CA2522994A1 - Nucleic acids and corresponding proteins entitled 109p1d4 useful in treatment and detection of cancer - Google Patents

Nucleic acids and corresponding proteins entitled 109p1d4 useful in treatment and detection of cancer Download PDF

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Publication number
CA2522994A1
CA2522994A1 CA002522994A CA2522994A CA2522994A1 CA 2522994 A1 CA2522994 A1 CA 2522994A1 CA 002522994 A CA002522994 A CA 002522994A CA 2522994 A CA2522994 A CA 2522994A CA 2522994 A1 CA2522994 A1 CA 2522994A1
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protein
cell
antibody
composition
nucleotide sequence
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CA002522994A
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French (fr)
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CA2522994C (en
Inventor
Arthur B. Raitano
Pia M. Challita-Eid
Wangmao Ge
Juan J. Perez-Villar
Steven B. Kanner
Aya Jakobovits
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Agensys Inc
Original Assignee
Agensys, Inc.
Arthur B. Raitano
Pia M. Challita-Eid
Wangmao Ge
Juan J. Perez-Villar
Steven B. Kanner
Aya Jakobovits
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Publication of CA2522994A1 publication Critical patent/CA2522994A1/en
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Publication of CA2522994C publication Critical patent/CA2522994C/en
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    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4748Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00Antineoplastic agents
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00Antineoplastic agents
    • A61P35/02Antineoplastic agents specific for leukemia
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00Drugs for immunological or allergic disorders
    • A61P37/02Immunomodulators
    • A61P37/04Immunostimulants
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705Receptors; Cell surface antigens; Cell surface determinants

Abstract

A novel gene 109P1D4 and its encoded protein, and variants thereof, are described wherein 109P1D4 exhibits tissue specific expression in normal adult tissue, and is aberrantly expressed in the cancers listed in Table i.
Consequently, 109P1D4 provides a diagnostic, prognostic, prophylactic and/or therapeutic target for cancer. The 109P1D4 gene or fragment thereof, or its encoded protein, or variants thereof, or a fragment thereof, can be used to elicit a humoral or cellular immune response; antibodies or T cells reactive with 109P1D4 can be used in active or passive immunization.

Claims (21)

1. A composition that comprises:
a) a peptide of eight, nine, ten, or eleven contiguous amino acids of a protein of Figure 2;
b) a peptide of Tables VIII-XXI;
c) a peptide of Tables XXII to XLV; or, d) a peptide of Tables XLVI to XLIX.
2. A composition of claim 1, which elicits an immune response.
3. A protein of claim 2 that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% homologous or identical to an entire amino acid sequence shown in Figure 2.
4. A protein of claim 2, which is bound by an antibody that specifically binds to a protein of Figure 2.
5. A composition of claim 2 wherein the composition comprises a cytotoxic T
cell (CTL) polypeptide epitope or an analog thereof, from the amino acid sequence of a protein of Figure 2.
6. A composition of claim 5 further limited by a proviso that the epitope is not an entire amino acid sequence of Figure 2.
7. A composition of claim 2 further limited by a proviso that the polypeptide is not an entire amino acid sequence of a protein of Figure 2.
8. A composition of claim 2 that comprises an antibody polypeptide epitope from an amino acid sequence of Figure 2.
9. A composition of claim 8 further limited by a proviso that the epitope is not an entire amino acid sequence of Figure 2.
10. A composition of claim 8 wherein the antibody epitope comprises a peptide region of at least 5 amino acids of Figure 2 in any whole number increment up to the end of said peptide, wherein the epitope comprises an amino acid position selected from:
a) an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of Figure 5, b) an amino acid position having a value less than 0.5 in the Hydropathicity profile of Figure 6;
c) an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of Figure 7;
d) an amino acid position having a value greater than 0.5 in the Average Flexibility profile of Figure 8;
e) an amino acid position having a value greater than 0.5 in the Beta-turn profile of Figure 9;
f) a combination of at least two of a) through e);
g) a combination of at least three of a) through e);
h) a combination of at least four of a) through e); or a combination of five of a) through e).
11. A polynucleotide that encodes a protein of claim 1.
12. A polynucleotide of claim 11 that comprises a nucleic acid molecule set forth in Figure 2.
13. A polynucleotide of claim 12 further limited by a proviso that the encoded protein is not an entire amino acid sequence of Figure 2.
14. A composition comprising a polynucleotide that is fully complementary to a polynucleotide of claim 11.
15. An 109P1D4 siRNA composition that comprises siRNA (double stranded RNA) that corresponds to the nucleic acid ORF sequence of the 109P1D4 protein or a subsequence thereof;
wherein the subsequence is 19, 20, 21, 22, 23, 24, or 25 contiguous RNA nucleotides in length and contains sequences that are complementary and non-complementary to at least a portion of the mRNA coding sequence.
16. A polynucleotide of claim 13 that further comprises an additional nucleotide sequence that encodes an additional peptide of claim 1.
17. A method of generating a mammalian immune response directed to a protein of Figure 2, the method comprising:
exposing cells of the mammal's immune system to a portion of a) a 109P1D4-related protein and/or b) a nucleotide sequence that encodes said protein, whereby an immune response is generated to said protein.
18. A method of generating an immune response of claim 17, said method comprising:
providing a 109P1 D4-related protein that comprises at least one T cell or at least one B cell epitope; and, contacting the epitope with a mammalian immune system T cell or B cell respectively, whereby the T cell or B cell is activated.
19. A method of claim 18 wherein the immune system cell is a B cell, whereby the activated B cell generates antibodies that specifically bind to the 109P1D4-related protein.
20. A method of claim 18 wherein the immune system cell is a T cell that is a cytotoxic T cell (CTL), whereby the activated CTL kills an autologous cell that expresses the 109P1D4-related protein.
21. A method of claim 18 wherein the immune system cell is a T cell that is a helper T cell (HTL), whereby the activated HTL secretes cytokines that facilitate the cytotoxic activity of a cytotoxic T cell (CTL) or the antibody-producing activity of a B cell.

