WO2009116860A1 - Marqueurs utilisés dans le pronostic de métastases chez les patients cancéreux - Google Patents

Marqueurs utilisés dans le pronostic de métastases chez les patients cancéreux Download PDF

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WO2009116860A1
WO2009116860A1 PCT/NL2009/050125 NL2009050125W WO2009116860A1 WO 2009116860 A1 WO2009116860 A1 WO 2009116860A1 NL 2009050125 W NL2009050125 W NL 2009050125W WO 2009116860 A1 WO2009116860 A1 WO 2009116860A1
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nucleotide sequence
expression
seq
polypeptide
gene
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Daniel S. Peeper
Christophe J. C. Desmet
Fabien Reyal
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Vereniging Het Nederlands Kanker Instituut
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    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
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    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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    • C12N2310/00—Structure or type of the nucleic acid
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/50—Physical structure
    • C12N2310/53—Physical structure partially self-complementary or closed
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/178—Oligonucleotides characterized by their use miRNA, siRNA or ncRNA

Definitions

  • the invention relates to an ex vivo method of prognosticating metastasis in a cancer patient comprising identifying differential modulation of a gene (relative to the expression of a same gene in a control) in a combination of genes selected from the groups consisting of genes represented by the following sequences SEQ ID NO: 1-76 and/or SEQ ID NO:77-108.
  • the invention also relates to the use of one of the following sequences selected from the following groups SEQ ID NO: 1-76 and/or SEQ ID NO:77- 108 as a medicament, preferably for preventing, delaying and/or treating metastasis in a cancer patient.
  • Mestatatic spread of tumour cells is the main cause of death in cancer patients. Efforts to improve on the current rates of survival include two major aims: first, to identify druggable genes that contribute to cancer metastasis and second, to stratify cancers based on sets of classifier genes into poor- and good-prognosis outcome groups, with direct consequences for treatment (Miller & Liu, 2007).
  • One major problem in the study of metastasis corresponds to the scarceness of in vivo models that recapitulate all steps of the metastatic process.
  • Several diagnostic portfolio comprising markers have already been identified as being linked with cancer (see for example EP 1 367 138 B). However, no diagnostic portfolio is known wherein a unique combination of genes has been identified based on functional metastasis experiments as further explained herein. The diagnostic portfolio of the invention has this unique property as explained later herein.
  • the inventors Using a robust rat tumor cell system, the inventors first identified the transcription factor Fos-related antigen- 1 (Fral, also referred to as FOSLl) as an essential promoter of cancer cell metastasis. They show that Fral is required for oncogene- induced epithelial to mesenchymal transition (EMT), thereby promoting migration and invasion of tumour cells. Correspondingly, they show that Fral is essential for the metastatic capacity of these rat tumour cells. Then, they demonstrate that the specific gene expression profile that is induced by Fral in rat tumour cells can be used to generate a classifier to stratify breast cancer patients based on their risk of developing distant metastasis.
  • FMT oncogene- induced epithelial to mesenchymal transition
  • an ex vivo method of prognosticating metastasis in a cancer patient comprising identifying differential modulation of a gene (relative to the expression of a same gene in a baseline) in a combination of genes selected from the groups consisting of genes represented by the following sequences SEQ ID NO: 1 -76 and/or SEQ ID NO:77-108.
  • prognosticating means either a predictive risk assessment of a cancer patient for metastasing (i.e. predict the presence of metastases in the future, or pre-symptomatic prediction of risk of metastasis) or an assessment of a metastasized cancer in a patient. It may also refer to the likelihood that a patient will respond to a given therapy or to the response of a patient to a therapy he has already been administered. Such a prognosticating method is crucial to have since usually once metastasis has been assessed in a cancer patient, his/her chances of survival decrease dramatically.
  • a "patient” may be an animal or a human being.
  • a patient is a human being.
  • metastasis preferably referred to "metastasis” as assessed in a cancer patient by ultrasound examination of lymph nodes, liver, thorax or any other organ suitable for ultrasound examination, lymph node dissection, scintigraphy of the bones or any other organs suitable for scintigraphy, standard radiography or any other technique suitable for the detection of metastasis. More preferably, “metastasis” refers to the “detection of a metastatic activity" within tumour cells in one of the in vivo animal models as described hereafter. Metastasis can be best studied in vivo in xenograft experiments in mice (nude mice or other suitable mouse strains).
  • tumour cells are injected either sub- cutaneously (as described in Douma S., et al (2004), Nature, 430:1034-1040), or orthotopically (that is, in the organ or tissue that corresponds to the tissue type of the tumour cells).
  • breast tumour cells are injected into a mammary gland (as described in Erler J.T., et al, (2006), Nature, 440: 1222-1226).
  • cell can be injected directly in the blood circulation of the mice (as described in Erler J.T., et al, (2006), Nature, 440: 1222-1226).
  • a visible metastatic lesion may comprise at least 4, 6, 8, 10, 12, 14, 15, 17, 19, 20, 22, 24, 25 tumour cells or more. Seeding and growth of metastases will occur at time points depending on the type of tumour cell, typically starting at several days after inoculation, or several weeks or months.
  • a “gene” preferably means a nucleotide acid molecule which is represented by a nucleotide acid sequence and which encodes a protein or polypeptide.
  • a gene may comprise a regulatory region.
  • a "cancer” in the expression a "cancer patient” preferably means that a cancer has already been diagnosed in a given patient.
  • metastasis can be prognosticated in any kind of cancer.
  • a cancer is such that it is already known to the skilled person that such cancer can potentially lead to metastasis.
  • a cancer is such that it is technically possible to isolate a sample containing a tumour cell.
  • a cancer may be melanoma, colon, prostate, lung, thyroid, or breast cancer.
  • a preferred cancer is breast cancer.
  • Modulated genes are preferably those that are differentially expressed as up regulated or down regulated in non-normal cells (tumour cells or metastasised tumour cells).
  • Up regulation and down regulation are relative terms meaning that a detectable difference (beyond the contribution of noise in the system used to measure it) is found in the amount of expression of the genes relative to a baseline.
  • a baseline preferably comes from a pool of non cancer patients, or preferably patients with cancer but without detectable metastasis.
  • a pool of these patients preferably contains 1, 3, 5, 10, 20, 30, 100, 400, 500, 600 or more patients.
  • the expression level of a gene of interest in the non-normal cells is then considered either up regulated or down regulated relative to a baseline level using the same measurement method.
  • a baseline is the measured gene expression of a large pool of cancer patients.
  • large means at least 50 cancer patients, at least 70, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600 or more.
  • the gene expression levels in this large pool of cancer patients is used in this application to generate a good and a poor prognostic centroids as extensively explained in the experimental part in the section entitled "Classifier generation”.
  • the assessment of the expression level of a gene in order to assess whether a gene is modulated is preferably performed using classical molecular biology techniques to detect mRNA levels, such as (real time) reverse transcriptase PCR (whether quantitative or semi-quantitative), mRNA (micro)array analysis or Northern blot analysis, or other methods to detect RNA.
  • the expression level of a gene is determined indirectly by quantifying the amount of the polypeptide encoded by said gene. Quantifying a polypeptide amount may be carried out by any known techniques. Preferably, polypeptide amount is quantified by Western blotting.
  • the quantification of an identified gene and/or corresponding polypeptide the quantification of a substrate of said corresponding polypeptide or of any compound known to be associated with the function of said corresponding polypeptide or the quantification of the function or activity of said corresponding polypeptide using a specific assay is encompassed within the scope of the prognosticating method of the invention.
  • the assessment of the expression level of a gene is carried out using (micro)arrays as later defined herein.
  • a sample from a patient is preferably used.
  • the expression level (of a gene or polypeptide) is determined ex vivo in a sample obtained from a patient.
  • a sample may be liquid, semi-liquid, semi-solid or solid.
  • a preferred sample comprises 100 or more tumour cells and/or a tumour tissue from a cancer patient to be tested taken in a biopsy.
  • a sample preferably comprises blood of a patient. The skilled person knows how to isolate and optionally purify RNA and/or protein present in such a sample.
  • RNA In case of RNA, the skilled person may further amplify it using known techniques.
  • An increase (or up regulation) (which is synonymous with a higher expression level) or decrease (or down regulation) (which is synonymous with a lower expression level) of the expression level of a gene (or steady state level of the encoded polypeptide) is preferably defined as being a detectable change of the expression level of a gene (or steady state level of the encoded polypeptide or any detectable change in the biological activity of the polypeptide) using a method as defined earlier on as compared to the expression level of a corresponding gene (or steady state level of the corresponding encoded polypeptide) in a baseline.
  • an increase or decrease of a polypeptide activity is quantified using a specific assay for the polypeptide activity.
  • an increase of the expression level of a gene means an increase of at least 5% of the expression level of said gene using arrays. More preferably, an increase of the expression level of a gene means an increase of at least 10%, even more preferably at least 20%, at least 30%, at least 40%, at least 50%, at least 70%, at least 90%, at least 150% or more.
  • a decrease of the expression level of a gene means a decrease of at least 5% of the expression level of said gene using arrays.
  • a decrease of the expression level of a gene means an decrease of at least 10%, even more preferably at least 20%., at least 30%, at least 40%, at least 50%, at least 70%, at least 90%, at least 150% or more.
  • an increase of the expression level of a polypeptide means an increase of at least 5% of the expression level of said polypeptide using western blotting. More preferably, an increase of the expression level of a polypeptide means an increase of at least 10%, even more preferably at least 20%, at least 30%, at least 40%, at least 50%, at least 70%, at least 90%, at least 150% or more.
  • a decrease of the expression level of a polypeptide means a decrease of at least 5% of the expression level of said polypeptide using western blotting. More preferably, a decrease of the expression level of a polypeptide means a decrease of at least 10%, even more preferably at least 20%, at least 30%, at least 40%, at least 50%, at least 70%, at least 90%, at least 150% or more.
