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Compositions for the treatment and diagnosis of breast cancer and methods for their use

Abstrict

Compositions and methods for the therapy and diagnosis of cancer, such as breast cancer, are disclosed. Compositions may comprise one or more breast tumor proteins, immunogenic portion thereof, or polynucleotides that encode such portions. Alternatively, a therapeutic composition may comprise an antigen presenting cell that expresses a breast tumor protein, or a T cell that is specific for cells expressing such a protein. Such compositions may be used, for example, for the prevention and treatment of diseases such as breast cancer. Diagnostic methods based on detecting a breast tumor protein, or mRNA encoding such a protein, in a sample are also provided.

Claims

What is claimed is:

1. An isolated polypeptide comprising SEQ ID NO:469.

2. A composition comprising a polypeptide according to claim 1, in combination with a physiologically acceptable carrier.

3. An isolated polypeptide according to claim 1, wherein the polypeptide comprises an amino acid sequence that is encoded by a polynucleotide of SEQ ID NO:463.

4. An immunogenic composition comprising a physiologically acceptable carrier and a polypeptide, wherein the polypeptide comprises SEQ ID NO:469.

5. An immunogenic composition according to claim 4, wherein the non-specific immune response enhancer is an adjuvant.

6. An immunogenic composition according to claim 4, wherein the immunostimulant induces a predominantly Type I response.

7. A fusion protein comprising at least one polypeptide, wherein the polypeptide comprises SEQ ID NO:469.

8. A fusion protein according to claim 7, wherein the fusion protein comprises an expression enhancer that increases expression of the fusion protein in a host cell transfected with a polynucleotide encoding the fusion protein.

9. A fusion protein according to claim 7, wherein the fusion protein comprises a T helper epitope that is not present within the polypeptide.

10. A fusion protein according to claim 7, wherein the fusion protein comprises an affinity tag.

11. A composition comprising a fusion protein according to claim 7, in combination with a physiologically acceptable carrier.

12. An immunogenic composition comprising a fusion protein according to claim 7, in combination with a non-specific immune response enhancer.

13. An immunogenic composition according to claim 12, wherein the non-specific immune response enhancer is an adjuvant.

14. An immunogenic composition according to claim 12, wherein the non-specific immune response enhancer induces a predominantly Type I response.

Description

TECHNICAL FIELD

The present invention relates generally to compositions and methods for the treatment of breast cancer. The invention is more particularly related to polypeptides comprising at least a portion of a protein that is preferentially expressed in breast tumor tissue and to polynucleotides encoding such polypeptides. Such polypeptides and polynucleotides may be in vaccines and pharmaceutical compositions for treatment of breast cancer.

BACKGROUND OF THE INVENTION

Breast cancer is a significant health problem for women in the United States and throughout the world. Although advances have been made in detection and treatment of the disease, breast cancer remains the second leading cause of cancer-related deaths in women, affecting more than 180,000 women in the United States each year. For women in North America, the life-time odds of getting breast cancer are one in eight.

No vaccine or other universally successful method for the prevention or treatment of breast cancer is currently available. Management of the disease currently relies on a combination of early diagnosis (through routine breast screening procedures) and aggressive treatment, which may include one or more of a variety of treatments such as surgery, radiotherapy, chemotherapy and hormone therapy. The course of treatment for a particular breast cancer is often selected based on a variety of prognostic parameters, including an analysis of specific tumor markers. See, e.g., Porter-Jordan and parameters, including an analysis of specific tumor markers. See, e.g., Porter-Jordan and Lippman, Breast Cancer 8:73-100 (1994). However, the use of established markers often leads to a result that is difficult to interpret, and the high mortality observed in breast cancer patients indicates that improvements are needed in the treatment, diagnosis and prevention of the disease.

Accordingly, there is a need in the art for improved methods for the treatment and diagnosis of breast cancer. The present invention fulfills these needs and further provides other related advantages.

SUMMARY OF THE INVENTION

The present invention provides compounds and methods for the treatment ad diagnosis of cancer, such as breast cancer. In one aspect, isolated polypeptides are provided comprising at least a portion of a breast tumor protein or a variant thereof. Certain portions and other variants are immunogenic, such that the ability of the variant to react with protein-specific antisera is not substantially diminished. With certain embodiments, the polypeptide comprises an amino acid sequence encoded by a polynucleotide selected from the group consisting of: (a) nucleotide sequences recited in SEQ ID NO: 1-61, 63-175, 178, 180, 182-313, 320-324, 342, 353, 366-368, 377, 382, 385, 389, 395, 397, 400, 408, 411, 413, 414, 416, 417, 419-423, 426, 427, 429, 431, 435-438, 441, 443-446, 450, 453, 454 and 463-468; (b) complements of said nucleotide sequences; and (c) variants of a sequence of (a) or (b). In specific embodiments, the inventive polypeptides comprise at least a portion of a tumor antigen that comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 62, 176, 179, 181 and 459-473.

In related aspects, isolated polynucleotides encoding the above polypeptides, or a portion thereof (such as a portion encoding at least 15 contiguous amino acid residues of a breast tumor protein), are provided. In specific embodiments, such polynucleotides comprise a sequence selected from the group consisting of sequences provided in SEQ ID NO: 1-61, 63-175, 178, 180, 182-313, 320-324, 342, 353, 366-368, 377, 382, 385, 389, 395, 397, 400, 408, 411, 413, 414, 416, 417, 419-423, 426, 427, 429, 431, 435-438, 441, 443-446, 450, 453, 454 and 463-468 and variants thereof. The present invention further provides expression vectors comprising the above polynucleotides, together with host cells transformed or transfected with such expression vectors. In preferred embodiments, the host cells are selected from the group consisting of E. coli, yeast and mammalian cells.