corresponds to the nucleic acid ORF sequence of the 109P1D4 protein or a subsequence thereof; wherein the subsequence is 19, 20, 21, 22, 23, 24, or 25 contiguous RNA nucleotides in length and contains sequences that are complementary and non-complementary to at least a portion of the mRNA coding sequence.

30. A composition of claim 28, further comprising a physiologically acceptable carrier.

31. A pharmaceutical composition that comprises the composition of claim 28 in a human unit dose form.

32. A composition of claim 28 wherein the substance comprises an antibody or fragment thereof that specifically binds to a protein of Figure 2.

33. An antibody or fragment thereof of claim 32, which is monoclonal.

34. An antibody of claim 32, which is a human antibody, a humanized antibody or a chimeric antibody.

35. A non-human transgenic animal that produces an antibody of claim 32.

36. A hybridoma that produces an antibody of claim 33.

37. A composition of claim 28 wherein the substance reduces or inhibits the viability, growth or reproduction status of a cell that expresses a protein of Figure 2.

38. A composition of claim 28 wherein the substance increases or enhances the viability, growth or reproduction status of a cell that expresses a protein of Figure 2.

39. A composition of claim 28 wherein the substance is selected from the group comprising:
a) an antibody or fragment thereof, either of which immunospecifically binds to a protein of Figure 2;
b) a polynucleotide that encodes an antibody or fragment thereof, either of which immunospecifically binds to a protein of Figure 2;
c) a ribozyme that cleaves a polynucleotide having a 109P1D4 coding sequence, or a nucleic acid molecule that encodes the ribozyme; and, a physiologically acceptable carrier; and d) human T cells, wherein said T cells specifically recognize a 109P1D4 peptide subsequence in the context of a particular HLA molecule;
e) a protein of Figure 2, or a fragment of a protein of Figure 2;
f) a nucleotide encoding a protein of Figure 2, or a nucleotide encoding a fragment of a protein of Figure 2;
g) a peptide of eight, nine, ten, or eleven contiguous amino acids of a protein of Figure 2;
h) a peptide of Tables VIII-XXI;
i) a peptide of Tables XXII to XLV;
j) a peptide of Tables XLVI to XLIX;

k) an antibody polypeptide epitope from an amino acid sequence of Figure 2;
l) a polynucleotide that encodes an antibody polypeptide epitope from an amino acid sequence of Figure 2; or m) an 109P1D4 siRNA composition that comprises siRNA (double stranded RNA) that corresponds to the nucleic acid ORF sequence of the 109P1D4 protein or a subsequence thereof; wherein the subsequence is 19, 20, 21, 22, 23, 24, or 25 contiguous RNA nucleotides in length and contains sequences that are complementary and non-complementary to at least a portion of the mRNA coding sequence.

40. A method of inhibiting viability, growth or reproduction status of cancer cells that express a protein of Figure 2, the method comprising:
administering to the cells the composition of claim 28, thereby inhibiting the viability, growth or reproduction status of said cells.