  • an increase of a polypeptide activity means an increase of at least 5% of said polypeptide activity using a suitable assay. More preferably, an increase of said polypeptide activity means an increase of at least 10%, even more preferably at least
  • a decrease of a polypeptide activity means a decrease of at least 5% of said polypeptide activity using a suitable assay. More preferably, a decrease of said polypeptide activity means a decrease of at least 10%, even more preferably at least
  • 76 or more genes as defined herein, and/or the steady state levels of said corresponding polypeptides are determined.
  • a gene whose expression level is determined is selected in a combination of genes selected from the groups consisting of genes represented by the following sequences SEQ ID NO: 1-76 and/or SEQ ID NO:77-108.
  • Each combination of 2 till 76 genes for the first group and/or of 2 till 33 genes for the second group may be used.
  • the 76 genes of the first group are being used.
  • the 33 genes of the second group are being used.
  • all the genes of both groups are used. Table 1 identifies the SEQ ID NO of all genes (cDNA, nucleotide sequence) and corresponding encoded polypeptides.
  • the first group consisting of genes represented by the following sequences SEQ ID NO: 1-76 and/or SEQ ID NO:77-108.
  • Each combination of 2 till 76 genes for the first group and/or of 2 till 33 genes for the second group may be used.
  • SEQ ID NO: 1-3 5, 7, 12-16, 18, 21, 28, 30-32, 34, 38, 40, 43-52, 55-57, 59-63, 65, 67, 69-70, 72-73, 65-76 are identified from the first group as having an expression level being up regulated in a method for prognosticating metastasis.
  • SEQ ID NO: 77-80, 83-84, 88, 90, 92-93, 96, 98, 100- 101, 104 are identified as having an expression level being up regulated in a method for prognosticating metastasis.
  • Remaining genes from both groups are identified as having their expression level being down regulated in a method for prognosticating metastasis.
  • a still reliable method for prognosticating metastasis may be carried out based on a sub combination of SEQ ID NO: 1-76 and/or SEQ ID NO: 77-108.
  • the most reliable group of genes for predicting (i.e. prognosticating) metastasis in a cancer patient, preferably in a human cancer patient is the one identified in a rat model cell line.
  • the most effective way of determining gene expression level uses (micro)arrays.
  • One gene to be used in a preferred prognosticating method is Fral identified as SEQ ID NO:21 or 88 in table 1.
  • Fra 1 is used in combination with at least one (at least, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, ...106) other gene(s) as identified in table 1.
  • a microarray is a solid support or carrier containing one or more immobilised nucleic acid or polypeptide fragments for analysing nucleic acid or amino acid sequences or mixtures thereof (see e.g. WO 97/27317 ', WO 97/22720, WO 97/43450, EP 0 799 897, EP 0 785 280, WO 97/31256, WO 97/27317, WO 98/08083 and Zhu and Snyder, 2001, Curr. Opin. Chem.
  • (Micro)array technology allows for the measurement of the steady-state mRNA level of thousands of genes simultaneously thereby presenting a powerful tool for identifying gene modulation for a given group of genes as identified herein.
  • Two microarray technologies are currently in wide use. The first are cDNA arrays and the second are oligonucleotide arrays. Although differences exist in the construction of these chips, essentially all downstream data analysis and output are the same. The product of these analyses are typically measurements of the intensity of the signal received from a labelled probe used to detect a cDNA sequence from the sample that hybridizes to a nucleic acid sequence at a known location on the microarray.
  • the intensity of the signal is proportional to the quantity of cDNA, and thus mRNA, expressed in a cell from a cancer patient to be tested.
  • mRNA mRNA
  • a large number of such techniques are available and useful. Preferred methods for determining gene expression can be found in US Patents 6,271,002 to Linsley, et al; 6,218,122 to Friend, et al; 6,218,114 to Peck, et al; and 6,004,755 to Wang, et al., the disclosure of each of which is incorporated herein by reference.
  • Analysis of the expression levels is conducted preferably by measuring expression levels using these techniques.
  • this is best done by generating a matrix of the expression intensities of genes in a test sample (RNA from cells from a cancer patient to be tested) using a single channel hybridisation on a microarray platform, and comparing these intensities with the one of a reference group or baseline (in this case, a good and a poor prognosis centroid as earlier identified herein).
  • the gene expression intensities from a non normal tissue can be compared with the expression intensities generated from non normal tissues of the same type.
  • a "control" refers to a large number of cancer patients as defined earlier herein preferably using the method as earlier defined herein.
  • each sample is assigned to a good prognosis or bad prognosis group using a Single Sample Predictor.
  • each patient is assigned to the nearest centroid as determined by the highest Spearman rank order correlation score between the gene expression value of the corresponding gene sets of each sample and the centroid values of the 'poor prognosis' and 'good prognosis' centroid.
  • a classifier of the invention is preferably used as described in Hu et al 2006.
  • a second ex vivo method wherein the method identified above is used to prognosticate the absence of metastasis in a cancer patient comprising identifying a lack of differential modulation of a gene (relative to the expression of a same gene in a control) in a combination of a gene selected from the groups consisting of genes represented by the following sequences SEQ ID NO: 1-76 and/or SEQ ID NO:77-108.
  • All elements (for example type of cancer, identity of a patient, way of identifying a modulation of a gene) of said second method have already been identified for the first method.
  • An absence of metastasis is preferably assessed the same way as earlier defined herein (scintigraphy or in an in vivo animal model). In a more preferred method, the absence of metastasis is prognosticated for a one, two, three, four, five year period or longer.
  • Another aspect of the invention relates to a diagnostic portfolio comprising or consisting of isolated nucleic acid (or nucleotide) sequences, their complements, or portions thereof of a combination of genes selected from the groups consisting of a gene represented by the following sequences SEQ ID NO: 1-76 and/or SEQ ID NO:77- 108. Diagnostic portfolios comprising or consisting of any combinations or sub combinations as defined herein are also encompassed by the present invention.
  • a preferred diagnostic portfolio comprises a matrix suitable for identifying the differential expression of the genes contained therein.
  • a more preferred diagnostic portfolio comprises a matrix, wherein said matrix is employed in a microarray. Said microarray is preferably a cDNA or oligonucleotide microarray.
  • Markers i.e. genes or nucleic acids, nucleotides
  • an article including a representation of the gene expression profiles that make up the portfolios useful for prognosticating metastasis or prognosticating an absence of metastasis. These representations are reduced to a medium that can be automatically read by a machine such as computer readable media (magnetic, optical, and the like).
  • the articles can also include instructions for assessing the gene expression profiles in such media.
  • the articles may comprise a CD ROM having computer instructions for comparing gene expression profiles of the portfolios of genes described above.
  • the articles may also have gene expression profiles digitally recorded therein so that they may be compared with gene expression data from a cancer patient sample. Alternatively, the profiles can be recorded in different representational format. A graphical recordation is one such format.
  • Different types of articles of manufacture according to the invention are media or formatted assays used to reveal gene expression profiles.
  • These can comprise or consist of, for example, microarrays in which sequence complements or probes are affixed to a matrix to which the sequences indicative of the genes of interest combine creating a readable determinant of their presence.
  • microarrays contains an optimized portfolio great savings in time, process steps, and resources are attained by minimizing the number of cDNA or oligonucleotides that must be applied to the substrate, reacted with the sample, read by an analyser, processed for results, and (sometimes) verified.
  • Kits made according to the invention include formatted assays for determining the gene expression profiles. These can include all or some of the materials needed to conduct the assays such as reagents and instructions.
  • kits for prognosticating metastasis or prognosticating the absence of metastasis in a cancer patient comprising reagents for detecting nucleic acid sequences, their complements, or portions thereof in a combination of genes selected from the groups consisting of genes represented by the following sequences SEQ ID NO: 1-76 and/or SEQ ID NO:77-108. Kits comprising or consisting of any combinations or sub combinations as defined herein are also encompassed by the present invention.
  • kits further comprises reagents for conducting a microarray analysis. More preferably, a kit further comprising a medium through which said nucleic acid sequences, their complements, or portions thereof are assayed. More preferably, said medium is a microarray. A kit may further comprise instructions.
  • the invention relates to a nucleic acid construct comprising all or a part of a nucleotide sequence that encodes a polypeptide that comprises an amino acid sequence that is encoded by a nucleotide sequence selected from: (a) a nucleotide sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99% identity with a nucleotide sequence selected from SEQ ID NO: 1-108; and/or,
  • nucleotide sequence that encodes an amino acid sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99% amino acid identity with an amino acid sequence encoded by a nucleotide sequence selected from SEQ ID NO: 1-108.
  • a nucleotide sequence is operably linked to a promoter that is capable of driving expression of said nucleotide sequence in a cell, more preferably a human and/or tumour cell. Even more preferably, the cell is a human breast cell.
  • a nucleic acid construct comprises all or a part of a nucleotide sequence that encodes a polypeptide that comprises an amino acid sequence that is encoded by a nucleotide sequence selected from:
  • nucleotide sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99% identity with a nucleotide sequence selected from SEQ ID NO: 1-4, 9, 12-13, 15, 19, 20, 21, 26-28, 32-33, 35, 42-45, 48, 54-55,56, 57-59, 61-65, 68, 70, 74-75, 77-79, 81, 82, 86, 88, 90, 93, 98, 101, 103, 105, 107 ; and/or,
  • nucleotide sequence that encodes an amino acid sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99% amino acid identity with an amino acid sequence encoded by a nucleotide sequence selected from SEQ ID NO: 1-4, 9, 12-13, 15, 19, 20, 21, 26-28, 32-33, 35, 42-45, 48, 54-55, 56, 57-59, 61-65, 68, 70, 74-75, 77-79, 81, 82, 86, 88, 90, 94, 98, 101, 103, 105, 107.
  • each identified nucleotide sequence correspond to a potentially druggable gene.
  • a druggable gene is a gene of which a protein product may be modulated (down regulated or up regulated) using a small molecule, an antibody (neutralising or agonist), and/or any other method of modulation (down regulation or up regulation) of a protein activity.
