WO2011076142A1 - Compositions et procédés pour le profilage de l'expression de micro-arn dans un plasma d'un cancer colorectal - Google Patents

Compositions et procédés pour le profilage de l'expression de micro-arn dans un plasma d'un cancer colorectal Download PDF

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WO2011076142A1
WO2011076142A1 PCT/CN2010/080233 CN2010080233W WO2011076142A1 WO 2011076142 A1 WO2011076142 A1 WO 2011076142A1 CN 2010080233 W CN2010080233 W CN 2010080233W WO 2011076142 A1 WO2011076142 A1 WO 2011076142A1
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hsa
mir
nucleic acid
expression
plasma
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PCT/CN2010/080233
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Zhaoyong Li
Ying Wu
Hongguang Zhu
Jian Li
Yiping Ren
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Fudan University
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Priority to CN201080064801.4A priority Critical patent/CN102933719B/zh
Publication of WO2011076142A1 publication Critical patent/WO2011076142A1/fr

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    • 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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/7105—Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y15/00—Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y5/00—Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
    • 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 compositions and methods for microRNA expression profiling in plasma of colorectal cancer.
  • CRC Colorectal cancer
  • CRC is characterized by the occurrence of a hyper-proliferative (dysplastic) epithelium in the colon, which first turns into inflammatory adenomatous polyps, then into adenomas, which are abnormal neoplasms (i.e. benign tumors) in the inner lining of the colon or rectum.
  • adenomas which are abnormal neoplasms (i.e. benign tumors) in the inner lining of the colon or rectum.
  • adenomas which are abnormal neoplasms (i.e. benign tumors) in the inner lining of the colon or rectum.
  • adenomas which are abnormal neoplasms (i.e. benign tumors) in the inner lining of the colon or rectum.
  • adenocarcinomas Usually, only a small subset of the adenomas formed (occurring with an incidence of 60-70% by age 60) progress into malignant adenocarcinomas. More
  • the current standard screening methods for CRC include colonoscopy and the fecal occult blood tests. Both tests, however, suffer from serious disadvantages.
  • the colonoscopy test is effective, but many people are hesitant to have this procedure due to its high cost, high discomfort and its potential for more significant side effects.
  • the fecal occult blood test is a simple and cheap test, but is relatively inaccurate.
  • no specific molecular markers have been identified so far that allow for a reliable diagnosis of CRC, preferably CRC manifested as an adenocarcinoma, and/or the progression of a benign adenoma into such a malignant tumor.
  • biomarkers would be of utmost clinical importance, particularly if these markers enable a diagnosis at an early stage of tumor progression in order to allow early stage treatment of carcinomas while avoiding unnecessary surgical intervention.
  • markers should enable the identification of a carcinoma at a stage where the presence of malignant cells is not yet detectable by in situ techniques or microscopic analysis of biopsy or resection material.
  • miRNAs small regulatory RNA molecules
  • nt nucleotides
  • miRNAs have advantages over mRNAs as cancer biomarkers, since they are very stable in vitro and long-lived in vivo (Lu, J. et al. (2005) Nature 435, 834-838; Lim, L.P. et al. (2005) Nature 433, 769-773).
  • MiRNAs are produced from primary transcripts that are processed to stem-loop structured precursors (pre-miRNAs) by the RNase III Drosha. After transport to the cytoplasm, another RNase III termed Dicer cleaves of the loop of the pre-miRNA hairpin to form a short double-stranded (ds) RNA, one strand of which is incorporated as mature miRNA into a miRNA-protein (miRNP).
  • ds short double-stranded
  • miRNA-protein miRNA-protein
  • the miRNA guides the miRNPs to their target mRNAs where they exert their function (Bartel, D.P. (2004) Cell 23, 281- 292; He, L. and Hannon, G.J. (2004) Nat Rev Genet 5, 522-531).
  • miRNAs can guide different regulatory processes.
  • Target mRNAs that are highly complementary to miRNAs are specifically cleaved by mechanisms identical to RNA interference (RNAi).
  • RNAi RNA interference
  • the miRNAs function as short interfering RNAs (siRNAs).
  • Target mRNAs with less complementarity to miRNAs are either directed to cellular degradation pathways or are translationally repressed without affecting the mRNA level.
  • the mechanism of how miRNAs repress translation of their target mRNAs is still a matter of controversy.
  • miRNAs can play roles in cancer as oncogenes or tumor suppressor genes, such as overexpressed mir- 17-92 in cancers, may function as oncogenes and promote cancer development by negatively regulating tumor suppressor genes and/or genes that control cell differentiation or apoptosis, as well as underexpressed let-7a, function as tumor suppressor genes and may inhibit cancers by regulating oncogenes and/or genes that control cell differentiation or apoptosis (Zhang, B. (2007) Dev Biol 302, 1-12), suggesting their contribution to cancer development and progression.
