WO2012114189A1 - Méthode pour prédire la survie d'un patient porteur d'un glioblastome à l'aide d'une signature de dix miarn - Google Patents

Méthode pour prédire la survie d'un patient porteur d'un glioblastome à l'aide d'une signature de dix miarn Download PDF

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WO2012114189A1
WO2012114189A1 PCT/IB2012/000312 IB2012000312W WO2012114189A1 WO 2012114189 A1 WO2012114189 A1 WO 2012114189A1 IB 2012000312 W IB2012000312 W IB 2012000312W WO 2012114189 A1 WO2012114189 A1 WO 2012114189A1
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mir
hsa
expression
glioblastoma
survival
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Kumaravel Somasundaram
Sujaya Srinivasan
Irene Rosita Pia PATRIC
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Indian Institute of Science IISC
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • 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
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/178—Oligonucleotides characterized by their use miRNA, siRNA or ncRNA

Definitions

  • the present invention relates to the field of cancer in particular to the method of predicting survival of glioblastoma patient using a ten-miRNA signature.
  • the grade IV astrocytoma Glioblastoma
  • Glioblastoma is the most common and malignant primary adult brain cancer (Furnari FB, Fenton T, Bachoo RM, Mukasa A, Stommel JM, et al. (2007) Malignant astrocytic glioma: genetics, biology, and paths to treatment. Genes Dev 21 : 2683- 2710).
  • the median survival is very poor. Since postoperative radiotherapy alone did not provide great benefit to GBM patients, several attempts have been made to find suitable adjuvant chemotherapy.
  • the present standard treatment appears to be maximal safe resection of the tumor followed by irradiation and temozolomide adjuvant chemotherapy.
  • MicroRNAs are endogenous non-coding small RNAs, which negatively regulate gene expression either by binding to the 3'UTR leading to inhibition of translation or degradation of specific mRNA. Since miRNAs can act as Oncogenes or tumor suppressor genes, they have been linked to a variety of cancers (Yue J, Tigyi G (2006) MicroRNA trafficking and human cancer. Cancer Biol Ther 5: 573-578). It has been shown that classification of multiple cancers based on miRNA expression signatures is more accurate than mRNA based signatures (Lu J, Getz G, Miska EA, Alvarez- Saavedra E, Lamb J, et al. (2005) MicroRNA expression profiles classify human cancers. Nature 435: 834-838).
  • Rao et al. profiled the expression of 756 miRNAs using 39 malignant astrocytoma and 7 normal brain samples and identified a 23-miRNA expression signatures which can discriminate anaplastic astrocytoma from glioblastoma.
  • Other studies investigated the target identification and functional characterization of specific miRNAs (Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee. DH, et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR.
  • microRNA-7 inhibits the epidermal growth factor receptor and the Akt pathway and is down-regulated in glioblastoma. Cancer Res 68: 3566-3572; Li Y, Guessous F, Zhang Y, Dipierro C, Kefas B, et al. (2009) MicroRNA-34a inhibits glioblastoma growth by targeting multiple oncogenes.
  • a diagnostic assay that would allow identifying high-risk patients at an earlier time point and thus improving the outcomes in patients treated with advanced glioblastoma therapeutics would be of great utility.
  • a diagnostic assay that would allow identifying high-risk patients at an earlier time point and thus improving the outcomes in patients treated with advanced glioblastoma therapeutics would be of great utility.
