Natriuretic Peptide Receptor As A Biomarker For Diagnosis And Prognosis Of Cancer

  *US10184942B2*
  US010184942B2                                 
(12)United States Patent(10)Patent No.: US 10,184,942 B2
 Mohapatra et al. (45) Date of Patent:Jan.  22, 2019

(54)Natriuretic peptide receptor as a biomarker for diagnosis and prognosis of cancer 
    
(75)Inventors: Subhra Mohapatra,  Lutz, FL (US); 
  Shyam Mohapatra,  Lutz, FL (US) 
(73)Assignee:UNIVERSITY OF SOUTH FLORIDA,  Tampa (unknown), Type: US Company 
(*)Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S.C. 154(b) by 492 days. 
(21)Appl. No.: 13/422,880 
(22)Filed: Mar.  16, 2012 
(65)Prior Publication Data 
 US 2012/0270923 A1 Oct.  25, 2012 
 Related U.S. Patent Documents 
(60)Provisional application No. 61/453,646, filed on Mar.  17, 2011.
 
Jan.  1, 2013 G 01 N 33 57415 F I Jan.  22, 2019 US B H C Jan.  1, 2013 C 07 K 16 286 L I Jan.  22, 2019 US B H C Jan.  1, 2013 C 12 N 15 1138 L I Jan.  22, 2019 US B H C Jan.  1, 2013 C 12 Q 1 6886 L I Jan.  22, 2019 US B H C Jan.  1, 2013 G 01 N 33 5743 L I Jan.  22, 2019 US B H C Jan.  1, 2013 G 01 N 33 57419 L I Jan.  22, 2019 US B H C Jan.  1, 2013 G 01 N 33 57434 L I Jan.  22, 2019 US B H C Jan.  1, 2013 G 01 N 33 57438 L I Jan.  22, 2019 US B H C Jan.  1, 2013 G 01 N 33 57446 L I Jan.  22, 2019 US B H C Jan.  1, 2013 G 01 N 33 57492 L I Jan.  22, 2019 US B H C Jan.  1, 2013 C 07 K 2317 34 L A Jan.  22, 2019 US B H C Jan.  1, 2013 C 12 N 2310 11 L A Jan.  22, 2019 US B H C Jan.  1, 2013 C 12 N 2310 12 L A Jan.  22, 2019 US B H C Jan.  1, 2013 C 12 N 2310 14 L A Jan.  22, 2019 US B H C Jan.  1, 2013 C 12 Q 2600 158 L A Jan.  22, 2019 US B H C Jan.  1, 2013 G 01 N 2333 72 L A Jan.  22, 2019 US B H C Jan.  1, 2013 G 01 N 2800 50 L A Jan.  22, 2019 US B H C Jan.  1, 2013 G 01 N 2800 52 L A Jan.  22, 2019 US B H C Jan.  1, 2013 G 01 N 2800 56 L A Jan.  22, 2019 US B H C
(51)Int. Cl. G01N 033/574 (20060101); C07K 016/28 (20060101); C12Q 001/6886 (20180101); C12N 015/113 (20100101)
(58)Field of Search  None

 
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       WO       WO 20/00/71576       A2                11/2000      
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       WO       WO 20/01/75164       A3                10/2001      
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       WO       WO 20/04/011498       A3                2/2004      
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       WO       WO 20/09/042173       A1                3/2009      
       WO       WO 20/09/073527       A2                6/2009      

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     * cited by examiner
 
     Primary Examiner —Alana Harris Dent
     Art Unit — 1643
     Exemplary claim number — 1
 
(74)Attorney, Agent, or Firm — Saliwanchik, Lloyd & Saliwanchik

(57)

Abstract

The invention pertains to biomarkers for clinical detection of malignancies, especially for early detection of cancers. More specifically, this invention pertains to the role of Natriuretic Peptide Receptor A (NPRA) in cancer (e.g., tumor) progression. Thus, the invention includes materials and methods for the detection and prognosis of malignancies. The invention also pertains to methods for treating malignancies.
16 Claims, 26 Drawing Sheets, and 33 Figures


CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] The present application claims the benefit of U.S. Provisional Application Ser. No. 61/453,646, filed Mar. 17, 2011, which is hereby incorporated by reference herein in its entirety, including any figures, tables, or drawings.

BACKGROUND OF THE INVENTION

[0002] Advances in the fields of genomics and proteomics have helped to advance basic knowledge of cancer biology leading to identification of cancer biomarkers and development of new methods of diagnosis and disease prognosis. Biomarkers are biological molecules that are indicators of physiologic state and also of change during a disease process.
[0003] The utility of a biomarker lies in its ability to provide an early indication of the disease, to monitor disease progression, to provide ease of detection, and to provide a factor measurable across populations. The sequencing of the human genome has set the pace for biomarker discovery and provided the impetus for the next level of molecular inquiry, which is represented by functional genomics or proteomics. These approaches have led to the identification of numerous molecular signatures for either prognosis or prediction of a diverse array of cancers linked to specific disease phenotypes. However, only a limited number of these have been validated, commercialized and brought forward to the clinic. To be clinically useful, a molecular signature should have independent predictive value superior to pathological staging. An alternative method of detecting biomarkers is referred to candidate approach, whereby a selected protein is tested as candidate biomarker by its expression levels and its physiological role in the cancer pathogenesis.
[0004] It has been reported that NPRA expression and signaling is important for tumor growth (3). NPRA-deficient mice showed significantly reduced antigen-induced pulmonary inflammation. NPRA deficiency also substantially protected C57BL/6 mice from lung, skin, and ovarian cancers. Furthermore, a nanoparticle-formulated interfering RNA for NPRA attenuated B16 melanoma tumors in mice. Ectopic expression of a plasmid encoding NP73-102, the NH(2)-terminal peptide of the ANP prohormone, which down-regulates NPRA expression, also suppressed lung metastasis of A549 cells in nude mice and tumorigenesis of Line 1 cells in immunocompetent BALB/c mice. The antitumor activity of NP73-102 was in part attributed to apoptosis of tumor cells. Western blot and immunohistochemistry staining indicated that the transcription factor, nuclear factor-kappaB, was inactivated, whereas the level of tumor suppressor retinoblastoma protein was up-regulated in the lungs of NPRA-deficient mice. Furthermore, expression of vascular endothelial growth factor was down-regulated in the lungs of NPRA-deficient mice compared with that in wild-type mice. These results suggest that NPRA is involved in tumor angiogenesis.
[0005] It was also reported that atrial natriuretic peptide receptor A (NPRA) protein is expressed in various tumor cell lines, including the androgen-independent human prostate cancer (PCa) cell line DU145, but not in NIH 3T3, a normal mouse fibroblast cell line, and NHBE, a normal human bronchial epithelial cell line. Further, NPRA protein is also detectable in the human PCa cell line PC3. However, to date the expression levels of NPRA in human tumor tissues is largely unknown and the clinical relevance of NPRA is unclear.
[0006] Prostate cancer (PCa) is the third leading cause of death among men in America [1, 2]. The mortality from PCa results from metastases to bones and lymph nodes and progression from androgen-dependent to androgen-independent disease. While androgen deprivation has been effective in treating androgen-dependent PCa, it is ineffective in treating advanced PCas, the primary cause of mortality. Epidemiological and histopathological studies have implicated inflammation in the pathogenesis of PCa [3-5]. Studies have consistently shown a decreased risk of PCa among men who regularly take aspirin or other non-steroidal anti-inflammatory drugs (NSAIDs) [6-8]. Despite beneficial effects, the side effects from using high doses of COX-2 inhibitors for cancer prevention are a major concern. These observations emphasize the need for development of new effective treatments for advanced PCa.
[0007] The family of natriuretic peptide hormones has broad physiologic effects. In addition to vasodilation, cardiovascular homeostasis, sodium excretion and inhibition of aldosterone secretion, they have been implicated in immunity and inflammation [9-18]. The effects of atrial natriuretic peptide (ANP) are mediated by its interaction with the cell surface natriuretic peptide receptor A (NPRA; high affinity) and natriuretic peptide receptor C (NPRC; low affinity). In patients with prostate tumors, the immune response plays a large part in the progression of the disease and it is likely that the NPRA system is involved; but the role of NPRA in human cancers remains unknown. The peptide NP73-102 [14], whose sequence is immediately N-terminal to the ANP peptide, is an inhibitor of NPRA (iNPRA). NP73-102 does not bind to NPRA but blocks its expression, and it has been shown that it possesses bronchodilatory, anti-inflammatory [14, 16, 19, 20] and anti-tumor activity [19].
[0008] It was previously reported that mice deficient in NPRA (NPRA-knockout, KO) exhibit significantly decreased inflammation [16, 19-21]. Furthermore, it was found that NPRA-KO mice do not permit growth of implanted human lung cancer, melanoma and ovarian cancer cells [19], suggesting that NPRA may be a novel therapeutic candidate.

BRIEF SUMMARY OF THE INVENTION

[0009] The invention pertains to biomarkers for clinical detection of a number of malignancies, especially for early detection of cancers. More specifically, this invention pertains to the role of Natriuretic Peptide Receptor A (NPRA) in cancer (e.g., tumor) progression, as its expression has been examined in a number of contexts, such as in benign prostatic hyperplasia (BPH), high grade PIN (prostatic intraepithelial neoplasm) and prostatic adenocarcinoma. NPRA expression was examined in a human PCa tissue microarray (TMA) containing 240 samples. The TMA samples included BPH, regular prostatic intraepithelial neoplasm (PIN-R), high PIN (PIN-H), prostate carcinoma (PC) with a Gleason score of 6, PC with a Gleason score of 7, PC with a Gleason score of 8 and up and androgen-independent (AI) PC. The TMA slide was stained using an in-house human NPRA antibody in a Ventana Discovery XT automated system and the data statistically analyzed. Epithelial cell NPRA staining was weak for the majority of BPH and PIN-R samples, weak to moderate in PIN-H, moderate to strong in Gleason-6 and uniformly strong in epithelial tumors of Gleason-7 and -8 and in AI samples. Moderate staining was seen in stromal and inflammatory cells. Analyses of medians by chi-square and P-K test showed a strong association between intensity of NPRA staining and PCa stage. In other embodiments of this invention the expression of NPRA was associated with early detection of colon cancer, detection of breast cancer, detection of pancreatic cancer, detection of markell cell carcinoma, GIST tumors and melanoma. Although NPRA expression was found not to be associated with ovarian cancer or melanoma, NPRA may constitute a diagnostic and prognostic marker in many other cancers. The contents of Wang et al., “Natriuretic Peptide Receptor A as a Novel Target for Prostate Cancer,” Molecular Cancer, 2011, 10:56, is incorporated herein by reference in its entirety.
[0010] One aspect of the invention provides a method of detecting a malignancy in a subject, comprising obtaining a sample of cells from the subject, and determining whether the expression level (abundance) or activity of NPRA in cells of the sample is elevated relative to an appropriate control (comparing the determined NPRA expression level to an appropriate control). NPRA expression levels can be determined by determining the amount of genetic material encoding NPRA (e.g., DNA or mRNA transcripts) or the amount NPRA protein.
[0011] The appropriate control may be, for example, an NPRA expression level or activity in normal cells of the individual, an NPRA expression level or activity in normal cells of another individual or a group of individuals, or other reference NPRA expression level or activity. Preferably, the normal cells are normal cells of the same cell type under study in the sample. A case in which NPRA level or activity is elevated (e.g., over-expressed) relative to NPRA level or activity in the normal control cells is indicative of cancer.
[0012] The appropriate control may be NPRA level or activity in one or more types of cancer cells. The appropriate control may be NPRA level or activity in one or more stages of a cancer, in order to accurately stage cancer in the sample for diagnosis and/or prognosis of the disease. The NPRA expression level or activity in cancer cells may be from cells of the individual (e.g., obtained from the individual at a prior time, such as before treatment or earlier in a treatment regimen), or before or after the cancer diagnosis. In some embodiments, the NPRA expression level or activity of the sample is compared to that of normal cells, cancer cells, or both. In some embodiments, the control cells are primary cells and not a cell line. In some embodiments, the control cells are cells of a cell line.
[0013] Cancers that may be detected include, but are not limited to, prostate cancer, colon cancer, breast cancer, pancreatic cancer, Merkell cell carcinoma, and GIST.
[0014] The sample may be any biological sample comprising the cells of interest, or genetic material (e.g., DNA or RNA) encoding NPRA or NPRA protein obtained from sample cells of interest. For example, the sample may comprise tumor cells from the subject. In some embodiments, the sample comprises tissue or cells adjacent to a tumor in the subject. In some embodiments, the mammalian subject is a human and the cells are human cells. In some embodiments, the cells are primary cells, and not cells of a cell line.
[0015] Optionally, the methods of the invention further comprise carrying out at least one confirmatory test for the cancer if NPRA is determined to be over-expressed. Confirmatory tests for cancer vary with the cancer type. For example, confirmatory tests for colorectal cancer include, but are not limited to, a blood test, test for blood in a stool sample, test for a target microorganism in a stool sample, colonoscopy, sigmoidoscopy, X-ray with barium, computerized axial tomography, and capsule tomography, or a combination of two or more of the foregoing.
[0016] Another aspect of the invention concerns a method of treating a malignancy in a subject from whom a sample of cells (e.g., tumor cells) has been determined to have elevated NPRA level or activity. In some embodiments, the method comprises obtaining a sample comprising cells from the subject; determining whether NPRA is over-expressed in the cells (e.g., relative to an appropriate control), wherein NPRA over-expression is indicative of the cancer; and treating the subject with a therapy for the cancer if NPRA is over-expressed. Optionally, the determined NPRA expression level can be compared to a control known to have one or more cancers. Optionally, the method further comprises carrying out at least one confirmatory test for the cancer if NPRA is determined to be over-expressed.
[0017] The therapy or therapies used for treating the subject determined to have a malignancy can be selected by a clinician (such as an oncologist) and will depend upon the cancer type. For example, in the case of colorectal cancer, the therapy may comprise bowel diversion therapy, a chemotherapeutic, and radiation therapy, or a combination of two or more of the foregoing. These and other appropriate treatment regimens and procedures that may used for treatment of cancer are known to those of ordinary skill in the art.
[0018] Normally, cancer progression is generally unpredictable, with cancer diagnosis providing little guidance as to whether the cancer will progress aggressively or spontaneously regress in an individual. The present invention provides diagnostic methods for differentiating low grade cancers (e.g., low grade tumors) from high grade cancers (e.g., high grade tumors) by correlating the level of NPRA to favorable or unfavorable prognosis. The basic method involves (a) obtaining a sample of cells suspected of containing cancer cells; (b) analyzing the sample for NPRA level or activity; (c) correlating the NPRA level or activity with a control or standard NPRA level or activity; and (d) relating a high NPRA level or activity relative to said standard NPRA level or activity as an indication of unfavorable cancer prognosis, and a low NPRA level or activity relative to said standard NPRA level or activity equal to said standard level or activity as an indication of favorable cancer prognosis. The standard value can be a predetermined level obtained from assaying cells known to have low NPRA level or activity. Alternatively the standard value can be determined from a range of NPRA levels or activities known to be associated with the different clinical outcomes of cancer progression.
[0019] Another aspect of the invention concerns a method of monitoring cancer in a subject diagnosed with cancer, comprising obtaining a sample comprising cells from the subject; determining the NPRA level or activity in the cells; comparing the determined NPRA level or activity to an NPRA level or activity in a sample of cells previously obtained from the subject.
[0020] Another aspect of the invention concerns a method of determining the expression of NPRA in cells of subject that has been diagnosed with cancer, comprising obtaining a sample comprising cells from the subject, and determining the amount of NPRA expression (e.g., the amount of NPRA messenger RNA or protein) in cells of the sample. In some embodiments, the method comprises obtaining a series of samples from the subject over time and determining the amount of NPRA expression in the samples to monitor NPRA expression over time. The NPRA expression levels determined can be compared to an appropriate control and compared to one another to determine the status of the cancer and/or the subject's responsiveness to a treatment.
[0021] Another aspect of the invention concerns an immunoassay for determining whether a subject has a malignancy by detecting elevated NPRA, and a kit for conducting the immunoassay, the kit comprising a first container comprising an anti-NPRA antibody of the invention.
[0022] Another aspect of the invention concerns an in vitro polymerase chain reaction (PCR) assay kit for determining whether a subject has a cancer by detecting over-expression of NPRA, the kit comprising a first container comprising PCR primers that amplify an NPRA transcript or cDNA generated therefrom; and a second container comprising a nucleic acid marker, said marker being and labeled and able to hybridize to said transcript or cDNA. Optionally, the kit further comprises printed instructions for determining over-expression of NPRA.
[0023] Another aspect of the invention is a purified or isolated immunological reagent, such as an antibody or antibody fragment, that binds to NPRA protein. Preferably, the immunological reagents binds to human NPRA. In some embodiments, the immunological reagent binds to both human and mouse NPRA. In some embodiments, the immunological reagent is a monoclonal antibody or polyclonal antibody. In some embodiments, the immunological reagent binds to an epitope within the amino acid sequence of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3. In some embodiments, the immunological reagent binds to an epitope comprising or consisting of the amino acid sequence SEQ ID NO:1, 2, or 3.
[0024] Another aspect of the invention is a method for inhibiting the growth of a malignant cell in vitro or in vivo, comprising administering an agent to the cell, wherein the agent inhibits the function of migration inhibitor factor (MIF) in the malignant cell. In some embodiments, the agent is administered in vivo to a human or non-human mammal. The agent may be administered in vivo systemically or locally, directly at the site of the malignant cells. For example, if the mammal has tumor comprising malignant cells, the agent may be administered directly to the tumor (e.g., intra-tumorally).
[0025] In some embodiments, the agent targets a nucleic acid sequence within the MIF gene or transcript and reduces expression of MIF in the malignant cell (e.g., complete silencing of gene expression or partial knockdown). In some embodiments, the malignant cell is a cancer cell selected from the group consisting of prostate cancer, colon cancer, breast cancer, pancreatic cancer, Merkell cell carcinoma, and gastrointestinal stromal tumor (GIST). In some embodiments, the agent is a nucleic acid inhibitor selected from an RNA interference (RNAi) molecule (e.g., siRNA, shRNA), microRNA (miRNA), antisense oligonucleotide, or ribozyme that targets a target nucleic acid sequence within the MIF gene or transcript and reduces expression of MIF in the malignant cell. In some embodiments, the nucleic acid inhibitor comprises a nucleic acid sequence that is complementary with a target sequence within the MIF gene or transcript.
[0026] In each aspect of the invention, the subject may be one that has been diagnosed with the malignancy (for example, prostate cancer, colon cancer, breast cancer, pancreatic cancer, Merkell cell carcinoma, GIST), or may be a subject that has not yet been diagnosed with the malignancy.
[0027] Another aspect of the invention includes a method for providing an NPRA expression profile useful for detecting and/or prognosing cancer.
[0028] The terms “CaP” and “PCa” are used interchangeably herein to refer to cancer of the prostate.