  • a nucleic acid construct comprises all or a part of a nucleotide sequence that encodes a polypeptide that comprises an amino acid sequence that is encoded by a nucleotide sequence selected from: (a) a nucleotide sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99% identity with a nucleotide sequence selected from SEQ ID NO: 77-79, 81, 82, 86, 88, 90, 93, 98, 101, 103, 105, 107 ; and/or, (b) a nucleotide sequence that encodes an amino acid sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99% amino acid identity with an amino acid sequence encoded by a nucleotide sequence selected from SEQ ID NO: 77-79, 81, 82, 86, 88, 90, 93, 98, 101, 103, 105, 107 .
  • Table 1 identified in bold preferred druggable genes of which a protein product is down regulated (identified as being up regulated in a patient with metastasis), and in italics and bold preferred druggable genes of which a protein product is up regulated (identified as being down regulated in a patient with metastasis):
  • each of SEQ ID NO: 4, 19, 20 26-27, 33, 42, 54, 64, 68, 74, 81, 86, 94, 103, 105, 107 is identified as a gene of which a protein product may be up regulated using a small molecule, an agonist antibody, and/or any other method of modulation (up regulation) of a protein activity. More preferably, SEQ ID NO: 4, 9, 19, 20, 26-27, 33, 35, 42, 54, 58, 64, 68, 74, 82 are selected since these genes were identified in the rat classifier.
  • each of SEQ ID NO: 1-3, 12-13, 15, 21, 28, 32, 43-45, 48, 55, 56, 57, 59, 61, 65, 70, 75, 77-79, 88, 90, 98, 101 is identified as a gene of which a protein product may be down regulated using a small molecule, a neutralising antibody, and/or any other method of modulation (down regulation) of a protein activity.
  • These druggable genes are preferred since it is technically expected to be easier to down regulate the expression of a given gene than the opposite. More preferably, SEQ ID NO: 77-79, 88, 90, 98, 101 are selected since these genes were identified in the human classifier.
  • a druggable gene is selected from the group consisting of: SEQ ID NO: 4, 20, 56, 101 and 105. Each sub combination of one, two, three, four of these genes and these five genes are encompassed by the present invention. The importance of these genes as druggable genes has been confirmed in another system. Even more preferably, a druggable gene is selected from the group consisting of SEQ ID NO: 101 and 105 since these genes were identified in the human classifier.
  • a druggable gene is selected from the group consisting of SEQ ID NO: 56 and 105 since each of these genes is identified as a gene of which a protein product may be down regulated using a small molecule, a neutralising antibody, and/or any other method of modulation (down regulation) of a protein activity.
  • a nucleic acid construct as defined herein preferably comprises all or a part of a nucleotide sequence that encodes a polypeptide that comprises an amino acid sequence that is encoded by a nucleotide sequence selected from:
  • nucleotide sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99% identity with a nucleotide sequence selected from SEQ ID NO: 4, 20, 56, 101, 105; and/or,
  • nucleotide sequence that encodes an amino acid sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99% amino acid identity with an amino acid sequence encoded by a nucleotide sequence selected from SEQ ID NO: 4, 20, 56, 101, 105.
  • a nucleic acid construct of the invention comprises or consists of a nucleotide sequence that encodes an RNAi agent, i.e. an RNA molecule that is capable of RNA interference or that is part of an RNA molecule that is capable of RNA interference.
  • RNAi agent i.e. an RNA molecule that is capable of RNA interference or that is part of an RNA molecule that is capable of RNA interference.
  • small RNA molecules such as siRNA (short interfering RNA, including e.g. a short hairpin RNA).
  • the nucleotide sequence that encodes the RNAi agent preferably has sufficient complementarity with a cellular nucleotide sequence to be capable of inhibiting the expression of a polypeptide that comprises an amino acid sequence that is encoded by a nucleotide sequence selected from: a) a nucleotide sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99 % identity with a sequence selected from SEQ ID NO: 1-3, 12-13, 15, 21, 28, 32, 43-45, 48, 55, 56, 57, 59, 61, 65, 70, 75, 77-79, 88, 98, 101, preferably 56, 105 as defined herein; and/or,
  • nucleotide sequence that encodes an amino acid sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99 % amino acid identity with an amino acid sequence encoded by a nucleotide sequence selected from SEQ ID NO: 1-3, 12-13, 15, 21, 28, 32, 43-45, 48, 55, 56, 57, 59, 61, 65, 70, 75, 77-79, 88, 98, 101, preferably 56, 105;
  • a nucleic acid construct of the invention comprises or consists of a nucleotide sequence that encodes an RNAi agent capable of inhibiting the expression of a polypeptide that comprises an amino acid sequence that is encoded by a nucleotide sequence selected from: a) a nucleotide sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99 % identity with SEQ ID NO: 1-3, 12-13, 15, 21, 28, 32, 43-45, 48, 55, 56, 57, 59, 61, 65, 70, 75 as defined herein; and/or,
  • nucleotide sequence that encodes an amino acid sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99 % amino acid identity with an amino acid sequence encoded by a nucleotide sequence selected from SEQ ID NO: 1-3, 12-13, 15, 21, 28, 32, 43-45, 48, 55, 56, 57, 59, 61, 65, 70, 75. These sequences are more preferred since they were identified in the rat classifier.
  • a nucleic acid construct of the invention comprises or consists of a nucleotide sequence that encodes an RNAi agent capable of inhibiting the expression of a polypeptide that comprises an amino acid sequence that is encoded by a nucleotide sequence selected from: a) a nucleotide sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99 % identity with SEQ ID NO: 21 or 88 as defined herein; and/or,
  • nucleotide sequence that encodes an amino acid sequence that has at least 60, 70, 80, 85, 90, 95, 98 or 99 % amino acid identity with an amino acid sequence encoded by a nucleotide sequence selected from SEQ ID NO: 21 or 88; wherein optionally the nucleotide sequence encoding the RNAi agent is operably linked to a promoter that is capable of driving expression of the nucleotide sequence in a cell, more preferably a human and/or tumour cell. Even more preferably, the cell is a human breast cell.
  • a promoter which may be present is preferably a promoter that is specific for a human and/or tumour cell and/or mammary cell.
  • a promoter chosen is specific for and functional in a human and/or tumour cell and/or mammary cell.
  • a promoter that is specific for a human and/or tumour cell and/or mammary is a promoter with a transcription rate that is higher in such a cell than in other types of cells.
  • the promoter's transcription rate in such a cell is at least 1.1, 1.5, 2.0 or 5.0 times higher than in a other types of cells as measured by PCR of the construct in such a cell as compared to other types of cells.
  • a nucleic acid construct as defined herein is for use as a medicament, preferably for preventing, delaying and/or treating metastasis in a cancer patient.
  • a nucleic acid construct is a viral gene therapy vector selected from gene therapy vectors based on an adenovirus, an adeno-associated virus (AAV), a herpes virus, a pox virus and a retrovirus.
  • a preferred viral gene therapy vector is an AAV or Lentiviral vector. Such vectors are further described herein below.
  • the invention relates to a use of a nucleic acid construct as defined herein for modulating the expression level of a gene and/or activity or steady state level of a polypeptide as defined herein, for the manufacture of a medicament for preventing and/or delaying and/or metastasis in a cancer patient, preferably in a method of the invention as defined herein.
  • the invention relates to a method for identification of a substance capable of preventing, delaying and/or treating metastasis in a cancer patient.
  • the method preferably comprises the steps of: (a) providing a test cell population capable of expressing a nucleotide sequence encoding a polypeptide of the invention; (b) contacting the test cell population with the substance; (c) determining the expression level of the nucleotide sequence or the activity or steady state level of the polypeptide in the test cell population contacted with the substance; (d) comparing the expression, activity or steady state level determined in (c) with the expression, activity or steady state level of the nucleotide sequence or of the polypeptide in a test cell population that has not been contacted with the substance; and, (e) identifying a substance that produces a difference in expression level, activity or steady state level of the nucleotide sequence or the polypeptide, between the test cell population that has been contacted with the substance and the test cell population that has not been contacted
  • the test cell comprises a nucleic acid construct of the invention.
  • the expression levels, activities or steady state levels of more than one nucleotide sequence or more than one polypeptide are compared.
  • a test cell population comprises mammalian cells, more preferably human and/or tumour cells.
  • a test cell population comprises bone-marrow and/or peripheral blood and/or pluripotent stem cells and/or mammary cells. These cells can be harvested, purified using techniques known to the skilled person.
  • a test cell population comprises a cell line.
  • the cell line is a human or rat cell line.
  • test cells are part of an in vivo animal model as earlier defined herein.
  • the invention also pertains to a substance that is identified in a method the aforementioned methods.
  • "preventing" metastasis means that during at least one, two, three, four, five years, or longer no metastatic lesion will be detected in an in vivo animal model as earlier defined herein and/or in a cancer patient using scintigraphy as earlier defined herein, wherein said tumour cells were treated with said substance by comparison with the potential development of a metastatic lesion in a non- treated control.
  • "delaying" metastasis means that the detection of a metastatic lesion in a given system using the same assays as defined in the previous paragraph treated with said substance is delayed of at least 1, 6, 12, 18, 24, 30, 36, 42, 48, 54, 60, 66 months or longer compared to the time at which detection of one metastatic lesion will occur in a corresponding control non treated with said substance.
  • "treating" metastasis means that there is a detectable decrease of the amount of metastatic lesions in a given system using the same assays as defined in the previous paragraph treated with said substance after at least one month (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 months or longer) compared to the amount of metastatic lesions in the same system which has not been treated.
  • a detectable decrease is preferably defined as being at least 1% decrease, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%,35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more till no metastase are detectable.
  • the invention provides a method for preventing, delaying and/or treating metastasis in a cancer patient, said method comprising pharmacologically altering the expression level of a gene and/or activity or the steady-state level of a polypeptide encoded by a nucleotide sequence selected from the druggable genes as earlier defined herein.