  • One aspect of the present invention relates to a process of determining survival prognosis in a subject with glioblastoma, wherein the process comprises measuring the level of miRNAs hsa-miR-20a, hsa-miR-106a, hsa-miR-17-5p, hsa-miR-31, hsa-miR-222, hsa-miR-148a, hsa- miR-221, hsa-miR- 146b, hsa-miR-200b and hsa-miR-193a in a biological sample, calculating a risk score of the biological sample using, wherein the risk score is calculated as (-0.39 x expression of hsa-mir-20a) + (-0.41 x expression of hsa-mir-106a) + (-0.39 x expression of hsa-mir-17-5p) + (0.28 x expression of hsa-mir
  • Another aspect of the present invention provides a process of determining survival prognosis in a subject with glioblastoma, wherein the process comprises determining expression level of miRNAs hsa-miR-20a, hsa-miR-106a, hsa-miR-17-5p, hsa-miR-31 , hsa- miR-222, hsa-miR-148a, hsa-miR-221 , hsa-miR-146b, hsa-miR-200b and hsa-miR-193a in a sample from a subject with 1 glioblastoma; and comparing the expression level of the miRNAs to the expression level of the miRNAs in a reference set of samples obtained from subjects with glioblastoma to determine prognosis, wherein increased expression level of hsa-miR-20a, hsa-miR-106a, h
  • kits for determining survival prognosis in a subject with glioblastoma comprising polynucleotides for analysis of miRNAs hsa-miR-20a, hsa-miR-106a, hsa-miR-17-5p, hsa-miR-31, hsa-miR-222, hsa-miR- 148a, hsa-miR-221 , hsa-miR-146b, hsa-miR-200b and hsa-miR-193a.
  • Yet another aspect of the present invention relates to a microarray card for determining survival prognosis in a subject with glioblastoma, wherein the microarray comprises hsa-miR- 20a, hsa-miR-106a, hsa-miR-17-5p, hsa-miR-31 , hsa-miR-222, hsa-miR-148a, hsa-miR-221 , hsa-miR-146b, hsa-miR-200b and hsa-miR-193a specific probe oligonucleotides.
  • Figure 1 shows Kaplan-Meier survival estimates overall survival of glioblastoma patients according to the 10 miRNA expression signature
  • Figure 2 shows ten miRNA Risk-Score Analysis of 1 1 1 GBM patients (training set)
  • the blue line represents the miRNA signature cutoff dividing patients into low-risk and high-risk groups
  • Figure 3 shows ten miRNA Risk-Score Analysis of 1 1 1 GBM patients (test set)
  • Figure 4 shows comparison of overall survival of low risk group vs. high risk group throughout the study period in the training, the testing, and the entire patient sets
  • sample or “biological sample” is any biological material obtained from an individual.
  • it may be a blood sample or ant tissue sample obtained by biopsy.
  • microRNA and “miRNA” used herein can be used interchangeably.
  • composition of the invention may be used in any method of the invention, and any method of the invention may be used to produce or to utilize any composition of the invention.
  • the present invention provides an assay or method to assess the prognosis in individual patients suffering form Glioblastoma (GBM), wherein the patient is under treatment selected from a group consisting of radiotherapy, chemotherapy, surgery, and combination thereof.
  • the assay disclosed in the present invention is based on analyzing expression of specific microRNA by performing microRNA profiling of the patient.
  • the present invention in particular discloses an assay for predicting the survival of patients suffering form Glioblastoma (GBM) using a ten mi-RNA signature.
  • the ten microRNA signature (Table 6) associated with Glioblastoma (GBM) as disclosed in the present invention are hsa-miR-20a (SEQ ID NO: 1), hsa-miR-106a (SEQ ID NO: 2), hsa-miR- 17-5p (SEQ ID NO: 3), hsa-miR-31(SEQ ID NO: 4), hsa-miR-222 (SEQ ID NO: 5), hsa-miR-148a (SEQ ID NO: 6), hsa-miR-221 (SEQ ID NO: 7), hsa-miR-146b (SEQ ID NO: 8), hsa-miR-200b (SEQ ID NO: 9), and hsa-miR-193a (SEQ ID NO: 10)
  • the ten microRNA signature as disclosed in the present invention can also be used to identify potential targets for GBM treatment, wherein the genes targeted by these micro-RNA can be identified using the methods known in the art. Further, the genes and its products can be used as potential target for treatment of GBM.
  • the expression level of the miRNAs can be determined using any process known in the art.
  • the process may involve any of a variety of techniques known to those of ordinary skill in the art. Examples of such techniques include reverse transcriptase (RT) PCR, PCR, allele specific oligonucleotide hybridization, size analysis, sequencing, hybridization, 5' nuclease digestion, single-stranded conformation polymorphism analysis, allele specific hybridization, primer specific extension, and oligonucleotide ligation assays.