BRIEF DESCRIPTION OF THE DRAWINGS

[0029] FIGS. 1A-1D show results of immunoblot analysis demonstrating specificity of an anti-NPRA antibody (antibody 3 specific to SEQ ID NO:3). In FIG. 1A, cell lysates were subjected to SDS-PAGE/immunoblot analysis with rabbit polyclonal antibody specific for human NPRA (top) and β-actin (bottom). FIG. 1B shows Western blotting for NPRA expression. β-actin expression was used as loading control. In FIGS. 1C and 1D, whole cell lysates of TRAMP-C1, C2 and C3 cell lines (FIG. 1C) and CaP2 and P2 cells (FIG. 1D) were analyzed by western blotting for NPRA expression.
[0030] FIG. 2 shows the strong immunoreactivity for NPRA in human prostate TMA. A 200× image of a representative sample from each disease stage is shown.
[0031] FIG. 3 is a graph showing the final NPRA scores for each sample of different stages of PCa. The bar represents the mean sample score for each category of PCa.
[0032] FIG. 4 shows the final scores for each sample of different stages of colon cancer are shown. These include, normal (n=24); adenoma (n=24) and adenocarcinoma (n=78). The bar represents the mean sample score for each category.
[0033] FIG. 5 shows the final scores for each sample of different stages of breast cancer are shown. These include, normal breast tissue (n=11); DCIS (n=14), IDC without metastases (n=28), IDC with metastases (n=31) and lymphnode metastases (n=21). The bar represents the mean sample score for each category.
[0034] FIG. 6 shows the final scores for each sample of different stages of pancreatic cancer are shown. These include, normal pancreatic duct (n=54); IDC (n=68), and neuroendocrine carcinoma (n=158). The bar represents the mean sample score for each category.
[0035] FIG. 7 shows the final scores for each sample of different stages of merkell cell carcinoma are shown. These include, normal skin (n=21); primary lesion (n=98), lymphnode involvement (n=65) and recurrent/metastatic (n=38). The bar represents the mean sample score for each category.
[0036] FIG. 8 shows the final scores for each sample of different stages of GIST tumors are shown. These include, normal skin (n=21); and GIST (n=124). The bar represents the mean sample score for each category.
[0037] FIGS. 9A-C demonstrate effects of NPRA deficiency. FIG. 9A shows that NPRA-deficiency impaired engraftment of TRAMP-C1 cells. Three groups of mice (wild type (WT), heterozygous (Het) and homozygous (NPRA-KO), (n=5 per group) were injected s.c. in the left and right flanks with 5×106 TRAMP-C1 cells per site. Mice were euthanized ten weeks after injection. Tumors were excised and weighed. Mean tumor weights ±SEM are shown in FIG. 9A. NPRA deficiency induced apoptosis of PCa cells. TRAMP-C1 cells were transiently transfected with psiNPRA (si1 and si2) and control plasmid (pU6). Cells were harvested 72 hrs later and whole cell lysates were analysed for NPRA and PARP by Western blotting. Results are shown in FIG. 9B. TRAMP-C1 cells were transfected with pU6 or psi-2 plasmids. Forty-eight hours after transfection, apoptosis was monitored by TUNEL assay. Results are shown in FIG. 9C.
[0038] FIGS. 10A-C show that NPRA depletion inhibits MIF expression. SuperArray analysis of prostate tissues of NPRA-KO and WT C57BL/6 mice. The relative expression level of genes that are altered in the prostate tissues of NPRA-KO vs. WT is shown in FIG. 10A. TRAMP-C1 cells were transfected with pshNPRAs or pNP73-102 plasmid. Whole cell lysates were extracted 72 hrs after transfection and examined for NPRA and MIF by Western blotting. Results are shown in FIGS. 10B and 10C.
[0039] FIGS. 11A-C show effects of iNPRA in TRAMP-C1 inoculated xenografts in immunocompetent mice, and correlation of NPRA expression with MIF expression. Four groups of C57BL/6 mice (n=7 per group) were injected s.c. in the right flank with 5×106 TRAMP-C1 cells. Two weeks later, tumor inoculated mice were treated with CNPs encapsulated with pVAX, pNP73-102, pVD or a combination of pNP73-102 and pVD i.p. twice a week until euthanized. The tumor size (FIG. 11A) was measured at the indicated days, and the weight was recorded after tumor resection (FIG. 11B). NPRA expression correlates with MIF expression in tumor lysates. Tumor lysates from B were analysed for NPRA and MIF by Western blotting. Results are shown in FIG. 11A. pVAX (lanes 1-3) and pNP73-102 (lanes 4-6). β-actin was used as a loading control.
[0040] FIGS. 12A-B show NPRA and MIF expression in primary prostate tumors. Prostate tissues were homogenized using a polytron and cell lysates were analyzed for NPRA and MIF by Western blotting. Results are shown in FIG. 12A. Lanes 1-4: lysates of TRAMP prostates. Lanes 5-6: lysates of C57BL/6 prostates. Whole cell lysates of tumor cell lines and control (normal) cells were analysed by Western blotting. Results are shown in FIG. 12B.
[0041] FIGS. 13A-C show immunofluorescence (A), and immunohistochemistry (B-C) with an anti-NPRA antibody. In FIG. 13A, the indicated cell lines were cultured on chamber slide and immunostained using anti-NPRA Ab. As a negative control, PC3 cells were incubated with secondary Ab alone (Control). In FIGS. 13B and 13C, two identical multi-tissue TMA slides containing colon, prostate, breast, and pancreas tumor tissues were used to optimize immunostaining. The slide in FIG. 13C was incubated with secondary Ab only.
[0042] FIGS. 14A-C show results of analysis of TRAMP-C1 (TR-C1), TRAMP-C2 (TR-C2), and TRAMP-C3 (TR-C3) cells. In FIG. 14A, TRAMP-C1, -C2 and -C3 cells were plated at 105 cells per plate for 4 days and viable cell numbers were enumerated at the indicated days by trypan blue dye-exclusion. In FIGS. 14B and 14C, TRAMP-C1 or TR-C3 cells were plated in 100 mm dishes at 1000 cells/dish. After 3 weeks, the colonies were stained, photographed (FIG. 14B) or counted (FIG. 14C).
[0043] FIG. 15 shows that pNP73-102 inhibits NPRA luciferase reporter activity. PC3 cells were co-transfected with pVAX, phNP73-102, pVD or pmNP73-102 and pNPRA-luc plasmid and pRenilla-luc plasmids. Forty-eight hrs after transfection, lysates were analysed for luciferase reporter activity. Relative luciferase activity ±SD is shown.
[0044] FIG. 16 shows results of blood pressure measurement in mice. Diastolic and systolic pressure of age matched wt (n=3), NPRA-KO (n=4) and TRAMP (n=4) male mice were measured using the CODA non-invasive blood pressure system (Kent Scientific). Data is presented as mean pressure ±SD.
[0045] FIGS. 17A-C show results of examination of NPRA and prostate specific membrane antigen (PSMA) expressions using a human PCa (tissue microarray (TMA) containing 240 samples, including BPH (n=24), low grade prostatic intraepithelial neoplasm (PIN-L; n=21), high grade PIN (PIN-H; n=14), AI PCa (n=15) and prostate carcinoma (GS 6, n=33; GS 7, n=82; GS 8 to 10; n=51). TMA slide was stained for NPRA (FIG. 17AA) and PSMA (FIG. 17B) using a Ventana Discovery XT automated system. Slides were scored for intensity and cellularity. The distribution of scores in each disease stage of PCa is shown. The bar represents the mean sample score. FIG. 17C is graph comparing PSMA and NPRA scores at different PCA disease states.

BRIEF DESCRIPTION OF THE SEQUENCES

[0046] SEQ ID NO: 1 is the NPRA target sequence of antibody 1 (CWAEDPQERPPFQQIR).
[0047] SEQ ID NO: 2 is the NPRA target sequence of antibody 2 (CSELWRVRWEDLQPSSLERHLRS).
[0048] SEQ ID NO: 3 is the NPRA target sequence of antibody 3 (IHLSSETKAVLEEFDGFELELR); ID: 1010.
[0049] SEQ ID NO: 4 is the amino acid sequence of mouse NPRA protein.
[0050] SEQ ID NO: 5 is the amino acid sequence of human NPRA protein.
[0051] SEQ ID NO: 6 is a nucleic acid sequence encoding human NPRA protein.

