WO2010089707A1

WO2010089707A1 - Methods and kits for determining sensitivity or resistance of prostate cancer to radiation therapy

Info

Publication number: WO2010089707A1
Application number: PCT/IB2010/050517
Authority: WO
Inventors: Zelig Eshhar; Eytan Domany; Lilach Agemy; Itai Kella; Avi Orr-Urtreger; Anat Bar-Shira
Original assignee: Yeda Research And Development Co. Ltd.; The Medical Research, Infrastructure, And Health Services Fund Of The Tel Aviv Medical Center
Priority date: 2009-02-04
Filing date: 2010-02-04
Publication date: 2010-08-12

Abstract

Provided are methods and kits for predicting the sensitivity or the resistance of prostate cancer to radiation therapy by determining the expression level of polynucleotides and/or their gene products which are differentially expressed in radiation sensitive or radiation resistant prostate cancers. Also provided are methods and kits for selecting a treatment regimen of a subject diagnosed with prostate cancer and/or selecting an optimal dosage of radiation therapy.

Description

METHODS AND KITS FOR DETERMINING SENSITIVITY OR RESISTANCE OF PROSTATE CANCER TO RADIATION THERAPY

FIELD AND BACKGROUND OF THE INVENTION The present invention, in some embodiments thereof, relates to genetic markers of radiation- sensitivity or resistance of prostate cancer cells, and, more particularly, to methods and kits for predicting the sensitivity or the resistance of prostate cancer cells to radiation therapy and determining dosage and treatment regimens of prostate cancer.

Prostate cancer is the most commonly diagnosed malignancy and the second leading cause of cancer related death in the Western male population. The adoption of screening based upon the measurement of the serum prostate specific antigen (PSA) has led to earlier detection of prostate cancer, where at presentation most tumors now appear confined to the prostate gland. Surgery (radical prostatectomy) and radiotherapy (external-beam or brachytherapy) are the mainstay of treatment of localized primary prostate cancer. Direct comparisons between patients treated with radiation and prostatectomy are difficult because of variation in tumor stage, and thus there is no consensus regarding the relative effectiveness of these two therapies.

Radiation therapy [ionizing radiation (IR)] as a curative modality for localized prostate cancer was instituted by Bagshow early in the 1950' s, and has undergone improvement. Today, external radiation therapy is given over a 7 to 8 week period with a total of 65-75 Gray (Gy) delivered in fractions to the prostate. However, using pro state- specific antigen levels as a marker for tumor control, patients who present with apparently organ-confined disease have a 5-year biochemical failure rate of 10-40 % after external-beam radiation therapy depending upon original Gleason score and pro state- specific antigen (Scott et al., 2004).

The reasons for local radiation therapy failure are multiple and vary. Tumor factors, such as location, size, and inadequate vascular supply (hypoxia), can all play a role in the lack of responsiveness of neoplasms to ionizing radiation. In addition, failure of radiation therapy may result from either resistance of certain tumor cells within the tumor to the applied dose, and/or from failure to provide the optimal effective dose of IR to the entire tumor mass. Resistant of cells to radiation therapy may be influenced by cellular and genetic factors, such as differential tissue- specific gene expression [e.g., p53, ataxia telangiectasia mutated (ATM) status (Canman, CE., et al., 1998; Chang, EH., 2000; Colletier, PJ., 2000; Fan, Z., et al., 2000; Lee, JM. and Bernstein, A. 1993)]. Thus, tumors from different patients may have the same histological diagnosis yet may vary in their responses to ionizing radiation. In this respect, a critical problem lies in the lack of specific parameters to accurately predict the outcome of PC radiotherapy.

Exposure of cells to ionizing radiation results in immediate and widespread oxidative damage, by stimulating various signal transduction pathways such as protein kinase C (PKC), c-Jun NH2-terminal kinase (JNK), ceramide and mitogen- activated protein kinase (MAPK) activation. Although the oxidative damage to lipid membrane can induce apoptosis, the most important subcellular target is DNA. Two events are recognized in the irradiated cell. The first one is radiation-induced DNA damage with conformational alterations recognized by the sensory monitoring system, leading to recruitment of DNA repair enzymes followed by restoration of higher-order DNA structure. The second one is an indirect effect in which recognition of DNA damage by sensor molecules (like ATM and ku 80), initiate signal transmitted to proteins that modulate the activity of gene regulated cellular responses. The outcome of this dynamic combination under certain circumstances is arrest of cell cycle that is coupled with DNA repair leading to cell survival, apoptotic cell death or senescence.

The main forms of DNA damage induced radiation include single-strand breaks (SSBs) and double-strand breaks (DSBs), sugar and base modifications, oxidative damage of bases, interstrand cross-links, DNA-protein cross-links and locally multiply damaged sites (LMDSs). Of these various forms of damage, probably the most dangerous ones are the DSBs and LMDSs since they are the origin of lethal effects, mutagenesis, genomic instability and carcinogenesis. IR initiates a complicated series of transcriptional alterations in the cell, many of which are dependent upon genetic background, dose, dose rate, stage of cell cycle and time after irradiation.

It has so far been rather difficult to document the individual's intrinsic radiosensitivity since it is depended on many factors. For example, both deficiencies in DNA repair pathways and regulation of cell death may result in higher vulnerability to IR. Cases of hypersensitivity to IR have been well known to radiation oncologists for many years. Around 5-7 % of cancer patients develop adverse side effects to external radiation therapy in normal (healthy) tissues within the treatment field. On the other hand, radiation therapists have also observed that certain cancer patients do not respond to standard radiation therapy and might benefit from higher doses of radiation that would offer a better likelihood of cure. DNA microarrays have become the major tool for the investigation of global gene expression in human disease and in biomedical research. Given the complexity of radiation-induced responses, microarray analysis, offers new opportunities to identify a wider range of genes and signaling pathways involved in the response to radiation. This wealth of data (Snyder, AR. and Morgan, WF, 2004) has provided investigators with valuable information about gene expression responses right after IR. As expected, it became apparent that there is no single response to radiation. Genetic background, cell type, dose, and dose rate all vary the transcriptional profile seen after exposure to irradiation.

Microarray technology has been used to identify markers which can predict resistance of cancerous cells to radiation therapy. For example, Hanna E., et al., (Cancer Research 61: 2376-2380, 2001) identified tumor-related genes as predictors of radiation response of squamous cell carcinoma and Kumagai K, et al., [Invest Ophthalmol Vis Sci. 47(6): 2300-4, 2006] identified upregulated and downregulated genes in RNA samples of radiation-sensitive and radiation-resistant cell lines of choroidal malignant melanomas.

Microarray studies performed on prostate cancer cells identified small clusters of genes discriminating recurrent versus nonrecurrent prostate cancer disease (Glinsky GV., et al., J. Clin. Invest. 113: 913-923, 2004). In addition, the present inventors used microarrays to identify differentially expressed genes between IR resistance and IR sensitive human prostate cancer xenografts and cell lines (Lilach Agemy, Itai KeIa, Rafi Pfeffer, Eytan Domany, Avi Orr-Urtreger, Bar Shira Anat and Zelig Eshhar. "GENETIC PREDISPOSITION OF THE SENSITIVITY OF PROSTATE CANCER TO RADIATHERAPY" presented in: American- Society of Gene Therapy 9th Annual meeting, Boltimor, June 2006 (Abstract 1017; poster presentation). Lilach Agemy, Alon Harmelin, Tova Waks, Ilan Leibovitch, Tatyana Rabin, M. Raphael Pfeffer and Zelig Eshhar. "Irradiation Enhances the Metastatic Development of Prostatic Small Cell Carcinoma Xenografts" presented in: second Integral Join American-Israeli Conference on Cancer, June 2006 (Abstract 0006; poster presentation).

Additional background art include Fait S, et al., 2003, Carcinogenesis, 24(11): 1837-1845; Kruse JJ, et al., 2004, Radiat Res., 161(l):28-38; Rosser CJ, et al., 2004, Cancer Gene Ther., l l(4):273-279; Kitahara O, et al., 2002, Neoplasia, 4(4):295- 303; Vallat L, et al., 2003, Blood, 101(11):4598-4606; Fukuda K, et al., 2004, Br J Cancer, 91(8):1543-1550; Fait S, et al., 2003, Carcinogenesis, 24(11):1837-1845; and Kruse JJ, et al., 2004, Radiat Res., 161(l):28-38.

SUMMARY OF THE INVENTION

According to an aspect of some embodiments of the present invention there is provided a method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy, the method comprising comparing a level of expression in a prostate cancer sample of at least one gene selected from the group consisting H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl to a reference expression data of the at least one gene obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy.

According to an aspect of some embodiments of the present invention there is provided a kit for predicting a sensitivity or a resistance of prostate cancer to radiation therapy, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, S100A16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl.

According to an aspect of some embodiments of the present invention there is provided a kit for selecting a treatment regimen of a subject diagnosed with prostate cancer, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, S100A16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl.

According to an aspect of some embodiments of the present invention there is provided a microarray comprising no more than 500 oligonucleotides wherein each of the oligonucleotides is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl.

According to an aspect of some embodiments of the present invention there is provided a method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy, the method comprising determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2 and ZNF718, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy.

According to an aspect of some embodiments of the present invention there is provided a method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy, the method comprising determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy.

According to an aspect of some embodiments of the present invention there is provided a method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy, the method comprising determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:204-218, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy.

According to an aspect of some embodiments of the present invention there is provided a method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy, the method comprising determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-218, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy.

According to an aspect of some embodiments of the present invention there is provided a method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy, the method comprising determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:l l, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy.

According to an aspect of some embodiments of the present invention there is provided a method of selecting a treatment regimen of a subject diagnosed with prostate cancer, the method comprising: (a) predicting the sensitivity or the resistance of the prostate cancer of the subject to radiation therapy according to the method of the invention; and (b) selecting the treatment regimen based on the sensitivity or resistance of the prostate cancer to radiation therapy, thereby selecting the treatment regimen of a subject diagnosed with prostate cancer.

According to an aspect of some embodiments of the present invention there is provided a method of selecting a treatment regimen of a subject diagnosed with prostate cancer, the method comprising: (a) determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of S100A16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2 and ZNF718, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy; and (b) selecting the treatment regimen based on the sensitivity or resistance of the prostate cancer to radiation therapy.

According to an aspect of some embodiments of the present invention there is provided a method of selecting a treatment regimen of a subject diagnosed with prostate cancer, the method comprising: (a) determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy; and (b) selecting the treatment regimen based on the sensitivity or resistance of the prostate cancer to radiation therapy.

According to an aspect of some embodiments of the present invention there is provided a method of selecting a treatment regimen of a subject diagnosed with prostate cancer, the method comprising: (a) determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:204-218, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy; and (b) selecting the treatment regimen based on the sensitivity or resistance of the prostate cancer to radiation therapy.

According to an aspect of some embodiments of the present invention there is provided a method of selecting a treatment regimen of a subject diagnosed with prostate cancer, the method comprising: (a) determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-218, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy; and (b) selecting the treatment regimen based on the sensitivity or resistance of the prostate cancer to radiation therapy. According to an aspect of some embodiments of the present invention there is provided a method of selecting a treatment regimen of a subject diagnosed with prostate cancer, the method comprising: (a) determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy; and (b) selecting the treatment regimen based on the sensitivity or resistance of the prostate cancer to radiation therapy.

According to an aspect of some embodiments of the present invention there is provided a kit for predicting a sensitivity or a resistance of prostate cancer to radiation therapy, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2 and ZNF718.

According to an aspect of some embodiments of the present invention there is provided a kit for predicting a sensitivity or a resistance of prostate cancer to radiation therapy, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203.

According to an aspect of some embodiments of the present invention there is provided a kit for predicting a sensitivity or a resistance of prostate cancer to radiation therapy, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:204-218. According to an aspect of some embodiments of the present invention there is provided a kit for predicting a sensitivity or a resistance of prostate cancer to radiation therapy, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-218.

According to an aspect of some embodiments of the present invention there is provided a kit for predicting a sensitivity or a resistance of prostate cancer to radiation therapy, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197.

According to an aspect of some embodiments of the present invention there is provided a kit for predicting a sensitivity or a resistance of prostate cancer to radiation therapy, comprising at least 2 and no more than 500 isolated nucleic acid sequences selected from the group consisting of SEQ ID NOs:233-308.

According to an aspect of some embodiments of the present invention there is provided a kit for predicting a sensitivity or a resistance of prostate cancer to radiation therapy, consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences selected from the group consisting of SEQ ID NOs:233-308 and optionally additional reagent(s) for facilitating detection of the expression level of at least one gene hybridizing to the isolated nucleic acid sequences, and/or packaging materials and/or instructions for use in predicting a sensitivity or a resistance of prostate cancer to radiation therapy.

According to an aspect of some embodiments of the present invention there is provided a kit for selecting a treatment regimen of a subject diagnosed with prostate cancer, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2 and ZNF718. According to an aspect of some embodiments of the present invention there is provided a kit for selecting a treatment regimen of a subject diagnosed with prostate cancer, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203.

According to an aspect of some embodiments of the present invention there is provided a kit for selecting a treatment regimen of a subject diagnosed with prostate cancer, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:204-218.

According to an aspect of some embodiments of the present invention there is provided a kit for selecting a treatment regimen of a subject diagnosed with prostate cancer, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-218. According to an aspect of some embodiments of the present invention there is provided a kit for selecting a treatment regimen of a subject diagnosed with prostate cancer, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197.

According to an aspect of some embodiments of the present invention there is provided a kit for selecting a treatment regimen of a subject diagnosed with prostate cancer, comprising at least 2 and no more than 500 isolated nucleic acid sequences selected from the group consisting of SEQ ID NOs:233-308.

According to an aspect of some embodiments of the present invention there is provided a kit for selecting a treatment regimen of a subject diagnosed with prostate cancer, consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences selected from the group consisting of SEQ ID NOs:233-308 and optionally additional reagent(s) for facilitating detection of the expression level of at least one gene hybridizing to the isolated nucleic acid sequences, and/or packaging materials and/or instructions for use in selecting a treatment regimen of a subject diagnosed with prostate cancer.

According to an aspect of some embodiments of the present invention there is provided a microarray comprising no more than 500 oligonucleotides wherein each of the oligonucleotides is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2 and ZNF718.

According to an aspect of some embodiments of the present invention there is provided a microarray comprising no more than 500 oligonucleotides wherein each of the oligonucleotides is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198,

83, 199, 200, 201, 202, 101, 181, 114, 111 and 203.

According to an aspect of some embodiments of the present invention there is provided a microarray comprising no more than 500 oligonucleotides wherein each of the oligonucleotides is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:204-218.

According to an aspect of some embodiments of the present invention there is provided a microarray comprising no more than 500 oligonucleotides wherein each of the oligonucleotides is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-218.

According to an aspect of some embodiments of the present invention there is provided a microarray comprising no more than 500 oligonucleotides wherein each of the oligonucleotides is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197.

According to some embodiments of the invention, a decrease above a predetermined threshold in the level of expression of the at least one gene selected from the group consisting of IMP3, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, CSAG2, ZNF718, TP53, PTEN, DUSP6, TNFRSFlOD, and BTGl in the prostate cancer sample relative to the reference expression data of the at least one gene obtained from the at least one prostate cancer sensitive sample predicts the resistance of the prostate cancer sample to radiation therapy. According to some embodiments of the invention, an increase above a predetermined threshold in the level of expression of the at least one gene selected from the group consisting of IMP3, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, CSAG2, ZNF718, TP53, PTEN, DUSP6, TNFRSFlOD, and BTGl in the prostate cancer sample relative to the reference expression data of the at least one gene obtained from the at least one prostate cancer resistant sample predicts the sensitivity of the prostate cancer sample to radiation therapy.

According to some embodiments of the invention, a decrease above a predetermined threshold in the level of expression of the at least one gene selected from the group consisting of H2AFJ, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, ANXA2P2, SMARCAl, HPCALl, FUNDCl, CASP4, LITAF, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl and AGTRl in the prostate cancer sample relative to the reference expression data of the at least one gene obtained from the at least one prostate cancer resistant sample predicts the sensitivity of the prostate cancer sample to radiation therapy. According to some embodiments of the invention, an increase above a predetermined threshold in the level of expression of the at least one gene selected from the group consisting of H2AFJ, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, ANXA2P2, SMARCAl, HPCALl, FUNDCl, CASP4, LITAF, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl and AGTRl in the prostate cancer sample relative to the reference expression data of the at least one gene obtained from the at least one prostate cancer sensitive sample predicts the resistance of the prostate cancer sample to radiation therapy.