  • RT reverse transcriptase
  • the sample can be any tissue sample obtained from the subject, such as but not limited to tumor sample obtained during surgery or biopsy.
  • the sample may be any tissue obtained by biopsy.
  • the expression level of the reference sample set can be obtained from a single subject or from a group of subjects.
  • the expression level of miRNA expression can be determined using any method known to those of ordinary skill in the art, such as any of the methods discussed above and elsewhere in this description.
  • the expression level is an average level of expression of hsa- miR-20a, hsa-miR-106a, hsa-miR-17-5p, hsa-miR-31 , hsa-miR-222, hsa-miR-148a, hsa-miR- 221, hsa-miR-146b, hsa-miR-200b and hsa-miR-193a obtained from a cohort of subjects with glioblastoma with a known poor outcome following a therapeutic intervention.
  • the reference level is an average level of expression of hsa- miR-20a, hsa-miR-106a, hsa-miR-17-5p, hsa-miR-31 , hsa-miR-222, hsa-miR-148a, hsa-miR- 221 , hsa-miR-146b, hsa-miR-200b and hsa-miR-193a obtained from a cohort of subjects with glioblastoma with a known good outcome following a therapeutic intervention.
  • Good outcome can be measured by any method known to those of ordinary skill in the art. For example, good outcome can be assessed as improvement in signs or symptoms of glioblastoma or prolonged survival compared to another cohort of subjects.
  • the expression level may be a single value of miRNA expression level, or it may be a range of values of miRNA expression level.
  • the expression level may also be depicted graphically as an area on a graph.
  • the formula for calculating the risk score is as provided below.
  • Risk score (-0.39 x expression of hsa-mir-20a) + (-0.41 x expression of hsa-mir- 106a) + (-0.39 x expression of hsa-mir-17-5p) + (0.28 x expression of hsa-mir-31) + (0.23 x expression of hsa-mir-222) + (0.19 x expression of hsa-mir-148a) + (0.24 x expression of hsa- mir-221) + (0.22 x expression of hsa-mir-146b) + (0.19 x expression of hsa-mir-200b) + (0.29 x expression of hsa-mir-193a).
  • a process to assess the prognosis in individual patients suffering form Glioblastoma comprises detecting expression levels of miRNAs hsa-miR-20a, hsa-miR-106a, hsa-miR-17-5p, hsa-miR-31 , hsa-miR-222, hsa-miR-148a, hsa-miR-221 , hsa-miR-146b, hsa- miR-200b and hsa-miR-193a in a sample obtained from the patient; calculating the risk score based on the expression of the said miRNAs and predicting survival of the patient based on the value of risk score, wherein the patient showing low risk score has greater chances of survival compared to the patient showing high risk score.
  • the process set forth herein further comprises obtaining a sample from the subject, the sample may be any sample as disclosed above, but in particular embodiment the sample is tumor samples obtained after surgery of glioblastoma patients.
  • a range of risk score wherein the risk score equal to or less than -0.7 of training set (reference samples set) indicates that the patient has a fair chance of survival.
  • a range of cut off value for risk score which is -1 1.38 to 2.33 for training set (reference samples set) and -6.45 to 1.82 for test set.
  • Still another embodiment of the present invention provides that the ten microRNA signature as disclosed in the present invention can predict GBM patient survival and other grades of glioma.