DETAILED DISCLOSURE OF THE INVENTION

[0052] The methods of the invention are particularly applicable to the diagnosis and prognosis (staging, i.e., determining the stage) of malignancies (e.g., cancer), such as prostate cancer, colon cancer, breast cancer, pancreatic cancer Merkell cell carcinoma, and gastrointestinal stromal tumor (GIST). The sample on which the assay is performed is preferably of body tissue and/or body fluid from a subject, but may be isolated primary cells from a subject, or cells cultured in vitro (e.g., from a cell line). In some embodiments, the cells in the sample are obtained from a subject and not derived from a cell line. The sample may be a piece of tissue or a fine needle aspirate (FNA) of cells from a subject, for example. In some embodiments, the biological sample is a sample of cells or tissue suspected to be cancer, or a tumor. The subject may be presenting with symptoms of cancer at the time the sample is taken from the subject and/or NPRA expression determined, or the subject may be asymptomatic. In the methods of the invention, analysis of a sample for NPRA level or activity can carried out at the nucleic acid or protein level. Depending upon the sample and the method of analysis selected, analysis may involve isolation of the nucleic acid (DNA or RNA) or protein, and other preparatory steps.
[0053] NPRA cDNA may be detected by use of one or more labeled specific oligonucleotide probes, the probes being chosen so as to be capable of annealing to part of the amplified cDNA sequence. Alternatively, labeled oligonucleotide primers and/or labeled mononucleotides could be used. There are a number of suitable detectable labels, which can be employed, including radiolabels.
[0054] The level of gene expression of NPRA can be determined by RT-PCR, or by using labeled antibodies that bind to NPRA protein, or other methods known in the art for determination of messenger RNA or protein. For example, labeled antibodies that bind to NPRA (anti-NPRA antibodies) can be used to stain cells expressing the proteins. If the cells normally express the NPRA protein but the antibodies to NPRA do not bind to the cells as indicated by the lack of production of the desired stain or other label (or diminished stain or other label), or the antibodies bind to the cells to the same extent as normal control cells as indicated by the production of stain or other label, this indicates that NPRA is not expressed or not over-expressed by the sample cells and that the subject does not have cancer (a negative result). Conversely, if the antibodies to NPRA bind to the cells as indicated by the production of the desired stain or other label to a greater extent than normal control cells, this indicates that NPRA is over-expressed by the sample cells and that the subject has cancer (a positive result).

Detecting a Cancer

[0055] According to the present invention, a cancer can be detected by determining whether or not NPRA is expressed in a tissue type that may or may not normally express NPRA, and to what extent. There are a number of ways to determine this including the use of antibodies to detect the presence of the proteins or by determining the presence and amount mRNA coding for NPRA. Gene expression analysis can be performed at the mRNA or protein level to detect differences in NPRA gene expression between populations of target cells of a subject and reference cells (e.g., an appropriate control) to determine whether or not NPRA is being expressed and to what extent. NPRA expression can be determined in multiple samples taken at different time points to monitor NPRA expression.
[0056] The methods of detecting cancer of the invention are preferably performed using human biological samples. Samples may be obtained directly from a subject (e.g., by biopsy) or the subject's sample may be obtained from a third party. The target cell population may include one or more subpopulations of cells. Appropriate isolation steps may be taken, and/or pretreatments carried out, to determine NPRA expression in the target cell type or types. The samples may be preserved or pre-treated, or prepared for histological and immunohistochemical analysis. In the case of blood samples, red blood cells can by lysed by treatment with hypotonic solutions from nucleated cells, and separation can be achieved by differential centrifugation and other methods known in the art. For example, a Ficoll-step-gradient procedure can be utilized. PBMC-enriched cell populations can be obtained using the buffy coat method. Biological samples may be cryopreserved prior to determination of NPRA expression.

Prognosis of Cancer

[0057] Another aspect of the invention comprises a method for predicting progression of a malignancy (e.g., a tumor) and prognosing the malignancy, comprising: (a) obtaining a sample suspected of containing malignant cells; (b) analyzing the sample for NPRA level or activity; (c) correlating the level or activity with a control NPRA level or activity; and (d) correlating a high NPRA level or activity with an indication of unfavorable prognosis and a low NPRA level or activity with a favorable prognosis. In some embodiments, the method comprises a method for prognosing cancer in mammalian subjects, comprising: (a) obtaining a sample suspected of containing cancer cells; (b) analyzing the sample for NPRA level or activity; (c) correlating the NPRA level or activity with a control NPRA level of activity; and (d) correlating a high NPRA level or activity with an indication of unfavorable prognosis and a low NPRA level or activity with a favorable prognosis. In some embodiments, the analyzing in step (b) comprises preparing a cell extract. In some embodiments, the analyzing in step (b) is under conditions selected to detect any NPRA level or activity, and the method further comprises analyzing a second aliquot of the sample for NPRA level or activity under conditions selected to detect NPRA level or activity only above the control NPRA level or activity; and associating high NPRA level or activity to the presence of NPRA in both the first and second aliquots and low NPRA level or activity to the presence of NPRA only in the first aliquot. In some embodiments, the analyzing step further comprises amplifying any NPRA genetic material in the reaction mixture by a polymerase chain reaction using at least one primer complementary to a NPRA sequence. In some embodiments, the analyzing step comprises detecting NPRA protein using an immunological reagent such as a monoclonal or polyclonal antibody. In some embodiments, the sample comprises tumor cells from the subject. In some embodiments, the sample comprises tissue or cells adjacent to a tumor in the subject. Samples may be obtained directly from a subject (e.g., by biopsy) or the subject's sample may be obtained from a third party.
[0058] A favorable prognosis can be tumor regression, which may be indicative of longer survival rates relative to patients with unfavorable prognosis. Optionally, the favorable or unfavorable prognosis is communicated to the subject. The communication may be given on a tangible medium or communicated verbally or by other methods.
[0059] Another aspect of the invention includes a method for providing an NPRA expression profile useful for detecting and/or prognosing cancer. The method comprises analyzing a biological sample (e.g., sample that may or may not contain malignant cells) from a subject for NPRA level or activity, wherein an elevated NPRA level or activity (relative to a reference NPRA level or activity, such as a normal control or less aggressive stage of the malignancy) is indicative of the presence of a malignancy or a more advanced stage of the malignancy. Optionally, the method further comprises communicating the results of the analysis to a health care provider. For example, the communication may involve providing a report containing the results of the analysis to the health care provider. In some embodiments, the report is transmitted to the health care provider electronically (e.g., via the internet) or on a tangible medium (e.g., paper or tangible electronic storage medium).

Use of Immunological Reagents to Detect the Expression of NPRA

[0060] For the purposes of this invention, the term “immunological reagents” is intended to encompass antisera and antibodies, particularly monoclonal and polyclonal antibodies, as well as fragments thereof (including F(ab), F(ab)2, F(ab)′ and Fv fragments) that bind to NPRA. Also included in the definition of immunological reagent are chimeric antibodies, humanized antibodies, and recombinantly-produced antibodies and fragments thereof, as well as aptamers (i.e., oligonucleotides capable of interacting with target molecules such as peptides). Immunological methods used in conjunction with the reagents of the invention include direct and indirect (for example, sandwich-type) labeling techniques, immunoaffinity columns, immunomagnetic beads, fluorescence activated cell sorting (FACS), enzyme-linked immunosorbent assays (ELISA), and radioimmune assay (RIA), most preferably FACS. For use in these assays, the immunological reagents can be labeled, using fluorescence, antigenic, radioisotopic or biotin labels, among others, or a labeled secondary or tertiary immunological detection reagent can be used to detect binding of the immunological reagents (e.g., in secondary antibody (sandwich) assays) used in determining the presence of NPRA. Examples of immunological reagents useful in the practice of this invention include antibodies, such as monoclonal antibodies that recognize NPRA. The immunological reagent may be specific to one or more isoforms of NPRA (e.g., one or more splice variants). Preferably, the immunological reagent is not specific with respect to NPRA isoform (i.e., binding to all NPRA isoforms, or at least the major NPRA isoforms). In some embodiments, the antibody detects (binds to) both human and mouse NPRA proteins or peptides.
[0061] The immunological reagents employed in the invention are preferably detectably-labeled, most preferably using fluorescent labels that have excitation and emission wavelengths adapted for detection using commercially-available instruments such as and most preferably fluorescence activated cell sorters. Examples of fluorescent labels useful in the practice of the invention include phycoerythrin (PE), fluorescein isothiocyanate (FITC), rhodamine (RH), Texas Red (TX), Cy3, Hoechst 33258, and 4′,6-diamidino-2-phenylindole (DAPI). Such labels can be conjugated to immunological reagents, such as antibodies and most preferably monoclonal antibodies using standard techniques.
[0062] In addition to the use of immunological methods for detection and determination of NPRA protein (e.g., ELISA, Western blots, immunoprecipitation), other detection methods for proteins that can be utilized to determine NPRA expression include, but are not limited to, mass spectrometry, protein array, and 2-D gel electrophoresis. For example, surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) allows rapid generation of high-throughput protein profiles from a large number of samples (see, for example, Liu et al., Cancer Invest. 2006, 24:747-753; Munro et al., Int. J. Cancer. 2006, 119:2642-2650; Simpkins et al., Pharmacogenomics. 2005, 6(6):647-653; Oh et al., Genome Inform. 2005, 16:195-204; Lakhan S. E., Diagn Pathol. 2006, 1:11; Novikova et al., Neurobiol Dis. 2006, 23:61-76; Lewczuk et al., Biol Psychiatry. 2004, 55:524-530; and Sanchez et al., Proteomics. 2004, 4:2229-2233, which are each incorporated herein by reference in its entirety).

SEQ ID NO:4 is the amino acid sequence of mouse NPRA protein:

[0063] 
[00001] [TABLE-US-00001]
  mprsrrvrpr lrallllppl lllrsghasd ltvavvlpvt ntsypwswar vgpavelalg  
 
  rvkarpdllp gwtvrmvlgs senaagvcsd taaplaavdl kwehspavfl gpgcvysaap
 
  vdrftahwrl plltagapal gigvkdeyal ttrtgpshvk lgdfvtalhr rlgwehqalv
 
  lyadrlgddr pcffivegly mrvrerinit vnhqefvegd pdhytkllrt vqrkgrviyi
 
  csspdafrnl mllaldaglt gedyvffhld vfgqslqgaq gpvpekpwer ddgqdrrarq
 
  rfqaakiity kepdnpeyle flkqlkllad kkfnftmedg lkniipasfh dglllyvqav
 
  tetlaqggtv tdgenitqrm wnrsfqgvtg ylkidrngdr dtdsplwdmd petgafrvvl
 
  nfngtsqelm aysehrlywp lgypppdipk cgfdnedpac nqdhfstlev lalvgslslv
 
  sflivsffiy rkmqlekelv selwrvrwed lqpsslerhl rsagsrltls grgsnygsll
 
  ttegqfqvfa ktayykgnlv avkrvnrkri eltrkvlfel khmrdvqneq ltrfvgactd
 
  ppniciltey cprgslqdil enesitldwm frysltndiv kgmlflhnga icshgnlkss
 
  ncvvdgrfvl kitdyglesf rdpepeqght lfakklwtap ellrmasppa rgsqagdvys
 
  fgiilqeial rsgvfyvegl dlspkeiier vtrgeqppfr psmdlqshle elgqlmqrcw
 
  aedpqerppf qqirlalrkf nkenssnild nllsrmeqya nnleelveer tqpyleekrk
 
  aeallyqilp hsvaeqlkrg etvqaeafds vtiyfsdivg ftalsaestp mqvvtllndl
 
  ytcfdavidn fdvykvetig daymvvsglp vrngqlhare varmalalld avrsfrighr
 
  pqeqlrlrig ihtgpvcagv vglkmprycl fgdtvntasr mesngealri hlssetkavl
 
  eefdgfelel rgdvemkgkg kvrsywllgd rgcssra
[0064] (GenBank Accession Number AAA37670; version AAA37670.1, GI: 309246; which is incorporated herein by reference)
SEQ ID NO:5 is the amino acid sequence of human NPRA protein:
[0065] 
[00002] [TABLE-US-00002]
  mfrysltndi vkgmlflhng aicshgnlks sncvvdgrfv lkitdygles frdldpeqgh  
 