According to some embodiments of the invention, the at least one gene is selected from the group consisting of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, MAGEA2, ZNF718, CASP8, LITAF, CASP4, CD24, GULPl, UCP2, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, RAB26, and BTGl.

According to some embodiments of the invention, the at least one gene is selected from the group consisting of Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, PSMB8, TFCP2, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208 and KRTCAP3.

According to some embodiments of the invention, the at least one gene is selected from the group consisting of H2AFJ, FTHl, PFN2, TFCP2, PSMB 8, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, and BTGl. According to some embodiments of the invention, the at least one gene is selected from the group consisting of Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, and ZNF718.

According to some embodiments of the invention, the at least one gene is selected from the group consisting of CASP8, LITAF, CASP4, CD24, GULPl, UCP2, H2AFJ, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, RAB26, and BTGl.

According to some embodiments of the invention, the at least one gene is selected from the group consisting of FTHl, PFN2, PSMB8, TFCP2, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB,

VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST,

PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ

ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2,

SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, and KRTC AP3.

According to some embodiments of the invention, the kit further comprising at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample.

According to some embodiments of the invention, the at least one prostate cancer sensitive sample comprises a radiation sensitive prostate cancer xenograft or a radiation sensitive prostate cancer cell line.

According to some embodiments of the invention, the at least one prostate cancer resistant sample comprises a radiation resistant prostate cancer xenograft or a radiation resistant prostate cancer cell line. According to some embodiments of the invention, the kit further comprising a reference sample which comprises a cell sample of prostate cancer with known sensitivity or resistance to radiation therapy.

According to some embodiments of the invention, the reference sample comprises a radiation sensitive prostate cancer xenograft or a radiation sensitive prostate cancer cell line. According to some embodiments of the invention, the reference sample comprises a radiation resistant prostate cancer xenograft or a radiation resistant prostate cancer cell line.

According to some embodiments of the invention, the treatment regimen comprises a radiation therapy selected from the range of 45-80 Gy when the prostate cancer is radiation sensitive.

According to some embodiments of the invention, the alteration is upregulation of the expression level of the at least one polynucleotide in the cell of the prostate cancer relative to the reference cell, whereas the at least one polynucleotide is selected from the group consisting of Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl and

FUNDCl.

According to some embodiments of the invention, the alteration is upregulation of the expression level of the at least one polynucleotide in the cell of the prostate cancer relative to the reference cell, whereas the at least one polynucleotide is selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201 and 202.

According to some embodiments of the invention, the alteration is upregulation of the expression level of the at least one polynucleotide in the cell of the prostate cancer relative to the reference cell, whereas the at least one polynucleotide is selected from the group consisting of SEQ ID NOs:204-210. According to some embodiments of the invention, the alteration is upregulation of the expression level of the at least one polynucleotide in the cell of the prostate cancer relative to the reference cell, whereas the at least one polynucleotide is selected from the group consisting of SEQ ID NOs: 11-97 and 169-173.

According to some embodiments of the invention, the alteration is upregulation of the expression level of the at least one polynucleotide in the cell of the prostate cancer relative to the reference cell, whereas the at least one polynucleotide is selected from the group consisting of SEQ ID NOs: 11, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169,

170, 171, 172, 173.

According to some embodiments of the invention, the alteration is upregulation of the level of expression of the at least one polynucleotide in the cell of the prostate cancer relative to the reference cell, whereas the at least one polynucleotide is selected from the group consisting of CSAG2, PPAPDClB, MAGEA2 and ZNF718. According to some embodiments of the invention, the alteration is upregulation of the level of expression of the at least one polynucleotide in the cell of the prostate cancer relative to the reference cell, whereas the at least one polynucleotide is selected from the group consisting of SEQ ID NOs: 101, 181, 114, 111 and 203. According to some embodiments of the invention, the alteration is upregulation of the level of expression of the at least one polynucleotide in the cell of the prostate cancer relative to the reference cell, whereas the at least one polynucleotide is selected from the group consisting of SEQ ID NOs:211-218.

According to some embodiments of the invention, the alteration is upregulation of the level of expression of the at least one polynucleotide in the cell of the prostate cancer relative to the reference cell, whereas the at least one polynucleotide is selected from the group consisting of SEQ ID NOs:98-168 and 174-197.

According to some embodiments of the invention, the alteration is upregulation of the level of expression of the at least one polynucleotide in the cell of the prostate cancer relative to the reference cell, whereas the at least one polynucleotide is selected from the group consisting of SEQ ID NOs: 101, 114, 119, 174-197.

According to some embodiments of the invention, detecting the level of expression is effected using an RNA detection method.

According to some embodiments of the invention, detecting the level of expression is effected using a protein detection method.

According to some embodiments of the invention, each of the isolated nucleic acid sequences is selected from the group consisting of an oligonucleotide molecule, a cDNA molecule, a genomic DNA molecule and an RNA molecule.

According to some embodiments of the invention, each of the isolated nucleic acid sequences comprises at least 10 and no more than 50 nucleic acids.

According to some embodiments of the invention, each of the isolated nucleic acid sequences is bound to a solid support.

According to some embodiments of the invention, the kit further comprising at least one reagent suitable for detecting hybridization of the isolated nucleic acid sequences to at least one RNA transcript of the at least one gene.

According to some embodiments of the invention, the kit further comprising at least one reagent suitable for detecting hybridization of the isolated nucleic acid sequences and at least one RNA transcript corresponding to the at least one specific polynucleotide sequence selected from the group consisting of Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2 and ZNF718. According to some embodiments of the invention, the kit further comprising at least one reagent suitable for detecting hybridization of the isolated nucleic acid sequences and at least one RNA transcript corresponding to the at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203. According to some embodiments of the invention, the kit further comprising at least one reagent suitable for detecting hybridization of the isolated nucleic acid sequences and at least one RNA transcript corresponding to the at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:204-218.

According to some embodiments of the invention, the kit further comprising at least one reagent suitable for detecting hybridization of the isolated nucleic acid sequences and at least one RNA transcript corresponding to the at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-218.

According to some embodiments of the invention, the kit further comprising at least one reagent suitable for detecting hybridization of the isolated nucleic acid sequences and at least one RNA transcript corresponding to the at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11, 30, 38,

44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197.

According to some embodiments of the invention, the kit further comprising packaging materials packaging the at least one reagent and instructions for use in determining the sensitivity or the resistance of the prostate cancer to radiation therapy

According to some embodiments of the invention, the kit further comprising packaging materials packaging the at least one reagent and instructions for use in selecting the treatment regimen of the subject diagnosed with prostate cancer.

According to some embodiments of the invention, each of the oligonucleotides comprises at least 10 and no more than 40 nucleic acids.

Unless otherwise defined, all technical and/or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and/or materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be necessarily limiting.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention is herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of the preferred embodiments of the present invention only, and are presented in the cause of providing what is believed to be the most useful and readily understood description of the principles and conceptual aspects of the invention. In this regard, no attempt is made to show structural details of the invention in more detail than is necessary for a fundamental understanding of the invention, the description taken with the drawings making apparent to those skilled in the art how the several forms of the invention may be embodied in practice. In the drawings: FIGs. IA-D are graphs depicting tumor growth following a single dose of in- vitro irradiation (FIG.s IA-B) or fractionated irradiation in vivo (FIGs. IC-D) of representative radiosensitive (FIGs. IA, 1C) and radioresistant (FIGs. IB and ID) prostate cancer xenografts. Tissue of CWR22 or LAPC9 xenografts (80-100 mg) were implanted subcutaneously (s.c.) to SCID mice either without or after increasing doses of irradiation (0-160 Gy). For fractionated irradiation experiment same xenografts were injected into right hind thigh of SCID mice and shielded mice were sub-lethally irradiated at the exposed hind leg by daily doses (five sessions per week) directed. Kinetics of tumor growth was measured until > 50 % of the mice in a certain group scored dead (the values represent average of mice that developed tumor). FIGs. IA and 1C - CWR22; FIGs. IB and ID - LAPC9. FIGs. 2A-B depict clustering results using super-paramagnetic clustering (SPC) for the 3730 probe sets that passed through one of three filters (described under "Material and Experimental Methods" of the Examples section which follows). FIG. 2A - Dendrogram of the genes that includes clusters (each box represent a cluster) of size 3 and larger. The arrows mark the six clusters analyzed; FIG. 2B - Expression matrix of the 12 RNA samples obtained from 5 prostate cancer (PC) xenografts. Samples 1, 3, 5, 8 and 11 were obtained from non-irradiated (0 Gy) prostate cancer xenografts; Samples 2, 4, 6, 7, 9, 10 and 12 were obtained from irradiated prostate cancer xenografts with the following maximal irradiation doses: Sample 2 - 40 Gy; Sample 4 - 20 Gy; Sample 6 - 20 Gy; Sample 7 - 60 Gy; Sample 9 (80 Gy); Sample 10 - 160 Gy; and Sample 12 - 120 Gy. The genes (row) are normalized and ordered according to the dendrogram on the left (clustering operation). The color represents induction (increase; red) or repression (decrease; blue). The six clusters are marked by black lines at the right hand side of the matrix. The 12 samples are divided according to their sensitivity to the IR (delineated at the matrix). The "radiosensitive" group includes WISH-PC23 (columns 1 and 2) and CWR22 (columns 3 and 4) xenografts; the "semi-radioresistant" group includes the LuCap35 (columns 5, 6 and 7) xenograft, and the "radioresistant" group includes the LAPC9 (columns 8, 9 and 10) and WISH-PC14 (columns 11 and 12) xenografts.

FIGs. 3A-D depict up regulated genes in the radioresistant samples. Cluster 2 (FIGs. 3A-B), an expression matrix consists of 157 probesets (rows) and 12 samples (columns); Cluster 3 (FIGs. 3C-D), an expression matrix consists of 66 probesets (rows) and 12 samples (columns). FIGs. 3A and 3C - The probesets are centered and normalized, and ordered according to the sorter algorithm. The color represents increase (red) or decrease of gene expression (blue). The samples are ordered according to their sensitivity to radiation (see bottom of the expression matrix). The sensitive group includes the WISH-PC23 (columns 1 and 2) and CWR22 (columns 3 and 4) xenografts, the semi-resistant group includes the LuCAP35 (columns 5, 6 and 7) xenograft, and the resistant group includes the LAPC9 (columns 8, 9 and 10) and WISH-PC14 (columns 11 and 12) xenografts. Samples 1, 3, 5, 8 and 11 were obtained from non-irradiated (0 Gy) prostate cancer xenografts; Samples 2, 4, 6, 7, 9, 10 and 12 were obtained from irradiated prostate cancer xenografts with the following maximal irradiation doses: Sample 2 - 40 Gy; Sample 4 - 20 Gy; Sample 6 - 20 Gy; Sample 7 - 60 Gy; Sample 9 (80 Gy); Sample 10 - 160 Gy; and Sample 12 - 120 Gy. FIGs. 3B and 3D - principal component analysis (PCA), which is a method that enables visualization of high dimension vectors in a two or three dimensional plane; for example, each of the 12 samples in cluster 2 can be defined as a vector in 157 dimensions. The sensitive, resistant and semi-sensitive groups are marked by red, black and green dots, respectively. FIGs. 4A-D depict up regulated genes in the radiosensitive samples. Cluster 5

(FIGs. 4A and 4C), an expression matrix consists of 117 probesets (rows) and 12 samples (columns); Cluster 6 (FIGs. 4B and 4D), an expression matrix consists of 116 probesets (rows) and 12 samples (columns). FIGs. 4A and 4C - The probesets are centered and normalized, and ordered according to the sorter algorithm. The color represents increase (red) or decrease of gene expression (blue). The samples are ordered according to their sensitivity to radiation (see bottom of the expression matrix). The sensitive group includes the WISH-PC23 (columns 1 and 2) and CWR22 (columns 3 and 4) xenografts, the semi-resistant group includes the LuCap35 (columns 5, 6 and 7) xenograft, and the resistant group includes the LAPC9 (columns 8, 9 and 10) and WISH- PC14 (columns 11 and 12) xenografts. Samples 1, 3, 5, 8 and 11 were obtained from non-irradiated (0 Gy) prostate cancer xenografts; Samples 2, 4, 6, 7, 9, 10 and 12 were obtained from irradiated prostate cancer xenografts with the following maximal irradiation doses: Sample 2 - 40 Gy; Sample 4 - 20 Gy; Sample 6 - 20 Gy; Sample 7 - 60 Gy; Sample 9 (80 Gy); Sample 10 - 160 Gy; and Sample 12 - 120 Gy. FIGs. 4B and 4D - depict principal component analysis (PCA), a visualization of the distance relation between the 12 samples. The sensitive, resistant and semi- sensitive groups are marked by red, black and green dots, respectively.

FIGs. 5A-C depict uniting clusters 2, 3, 5 and 6. FIG. 5A - An expression matrix consisting of 456 probesets (rows) and 12 samples (columns). The probesets are centered and normalized, and ordered according to the sorter algorithm. The color represents increase (red) or decrease in gene expression (blue). The samples are ordered according to their sensitivity to the IR (see bottom of the expression matrix). The sensitive group includes the WISH-PC23 (columns 1 and 2) and CWR22 (columns 3 and 4) xenografts, the semi-resistant group includes the LuCap35 (columns 5, 6 and 7) xenograft, and the resistant group includes the LAPC9 (columns 8, 9 and 10) and WISH- PC 14 (columns 11 and 12) xenografts. FIG. 5B - A visualization of the distance relation between the 12 samples by PCA analysis. The sensitive, resistant and semi-resistant groups are marked by red, black and green dots, respectively. FIG. 5C - Representation of the distance relationship between the 12 samples by PCA analysis. The Sensitive, Resistant and Semi-resistant samples are marked by red, black and green dots, respectively. X, Y and Z axes represent the first, second and third principal components, respectively.

FIGs. 6A-D depict correlation of mRNA expression between gene chip analysis and Real Time PCR. RNA samples from three individual mice, each of a different generation of the same xenograft, and the RNA sample (of the same xenograft) used on the Affymetrix chip were tested by Real Time PCR. The data is presented as the relative expression value for LAPC9-resistant xenograft compared with sensitive xenografts (CWR22 or WISH PC23) or the intermediate phenotype (LuCAP35). TPTl, a control gene that was used for normalization for each sample. FIG. 6A - H2AFJ variant 2; FIG. 6B - UCP2; FIG. 6C - PTEN; FIG. 6D - RAB26.

FIG. 7 depicts clustering of genes whose expression differentiates between the radio- sensitive and the radio-resistant phenotypes, and are shared by both PC xenografts and cell lines. The expression matrix contains 46 probe sets (corresponding to 42 genes) out of the 456 previously identified probesets that best distinguish between the radioresistant/sensitive phenotypes (using t-test, FDR 10 %) in the xenogratfs and in the cell line data. The color bars at the bottom mark the Sensitive (red) and the Resistant (black) samples.

FIGs. 8A-B depict two hypothetical models for radioresistance/sensitivity of prostate cancer xenografts FIG. 8 A - Model a (one): two distinct subpopulations within a given xenograft; FIG. 8B - Model b (two): each xenograft contains a homogeneous population of cells that have equal chance to survive/die after irradiation. DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION

The present invention is of genetic markers which are differentially expressed in radiation sensitive or radiation resistant prostate cancer cells and which can be used to predict the sensitivity or the resistance of prostate cancer to radiation therapy. Specifically, the present invention can be used to select treatment regimens and dosage of subjects diagnosed with prostate cancer.

The principles and operation of the methods or kits of predicting sensitivity and the methods of increasing the sensitivity of the prostate cancer to radiation therapy according to the present invention may be better understood with reference to the drawings and accompanying descriptions.

Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways. Also, it is to be understood that the phraseology and terminology employed herein is for the purpose of description and should not be regarded as limiting.

The present inventors have uncovered differentially expressed genes which are associated with radiation sensitive or radiation resistance prostate cancer and which can be used to predict the sensitivity or the resistance of prostate cancer to radiation therapy, select treatment regimen in subjects diagnosed with prostate cancer and determine a dosage of radiation therapy suitable for treating prostate cancer.

