later in the animal's life. MHC class II molecules, whose expression is typically restricted to professional antigen-presenting cells (APCs) such as dendritic cells (DCs), are typically loaded with peptides that have been internalized from the extracellular environment. Binding of complementary TCR from a naive CD4+ T cell to the MHC P-peptide complex in the presence of various factors, including T-cell adhesion molecules (CD54, CD48) and costimulatory molecules (CD40, CD80, CD86), induces the maturation of CD4+ T cells into effector cells (e.g., T H 1, T H 2, T H 17, T FH , regulatory T cells). These effector CD4+ T cells can promote the differentiation of B cells into antibody-secreting plasma cells and promote the differentiation of antigen-specific CD8+ CTLs, thereby helping to induce an adaptive immune response to foreign antigens that includes both short-term effector functions and long-term immunological memory. DCs can perform the process of peptide antigen cross-presentation by delivering exogenous antigens (such as a peptide or protein released by a pathogen or tumor cell) to their MHC I molecules, facilitating the generation of immunological memory by providing an alternative pathway for stimulating the expansion of naive CD8+ T cells. Immunological memory (particularly antigen-specific B cells/antibodies and antigen-specific CTLs) are critical players in the fight against microbial infections, and immunological memory has been used to develop numerous vaccines that prevent diseases caused by important pathogenic microbes. Immunological memory is also known to play a key role in tumor control, but very few effective cancer vaccines have been developed. Cancer is the second leading cause of morbidity, accounting for nearly 1 in 6 deaths worldwide. Of the 8.8 million cancer deaths in 2015, lung cancer (1.69 million) was responsible for the largest number of deaths, followed by liver cancer (788,000), colorectal cancer (774,000), stomach cancer (754,000), and breast cancer (571,000). The economic burden of cancer in 2010 was estimated at US$1.16 trillion, and the number of new cases is expected to increase by approximately 70% over the next two decades (World Health Organization Cancer Facts, 2017). Current treatment options for cutaneous melanoma vary widely and depend largely on the tumor location and stage of the disease. The primary treatment for nonmetastatic melanoma is surgical removal of the tumor and surrounding tissue. More advanced melanomas may require treatments including lymph node dissection, radiation therapy, or chemotherapy. Immune checkpoint blockade strategies, including the use of antibodies targeting negative immune regulators such as PD-1/PD-L1 and CTLA4, have recently revolutionized the treatment of various malignancies, including melanoma (Ribas, A., & Wolchok, J. D. (2018) Science, 359:1350–1355). The extraordinary value of checkpoint blockade therapies and the well-established link between their clinical benefit and patients' adaptive immune responses (particularly T-cell immune responses) to their own cancer antigens have re-energized the search for effective cancer vaccines, vaccination methods, and cancer vaccine antigens. - 1 053293 Human endogenous retroviruses (HERVs) are remnants of ancient integrations of exogenous infectious retroviruses into germline cells. HERVs belong to a group of endogenous retroelements characterized by the presence of long terminal repeats (LTRs) flan