WO2014085906A1 - Biomarqueurs micro-arn pour le cancer de la prostate - Google Patents

Biomarqueurs micro-arn pour le cancer de la prostate Download PDF

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Publication number
WO2014085906A1
WO2014085906A1 PCT/CA2013/001005 CA2013001005W WO2014085906A1 WO 2014085906 A1 WO2014085906 A1 WO 2014085906A1 CA 2013001005 W CA2013001005 W CA 2013001005W WO 2014085906 A1 WO2014085906 A1 WO 2014085906A1
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mir
hsa
gene product
risk
prostate cancer
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PCT/CA2013/001005
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George Yousef
Klaus Jung
Neil Eric FLESHNER
Richardson John D'Arcy HONEY
Annika FENDLER
Carsten STEPHAN
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St. Michael's Hospital
Charite University Hospital
University Health Network
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Publication of WO2014085906A1 publication Critical patent/WO2014085906A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/02—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • 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
    • 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
    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering N.A.
    • C12N2310/141—MicroRNAs, miRNAs
    • 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
    • C12Q2600/118—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
    • C12Q2600/178—Oligonucleotides characterized by their use miRNA, siRNA or ncRNA

Definitions

  • the biomarker set or miR gene product signature comprises miR-135a, miR-152, miR-429, miR-19a, miR-374b, miR-374a, miR-20b, miR-29c, and miR-218.
  • the invention provides a method of determining whether a human subject has aggressive disease for prostate cancer characterized by a Gleason score of 4, comprising: measuring the level of at least one miR gene product signature in a test sample of prostate cancer from the human subject, the miR gene product signature comprising or consisting of at least one miR gene product of Table 10 including their corresponding homologues and complementary sequences; and determining the risk of aggressive disease in the subject; wherein an alteration in the level of the miR gene product in the test sample, relative to a corresponding level of miR gene product in a control sample, is indicative of the human subject having an increased risk of aggressive disease; the alteration being wherein the level of one or more of the miRNAs shown as down-regulated in Table 10 is below the level of the control sample, and the level of one or more of the miRNAs shown as up-regulated in Table 10 is above the level of the control sample.
  • the at least one miRNA that has levels below the levels of the control sample is miR-29c.
  • the sample is serum or urine and the miR gene products of SEQ ID NOs: 1 to 47, in particular the mature miRNAs of SEQ ID NOs: 1 to 29, more particularly SEQ ID NOs: 1 to 21 , including their corresponding homologues and complementary sequences, are analyzed.
  • the at least one miR gene product comprises or consists of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, 14, 15, 20 or all of the miR gene products of SEQ ID NOs: 1 to 21 , including their corresponding homologues and complementary sequences.
  • the at least one miR gene product comprises or consists of at least 2, 3, 4, 5 or all of the miR gene products of SEQ ID NOs: 22 to 29, including their corresponding homologues and complementary sequences.
  • the at least one miR gene product comprises or consists of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, 14, 15 or all of the miR gene products of SEQ ID NOs: 30 to 47, including their corresponding homologues and complementary sequences.
  • the at least one miR gene product comprises miR-152, miR-331-3p, and one, two, three, four, five, six, seven or all of miR-135a, miR-141 , miR-19a, miR-374b, miR-29c, miR-26b, miR-664a-3p, miR- 664a-5p, miR-148a, and miR-30d, including their corresponding homologues and complementary sequences.
  • miR-331 -3p miR-135a, miR-141 , miR-19a, miR-374b, miR-29c, miR-26b, miR- 664a-3p, miR-664a-5p, miR-148a, and miR-30d, including their corresponding homologues and complementary sequences.
  • control is a standard value representing the average value or average range of values obtained from a plurality of patient samples (such as an average value or range of values of miR gene product expression for those miR gene products listed in Table 1 , 2, 3, 4 or 5, in particular SEQ ID NOs: 1 to 29, more particularly, SEQ ID NOs: 1 to 21 , and/or SEQ ID NOs: 48 to 140, in particular SEQ ID NOs: 48 to 103, including their corresponding homologues and complementary sequences).