As is shown in the Examples section which follows, the present inventors have determined the radiosensitivity or radioresistance of prostatic adenocarcinoma xenografts and prostate cancer cell lines (Table 1, Figures IA-D, Example 1), and further subjected RNA derived from radiation sensitive or radiation resistance xenografts to microarray analysis. As is further shown in Figures 2A-B, 3A-D, 4A-D and 5A-C and is described in Example 2 of the Examples section which follows, six stable gene clusters were observed. Of these, four clusters could divide the samples into major subgroups: IR-resistant and IR-sensitive phenotypes. The four clusters consisted of 158 probsets [correspondent to 112 genes, including 14 expressed sequence tags (ESTs)] that showed more than 3 fold change in transcription (RNA expression level). 87 probesets displayed elevated expression (clusters 2 and 3, Tables 2 and 3, respectively), and 71 probesets displayed decreased expression (clusters 5 and 6, Tables 4 and 5, respectively) in the radioresistant xenografts relative to the radiosensitive xenografts. Real Time PCR analysis of representative genes validated the gene array data (Figures 6A-D, Example 3). As is further shown in Table 6 and Figure 7 and described in Example 4 of the Examples section which follows, analysis of the expression pattern of the probesets included in clusters 2, 3, 5 and 6 in an independent set of prostate cancer cell lines which are radiation resistant or radiation sensitive and comparison of such expression pattern to that obtained in radiation sensitive or radiation resistant prostate cancer xenografts revealed a group of 41 unique genes (FTHl, PFN2, PSMB8, TFCP2, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, KRTCAP3; 42 probesets) which best distinguished between the radioresistant/sensitive phenotypes (t-test, p < 0.01; FDR 10 %). Moreover, analysis of the average expression levels of all differentiating genes/markers identified in this study in all prostate cancer samples (xenografts and cell lines) revealed a group of 10 unique genes (Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, and ZNF718; e.g., represented by SEQ ID NOs:204-218, 91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203) which provide a significant prediction power of the sensitivity or resistance of a prostate cancer sample to radiation therapy (Example 5, Table 7). In addition, Tables 8 and 9 (Example 5 of the Examples section which follows) summarize the ratio of expression levels between several genes (CASP8, LITAF, CASP4, CD24, GULPl, UCP2, H2AFJ, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, RAB26, BTGl) which are differentially expressed between IR resistant and sensitive prostate cancer cell samples phenotypes according to their functional affiliation.

Altogether, these results demonstrate for the first time that genetic markers can discriminate between radiosensitive and radioresistant prostate cancer cells, and suggest the use of such differentially expressed genes in predicting sensitivity of prostate cancer cells to radiation therapy.

Thus, according an aspect of some embodiments of the invention, there is provided a method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy. The method is effected by comparing a level of expression in a prostate cancer sample of at least one gene selected from the group consisting H2AFJ, S100A16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl to a reference expression data of the at least one gene obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy. As used herein, the phrase "radiation therapy" refers to a high-energy radiation which is capable of at least causing a growth arrest of cancer cells and optimally killing the cancer cell and/or shrinking tumors. Generally, the phrase "radiation therapy" refers to an ionizing radiation such as X-ray, beta particles and/or gamma rays. Radiation therapy may be applied to the cancer cells or the tumors from an external radiation source (e.g., machine) placed outside the body (external radiation therapy) or can be delivered via radioisotopes which are administered close to the cancer cells or the tumor (e.g., brachy therapy). It will be appreciated that radiation therapy may be given at a single dose, or preferably, in fractions so that multiple doses are given for a period of several weeks. For example, for the treatment of prostate cancer, radiation therapy is given over a 7 to 8 week period with a total of 65-80 Gray (Gy) delivered in fractions (e.g., in the range of 1.8 to 2 Gy) to the prostate.

As used herein, the phrase "predicting a sensitivity or a resistance of prostate cancer to radiation therapy" refers to determining susceptibility of the prostate cancer cells to the radiation therapy, e.g., the degree of sensitivity or resistance of the prostate cancer to the radiation therapy.

As used herein "radiation resistant prostate cancer" refers to prostate cancer cells of which at least about 50 % of cells survive radiation therapy, e.g., being capable of growing and/or proliferating following radiation therapy. According to some embodiments of the invention, in a radiation resistant prostate cancer at least about 55 %, at least about 60 %, at least about 65 %, at least about 70 %, at least about 75 %, at least about 80 %, at least about 85 %, at least about 90 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, e.g., 100 % of the cells are capable of growing and/or proliferating following radiation therapy.

As used herein "radiation sensitive prostate cancer" refers to prostate cancer cells of which at least about 50 % of cells are growth arrest and/or killed as a result of radiation therapy. According to some embodiments of the invention, in a radiation sensitive prostate cancer at least about 55 %, at least about 60 %, at least about 65 %, at least about 70 %, at least about 75 %, at least about 80 %, at least about 85 %, at least about 90 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, e.g., 100 % of the cells are growth arrest and/or killed as a result of radiation therapy.

It should be noted that the growth and/or proliferation of prostate cancer cells can be determined in vitro (e.g., using known cell viability, proliferation, live/dead assays), ex vivo (e.g., by monitoring the ability of the cells to generate tumors in animals) and/or in vivo (e.g., by monitoring tumor growth in a subject). As used herein, the phrase "level of expression" refers to the degree of gene expression and/or gene product activity in a specific prostate cancer sample (e.g., a cell or a cell sample of the prostate cancer). For example, up-regulation or down-regulation of various genes can affect the level of the gene product (i.e., RNA and/or protein) in a specific sample. Sequence information regarding gene products (i.e., RNA transcripts and polypeptide sequences) of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl can be found in Tables 6, 7, 8 and 9 in the Examples section which follows. In addition, probes which can be used to detect transcripts of these genes (e.g., affymetrix probesets), are provided in 6, 7, 8 and 9 in the Examples section which follows. It should be noted that the level of expression can be determined in arbitrary absolute units, or in normalized units (relative to known expression levels of a control reference, e.g., a prostate cancer sample with known sensitivity or resistant to radiation therapy). For example, when using DNA chips, the expression levels are normalized according to the chips' internal controls or by using quantile normalization such as RMA (Robust Multichip Average).

VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST,

PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ

ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2,

According to some embodiments of the invention, the method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy is effected by comparing the level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-218, in a prostate cancer sample to a reference expression data of the at least one polynucleotide sequence obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy.

According to some embodiments of the invention, the method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy is effected by comparing the level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114,

111 and 203 in a prostate cancer sample to a reference expression data of the at least one polynucleotide sequence obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy.

According to some embodiments of the invention, the method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy is effected by comparing the level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:204-218 in a prostate cancer sample to a reference expression data of the at least one polynucleotide sequence obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy.

According to an embodiment of the invention, the method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy is effected by comparing the level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197 in a prostate cancer sample to a reference expression data of the at least one polynucleotide sequence obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy.

According to some embodiments of the invention, the at least one gene comprises at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least about 10 genes (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18 or 19 genes), at least about 20 genes (e.g., 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 genes), at least about 30 genes (e.g., 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 genes), at least about 40 genes (e.g., 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 genes), at least about 50 genes (e.g., 50, 51, 52, 53, 54, 55, 56, 57, 58, 59 genes), at least about 60 genes (e.g., 60, 61, 62, 63 or 64 genes) selected from the group consisting of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl. For example, the at least one gene can include H2AFJ, PSMB8, RHOQ, ACAA2, TUB A3 and Sl 0OA 16. Additionally or alternatively, the at least one gene can include METTL7A, MAGEA2, and KRTC AP3. Additionally or alternatively, the at least one gene can include H2AFJ, PSMB8, RHOQ, ACAA2, TUBA3, S100A16 and METTL7A, MAGEA2, and KRTC AP3. It should be noted that any combination of genes from the list consisting of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl can be used according to the method of the invention.

According to some embodiments of the invention, the at least one gene comprises at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least about 10 genes (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18 or 19 genes), at least about 20 genes (e.g., 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 genes), at least about 30 genes (e.g., 30, 31, 32 genes) selected from the group consisting of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, MAGEA2, ZNF718, CASP8, LITAF, CASP4, CD24, GULPl, UCP2, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, RAB26, and BTGl. For example, the at least one gene can include H2AFJ, Sl 0OA 16, MALL,

SMARCAl, HPCALl. Additionally or alternatively, the at least one gene can include H2AFJ, MAGEA2, ZNF718, CASP8, CASP4, CD24, UCP2, IFITM3, GUCY1A3. Additionally or alternatively, the at least one gene can include TP53, DUSP6, PTEN, TNFRSFlOD and IMP-3. It should be noted that any combination of genes from the list consisting of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, MAGEA2, ZNF718, CASP8, LITAF, CASP4, CD24, GULPl, UCP2, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, RAB26, and BTGl can be used according to the method of the invention.

According to some embodiments of the invention, the at least one gene comprises at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least about 10 genes (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18 or 19 genes), at least about 20 genes (e.g., 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 genes), at least about 30 genes (e.g., 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 genes), at least about 40 genes (e.g., 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 genes), e.g., 50 or 51 genes selected from the group consisting of Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, PSMB8, TFCP2, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208 and KRTCAP3.

According to some embodiments of the invention, the at least one gene comprises at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least about 10 genes (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18 or 19 genes), at least about 20 genes (e.g., 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 genes), at least about 30 genes (e.g., 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 genes), at least about 40 genes (e.g., 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 genes), at least 50 genes (e.g., 50, 51, 52, 53, 54, 55, 56, 57, 58 or 59 genes) selected from the group consisting of H2AFJ, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO:186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, and BTGl. According to some embodiments of the invention, the at least one gene comprises at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least about 10 genes selected from the group consisting of

S100A16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, and ZNF718.

According to some embodiments of the invention, the at least one gene comprises at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least about 10 genes (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18 or 19 genes), at least about 20 genes (e.g., 20, 21 genes) selected from the group consisting of CASP8, LITAF, CASP4, CD24, GULPl, UCP2, H2AFJ, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, RAB26, and BTGl.

According to some embodiments of the invention, the at least one gene comprises at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least about 10 genes (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18 or 19 genes), at least about 20 genes (e.g., 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 genes), at least about 30 genes (e.g., 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 genes), at least about 40 genes (e.g., 40, 41 genes) selected from the group consisting of FTHl, PFN2, PSMB8, TFCP2, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO:184, a gene encoding SEQ ID NO:185, a gene encoding SEQ ID NO:186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, and KRTCAP3. According to some embodiments of the invention, the method is effected by comparing the level of expression of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least 10 polynucleotide sequences, at least 11, e.g., 12 polynucleotide sequences selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203 in a prostate cancer sample to a reference expression data of the at least one polynucleotide obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy.

According to some embodiments of the invention, the method is effected by comparing the level of expression of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, e.g., 10 polynucleotide sequences selected from the group consisting of SEQ ID NOs:204-218 in a prostate cancer sample to a reference expression data of the at least one polynucleotide obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy. . According to some embodiments of the invention, the method is effected by comparing the level of expression of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least 10 polynucleotide sequences, at least 20, at least 30, at least 40, at least 50 polynucleotide sequences selected from the group consisting of SEQ ID NOs: 11- 197 in a prostate cancer sample to a reference expression data of the at least one polynucleotide obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy.

According to some embodiments of the invention, the method is effected by determining the level of expression of at least one polynucleotide of clusters 2 and/or 3 (which genes are upregulated in radiation resistant prostate cancer cells) and/or of clusters 4 and/or 5 (which genes are downregulated in radiation resistant prostate cancer cells) and comparing the level of the at least one polynucleotide in a prostate cancer sample to a reference expression data of the at least one polynucleotide obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy.

According to some embodiments of the invention, the method is effected by comparing the level of expression of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least 10 polynucleotide sequences, at least 20, at least 30 polynucleotide sequences selected from the group consisting of SEQ ID NOs:l l, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197 in a prostate cancer sample to a reference expression data of the at least one polynucleotide obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy. According to some embodiments of the invention, detecting/determining the level of expression of the genes of some embodiments of the invention is effected using RNA or protein molecules which are extracted from a prostate cancer cell sample.

As used herein the phrase "prostate cancer sample" refers to any cell content and/or cell secreted content which contains RNA and/or proteins of the prostate cancer cells. Prostate cancer may be adenocarcinoma of the prostate or small cell carcinoma of the prostate. Preferably, the prostate cancer cell of the present invention is adenocarcinoma of the prostate. Examples include a prostate cancer biopsy (e.g., frozen tissue, cryosection, archival or fixed pathological specimens), blood sample, prostate cancer cell line, prostate cancer xenograft. It should be noted that a "cell of the prostate cancer" may also optionally comprise a prostate cancer cell that has not been physically removed from the subject (e.g., in vivo detection).

According to some embodiments of the invention, the prostate cancer sample is a prostate cancer tissue biopsy which can be obtained using a scalpel or a syringe needle from a prostate cancer tumor. Methods of extracting RNA or protein molecules from cells are well known in the art.

Once obtained, the RNA or protein molecules are preferably characterized for the expression and/or activity level of various RNA and/or protein molecules using methods known in the arts. Non-limiting examples of methods of detecting transcribed RNA molecules in a cell sample include Northern blot analysis, RT-PCR, RNA in situ hybridization (using e.g., DNA or RNA probes to hybridize RNA molecules present in the cells or tissue sections), in situ RT-PCR (as described in Nuovo GJ, et al. Am J Surg Pathol. 1993, 17: 683-90; Komminoth P, et al. Pathol Res Pract. 1994, 190: 1017-25), and oligonucleotide microarray (e.g., by hybridization of polynucleotide sequences derived from a sample to oligonucleotides attached to a solid surface [e.g., a glass wafer) with addressable location, such as Affymetrix microarray (Affymetrix®, Santa Clara, CA)]. Non-limiting examples of methods of detecting the level and/or activity of specific protein molecules in a cell sample include Enzyme linked immunosorbent assay (ELISA), Western blot analysis, radio-immunoassay (RIA), Fluorescence activated cell sorting (FACS), immunohistochemical analysis, in situ activity assay (using e.g., a chromogenic substrate applied on the cells containing an active enzyme), in vitro activity assays (in which the activity of a particular enzyme is measured in a protein mixture extracted from the cells), quantitative two-dimensional (2-D) electrophoresis, dot blot analysis, protein array and the like.

As used herein the phrase "reference expression data" refers to the expression level of the gene in a prostate cancer sample with known sensitivity or resistant to radiation therapy, i.e., a radiation sensitive or a radiation resistance prostate cancer sample. Such as an expression level can be known from the literature, from the database, or from biological samples comprising RNA or protein molecules obtained from a reference cell. As used herein the phrase "reference cell" refers to any cell of a prostate cancer with known sensitivity to radiation therapy, i.e., a radiation sensitive or a radiation resistance cell. Such a reference cell can be obtained from a blood sample of a subject diagnosed with prostate cancer, from a biopsy of prostate cancer, from a cell line or xenograft derived therefrom. According to some embodiments of the invention, the reference expression data is obtained from at least one resistant prostate cancer sample (e.g., from one resistant prostate cancer sample), e.g., from at least 2, from at least 3, from at least 4, from at least 5, from at least 6, from at least 7, from at least 8, from at least 9, from at least 10, from at least 20, from at least 30, from at least 40, from at least 50, from at least 100 or more resistant prostate cancer samples.

According to some embodiments of the invention, the reference expression data is obtained from at least one sensitive prostate cancer sample (e.g., from one sensitive prostate cancer sample), e.g., from at least 2, from at least 3, from at least 4, from at least 5, from at least 6, from at least 7, from at least 8, from at least 9, from at least 10, from at least 20, from at least 30, from at least 40, from at least 50, from at least 100 or more one sensitive prostate cancer samples. It should be noted that when more than one prostate cancer samples (i.e., resistant or sensitive prostate cancer samples) is used, the reference expression data may comprise an average of the expression level of several or all samples, and those of skills in the art are capable of averaging expression levels from 2 or more samples, using e.g., normalized expression values.

According to some embodiments of the invention, the reference expression data (or the reference cell) is obtained from a radiation sensitive prostate cancer xenograft or a radiation sensitive prostate cancer cell line.

Non-limiting examples of radiation sensitive prostate cancer xenograft include WISH-PC23 and CWR22. Non-limiting examples of radiation sensitive prostate cancer cell line include LAPC4, LnCAP10995 (ATCC No. CRL- 10995), LnCAP1740 and 22RV-1 (ATCC No. CRL-2505). Such xenografts and cell lines can be obtained from the American Type Culture Collection (Manassas, VA) or can be established in vitro from prostatic carcinoma essentially as described in the Examples section which follows.

Since as is shown in Tables 2 and 3 and is described in Example 2 of the Examples section which follows, 87 polynucleotide sequences displayed elevated expression (gene transcription) in the radioresistant xenografts relative to the radiosensitive xenografts, in order to predict the sensitivity of the prostate cancer to radiation therapy, the level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-97 is determined and compared to the level of expression of the same polynucleotide sequences in a reference sample derived from a radiation sensitive prostate cancer (e.g., WISH-PC23, CWR22) or to an average level of expression of two or more radiation sensitive prostate cancer reference samples, wherein an upregulation (increase) in the expression level of the at least one polynucleotide sequence above a predetermined threshold relative to the reference sample is indicative of a radiation resistant prostate cancer.