  • the expression level of a gene and/or activity and/or steady-state level of a polypeptide of the invention is altered in order to mimick its physiological level in a cancer patient known not have metastasis (no detectable metastase) or in a healthy subject.
  • the activity or steady-state level of a polypeptide of the invention may be altered at the level of the polypeptide itself, e.g. by providing a polypeptide of the invention to a patient, preferably to a cell of a patient, more preferably to a tumour cell of a patient, said polypeptide being from an exogenous source, or by adding an antagonist or inhibitor of a polypeptide to a patient, preferably to a cell, more preferably to a tumour cell of said cancer patient such as e.g. an antibody against a polypeptide, preferably a neutralizing antibody.
  • a polypeptide may conveniently be produced by expression of a nucleic acid encoding a polypeptide in a suitable host cell as described below.
  • An antibody against a polypeptide of the invention may be obtained as described below.
  • the activity or steady-state level of a polypeptide is altered by regulating the expression level of a nucleotide sequence encoding a polypeptide.
  • the expression level of a nucleotide sequence is regulated in a human and/or tumour cell.
  • the expression level of a polypeptide of the invention may be increased by introduction of an expression construct (or vector) into a human and/or tumour cell, whereby an expression vector comprises a nucleotide sequence encoding a polypeptide, and whereby a nucleotide sequence is under control of a promoter capable of driving expression of a nucleotide sequence in a human and/or tumour cell.
  • the expression level of a polypeptide may also be increased by introduction of an expression construct into a human and/or tumour cell, whereby a construct comprises a nucleotide sequence encoding a factor capable of trans-activation of an endogenous nucleotide sequence encoding a polypeptide.
  • the expression level of a polypeptide of the invention may be decreased by providing an antisense molecule to a human and/or tumour cell, whereby an antisense molecule is capable of inhibiting the biosynthesis (usually the translation) of a nucleotide sequence encoding a polypeptide.
  • An antisense molecule may be provided to a cell as such or it may be provided by introducing an expression construct into a human and/or tumour cell, whereby an expression construct comprises an antisense nucleotide sequence that is capable of inhibiting the expression of a nucleotide sequence encoding a polypeptide, and whereby an antisense nucleotide sequence is under control of a promoter capable of driving transcription of an antisense nucleotide sequence in a human and/or tumour cell.
  • the expression level of a polypeptide may also be decreased by introducing an expression construct into a human and/or tumour cell, whereby an expression construct comprises a nucleotide sequence encoding a factor capable of trans-repression of an endogenous nucleotide sequence encoding a polypeptide.
  • An antisense or interfering nucleic acid molecule may be introduced into a cell directly "as such", optionally in a suitable formulation, or it may be produce in situ in a cell by introducing into a cell an expression construct comprising a (antisense or interfering) nucleotide sequence that is capable of inhibiting the expression of a nucleotide sequence encoding a polypeptide, whereby, optionally, an antisense or interfering nucleotide sequence is under control of a promoter capable of driving expression of an nucleotide sequence in a human and/or tumour cell.
  • the meaning of "increase or decrease the expression of a gene (nucleotide) or corresponding polypeptide" is the same as given in the section entitled “ex vivo methods”.
  • a method of the invention preferably comprises the step of administering to a cancer patient a therapeutically effective amount of a pharmaceutical composition comprising a nucleic acid construct for modulating the activity or steady state level of a polypeptide and/or a neutralizing antibody and/or a polypeptide as defined herein.
  • a nucleic acid construct may be an expression construct as further specified herein below.
  • an expression construct is a viral gene therapy vector selected from a gene therapy vector based on an adenovirus, an adeno-associated virus (AAV), a herpes virus, a pox virus and a retrovirus.
  • a preferred viral gene therapy vector is an AAV or Lentiviral vector.
  • a nucleic acid construct may be for inhibiting expression of a polypeptide of the invention such as an antisense molecule or an RNA molecule capable of RNA interference (see below).
  • a human and/or tumour cell is preferably a cell from a cancer patient suspected to have a high risk of having a metastasised cancer, due for example to its age and/or its genetic background and/or to its diet and/or to the type of cancer he has.
  • a method of the invention is applied on a cell from a cancer patient diagnosed as having a risk of having a metastasised cancer.
  • a prognosticating method used is preferably one of the inventions already earlier described herein.
  • a human and/or tumour cell chosen to be treated are preferably isolated from the patient they belong to ⁇ ex vivo method).
  • Cells are subsequently treated by altering the activity or the steady state level of a polypeptide of the invention.
  • This treatment is preferably performed by infecting them with a polypeptide and/or a nucleic acid construct of the invention and/or a neutralizing antibody as earlier defined herein.
  • treated cells are placed back into the patient they belong to.
  • the invention mentioned herein may be combined with standard treatments of metastasis such as chemotherapy and/or radiation.
  • metastasis such as chemotherapy and/or radiation.
  • gene therapy is a possibility for preventing, delaying and/or treating metastasis, other possible treatments may also be envisaged.
  • treatment by ""small molecule” drugs to steer certain molecular pathways in the desired direction is also preferred. These small molecules are preferably identified by the screening method of the invention as defined later herein.
  • SEQ ID NO is not limited to this specific sequence as disclosed.
  • Each gene sequence or nucleotide sequence as identified herein encodes a given protein or polypeptide as identified in table 1.
  • SEQ ID NO a specific nucleotide sequence SEQ ID NO (take SEQ ID NO:1 as example)
  • nucleotide sequences the complementary strand of which hybridizes to a nucleic acid molecule of sequence of (i) or (ii); iv.a nucleotide sequence the sequence of which differs from the sequence of a nucleic acid molecule of (iii) due to the degeneracy of the genetic code. iv. a nucleotide sequence that encodes an amino acid sequence that has at least
  • nucleotide sequence or amino acid sequence described herein by virtue of its identity percentage (at least 60%) with a given nucleotide sequence or amino acid sequence respectively has in a further preferred embodiment an identity of at least 65%
  • sequence identity is determined by comparing the whole length of the sequences as identified herein.
  • sequence identity is herein defined as a relationship between two or more amino acid (polypeptide or protein) sequences or two or more nucleic acid
  • identity also means the degree of sequence relatedness between amino acid or nucleic acid sequences, as the case may be, as determined by the match between strings of such sequences. "Similarity" between two amino acid sequences is determined by comparing the amino acid sequence and its conserved amino acid substitutes of one polypeptide to the sequence of a second polypeptide. "Identity” and “similarity” can be readily calculated by known methods, including but not limited to those described in (Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A.
  • Preferred methods to determine identity are designed to give the largest match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Preferred computer program methods to determine identity and similarity between two sequences include e.g. the GCG program package (Devereux, J., et al, Nucleic Acids Research 12 (1): 387 (1984)), BestFit, BLASTP, BLASTN, and FASTA (Altschul, S. F. et al., J. MoI. Biol. 215:403-410 (1990).
  • the BLAST X program is publicly available from NCBI and other sources (BLAST Manual, Altschul, S., et al., NCBI NLM NIH Bethesda, MD 20894; Altschul, S., et al., J. MoI. Biol. 215:403-410 (1990).
  • the well-known Smith Waterman algorithm may also be used to determine identity.
  • Preferred parameters for polypeptide sequence comparison include the following: Algorithm: Needleman and Wunsch, J. MoI. Biol. 48:443-453 (1970); Comparison matrix: BLOSSUM62 from Hentikoff and Hentikoff, Proc. Natl. Acad. Sci. USA. 89:10915-10919 (1992); Gap Penalty: 12; and Gap Length Penalty: 4.
  • a program useful with these parameters is publicly available as the "Ogap" program from Genetics Computer Group, located in Madison, WI.
  • the aforementioned parameters are the default parameters for amino acid comparisons (along with no penalty for end gaps).
  • Preferred parameters for nucleic acid comparison include the following:
  • amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide- containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulphur-containing side chains is cysteine and methionine.
  • Preferred conservative amino acids substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine- valine, and asparagine-glutamine.
  • Substitutional variants of the amino acid sequence disclosed herein are those in which at least one residue in the disclosed sequences has been removed and a different residue inserted in its place.
  • the amino acid change is conservative.
  • Preferred conservative substitutions for each of the naturally occurring amino acids are as follows: Ala to ser; Arg to lys; Asn to gin or his; Asp to glu; Cys to ser or ala; GIn to asn; GIu to asp; GIy to pro; His to asn or gin; He to leu or val; Leu to ile or val; Lys to arg; gin or glu; Met to leu or ile; Phe to met, leu or tyr; Ser to thr; Thr to ser; Trp to tyr; Tyr to trp or phe; and, Val to ile or leu.
  • a polypeptide for use in the present invention can be prepared using recombinant techniques, in which a nucleotide sequence encoding said polypeptide of interest is expressed in a suitable host cell.
  • the present invention thus also concerns the use of a nucleic acid construct, preferably being a vector comprising a nucleic acid molecule being represented by a nucleotide sequence as defined above.
  • the vector is a replicative vector comprising on origin of replication (or autonomously replication sequence) that ensures multiplication of the vector in a suitable host for the vector.
  • the vector is capable of integrating into a host cell's genome, e.g.
  • a particularly preferred vector is an expression vector wherein a nucleotide sequence encoding a polypeptide as defined above, is operably linked to a promoter capable of directing expression of the coding sequence in a host cell for the vector.
  • promoter refers to a nucleic acid fragment that functions to control the transcription of one or more genes, located upstream with respect to the direction of transcription of the transcription initiation site of the gene, and is structurally identified by the presence of a binding site for DNA-dependent RNA polymerase, transcription initiation sites and any other DNA sequences, including, but not limited to transcription factor binding sites, repressor and activator protein binding sites, and any other sequences of nucleotides known to one of skill in the art to act directly or indirectly to regulate the amount of transcription from the promoter.
  • a “constitutive” promoter is a promoter that is active under most physiological and developmental conditions.
  • an “inducible” promoter is a promoter that is regulated depending on physiological or developmental conditions.