  • a control or standard may be a laboratory standard or value set based on a known or predetermined population value. Laboratory standards or values can be in the form of a graph or table that permits comparison of measured experimentally determined values.
  • a control may also be another sample (e.g., earlier sample from the patient).
  • the sample is a mammalian tissue sample.
  • the tissue is a prostate tissue sample, in particular a prostate tumor tissue sample.
  • “Significant difference" in levels or amounts of miR gene products in a sample compared to a control or standard may represent levels that are higher or lower than the standard error of the detection method.
  • the levels may be 1.5, 2, 3, 4, 5, or 6 times higher or lower than the control or standard.
  • the term “treat” or “treating” refers to any method used to partially or completely alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of and/or reduce incidence of one or more symptoms or features of a particular condition. Treatment may be administered to a subject who does not exhibit signs of a condition and/or exhibits only signs of the condition for the purpose of decreasing the risk of developing pathology associated with the condition. Thus, depending on the state of the subject, the term in some aspects of the invention may refer to preventing a condition, and includes preventing the onset, or preventing the symptoms associated with a condition. The term also includes maintaining the condition and/or symptom such that the condition and/or symptom do not progress in severity.
  • hsa-miR-148a, hsa-miR-135a, hsa-miR- 152, hsa-miR-429, hsa- miR-141 , hsa-miR-19a, hsa-miR-19b, hsa-miR-374b, hsa-miR-26b, hsa-miR-374a, hsa-miR-29c, hsa-miR-454, hsa-miR-30-3p, hsa-miR-20a, hsa-miR-218, hsa-miR- 196b, hsa-miR-203, hsa-miR-106a, hsa-miR-17 and/or hsa-miR-26a are down- regulated by at least 2-fold in high risk patients.
  • the at least one miR gene product comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, 14, 15 or all of the miR gene products of Table 10, including their corresponding homologues and complementary sequences. In aspects of the invention the at least one miR gene product comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 20, 25 or all of the miR gene products of Table 1 1, including their corresponding homologues and complementary sequences. In an aspect, the at least one miR gene product comprises at least one, two, three, four, five, six, eight, ten, twelve, fifteen, twenty or all the miR gene product(s) in Table 1 , including their corresponding homologues and complementary sequences.
  • the at least one miR gene product comprises hsa- miR-29c or hsa-miR-34a, including their corresponding homologues and complementary sequences.
  • miR-152 and miR-148 is decreased by at least about 0.-5 to 5-fold, 1 - to 3-fold, or 2-fold
  • miR-331 -3p is increased by at least about 0.5- to 5-fold, 1 - to 3-fold, or 2-fold, or a combination thereof, in the biological sample of the subject with high risk prostate cancer relative to the control (e.g. healthy individual).
  • RNA expression assays such as microarray analysis and in situ hybridization (Parker & Barnes, Methods in Molecular Biology 106: 247-283, 1999; RNAse protection assays (Hod, Biotechniques 13: 852-854, 1992); PCR based methods such as reverse transcription PCR (RT-PCR) (Weis et al., Trends in Genetics, 8:263-264, 1992) and in situ PCR.
  • RT-PCR reverse transcription PCR
  • Methods to profile gene expression may also employ antibodies that can recognize sequence-specific duplexes such as RNA duplexes and DNA-RNA hybrid duplexes.
  • methods based on sequencing include without limitation, serial analysis of gene expression (SAGE), deep sequencing (Creighton et al., Brief Bioinform. 10(5):490-2009) and gene expression analysis by massively parallel signature sequencing (MPSS).
  • SAGE serial analysis of gene expression
  • MPSS massively parallel signature sequencing
  • the analysis step may be further accomplished by quantitatively detecting the presence of miR gene products in the amplification product, and comparing the quantity of miR gene products detected against a panel of expected values for the known presence or absence of the miR gene products in control samples derived using similar primers.