Additionally or alternatively, since as is shown in Tables 4 and 5 and is described in Example 2 of the Examples section which follows, the level of expression of 71 polynucleotide sequences was downregulated in the radioresistant xenografts relative to the radiosensitive xenografts, in order to predict the sensitivity of the prostate cancer to radiation therapy, the level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:98-168 is determined and compared to the level of expression of the same polynucleotide sequences in a reference sample derived from a radiation sensitive prostate cancer (e.g., WISH-PC23, CWR22) or to an average level of expression of two or more radiation sensitive prostate cancer reference samples, wherein downregulation (decrease) in the expression level of the at least one polynucleotide sequence above a predetermined threshold relative to the reference sample is indicative of a radiation resistant prostate cancer.

According to some embodiment of the present invention, the reference expression data (or the reference cell) is obtained from a radiation resistant prostate cancer xenograft or a radiation resistant prostate cancer cell line.

Non-limiting examples of radiation resistant prostate cancer xenograft include WISH-PC14 and LAPC9. Non-limiting examples of radiation resistant prostate cancer cell line include PC-3 (ATCC No. CRL- 1435), DU- 145 (ATCC No. HTB-81) and CL- 1. Such xenografts and cell lines can be obtained from the American Type Culture Collection (Manassas, VA) or can be established in vitro from prostatic carcinoma essentially as described in the Examples section which follows.

Since as is shown in Tables 2 and 3 and is described in Example 2 of the Examples section which follows, the expression level of 87 polynucleotide sequences was downregulated in the radiosensitive xenografts relative to the radioresistant xenografts, in order to predict the sensitivity of the prostate cancer to radiation therapy, the level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-97 is determined and compared to the level of expression of the same polynucleotide sequences in a reference sample derived from a radiation resistant prostate cancer (e.g., WISH-PC14 and LAPC9) or to an average level of expression of two or more radiation resistant prostate cancer reference samples, wherein downregulation (decrease) in the expression level of the at least one polynucleotide sequence above a predetermined threshold relative to the reference sample is indicative of a radiation sensitive prostate cancer.

Additionally or alternatively, since as is shown in Tables 4 and 5 and is described in Example 2 of the Examples section which follows, the level of expression of 71 polynucleotide sequences was upregulated (increased) in the radiosensitive xenografts relative to the radioresistant xenografts, in order to predict the sensitivity of the prostate cancer to radiation therapy, the level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:98-168 is determined and compared to the level of expression of the same polynucleotide sequences in a reference sample derived from a radiation resistant prostate cancer (e.g., WISH-PC14 and LAPC9) or to an average level of expression of two or more radiation resistant prostate cancer reference samples, wherein upregulation (increase) in the expression level of the at least one polynucleotide sequence above a predetermined threshold relative to the reference sample is indicative of a radiation sensitive prostate cancer. As used herein the phrase "an alteration above a predetermined threshold" refers to a fold increase or decrease (i.e., degree of upregulation or downregulation, respectively) which is higher than a predetermined threshold such as at least twice, at least three times, at least four time, at least five times, at least six times, at least seven times, at least eight times, at least nine times, at least 20 times, at least 50 times, at least 100 times, at least 200 times, at least 500 times, at least 1000 times, at least 2000 times, at least 3000 times relative to the reference sample.

For example, as is shown in Tables 2 and 3, while the level of expression of the polynucleotide sequences set forth by SEQ ID NOs: 14, 15, 17, 24, 26, 29, 35, 45, 49, 60, 64, 65, 80, 82, 83 and 96, is at least 10 times higher in radiation resistant prostate cancer cells as compared to radiation sensitive prostate cancer cells, the level of expression of the polynucleotide sequences set forth by SEQ ID NOs:22, 28, 36, 42, 84 or the polynucleotides set forth by SEQ ID NOs:21 and 44 is at least 50 or 150 times, respectively, higher in radiation resistant prostate cancer cells as compared to radiation sensitive prostate cancer cells. In addition, as shown in Table 6, the level of expression of the polynucleotide sequences set forth by SEQ ID NOs: 11, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173 is higher in radiation resistant prostate cancer cells as compared to radiation sensitive prostate cancer cells.

In addition, as shown in Table 7, the level of expression of the polynucleotide sequences set forth by SEQ ID NOs:91, 198, 83, 199, 200, 201 or 202 is higher in radiation resistant prostate cancer cells as compared to radiation sensitive prostate cancer cells. In addition, as is further shown in Tables 4 and 5, while the level of expression of the polynucleotide sequences set forth by SEQ ID NOs:99, 104, 112, 113, 114, 118, 122, 125, 129, 130, 132, 135, 136, 138, 146, 152, 153, 156, 158, 159, 164, 165 and 166, is at least 10 times higher in radiation sensitive prostate cancer cells as compared to radiation resistant prostate cancer cells, the level of expression of the polynucleotide sequences set forth by SEQ ID NOs: 107, 108, 109, 117, 139, 143, 147, 157, 162 and 167, the polynucleotides set forth by SEQ ID NOs: 101, 105, 111, 140 and 145, or the polynucleotides set forth by SEQ ID NOs: 141, 142 and 144 is at least 50, 150 or 1000 times, respectively, higher in radiation sensitive prostate cancer cells as compared to radiation resistant prostate cancer cells.

In addition, as shown in Table 6, the level of expression of the polynucleotide sequences set forth by SEQ ID NOs: 101, 114, 119, 174-197 is higher in radiation sensitive prostate cancer cells as compared to radiation resistant prostate cancer cells.

In addition, as shown in Table 7, the level of expression of the polynucleotide sequences set forth by SEQ ID NOs: 101, 181, 114, 111 or 203 is higher in radiation sensitive prostate cancer cells as compared to radiation resistant prostate cancer cells.

According to some embodiments of the invention, a decrease above a predetermined threshold in the level of expression of the at least one gene selected from the group consisting of IMP3, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, CSAG2, ZNF718, TP53, PTEN, DUSP6, TNFRSFlOD, and BTGl in the prostate cancer sample relative to the reference expression data of the at least one gene obtained from the at least one prostate cancer sensitive sample predicts the resistance of the prostate cancer sample to radiation therapy.

According to some embodiments of the invention, an increase above a predetermined threshold in the level of expression of the at least one gene selected from the group consisting of IMP3, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, CSAG2, ZNF718, TP53, PTEN, DUSP6, TNFRSFlOD, and BTGl in the prostate cancer sample relative to the reference expression data of the at least one gene obtained from the at least one prostate cancer resistant sample predicts the sensitivity of the prostate cancer sample to radiation therapy.

According to some embodiments of the invention, a decrease above a predetermined threshold in the level of expression of the at least one gene selected from the group consisting of H2AFJ, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, ANXA2P2, SMARCAl, HPCALl, FUNDCl, CASP4, LITAF, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl and AGTRl in the prostate cancer sample relative to the reference expression data of the at least one gene obtained from the at least one prostate cancer resistant sample predicts the sensitivity of the prostate cancer sample to radiation therapy.

According to some embodiments of the invention, an increase above a predetermined threshold in the level of expression of the at least one gene selected from the group consisting of H2AFJ, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, ANXA2P2, SMARCAl, HPCALl, FUNDCl, CASP4, LITAF, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl and AGTRl in the prostate cancer sample relative to the reference expression data of the at least one gene obtained from the at least one prostate cancer sensitive sample predicts the resistance of the prostate cancer sample to radiation therapy. Thus, the method of predicting the sensitivity or resistance of prostate cancer to radiation therapy according to the present invention enables the classification of prostate cancer cells to radiation resistant or radiation sensitive cells. It will be appreciated that some prostate cancer cells may have a semi-resistant or a semi- sensitive phenotype with respect to radiation therapy. Accordingly, such prostate cancer cells may share an expression profile with radiation resistant and radiation sensitive prostate cancer cells. A non-limiting example of a prostate cancer cell sample with a semi-resistant radiation therapy phenotype is the LuCaP35 prostate cancer xenograft described in the Examples section which follows.

Determination of the radiosensitivity or radioresistance of a prostate cancer cell sample can be used to select the treatment regimen of a subject being diagnosed with prostate cancer.

According to an aspect of some embodiments of the invention there is provided a method of selecting a treatment regimen of a subject diagnosed with prostate cancer. The method is effected by (a) predicting the sensitivity or the resistance of the prostate cancer of the subject to radiation therapy according to the method of the invention and (b) selecting the treatment regimen based on the sensitivity or resistance of the prostate cancer to radiation therapy.

According to some embodiments of the invention, a presence of a radiation sensitive prostate cancer is indicative of selecting radiation therapy as the treatment regimen of the subject diagnosed with prostate cancer. According to some embodiments of the invention, the method of selecting a treatment regimen of a subject diagnosed with prostate cancer is effected by determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-218, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy, whereas a presence of a radiation sensitive prostate cancer is indicative of selecting radiation therapy as the treatment regimen of the subject diagnosed with prostate cancer. According to some embodiments of the invention, the method of selecting a treatment regimen of a subject diagnosed with prostate cancer is effected by determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy, whereas a presence of a radiation sensitive prostate cancer is indicative of selecting radiation therapy as the treatment regimen of the subject diagnosed with prostate cancer.

According to some embodiments of the invention, the method of selecting a treatment regimen of a subject diagnosed with prostate cancer is effected by determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:204-218, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy, whereas a presence of a radiation sensitive prostate cancer is indicative of selecting radiation therapy as the treatment regimen of the subject diagnosed with prostate cancer.

According to some embodiments of the invention, the method of selecting a treatment regimen of a subject diagnosed with prostate cancer is effected by determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy, whereas a presence of a radiation sensitive prostate cancer is indicative of selecting radiation therapy as the treatment regimen of the subject diagnosed with prostate cancer. As used herein the term "subject" refers to a male mammal, preferably human being, who is diagnosed with prostate cancer. It will be appreciated that the diagnosis of prostate cancer (e.g., determining presence of cancer, classifying disease, determining the severity of the disease) can take place at early stages of the disease (e.g., when the cancer is confined to the prostate tissue) as well as at advanced stages of the disease, when the cancer has spread beyond the prostate tissue.

Thus, the presence of radiation sensitive prostate cancer cells of a subject is indicative of selecting radiotherapy as a preferred treatment regimen. On the other hand, the presence of radiation resistant prostate cancer cells of a subject suggests that the tumor is refractory to IR and therefore the subject should preferably be subjected to alternative treatment (e.g., radical prostectomy, with or without radiation therapy, with or without hormonal therapy such as androgen suppression (ablation) which is achieved, for example, with a gonadotropin-releasing-hormone agonist with or without antiandrogen therapy and the like).

It will be appreciated that the classification of prostate cancer cells as being sensitive or resistant to radiation therapy may also affect the selection of optimal dosage for treating the prostate cancer in the subject. According to an aspect of some embodiments of the invention there is provided a method of determining an optimal dosage of radiation therapy for treatment of prostate cancer. The method is effected by (a) predicting the sensitivity or the resistance of the prostate cancer of the subject to radiation therapy according to the method of the invention; and (b) selecting the optimal dosage of radiation therapy for the treatment of prostate cancer, thereby determining the optimal dosage of the radiation therapy for the treatment of the prostate cancer.

According to some embodiments of the invention, the method of determining an optimal dosage of radiation therapy for treatment of prostate cancer is effected by (a) determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-218 (e.g., a polynucleotide selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203; a polynucleotide selected from the group consisting of SEQ ID NOs:204-218; or a polynucleotide selected from the group consisting of SEQ ID NOs:l l, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197), wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to radiation therapy, and (b) selecting the optimal dosage of radiation therapy for the treatment of prostate cancer. According to some embodiments of the invention, a presence of radiation sensitive prostate cancer is indicative of using a dosage of the radiation therapy selected from the range of about 45-80 Gy, e.g., about 65-80 Gy, e.g., about between 65-78 Gy;

According to some embodiments of the invention, a presence of radiation sensitive prostate cancer is indicative for using a combination of external beam radiation and brachy therapy. For example, an external beam radiation therapy can involve the administration of a dosage of about 45 Gy (e.g., in fractions of about 2 Gy, for 5 times/week, 4-5 weeks) and brachy therapy can involve an internal radiation of more than 100 Gy (see Pisansky TM., 2006). According to some embodiments of the invention, a presence of radiation resistant prostate cancer is indicative of using a dosage of radiation therapy selected from the range of about 75-80 Gy combined with radiotherapy to the pelvic lymph nodes and/or neoadjuvant or adjuvant androgen suppression therapy (see Pisansky TM., 2006). According to some embodiments of the invention, a presence of radiation resistant prostate cancer is indicative of treating the subject with radical prostectomy, with or without radiation therapy.

It will be appreciated that the combination of an efficient radiation therapy (which is selected according to the method described hereinabove) with a radical prostatectomy may increase the prognosis of a subject diagnosed with prostate cancer. On the other hand, the presence of prostate cancer cells which are resistant to radiation therapy may indicative poor prognosis of the subject being diagnosed with prostate cancer.

Thus, according to yet another aspect of the present invention there is provided a method of predicting a prognosis of a subject diagnosed with prostate cancer following radiation therapy. The method is effected by predicting the sensitivity or the resistance of the prostate cancer of the subject to radiation therapy according to the method of the invention; wherein a presence of radiation resistance prostate cancer is indicative of poor prognosis of the subject; thereby determining the prognosis of the subject diagnosed with prostate cancer following radiation therapy.

According to some embodiments of the invention the method of predicting a prognosis of a subject diagnosed with prostate cancer following radiation therapy is effected by determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11- 218, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to the radiation therapy; wherein a presence of radiation resistance prostate cancer is indicative of poor prognosis of the subject; thereby determining the prognosis of the subject diagnosed with prostate cancer following radiation therapy. According to an embodiment of the invention the method of predicting a prognosis of a subject diagnosed with prostate cancer following radiation therapy is effected by determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to the radiation therapy; wherein a presence of radiation resistance prostate cancer is indicative of poor prognosis of the subject; thereby determining the prognosis of the subject diagnosed with prostate cancer following radiation therapy.

According to an embodiment of the invention the method of predicting a prognosis of a subject diagnosed with prostate cancer following radiation therapy is effected by determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs:204- 218, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to the radiation therapy; wherein a presence of radiation resistance prostate cancer is indicative of poor prognosis of the subject; thereby determining the prognosis of the subject diagnosed with prostate cancer following radiation therapy. According to an embodiment of the invention the method of predicting a prognosis of a subject diagnosed with prostate cancer following radiation therapy is effected by determining in a cell of the prostate cancer a level of expression of at least one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197, wherein an alteration above a predetermined threshold in the level of expression of the at least one polynucleotide sequence in the cell relative to a level of expression of the at least one polynucleotide sequence in a reference cell is indicative of the sensitivity or the resistance of the prostate cancer to the radiation therapy; wherein a presence of radiation resistance prostate cancer is indicative of poor prognosis of the subject; thereby determining the prognosis of the subject diagnosed with prostate cancer following radiation therapy.

It will be appreciated that the reagents utilized by any of the methods of the present invention which are described hereinabove can form a part of a diagnostic kit/article of manufacture.

The kit of the some embodiments of the invention is for predicting a sensitivity or a resistance of prostate cancer to radiation therapy. The kit comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, S100A16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl. The kit of the some embodiments of the invention is for selecting a treatment regimen of a subject diagnosed with prostate cancer. The kit comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, S100A16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl.

According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl, and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow.

According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, PSMB8, RHOQ, ACAA2, TUBA3 and S100A16 and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow.

According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of METTL7A, MAGEA2, and KRTCAP3 and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow.

According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, PSMB 8, RHOQ, ACAA2, TUB A3, S100A16 and METTL7A, MAGEA2, and KRTCAP3 and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow.

According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, MAGEA2, ZNF718, CASP8, LITAF, CASP4, CD24, GULPl, UCP2, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, RAB26, and BTGl and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow.

According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, S100A16, MALL, SMARCAl, HPCALl and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow.

According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, MAGEA2, ZNF718, CASP8, CASP4, CD24, UCP2, IFITM3, GUCY1A3 and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow. According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of TP53, DUSP6, PTEN, TNFRSFlOD and IMP-3 and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow.

According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, PSMB8, TFCP2, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208 and KRTCAP3 and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow.

According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAM118A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, and BTGl and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow.

According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, and ZNF718 and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow.