  • a “tissue specific” promoter is only active in specific types of differentiated cells/tissues, such as preferably a human and/or tumour and/or mammary cell or tissue derived thereof.
  • An expression vector may allow a polypeptide of the invention as defined above to be prepared using recombinant techniques in which a nucleotide sequence encoding said polypeptide is expressed in a suitable cell, e.g. cultured cells or cells of a multicellular organism, such as described in Ausubel et al., "Current Protocols in Molecular Biology", Greene Publishing and Wiley-Interscience, New York (1987) and in Sambrook and Russell (2001, supra); both of which are incorporated herein by reference in their entirety. Also see, Kunkel (1985) Proc. Natl. Acad. Sci. 82:488 (describing site directed mutagenesis) and Roberts et al. (1987) Nature 328:731-734 or Wells, J.A., et al. (1985) Gene 34: 315 (describing cassette mutagenesis).
  • a nucleic acid encoding said polypeptide is used in an expression vector.
  • expression vector generally refers to nucleotide sequences that are capable of effecting expression of a gene in hosts compatible with such sequences. These expression vectors typically include at least suitable promoter sequences and optionally, transcription termination signals. Additional factors necessary or helpful in effecting expression can also be used as described herein.
  • a nucleic acid or DNA encoding said polypeptide is incorporated into a DNA construct capable of introduction into and expression in an in vitro cell culture.
  • DNA constructs are suitable for replication in a prokaryotic host, such as bacteria, e.g., E. coli, or can be introduced into a cultured mammalian, plant, insect, e.g., Sf9, yeast, fungi or other eukaryotic cell lines.
  • DNA constructs prepared for introduction into a particular host typically include a replication system recognized by the host, the intended DNA segment encoding the desired polypeptide, and transcriptional and trans lational initiation and termination regulatory sequences operably linked to the polypeptide-encoding segment.
  • a DNA segment is "operably linked" when it is placed into a functional relationship with another DNA segment.
  • a promoter or enhancer is operably linked to a coding sequence if it stimulates the transcription of the sequence.
  • DNA for a signal sequence is operably linked to DNA encoding a polypeptide if it is expressed as a pre protein that participates in the secretion of said polypeptide.
  • DNA sequences that are operably linked are contiguous, and, in the case of a signal sequence, both contiguous and in reading phase.
  • enhancers need not be contiguous with the coding sequences whose transcription they control. Linking is accomplished by ligation at convenient restriction sites or at adapters or linkers inserted in lieu thereof.
  • an appropriate promoter sequence generally depends upon the host cell selected for the expression of the DNA segment.
  • suitable promoter sequences include prokaryotic, and eukaryotic promoters well known in the art (see, e.g. Sambrook and Russell, 2001 , supra).
  • the transcriptional regulatory sequences typically include a heterologous enhancer or promoter that is recognised by the host.
  • the selection of an appropriate promoter depends upon the host, but promoters such as the trp, lac and phage promoters, tRNA promoters and glycolytic enzyme promoters are known and available (see, e.g. Sambrook and Russell, 2001, supra).
  • Expression vectors include the replication system and transcriptional and translational regulatory sequences together with the insertion site for the polypeptide encoding segment can be employed. Examples of workable combinations of cell lines and expression vectors are described in Sambrook and Russell (2001, supra) and in Metzger et al. (1988) Nature 334: 31-36.
  • suitable expression vectors can be expressed in, yeast, e.g. S.cerevisiae, e.g., insect cells, e.g., Sf9 cells, mammalian cells, e.g., CHO cells and bacterial cells, e.g., E. coli.
  • the host cells may thus be prokaryotic or eukarotic host cells.
  • a host cell may be a host cell that is suitable for culture in liquid or on solid media.
  • a host cell is preferably used in a method for producing a polypeptide of the invention as defined above or in a method for identification of a substance as defined herein.
  • Said method may comprise the step of culturing a host cell under conditions conducive to the expression of said polypeptide.
  • the method may comprise recovery of said polypeptide.
  • a polypeptide may e.g. be recovered from the culture medium by standard protein purification techniques, including a variety of chromatography methods known in the art per se.
  • a host cell is a cell that is part of a multi cellular organism such as a transgenic plant or animal, preferably a non-human animal.
  • a transgenic plant comprises in at least a part of its cells a vector as defined above. Methods for generating transgenic plants are e.g. described in U.S. 6,359,196 and in the references cited therein. Such transgenic plant or animal may be used in a method for producing a polypeptide of the invention as defined above and/or in a method for identification of a substance both as defined herein.
  • a preferred method comprises the step of recovering a part of a transgenic plant comprising in its cells the vector or a part of a descendant of such transgenic plant, whereby the plant part contains said polypeptide, and, optionally recovery of said polypeptide from the plant part.
  • the transgenic animal comprises in its somatic and germ cells a vector as defined above.
  • the transgenic animal preferably is a non-human animal. Methods for generating transgenic animals are e.g. described in WO 01/57079 and in the references cited therein.
  • transgenic animals may be used in a method for producing a polypeptide of the invention as defined above, the method comprising the step of recovering a body fluid from a transgenic animal comprising the vector or a female descendant thereof, wherein the body fluid contains said polypeptide, and, optionally recovery of said polypeptide from said body fluid.
  • the body fluid containing the polypeptide preferably is blood or more preferably milk.
  • Another method for preparing a polypeptide is to employ an in vitro transcription/translation system.
  • DNA encoding a polypeptide is cloned into an expression vector as described supra.
  • the expression vector is then transcribed and translated in vitro.
  • the translation product can be used directly or first purified.
  • a polypeptide resulting from in vitro translation typically do not contain the post- translation modifications present on polypeptides synthesised in vivo, although due to the inherent presence of microsomes some post-translational modification may occur.
  • Methods for synthesis of polypeptides by in vitro translation are described by, for example, Berger & Kimmel, Methods in Enzymology, Volume 152, Guide to Molecular Cloning Techniques, Academic Press, Inc., San Diego, CA, 1987.
  • Some aspects of the invention concern the use of anucleic acid construct or expression vector comprising a nucleotide sequence as defined above, wherein the vector is a vector that is suitable for gene therapy.
  • Vectors that are suitable for gene therapy are described in Anderson 1998, Nature 392: 25-30; Walther and Stein, 2000, Drugs 60: 249-71; Kay et al, 2001, Nat. Med. 7: 33-40; Russell, 2000, J. Gen. Virol. 81: 2573-604; Amado and Chen, 1999, Science 285: 674-6; Federico, 1999, Curr. Opin. BiotechnoLlO: 448-53; Vigna and Naldini, 2000, J. Gene Med.
  • Particularly suitable gene therapy vectors include Adenoviral and Adeno-associated virus (AAV) vectors. These vectors infect a wide number of dividing and non-dividing cell types including neuronal cells.
  • Adenoviral vectors are capable of high levels of transgene expression.
  • these viral vectors are most suited for therapeutic applications requiring only transient expression of the transgene (Russell, 2000, J. Gen. Virol. 81: 2573-2604; Goncalves, 2005, Virol J. 2(1):43) as indicated above.
  • Preferred adenoviral vectors are modified to reduce the host response as reviewed by Russell (2000, supra).
  • AAV serotype 2 is an effective vector and therefore a preferred AAV serotype.
  • a preferred retroviral vector for application in the present invention is a lentiviral based expression construct. Lentiviral vectors have the unique ability to infect non- dividing cells (Amado and Chen, 1999 Science 285: 674-6).
  • gene therapy vectors will be as the expression vectors described above in the sense that they comprise a nucleotide sequence encoding a polypeptide of the invention to be expressed, whereby said nucleotide sequence is operably linked to the appropriate regulatory sequences as indicated above.
  • Such regulatory sequence will at least comprise a promoter sequence.
  • Suitable promoters for expression of a nucleotide sequence encoding said polypeptide from gene therapy vectors include e.g.
  • CMV cytomegalovirus
  • LTRs viral long terminal repeat promoters
  • MMLV murine moloney leukaemia virus
  • HTLV-I hematoma virus
  • SV 40 simian virus 40
  • herpes simplex virus thymidine kinase promoter Suitable promoters are described below.
  • inducible promoter systems have been described that may be induced by the administration of small organic or inorganic compounds.
  • Such inducible promoters include those controlled by heavy metals, such as the metallothionine promoter (Brinster et al. 1982 Nature 296: 39-42; Mayo et al. 1982 Cell 29: 99-108), RU-486 (a progesterone antagonist) (Wang et al. 1994 Proc. Natl. Acad. Sci. USA 9]_: 8180-8184), steroids (Mader and White, 1993 Proc. Natl. Acad. Sci. USA 90: 5603-5607), tetracycline (Gossen and Bujard 1992 Proc. Natl. Acad. Sci.
  • tTAER system that is based on the multi-chimeric transactivator composed of a tetR polypeptide, as activation domain of VP 16, and a ligand binding domain of an estrogen receptor (Yee et al., 2002, US 6,432,705).
  • RNA polymerase III RNA polymerase III
  • the RNA polymerase III is responsible for the synthesis of a large variety of small nuclear and cytoplasmic non-coding RNAs including 5S, U6, adenovirus VAl, Vault, telomerase RNA, and tRNAs.
  • the promoter structures of a large number of genes encoding these RNAs have been determined and it has been found that RNA pol III promoters fall into three types of structures (for a review see Geiduschek and Tocchini- Valentini, 1988 Annu. Rev.
  • RNA pol III promoters Particularly suitable for expression of siRNAs are the type 3 of the RNA pol III promoters, whereby transcription is driven by cis-acting elements found only in the 5'-flanking region, i.e. upstream of the transcription start site.
  • Upstream sequence elements include a traditional TATA box (Mattaj et al, 1988 Cell 55, 435-442), proximal sequence element and a distal sequence element (DSE; Gupta and Reddy, 1991 Nucleic Acids Res. 19, 2073-2075).