In another aspect, the present invention provides fusion proteins comprising a first and a second inventive polypeptide or, alternatively, an inventive polypeptide and a known breast tumor antigen.

The present invention also provides pharmaceutical compositions comprising at least one of the above polypeptides, or a polynucleotide encoding such a polypeptide, and a physiologically acceptable carrier, together with vaccines. For prophylactic or therapeutic use, comprising at least one such polypeptide or polynucleotide in combination with an immunostimulant. Pharmaceutical compositions and vaccines comprising one or more of the above fusion proteins are also provided.

The present invention further provides pharmaceutical compositions that comprise: (a) an antibody or antigen-binding fragment thereof that specifically binds to a breast tumor protein, and (b) a physiologically acceptable carrier.

Within further aspects, the present invention provides pharmaceutical compositions comprising: (a) an antigen presenting cell that expresses a polypeptide as described above and (b) a pharmaceutically acceptable carrier or excipient. Antigen presenting cells include dentritic cells, macrophages, monocytes, fibroblasts and B cells.

Within related aspects, vaccines are provided that comprise: (a) an antigen presenting cell that expresses a polypeptide as described above and (b) an immunostimulant.

In yet another aspect, methods are provided for inhibiting the development of breast cancer in a patient, comprising administering an effective amount of at least one of the above pharmaceutical compositions and/or vaccines.

The present invention further provides, within other aspects, methods for removing tumor cells from a biological sample, comprising contacting a biological sample with T cells that specifically react with a breast tumor protein, wherein the step of contacting is performed under conditions and for a time sufficient to permit the removal of cells expressing the protein from the sample.

Within related aspects, methods are provided for inhibiting the development of a cancer in a patient, comprising administering to a patient a biological sample treated as described above.

Methods are further provided, within other aspects, for stimulating and/or expanding T cells specific for a breast tumor protein, comprising contacting T cells with one or more of: (i) a polypeptide as described above; (ii) a polynucleotide encoding such a polypeptide; and/or (iii) an antigen presenting cell that expresses such a polypeptide; under conditions and for a time sufficient to permit the stimulation and/or expansion of T cells. Isolated T cell populations comprising T cells prepared as described above are also provided.

Within further aspects, the present invention provides methods for inhibiting the development of a cancer a patient, comprising administering to a patient an effective amount of a T cell population as described above.

The present invention further provides methods for inhibiting the development of a cancer in a patient comprising the steps of: (a) incubating CD4.sup.+ and/or CD8.sup.+ T cells isolated from a patient with one or more of: (i) a polypeptide comprising at least an immunogenic portion of a breast tumor protein; (ii) a polynucleotide encoding such a polypeptide; and (iii) an antigen-presenting cell that expressed such a polypeptide; and (b) administering to the patient an effective amount of the proliferated T cells, and thereby inhibiting the development of a cancer in the patient. Proliferated cells may, but need not, be cloned prior to administration to the patient.

The polypeptides disclosed herein may be usefully employed in the diagnosis and monitoring of breast cancer. In one aspect of the present invention, methods are provided for detecting a cancer in a patient, comprising: (a) contacting a biological sample obtained from a patient with a binding agent that is capable of binding to one of the above polypeptides, and (b) detecting in the sample an amount of polypeptide that binds to the binding agent; and (c) comparing the amount of polypeptide with a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in a patient. In preferred embodiments, the biding agent is an antibody, most preferably a monoclonal antibody. The cancer may be breast cancer.

In related aspects, methods are provided for monitoring the progression of a cancer in a patient, comprising: (a) contacting a biological sample obtained from a patient with a binding agent that is capable of binding to one of the above polypeptides; (b) detecting in the sample an amount of a polypeptide that binds to the binding agent; (c) repeating steps (a) and (b) using a biological sample obtained from the patient at a subsequent point in time; and (d) comparing the amounts of polypeptide detected in steps (b) and (c).

Within related aspects, the present invention provides antibodies, preferably monoclonal antibodies, that bind to the inventive polypeptides, as well as diagnostic kits comprising such antibodies, and methods of using such antibodies to inhibit the development of breast cancer.

The present invention further provides, within other aspects, methods for determining the presence or absence of a cancer in a patient, comprising the steps of: (a) contacting a biological sample obtained from a patient with an oligonucleotide that hybridizes to a polynucleotide that encodes a breast tumor protein: (b) detecting in the sample a level of a polynucleotide, preferably mRNA, that hybridizes to the oligonucleotide; and (c) comparing the level of polynucleotide that hybridizes to the oligonucleotide with a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient. Within certain embodiments, the amount of mRNA is detected via polymerase chain reaction using, for example, at least one oligonucleotide primer that hybridizes to a polynucleotide encoding a polypeptide as recited above, or a complement of such a polynucleotide. Within other embodiments, the amount of mRNA is detected using a hybridization technique, employing an oligonucleotide probe that hybridizes to a polynucleotide that encodes a polypeptide as recited above, or a complement of such a polynucleotide.

In related aspects, diagnostic kits comprising the above olignoucleotide probes or primers are provided.

These and other aspects of the present invention will become apparent upon reference to the following detailed description. All references disclosed herein are hereby incorporated by reference in their entirety as if each was incorporated individually.

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