  • the invention provides a method of identifying a subject with high risk prostate cancer (i.e., early biochemical failure, aggressive disease, and/or recurrence or relapse) comprising the steps of: providing one or more sample from the subject, wherein the sample is selected from the group consisting of a tissue sample, a cell homogenate, and one or more biological fluid comprising blood, plasma, serum, lymph or urine, and determining differential expression of at least one miR gene product of Table 1 , 2, 3, 4, 5, 10 and/or 1 1 , in particular Table 1 or 3, including corresponding homologues and complementary sequences, in the sample using a microarray, wherein differential expression of the at least one miR gene product is indicative of the presence of high risk disease in the subject.
  • a variety of data processor programs and formats can be used to store information on the miR gene product and other biomarkers on computer readable medium.
  • the information can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and Microsoft Word, or represented in the form of an ASCII file, stored in a USB or database application, such as DB2, Sybase, Oracle, or the like.
  • Any number of dataprocessor structuring formats e.g., text file or database
  • kits for carrying out the methods of the invention.
  • Kits may typically comprise two or more components required for performing a diagnostic or screening assay.
  • Components include but are not limited to compounds, reagents, containers, and/or equipment.
  • the components may be packaged with the necessary materials into suitable containers. Controls (such as positive and negative controls) can also be included in some kits.
  • kits including at least two probes for at least one miR gene product chosen from or selected from any of the miR gene products of SEQ ID NOs: 1 to 29 and 48 to 140, in particular SEQ ID NOs: 1 to 21 and 48 to 103, including homologues and complementary sequences thereof.
  • the invention provides a kit for assessing the potential of a test compound to contribute to high risk prostate cancer.
  • the kit comprises diseased cells and reagents for assessing at least one miR gene product, and optionally other markers associated with high risk prostate cancer.
  • the invention provides a method for assessing the potential efficacy of a test compound for modulating high risk prostate cancer in a patient, the method comprising comparing:
  • Erbb3 and the activated Erbb/PBK/Akt/NFicP pathway were suggested to predict biochemical recurrence of PCa in patients treated with radical prostatectomy (31). Moreover, Erbb3 is reported to be responsible for therapy resistance in different cancers, and is a promising therapeutic target for cancer gene therapy (32).
  • the miRNA is transfected in PCa cell lines that have minimal endogenous expression of the miRNA, using commercially available synthetic miRNAs (e.g. PC3, LNCaP and DU145 PCA cell lines). The endogenous level of miRNA expression is quantitated in each of these cells by qRT- PCR.
  • anti-miRNAs or siRNAs are used for knocking down of miRNA expression. Synthetic miRNAs and miRNA inhibitors are commercially available, and can be easily transfected with high efficiency using siPORT NeoFX (Ambion, Inc) (67-72). The concentration of 30 nM was found to be optimal for transfection.
  • Transfection efficiency is assessed by transfecting cells with Cy-3 -labeled random miRNA pool and is also confirmed by qRT-PCR. Appropriate controls are used, including untransfected cells; cells treated with transfection reagent only, transfection with a random pool of miRNAs; and cells co-transfected with the miRNA and its inhibitor, as in recent publications (60, 68, 73). Also, knocking down of the miRNA abolishes the effect of overexpression. Each experiment is done in three independent biological replicates, each including technical triplicates.
  • miR-29c is strongly predicted to target 29 types of collagens, and thus collagens may be the predominant functional targets of this miRNA.
  • the following predicted targets of miR-29 and miR-141 were selected for validation: extracellular matrix components collagen COL1A and, COL4A1 and MMP-2, and the EMT regulators ZEB1 and ZEB2.
  • miRNA expression is quantified by qRT-PCR and expression levels of their targets are measured by qRT-PCR (for mRNA changes) and immunohistochemistry or ELISA (to measure the protein levels).
  • the protein concentration of the target is compared before and after transfecting the targeting miRNA by western blot or ELISA. Appropriate endogenous controls are included, (60, 68, 73). Each experiment is done in three independent biological replicates.
  • MicroRNA expression in melanocyte nevi the usefulness of formalin-fixed, paraffin-embedded material for miRNA microarray profiling. J Invest Dermatol 2009;129: 1219-24.
  • Circulating microRNAs as potential markers of human drug-induced liver injury Hepatology 201 1 ;54: 1767-76.