  • miRNA profiling is used to create signatures for a variety of cancers, indicating that the profile will help further establish molecular diagnosis, prognosis and therapy.
  • the aberrant expression of miRNAs in human cancer indicates the potential of these miRNAs as biomarkers and targets for molecular therapy.
  • blood is thought to be ideal for screening high risk individuals, leading to early detection, diagnosis, monitoring and efficient treatment of cancers- since blood can be collected easily in a minimally invasive manner.
  • tumor-derived miRNAs are present in human plasma or serum in a remarkably stable form that is protected from endogenous RNase activity.
  • These tumor-derived miRNAs in serum or plasma are at levels sufficient to be measurable as biomarkers for cancer detection.
  • the levels of plasma and serum miRNAs correlate strongly, suggesting that either plasma or serum samples will be suitable for clinical applications using miRNAs as cancer diagnostic biomarkers (Mitchell, P.S.
  • miRNA microRNA
  • the present invention relates to a diagnostic kit of molecular markers in blood for identifying colorectal cancer, the kit comprising a plurality of nucleic acid molecules, each nucleic acid molecule encoding a microRNA sequence, wherein one or more of the plurality of nucleic acid molecules are differentially expressed in the target plasma as compared to healthy controls, and wherein the differentially expressed signatures are derived from tumor-related or plasma- specific signatures, and wherein the one or more differentially expressed nucleic acid molecules together represent a nucleic acid expression signature that is indicative for the presence of colorectal cancer.
  • the nucleic acid expression signature may comprise at least thirty-five acid molecules, preferably at least twelve nucleic acid molecules, and particularly preferably at least six nucleic acid molecules.
  • the nucleic acid expression signature comprises at least one nucleic acid molecule encoding a microRNA sequence whose expression is up-regulated in the one or more target plasma compared to the one or more healthy controls and at least one nucleic acid molecule encoding a microRNA sequence whose expression is down-regulated in the one or more target plasma compared to the one or more healthy controls.
  • the nucleic acid expression signature comprises any one or more of the nucleic acid molecules encoding tumor-related signatures: hsa-miR- 409-3p, hsa-miR-25, hsa-miR-93, hsa-miR-96, hsa-miR-301a, hsa-miR-342-3p, hsa- miR-19b, hsa-miR-451, hsa-miR-486-5p, hsa-miR-187*, hsa-miR-92a, hsa-miR-19a, hsa-miR-20b, hsa-miR-20a, hsa-miR-139-3p, hsa-miR-107, hsa-miR-17, hsa-miR-140- 3p, hsa-miR-30e,
  • the expression of any one or more of the nucleic acid molecules encoding hsa-miR-409-3p and hsa-mir-671-3p is up-regulated and the expression of any one or more of the nucleic acid molecules encoding hsa-miR-25, hsa- miR-93, hsa-miR-96, hsa-miR-301a, hsa-miR-342-3p, hsa-miR-19b, hsa-miR-451, hsa- miR-486-5p, hsa-miR-187*, hsa-miR-92a, hsa-miR-19a, hsa-miR-20b, hsa-miR-20a, hsa-miR-139-3p, hsa-miR-107, hsa-miR-17, hsa-mi
  • the nucleic acid expression signature comprises any one or more of the nucleic acid molecules encoding tumor-related signatures: hsa- miR-409-3p, hsa-miR-25, hsa-miR-93, hsa-miR-96, hsa-miR-301a, hsa-miR-342-3p, hsa-miR-19b, hsa-miR-451 and plasma- specific signatures: hsa-mir-671-3p, hsa-mir- 16-2*, hsa-miR-30c-l*, hsa-miR-548c-5p.
  • the expression of any one or more of the nucleic acid molecules encoding hsa-miR-409-3p and hsa-mir-671-3p is up-regulated and the expression of any one or more of the nucleic acid molecules encoding hsa-miR-25, hsa- miR-93, hsa-miR-96, hsa-miR-301a, hsa-miR-342-3p, hsa-miR-19b, hsa-miR-451, hsa- mir-16-2*, hsa-miR-30c-l* and hsa-miR-548c-5p is down-regulated in the one or more target plasma compared to the one or more healthy controls.
  • the nucleic acid expression signature comprises any one or more of the nucleic acid molecules encoding tumor-related signatures: hsa-miR-409-3p, hsa-miR-25, hsa-miR-93, hsa-miR-96, and plasma- specific signatures: hsa-mir-671-3p, hsa-mir-16-2*.