  tvyakklwta pellrmaspp vrgsqagdvy sfgiilqeia lrsgvfhveg ldlspkeiie
 
  rvtrgeqppf rpslalqshl eelgllmqrc waedpqerpp fqqirltlrk fnrenssnil
 
  dnllsrmeqy annleelvee rtqayleekr kaeallyqil phsvaeqlkr getvqaeafd
 
  svtiyfsdiv gftalsaest pmqvvtllnd lytcfdavid nfdvykveti gdaymvvsgl
 
  pvrngrlhac evarmalall davrsfrirh rpqeqlrlri gihtgpvcag vvglkmpryc
 
  lfgdtvntas rmesngealk ihlssetkav leefggfele lrgdvemkgk gkvrt

(GenBank Accession Number AAD14112; version AAD14112.1, GI: 4261812; which is incorporated herein by reference)
Other versions of the human mouse NPRA protein sequences include:
GenBank Accession Number AAF01340 (version AAF01340.1, GI: 6013455);
GenBank Accession Number CAI3613 (version CAI13613.1, GI: 55962127);
GenBank Accession Number AAI10660 (version AAI10660.1, GI: 83404966); and
GenBank Accession Number AAA66945 (version AAA66945, GI: 473634), which are each incorporated herein by reference.
Detection of NPRA Using Nucleic Acid Hybridization Techniques
[0066] The expression of NPRA can be determined using nucleic acids and associated hybridization methods to detect the presence of mRNA within a cell of interest. For example, a nucleic acid that is complementary to and hybridizes under stringent conditions to the mRNA of a portion of NPRA can be detectably labeled. Such a detectably labeled nucleic acid molecule can be contacted with a cell or an extract of a cell to detect the presence and amount of the mRNA that encodes NPRA. The amount of nucleic acids that encode NPRA is assumed to correlate with the expression of the NPRA in a cell. The selection of an appropriate nucleic acid molecule for use as a probe can be made by studying the nucleic acid sequences of human NPRA and determining an appropriate length. A unique sequence should be determined that selectively hybridizes under stringent conditions to the mRNA of NPRA. The probe may be specific to one or more isoforms of NPRA. Preferably, the probe is not specific with respect to NPRA isoform (i.e., detecting all NPRA isoforms, or at least the major NPRA isoforms).
[0067] The term “stringent conditions” as used herein refers to parameters with which the art is familiar. Nucleic acid hybridization parameters may be found in references which compile such methods, e.g., Molecular Cloning: A Laboratory Manual, J. Sambrook, et al., eds., Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, or Current Protocols in Molecular Biology, F. M. Ausubel, et al., eds., John Wiley & Sons, Inc., New York. More specifically, stringent conditions, as used herein, refers, for example, to hybridization at 65 degrees C. in hybridization buffer (3.5×SSC, 0.02% Ficoll, 0.02% polyvinyl pyrrolidone, 0.02% Bovine Serum Albumin, 2.5 mM NaH2 PO4 (pH7), 0.5% SDS, 2 mM EDTA). SSC is 0.15 M sodium chloride/0.015 M sodium citrate, pH7; SDS is sodium dodecyl sulphate; and EDTA is ethylenediaminetetracetic acid. After hybridization, the membrane upon which the DNA is transferred is washed, for example, in 2×SSC at room temperature and then at 0.1-0.5×SSC/0.1×SDS at temperatures up to 68 degrees C.
[0068] There are other conditions, reagents, and so forth which can be used, which result in a similar degree of stringency. The skilled artisan will be familiar with such conditions, and thus they are not provided here. It will be understood, however, that the skilled artisan will be able to manipulate the conditions in a manner to permit the clear identification of NPRA (e.g., by using lower stringency conditions). The skilled artisan also is familiar with the methodology for screening cells and libraries for expression of such molecules which then are routinely isolated, followed by isolation of the pertinent nucleic acid molecule and sequencing.
[0069] One method for detecting the NPRA transcripts in genetic material derived from a subject's cells uses polymerase chain reaction (PCR) technology. PCR technology is practiced routinely by those having ordinary skill in the art and its uses in diagnostics are well known and accepted. Methods for practicing PCR technology are disclosed in “PCR Protocols: A Guide to Methods and Applications”, Innis, M. A., et al. Eds. Academic Press, Inc. San Diego, Calif. (1990). Applications of PCR technology are disclosed in “Polymerase Chain Reaction” Erlich, H. A., et al., Eds. Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989). U.S. Pat. No. 4,683,202, U.S. Pat. No. 4,683,195, U.S. Pat. No. 4,965,188 and U.S. Pat. No. 5,075,216 describe methods of performing PCR. PCR may be routinely practiced using Perkin Elmer Cetus GENE AMP RNA PCR kit.
[0070] PCR technology allows for the rapid generation of multiple copies of DNA sequences by providing 5′ and 3′ primers that hybridize to sequences present in an RNA or DNA molecule, and further providing free nucleotides and an enzyme which fills in the complementary bases to the nucleotide sequence between the primers with the free nucleotides to produce a complementary strand of DNA. The enzyme will fill in the complementary sequences adjacent to the primers. If both the 5′ primer and 3′ primer hybridize to nucleotide sequences on the same small fragment of nucleic acid, exponential amplification of a specific double-stranded size product results. If only a single primer hybridizes to the nucleic acid fragment, linear amplification produces single-stranded products of variable length.
[0071] PCR primers can be designed routinely by those having ordinary skill in the art using sequence information. The nucleotide sequences of NPRA transcripts are known in the art. To perform this method, RNA is extracted from cells in a sample and tested or used to make cDNA using well known methods and readily available starting materials.
[0072] Those having ordinary skill in the art can readily prepare PCR primers. A set of primers generally contains two primers. When performing PCR on extracted mRNA or cDNA generated therefrom, if the NPRA transcript or cDNA generated therefrom is present, multiple copies of the mRNA or cDNA will be made. If it is not present, PCR will not generate a discrete detectable product. Primers are generally 8-50 nucleotides, preferably about 15-35 nucleotides, more preferably 18-28 nucleotides, which are identical or complementary to and therefor hybridize to the NPRA transcript or cDNA generated therefrom. In preferred embodiments, the primers are each 15-35 nucleotides in length, and more preferably 18-28 nucleotides in length. The primer must hybridize to the sequence to be amplified.
[0073] Typical primers are 18-28 nucleotides in length and generally have 500 to 60% G+C composition. The entire primer is preferably complementary to the sequence to which it must hybridize. Preferably, primers generate PCR products 100 base pairs to 2000 base pairs. However, it is possible to generate products of 50 to up to 10 kb and more. If mRNA is used as a template, the primers must hybridize to mRNA sequences. If cDNA is used as a template, the primers must hybridize to cDNA sequences.
[0074] The mRNA or cDNA is combined with the primers, free nucleotides and enzyme following standard PCR protocols. The mixture undergoes a series of temperature changes. If the NPRA transcript or cDNA generated therefrom is present, that is, if both primers hybridize to sequences on the same molecule, the molecule comprising the primers and the intervening complementary sequences will be exponentially amplified. The amplified DNA can be easily detected by a variety of well known means. If no NPRA transcript or cDNA generated therefrom is present, no PCR product will be exponentially amplified. The PCR technology therefore provides an extremely easy, straightforward and reliable method of detecting the NPRA transcript in a sample.
[0075] PCR product may be detected by several well known means. The preferred method for detecting the presence of amplified DNA is to separate the PCR reaction material by gel electrophoresis and stain the gel with ethidium bromide in order to visual the amplified DNA if present. A size standard of the expected size of the amplified DNA is preferably run on the gel as a control.
[0076] In some instances, such as when unusually small amounts of RNA are recovered and only small amounts of cDNA are generated therefrom, it is desirable to perform a PCR reaction on the first PCR reaction product. That is, if difficult to detect quantities of amplified DNA are produced by the first reaction, a second PCR can be performed to make multiple copies of DNA sequences of the first amplified DNA. A nested set of primers are used in the second PCR reaction. The nested set of primers hybridize to sequences downstream of the 5′ primer and upstream of the 3′ primer used in the first reaction.

SEQ ID NO:6 is a nucleic acid sequence encoding human NPRA.

[0077] 
[00003] [TABLE-US-00003]
  acactccctg gggcaggcgc tcacgcacgc tacaaacaca cactcctctt tcctccctcg  
 