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Abstract

L'invention concerne en général de nouveaux biomarqueurs pour la détection du cancer de la prostate, et plus particulièrement l'analyse de produits de gène micro-ARN (miARN) et de signatures micro-ARN dans des cancers de la prostate à risque faible et élevé.
PCT/CA2013/001005 2012-12-03 2013-12-03 Biomarqueurs micro-arn pour le cancer de la prostate WO2014085906A1 (fr)

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Cited By (13)

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Publication number Priority date Publication date Assignee Title
WO2016115312A1 (fr) 2015-01-14 2016-07-21 Ohio State Innovation Foundation Modèles prédictifs à base de micro-arn pour le diagnostic et le pronostic du cancer de la prostate
CZ306080B6 (cs) * 2015-02-17 2016-07-27 Masarykova Univerzita Způsob absolutní kvantifikace exprese miRNA, zejména miR-34a a/nebo miR-150, a jeho použití v diagnostice a prognostice B-buněčných malignit
WO2016134727A1 (fr) * 2015-02-27 2016-09-01 Exiqon A/S Procédé à base de micro-arn pour évaluer le pronostic d'un patient atteint du cancer de la prostate
WO2016139092A1 (fr) * 2015-03-04 2016-09-09 Hummingbird Diagnostics Gmbh Signature de la santé
CN106367415A (zh) * 2015-07-24 2017-02-01 复旦大学 人MIR135a－3p在制备诊断及治疗前列腺癌的制剂中的用途
WO2017031086A1 (fr) * 2015-08-14 2017-02-23 Northwestern University Identification par la plateforme scano-mir d'une signature de microarn circulant distincte pour le diagnostic d'une maladie
WO2017214436A1 (fr) * 2016-06-08 2017-12-14 MiR DIAGNOSTICS Procédés et compositions pour le diagnostic et le traitement du cancer de la prostate
CN107488733A (zh) * 2017-10-10 2017-12-19 广州医科大学附属第二医院 miR‑133b在前列腺癌骨转移诊断、预测、治疗中的应用
CN107488734A (zh) * 2017-10-10 2017-12-19 广州医科大学附属第二医院 miR‑19a‑3p在制备前列腺癌骨转移诊断试剂和治疗药物中的应用
WO2018049506A1 (fr) * 2016-09-14 2018-03-22 Ontario Institute For Cancer Research (Oicr) Marqueur du cancer de la prostate miarn
CN109913555A (zh) * 2019-04-23 2019-06-21 武汉科技大学 一种前列腺癌诊断标志物、测定方法及其应用
US10400288B2 (en) 2015-02-11 2019-09-03 Aarhus Universitet MicroRNA-based method for early detection of prostate cancer in urine samples
WO2020190819A1 (fr) * 2019-03-15 2020-09-24 Mir Scientific, Llc Méthodes de prédiction du cancer de la prostate et leurs utilisations