41. The method of claim 40, wherein the composition comprises an antibody or fragment thereof, either of which specifically bind to a 109P1D4-related protein.

42. The method of claim 40, wherein the composition comprises (i) a 109P1 D4-related protein or, (ii) a polynucleotide comprising a coding sequence for a 109P1D4-related protein or comprising a polynucleotide complementary to a coding sequence for a 109P1D4-related protein.

43. The method of claim 40, wherein the composition comprises a ribozyme that cleaves a polynucleotide that encodes a protein of Figure 2.

44. The method of claim 40, wherein the composition comprises human T cells to said cancer cells, wherein said T cells specifically recognize a peptide subsequence of a protein of Figure 2 while the subsequence is in the context of the particular HLA molecule.

45. The method of claim 40, wherein the composition comprises a vector that delivers a nucleotide that encodes a single chain monoclonal antibody, whereby the encoded single chain antibody is expressed intracellularly within cancer cells that express a protein of Figure 2.

46. A method of delivering an agent to a cell that expresses a protein of Figure 2, said method comprising:
providing the agent conjugated to an antibody or fragment thereof of claim 32;
and, exposing the cell to the antibody-agent or fragment-agent conjugate.

47. A method of inhibiting viability, growth or reproduction status of cancer cells that express a protein of Figure 2, the method comprising:
administering to the cells the composition of claim 28, thereby inhibiting the viability, growth or reproduction status of said cells.

48. A method of targeting information for preventing or treating a cancer of a tissue listed in Table I to a subject in need thereof, which comprises:

detecting the presence or absence of the expression of a polynucleotide associated with a cancer of a tissue listed in Table I in a sample from a subject, wherein the expression of the polynucleotide is selected from the group consisting of:
(a) a nucleotide sequence in Figure 2;
(b) a nucleotide sequence which encodes a polypeptide encoded by a nucleotide sequence in Figure 2;
(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by a nucleotide sequence in Figure 2;
directing information for preventing or treating the cancer of a tissue listed in Table I to a subject in need thereof based upon the presence or absence of the expression of the polynucleotide in the sample.
49. The method of claim 48, wherein the information comprises a description of detection procedure or treatment for a cancer of a tissue listed in Table I.
50. A method for identifying a candidate molecule that modulates cell proliferation, which comprises:
(a) introducing a test molecule to a system which comprises a nucleic acid comprising a nucleotide sequence selected from the group consisting of:
(i) the nucleotide sequence of SEQ ID NO:1;
(ii) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence set forth in Figure 3;
(iii) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence set forth in Figure 3; and (iv) a fragment of a nucleotide sequence of (i), (ii), or (iii); or introducing a test molecule to a system which comprises a protein encoded by a nucleotide sequence of (i), (ii), (iii), or (iv); and (b) determining the presence or absence of an interaction between the test molecule and the nucleotide sequence or protein, whereby the presence of an interaction between the test molecule and the nucleotide sequence or protein identifies the test molecule as a candidate molecule that modulates cell proliferation.
51. The method of claim 50, wherein the system is an animal.
52. The method of claim 50, wherein the system is a cell.
53. The method of claim 50, wherein the test molecule comprises an antibody or antibody fragment that specifically binds the protein encoded by the nucleotide sequence of (i), (ii), (iii), or (iv).
54. A method for treating a cancer of a tissue listed in Table I in a subject, which comprises administering a candidate molecule identified by the method of claim 50 to a subject in need thereof, whereby the candidate molecule treats a cancer of a tissue listed in Table I in the subject.
55. A method for identifying a candidate therapeutic for treating a cancer of a tissue listed in Table I, which comprises:

(a) introducing a test molecule to a system which comprises a nucleic acid comprising a nucleotide sequence selected from the group consisting of:

(i) the nucleotide sequence of SEQ ID NO:1;
(ii) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence set forth in Figure 3;
(iii) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence set forth in Figure 3; and (iv) a fragment of a nucleotide sequence of (i), (ii), or (iii); or introducing a test molecule to a system which comprises a protein encoded by a nucleotide sequence of (i), (ii), (iii), or (iv); and (b) determining the presence or absence of an interaction between the test molecule and the nucleotide sequence or protein, whereby the presence of an interaction between the test molecule and the nucleotide sequence or protein identifies the test molecule as a candidate therapeutic for treating a cancer of a tissue listed in Table I.