  • U6 small nuclear RNA U6 small nuclear RNA
  • 7SK 7SK
  • Y Y
  • MRP Hl
  • Hl telomerase RNA genes
  • the gene therapy vector may optionally comprise a second or one or more further nucleotide sequence coding for a second or further polypeptide.
  • the second or further polypeptide may be a (selectable) marker polypeptide that allows for the identification, selection and/or screening for cells containing the expression construct. Suitable marker proteins for this purpose are e.g.
  • the fluorescent protein GFP and the selectable marker genes HSV thymidine kinase (for selection on HAT medium), bacterial hygromycin B phosphotransferase (for selection on hygromycin B), Tn5 aminoglycoside phosphotransferase (for selection on G418), and dihydro folate reductase (DHFR) (for selection on methotrexate), CD20, the low affinity nerve growth factor gene.
  • HSV thymidine kinase for selection on HAT medium
  • bacterial hygromycin B phosphotransferase for selection on hygromycin B
  • Tn5 aminoglycoside phosphotransferase for selection on G418)
  • DHFR dihydro folate reductase
  • the second or further nucleotide sequence may encode a polypeptide that provides for fail-safe mechanism that allows to cure a subject from the transgenic cells, if deemed necessary.
  • a nucleotide sequence often referred to as a suicide gene, encodes a polypeptide that is capable of converting a pro drug into a toxic substance that is capable of killing the transgenic cells in which said polypeptide is expressed.
  • Suitable examples of such suicide genes include e.g.
  • a gene therapy vector is preferably formulated in a pharmaceutical composition comprising a suitable pharmaceutical carrier as defined below.
  • RNA interference For knock down of expression of a specific polypeptide of the invention of the invention, a gene therapy vector or other expression construct is used for the expression of a desired nucleotide sequence that preferably encodes an RNAi agent, i.e. an RNA molecule that is capable of RNA interference or that is part of an RNA molecule that is capable of RNA interference.
  • RNA molecules are referred to as siRNA (short interfering RNA, including e.g. a short hairpin RNA).
  • the siRNA molecules may directly, e.g. in a pharmaceutical composition that is administered within or in the neighbourhood of a human and/or tumour and/or mammary cell.
  • a desired nucleotide sequence comprises an antisense code DNA coding for the antisense RNA directed against a region of the target gene mRNA, and/or a sense code DNA coding for the sense RNA directed against the same region of the target gene mRNA.
  • the antisense and sense code DNAs are operably linked to one or more promoters as herein defined above that are capable of expressing the antisense and sense RNAs, respectively.
  • siRNA means a small interfering RNA that is a short-length double-stranded RNA that are not toxic in mammalian cells (Elbashir et al, 2001, Nature 41J_: 494-98; Caplen et al, 2001, Proc. Natl.
  • siRNAs can be, e.g. at least 15, 18 or 21 nucleotides and up to 25, 30, 35 or 49 nucleotides long.
  • the double-stranded RNA portion of a final transcription product of siRNA to be expressed can be, e.g. at least 15, 18 or 21 nucleotides and up to 25, 30, 35 or 49 nucleotides long.
  • Antisense RNA is an RNA strand having a sequence complementary to a target gene mRNA, and thought to induce RNAi by binding to the target gene mRNA.
  • Sense RNA has a sequence complementary to the antisense RNA, and annealed to its complementary antisense RNA to form siRNA.
  • target gene in this context refers to a gene whose expression is to be silenced due to siRNA to be expressed by the present system, and can be arbitrarily selected. As this target gene, for example, genes whose sequences are known but whose functions remain to be elucidated, and genes whose expressions are thought to be causative of diseases are preferably selected.
  • a target gene may be one whose genome sequence has not been fully elucidated, as long as a partial sequence of mRNA of the gene having at least 15 nucleotides or more, which is a length capable of binding to one of the strands (antisense RNA strand) of siRNA, has been determined. Therefore, genes, expressed sequence tags (ESTs) and portions of mRNA, of which some sequence (preferably at least 15 nucleotides) has been elucidated, may be selected as the "target gene” even if their full length sequences have not been determined.
  • ESTs expressed sequence tags
  • the double-stranded RNA portions of siRNAs in which two RNA strands pair up are not limited to the completely paired ones, and may contain non pairing portions due to mismatch (the corresponding nucleotides are not complementary), bulge (lacking in the corresponding complementary nucleotide on one strand), and the like. Non pairing portions can be contained to the extent that they do not interfere with siRNA formation.
  • the "bulge” used herein preferably comprise 1 to 2 non pairing nucleotides, and the double-stranded RNA region of siRNAs in which two RNA strands pair up contains preferably 1 to 7, more preferably 1 to 5 bulges.
  • the "mismatch" used herein is contained in the double-stranded RNA region of siRNAs in which two RNA strands pair up, preferably 1 to 7, more preferably 1 to 5, in number.
  • one of the nucleotides is guanine, and the other is uracil.
  • Such a mismatch is due to a mutation from C to T, G to A, or mixtures thereof in DNA coding for sense RNA, but not particularly limited to them.
  • the double-stranded RNA region of siRNAs in which two RNA strands pair up may contain both bulge and mismatched, which sum up to, preferably 1 to 7, more preferably 1 to 5 in number.
  • Such non pairing portions can suppress the below-described recombination between antisense and sense code DNAs and make the siRNA expression system as described below stable. Furthermore, although it is difficult to sequence stem loop DNA containing no non pairing portion in the double-stranded RNA region of siRNAs in which two RNA strands pair up, the sequencing is enabled by introducing mismatches or bulges as described above. Moreover, siRNAs containing mismatches or bulges in the pairing double-stranded RNA region have the advantage of being stable in E. coli or animal cells.
  • the terminal structure of siRNA may be either blunt or cohesive (overhanging) as long as siRNA enables to silence the target gene expression due to its RNAi effect.
  • the cohesive (overhanging) end structure is not limited only to the 3' overhang, and the 5' overhanging structure may be included as long as it is capable of inducing the RNAi effect.
  • the number of overhanging nucleotide is not limited to the already reported 2 or 3, but can be any numbers as long as the overhang is capable of inducing the RNAi effect.
  • the overhang consists of 1 to 8, preferably 2 to 4 nucleotides.
  • the total length of siRNA having cohesive end structure is expressed as the sum of the length of the paired double-stranded portion and that of a pair comprising overhanging single-strands at both ends. For example, in the case of 19 bp double-stranded RNA portion with 4 nucleotide overhangs at both ends, the total length is expressed as 23 bp. Furthermore, since this overhanging sequence has low specificity to a target gene, it is not necessarily complementary (antisense) or identical (sense) to the target gene sequence.
  • siRNA may contain a low molecular weight RNA (which may be a natural RNA molecule such as tRNA, rRNA or viral RNA, or an artificial RNA molecule), for example, in the overhanging portion at its one end.
  • RNA which may be a natural RNA molecule such as tRNA, rRNA or viral RNA, or an artificial RNA molecule
  • the terminal structure of the "siRNA” is necessarily the cut off structure at both ends as described above, and may have a stem-loop structure in which ends of one side of double-stranded RNA are connected by a linker RNA (a "shRNA").
  • the length of the double-stranded RNA region can be, e.g. at least 15, 18 or 21 nucleotides and up to 25, 30, 35 or 49 nucleotides long.
  • the length of the double-stranded RNA region that is a final transcription product of siRNAs to be expressed is, e.g. at least 15, 18 or 21 nucleotides and up to 25, 30, 35 or 49 nucleotides long.
  • the linker portion may have a clover- leaf tRNA structure.
  • the linker portion may include introns so that the introns are excised during processing of precursor RNA into mature RNA, thereby allowing pairing of the stem portion.
  • either end (head or tail) of RNA with no loop structure may have a low molecular weight RNA.
  • this low molecular weight RNA may be a natural RNA molecule such as tRNA, rRNA, snRNA or viral RNA, or an artificial RNA molecule.
  • a DNA construct of the present invention comprise a promoter as defined above. The number and the location of the promoter in the construct can in principle be arbitrarily selected as long as it is capable of expressing antisense and sense code DNAs.
  • a tandem expression system can be formed, in which a promoter is located upstream of both antisense and sense code DNAs. This tandem expression system is capable of producing siRNAs having the aforementioned cut off structure on both ends.
  • stem-loop siRNA expression system antisense and sense code DNAs are arranged in the opposite direction, and these DNAs are connected via a linker DNA to construct a unit.
  • a promoter is linked to one side of this unit to construct a stem- loop siRNA expression system.
  • the linker DNA there is no particular limitation in the length and sequence of the linker DNA, which may have any length and sequence as long as its sequence is not the termination sequence, and its length and sequence do not hinder the stem portion pairing during the mature RNA production as described above.
  • DNA coding for the above-mentioned tRNA and such can be used as a linker DNA.
  • the 5' end may be have a sequence capable of promoting the transcription from the promoter. More specifically, in the case of tandem siRNA, the efficiency of siRNA production may be improved by adding a sequence capable of promoting the transcription from the promoters at the 5' ends of antisense and sense code DNAs. In the case of stem-loop siRNA, such a sequence can be added at the 5' end of the above-described unit. A transcript from such a sequence may be used in a state of being attached to siRNA as long as the target gene silencing by siRNA is not hindered.
  • the antisense and sense RNAs may be expressed in the same vector or in different vectors.
  • a terminator of transcription may be a sequence of four or more consecutive adenine (A) nucleotides.
  • Some aspects of the invention concern the use of an antibody or antibody- fragment that specifically binds to a polypeptide of the invention as defined above.
  • Methods for generating antibodies or antibody- fragments that specifically bind to a given polypeptide are described in e.g. Harlow and Lane (1988, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY) and WO 91/19818; WO 91/18989; WO 92/01047; WO 92/06204; WO 92/18619; and US 6,420,113 and references cited therein.
  • the term "specific binding,” as used herein, includes both low and high affinity specific binding.