  • a process of determining survival prognosis in a subject with glioblastoma comprises measuring the level of miRNAs hsa-miR-20a, hsa-miR-106a, hsa-miR-17-5p, hsa-miR-31 , hsa-miR-222, hsa-miR-148a, hsa-miR-221 , hsa-miR-146b, hsa-miR-200b and hsa-miR-193a in a biological sample, calculating a risk score of the biological sample using, wherein the risk score is calculated as (-0.39 x expression of hsa-mir-20a) + (-0.41 x expression of hsa-mir-106a) + (- 0.39 x expression of hsa-mir-17-5p) + (0.28 x expression of hs
  • Another embodiment of the present invention there is provided a process of determining survival prognosis in a subject with glioblastoma, wherein the process comprises determining expression level of miRNAs hsa-miR-20a, hsa-miR-106a, hsa-miR-17-5p, hsa-miR-31, hsa- miR-222, hsa-miR-148a, hsa-miR-221, hsa-miR-146b, hsa-miR-200b and hsa-miR-193a in a sample from a subject with glioblastoma; and comparing the expression level of the miRNAs to the expression level of the miRNAs in a reference set of samples obtained from subjects with glioblastoma to determine prognosis, wherein increased expression level of hsa-miR-20a, hsa-miR- 106a, hs
  • kits for determining survival prognosis in a subject with glioblastoma comprising polynucleotides for analysis of microRNAs hsa-miR-20a, hsa-miR- 106a, hsa-miR-17-5p, hsa-miR-31, hsa-miR- 222, hsa-miR-148a, hsa-miR-221 , hsa-miR- 146b, hsa-miR-200b and hsa-miR-193a.
  • the kit as disclosed in the present invention further comprises a set of primers specific for transcription or reverse transcription of miRNAs hsa-miR-20a, hsa-miR- 106a, hsa-miR- 17-5p, hsa-miR-31 , hsa-miR-222, hsa-miR- 148a, hsa-miR-221, hsa-miR- 146b, hsa-miR-200b and hsa-miR- 193a.
  • the kit as disclosed in the present invention further comprises a miRNA array card, wherein the one or more polynucleotides are arrayed on said card.
  • microarray card for determining survival prognosis in a subject with glioblastoma
  • the microarray comprises hsa-miR- 20a, hsa-miR- 106a, hsa-miR- 17-5p, hsa-miR-31 , hsa-miR-222, hsa-miR- 148a, hsa-miR-221 , hsa-miR- 146b, hsa-miR-200b and hsa-miR- 193a specific probe oligonucleotides.
  • Some embodiments of the process of the present invention involve analysis of miRNA expression level or gene expression level.
  • Methods for analyzing gene expression or expression of miRNA include, but are not limited to, methods based on hybridization analysis of polynucleotides, sequencing of polynucleotides, and analysis of pratein expression such as proteomics-based methods.
  • Commonly used methods for the quantification of mRNA expression level in a sample include northern blotting and in situ hybridization, RNAse protection assays, and PCR-based methods, such as reverse transcription polymerase chain reaction (RT-PCR).
  • RT-PCR reverse transcription polymerase chain reaction
  • antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes.
  • SAGE Gene Expression Analysis
  • MPSS massively parallel signature sequencing
  • Gene expression level or miRNA expression level can be analyzed using techniques that employ PCR. PCR is useful to amplify and detect transcripts from a sample. Examples of
  • RT-PCR is a sensitive quantitative method that can be used to compare mRNA levels in different samples (e.g., endomyocardial biopsy samples) to examine gene expression signatures.
  • RNA is isolated from a sample.
  • total RNA may be isolated from a sample of heart tissue.
  • mRNA may also be extracted, for example, from frozen or archived paraffin-embedded and fixed tissue samples. Methods for mRNA extraction are known in the art.
  • RNA is then reverse transcribed into cDNA.
  • the cDNA is amplified in a PCR reaction.
  • a variety of reverse transcriptases are known in the art.
  • the reverse transcription step is typically primed using specific primers, random hexamers, or oligo-dT primers, depending on the conditions and desired readout.
  • extracted RNA can be reverse-transcribed using a GeneAmp RNA PCR kit, following the manufacturer's instructions.
  • the derived cDNA can then be used as a template in the subsequent PCR reaction.
  • the PCR reaction may employ the Taq DNA polymerase, which has a 5 '-3' nuclease activity but lacks a 3 '-5' proofreading endonuclease-activity.
  • Two oligonucleotide primers are used to generate an amplicon in the PCR reaction.
  • a third oligonucleotide, or probe is used to detect nucleotide sequence located between the two PCR primers.
  • the probe is non-extendible by Taq DNA polymerase enzyme, and typically is labeled with a reporter fluorescent dye and a quencher fluorescent dye.