  cgcgccctct ctcatccttc ttcacgaagc gctcactcgc accctttctc tctctctctc
 
  tctctctcta acacgcacgc acactcccag ttgttcacac tcgggtcctc tccagcccga
 
  cgttctcctg gcacccacct gctccgcggc gccctgcgcg cccccctcgg tcgcgcccct
 
  tgcgctctcg gcccagaccg tcgcagctac agggggcctc gagccccggg gtgagcgtcc
 
  ccgtcccgct cctgctcctt cccataggga cgcgcctgat gcctgggacc ggccgctgag
 
  cccaagggga ccgaggaggc catggtagga gcgctcgcct gctgcggtgc ccgctgaggc
 
  catgccgggg ccccggcgcc ccgctggctc ccgcctgcgc ctgctcctgc tcctgctgct
 
  gccgccgctg ctgctgctgc tccggggcag ccacgcgggc aacctgacgg tagccgtggt
 
  actgccgctg gccaatacct cgtacccctg gtcgtgggcg cgcgtgggac ccgccgtgga
 
  gctggccctg gcccaggtga aggcgcgccc cgacttgctg ccgggctgga cggtccgcac
 
  ggtgctgggc agcagcgaaa acgcgctggg cgtctgctcc gacaccgcag cgcccctggc
 
  cgcggtggac ctcaagtggg agcacaaccc cgctgtgttc ctgggccccg gctgcgtgta
 
  cgccgccgcc ccagtggggc gcttcaccgc gcactggcgg gtcccgctgc tgaccgccgg
 
  cgccccggcg ctgggcttcg gtgtcaagga cgagtatgcg ctgaccaccc gcgcggggcc
 
  cagctacgcc aagctggggg acttcgtggc ggcgctgcac cgacggctgg gctgggagcg
 
  ccaagcgctc atgctctacg cctaccggcc gggtgacgaa gagcactgct tcttcctcgt
 
  ggaggggctg ttcatgcggg tccgcgaccg cctcaatatt acggtggacc acctggagtt
 
  cgccgaggac gacctcagcc actacaccag gctgctgcgg accatgccgc gcaaaggccg
 
  agttatctac atctgcagct cccctgatgc cttcagaacc ctcatgctcc tggccctgga
 
  agctggcttg tgtggggagg actacgtttt cttccacctg gatatctttg ggcaaagcct
 
  gcaaggtgga cagggccctg ctccccgcag gccctgggag agaggggatg ggcaggatgt
 
  cagtgcccgc caggcctttc aggctgccaa aatcattaca tataaagacc cagataatcc
 
  cgagtacttg gaattcctga agcagttaaa acacctggcc tatgagcagt tcaacttcac
 
  catggaggat ggcctggtga acaccatccc agcatccttc cacgacgggc tcctgctcta
 
  tatccaggca gtgacggaga ctctggcaca tgggggaact gttactgatg gggagaacat
 
  cactcagcgg atgtggaacc gaagctttca aggtgtgaca ggatacctga aaattgatag
 
  cagtggcgat cgggaaacag acttctccct ctgggatatg gatcccgaga atggtgcctt
 
  cagggttgta ctgaactaca atgggacttc ccaagagctg gtggctgtgt cggggcgcaa
 
  actgaactgg cccctggggt accctcctcc tgacatcccc aaatgtggct ttgacaacga
 
  agacccagca tgcaaccaag atcacctttc caccctggag gtgctggctt tggtgggcag
 
  cctctccttg ctcggcattc tgattgtctc cttcttcata tacaggaaga tgcagctgga
 
  gaaggaactg gcctcggagc tgtggcgggt gcgctgggag gacgttgagc ccagtagcct
 
  tgagaggcac ctgcggagtg caggcagccg gctgaccctg agcgggagag gctccaatta
 
  cggctccctg ctaaccacag agggccagtt ccaagtcttt gccaagacag catattataa
 
  gggcaacctc gtggctgtga aacgtgtgaa ccgtaaacgc attgagctga cacgaaaagt
 
  cctgtttgaa ctgaagcata tgcgggatgt gcagaatgaa cacctgacca ggtttgtggg
 
  agcctgcacc gaccccccca atatctgcat cctcacagag tactgtcccc gtgggagcct
 
  gcaggacatt ctggagaatg agagcatcac cctggactgg atgttccggt actcactcac
 
  caatgacatc gtcaagggca tgctgtttct acacaatggg gctatctgtt cccatgggaa
 
  cctcaagtca tccaactgcg tggtagatgg gcgctttgtg ctcaagatca ccgactatgg
 
  gctggagagc ttcagggacc tggacccaga gcaaggacac accgtttatg ccaaaaagct
 
  gtggacggcc cctgagctcc tgcgaatggc ttcaccccct gtgcggggct cccaggctgg
 
  tgacgtatac agctttggga tcatccttca ggagattgcc ctgaggagtg gggtcttcca
 
  cgtggaaggt ttggacctga gccccaaaga gatcatcgag cgggtgactc ggggtgagca
 
  gccccccttc cggccctccc tggccctgca gagtcacctg gaggagttgg ggctgctcat
 
  gcagcggtgc tgggctgagg acccacagga gaggccacca ttccagcaga tccgcctgac
 
  gttgcgcaaa tttaacaggg agaacagcag caacatcctg gacaacctgc tgtcccgcat
 
  ggagcagtac gcgaacaatc tggaggaact ggtggaggag cggacccagg catacctgga
 
  ggagaagcgc aaggctgagg ccctgctcta ccagatcctg cctcactcag tggctgagca
 
  gctgaagcgt ggggagacgg tgcaggccga agcctttgac agtgttacca tctacttcag
 
  tgacattgtg ggtttcacag cgctgtcggc ggagagcaca cccatgcagg tggtgaccct
 
  gctcaatgac ctgtacactt gctttgatgc tgtcatagac aactttgatg tgtacaaggt
 
  ggagacaatt ggcgatgcct acatggtggt gtcagggctc cctgtgcgga acgggcggct
 
  acacgcctgc gaggtagccc gcatggccct ggcactgctg gatgctgtgc gctccttccg
 
  aatccgccac cggccccagg agcagctgcg cttgcgcatt ggcatccaca caggacctgt
 
  gtgtgctgga gtggtgggac tgaagatgcc ccgctactgt ctctttgggg atacagtcaa
 
  cacagcctca agaatggagt ctaatgggga agccctgaag atccacttgt cttctgagac
 
  caaggctgtc ctggaggagt ttggtggttt cgagctggag cttcgagggg atgtagaaat
 
  gaagggcaaa ggcaaggttc ggacctactg gctccttggg gagaggggga gtagcacccg
 
  aggctgacct gcctcctctc ctatccctcc acacctccct accctgtgcc agaagcaaca
 
  gaggtgccag gcctcagcct cacccacagc agccccatcg ccaaaggatg gaagtaattt
 
  gaatagctca ggtgtgctga ccccagtgaa gacaccagat aggacctctg agaggggact
 
  ggcatggggg gatctcagag cttacaggct gagccaagcc cacggccatg cacagggaca
 
  ctcacacagg cacacgcacc tgctctccac ctggactcag gccgggctgg gctgtggatt
 
  cctgatcccc tcccctcccc atgctctcct ccctcagcct tgctaccctg tgacttactg
 
  ggaggagaaa gagtcacctg aaggggaaca tgaaaagaga ctaggtgaag agagggcagg
 
  ggagcccaca tctggggctg gcccacaata cctgctcccc cgaccccctc cacccagcag
 
  tagacacagt gcacagggga gaagaggggt ggcgcagaag ggttgggggc ctgtatgcct
 
  tgcttctacc atgagcagag acaattaaaa tctttattcc agtgaaaaaa aaaaaaaaaa a

(GenBank Accession Number NM_000906; Version NM_000906.3, GI: 67830410, which is incorporated herein by reference)
[0078] The present invention includes diagnostic kits comprising oligonucleotides which are useful as primers for performing PCR methods to amplify the NPRA transcript or cDNA generated therefrom.
[0079] According to the invention, diagnostic kits can be assembled which are useful to practice methods of detecting the presence of the NPRA transcript or cDNA generated therefrom in biological samples. Such diagnostic kits comprise oligonucleotides which are useful as primers for performing PCR methods. It is preferred that diagnostic kits according to the present invention comprise a container comprising a size marker to be run as a standard on a gel used to detect the presence of amplified DNA. The size marker is the same size as the DNA generated by the primers in the presence of the NPRA transcript or cDNA generated therefrom. Additional components in some kits include instructions for carrying out the assay. Additionally, the kit may optionally comprise depictions or photographs that represent the appearance of positive and negative results.
[0080] PCR assays are useful for detecting the NPRA transcript in homogenized tissue samples and cells in body fluid samples, such as blood.
[0081] Another method of determining whether a sample contains cells expressing NPRA is by branched chain oligonucleotide hybridization analysis of mRNA extracted from a sample. Branched chain oligonucleotide hybridization may be performed as described in U.S. Pat. No. 5,597,909, U.S. Pat. No. 5,437,977 and U.S. Pat. No. 5,430,138, which are each incorporated herein by reference. Reagents may be designed following the teachings of those patents and that sequence of the NPRA transcript.
[0082] Another method of determining whether a sample contains cells expressing NPRA is by Northern Blot analysis of mRNA extracted from a biological sample, such as blood. The techniques for performing Northern blot analyses are well known by those having ordinary skill in the art and are described in Sambrook, J. et al., (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. mRNA extraction, electrophoretic separation of the mRNA, blotting, probe preparation and hybridization are all well known techniques that can be routinely performed using readily available starting material.
[0083] The mRNA is extracted using poly dT columns and the material is separated by electrophoresis and, for example, transferred to nitrocellulose paper. Labeled probes made from an isolated specific fragment or fragments can be used to visualize the presence of a complementary fragment fixed to the paper. Probes useful to identify mRNA in a Northern Blot have a nucleotide sequence that is complementary to one or more sequences of the NPRA transcript. Those having ordinary skill in the art can use the sequence information included herein to design such probes or to isolate and clone the NPRA transcript or cDNA generated therefrom to be used as a probe. Such probes are at generally least 15 nucleotides, preferably 30-200, more preferably 40-100 nucleotide fragments and may be the entire NPRA transcript.
[0084] According to the invention, diagnostic kits can be assembled, which are useful to practice methods of detecting the presence of the NPRA transcript in biological samples by Northern blot analysis. Such diagnostic kits comprise oligonucleotides which are useful as probes for hybridizing to the mRNA. The probes may be radiolabeled. It is preferred that diagnostic kits according to the present invention comprise a container comprising a size marker to be run as a standard on a gel. It is preferred that diagnostic kits according to the present invention comprise a container comprising a positive control which will hybridize to the probe. Additional components in some kits include instructions for carrying out the assay (e.g., written or embossed on packaging or on one or more containers). Additionally, the kit may optionally comprise depictions or photographs that represent the appearance of positive and negative results. Northern blot analysis is useful for detecting the NPRA transcript in tissue samples and cells in body fluid samples.
[0085] Another method of detecting the presence of the NPRA transcript is by oligonucleotide hybridization technology. Oligonucleotide hybridization technology is well known to those having ordinary skill in the art. Briefly, detectable probes which contain a specific nucleotide sequence that will hybridize to nucleotide sequence of the NPRA transcript. RNA or cDNA made from RNA from a sample is fixed, usually to filter paper or the like. The probes are added and maintained under conditions that permit hybridization only if the probes fully complement the fixed genetic material. The conditions are sufficiently stringent to wash off probes in which only a portion of the probe hybridizes to the fixed material. Detection of the probe on the washed filter indicate complementary sequences.
[0086] Probes useful in oligonucleotide assays at least 18 nucleotides of complementary DNA and may be as large as a complete complementary sequence to the NPRA transcript. In some preferred embodiments, the probes of the invention are 30-200 nucleotides, preferably 40-100 nucleotides.
[0087] One having ordinary skill in the art, using the human NPRA sequence information disclosed herein can design probes which are fully complementary to at least a portion of the NPRA transcript. Hybridization conditions can be routinely optimized to minimize background signal by non-fully complementary hybridization. In some preferred embodiments, the probes are full length clones. Probes are at least 15 nucleotides, preferably 30-200, more preferably 40-100 nucleotide fragments and may be the entire NPRA transcript.
[0088] The present invention includes labeled oligonucleotides which are useful as probes for performing oligonucleotide hybridization. That is, the binding portion of the probe can be fully complementary with the NPRA transcript. For example, the mRNA sequence includes portions encoded by different exons. The labeled probes of the present invention are labeled with radiolabeled nucleotides or are otherwise detectable by readily available nonradioactive detection systems.
[0089] According to the invention, diagnostic kits can be assembled which are useful to practice oligonucleotide hybridization methods of the invention. Such diagnostic kits comprise a labeled oligonucleotide which encodes portions of the NPRA transcript. It is preferred that labeled probes of the oligonucleotide diagnostic kits according to the present invention are labeled with a radionucleotide. The oligonucleotide hybridization-based diagnostic kits according to the invention preferably comprise DNA samples that represent positive and negative controls. A positive control DNA sample is one that comprises a nucleic acid molecule which has a nucleotide sequence that is fully complementary to the probes of the kit such that the probes will hybridize to the molecule under assay conditions. A negative control DNA sample is one that comprises at least one nucleic acid molecule, the nucleotide sequence of which is partially complementary to the sequences of the probe of the kit. Under assay conditions, the probe will not hybridize to the negative control DNA sample. Additional components in some kits include instructions for carrying out the assay. Additionally the kit may optionally comprise depictions or photographs that represent the appearance of positive and negative results. Oligonucleotide hybridization techniques are useful for detecting the NPRA transcript in tissue samples (e.g., tissue homogenates) and cells in body fluid samples.
[0090] Thus, the present invention relates to in vitro kits for evaluating biological samples to determine the level of NPRA (e.g., NPRA cDNA, NPRA mRNA, NPRA protein, NPRA activity) and to reagents and compositions useful to practice the same. Techniques for determining the presence of mRNA of a polypeptide have resulted in the production of various microarrays, bioarray, biochips and biochip arrays, which may be employed with the invention. As used herein, the terms “microarray,” “bioarray,” “biochip” and “biochip array” refer to an ordered spatial arrangement of immobilized biomolecular probes arrayed on a solid supporting substrate. Preferably, the biomolecular probes are immobilized on second linker moieties in contact with polymeric beads, wherein the polymeric beads are immobilized on first linker moieties in contact with the solid supporting substrate. Biochips, as used in the art, encompass substrates containing arrays or microarrays, preferably ordered arrays and most preferably ordered, addressable arrays, of biological molecules that comprise one member of a biological binding pair. Typically, such arrays are oligonucleotide arrays comprising a nucleotide sequence that is complementary to at least one sequence of a nucleic acid that encodes NPRA. Alternatively, and preferably, proteins, peptides or other small molecules can be arrayed in such biochips for performing, inter alia, immunological analyses (wherein the arrayed molecules are antigens) or assaying biological receptors (wherein the arrayed molecules are ligands, agonists or antagonists of said receptors). Useful microarrays for detecting differential gene expression are described, for example, in U.S. Pat. No. 6,040,138 to Lockhart et al. (commercially-available from Affymetrix, Inc., Santa Clara, Calif.) and U.S. Pat. No. 6,004,755 to Wang (commercially-available from Incyte Inc., Palo Alto, Calif.) and are also commercially available, inter alia, from Research Genetics (Huntsville, Ala.).
[0091] Gene expression analysis can be performed to detect differences in gene expression between populations of target cells of a subject and reference cells (e.g., an appropriate control) to determine whether or not NPRA is being expressed and/or to what extent. The target cell population may include one or more subpopulations of cell types. Hybridization of gene expression microarrays can be used to produce patterns of gene expression of NPRA. Identification of genes and patterns of genes differentially expressed in the target cells is established by comparison of the gene expression pattern obtained by performing the microarray hybridization analysis on cDNA from target cells in comparison to that of normal cells.
[0092] In the methods of the invention, elevated NPRA level or activity can be used to diagnose or provide prognosis (predict progression of) a malignancy (e.g., cancer). Methods for determining NPRA activity are known in the art (Patel J. B. et al., Am. J. Physiol. Heart Circ. Physiol., 2005, 289:H777-H784, which is incorporated herein by reference).
[0093] In some embodiments, various methodologies of the instant invention include a step that involves comparing NPRA level or activity in a sample obtained from a subject to a “suitable control,” also referred to interchangeably herein as an “appropriate control.” Thus, in accordance with the invention, it can be determined whether a subject has, or more likely to have, a cancer, based on NPRA expression in relevant cells from the subject (e.g., based on comparison to an appropriate control). A “suitable control” or “appropriate control” in this context is a predetermined value associated with NPRA useful for comparison purposes, which can take many different forms. Exemplary forms include, but are not limited to, for example, a transcription rate, mRNA level, translation rate, protein level, protein structure, biological activity, cellular characteristic or property, genotype, phenotype, receptor activity etc. associated with NPRA. In one embodiment, a “suitable control” is a predetermined NPRA activity, which is compared to NPRA activity in a sample obtained from a subject being identified as having or not having a cancer associated with (correlating with) NPRA over-expression as described herein. In another embodiment, a “suitable control” is a predetermined NPRA level, which is compared to an NPRA level in a sample obtained from a subject being identified as having or not having a cancer associated with (correlating with) NPRA over-expression as described herein. In another embodiment, a “suitable control” is a predetermined NPRA level, which is compared to an NPRA level in a sample derived from a subject in which a clinical measure was achieved, for example an NPRA level obtained from cells in a subject who reached, or failed to reach, a particular clinical outcome following treatment of the cancer.
[0094] In some embodiments, a “suitable control” or an “appropriate control” can be a single cut-off value, such as a median or mean. A single cut-off value can be established, for example, based upon comparative groups, such as in groups having an NPRA level or activity which correlates with lack of, or resistance to, a cancer, and groups having an NPRA level or activity which does not confer or correlate with resistance to lack of, or resistance to, a cancer. For example, samples can be obtained from various individuals or blood or tissue banks and an NPRA level or activity can be measured in each sample. Consequently, a single cut-off value can be based on the mean of an NPRA level or activity in samples which correlate with lack of, or resistance to, a cancer. Another comparative group can be, for example, an NPRA level or activity in a group of individuals with a family history of a cancer, or a family history with a lack of, resistance to, a cancer. Optionally, the determined NPRA can be compared to a control in which the control is an NPRA level or activity from a subject, or a mean NPRA level or activity from a group of subjects, known to have one or more cancers. In practice, the readout or output for determination of NPRA may be qualitative, quantitative, or semi-quantitative. Preferably, a quantitative value of NPRA level or activity is determined, which is compared to that of an appropriate control.
[0095] The terms “subject,” “individual,” and “patient”, as used herein, refers to a human or non-human mammal, of any age or gender.
[0096] As used herein, the terms “treat,” “treating,” and “treatment” refer to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) an undesired physiological change or disorder, such as the development or spread of cancer, in a subject. For purposes of this invention, beneficial or desired clinical results include, but are not limited to, alleviation of symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable. “Treatment” can also mean prolonging survival as compared to expected survival if not receiving treatment. Those in need of treatment include those already with the condition or disorder as well as those prone to have the condition or disorder or those in which the condition or disorder is to be prevented. In some embodiments, the treatment includes one disclosed in U.S. Patent Publication Nos. 2009/0176706 (Mohapatra); 2008/0214437 (Mohapatra et al.); 2007/0265204 (Mohapatra et al.); and 20050272650 (Mohapatra), which are each incorporated herein by reference.
[0097] As used herein, the terms “cancer” and “cancerous” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. Examples of cancer include but are not limited to, carcinoma, lymphoma, blastoma, sarcoma, and leukemia. More particular examples of such cancers include, but are no limited to, breast cancer, prostate cancer, colon cancer, squamous cell cancer, small-cell lung cancer, non-small cell lung cancer, gastrointestinal cancer, pancreatic cancer, cervical cancer, ovarian cancer, liver cancer, e.g., hepatic carcinoma, bladder cancer, colorectal cancer, endometrial carcinoma, kidney cancer, and thyroid cancer. The terms “cancer” and “malignancy” are used interchangeably herein.
[0098] Other non-limiting examples of cancers are basal cell carcinoma, biliary tract cancer; bone cancer; brain and CNS cancer; choriocarcinoma; connective tissue cancer; esophageal cancer; eye cancer; cancer of the head and neck; gastric cancer; GIST, intra-epithelial neoplasm; larynx cancer; lymphoma including Hodgkin's and Non-Hodgkin's lymphoma; melanoma; myeloma; neuroblastoma; oral cavity cancer (e.g., lip, tongue, mouth, and pharynx); pancreatic cancer; retinoblastoma; rhabdomyosarcoma; rectal cancer; cancer of the respiratory system; sarcoma; skin cancer; stomach cancer; testicular cancer; uterine cancer; cancer of the urinary system, as well as other carcinomas and sarcomas. In some embodiments of the invention, the cancer is not ovarian cancer or melanoma.
[0099] As used herein, the term “tumor” refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. For example, a particular cancer may be characterized by a solid mass tumor. The solid tumor mass, if present, may be a primary tumor mass. A primary tumor mass refers to a growth of cancer cells in a tissue resulting from the transformation of a normal cell of that tissue. In most cases, the primary tumor mass is identified by the presence of a cyst, which can be found through visual or palpation methods, or by irregularity in shape, texture or weight of the tissue. However, some primary tumors are not palpable and can be detected only through medical imaging techniques such as X-rays (e.g., mammography), or by needle aspirations. The use of these latter techniques is more common in early detection. Molecular and phenotypic analysis of cancer cells within a tissue will usually confirm if the cancer is endogenous to the tissue or if the lesion is due to metastasis from another site.
[0100] As used in this specification, including the appended claims, the singular “a”, “an”, and “the” include plural reference unless the contact dictates otherwise. Thus, for example, a reference to “an antibody” includes more than one such antibody. A reference to “a cell” includes more than one such cell, and so forth.
[0101] The terms “comprising”, “consisting of” and “consisting essentially of” are defined according to their standard meaning. The terms may be substituted for one another throughout the instant application in order to attach the specific meaning associated with each term.
[0102] Without wishing to be bound by theory, it is contemplated that any suitable characteristic associated with NPRA such as, for example, mRNA level, polypeptide amount, NPRA activity, transcription rate, translation rate etc., may be used as an indicator for identifying subjects that are suffering from a cancer, and for prognosing cancer. In some embodiments, NPRA activity or level, for example, the amount of NPRA polypeptide present, is used as an indicator for identifying subjects suitable for a further diagnostic test for cancer. In other embodiments, NPRA level or activity is used as an indicator for identifying subjects suitable for treatment of a cancer.