According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of CASP8, LITAF, CASP4, CD24, GULPl, UCP2, H2AFJ, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, RAB26, and BTGl and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow. According to some embodiments of the invention, the kit consisting essentially of at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of FTHl, PFN2, PSMB8, TFCP2, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, and KRTCAP3 and additional reagent(s) as described below for facilitating detection of the expression level of the at least one gene, and/or packaging materials and instructions for use as described hereinbelow. According to some embodiments of the invention, the kit comprises at least 2 and no more than 500 isolated nucleic acid sequences, preferably, at least 4 and no more than 500 isolated nucleic acid sequences, preferably, at least 4 and no more than 400 isolated nucleic acid sequences, preferably, at least 10 and no more than 300 isolated nucleic acid sequences, preferably, at least 10 and no more than 198 isolated nucleic acid sequences, preferably, at least 20 and no more than 157 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-218.

According to some embodiments of the invention, the kit comprises at least 2 and no more than 500 isolated nucleic acid sequences, preferably, at least 4 and no more than 500 isolated nucleic acid sequences, preferably, at least 4 and no more than 400 isolated nucleic acid sequences, preferably, at least 10 and no more than 300 isolated nucleic acid sequences, preferably, at least 10 and no more than 198 isolated nucleic acid sequences, preferably, at least 20 and no more than 157 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203.

According to some embodiments of the invention, the kit comprises at least 2 and no more than 500 isolated nucleic acid sequences, preferably, at least 4 and no more than 500 isolated nucleic acid sequences, preferably, at least 4 and no more than 400 isolated nucleic acid sequences, preferably, at least 10 and no more than 300 isolated nucleic acid sequences, preferably, at least 10 and no more than 198 isolated nucleic acid sequences, preferably, at least 20 and no more than 157 isolated nucleic acid sequences, wherein each of the at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:204-218.

The isolated nucleic acid sequences included in the kit of the present invention can be single- stranded or double- stranded, naturally occurring or synthetic nucleic acid sequences such as oligonucleotides, RNA molecules, genomic DNA molecules, cDNA molecules and/or cRNA molecules. The isolated nucleic acid sequences of the kit can be composed of naturally occurring bases, sugars, and covalent internucleoside linkages (e.g., backbone), as well as non-naturally occurring portions, which function similarly to respective naturally occurring portions.

Synthesis of the isolated nucleic acid sequences of the kit can be performed using enzymatic synthesis or solid-phase synthesis. Equipment and reagents for executing solid-phase synthesis are commercially available from, for example, Applied Biosystems. Any other means for such synthesis may also be employed; the actual synthesis of the oligonucleotides is well within the capabilities of one skilled in the art and can be accomplished via established methodologies as detailed in, for example: Sambrook, J. and Russell, D. W. (2001), "Molecular Cloning: A Laboratory Manual"; Ausubel, R. M. et al, eds. (1994, 1989), "Current Protocols in Molecular Biology," Volumes I-III, John Wiley & Sons, Baltimore, Maryland; Perbal, B. (1988), "A Practical Guide to Molecular Cloning," John Wiley & Sons, New York; and Gait, M. J., ed. (1984), "Oligonucleotide Synthesis"; utilizing solid-phase chemistry, e.g. cyanoethyl phosphoramidite followed by deprotection, desalting, and purification by, for example, an automated trityl-on method or HPLC.

According to some embodiments of the invention, each of the isolated nucleic acid sequences included in the kit of present invention comprises at least 10 and no more than 50 nucleic acids, more preferably, at least 15 and no more than 45, more preferably, between 15-40, more preferably, between 20-35, more preferably, between 20-30, even more preferably, between 20-25 nucleic acids.

The kit preferably includes at least one reagent as described hereinabove which is suitable for facilitating detection of the expression level of the at least one gene of the invention (as described above), e.g., the polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11-218; at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203; at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:204-218; or at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs: 11, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197. Examples include reagents suitable for hybridization or annealing of a specific polynucleotide of the kit to a specific target polynucleotide sequence (e.g., RNA transcript derived from the prostate cancer cell sample or a cDNA derived therefrom) such as formamide, sodium chloride, and sodium citrate), reagents which can be used to labeled polynucleotides (e.g., radiolabeled nucleotides, biotinylated nucleotides, digoxigenin-conjugated nucleotides, fluorescent-conjugated nucleotides) as well as reagents suitable for detecting the labeled polynucleotides (e.g., antibodies conjugated to fluorescent dyes, antibodies conjugated to enzymes, radiolabeled antibodies and the like).

Additionally or alternatively, the kit of the present invention comprises at least one reagent suitable for detecting the expression level and/or activity of at least one polypeptide encoded by at least one polynucleotide selected from the group consisting of SEQ ID NOs: 11-218; at least one polypeptide encoded by at least one polynucleotide selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203; at least one polypeptide encoded by at least one polynucleotide selected from the group consisting of SEQ ID NOs:204-218; or at least one polypeptide encoded by at least one polynucleotide selected from the group consisting of SEQ ID NOs:l l, 30, 38, 44, 59, 62, 65, 82, 83, 91, 169, 170, 171, 172, 173, 101, 114, 119, 174-197. For example, the kit may comprise at least one reagent suitable for detecting the expression level and/or activity of at least one polypeptide selected from the group consisting of: S100A16 (GenBank Accession No. NP_525127.1; SEQ ID NO:219), MALL (GenBank Accession No. NP_005425.1; SEQ ID NO:220), SMARCAl (GenBank Accession No. NP_003060.2; SEQ ID NO:221), HPCALl (GenBank Accession Nos. NP_002140.2, and NP_602293.1; SEQ ID NOs:222, and 223), FUNDCl (GenBank Accession No. NP_776155.1; SEQ ID NO:224), CSAG2 (GenBank Accession No. NP_004900.2; SEQ ID NO:225), PPAPDClB (GenBank Accession Nos. NPJ)01096029.1, NP_115872.2, and NP_001096030.1; SEQ ID NOs:226, 227, and 228), MAGEA2 (GenBank Accession Nos. NP_005352.1, NP_786884.1, and NP_786885.1; SEQ ID NO:229, 230, and 231), ZNF718 (GenBank Accession No. NPJ)01034216.1; SEQ ID NO:232). Such a reagent can be, for example, an antibody capable of specifically binding to at least one epitope of the polypeptide. Additionally or alternatively, the reagent included in the kit can be a specific substrate capable of binding to an active site of the polypeptide. In addition, the kit may also include reagents such as fluorescent conjugates, enzymes, secondary antibodies and the like which are suitable for detecting the binding of a specific antibody and/or a specific substrate to the polypeptide.

According to some embodiments of the invention, the kit includes a reference cell which comprises a cell sample of prostate cancer with a known sensitivity (sensitive or resistant prostate cancer sample) to radiation therapy as described hereinabove.

The kit of the present invention preferably includes packaging material packaging the at least one reagent and a notification in or on the packaging material. Such a notification identifies the kit for use in predicting the sensitivity or the resistance of prostate cancer to radiation therapy, selecting a treatment regimen of a subject diagnosed with prostate cancer, determining an optimal dosage of radiation therapy for treatment of prostate cancer and/or predicting a prognosis of a subject diagnosed with prostate cancer following radiation therapy. The kit may also include appropriate buffers and preservatives for improving the shelf life of the kit.

It will be appreciated that the isolated nucleic acid sequences included in the kit of the present invention can be bound to a solid support e.g., a glass wafer in a specific order, i.e., in the form of a microarray. Alternatively, isolated nucleic acid sequences can be synthesized directly on the solid support using well-known prior art approaches (Seo TS, et al, 2004, Proc. Natl. Acad. Sci. USA, 101: 5488-93.). In any case, the isolated nucleic acid sequences are attached to the support in a location specific manner such that each specific isolated nucleic acid sequence has a specific address on the support (i.e., an addressable location) which denotes the identity (i.e., the sequence) of that specific isolated nucleic acid sequence.

According to some embodiments of the present invention the microarray comprising no more than 500 oligonucleotides wherein each of the oligonucleotides is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, S100A16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUB A3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl.

According to some embodiments of the present invention the microarray comprises no more than 500 isolated nucleic acid sequences, wherein each of the isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:l l-218.

According to some embodiments of the present invention the microarray comprises no more than 500 isolated nucleic acid sequences, wherein each of the isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203.

According to some embodiments of the present invention the microarray comprises no more than 500 isolated nucleic acid sequences, wherein each of the isolated nucleic acid sequences is capable of specifically recognizing at least one specific polynucleotide sequence selected from the group consisting of SEQ ID NOs:204-218.

As used herein the term "about" refers to ± 10 %.

The terms "comprises", "comprising", "includes", "including", "having" and their conjugates mean "including but not limited to". The term "consisting of means "including and limited to".

The term "consisting essentially of" means that the composition, method or structure may include additional ingredients, steps and/or parts, but only if the additional ingredients, steps and/or parts do not materially alter the basic and novel characteristics of the claimed composition, method or structure.

As used herein, the singular form "a", "an" and "the" include plural references unless the context clearly dictates otherwise. For example, the term "a compound" or "at least one compound" may include a plurality of compounds, including mixtures thereof.

Throughout this application, various embodiments of this invention may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.

Whenever a numerical range is indicated herein, it is meant to include any cited numeral (fractional or integral) within the indicated range. The phrases "ranging/ranges between" a first indicate number and a second indicate number and "ranging/ranges from" a first indicate number "to" a second indicate number are used herein interchangeably and are meant to include the first and second indicated numbers and all the fractional and integral numerals therebetween.

As used herein the term "method" refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, pharmacological, biological, biochemical and medical arts.

As used herein, the term "treating" includes abrogating, substantially inhibiting, slowing or reversing the progression of a condition, substantially ameliorating clinical or aesthetical symptoms of a condition or substantially preventing the appearance of clinical or aesthetical symptoms of a condition. It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination or as suitable in any other described embodiment of the invention. Certain features described in the context of various embodiments are not to be considered essential features of those embodiments, unless the embodiment is inoperative without those elements.

Various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below find experimental support in the following examples.

EXAMPLES

Reference is now made to the following examples, which together with the above descriptions, illustrate the invention in a non-limiting fashion.

Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, "Molecular Cloning: A laboratory Manual" Sambrook et al, (1989); "Current Protocols in Molecular Biology" Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., "Current Protocols in Molecular Biology", John Wiley and Sons, Baltimore, Maryland (1989); Perbal, "A Practical Guide to Molecular Cloning", John Wiley & Sons, New York (1988); Watson et al., "Recombinant DNA", Scientific American Books, New York; Birren et al. (eds) "Genome Analysis: A Laboratory Manual Series", VoIs. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; "Cell Biology: A Laboratory Handbook", Volumes I-III Cellis, J. E., ed. (1994); "Current Protocols in Immunology" Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), "Basic and Clinical Immunology" (8th Edition), Appleton & Lange, Norwalk, CT (1994); Mishell and Shiigi (eds), "Selected Methods in Cellular Immunology", W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; "Oligonucleotide Synthesis" Gait, M. J., ed. (1984); "Nucleic Acid Hybridization" Hames, B. D., and Higgins S. J., eds. (1985); "Transcription and Translation" Hames, B. D., and Higgins S. J., Eds. (1984); "Animal Cell Culture" Freshney, R. L, ed. (1986); "Immobilized Cells and Enzymes" IRL Press, (1986); "A Practical Guide to Molecular Cloning" Perbal, B., (1984) and "Methods in Enzymology" Vol. 1-317, Academic Press; "PCR Protocols: A Guide To Methods And Applications", Academic Press, San Diego, CA (1990); Marshak et al., "Strategies for Protein Purification and Characterization - A Laboratory Course Manual" CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. All the information contained therein is incorporated herein by reference.

GENERAL MATERIALS AND EXPERIMENTAL METHODS Xenografts and cell lines - Prostate cancer cell lines LNCaP1740, LNCaP10995, PC-3, DU- 145, 22RvI, were purchased from American Type Culture Collection (Manassas, VA); LAPC4 was obtain from Charles L Sawyers (University of California, Los Angeles, California, USA); CL-I was obtain Belldegrun AS (University of California at Los Angeles, Los Angeles, California, USA). The establishment and characterization of WISH-PC 14, human adenocarcinoma xenograft, is described in detail elsewhere (Bar-Shira, A. et al., 2002). The WISH-PC23 adenocarcinoma xenograft was established from prostatic carcinoma harvested during palliative trans urethral resection of the prostate performed in a patient with local progression of adenocarcinoma of the prostate, Gleason score 6 (3+3). The patient was previously treated with external beam radiotherapy and total androgen blockade. At the time of tumor progression, there were symptoms of bladder outlet, urethral obstruction, and a PSA rise to 18.; LuCaP35 xenograft was developed and provided by R.L. Vessella (University of Washington School of Medicine, Seattle, Washington, USA); LAPC9 was developed and provided by Charles L Sawyers (University of California, Los Angeles, USA); CWR22 was developed by Case Western Reserve University and provided by the University of North Carolina-Chapel Hill. All xenografts were maintained by serial transfers in 4-10-week-old SCID mice (c.b-17/Icr Beige). Mice were grown in the pathogen-free facilities of the Weizmann Institute of Science. All of the surgical procedures were performed under ketamin + xylazine anesthesia (127.5 and 4.5 mg/kg respectively) according to the IACUC regulations.

Cell culture - Cells were grown in RPMI 1640 media supplemented with 2 mM glutamine, 100 μg/mL penicillin, 100 μg/mL streptomycin, and 10 % FCS (CL-I supplemented with charcoal stripped FCS). Special supplement to cell lines used in these studies were as follows: LNCaP1740, LNCaP10995 and LAPC4 were grown with 10^"9 M testosterone and insulin (Sigma). DU-145 were grown with insulin (Sigma). Cells cultured in RPMI-based media were incubated in a humidified 37 ⁰C incubator with a 5 % CO₂ atmosphere.

Single dose irradiation procedures

A. Xenograft irradiation - Single-cell suspensions of xenograft fragments were prepared by dissociating and mincing the xenografts through a stainless still mesh followed by separation over Ficoll-Paque 400. The cell suspensions or the tumor tissues were irradiated by a Cobalt 60 source, emitting 65 cGy/min (Gammabeam-150, MDS Nordion). After irradiation, cells or tissue in HBSS medium were mixed with Matrigel^R™ (Becton Dickinson, Bedford, MA) and implanted (5 x 10⁶ cells or small pieces of tumor (80-100 mg/mouse) subcutaneously (s.c.) in male SCID 6-10-week-old mice. Tumor growth was followed for up to a year after inoculation.

B. Cell irradiation - Prostate cancer cell cultures were plated in 6-well tissue culture plate (Falcon) at 60 % to 70 % confluence irradiations were done in the dish using Cobalt 60 source, operating at a rate of 65 cGy/min (Gammabeam-150, MDS Nordion). The cells were irradiated at 5, 10, 40, 80 or 160 Gy and returned to an incubator after the irradiations and maintained at 37 ⁰C. Cells were fed every 3 days with complete medium until colonies were appeared, then cells were transferred from 6- well tissue culture plate to 25 mm flask and 75 mm flask to follow after capability of survival cells to prorogate. Fractionated radiation procedures - Male SCID were inoculated with tumor cells 5 x 10⁶ cells in 0.1 ml volume of Matrigel/medium into the right hind thigh of the animal. Prior to inoculation, local anesthesia with xylocaine 10 % spray (Astra Sweden) was applied to the right hind leg of the animal. When tumor volumes reached approximately 150-200 mm³, anesthetized mice (under ketamin + xylazine 127.5 and 4.5 mg/kg, respectively) were shielded allowing only the right hind leg to be exposed. Mice (five /group) received fractionated radiation using the Caesium 137 source, operating at a dose rate of 100 centiGy/min (Gammacell 40 Exactor, MDS Nordion). Treatment was given daily for five consecutive days per week, followed by a two day break, for the total number of fraction as indicated. Tumor growth was followed for up to 1 year after irradiation.

Monitoring tumor growth - Tumor size was determined at weekly intervals by caliper measurements of length, width, and depth, and the tumor volume (mm³) was approximated using the formula: length x width x depth x 0.5236 [Gleave ME, Hsieh JT, Wu HC, von Eschenbach AC, Chung LW. Serum prostate specific antigen levels in mice bearing human prostate LNCaP tumors are determined by tumor volume and endocrine and growth factors. Cancer Res 1992;52(6): 1598- 1605]. Single dose irradiation groups were monitored for 10 months and in the fractionated radiation groups, and recording of the results of a group was stopped when < 50 % of the mice in a certain group scored dead. Mice were removed from the experiments and euthanised when the tumor volume exceeded 1200 mm³.

Samples were collected from 12 xenografts; either un-irradiated or from xenografts 2-6 months after their irradiation (depend on the tumor establishment after IR) using the highest tolerated dose: CWR22 (un-irradiated and survivors of 20Gy), WISH PC-23 (un-irradiated and survivors of 40Gy), LuCAP35 (un-irradiated and survivors of 20Gy and 60Gy), LAPC9 (un-irradiated and survivors of 80Gy and 160Gy) and WISH PC- 14 (un-irradiated and survivors of 120Gy). Samples of irradiated xenografts that developed in mice were kept frozen in liquid nitrogen until their processing for gene array.