  • any laser-induced emission from the reporter dye is quenched by the quenching dye when the two dyes are located close together as they are on the probe.
  • the Taq DNA polymerase enzyme cleaves the probe in a template- dependent manner.
  • the resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore.
  • One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative analysis.
  • RT-PCR can be performed using commercially available equipment.
  • RT-PCR is usually performed using an internal standard.
  • a suitable internal standard is expressed at a constant level among different tissues, and is unaffected by the experimental variable.
  • Microarrays permit simultaneous analysis of a large number of gene expression products.
  • polynucleotides of interest are plated, or arrayed, on a microchip substrate.
  • the arrayed sequences are then hybridized with nucleic acids (e.g., DNA or RNA) from cells or tissues of interest.
  • the source of mRNA typically is total RNA. If the source of mRNA is endomyocardial tissue, mRNA can be extracted.
  • probes to at least 10, 25, 50, 100, 200, 500, 1000, 1250, 1500, or 1600 polynucleotides are immobilized on an array substrate (for example, a porous or nonporous solid support, such as a glass, plastic, or gel surface).
  • the probes can include DNA, RNA, copolymer sequences of DNA and RNA, DNA and/or RNA analogues, or combinations thereof.
  • a microarray includes a support with an ordered array of binding (e.g., hybridization) sites for each individual polynucleotide of interest.
  • the microarrays can be addressable arrays, such as positionally addressable arrays where each probe of the array is located at a known, predetermined position on the solid support such that the identity of each probe can be determined from its position in the array.
  • Each probe on the microarray can be between about 10-50,000 nucleotides in length.
  • the probes of the microarray can consist of nucleotide sequences with lengths: less than 1,000 nucleotides, such as sequences 10-1 ,000, or 10-500, or 10-200 nucleotides in length.
  • An array can include positive control probes, such as probes known to be complementary and hybridizable to sequences in the test sample, and negative control probes such as probes known to not be complementary and hybridizable to sequences in the test sample.
  • GBM Glioblastoma
  • GBM Glioblastoma
  • TCGA Cancer Genome Atlas
  • MGMT gene promoter methylation status is of great interest in recent times because it predicted response of GBM patients receiving temozolomide chemotherapy in addition to irradiation (Stupp R, Hegi ME, Mason WP, van den Bent MJ, Taphoorn MJ, et al. (2009) Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. Lancet Oncol 10: 459-466).
  • the ten miRNA signature identified in this study included three miRNAs (miR-20a, miR-106a and miR-17-5p) that were protective and seven miRNAs (hsa-miR-31, hsa-miR- 222, hsa-miR-148a, hsa-miR-221, hsa-miR-146b, hsa-miR-200b and hsa-miR-193a) that were risky with respect to their association between their expression and patient survival.
  • the protective miRNAs were expressed at a higher level in the low risk group compared to the high risk group and the risky miRNAs were expressed at a higher level in the high risk group than in the low risk group.
  • the protective and risky nature of these miRNAs is suggestive of their functions being either inhibitory or promoting, respectively of various properties of cancer cells like proliferation, migration and invasion etc.
  • miR-31 has been shown to be an inhibitor of breast cancer metastasis by targeting
  • RhoA, RDX and ITGA which are involved in tumor motility, invasion and resistance to anoikis (Valastyan S, Reinhardt F, Benaich N, Calogrias D, Szasz AM, et al. (2009) A pleiotropically acting microRNA, miR-31, inhibits breast cancer metastasis. Cell 137: 1032- 1046).
  • miR-31 has also been shown to be an oncogenic miRNA in lung cancer by targeting tumor suppressor genes and in head and neck cancer by targeting factor-inhibiting hypoxia-inducible factor (FIH) (Liu CJ, Tsai MM, Hung PS, Kao SY, Liu TY, et al.
  • FHI hypoxia-inducible factor
  • miR-31 ablates expression of the HIF regulatory factor FIH to activate the HIF pathway in head and neck carcinoma. Cancer Res 70: 1635-1644; Liu X, Sempere LF, Ouyang H, Memoli VA, Andrew AS, et al. MicroRNA-31 functions as an oncogenic microRNA in mouse and human lung cancer cells by repressing specific tumor suppressors. J Clin Invest 120: 1298-1309).