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Cited By (26)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10480033B2 (en) 2015-01-14 2019-11-19 Ohio State Innovation Foundation MiRNA-based predictive models for diagnosis and prognosis of prostate cancer
EP3245302A4 (fr) * 2015-01-14 2018-10-31 Ohio State Innovation Foundation Modèles prédictifs à base de micro-arn pour le diagnostic et le pronostic du cancer de la prostate
WO2016115312A1 (fr) 2015-01-14 2016-07-21 Ohio State Innovation Foundation Modèles prédictifs à base de micro-arn pour le diagnostic et le pronostic du cancer de la prostate
US10400288B2 (en) 2015-02-11 2019-09-03 Aarhus Universitet MicroRNA-based method for early detection of prostate cancer in urine samples
CZ306080B6 (cs) * 2015-02-17 2016-07-27 Masarykova Univerzita Způsob absolutní kvantifikace exprese miRNA, zejména miR-34a a/nebo miR-150, a jeho použití v diagnostice a prognostice B-buněčných malignit
WO2016134727A1 (fr) * 2015-02-27 2016-09-01 Exiqon A/S Procédé à base de micro-arn pour évaluer le pronostic d'un patient atteint du cancer de la prostate
US10358681B2 (en) 2015-02-27 2019-07-23 Aarhus Universitet Microrna-based method for assessing the prognosis of a prostate cancer patient
JP2018507692A (ja) * 2015-02-27 2018-03-22 エクシコン エ／エス マイクロｒｎａに基づく前立腺がん患者の予後評価方法
WO2016139092A1 (fr) * 2015-03-04 2016-09-09 Hummingbird Diagnostics Gmbh Signature de la santé
CN107820519A (zh) * 2015-03-04 2018-03-20 蜂鸟诊断有限责任公司 健康标志
CN107820519B (zh) * 2015-03-04 2022-01-11 蜂鸟诊断有限责任公司 健康标志
CN106367415A (zh) * 2015-07-24 2017-02-01 复旦大学 人MIR135a－3p在制备诊断及治疗前列腺癌的制剂中的用途
WO2017031086A1 (fr) * 2015-08-14 2017-02-23 Northwestern University Identification par la plateforme scano-mir d'une signature de microarn circulant distincte pour le diagnostic d'une maladie
WO2017214436A1 (fr) * 2016-06-08 2017-12-14 MiR DIAGNOSTICS Procédés et compositions pour le diagnostic et le traitement du cancer de la prostate
CN110023511A (zh) * 2016-06-08 2019-07-16 Mir科學有限責任公司 用于前列腺癌诊断及治疗的方法及组合物
JP2019528758A (ja) * 2016-06-08 2019-10-17 エムアイアール サイエンティフィック，エルエルシー 前立腺癌の診断および治療のための方法および組成物
WO2018049506A1 (fr) * 2016-09-14 2018-03-22 Ontario Institute For Cancer Research (Oicr) Marqueur du cancer de la prostate miarn
CN107488734B (zh) * 2017-10-10 2019-11-05 广州医科大学附属第二医院 miR-19a-3p在制备前列腺癌骨转移诊断试剂和治疗药物中的应用
CN107488734A (zh) * 2017-10-10 2017-12-19 广州医科大学附属第二医院 miR‑19a‑3p在制备前列腺癌骨转移诊断试剂和治疗药物中的应用
CN107488733A (zh) * 2017-10-10 2017-12-19 广州医科大学附属第二医院 miR‑133b在前列腺癌骨转移诊断、预测、治疗中的应用
WO2020190819A1 (fr) * 2019-03-15 2020-09-24 Mir Scientific, Llc Méthodes de prédiction du cancer de la prostate et leurs utilisations
CN113614249A (zh) * 2019-03-15 2021-11-05 美尔科学有限责任公司 预测前列腺癌的方法及其用途
JP2022524382A (ja) * 2019-03-15 2022-05-02 エムアイアール サイエンティフィック，エルエルシー 前立腺がんを予測するための方法およびその使用
US11661633B2 (en) 2019-03-15 2023-05-30 Mir Scientific Llc Methods for predicting prostate cancer and uses thereof
CN109913555A (zh) * 2019-04-23 2019-06-21 武汉科技大学 一种前列腺癌诊断标志物、测定方法及其应用
CN109913555B (zh) * 2019-04-23 2022-09-06 湖北民族大学 一种前列腺癌诊断标志物、测定方法及其应用

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