Microarray experiments - Total RNA was extracted from frozen (liquid N2) tissues of PC xenografts and cell lines using TRI Reagent (Sigma) and cleaned by using RNEasy Mini kit (Qiagen, Hilden , Germany) according to the manufacturer's instruction. Gene expression was measured using Human Genome U133 Plus 2.0 GeneChips (Affymetrix, Santa Clara, CA). The microarray consists of sets of DNA probes, each chosen carefully to record expression of a specific gene. The set of probes relating to a specific gene is referred to as a probeset, where, each probe that is part of a probeset is a sequence of 20-25 bases taken from the transcribed region of the gene. The expression value of a given probeset is calculated as the average expression level of all the probes in the probeset. Note that some genes have more than one probeset. GeneChips were prepared, hybridized, and scanned according to the manufacturer's instruction. Briefly, 10 μg total RNA was reverse transcribed with a poly-(T) primer containing a T7 promoter, and the cDNA made double-stranded. An in vitro transcription was done to produce biotinylated cRNA, which was then hybridized to the GeneChips. The chips were washed and stained with streptavidin phycoerythrin using an Affymetrix FS-450 fluidics station, and data was collected with Affymetrix GeneChip Scanner 3000.

Clustering analysis - Clustering analysis of the gene array data was performed as follows. First, probesets that were present (P ≤ 0.05) at least in one sample (out of 12) were selected. 31690 (out of 54,613) probeset passed this filter. Next, the 3 filtering process was performed as following:

1. Probesets that their expression levels in the irradiated samples, increased above 3 fold (over their non-irradiated pairs); 967 probesets passed this filter.

2. The 2000 most variable probe-sets measured based on the 12 samples.

3. The 1650 probesets that best distinguish the sensitive from the resistant xenografts (RankSum test P < 0.05, FDR 5 %). For this process the LuCAP35 line

(which demonstrated intermediate radioresistance phenotype) was ascribed with the resistant xenografts (LAPC9, WISH-PC14); while ascribing LuCAP35 to the sensitive xenografts (CWR22 and WISH PC-23) RankSum test yielded 593 significant genes (P < 0.05, FDR 5 %). The clustering analysis was based on the 3,730 probe sets that fulfilled at least one of the three aforementioned filtering criterions.

The gene clustering operation was performed using the Super-Paramagnetic Clustering algorithm (Blatt M, Wiseman S, Domany E. Superparamagnetic clustering of data; 1996. 3251-3254). For the sample clustering operations the SPIN algorithm (Tsafrir D, Tsafrir I, Ein-Dor L, Zuk O, Notterman DA, Domany E. Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices; 2005. 2301-2308) was used. Statistical Analysis - Statistical analysis was performed using JMP statistical software (SAS Institute, Inc., Cary, NC). Tumor volume data were analyzed by the Fit model, to test the effect of different doses of irradiation during the experimental period.

Real time PCR - RNA was reverse transcribed to cDNA from 1 μg of total RNA by using the Reverse Transcription System kit (Promega Crop.), which was then subjected to Q-RT-PCR performed essentially according to the manufacturer's instructions. Specific primer pairs were designed using LightCycler probe design software (Roche) and were used to amplify specific genes in the presence of 3 mM MgCl₂. PCR was performed in duplicate/triplicate in a total volume of 10 μl of LightCycler HotStart DNA SYBR Green I mix (Roche) containing primer and 2.5 μl of cDNA. PCR amplification was preceded by incubation of the mixture for 10 minutes at 95 ⁰C, and the amplification step consisted of 35-45 cycles of denaturation, annealing, and extension. Denaturation was performed for 10 seconds at 95 ⁰C, annealing was performed at 60 ⁰C for 10 seconds, and the extension was performed at 72 ⁰C for 14 seconds, with fluorescence detection at 72 ⁰C after each cycle. After the final cycle, melting point analyses of all samples were performed within the range of 70-99 ⁰C with continuous fluorescence detection. A standard curve was generated from one sample in each run. Expression levels of TPTl [5¹-GCACATCCTTGCTAATTTCA-3¹ (SEQ ID NO:1) and 3'-CAAGCAGAAGCCAGTTAT-S' (SEQ ID NO:2); 207 bp RT-PCR product] were used for sample normalization. Results for each gene are presented as the relative expression of LAPC9 xenograft levels. The primers used in these studies were as follows: human RAB26 [5¹-AGTGGACAGACTTTGCC-3¹ (SEQ ID NO:3) and 3'- GCACG ATGTGATTAGCCAG-S¹ (SEQ ID NO:4); 193 bp RT-PCR product], human H2A variant 2 [5¹-TGTTGGAGTACCTTACGG-3¹ (SEQ ID NO:5) and 3'- GCGTCAGGGTCATTTG-S¹ (SEQ ID NO:6); 236 bp RT-PCR product], human PTEN [5¹-AGTGGCTAAAGAGCTTTG-3¹ (SEQ ID NO:7) and 3'-

ATGGTATATGGTCCAGAGT-S¹ (SEQ ID NO:8); 196 bp RT-PCR product], and human UCP2 [5¹-GATACCAAAGCACCGTC-3¹ (SEQ ID NO:9) and 3'- GAAGTGAAGAAGTGGCAAGG-S¹ (SEQ ID NO: 10), 196 bp RT-PCR product]. EXAMPLE 1

RADIOSENSITIVITY OF HUMAN PROSTATIC ADENOCARCINOMA XENOGRAFTS AND CELLS LINES TO IONIZING RADIATION

To identify a transcription profile related to radiosensitivity/resistance phenotype of prostate cancer (PC), the present inventors have determined the effect of different doses of IR in-vitro (single dose) and in-vivo (both single and fractionated doses) of human PC xenografts and classified the xenografts and cell lines to radiosensitive and radioresistant groups, as follows.

Experimental Results

Variability of xenografts and cell lines to irradiation dose - The growth of subcutaneously injected human prostate cancer (PC) xenograft tumor cells following a range of a single doses of IR in-vitro was evaluated in SCID mice. The range chosen for irradiation, between 4 to 160 Gy, relied on the maximal level of radiation employed in clinical practice (using brachy therapy), which is higher than 140 Gy [Langley SE, Laing R. Prostate brachytherapy has come of age: a review of the technique and results. BJU Int 2002;89(3):241-249]. Table 1, hereinbelow, summarizes the highest dose of IR beyond which no tumor grew. Thus, as shown in Table 1, hereinbelow, human prostate cancer xenografts established in the present inventors' laboratory (WISH PC- 14, WISH PC-2, WISH PC-23) as well other adenocarcinoma xenografts from other laboratories (CWR22, LuCAP35 and LAPC9), and cell lines (CL-I, LNCaP10995, LNCaP1740, LAPC4, PC-3, 22RV-1 and DU- 145) show variability in their resistance to radiation in the range of 4-160 Gy.

Table 1

Maximal irradiation dose at which prostate adenocarcinoma grew following a single dose irradiation

Table 1: Maximal irradiation dose at which prostate adenocarcinoma grew following a single dose irradiation or a fractionated dose. Tissue or cells of the prostate cancer xenografts (80-100 mg/5xlθ⁶ cells/) were put in dishes and irradiated at various doses 5, 10, 40, 80 or 160 Gy before their subcutaneous implantation into SCID mice. The cells or xenograft beads were then injected/implanted s.c. to SCID mice. For fractionated irradiation in vivo, cells derived from xenografts or small pieces were implanted into the right hind thigh of SCID mice. After reaching a size of around 200 mm³, mice were shielded except for their tumor bearing leg and were sub-lethally irradiated by daily doses (five sessions per week) for the total dose as indicated. The values shown represent maximal irradiation dose in which PC xenografts or in-vivo cells grew. Samples were taken from all xenografts before and after irradiation.

Thus, while the LAPC4, LnCAP10995, LnCAP1740 and 22RV-1 prostate cancer cell lines exhibited sensitivity to radiation therapy, the PC-3, DU- 145 and CL-I prostate cancer cell lines exhibited resistance to radiation therapy.

Identification of radiosensitive and radioresistant PC xenografts - Two phenotypes were observed in most PC xenografts tested (Figures IA-D) regardless if irradiated by a single dose (Figures IA-B) or fractionated doses (Figures IC-D): IR sensitive [exemplified by the CWR22 xenograft, (Figures IA, C), which grew in mice following a single ex-vivo dose of 20 Gy but did not develop into a tumor for a year following their irradiation with >20 Gy] and IR resistant [exemplified by the LAPC xenograft, (Figures IB and D), which formed tumors even following a dose of 160 Gy]. Importantly, in both of the phenotypes, no change in growth rate has been observed following irradiation as compared to prior to IR. With increased doses of irradiation, the lag time before tumor growth in vivo was prolonged and the number of mice that developed tumors decreased. The lag time increment, as well as the fraction of mice that developed tumors following IR, are a function of the number of cells that survived IR. The delay in tumor appearance reflects a decline in the viable cell number resulting from the IR.

The maximum single dose at which mice developed the IR sensitive xenograft

(CWR22) was 20 Gy (Figure IA). No tumor appeared following irradiation in the range of 40-160 Gy even a year after tumor cell inoculation (data not shown). In the IR resistant xenografts such as LAPC9 tumors grew even following to a dose of 160 Gy

(Figure IB).

To test whether a similar phenotypic distribution holds for fractionated irradiation, as is actually administered clinically, mice were treated according to a protocol clinically applied to prostate cancer patients, including a total of 65-78 Gy delivered in 1.8-2 Gy doses over a 7 to 8 week period. The human PC xenografts were injected into the hind limb of SCID mice and when tumor volume reached the volume of 150-200 mm³, mice were irradiated using the Caesium 137 source at the indicated doses. In view of the fact that fractionated radiation is more effective than a single dose, the total dose administered was close to the maximal dose obtained by single dose irradiation. For example, 80 % of CWR22, a xenograft that is sensitive to a single dose of radiation (20 Gy), relapsed after fractionated irradiation of total dose of 14 Gy (2 Gy x 7) but no relapses were observed with total doses of 20 Gy (2 Gy x 10) and 26 Gy (2 Gy x 13) (Figure 1C). Fractionated irradiation of LAPC9, the most radiation resistant xenograft, showed that following to total dose of 60 Gy (2.5 Gy x 24) tumors relapsed in four out of five mice, but no relapses were observed with a total dose of 80 Gy (2.5 Gy x 30) (Figure ID). These data support the phenotypic classification that was determined based on a single dose of irradiation and reiterates the advantage and benefit of fractionated radiation over a single dose radiotherapy, being more effective and causing less side effects to neighboring non-replicating healthy tissues.

Altogether, these results demonstrate the classification of the prostate cancer cell lines and xenografts of the present invention to radiosensitive or radioresistant for the subsequent gene expression profile analysis. EXAMPLE 2 RESISTANT I SENSITIVE SIGNATURE

To find out whether there is a genetic signature that can differentiate between irradiation sensitive and resistant PC cells and to determine which of the models outlined above is correct, RNA from non-irradiated and irradiated PC xenografts of both irradiation resistant and sensitive phenotypes was subjected to gene microarray (Affymetrix, U133P2) containing probes corresponding to 54,613 human transcripts and clustering analysis as described under General Materials and Experimental Methods hereinabove. Gene expression profiling of 12 experimental samples was performed, four of which were derived from radiation-sensitive xenografts: CWR22 (unirradiated and cells surviving 20 Gy) and WISH PC-23 (unirradiated cells, and those surviving 40 Gy), and five samples were processed from radiation-resistant xenografts: LAPC9 (unirradiated and cells surviving of 80 Gy and 160 Gy) and WISH PC- 14 (unirradiated and cells surviving of 120 Gy). Another xenograft sample was LuCAP35 (un-irradiated and surviving of 20 Gy and 60 Gy) which represented an intermediate level of IR sensitivity (Table 1, hereinabove).

Unsupervised analysis of the data was conducted to search for clusters shared by either IR resistant or sensitive PC xenografts. The 3,730 probesets that passed one of the four filtering processes were clustered (employing the Super-Paramagnetic Clustering algorithm (SPC) [Blatt M, Wiseman S, Domany E. Superparamagnetic clustering of data. Physical Review Letters 1996;76(18):3251-3254] based on the phenotypes of the xenograft samples. Additionally, principal component analysis (PCA) was performed on the samples, separately for each of the clusters and for the union of the four clusters, in order to evaluate the relationships between the transcription profiles of the tested samples. The 3,730 probe sets yielded six stable clusters (Figure 2b). Because the same gene expression profiles have been obtained for none and irradiated cells (see comparison below) the analysis used data from both samples. The samples were then clustered, one at a time, based on each stable gene cluster of the 6 clusters shown in Figure 2b. Four gene clusters (clusters 2, 3, 5 and 6; Figures 3A, 3C, 4A and 4C) were identified displaying different behavior between the resistant versus the sensitive xenografts in non-irradiated cells Two clusters (Clusters 2 and 3) showed higher expression levels in the resistant xenografts (WISH-PC14 and LAPC9; Figures 3a and c), while the other two clusters (Clusters 5 and 6) were more highly expressed in the IR sensitive xenografts (CWR22 and WISH-PC23; Figures 4A and C). The LuCAP35 cell line displayed a non-uniform behavior; for some groups of genes it clustered with the IR resistant samples (clusters 2 and 6; Figures 3A and 4C) while for others it clustered with the sensitive samples (clusters 3 and 5; Figures 3C and 4A). Cluster 2 consisted of 157 probe-sets and cluster 3 consisted of 66 probe-sets that were highly expressed in the resistant samples. A set of 87 (SEQ ID NOs: 11-97) (including 7 ESTs) probesets (out of the 223 probesets contained in clusters 2 and 3) displayed at least 3-fold up-regulation in the resistant samples, compared to the average expression levels of the sensitive samples. The up-regulated genes that were highly expressed in the IR resistant samples (Tables 2 and 3, hereinbelow) included a number of genes involved in cell survival and death such as the cell growth genes SNN, KLK2, ACPP; angiogenesis factors AGTRl, ILlRl, ZNF323, FMNL2, KLF13 and PTK7; DNA repair genes, e.g. H2AFJ, HIST1H2BK, HIST1H2BD and SMARCAl; cell death genes

CASP8 and 4, LITAF, GULP and UCP2; and an inhibition of cell growth gene IFITM3.

The opposite picture was seen in clusters 5 and 6 (Tables 4 and 5, hereinbelow) which consisted of 117 and 116 probe-sets, respectively, which were highly expressed in the IR sensitive cells relative to the resistant lines. A set of 71 probesets (SEQ ID NOs:98-168) (including 7 ESTs) out of the 233 probe sets contained in these clusters displayed up-regulation of at least 3-fold in the sensitive samples, compared to the average expression levels of the resistant samples. The up-regulated genes that were highly expressed in IR sensitive samples include a number of genes that are involved in cell death and survival: Cell death and apoptosis genes such as TP53, PTEN, DUSP6. On the other hand, an increased expression of Growth and survival promoting genes, including ETS2, CFCl, RAB26, and ATF7 was found.

Figures 5A-C display a united expression profile of these clusters. The LuCAP35 xenograft displayed a non-uniform behavior, while in some cases it clustered with the resistant samples and in some cases it clustered with the sensitive samples. LuCap35 displays a radioresistant behavior in cluster 2 and radiosensitive behavior in cluster 3 (Figures 5a-b). Gene clusters that appear in Figures 5A-B consist of probe sets that are highly expressed in the resistant samples (Figures 3A-D) together with the opposite pattern seen in the clusters displayed in Figures 4A-D, in which the sensitive samples characterized by high expression levels compared to the resistant samples. In this case LuCap35 xenograft also displayed inconsistent behavior, and was clustered with the sensitive samples in Figure 5 A and with the resistant samples in Figure 5B. The PCA analysis shown in Figure 5C clearly shows the same differences that have been seen in the clustering analysis. It demonstrates that the groups representing the resistant xenografts (WISH-PC14 and LAPC9), the sensitive ones (CWR22 and WISH-PC23) and LuCAP35 each differ in their gene expression profiles. This observation may reflect the inherent properties of the response to irradiation. Altogether, the data presented so far identify 456 probesets (113 genes) that differentiate between the IR resistant and IR sensitive phenotypes.