  • Specific binding can be exhibited, e.g., by a low affinity antibody or antibody-fragment having a Kd of at least about 10 "4 M. Specific binding also can be exhibited by a high affinity antibody or antibody- fragment, for example, an antibody or antibody- fragment having a Kd of at least about of 10 "7 M, at least about 10 "8 M, at least about 10 "9 M, at least about 10 "10 M, or can have a Kd of at least about 10 "11 M or 10 "12 M or greater.
  • Peptide-like molecules referred to as peptidomimetics
  • non-peptide molecules that specifically bind to a polypeptide of the invention or to its receptor polypeptide and that may be applied in any of the methods of the invention as defined herein (for example for altering the activity or steady state level of a polypeptide of the invention) as an agonist or antagonist of a polypeptide of the invention and they may be identified using methods known in the art per se, as e.g. described in detail in US 6,180,084 which incorporated herein by reference. Such methods include e.g. screening libraries of peptidomimetics, peptides, DNA or cDNA expression libraries, combinatorial chemistry and, particularly useful, phage display libraries. These libraries may be screened for an agonist or antagonist of a polypeptide by contacting the libraries with a substantially purified polypeptide of the invention, a fragment thereof or a structural analogue thereof.
  • the invention further relates to a pharmaceutical preparation
  • a pharmaceutical preparation comprising as active ingredient an ingredient selected from the group consisting of: a polypeptide, a nucleic acid, a nucleic acid construct, a gene therapy vector and an antibody. All these ingredients were already defined herein.
  • Said preparation or composition preferably comprises at least one pharmaceutically acceptable carrier in addition to an active ingredient.
  • a polypeptide or antibody of the invention as purified from mammalian, insect or microbial cell cultures, from milk of transgenic mammals or other source is administered in purified form together with a pharmaceutical carrier as a pharmaceutical composition.
  • a pharmaceutical carrier as a pharmaceutical composition.
  • a pharmaceutical carrier can be any compatible, non-toxic substance suitable to deliver a polypeptide, antibody or gene therapy vector to a patient.
  • Sterile water, alcohol, fats, waxes, and inert solids may be used as a carrier.
  • a pharmaceutically acceptable adjuvant, buffering agent, dispersing agent, and the like, may also be incorporated into a pharmaceutical composition.
  • concentration of a polypeptide or antibody o f the invention in a pharmaceutical composition can vary widely, i.e., from less than about 0.1% by weight, usually being at least about 1% by weight to as much as 20% by weight or more.
  • an active ingredient can be administered in solid dosage forms, such as capsules, tablets, and powders, or in liquid dosage forms, such as elixirs, syrups, and suspensions.
  • An active component or ingredient can be encapsulated in gelatin capsules together with an inactive ingredient and a powdered carrier, such as glucose, lactose, sucrose, mannitol, starch, cellulose or cellulose derivatives, magnesium stearate, stearic acid, sodium saccharin, talcum, magnesium carbonate and the like.
  • inactive ingredients examples include red iron oxide, silica gel, sodium lauryl sulfate, titanium dioxide, edible white ink and the like.
  • Similar diluents can be used to make compressed tablets. Both tablets and capsules can be manufactured as sustained release products to provide for continuous release of medication over a period of hours. Compressed tablets can be sugar coated or film coated to mask any unpleasant taste and protect the tablet from the atmosphere, or enteric-coated for selective disintegration in the gastrointestinal tract.
  • Liquid dosage forms for oral administration can contain colouring and flavouring to increase patient acceptance.
  • a polypeptide, antibody or nucleic acid construct or gene therapy vector is preferably administered parentally or systemically.
  • a polypeptide, antibody, nucleic acid construct or vector for preparations must be sterile. Sterilisation is readily accomplished by filtration through sterile filtration membranes, prior to or following lyophilisation and reconstitution.
  • One preferred route of administration is systemic, more preferably orally.
  • Another preferred route is a parental route for administration of A polypeptide, antibody nucleic acid construct or vector is in accord with known methods, e.g. injection or infusion by subcutaneous, intravenous, intraperitoneal, intramuscular, intraarterial, intralesional, intracranial, intrathecal, transdermal, nasal, buccal, rectal, or vaginal routes.
  • the route for administration is intravenous or subcutaneous.
  • a polypeptide, antibody nucleic acid construct or vector is administered continuously by infusion or by bolus injection.
  • a typical composition for intravenous infusion could be made up to contain 10 to 50 ml of sterile 0.9% NaCl or 5% glucose optionally supplemented with a 20% albumin solution and 1 to 50 ⁇ g of the polypeptide, antibody nucleic acid construct or vector.
  • a typical pharmaceutical composition for intramuscular injection would be made up to contain, for example, 1 - 10 ml of sterile buffered water and 1 to 100 ⁇ g of a polypeptide, antibody, nucleic acid construct or vector of the invention.
  • a pharmaceutical composition is preferably administered to a cancer patient as earlier defined herein in an amount sufficient to reduce the severity of symptoms and/or prevent or arrest further development of symptoms.
  • An amount adequate to accomplish this is defined as a "therapeutically-" or “prophylactically-effective dose”.
  • Such effective dosages will depend on the severity of the condition and on the general state of the patient's health.
  • a therapeutically- or prophylactically-effective dose preferably is a dose, which is sufficient to reverse the symptoms, i.e. to prevent, delay and/or treat metastasis as earlier defined herein.
  • a polypeptide or antibody is usually administered at a dosage of about 1 ⁇ g/kg subject body weight or more per week to a subject. Often dosages are greater than 10 ⁇ g/kg per week. Dosage regimes can range from 10 ⁇ g/kg per week to at least 1 mg/kg per week.
  • dosage regimes are 10 ⁇ g/kg per week, 20 ⁇ g/kg per week, 30 ⁇ g/kg per week, 40 ⁇ g/kg week, 60 ⁇ g/kg week, 80 ⁇ g/kg per week and 120 ⁇ g/kg per week.
  • 10 ⁇ g/kg, 20 ⁇ g/kg or 40 ⁇ g/kg is administered once, twice or three times weekly. Treatment is preferably administered by parenteral route.
  • the verb "to comprise” and its conjugations is used in its non-limiting sense to mean that items following the word are included, but items not specifically mentioned are not excluded.
  • the verb "to consist” may be replaced by "to consist essentially of meaning that a polypeptide or a nucleic acid construct or an antibody or a composition as defined herein may comprise additional component(s) than the ones specifically identified, said additional component(s) not altering the unique characteristic of the invention.
  • reference to an element by the indefinite article “a” or “an” does not exclude the possibility that more than one of the element is present, unless the context clearly requires that there be one and only one of the elements.
  • the indefinite article “a” or “an” thus usually means “at least one”.
  • Fral is upregulated upon oncogenic transformation of non-malignant rat epithelial cells
  • a Phase contrast micrographs of RK3E and RIE rat epithelial cells expressing ligand-activated TrkB or empty vector
  • b Microarray analysis of TrkB- expressing RK3E and RIE cells. The top 10 genes up- or down-regulated in both cell systems are shown,
  • d Gel shift analysis measuring AP-I DNA-binding activity (first 2 left lanes).
  • FIG. 1 Silencing of Fral abolishes distant metastasis in vivo.
  • a Representative images of pulmonary metastases in mice carrying subcutaneous control or Fral- silenced TrkB-expressing RK3E tumors, at 3 weeks post-inoculation,
  • b Macroscopic quantification of pulmonary metastases described in a.
  • c Haematoxylin-eosin staining of histological lung sections described in a.
  • d Microscopic quantification of pulmonary metastases. The total number of metastases in 8 independent sections per mouse is indicated, representative of three independent experiments.
  • FIG. 4 Fral depletion strongly suppresses EMT and metastatic potential of human breast cancer cells
  • a Bright-field and fluorescence images of the lungs of mice that were injected with LM2 human breast cancer cells expressing independent Fral shRNAs as indicated, photographed at 35 days after inoculation
  • c Phase contrast micrographs of LM2 cells expressing shRNAs as indicated
  • d. Phalloidin staining visualizing the cytoskeleton of control and Fral -silenced LM2 cells, e. Migration properties of LM2 cells as a function of Fral depletion (n 3, error bars: S. D.).
  • f Fral depletion strongly suppresses EMT and metastatic potential of human breast cancer cells
  • a Bright-field and fluorescence images of the lungs of mice that were injected with LM2 human breast cancer cells expressing independent Fral shRNAs as indicated
  • DMFS Distant metastasis- free survival
  • Figure 10. Generation of a human function-associated Fral classifier predictive of clinical outcome of breast cancer. Distant metastasis- free survival (DMFS) of breast cancer patients from the mentioned data sets that expressed (red line) or not (blue line) the human Fral classifier. The human Fral classifier was derived from the expression profile of LM2 cells silenced or not for Fral. For comparison, the DMFS of breast cancer patients stratified using the Fral classifier derived from rat data is displayed (shaded bottom right panel).
  • DMFS Distant metastasis- free survival
  • Fral is overexpressed in numerous human cancer cell lines (Milde-Langosch 2005), notably those of mammary origin (Belguise et al., 2005) ( Figure 8). Accordingly, Fral is often overexpressed in breast cancer and a weakly significant association between Fral expression levels and nodal involvement was previously reported (Milde-Langosch et al., 2004).
  • Fral is required for human breast cancer cell metastasis, we silenced Fral using lentiviral vectors encoding two independent shRNAs in LM2 cells, which correspond to human breast cancer cells that display a high metastatic tropism to the lungs and are highly metastatic in nude mice (Massague et al., 2005).
  • Fral is a transcription factor
  • the changes it induces in the transcriptome of cancer cells should comprise genetic markers or genes causally implicated in metastasis. We thus predicted that the expression levels of such genes would have prognostic value in cancer patients.
  • the often >100 genetic alterations commonly seen in human cancer cell systems generate such a complex genetic environment that it precludes extracting a robust genetic predictive classifier.
  • rat RK3E epithelial cells that we have previously shown to represent a genetically simple and straightforward cell system that relies on the expression of a ligand-activated TrkB gene for its oncogenic and metastatic capacity in nude mice.