  • Both miR-221 and 222 have shown to be upregulated in multiple cancers including glioblastoma, linked to promoting proliferation and radioresistance by targeting PTEN, p27 and p57 (Chun-Zhi Z, Lei H, An-Ling Z, Yan-Chao F, Xiao Y, et al. MicroRNA-221 and microRNA-222 regulate gastric carcinoma cell proliferation and radioresistance by targeting PTEN. BMC Cancer 10: 367; Gillies JK, Lorimer IA (2007) Regulation of p27Kipl by miRNA 221/222 in glioblastoma.
  • p27Kipl a target of miR-221 and 222
  • p27Kipl a target of miR-221 and 222
  • miR-148a has been shown to regulate DNA methylation by targeting DNA methylatransferase 1 (DNMT1) (Pan W, Zhu S, Yuan M, Cui H, Wang L, et al. MicroRNA-21 and microRNA- 148a contribute to DNA hypomethylation in lupus CD4+ T cells by directly and indirectly targeting DNA methyltransferase 1. J Immunol 184: 6773-6781).
  • DNMT1 DNA methylatransferase 1
  • miR-200b While Xia et al identified it to promote S-phase entry by targeting RND3 and increasing cyclin Dl expression, other reports suggest miR-200 to be an inhibitor of epithelial-to mesenchymal transition with decreased cell migration and increased sensitivity to EGFR-blocking agents ( Xia H, Qi Y, Ng SS, Chen X, Li D, et al. (2009) microRNA- 146b inhibits glioma cell migration and invasion by targeting MMPs. Brain Res 1269: 158-165; Adam L, Zhong M, Choi W, Qi W, Nicoloso M, et al. (2009) miR-200 expression regulates epithelial-to-mesenchymal transition in bladder cancer cells and reverses resistance to epidermal growth factor receptor therapy. Clin Cancer Res 15: 5060-5072).
  • miR-193a In malignant cutaneous melanoma, while increased expression of miR-193a is associated with poor survival, miR-193a has been identified as epigenetically silenced tumor suppressor miRNA in oral cancer (Caramuta S, Egyhazi S, Rodolfo M, Witten D, Hansson J, et al. MicroRNA expression profiles associated with mutational status and survival in malignant melanoma. J Invest Dermatol 130: 2062-2070; Kozaki K, Imoto I, Mogi. S, Omura K, Inazawa J (2008) Exploration of tumor-suppressive microRNAs silenced by DNA hypermethylation in oral cancer. Cancer Res 68: 2094-2105).
  • miR-106a one of the protective miRNAs was found to be over-expressed and oncogenic in human T-Cell leukemia (Landais S, Landry S, Legault P, Rassart E (2007) Oncogenic potential of the miR- 106-363 cluster and its implication in human T-cell leukemia. Cancer Res 67: 5699-5707). However, in good correlation with our data, low expression of miR- 106a was found to be associated with poor patient survival in glioma and colon cancer (Zhi F, Chen X, Wang S, Xia X, Shi Y, et al.
  • hsa-miR-21 , hsa-miR-181b and hsa- miR-106a as prognostic indicators of astrocytoma.
  • the miR- 17-92 cluster which contains two protective miRNAs, miR-17-5p and miR-
  • miR- 17-92 has been shown to be deleted and found to inhibit cell proliferation upon overexpression suggesting miR- 17-92 cluster may have context dependent functions (Bonauer A, Dimmeler S (2009) The microRNA- 17-92 cluster: still a miRacle? Cell Cycle 8: 3866-3873).
  • Our results show that both miR-17-5p and miR-20a are upregulated in GBMs with higher expression correlating with increased survival.
  • the ten miRNA signature identified in this study, classifies patients successfully into low risk and high risk groups in both training and testing sets. This may help clinicians to identify patients belonging to high risk for more effective adjuvant therapy in addition to the standard treatment protocol. We also found that the ten miRNA signature is an independent predictor of GBM patient survival.