56. The method of claim 55, wherein the system is an animal.
57. The method of claim 55, wherein the system is a cell.
58. The method of claim 55, wherein the test molecule comprises an antibody or antibody fragment that specifically binds the protein encoded by the nucleotide sequence of (i), (ii), (iii), or (iv).
CA2522994A 2003-04-30 2004-04-30 Nucleic acids and corresponding proteins entitled 109p1d4 useful in treatment and detection of cancer Expired - Fee Related CA2522994C (en)

Applications Claiming Priority (3)

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US46700203P 2003-04-30 2003-04-30
US60/467,002 2003-04-30
PCT/US2004/013568 WO2004098515A2 (en) 2003-04-30 2004-04-30 Nucleic acids and corresponding proteins entitled 109p1d4 useful in treatment and detection of cancer

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CA2522994A1 true CA2522994A1 (en) 2004-11-18
CA2522994C CA2522994C (en) 2012-09-25

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EP (1) EP1622571A4 (en)
JP (2) JP2007525183A (en)
AU (2) AU2004235755A1 (en)
CA (1) CA2522994C (en)
WO (1) WO2004098515A2 (en)

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US8010189B2 (en) 2004-02-20 2011-08-30 Brainsgate Ltd. SPG stimulation for treating complications of subarachnoid hemorrhage
US8055347B2 (en) 2005-08-19 2011-11-08 Brainsgate Ltd. Stimulation for treating brain events and other conditions
US9233245B2 (en) 2004-02-20 2016-01-12 Brainsgate Ltd. SPG stimulation
EP1864134A4 (en) * 2005-02-07 2010-10-20 Univ Columbia Methods to treat or prevent hormone-resistant prostate cancer using sirna specific for protocadherin-pc, or other inhibitors of protocadherin-pc expression or activity
NZ587704A (en) * 2006-03-31 2012-04-27 Alnylam Pharmaceuticals Inc Use of dsRNA for inhibiting expression of Eg5 gene
JP6236948B2 (en) * 2013-07-17 2017-11-29 東ソー株式会社 Antibody eluate and antibody purification method using the eluate
EP2878335B1 (en) 2013-11-10 2018-01-03 Brainsgate Ltd. Implant and delivery system for neural stimulator
IL303543A (en) 2015-02-18 2023-08-01 Enlivex Therapeutics Rdo Ltd Combination immune therapy and cytokine control therapy for cancer treatment
US11000548B2 (en) 2015-02-18 2021-05-11 Enlivex Therapeutics Ltd Combination immune therapy and cytokine control therapy for cancer treatment
US11318163B2 (en) 2015-02-18 2022-05-03 Enlivex Therapeutics Ltd Combination immune therapy and cytokine control therapy for cancer treatment
US11304976B2 (en) 2015-02-18 2022-04-19 Enlivex Therapeutics Ltd Combination immune therapy and cytokine control therapy for cancer treatment
US11497767B2 (en) 2015-02-18 2022-11-15 Enlivex Therapeutics R&D Ltd Combination immune therapy and cytokine control therapy for cancer treatment
US11596652B2 (en) 2015-02-18 2023-03-07 Enlivex Therapeutics R&D Ltd Early apoptotic cells for use in treating sepsis
CA2982452A1 (en) 2015-04-21 2016-10-27 Enlivex Therapeutics Ltd. Therapeutic pooled blood apoptotic cell preparations and uses thereof
US10271907B2 (en) 2015-05-13 2019-04-30 Brainsgate Ltd. Implant and delivery system for neural stimulator
EP3416661A4 (en) 2016-02-18 2020-03-04 Enlivex Therapeutics Ltd. Combination immune therapy and cytokine control therapy for cancer treatment
TWI795381B (en) * 2016-12-21 2023-03-11 比利時商健生藥品公司 Pyrazole derivatives as malt1 inhibitors

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EP1572987A4 (en) * 2000-02-03 2005-11-30 Nuvelo Inc Novel nucleic acids and polypeptides
WO2002083921A2 (en) * 2001-04-10 2002-10-24 Agensys, Inc. Nuleic acids and corresponding proteins useful in the detection and treatment of various cancers

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AU2008212020A1 (en) 2008-09-25
CA2522994C (en) 2012-09-25
WO2004098515A2 (en) 2004-11-18
AU2008212020B2 (en) 2012-05-24
JP2007525183A (en) 2007-09-06
EP1622571A2 (en) 2006-02-08
JP2011152132A (en) 2011-08-11
WO2004098515A3 (en) 2009-04-30
AU2004235755A1 (en) 2004-11-18
EP1622571A4 (en) 2012-05-02

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