Analyzing the xenografts samples by PCA based on the four aforementioned clusters nicely demonstrates that the radioresistant xenografts (WISH-PC 14 and LAPC9), the radiosensitive (CWR22 and WISH-PC23) and LuCap35 differ in their genes expression profiles (Figures 3-4). This observation may indicate an existence of intrinsic properties that are involved in response to irradiation. The list of genes that appear in these clusters is shown in Tables 2-5. The Tables divide the genes according to their function (when known). For clusters 2, 3 (Tables 2, 3) the ratio between the gene expression in each of the two radioresistant xenografts (LAPC9 and WISH-PC14) and the mean expression of the radiosensitive xenografts. In Tables 4 and 5 displaying the genes in clusters 5 and 6, the opposite ratio is given.

Altogether, the genes identified herein can serve as the cohort of genes whose pattern of expression in a given prostate cancer biopsy should serve as a genetic signature to predict the response of the tumor to ionizing irradiation. Table 2 depicts the genes of cluster 2 which were upregulated in radiation resistant prostate cancer cells (or downregulated in radiation sensitive prostate cancer cells). Table 2 Cluster 2: genes upregulated in radiation resistant prostate cancer

Table 2.

Table 3 depicts the genes of cluster 3 which were upregulated in radiation resistant prostate cancer cells (or downregulated in radiation sensitive prostate cancer cells). Table 3 Cluster 3: genes upregulated in radiation resistant prostate cancer

Table 3.

Table 4 depicts the genes of cluster 5 which were downregulated in radiation resistant prostate cancer cells (or upregulated in radiation sensitive prostate cancer cells). Table 4 Cluster 5: genes downregulated in radiation resistant prostate cancer

Table 4.

Table 5 depicts the genes of cluster 6 which were downregulated in radiation resistant prostate cancer cells (or upregulated in radiation sensitive prostate cancer cells).

Table 5 Cluster 6: genes downregulated in radiation resistant prostate cancer

Table 5.

Interestingly, the non-irradiated and the irradiated sample pairs showed extremely high similarity in their gene-expression profiles. Since the immediate effect of irradiation is associated with modified gene expression due to DNA damage and repair, induction of pro-apoptotic processes and other mechanisms described in the background section, it is reasoned that this effect reflects the relatively long time period (3 months) that elapsed between the irradiation to the time of gene-expression analysis (which was performed on cancer cells that survived the irradiation). In such a case most of the biological processes activated following irradiation has been already inactive. These data support a model in which the xenografts tested represent a homogeneous cell population in their response to the random effect of IR rather than a mixture of two distinct sensitive and resistant sub-populations.

Notably, similar analysis of cultured PC cell lines in unsupervised fashion yielded significantly identical patterns of gene expression as was obtained for the xenografts described above (data not shown).

Thus, these results demonstrate, for the first time, the identification of gene markers which differentiate between radiosensitive and radioresistant prostate cancer cells. Thus, these gene markers can be used to predict the response of the prostate cancer tumors to ionizing irradiation and thus can serve as a tool for selecting the suitable treatment regimen for each prostate cancer patient (e.g., chemotherapy, surgery, radiation therapy or combination thereof). Moreover, these gene markers can be used to determine the dosing of radiation therapy in prostate cancer patients.

This study may also lead to identifying genes and gene regulatory pathways related to the resistance of cells to ionizing radiotherapy. EXAMPLE 3 VALIDATION OF ARRAY RESULTS BY Q-RT-PCR

To confirm the changes in expression of candidate genes from the GeneChip, and to compare the expression level between the types of IR phenotypes relative to resistant xenograft LAPC9, the present inventors have employed Quantitative RT-PCR (Q-RT- PCR), as follows.

Experimental Results

Validation of array data by Q-RT-PCR - For validation of array results, one gene per cluster was selected, based on the gene expression analysis described in Example 2, hereinabove (cluster 2- H2AFJ, cluster 3-UCP2, cluster 5-RAB26, cluster 6- PTEN). For Q-RT-PCR analysis, the sample previously used in GeneChip analysis was employed and two other samples from different mice and generation for each xenografts. The RNA expression level of each of the analyzed genes was calculated relative to TPTl expression. Figures 6a-d depict the relative expression of each of the tested genes [H2AFJ (Figure 6A), UCP2 (Figure 6B), PTEN (Figure 6C) and RAB26 (Figure 6D)] in the LAPC9 resistant xenograft as compared to the expression in the CWR22 or WISH PC-23 sensitive xenografts of the LuCAP35 semiresistant xenograft. Thus, in both of the genes that were upregulated (H2AFJ and UCP2) in resistant xenografts, a significantly higher expression was found as compared with the expression of the same genes in the GeneChip analysis. In the genes that were down-regulated in the resistant xenografts, it was found that PTEN exhibited higher expression than its expression in the GeneChip analysis and RAB26 exhibited lower expression but the same tendency of expression as in the GeneChip analysis (Figures 6A-D).

Altogether, these results demonstrate that changes in the expression of 4 genes that were detected by Q-RT-PCR, correlated well with the microarray data.

EXAMPLE 4

TESTING THE DIFFERENTIATING GENES ONA NEW SET OF SENSITIVE OR RESISTANTPROSTATE CANCER CELL LINES To confirm the data obtained from the PC xenograft analysis and to select a limited list of genes capable of differentiating between sensitive and resistant samples, an additional and independent set of 7 PC cell lines (radiation resistant cell lines: CL-I, DU-145 and PC-3; radiation sensitive cell lines: 22Rv-I, LNCaP1740, LNCaP10995 and LAPC4) was employed. RNA isolated from these cells was subjected to gene array on the same array described hereinabove. The expression profile of the 456 probesets that differentiated between the IR resistant and sensitive xenografts were tested on the cell-line data. Using this approach, 41 unique genes (42 probesets) were identified that best distinguished between the radioresistant/sensitive phenotypes ((using t-test (p < 0.01), FDR 10 % (Figure 7; Table 6, hereinbelow).

Table 6 Differentiating genes between radiation resistance and sensitive phenotypes in both prostate cancer xenografts and cells lines

Table 6: Presented are the Affymetrix probe set and sequence identifiers and the genes (and sequence identifiers of their encoded transcripts and polypeptides) which are differentially expressed between radiation resistance and sensitive prostate cancer xenografts and cell lines. Also provided are the average ratios between the expression level of resistance to sensitive for the prostate cancer xenografts and for cell lines. The resistance xenografts were LAPC9 and WISH14; the sensitive xenografts were WISH23 and CWR22; the resistance cell lines were CL-I, DU- 145, and PC-3; the sensitive cell lines were LNCaP1740, LNCaP10995 and LAPC4. P values were calculated using the t test. Symb. = symbol; Polyn. = polynucleotide; Polyp. = polypeptide. Thus, these data reveal a set of 41 unique candidate genes (Table 6) whose expression provides a transcriptional signature to predict the response of a prostate tumor_to radiotherapy.

EXAMPLE 5

DETERMINATION OF THE SENSITIVITY OR RESISTANCE OF PROSTATE CANCER TO RADIATION THERAPY USING DIFFERENTIATION GENES

To identify genes/markers which can predict the sensitivity or resistance of a prostate cancer sample to radiation therapy, the expression analysis profile data of the 456 probesets shown in Figure 5A of all prostate cancer xenografts and cell lines described in the "General Materials and Experimental Methods" section hereinabove was combined and the average values were computed (Table 7, below). Using this approach, 10 unique genes (12 probesets) were identified that best distinguished between the radioresistant/sensitive phenotypes [(using t-test (p < 0.01), FDR 10 %, Table 7]. These include the polynucleotides set forth by SEQ ID NOs:91, 198, 83, 199, 200, 201 and 202 which are upregulated in radiation resistance prostate cancer samples and are downregulated in radiation sensitive prostate cancer samples; and the polynucleotides set forth by SEQ ID NO: 101, 181, 114, 111 and 203 which are downregulated in radiation resistance prostate cancer samples and are upregulated in radiation sensitive prostate cancer samples. These results suggest the use of each of the differentiating genes (SEQ ID NOs:204-218) or probsets (SEQ ID NOs:91, 198, 83, 199, 200, 201, 202, 101, 181, 114, 111 and 203) presented in Table 7 or any combination thereof to determine the sensitivity or resistance of a prostate cancer sample to radiation therapy.

Table 7

Differentiating genes between radiation resistance and sensitive phenotypes of prostate cancer

Table 7: Presented are the Affymetrix probe set identifiers and genes along with the sequence identifiers (SEQ ID NO:) of their encoded transcripts and polypeptides which are differentially expressed between radiation resistance and sensitive prostate cancer samples (xenografts and cell lines). Also provided are the average ratios between the expression level of resistance to sensitive (R/S) for the prostate cancer samples (xenografts and cell lines). The resistance xenografts were LAPC9 and WISH14; the sensitive xenografts were WISH23 and CWR22; the resistance cell lines were CL-I, DU-145, and PC-3 ; the sensitive cell lines were LNCaP1740, LNCaP10995, LAPC4 and 22RvI. Polyn. = polynucleotide; Polyp. = polypeptide.

The following genes were found to be upregulated in radiation resistance (or downregulated in radiation sensitive) prostate cancer samples:

1. S100A16 [GenBank Accession No. NM_080388.1 (SEQ ID NO:204) for the polynucleotide, and NP_525127.1 (SEQ ID NO:219) for the polypeptide]. 2. ANXA2P2 [GenBank Accession No. NR_003573.1 (SEQ ID NO:205) for the polynucleotide].

3. MALL [GenBank Accession No. NM_005434.3 (SEQ ID NO:206) for the polynucleotide, and NP_005425.1 (SEQ ID NO:220) for the polypeptide]. 4. SMARCAl [GenBank Accession No. NM_003069.2 (SEQ ID NO:207) for the polynucleotide, and NP_003060.2 (SEQ ID NO:221) for the polypeptide].

5. HPCALl transcript variant 1 [GenBank Accession No. NM_002149.2 (SEQ ID NO:208) for the polynucleotide, and NP_002140.2 (SEQ ID NO:222) for the polypeptide]; HPCALl transcript variant 2 [GenBank Accession No. NM_134421.1 (SEQ ID NO:209) for the polynucleotide, and NP_602293.1 (SEQ ID NO:223) for the polypeptide].

6. FUNDCl [GenBank Accession No. NM_173794.2 (SEQ ID NO:210) for the polynucleotide, and NP_776155.1 (SEQ ID NO:224) for the polypeptide].

The following genes were found to be downregulated in radiation resistance (or upregulated in radiation sensitive) prostate cancer samples:

1. CSAG2 [GenBank Accession No. NM_004909.3 (SEQ ID NO:211) for the polynucleotide, and NP_004900.2 (SEQ ID NO:225) for the polypeptide].

2. PPAPDClB transcript variant 1 [GenBank Accession No. NMJ)Ol 102559 (SEQ ID NO:212), for the polynucleotide, and NPJ)01096029.1 (SEQ ID NO:226) for the polypeptide]; PPAPDClB transcript variant 2 [GenBank Accession No. NMJB2483 (SEQ ID NO:213), for the polynucleotide, and NP_115872.2 (SEQ ID NO:227) for the polypeptide]; PPAPDClB transcript variant 3 [GenBank Accession No. NMJ)Ol 102560 (SEQ ID NO:214), for the polynucleotide, and NPJ)01096030.1 (SEQ ID NO:228) for the polypeptide]. 3. MAGEA2 transcript variant 1 [GenBank Accession No. NMJJ05361 (SEQ

ID NO:215) for the polynucleotide, and NP_005352.1 (SEQ ID NO:229) for the polypeptide]; MAGEA2 transcript variant 2 [GenBank Accession No. NM_175742 (SEQ ID NO:216) for the polynucleotide, and NP_786884.1 (SEQ ID NO:230) for the polypeptide]; MAGEA2 transcript variant 3 [GenBank Accession No. NM_175743 (SEQ ID NO:217) for the polynucleotide, and NP_786885.1 (SEQ ID NO:231) for the polypeptide]. 4. ZNF718 [GenBank Accession No. NM_001039127 (SEQ ID NO:218) for the polynucleotide, and NP_001034216.1 (SEQ ID NO:232) for the polypeptide].

Tables 8 and 9, hereinbelow, summarize the ratio of expression levels between several genes which are differentially expressed between IR resistant and sensitive prostate cancer cell samples phenotypes according to their functional affiliation.

Table 8

Genes which are unregulated in radiation resistant as compared to radiation sensitive prostate cancer samples

Table 8. Provided are the Affymetrix probe set identifiers and genes along with the sequence identifiers (SEQ ID NO:) of their encoded transcripts and polypeptides which are upregulated in radiation resistant prostate cancer samples as compared to radiation sensitive prostate cancer cell samples. The apoptosis genes include CASP8, LITAF, CASP4, CD24, GULPl, UCP2; the DNA repair genes include H2AFJ, HIST1H2BK and, HIST1H2BD; the proliferation related genes include ILlRl; the inhibition of cell growth related genes include IFITM3; the angiogenesis related genes include GUCYl A3, NRPl and AGTRl. Polyn. = polynucleotide; Polyp. = polypeptide.

Table 9

Genes which are upregulated in radiation sensitive as compared to radiation resistant prostate cancer samples

Table 9: Provided are the Affymetrix probe set identifiers and genes along with the sequence identifiers (SEQ ID NO:) of their encoded transcripts and polypeptides which are upregulated in radiation sensitive prostate cancer samples as compared to radiation resistant prostate cancer cell samples. Apoptosis genes include TP53, DUSP6, PTEN, TNFRSFlOD; proliferation related (associated) genes include IMP-3 and RAB26; and growth arrest related (associated) genes include BTGl.Polyn. = polynucleotide; Polyp. = polypeptide.

Models for radioresistance/sensitivity of prostate cancer - Without being bound by any theory, the present inventors suggest that two possible models for the different responses seen following irradiation can be considered:

Model a (Figure 8A): Existence of two distinct subpopulations within a given xenograft. According to this model, the cell population within each xenograft consists of a mixture of two types- IR sensitive (S) and IR resistant (R) cells. Most of the sensitive cells die a short time after IR (some sensitive cells survive because of the stochastic effects of IR), while most of the resistant cells survive (though a small fraction will also die).

According to this model, in a sensitive xenograft, most of the population before IR consists of sensitive cells and only a small fraction contains resistant cells. A few months after exposure to IR, the ensemble of the cell population changes and the resistant population dominates. In the resistant xenografts, the majority of the cells resist IR. After a few months, there is a reduction in the sensitive population, but since it was small to begin with, the composition of the population before and after the IR does not change significantly. Thus, according to this model, the prediction is that following irradiation, sensitive xenografts will convert from dominantly sensitive (S) to dominantly resistant (R) sub-populations. This would be expected to cause a change in the gene expression profile before versus after IR. For the resistant xenografts, no significant change is expected to occur within the sub-populations after irradiation and therefore no change in gene expression is expected. Model b (Figure 8B): Each xenograft is homogeneous, and all cells within a xenograft have about the same chance to survive/die after irradiation. According to this model, each tumor contains a cell population that responds uniformly to radiation. Thus, every cell in a given xenograft has nearly the same probability of dying from IR. The probability of dying is greater for a sensitive cell, than for a resistant one. Thus, a short time after radiation, most of the cells in the sensitive xenograft die, but only a small fraction of those in the resistant xenograft die. According to this model, the prediction is that a few months after IR the population ensemble of each phenotype to remain unchanged. According to this model, no significant gene expression changes (before and after irradiation) are expected in the tumors on a population level, in either the sensitive or in the resistant xenografts.

The similarity in the gene expression patterns between the non-irradiated and irradiated xenografts support Model b (Figure 8b), which asserts a random effect of the irradiation on a homogeneous population of cells. Each xenograft has a different intrinsic phenotype that influences its capability to survive the IR.

Analysis and Discussion

In this study, the inventors have established the gene expression profile that distinguishes between radiation resistant and radiation sensitive human prostate cancer. For decades, IR has been used therapeutically to treat primary prostate tumors and its bone metastases. Currently, there is a high failure rate (5-year biochemical failure rate of 10-40 %) after external-beam radiation therapy. It is expected that the present teachings would help in selecting patients who can benefit from this therapeutic approach, to predict the long term treatment outcome, or to identify prostate cancer patients who are not expected to respond to radiotherapy. Such patients could be offered alternative treatment modalities (e.g. surgery).