EXEMPLIFIED EMBODIMENTS

Embodiment 1

[0103] A method of detecting a malignancy in a mammalian subject, comprising obtaining a sample comprising cells from the subject, and determining whether the level or activity of natriuretic peptide receptor A (NPRA) is elevated in the cells, wherein elevated NPRA level or activity is indicative of a malignancy.

Embodiment 2

[0104] The method of embodiment 1, wherein the malignancy is a cancer selected from the group consisting of prostate cancer, colon cancer, breast cancer, pancreatic cancer, Merkell cell carcinoma, and gastrointestinal stromal tumor (GIST).

Embodiment 3

[0105] The method of embodiment 1, wherein the malignancy is not ovarian cancer or melanoma.

Embodiment 4

[0106] The method of embodiment 1, further comprising carrying out one or more confirmatory tests for the malignancy if the level or activity NPRA is elevated.

Embodiment 5

[0107] The method of any preceding embodiment, wherein the sample is a tissue sample.

Embodiment 6

[0108] The method of any preceding embodiment, wherein the sample comprises tissue or cells that is adjacent a tumor in the subject.

Embodiment 7

[0109] The method of any preceding embodiment, wherein the sample comprises tumor cells.

Embodiment 8

[0110] The method of any preceding embodiment, further comprising advising the subject of treatment options for treating the malignancy if the level or activity of NPRA is elevated.

Embodiment 9

[0111] A method of treating a malignancy in a mammalian subject, comprising obtaining a sample comprising cells from the subject, determining whether the level or activity of natriuretic peptide receptor A (NPRA) is elevated in the cells, wherein elevated NPRA level or activity is indicative of a malignancy, and treating the subject with a therapy for the malignancy if the NPRA level or activity is elevated.

Embodiment 10

[0112] The method of embodiment 9, wherein the malignancy is selected from the group consisting of prostate cancer, colon cancer, breast cancer, pancreatic cancer, Merkell cell carcinoma, and GIST.

Embodiment 11

[0113] The method of embodiment 9 or 10, further comprising carrying out one or more confirmatory tests for the malignancy if the NPRA level or activity is elevated.

Embodiment 12

[0114] The method of any of one of embodiments 9 to 11, wherein the therapy comprises surgery, chemotherapy, radiation therapy, or a combination of two or more of the foregoing.

Embodiment 13

[0115] The method of any one of embodiments 9 to 12, wherein the sample is a tissue sample.

Embodiment 14

[0116] The method of any of one of embodiments 9 to 13, wherein the sample is a tumor cells.

Embodiment 15

[0117] The method of any one of embodiments 9 to 14, wherein the sample comprises tissue or cells that is adjacent a tumor in the subject.

Embodiment 16

[0118] A method of determining the level or activity of natriuretic peptide receptor A (NPRA) in cancer cells of a mammalian subject, comprising obtaining a sample of cancer cells from the subject, and determining the level or activity of NPRA in the cells.

Embodiment 17

[0119] The method of embodiment 16, wherein the cancer cells are selected from the group consisting of prostate cancer, colon cancer, breast cancer, pancreatic cancer, Merkell cell carcinoma, and GIST.

Embodiment 18

[0120] An in vitro polymerase chain reaction (PCR) assay kit for determining whether a subject has a malignancy by detecting elevated level or activity of natriuretic peptide receptor A (NPRA), said kit comprising a first container comprising polymerase chain reaction (PCR) primers that amplify an NPRA transcript or cDNA generated therefrom; and a second container comprising a nucleic acid marker, said marker being and labeled and able to hybridize to said transcript or cDNA.

Embodiment 19

[0121] A method for predicting progression of a malignancy and prognosing the malignancy in a mammalian subject, comprising: (a) obtaining a sample suspected of containing malignant cells; (b) analyzing the sample for NPRA level or activity; (c) correlating the level or activity with a control NPRA level or activity; and (d) correlating a high NPRA level or activity with an indication of unfavorable prognosis and a low NPRA level or activity with a favorable prognosis.

Embodiment 20

[0122] A method for prognosing cancer in mammalian subjects, comprising: (a) obtaining a sample suspected of containing cancer cells; (b) analyzing the sample for NPRA level or activity; (c) correlating the NPRA level or activity with a control NPRA level of activity; and (d) correlating a high NPRA level or activity with an indication of unfavorable prognosis and a low NPRA level or activity with a favorable prognosis.

Embodiment 21

[0123] The method of embodiment 20, wherein the analyzing in step (b) comprises preparing a cell extract.

Embodiment 22

[0124] The method of embodiment 20, wherein the analyzing in step (b) is under conditions selected to detect any NPRA level or activity, and the method further comprises analyzing a second aliquot of the sample for NPRA level or activity under conditions selected to detect NPRA level or activity only above the control NPRA level or activity; and associating high NPRA level or activity to the presence of NPRA in both the first and second aliquots and low NPRA level or activity to the presence of NPRa only in the first aliquot.

Embodiment 23

[0125] The method of embodiment 20, wherein the analyzing step further comprises amplifying any NPRA genetic material in the reaction mixture by a polymerase chain reaction using at least one primer complementary to a NPRA sequence.

Embodiment 24

[0126] The method of embodiment 20, wherein the analyzing step comprises detecting NPRA protein using an immunological reagent.

Embodiment 25

[0127] The method of embodiment 24, wherein the immunological agent is a monoclonal or polyclonal antibody.

Embodiment 26

[0128] The method of any one of embodiments 20 to 25, the sample comprises tumor cells from the subject.

Embodiment 27

[0129] The method of any one of embodiments 20 to 26, wherein the sample comprises tissue or cells adjacent to a tumor in the subject.

Embodiment 28

[0130] The method of any one of embodiments 20 to 27, wherein a favorable prognosis comprises tumor regression.

Embodiment 29

[0131] The method of any one of embodiments 18 to 28, wherein the favorable prognosis comprises longer survival rates relative to patients with unfavorable prognosis.

Embodiment 30

[0132] The method of any one of embodiments 20 to 29, further comprising communicating the favorable or unfavorable prognosis to the subject.

Embodiment 31

[0133] A purified or isolated antibody or antibody fragment that selectively binds to an epitope within the amino acid sequence comprising or consisting of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3.

Embodiment 32

[0134] A purified or isolated antibody or antibody fragment that selectively binds to both human and mouse natriuretic peptide receptor A (NPRA).

Embodiment 33

[0135] The antibody or antibody fragment of embodiment 32, wherein the antibody or antibody fragment selectively hinds to an epitope within the amino acid sequence comprising or consisting of SEQ ID NO:3.

Embodiment 34

[0136] A method for inhibiting the growth of a malignant cell in vitro or in vivo, comprising administering an agent to the cell, wherein the agent inhibits the function of migration inhibitor factor (MIF) in the malignant cell.

Embodiment 35

[0137] The method of embodiment 34, wherein the agent targets a nucleic acid sequence within the MIF gene or transcript and reduces expression of MIF in the malignant cell.

Embodiment 36

[0138] The method of embodiment 34 or 35, wherein the malignant cell is a cancer cell selected from the group consisting of prostate cancer, colon cancer, breast cancer, pancreatic cancer, Merkell cell carcinoma, and gastrointestinal stromal tumor (GIST).

Embodiment 37

[0139] The method of any one of embodiments 34-36, wherein the agent comprises an RNA interference (RNAi) molecule (e.g., siRNA or shRNA), microRNA (miRNA), antisense oligonucleotide, or ribozyme.

Embodiment 38

[0140] A method for providing an NPRA expression profile useful for detecting and/or prognosing cancer, comprising analyzing a biological sample (e.g., sample that may or may not contain malignant cells) from a subject for NPRA level or activity, wherein an elevated NPRA level or activity (relative to a reference NPRA level or activity, such as a normal control or less aggressive stage of the malignancy) is indicative of the presence of a malignancy or a more advanced stage of the malignancy.

Embodiment 39

[0141] The method of embodiment 38, further comprising communicating the results of the analysis to a health care provider.

Embodiment 40

[0142] The method of embodiment 39, wherein the communication includes transmitting a report to the health care provider electronically (e.g., via the internet) or on a tangible medium (e.g., paper or tangible electronic storage medium).
[0143] All patents, patent applications, provisional applications, and publications referred to or cited herein, supra or infra, are incorporated by reference in their entirety, including all figures and tables, to the extent they are not inconsistent with the explicit teachings of this specification.
[0144] Following are examples which illustrate procedures for practicing the invention. These examples should not be construed as limiting. All percentages are by weight and all solvent mixture proportions are by volume unless otherwise noted.

Materials and Methods

[0145] Cells and Beta-Actin Antibody.
[0146] Normal prostate epithelial cell (PrEC) was purchased from Lonza (Allendale). RWPE, Tramp-C1 and -C3 cells were purchased from the American Type Culture Collection (Manassas, Va., USA). DU145, PC3, benign prostatic hyperplasia (BPH), LNCaP, C4-2, the rat gastric mucosa cell line (RGM1), P2 and CaP2 were described before [22-25]. The beta-actin antibody was obtained from Sigma, the PARP antibody from Santa Cruz Biotechnology, and the MIF antibody from Abcam. Lipofectamine 2000 reagent was obtained from Invitrogen.
[0147] NPRA Antibody Production and Purification.
[0148] Antibody against NPRA was generated by injecting rabbits (New Zealand white) with 400 μg of synthetic NPRA peptide (amino acid 1010-1031 of mouse NPRA protein, which is homologous to rat and human NPRA) conjugated to keyhole limpet hemocyanin (BioSynthesis, Inc., Lewisville Tex.). Antibody was purified by applying serum to a column of protein A/G agarose (Invitrogen, Carlsbad, Calif.) equilibrated with 20 mM Tris, pH 7.5, 150 mM NaCl, and eluting with 100 mM citrate, pH 3.0. The eluate was neutralized with 5 M NaOH, glycerol was added to 50% and the purified aliquots were stored at −20° C.
[0149] Tissue Microarray (TMA) Staining.
[0150] A human prostate cancer TMA containing 240 samples, prepared in the histology laboratory of the Moffitt Cancer Center Tissue Core Facility was used to test for expression of NPRA and MIF. The TMA slide was stained using a Ventana Discovery XT automated system (Ventana Medical Systems, Tucson, Ariz.), according to the manufacturer's protocol. Briefly, slides were deparaffinized on the automated system with EZ Prep solution (Ventana). Following heat-induced antigen retrieval, the slide was incubated with NPRA antibody (1:300) or MIF antibody (R&D System, MN) for 32 min and Ventana anti-rabbit or anti-goat secondary antibody for 20 min. The detection system used was the Ventana OmniMap kit, and the slide was then counterstained with hematoxylin and dehydrated.
[0151] Data Analysis.
[0152] The TMA slide was scored for intensity and cellularity by an expert pathologist. Positive staining for NPRA or MIF was scored into four grades, according to the intensity: 0, 1+, 2+ and 3+. The percentage of NPRA-positive cells was scored into three categories: 1 (0-33%), 2 (34-64%) and 3 (65-100%). The product of the intensity and percentage scores was used as the final score. The final score was classified as: 0, negative; 1-3, weak; 4-6, moderate; and 7-9, strong. Both the Kruskal-Wallis test and the Wilcoxon-Mann-Whitney test were used to compare the scores by groups. Comparisons were done for (1) PIN-L vs. BPH; (2) PIN-H vs. BPH; (3) Gleason-6 vs. BPH; (4) Gleason-7 vs. BPH; (5) Gleason-8 to 10 vs. BPH and (6) AI vs. BPH. Spearman's correlation coefficient was used to analyze the relationship between NPRA or MIF expression and Gleason's grading score.
[0153] Animals.
[0154] Male C57BL/6 mice were purchased from the National Cancer Institute. Male C57BL/6 NPRA-KO or NPRA-het were described before [19]. All mice were maintained in a pathogen-free environment and all procedures were reviewed and approved by the University of South Florida Institutional Animal Care and Use Committee.
[0155] Preparation of Plasmid Nanoparticles and Administration to Mice.
[0156] Plasmids encoding NP73-102, hNP73-102 and VD were constructed as described previously [14, 19]. Plasmids encoding siRNAs against NPRA were described previously [19]. Plasmids encoding shNPRAs were purchased from Origene. For transfection, epithelial cells at 60% confluence (log phase) were incubated in complete medium at 37° C. with plasmid DNA (1 μg/106 cells) complexed with lipofectamine (GibcoBRL Life Technologies, Carlsbad, Calif.). For tumor cell inoculation, TRAMP-C1 cells were trypsinized, washed and resuspended in PBS at 5×107 cells per ml. Mice were injected s.c. in the flank with 100 uL of resuspended cancer cells. For evaluating the effects of iNPRA in modulating tumor progression, plasmids were encapsulated in chitosan nanoparticles (25 ug of plasmid plus 125 ug of chitosan), were administered i.p. twice a week until sacrificed. Tumor sizes were measured by calipers, and at the end of experiment (day 62), the mice were euthanized and the tumors were removed and weighed. Proteins from tumors were extracted and examined for NPRA and MIF expression by Western blotting.
[0157] Western Blot Analysis.
[0158] Western blot assay was performed as previously described [25]. Cells were lysed, total cellular protein (120 μg) was separated by SDS-PAGE, blotted to nitrocellulose, and incubated with antibodies to specific proteins. Bands were visualized by enhanced chemiluminescence (Amersham Life Sciences, Piscataway, N.J.) on Kodak X-OMAT-AR film.
[0159] SuperArray Analysis of Prostate Tissues.
[0160] NPRA-KO and WT C57BL/6 mice (n=4) were injected i.p. with LPS (1 mg/kg body weight) for 3 hrs, prior to prostate harvesting. Total RNA was isolated using an RNAeasy kit (QIAGEN, Valencia, Calif.) and a pool of total RNA by group hybridized to the mouse autoimmune and inflammatory response Oligo GEarray (SuperArray Frederick, Md.), according to the manufacturer's instructions. The X-ray films were scanned, and the spots were analyzed using SuperArray Software. The relative expression level was determined by comparing the signal intensity of each gene in the array after normalization to the signal of a set of housekeeping genes.
[0161] Statistics.
[0162] The number of mice used in each test group was a minimum of 4. Experiments were repeated at least once, and measurements were expressed as means±SD. Pairs of groups were compared through the use of Student's t tests. Differences between groups were considered significant at p=0.05.