  • This signature derived from rat data was then humanised by identifying the human orthologs of the rat genes.
  • TFBS transcription factor binding site enrichment analysis
  • the genes of the rat Fral signature that showed prognostic value in a set of 613 breast cancer patients were used to generate the Fral classifier (see Figure 5a for a description of the procedure).
  • the difference in distant metastasis-free survival between good and poor prognosis groups as classified by the Fral classifier was highly significant in all three series.
  • the hazard ratio of poor versus good prognosis groups as determined by the Fral classifier was also elevated in all three series (Table 2).
  • the Fral classifier was particularly potent in predicting outcome within the 5 first years following diagnosis.
  • the Kaplan-Meier curve obtained for the Fral classifier was very similar to the one obtained with the Mammaprint® classifier (Van't Veer et al, 2002, Nature;415:530-536; Figure 5c).
  • a performance analysis showed a sensitivity of 74%, a specificity of 62%, a positive predictive value of 50% and a negative predictive value of 82% (84%, 51%, 47%, 86% for the Mammaprint classifier respectively), showing that the Fral classifier performs as good as the Mammaprint.
  • LM2 cells were derived from a breast cancer cell line containing multiple complex genetic alterations which might interfere with normal Fral function and therefore "blur" the Fral signature.
  • the rat cell system was derived directly from non malignant cells that owed their oncogenic and metastatic actions to only a single and defined oncogenic event. This, therefore, emphasizes the value of the unique approach that we used: extract a genetic classifier from a relatively simple cancer cell system and impose that onto genetically much more complex human cancers.
  • the Fral classifier is the first that is based on a single transcription factor (Fral) with a direct link between its biological role (that is, its role in cancer cell metastasis) with its role in regulating the transcriptome. It thus denotes a functional link (whether being directly or indirectly) between Fral , its downstream effector genes and disease outcome. This is in contrast to currently used signatures, which represent merely a list of biomarkers that were generated by bio informatics approaches.
  • RIE and RK3E cells were transduced with human TrkB and BDNF expression constructs as previously described (Geiger et al, 2007).
  • the pRetroSuper and HlP vectors were used as previously described (Brummelkamp et al., 2002; Ivanova et al., 2006).
  • Anti-Fral, ⁇ -catenin, ⁇ -catenin, smooth-muscle actin and vimentin antibodies were from Santa Cruz, anti-E-cadherin N-cadherin and ⁇ -tubulin antibodies were from Becton Dickinson.
  • RIE cells (a kind gift from a kind gift from R.D. Beauchamp, Surgical Oncology Research Laboratories, Vanderbilt University Medical Center, Arlington, TN, and K.D. Brown, Signalling Programme, The Babraham Institute, Cambridge, United Kingdom), RK3E cells (ATCC #CRL-1895), MDA-MB-231 (a kind gift from Dr L. Smit, Department of Molecular Carcinogenesis, the Netherlands Cancer Institute, Asterdam, the Netherlands), LM2 cells (subline#4173, a kind gift from Prof. Dr. J.
  • cells were seeded at 3.10 5 (RK3E) or 1.10 6 (LM2 and MDA231) per 100-mm dish. For each cell line, cells from three dishes were trypsinized and counted every two days.
  • Retroviral transductions were performed using Phoenix cells as producers of viral supernatants as described previously Retroviral silencing of Fral in RK3E cells was performed using the pRS-puro vector with the following targeting sequences: Sh-Fral-1 (TAACTAGCCTAGAACACTA) and Sh- Fral -2 (GAAGTTCC ACCTTGTGCC A). As negative control, pRS-puro without insert was used.
  • RK3E cells were infected 4 times with viral supernatant and selected for puromycin resistance.
  • the RK3E Fral KD and control clones were generated by seeding 100 transduced cells per 100-mm dish, picking up clonal colonies and analyzing them for Fral expression levels by western-blotting.
  • Lentiviral transductions were performed using 293 T cells as producers of viral supernatants as described previously (Ivanova et al., 2006). Lentiviral silencing of Fral in LM2 and MDA-MB-231 cells was performed using the HlP vector with the following targeting sequences: Sh-Fral-1 (GTAGATCCTTAGAGGTCCT) and Sh- Fral-2 (GGCCTGTGCTTGAACCTGA). As negative control, HlP without insert was used. Cells were infected once (2.10 6 cells with 15.10 6 viral particles) and GFP -positive cells were selected by fluorescence activated cell sorting.
  • tumour cells In vivo injections of tumour cells
  • mice Female Balb/c nude mice aged 6-8 weeks were used for all xenografting experiments.
  • RK3E clones were injected sub-cutaneously (10 5 viable cells in 150 ⁇ l PBS in both flanks). Tumour width (W) and length (L) was measured twice a week using a calliper and tumour volume was estimated using the formula (L. W 12). Mice were sacrificed when the length tumour reached a size of 15 mm or when the tumours started to ulcerate.
  • LM2 cells were injected in the lateral tail vein (10 6 viable cells in 150 ⁇ l PBS). All animals were sacrificed one month after injection.
  • mice were killed using CO 2 asphyxiation, entire lungs were removed and dissected into left and right lungs.
  • Left lobes were fixed in formaldehyde and imaged within 2 hours under bright-field and fluorescence microscopy (LM2 cells).
  • Right lobes were fixed and contrasted in EAF and examined under a stereoscope (RK3E and LM2 cells).
  • Macroscopic lung metastases were identified as aberrant white masses on the surface of the lungs. For histological assessment of metastases, 8 sections from independent positions in the lungs were stained with hemoatoxylin-eosin. The number of metastases per section was summed over the different sections of the same lungs.
  • RNA from two independent experiments was isolated, purified and amplified.
  • Amplified (a)RNA was subsequently labeled either with Cy5 or Cy3.
  • Labeled aRNA was hybridized to oligo-arrays (Operon v3 library for human samples, Agilent 4x whole genome arrays for rat samples) and a dye-swap was performed for each experimental sample. The raw data are presented in Supplemental Data. Classifier generation
  • Chip pseudo-images were produced to assess artefacts on arrays that didn't pass the preceding quality control tests.
  • Selected arrays were normalized according to a three step procedure using the RMA expression measure algorithm (www.bioconductor.org): RMA background correction convolution, median centering of each gene across arrays separately for each data set and quantile normalization of all arrays.
  • RMA expression measure algorithm www.bioconductor.org
  • the experimental Fral signature was derived from the microarray analysis of FralKD clones versus control cells. Probes that were significantly regulated in both FralKD clones were considered as part of the rat signature. They were converted to their corresponding Ensembl gene IDs using Martview from BioMart Still using Martview, the human homologues of the rat genes were identified and matched to their corresponding probes on Affymetrix Ul 33 A arrays. Out of this humanized probe set, probes were extracted that exhibited a significant logrank test p value (p ⁇ 0.05) in the 613 samples. Then, we defined a k- means classifier. The 'poor prognosis' centroid was derived from the samples with a metastatic event before 60 months of follow-up.
  • the 'good prognosis' centroid was derived from the samples with no metastatic event and a follow-up longer than 60 months.
  • the humanized probe set multiple probes fitting with the same Entrez IDs, we selected a single Affymetrix ⁇ HGU- 133 A probe for each Entrez ID in the following manner. First, probes were favoured based on the Affymetrix algorithm probe extension (favoring ' at' over '_x_at' over ' s at'). Second, when multiple probes with the same extension mapped to the same Entrez ID, we selected the one with the highest absolute difference between the corresponding value of the metastatic centroid and the non metastatic centroid. The resulting 76 probes constituted the human Fral classifier.
  • the human Fral classifier was generated using the same procedure, from an experimental Fral signature derived from microarray analysis of LM2 cells (subclone 4173) expressing two independent knock-down constructs for Fral versus control LM2 cells. Only the human homology search was not performed as the array was directly performed on human cells.
  • Each sample in the independent validation set was assigned to the nearest centroid as determined by the highest Spearman rank order correlation score between the gene expression value of the corresponding probe sets of each sample and the centroid values of the 'poor prognosis' and 'good prognosis' centroid.
  • TFBS Transcription Factor Binding Site motif
  • Hu Z. et al The molecular portraits of breast tumors are conserved across microarray platforms, BMC Genomics, (2006), 7:96, published on http://www.biomedcentral.com/1471 -2164/7/96. Lenhard, B. & Wasserman, W. W. TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics. 2002;18: 1135-1136.

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Abstract

Cette invention concerne une méthode ex vivo de pronostic des métastases chez un patient cancéreux comprenant l’identification d’une modulation différentielle d’un gène (par rapport à l’expression d’un même gène chez un témoin) dans une association de gènes sélectionnés dans les groupes constitués par des gènes représentés par les séquences suivantes SEQ ID NO:1-76 et/ou SEQ ID NO:77-108. L’invention concerne également l’utilisation de l’une des séquences suivantes choisies parmi les groupes suivants SEQ ID NO:1-76 et/ou SEQ ID NO:77- 108 en tant que médicament, de préférence pour prévenir, retarder et/ou traiter les métastases chez un patient cancéreux.
PCT/NL2009/050125 2008-03-17 2009-03-16 Marqueurs utilisés dans le pronostic de métastases chez les patients cancéreux WO2009116860A1 (fr)

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JP2013505232A (ja) * 2009-09-16 2013-02-14 スティヒティング ヘット ネーデルラント カンカー インスティテュート 癌治療のための薬剤標的としてのＦｒａ−１標的遺伝子
US8802826B2 (en) 2009-11-24 2014-08-12 Alethia Biotherapeutics Inc. Anti-clusterin antibodies and antigen binding fragments and their use to reduce tumor volume
US9512211B2 (en) 2009-11-24 2016-12-06 Alethia Biotherapeutics Inc. Anti-clusterin antibodies and antigen binding fragments and their use to reduce tumor volume
US9822170B2 (en) 2012-02-22 2017-11-21 Alethia Biotherapeutics Inc. Co-use of a clusterin inhibitor with an EGFR inhibitor to treat cancer
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