To prevent artifacts corresponding to the immediate effects of IR on gene expression, the experimental system was based on human PC xenografts whose radioresistant/sensitive phenotype was previously determined (Table 1). In general, tumor xenografts are better representative of the patient's prostate cancer cell sample than cell lines. By analysis of the gene array the inventors identified four gene clusters displaying different expression behavior across the resistant and the sensitive xenografts (Figures 3A-D and 4A-D). Two clusters showed higher expression levels in the resistant xenografts and the other two clusters showed higher expression levels in the sensitive xenografts. The expression of 113 genes was significantly changed (p < 0.01 and at least 3 fold) in sensitive compared to resistant xenografts. By comparing this list of genes derived from the PC xenografts to the data obtained using PC cell lines 41 genes shared a similar pattern in distinguishing between the irradiation sensitive and resistant phenotypes (Figure 7; Table 6). These genes represent a primary list of genes whose expression may represent a genetic signature to predict the outcome of a given prostate tumor to radiotherapy. The genes in the list represent several cellular mechanisms (such as DNA repair, cell death (apoptosis, oncosis), angiogenesis and cell growth (Tables 2, 3, 4 and 5). As such, they embody the complexity of the molecular processes involved in radioresistance/sensitivity. TP53 and PTEN were previously reported to be related to radioresistance [Colletier PJ, et al, 2000, Int J Radiat Oncol Biol Phys 48(5):1507-1512; Lee JM, and Bernstein A. 1993. Proc Natl Acad Sci U S A ;90(12):5742-5746; Fan Z, et al., 2000, Cancer Gene Ther,7(10):1307-1314; and Rosser CJ, et al., 2004. Cancer Gene Ther l l(4):273-279]. These two tumor suppressor and pro-apoptotic genes are up regulated after radiotherapy, and it was found that deregulation (or deletion of these genes) contributes to the radiation resistance of some cancers (e.g. prostate, glioma) [Chang EH, et al., 2000, MoI Med Today, 6(9):358-364]. In the present study, these two genes were down-regulated or not-expressed in the radioresistant xenografts. Comparing the data obtained in this study concerning the effect of IR on PC xenografts, with data obtained from other types of human cancers could identify a common set of genes related to the radiorestant/sensitive phenotypes. To date, only a few groups investigated the long-term transcriptional response to irradiation. Kitahara et al examined the molecular profiles of radioresistant cervical squamous cell cacinoma versus sensitive cancers and showed that the expression of 62 genes could predict IR resistant versus sensitive tumors [Kitahara O, et al., 2002, Neoplasia, 4(4):295-303]. Vallat et al compared the gene expression of B-cell chronic lympocytic leukemia (B- CLL) cells that were either sensitive or resistant to radiation. Sixteen genes were differentially regulated by at least 2 fold in the resistant cells [Vallat L, et al., 2003, Blood 101(11):4598-4606]. Fukuda et al studied six oesophageal cancer cell lines that were treated with continuous fractionated irradiation and compared expression profiles of each parent to its radioresistant clones using an cDNA microarray. Nineteen up- regulated and 28 down-regulated genes were common to radioresistant cell lines [Fukuda K, et al., 2004, Br J Cancer, 91(8):1543-1550]. The study of the cervical cancer (Kitahara O., et al., 2002) response to IR, suggested that radioresistance is maintained via increased expression of a DNA repair component (XRCC5/Ku80), while in leukemia it is potentially mediated by upregulation of anti-apoptotic (e.g. c-IAPl, c-rel) and growth control (c-myc) gene (Vallat L, et al., 2003). Radiosensitivity in these studies was associated with an increased expression of MAP kinase signaling genes (Kitahara O, et al., 2002; Vallat L., et al., 2003). In oesophageal carcinoma cells (Fukuda K, et al., 2004), IR resistance was shown to be related to upregulation of anti-apoptotic (BIRC2 related to IAP family) and growth control (COX and CD73). Interestingly, none of these gene products were included in the list of genes identified in Tables 6, 7, 8 and 9. The gene identified in the present study show an increased expression of DNA repair associated genes such as H2AFJ, HIST1H2BK, HIST1H2BD and loss of the two tumor suppressor genes (PTEN and p53) in the radioresistant samples. In the radiosensitive PC xenografts an increase in growth factors related to the EGF gene family (CFCl), RAS oncogene family (RAB26) and IGF-2 binding protein 3 (Table 3). Taken together, the present study indicates that several key functional pathways are associated with the cell fate following irradiation. Resistant prostate cancer samples displayed an increase in DNA repair components and decrease in apoptotic components, both are the hallmarks of the radioresistant phenotype. Similarly, in IR-sensitive tumors, a common feature is the elevation of growth factor gene expression. Apparently, such an increase is associated with enhanced cell division, thereby rendering the cell more sensitive to IR.

The transcriptional patterns that distinguish between radioresistant and radiosensitive prostate cancer xenografts serve as a predictive tool, to determine right at early diagnosis, which PC patient will benefit from irradiation or resort to other treatment. These findings suggest that both radioresistant and radiosensitive tumors are composed from homogeneous population in term of their response to irradiation, and imply that with a proper design of the irradiation dose and schedule of administration thereof to the radiosensitive tumors, a complete cure of localized primary tumors with less side effects is feasible.

Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims.

All publications, patents and patent applications mentioned in this specification are herein incorporated in their entirety by reference into the specification, to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. To the extent that section headings are used, they should not be construed as necessarily limiting.

REFERENCES

(Additional references are cited in text)

1. Blatt, M., S. Wiseman, and E. Domany. 1996. Superparamagnetic clustering of data. Physical Review Letters 76:3251-3254.

2. Tsafrir, D., I. Tsafrir, L. Ein-Dor, O. Zuk, D. A. Notterman, and E. Domany. 2005. Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices. Bioinformatics 21:2301-8.

3. Scott, S. L., Gumerlock, P. H., Beckett, L., Li, Y., and Goldberg, Z. Survival and cell cycle kinetics of human prostate cancer cell lines after single- and multifraction exposures to ionizing radiation. Int J Radiat Oncol Biol Phys, 59: 219-227, 2004

4. Canman, C. E., Lim, D. S., Cimprich, K. A., Taya, Y., Tamai, K., Sakaguchi, K., Appella, E., Kastan, M. B., and Siliciano, J. D. Activation of the ATM kinase by ionizing radiation and phosphorylation of p53. Science, 281: 1677-1679., 1998.

5. Chang, E. H., Pirollo, K. F., and Bouker, K. B. Tp53 gene therapy: a key to modulating resistance to anticancer therapies? MoI Med Today, 6: 358-364., 2000.

6. Colletier, P. J., Ashoori, F., Cowen, D., Meyn, R. E., Tofilon, P., Meistrich, M. E., and Pollack, A. Adenoviral- mediated p53 transgene expression sensitizes both wild- type and null p53 prostate cancer cells in vitro to radiation. Int J Radiat Oncol Biol Phys, 48: 1507-1512., 2000.

7. Fan, Z., Chakravarty, P., Alfieri, A., Pandita, T. K., Vikram, B., and Guha, C. Adenovirus-mediated antisense ATM gene transfer sensitizes prostate cancer cells to radiation. Cancer Gene Ther, 7: 1307-1314., 2000.

8. Lee, J. M. and Bernstein, A. p53 mutations increase resistance to ionizing radiation. Proc Natl Acad Sci U S A, 90: 5742-5746., 1993.

9. Snyder, A. R. and Morgan, W. F. Gene expression profiling after irradiation: clues to understanding acute and persistent responses? Cancer Metastasis Rev, 23: 259- 268, 2004.

10. Bar-Shira, A., Pinthus, J. H., Rozovsky, U., Goldstein, M., Sellers, W. R., Yaron, Y., Eshhar, Z., and Orr-Urtreger, A. Multiple genes in human 20ql3 chromosomal region are involved in an advanced prostate cancer xenograft. Cancer Res, 62: 6803-6807, 2002. 11. Pisansky TM. External-beam radiotherapy for localized prostate cancer. The New England Journal of Medicine, 355(15):1583-1591, 2006.

12. Rosser CJ, Tanaka M, Pisters LL, Tanaka N, Levy LB, Hoover DC, Grossman HB, McDonnell TJ, Kuban DA, Meyn RE. Adenoviral-mediated PTEN transgene expression sensitizes Bcl-2-expressing prostate cancer cells to radiation. Cancer Gene Ther 2004;l l(4):273-279.

13. Kitahara O, Katagiri T, Tsunoda T, Harima Y, Nakamura Y. Classification of sensitivity or resistance of cervical cancers to ionizing radiation according to expression profiles of 62 genes selected by cDNA microarray analysis. Neoplasia 2002;4(4):295- 303

14. Vallat L, Magdelenat H, Merle-Beral H, Masdehors P, Potocki de Montalk G, Davi F, Kruhoffer M, Sabatier L, Orntoft TF, Delic J. The resistance of B-CLL cells to DNA damage-induced apoptosis defined by DNA microarrays. Blood 2003;101(l l):4598-4606.

15. Fukuda K, Sakakura C, Miyagawa K, Kuriu Y, Kin S, Nakase Y, Hagiwara A, Mitsufuji S, Okazaki Y, Hayashizaki Y, Yamagishi H. Differential gene expression profiles of radioresistant oesophageal cancer cell lines established by continuous fractionated irradiation. Br J Cancer 2004;91(8):1543-1550.

16. Fait S, Holmberg K, Lambert B, Wennborg A. Long-term global gene expression patterns in irradiated human lymphocytes. Carcinogenesis 2003;24(l l):1837-1845.

17. Kruse JJ, te Poele JA, Velds A, Kerkhoven RM, Boersma LJ, Russell NS, Stewart FA. Identification of differentially expressed genes in mouse kidney after irradiation using microarray analysis. Radiat Res 2004;161(l):28-38.

Claims

WHAT IS CLAIMED IS:

1. A method of predicting a sensitivity or a resistance of prostate cancer to radiation therapy, the method comprising comparing a level of expression in a prostate cancer sample of at least one gene selected from the group consisting H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl to a reference expression data of said at least one gene obtained from at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample, thereby predicting the sensitivity or the resistance of prostate cancer to radiation therapy.

2. The method of claim 1, wherein a decrease above a predetermined threshold in said level of expression of said at least one gene selected from the group consisting of IMP3, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, CSAG2, ZNF718, TP53, PTEN, DUSP6, TNFRSFlOD, and BTGl in said prostate cancer sample relative to said reference expression data of said at least one gene obtained from said at least one prostate cancer sensitive sample predicts the resistance of the prostate cancer sample to radiation therapy.

3. The method of claim 1, wherein an increase above a predetermined threshold in said level of expression of said at least one gene selected from the group consisting of IMP3, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, CSAG2, ZNF718, TP53, PTEN, DUSP6, TNFRSFlOD, and BTGl in said prostate cancer sample relative to said reference expression data of said at least one gene obtained from said at least one prostate cancer resistant sample predicts the sensitivity of the prostate cancer sample to radiation therapy.

4. The method of claim 1, wherein a decrease above a predetermined threshold in said level of expression of said at least one gene selected from the group consisting of H2AFJ, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, ANXA2P2, SMARCAl, HPCALl, FUNDCl, CASP4, LITAF, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl and AGTRl in said prostate cancer sample relative to said reference expression data of said at least one gene obtained from said at least one prostate cancer resistant sample predicts the sensitivity of the prostate cancer sample to radiation therapy.

5. The method of claim 1, wherein an increase above a predetermined threshold in said level of expression of said at least one gene selected from the group consisting of H2AFJ, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, ANXA2P2, SMARCAl, HPCALl, FUNDCl, CASP4, LITAF, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl and AGTRl in said prostate cancer sample relative to said reference expression data of said at least one gene obtained from said at least one prostate cancer sensitive sample predicts the resistance of the prostate cancer sample to radiation therapy.

6. A kit for predicting a sensitivity or a resistance of prostate cancer to radiation therapy, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of said at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO:186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl.

7. A kit for selecting a treatment regimen of a subject diagnosed with prostate cancer, comprising at least 2 and no more than 500 isolated nucleic acid sequences, wherein each of said at least 2 and no more than 500 isolated nucleic acid sequences is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO:186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl.

8. A microarray comprising no more than 500 oligonucleotides wherein each of said oligonucleotides is capable of specifically recognizing at least one gene selected from the group consisting of H2AFJ, Sl 0OA 16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, UCP2, TUBA3, CKLFSF3, GDAPl, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO:186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP3 and BTGl.

9. The method of claim 1, the kit of claim 6 or 7 or the microarray of claim 8, wherein said at least one gene is selected from the group consisting of H2AFJ, S100A16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, MAGEA2, ZNF718, CASP8, LITAF, CASP4, CD24, GULPl, UCP2, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, RAB26, and BTGl.

10. The method of claim 1, the kit of claim 6 or 7 or the microarray of claim 8, wherein said at least one gene is selected from the group consisting of S100A16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, ZNF718, FTHl, PFN2, PSMB8, TFCP2, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO:195, LOC646208 and KRTCAP3.

11. The method of claim 1, the kit of claim 6 or 7 or the microarray of claim 8, wherein said at least one gene is selected from the group consisting of H2AFJ, FTHl, PFN2, TFCP2, PSMB8, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, KRTCAP3, LITAF, CASP4, CD24, GULPl, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, and BTGl.

12. The method of claim 1, the kit of claim 6 or 7 or the microarray of claim 8, wherein said at least one gene is selected from the group consisting of S100A16, ANXA2P2, MALL, SMARCAl, HPCALl, FUNDCl, CSAG2, PPAPDClB, MAGEA2, and ZNF718.

13. The method of claim 1, the kit of claim 6 or 7 or the microarray of claim 8, wherein said at least one gene is selected from the group consisting of CASP8, LITAF, CASP4, CD24, GULPl, UCP2, H2AFJ, HIST1H2BK, HIST1H2BD, ILlRl, IFITM3, GUCY1A3, NRPl, AGTRl, TP53, DUSP6, PTEN, TNFRSFlOD, IMP-3, RAB26, and BTGl.

14. The method of claim 1, the kit of claim 6 or 7 or the microarray of claim 8, wherein said at least one gene is selected from the group consisting of FTHl, PFN2, PSMB8, TFCP2, RHOQ, CASP8, ACAA2, SMARCAl, UCP2, TUBA3, MALL, CKLFSF3, GDAPl, S100A16, PPIB, VDP, CDC40, METTL7A, MAGEA2, ELL3, RAB26, FAMl 18A, TRAG3, CNST, PPAPDClB, CLN8, WDR5B, a gene encoding SEQ ID NO: 184, a gene encoding SEQ ID NO: 185, a gene encoding SEQ ID NO: 186, IDHl, ZNF124, RWDD2, COX7A2, SETD7, ARRDC4, SLAINl, C6orfl51, a gene encoding SEQ ID NO: 195, LOC646208, and KRTCAP3.

15. A method of selecting a treatment regimen of a subject diagnosed with prostate cancer, the method comprising:

(a) predicting the sensitivity or the resistance of the prostate cancer of the subject to radiation therapy according to the method of any of claims 1-5 and 9-14; and

(b) selecting the treatment regimen based on said sensitivity or resistance of the prostate cancer to radiation therapy.

16. The method of claim 15, wherein the treatment regimen comprises a radiation therapy selected from the range of 45-80 Gy when the prostate cancer is radiation sensitive.

17. The kit of any of claims 6, 7, and 9-14, further comprising at least one prostate cancer resistant sample and/or at least one prostate cancer sensitive sample.

18. The method of any of claims 1-5 and 9-14 or the kit of claim 17, wherein said at least one prostate cancer sensitive sample comprises a radiation sensitive prostate cancer xenograft or a radiation sensitive prostate cancer cell line.

19. The method of any of claims 1-5 and 9-14 or the kit of claim 17, wherein said at least one prostate cancer resistant sample comprises a radiation resistant prostate cancer xenograft or a radiation resistant prostate cancer cell line.

20. The method of any of claims 1-5, 9-16 and 18-19, wherein said level of expression is determined using an RNA detection method.

21. The kit of any of claims 6, 7, 9-14 and 17-20, wherein each of said isolated nucleic acid sequences is selected from the group consisting of an oligonucleotide molecule, a cDNA molecule, a genomic DNA molecule and an RNA molecule.

22. The kit of any of claims 6, 7, 9-14 and 17-20, wherein each of said isolated nucleic acid sequences comprises at least 10 and no more than 50 nucleic acids.

23. The kit of any of claims 6, 7, 9-14 and 17-20, wherein each of said isolated nucleic acid sequences is bound to a solid support.

24. The kit of claim 6, 7, 9-14 and 17-20, further comprising at least one reagent suitable for detecting hybridization of said isolated nucleic acid sequences to at least one RNA transcript of said at least one gene.

25. The kit of claim 6, 9-14 and 17-20, further comprising packaging materials packaging said at least one reagent and instructions for use in determining the sensitivity or the resistance of the prostate cancer to radiation therapy.

26. The kit of claim 7, 9-14 and 17-20, further comprising packaging materials packaging said at least one reagent and instructions for use in selecting the treatment regimen of the subject diagnosed with prostate cancer.

27. The microarray of claim 8, wherein each of said oligonucleotides comprises at least 10 and no more than 40 nucleic acids.