Example 1—Development of Antibody Specific for Human NPRA

[0163] To examine the expression of NPRA protein in human PCa, the present inventors raised antibodies to three NPRA peptides (SEQ ID NOs: 1-3) conjugated with KLH in rabbits. The specificity of the anti-NPRA antibody was confirmed by immunoblot analysis. Three antibodies were screened, of which only one (antibody SEQ ID NO: 3) enables detection of human NPRA expression in a very specific manner while another is reactive to mouse, but not human, NPRA. As shown in FIGS. 1A and 1B, an approximately 120 kDa band corresponding to NPRA was detected only in human PCa cell lines, PC3 and DU145, but not in rat Rat gastric mucosa cell line, RGM1. The later does not express NPRA (6). The specificity of the anti-NPRA antibody was further confirmed in cell lysates prepared from PC3 cells transfected with a NPRA inhibitor.

Example 2—Examining NPRA Expression in Human PCa Specimens

[0164] A human PCa tissue microarray (TMA) containing 240 samples, prepared in the histology laboratory of the Moffitt Cancer Center Tissue Core Facility was used to test for NPRA expression during PCa progression. The prostate TMA included 24 samples of benign prostatic hyperplasia (BPH), 21 samples of regular prostatic intraepithelial neoplasm (PIN-R), 14 samples of high PIN (PIN-H), 33 samples of prostate carcinoma (PC) with a Gleason score of 6, 82 samples of PC with a Gleason score of 7, 15 samples of androgen independent (AI) PC, and 51 samples of PC with a Gleason score of 8 and up was selected for immunohistochemical staining with our human NPRA antibody. The TMA slide was stained using a Ventana Discovery XT automated system (Ventana Medical Systems, Tucson, Ariz.), as per the manufacturer's protocol. Briefly, slides were deparaffinized on the automated system with EZ Prep solution (Ventana). Following the heat-induced antigen retrieval the slide was incubated with NPRA antibody (1:300) for 32 min and Ventana anti-rabbit secondary antibody for 20 min. The detection system used was the Ventana OmniMap kit, and the slide was then counterstained with Hematoxylin and dehydrated. A representative image (200×) of one sample from each disease stage is shown in FIG. 2. The results demonstrate that the majority of epithelial cells in BPH and PIN-R expressed NPRA with weak intensity, in PIN-H with weak-moderate intensity and in Gleason-6 samples with moderate-strong intensity. Weak and focal staining of stromal/inflammatory cells was also observed in these samples.
[0165] In contrast, NPRA staining was uniform, strong and prominent in epithelial tumors of Gleason-7 and -8 and in AI samples. Stromal/inflammatory cells of Gleason-7 and Gleason-8 also showed NPRA expression with moderate intensity. The TMA slide was scored for intensity and cellularity by Dr. Domenico Coppola, Scientific Director, Tissue Core Facility at the H. Lee Moffitt Cancer Center. The positive reaction of NPRA was scored into four grades, according to the intensity of the staining: 0, 1+, 2+ and 3+. The percentage of NPRA positive cells was scored into three categories: 1 (0-33%), 2 (34-64%) and 3 (65-100%). The product of the intensity and percentage scores was used as the final score. The final score was classified as: 0, negative; 1-3, weak; 4-6, moderate; and 7-9, strong. FIG. 3 shows the distribution of scores in each disease stage. The results suggest that mean sample score increased during PCa progression.
[0166] NPRA expression studies in human tissues have been limited by lack of availability of appropriate antibodies to NPRA. The antibodies that are commercially available are very poor in quality and do not provide consistent results. The present inventors developed an antibody to NPRA in rabbits using a specific antigenic peptide (amino acid 1010-1031 of mouse NPRA protein, which is homologous to rat and human NPRA). As shown in FIG. 1A, an approximately 120 kDa band corresponding to NPRA was detected only in human PCa cell lines, PC3 and DU145 that express NPRA, but not in the RGM1 cell line that does not express NPRA [22]. The specificity of the anti-NPRA antibody was confirmed by ELISA assay (data not shown), and by immunofluorescence and immunohistochemistry assays (FIG. 13A).
[0167] The inventors examined NPRA expression by western blotting in various types of PCa tumors and compared it with normal prostate epithelial (PrEC and RWPE) and benign prostatic hyperplasia (BPH) cells. Results of the western blot show that NPRA is expressed abundantly in the androgen-dependent PCa cell line, LNCaP and androgen-independent cell lines C4-2, PC3 and DU145, but not in PrEC cells and only weakly in RWPE and BPH cells (FIG. 1B). Lysates of normal RGM1 that does not express NPRA were used as control. NPRA is also highly expressed in transplantable syngeneic tumor lines derived from TRAMP (transgenic adenocarcinoma mouse prostate) mice which get spontaneous PCa. NPRA is strongly expressed in the tumorigenic TRAMP-C1 and -C2 PCa cell lines but less abundantly in the non-tumorigenic TRAMP-C3 PCa cell line (FIG. 1C) [26]; the latter shows a three-fold reduction in growth and colonization potential compared to TRAMP-C1 and C2 cells (FIGS. 14A-C). In addition, increased NPRA expression was seen in prostate epithelial lines from intact conditional homozygous Pten knock-out mice (PTEN-CaP2) that are tumorigenic compared to heterozygous Pten knock-out mice (PTEN-P2) (FIG. 1D) [23]. These results suggest that NPRA is more abundantly expressed in PCa cells than normal or benign prostate epithelial cells.

Example 3—Association of NPRA Expression with PCa Progression

[0168] The clinical relevance of NPRA expression during human PCa development was examined in BPH, high grade PIN (prostatic intraepithelial neoplasm) and prostatic adenocarcinoma using a human PCa tissue microarray (TMA) containing 240 samples. The TMA samples included BPH (n=24), low grade prostatic intraepithelial neoplasm (PIN-L) (n=21), high PIN (PIN-H) (n=14), prostate carcinoma (PC) with a Gleason score of 6 (n=33), PC with a Gleason score of 7 (n=82), PC with a Gleason score of 8 to 10 (n=51) and androgen-independent (AI) PC (n=15). The TMA slide was immuno-stained with a rabbit anti-human NPRA antibody using a Ventana Discovery XT automated system (Ventana Medical Systems, Tucson, Ariz.) and the data were statistically analyzed. A representative image (200×) of one sample from each disease stage is shown in FIG. 2. The results demonstrate that the majority of epithelial cells in BPH and PIN-L were weakly stained with NPRA, and that the PIN-H samples were weakly to moderately positive for NPRA. Gleason-6 PCa samples exhibited moderate to strong NPRA immunoreactivity. Weak and focal staining of stromal/inflammatory cells was also observed in these samples. In contrast, NPRA staining was uniformly strong and prominent in Gleason 7-10 and in AI PCa samples. Stromal/inflammatory cells in these samples also showed moderate NPRA expression.
[0169] The TMA slide was scored for intensity and cellularity by an expert pathologist. The final score was classified as: 0, negative; 1-3, weak; 4-6, moderate; and 7-9, strong. FIG. 2B shows the distribution of scores in each disease stage. The results show that the mean sample score increased during PCa progression. Table 1 displays a median analysis of NPRA expression in the TMA for 240 subjects. Across all 240 subjects, the median score was 4. Table 2 shows the frequency in each disease group of having a score falling at or below the median and having one above the median. The number of observations in the BPH group with a score >4 was zero, while for Gleason-6, Gleason-7, Gleason-8-10 and AI groups the numbers were respectively 14 (of 33), 43 (of 82), 34 (of 51) and 8 (of 15). A chi-square (two-way frequency table) value of 50.761 with asymptomatic significance of p<0.0001 was obtained, suggesting that the relationship between NPRA expression and PCa stage is very strong. A Kruskal-Wallis test indicated that the difference in NPRA expression among the seven diagnostic groups was highly significant (p<0.0001). The pairwise Wilcoxon-Mann-Whitney tests and p values in Table 1 show that NPRA expression is strongly associated with PCa progression. The elevated NPRA expression in high-grade tumors may reflect its role in tumor-stromal interaction. Since the outcomes of the Kruskal-Wallis and Wilcoxon-Mann-Whitney tests are of ordinal value and do not follow the normal distribution that the ANOVA or t-test requires a non-parametric version of these two methods was used.
[0170] 
[00004] [TABLE-US-00004]
    TABLE 1
   
    Std.     Percentiles
        Devi-   Mini-   Max-     50th  
    N   Mean   ation   mum   imum   25th   (Median)   75th
 
  Score   240   4.66   2.431   1.00   9.00   3.00   4.00   6.00
  Disease   240   4.57   1.8711   1.00   7.00   4.00   5.00   6.00
 
[0171] 
[00005] [TABLE-US-00005]
  TABLE 2
 
      PIN     PC   PC     PC
      (Reg-   PIN   Gleason   Gleason   PC   Gleasons
  Score   B PH   ular)   (High)   6   7   (AI)   8-10
 
 
  >Median   0   1   2   14   43   8   34
  ≤Median   24   20   12   19   39   7   17
 

Thus, taken together, these results demonstrate a statistically significant difference in staining between BPH, PIN and prostatic adenocarcinoma, suggesting that NPRA expression is strongly associated with PCa progression. Hence, targeting NPRA signaling in PCa is highly relevant.
[0172] NPRA is more abundantly expressed in human PCa cells than in normal cells or prostate epithelial cells associated with benign prostatic hyperplasia (BPH), and its expression positively correlates with the Gleason score (GS) in clinically aggressive human PCa tissue (FIG. 17A). Thus, in accordance with the invention, NPRA expression levels may be used to detect and distinguish human PCa from normal cells and BPH. Additionally, since NPRA expression positively correlates with GS in aggressive PCa tissue, NPRA expression levels may be used to classify (stage) prostate cancer as to its clinical aggressiveness. The inventors used an identical PCa tissue microarray (TMA) to compare the expression of NPRA and prostate specific membrane antigen (PSMA), a transmembrane protein whose expression is increased in hormone-refractory PCa (FIG. 17B). NPRA expression correlated significantly with PSMA expression (Spearman's, r=1.000; p=0.0028, two-tailed) in each disease stage, but was more predictive in PCa with a core diagnosis of GS-7 (p<0.0001) and GS-8 (p<0.05) (FIG. 17C; Mann-Whitney test).

Example 4—Association of NPRA Expression with Colorectal Cancer

[0173] The present inventors analyzed the data two different ways, each of which indicates that NPRA expression is associated with colorectal cancer. The colon cancer TMA included normal (n=24); adenoma (n=24) and adenocarcinoma (n=78). The TMA slide was scored for intensity and cellularity. The results are shown in FIG. 4, which shows the distribution of scores in each disease stage. The results suggest that mean sample score increased during colorectal cancer.

Example 5—Association of NPRA Expression with Breast Cancer

[0174] The present inventors analyzed the data two different ways, each of which indicates that NPRA expression is associated with breast cancer. The breast cancer TMA included normal breast tissue (n=11); DCIS (n=14), IDC without metastases (n=28), IDC with metastases (n=31) and lymph node metastases (n=21). The TMA slide was scored for intensity and cellularity. The results are shown in FIG. 5, which shows the distribution of scores in each disease stage. The results suggest that mean sample score increased during breast cancer.

Example 6—Association of NPRA Expression with Pancreatic Cancer

[0175] The present inventors analyzed the data two different ways, each of which indicates that NPRA expression is associated with pancreatic cancer. The breast cancer TMA included pancreatic duct (n=54); IDC (n=68), and neuroendocrine carcinoma (n=158). The TMA slide was scored for intensity and cellularity. The results are shown in FIG. 6, which shows the distribution of scores in each disease stage. The results suggest that mean sample score increased during pancreatic cancer.

Example 7—Association of NPRA Expression with Merckell Cell Carcinoma

[0176] The present inventors analyzed the data two different ways, each of which indicates that NPRA expression is associated with pancreatic cancer. The merckell cell carcinoma TMA included normal skin (n=21); primary lesion (n=98), lymphnode involvement (n=65) and recurrent/metastatic (n=38). The TMA slide was scored for intensity and cellularity. The results are shown in FIG. 7, which shows the distribution of scores in each disease stage. The results suggest that mean sample score increased during merckell cell carcinoma.

Example 8—Association of NPRA Expression with GIST

[0177] The present inventors analyzed the data two different ways, each of which indicates that NPRA expression is associated with GIST cancer. The GIST TMA included normal skin (n=21); GIST tumor (n=124). The TMA slide was scored for intensity and cellularity. The results are shown in FIG. 8, which shows the distribution of scores in each disease stage. The results suggest that mean sample score increased in GIST.

Example 9—NPRA Deficiency Impairs Engraftment of PCA Cells

[0178] The present inventors proposed that NPRA might be important for prostate tumor growth. The role of NPRA in modulating PCa progression was tested using TRAMP-C1 cells, which form tumors when grafted subcutaneously into syngeneic C57BL/6 hosts [26]. For in vivo assays, C57BL/6 (WT), NPRA-heterozygous (NPRA-het) and NPRA-KO mice were injected subcutaneously with TRAMP-C1 cells. Mice were euthanized seven weeks after injection and tumor sizes and weights were compared (FIG. 9A). TRAMP-C1 cells failed to engraft in NPRA-KO mice and no visible tumors were detected in the homozygous group ten weeks after tumor cell injection. Some tumor growth was observed in NPRA-het mice, but at a significantly reduced level compared to that in WT C57BL/6 mice, suggesting that host NPRA gene dosage is a determining factor for the growth of tumor cells in these mice. The role of NPRA deficiency in the survival of TRAMP-C1 cells was tested in vitro by ectopic expression of a plasmid encoding small interfering RNA against NPRA (siNPRA). Expression of siNPRA-2, but not siNPRA-1, significantly reduced expression of NPRA (FIG. 9B). Apoptosis was detected by western blotting for PARP cleavage (FIG. 9B) and by the terminal transferase dUTP nick end labeling (TUNEL) assay (FIG. 9C). Downregulation of NPRA expression by siNPRA-2 induced significant apoptosis in PCa cells.