  • miRNA signature can predict GBM patient's survival also likely to generate potential molecular targets for the development of anticancer therapy. Since miRNAs can target multiple genes, more thorough studies are needed to understand the mechanism of action of these miRNAs which is likely to result in better understanding of glioma.
  • the present invention discloses a ten miRNA signature that can predict GBM patient survival with a lot of potential prognostic and therapeutic implications for the GBM patient management.
  • Table 1 gives the age and gender distribution of the patients in both sets and the entire set.
  • miRNA expression data corresponding to 305 miRNAs derived from the training set was subjected to Cox proportional hazard regression analysis to identify miRNAs, whose expression profile could be significantly correlated to patient survival.
  • a risk score formula was obtained for predicting the patient survival.
  • the 10 miRNA expression signature risk score was calculated for all patients in the training set.
  • the expression level of each miRNA was assessed by Cox regression analysis using the BRB array tools (Simon R, Lam A, Li MC, Ngan M, Menenzes S, et al. (2007) Analysis of Gene Expression Data Using BRB-Array Tools. Cancer Inform 3: 1 1 -1 7) package in the training set, and the most significant miRNAs were identified, using the permutation test method, with 10,000 permutations.
  • Risk score (-0.39 x expression of hsa-mir-20a) + (-0.41 x expression of hsa-mir-
  • the significant miRNAs that formed the signature were of two types-risky and protective. Risky miRNAs were defined as those that had hazard ratio for death greater than 1. Protective miRNAs were defined as those that had hazard ratio for death less than 1. Using this definition, we found 3 protective miRNAs and 7 risky miRNAs.
  • Table 1 The age and gender distribution of the patients
  • Table 3 Validation of the 10 miRNA expression signature for survival prediction in the testin set (%) [95% CI) (months, (%) (%) (%)

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  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Cette invention concerne une signature de dix miARN qui distingue un patient porteur d'un glioblastome à risque élevé d'un patient porteur d'un glioblastome à bas risque, les miARN étant : hsa-miR-20a, hsa-miR- 106a, hsa-miR-17-5p, hsa-miR-31, hsa-miR-222, hsa-miR-148a, hsa-miR-221, hsa-miR-146b, hsa-miR-200b et hsa-miR-193a. Cette invention concerne également des procédés et une trousse pour déterminer le pronostic de survie chez un sujet porteur d'un glioblastome.
PCT/IB2012/000312 2011-02-22 2012-02-22 Méthode pour prédire la survie d'un patient porteur d'un glioblastome à l'aide d'une signature de dix miarn Ceased WO2012114189A1 (fr)

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EP3502269A1 (fr) * 2013-07-09 2019-06-26 University of Central Lancashire Détection du cancer du cerveau
WO2021250106A1 (fr) * 2020-06-10 2021-12-16 INSERM (Institut National de la Santé et de la Recherche Médicale) Méthode de traitement et de pronostic du cancer comme le glioblastome

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WO2010066384A1 (fr) * 2008-12-10 2010-06-17 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. Compositions et procédés pour le profilage de l'expression de micro-arn de cellules souches cancéreuses

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"The Cancer Genome Atlas (TCGA) archive unc.edu_GBM.H-miRNA 8x15K.Level-1.1.7.0", May 2007 (2007-05-01), Retrieved from the Internet <URL:https://tcga-data.nci.nih.gov/tcgafiles/ftpauth/distro_ftpusers/anonymous/tumor/gbm/cgcc/unc.edu/h-mirna_8x1Sk/mirna/unc.edu_GBM.H-miRNA_8x1SK.Level_1.1.7.0/US14702406_251643612132_S01_miRNA-v1_95_May07_1_1.txt> [retrieved on 20120412] *
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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3502269A1 (fr) * 2013-07-09 2019-06-26 University of Central Lancashire Détection du cancer du cerveau
WO2021250106A1 (fr) * 2020-06-10 2021-12-16 INSERM (Institut National de la Santé et de la Recherche Médicale) Méthode de traitement et de pronostic du cancer comme le glioblastome

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