Example 10—NPRA Down-Regulation Inhibits Migration Inhibitory Factor (MIF) Expression

[0179] It has been previously that NPRA-deficient mice fail to mount an inflammatory response, as exemplified by the lack of goblet cell hyperplasia and infiltration of eosinophils in the lungs of NPRA-KO mice compared to those of WT mice, when sensitized and challenged with ovalbumin [19]. The lack of inflammatory response correlated with reduced levels of inflammatory cytokines IL-4, IL-5 and IL-6 in the bronchoalveolar lavage (BAL) fluid of the NPRA-KO mice relative that of WT mice [19, 27]. To examine whether the anti-tumor effects of iNPRA were due to lack of local inflammation in prostate tissue, the inventors injected mice with lipopolysaccharide (LPS), a potent inducer of local inflammation and compared prostate tissues for alterations in gene expression in WT and NPRA-KO mice. Prostate tissue was collected from LPS-treated and control mice, and total RNA was examined for differential gene expression using a mouse autoimmune and inflammatory response oligo GEarray (SuperArray, MD). Analysis of genes altered (more than two-fold) during LPS challenge in WT and NPRA-KO mice identified 24 genes that are either upregulated (15) or downregulated (9) in the prostate tissue of NPRA-KO mice compared to their expression levels in control mice. A few of the genes that are down-regulated during LPS stimulation in NPRA-KO mice is shown in FIG. 4A, and include: fibronectin 1 (Fn1), which is involved in the acute phase response [28], granulin [29] and S100 calcium binding protein A 11 (S100a11) [30], which are cytokines, IL6 signal transducer (IL6st; also known as gp130), a cytokine receptor [31, 32] and MIF, which is involved in the inflammatory response [33].
[0180] Since MIF has been reported to be involved in PCa progression [24, 33, 34], the possibility that NPRA depletion modulates MIF expression was tested using shRNAs for NPRA in TRAMP-C1 cells. As shown in FIG. 10B, transfection of TRAMP-C1 cells with shNPRA-1 and shNPRA-2 reduced NPRA expression >80% and also decreased MIF expression >90%. Since overexpression of plasmid-encoded NP73-102 downregulates NPRA (FIG. 15), pNP73-102 was also used as an inhibitor of NPRA (INFRA) in this study. Ectopic expression of the plasmid encoding NP73-102, but not the pVAX vector, reduced both NPRA and MIF expression >50% in TRAMP-C1 cells (FIG. 10C).

Example 11—iNPRA Inhibits Tumor Burden by Down-Regulating MIF

[0181] To rule out the possibility that impaired engraftment of TRAMP-C1 cells in NPRA-KO mice is due to immune rejection, the inventors examined the potential of NPRA inhibition to block the growth of TRAMP-C1 cells in immunocompetent C57BL/6 mice. Mice were inoculated with TRAMP-C1 cells and divided into four groups. Two weeks later, mice in each group were injected i.p. twice a week with chitosan nanoparticles (CNPs) encapsulating plasmid DNA (25 ug/mouse) encoding empty vector (pVAX), pNP73-102, a control peptide encoding human vessel dilator (pVD) or a combination of 12.5 ug each of pNP73-102 and pVD, using methods as described [19, 20]. Mice were monitored for tumor growth and tumor sizes were recorded on the indicated days (FIG. 11A). Tumor growth was significantly inhibited in mice treated with pNP73-102 compared to pVAX- or pVD-treated groups. Mice were euthanized on day 65 after treatment, and tumor weights were measured and compared (FIG. 11B). As shown in FIGS. 11A and 11B, a significant reduction (p<0.05) in tumor burden was seen in mice treated with 25 ug of pNP73-102 but not with the pVAX or pVD plasmids. Mice treated with 12.5 ug pNP73-102 showed only moderate inhibition of tumor burden. The plasmid pVD encodes a peptide corresponding to human VD and is not homologous with mouse VD; thus, lack of any anti-tumor effects in pVD-treated mice suggests the specificity of these peptides in vivo. To understand the anti-tumor effects of pNP73-102, the inventors examined NPRA and MIF expression in TRAMP-C1-engrafted tumor lysates from representative control (pVAX) and pNP73-102-treated mice. The results (FIG. 11C) show that treatment of mice with pNP73-102, but not with pVAX, significantly reduced expression of NPRA and MIF; therefore, expression of these proteins may be linked to growth of primary tumors in TRAMP-C1-inoculated C57BL/6 mice.
[0182] The inventors also examined NPRA and MIF expression in primary prostate tumors from TRAMP mice. Western blots showed that NPRA and MIF are detected in the lysates of primary prostate tumors from TRAMP mice of varying ages (18-30 weeks of age) (FIG. 12A; lanes 1-4) but not in prostates from age-matched WT C57BL/6 mice (18 and 28 weeks of age) (FIG. 12A; lanes 5-6). These results suggest that tumor cell lines, as well as primary prostate tumors of TRAMP mice, show significantly higher levels of NPRA and MIF compared to normal cells or prostate cells from C57BL/6 mice. The inventors also compared NPRA and MIF expression in total cell lysates of human PCa cells by Western blotting. Results presented in FIG. 12B suggest that increased MIF was seen in the lysates of PC3 and DU145 cells that express NPRA abundantly (FIG. 1B) compared to the lysates of BPH and RWPE. The results of these studies suggest that NPRA regulates MIF expression in PCa cells.
[0183] There remain several challenges in PCa research: the lack of specific clinical markers for early diagnosis and prognosis of PCa and the need to identify drugs that target AI-PCa tumor cells directly without damaging healthy cells. In this study, the inventors show that NPRA is a biomarker for PCa and candidate for PCa therapy.
[0184] An important finding of this study is the demonstration that NPRA is significantly over-expressed in mouse and human PCa cells compared to normal cells. Screening of a human PCa TMA containing 240 tissue samples shows that NPRA is also over-expressed in human tissues including high grade PIN (prostatic intraepithelial neoplasm) and prostatic adenocarcinoma. The benign hyperplastic glands exhibited significantly lower NPRA expression than localized PCas. These data are consistent with the previous report and with the data in this study, showing that NPRA is highly expressed in both human and mouse PCa cell lines and in advanced PCa tissues, but not in a normal prostate epithelial cell line or in a benign prostate hyperplasia epithelial cell line [19, 35, 36]. It is to be noted that NPRA was expressed in androgen dependent cell line LNCaP but not in stromal cell line, WPMY. However, expression of ANP was detected in the culture supernatant of PC3 and DU145 PCa cells and WPMY stromal cells but not in normal prostate epithelial cells or LNCaP cells (unpublished observation). The inventors found a significant association between NPRA expression and Gleason score and pathological stage. Results from the TMA studies show that NPRA is an independent predictor of advanced PCa, and may therefore be useful as a clinical marker. Although, a number of marker antigens have been reported for PCa, none of them is specific enough to pass the clinical test for use in PCa prognosis. Given the strong positive correlation (r=0.64, p<0.005) between NPRA expression and the severity of the clinical stage, particularly in AI-PCa, NPRA may prove to be an effective clinical prognostic marker.
[0185] This study also suggests that NPRA may be a drug target for treating PCa and other cancers. Using the TRAMP-C1 spontaneous PCa model, the inventors demonstrated that NPRA-KO mice, which have normal heart, kidney and vascular function, have no detectable increase in postnatal mortality, do not permit growth of implanted PCa cells and have a normal life-span of over 24 months. Tumor growth is observed in NPRA-het mice but at a significantly reduced level compared to that in WT C57BL/6 mice, which indicates that host NPRA gene dosage is a determining factor for the growth of tumor cells in mice. This finding is consistent with the reports that ANP peptides (ANP and VD) inhibit the proliferation of PCa cells in vitro and in mice [35]. This is presumably due to the feedback inhibition of NPRA expression caused by high doses of ANP or other natriuretic peptides, such as NP73-102 [18, 35, 37, 38]. Thus, while low doses of these peptides stimulate NPRA signaling, high doses inhibit NPRA signaling and show anticancer effects. In sum, NPRA provides a heretofore undescribed target for PCa. This hypothesis is also supported by the observation that NPRA is an upstream regulator of IL-6, which has been reported as a target for PCa therapy [39, 40].
[0186] In view of the finding that pNP73-102 inhibits NPRA expression, the inventors examined its role in treating PCa. TRAMP-C1 cells injected into C57BL/6 mice induced tumors in the control mice but not in pNP73-102-treated mice. These findings demonstrate the potential utility of pNP73-102 for the treatment of PCa. Although the mechanism of tumor inhibition by pNP73-102 is unknown, the evidence that pNP73-102 significantly decreases the expression of NPRA suggests that this may be the explanation for its antitumor effect. A perceived limitation in iNPRA therapy for PCa is the normal physiological role of NPRA in blood pressure regulation. To address this issue, the inventors compared blood pressure of NPRA-KO mice with that of TRAMP mice and found no relationship between NPRA expression, blood pressure levels and PCa incidence (FIG. 16), which is consistent with studies in humans that showed no relationship between blood pressure and PCa [41, 42].
[0187] Another major finding of this study is that the antitumor effects of limiting NPRA expression may be due to a reduction in inflammation in the tumor environment. The evidence herein shows that a number of molecules may be regulated by NPRA signaling including MIF and IL-6, both of which have been implicated in PCa development. Increased MIF mRNA expression and serum MIF levels have been associated with progression of PCa when tumor and benign tissue from matched samples were compared [33, 34, 43]. Elevated IL-6 levels are found in patients with metastatic PCa and are associated with a poor prognosis [44]. Furthermore, aberrant expression of the IL-6 gene and increased production of IL-6 are associated with advanced bone metastasis and increased morbidity [44-47], as well as resistance to chemotherapy [48]. There are three lines of evidence supporting the idea that NPRA is an upstream regulator of MIF in PCa cells: (i) A 2.5-fold reduction in MIF mRNA was found after LPS treatment of NPRA-KO mice compared to WT mice; (ii) MIF expression was detectable in the prostate tissues of TRAMP mice, but not in WT mice; and (iii) NPRA down-regulation reduced MIF expression in cultured TRAMP-C1 cells and xenografts. Consistent with these observations, a PCa TMA stained for NPRA showed expression of MIF.
[0188] Since intratumoral expression of MIF was correlated with serum IL-6 in patients with non-small cell lung cancer [49] and IL-6 was shown to be one of the potential MIF-regulated genes in DU145 cells [24], the inventors propose that NPRA can regulate IL-6 in PCa cells via MIF. In support of this hypothesis, the inventors found elevated IL-6 in the serum of TRAMP mice during PCa development. These data support previously reported studies, where lung tissues of NPRA-KO mice failed to induce IL-6 during OVA-induced inflammatory challenge and showed reduced expression of activated p65- and p50-NF-kB [19, 20]. Together, these studies show that NPRA may affect PCa progression by regulating MIF and possibly IL-6 expression, both of which have been linked to PCa.
[0189] The results herein demonstrate that increased NPRA expression is strongly associated with progression of human PCa and that NPRA deficiency prevents growth of transplanted PCa cells and inhibits tumor burden in TRAMP mice in part by down-regulating MIF in PCa cells.
[0190] It should be understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and the scope of the appended claims. In addition, any elements or limitations of any invention or embodiment thereof disclosed herein can be combined with any and/or all other elements or limitations (individually or in any combination) or any other invention or embodiment thereof disclosed herein, and all such combinations are contemplated with the scope of the invention without limitation thereto.

REFERENCES

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Claims

1. A method for predicting progression of a malignancy and prognosing the malignancy in a human subject diagnosed with the malignancy, comprising:
(a) obtaining a tissue sample suspected of containing malignant cells from the human subject diagnosed with the malignancy;
(b) determining a level of human natriuretic peptide receptor A (NPRA) protein in the tissue sample using an immunohistochemical assay, wherein the human NPRA protein comprises the amino acid sequence of SEQ ID NO:5, and wherein the immunohistochemical assay comprises: (i) contacting the tissue sample with a polyclonal antibody, or fragment thereof, that binds to the human NPRA protein, forming a complex, wherein the polyclonal antibody, or fragment thereof, is capable of binding to an epitope of mouse NPRA protein within the amino acid sequence of SEQ ID NO:3, and (ii) detecting the complex between the polyclonal antibody, or fragment thereof, and the human NPRA protein;
(c) comparing the level determined in (b) with a control NPRA level, wherein a high human NPRA protein level is indicative of an unfavorable prognosis and a low human NPRA protein level is indicative of a favorable prognosis; and
(d) repeating (a)-(c) one or more times over time, to monitor the malignancy over time.
2. The method of claim 1, wherein the tissue sample comprises tumor cells from the human subject.
3. The method of claim 1, wherein a favorable prognosis comprises tumor regression and/or longer survival rates relative to patients with unfavorable prognosis.
4. The method of claim 1, wherein the malignancy is selected from the group consisting of prostate cancer, colon cancer, breast cancer, pancreatic cancer, Merkell cell carcinoma, and gastrointestinal stromal tumor (GIST).
5. The method of claim 1, wherein the malignancy is colon cancer.
6. The method of claim 5, further comprising carrying out at least one confirmatory test for the colon cancer.
7. The method of claim 1, further comprising treating the human subject for the malignancy.
8. The method of claim 1, further comprising communicating the prognosis to the human subject.
9. The method of claim 1, wherein the human subject has undergone initiation of a regimen for treatment of the malignancy prior to said obtaining of (a).
10. The method of claim 9, wherein the control NPRA level is an NPRA level in a tissue sample obtained from the human subject earlier in the treatment regimen.
11. The method of claim 1, wherein the control NPRA level comprises a plurality of control NPRA levels, and wherein each control NPRA level corresponds to a different stage or grade of the malignancy.
12. The method of claim 11, wherein the malignancy is prostate cancer, and wherein the stage or grade of the malignancy comprises a Gleason score.
13. The method of claim 1, wherein the malignancy is prostate cancer.
14. The method of claim 1, wherein the immunohistochemical assay is a tissue microarray.
15. The method of claim 1, further comprising cryopreserving the tissue sample prior to said determining.
16. The method of claim 1, wherein the polyclonal antibody is a rabbit polyclonal antibody.
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