  • the expression of any one or more of the nucleic acid molecules encoding hsa-miR-409-3p and hsa-mir-671-3p is up-regulated and the expression of any one or more of the nucleic acid molecules encoding hsa-miR-25, hsa- miR-93, hsa-miR-96 and hsa-mir-16-2* is down-regulated in the one or more target plasma compared to the one or more healthy controls.
  • the nucleic acid expression signature comprises any one or more nucleic acid combinations encoding hsa-miR-409-3p/hsa- miR-16-2* hsa-miR-409-3p/hsa-miR-96, hsa-miR-671-3p/hsa-miR-548c-5p, hsa-miR- 671 -3p hsa-miR- 16-2*, hsa-miR-671 -3p hsa-miR-30c- 1 *, hsa-miR-671 -3p/hsa-miR- 342-3p, hsa-miR-67 l-3p/hsa-miR-96, hsa-miR-67 l-3p hsa-miR-30 la, hsa-miR-671- 3p/hsa-miR-345, hsa-miR
  • the present invention relates to a diagnostic kit of molecular markers for discriminating colorectal cancer from healthy individuals, hepatocellular carcinoma and lung cancer, the kit comprising a plurality of nucleic acid molecules, each nucleic acid molecule encoding a microRNA sequence, wherein one or more of the plurality of nucleic acid molecules are differentially expressed in the target plasma and in one or more healthy individuals, hepatocellular carcinoma and lung cancer, and wherein the one or more differentially expressed nucleic acid molecules together represent a nucleic acid expression signature that is indicative for the presence of colorectal cancer.
  • the nucleic acid expression signature may comprise at least twenty-three nucleic acid molecules, preferably at least eighteen nucleic acid molecules, and particularly preferably at least six nucleic acid molecules.
  • the nucleic acid expression signature comprises at least one nucleic acid molecule encoding a microRNA sequence whose expression is up-regulated in the one or more target plasma compared to the one or more healthy individuals, hepatocellular carcinoma and lung cancer, and at least one nucleic acid molecule encoding a microRNA sequence whose expression is down-regulated in the one or more target plasma compared to the one or more healthy individuals, hepatocellular carcinoma and lung cancer.
  • the nucleic acid expression signature comprises any one or more of the nucleic acid molecules encoding tumor-related signatures: hsa- miR-409-3p, hsa-miR-129-3p, hsa-miR-33b*, hsa-miR-7, hsa-miR-196b, hsa-miR-93, hsa-miR-486-5p, hsa-miR-25, hsa-miR-92a, hsa-miR-19b; plasma-specific signatures: hsa-miR-671-3p and hsa-miR-16-2*, hsa-miR-92b, hsa-miR-129*, hsa-miR-563, hsa- miR-602, hsa-miR-1227, hsa-miR-196a and internal stable controls: hsa- miR
  • the expression of any one or more of the nucleic acid molecules encoding hsa-miR-409-3p, hsa-mir-671-3p, hsa-miR-33b*, hsa-miR-92b, hsa-miR-149, hsa-miR-129*, hsa-miR-563, hsa-miR-129-3p, hsa-miR-634, hsa-let-7b*, hsa-miR-602 and hsa-miR-1227 is up-regulated and the expression of any one or more of the nucleic acid molecules encoding hsa-miR-16-2*, hsa-miR-7, hsa-miR-196a, hsa- miR-196b, hsa-miR-486-5p, hsa-miR-93, hsa
  • the nucleic acid expression signature comprises any one or more of the nucleic acid molecules encoding tumor-related signatures: hsa- miR-409-3p, hsa-miR-129-3p, hsa-miR-33b*, hsa-miR-7 and plasma- specific signatures: hsa-miR-671-3p and hsa-miR-16-2*.
  • the expression of any one or more of the nucleic acid molecules encoding hsa-miR-409-3p, hsa-miR-129-3p, hsa-miR-33b*, hsa-miR-671-3p is up-regulated and the expression of any one or more of the nucleic acid molecules encoding hsa-miR-16-2* and hsa-miR-7 is down-regulated in the one or more target plasma compared to the one or more healthy individuals, hepatocellular carcinoma and lung cancer.
  • the nucleic acid expression signature comprises any one or more nucleic acid combinations encoding hsa-miR-33b*/hsa- miR-196a, hsa-miR-92b/hsa-miR-196a, hsa-miR-563/hsa-miR-196a, hsa-miR- 1227/hsa-miR-196a, hsa-miR-129-3p/hsa-miR-16-2*, hsa-miR-129*/hsa-miR-16-2*, hsa-miR-92b/hsa-miR- 16-2*, hsa-miR- 129*/hsa-miR- 196a, hsa-miR- 1227/hsa-miR- 16- 2*, hsa-miR- 129-3p/hsa
  • the present invention relates to a method for identifying one or more target plasma exhibiting colorectal cancer, the method comprising: (a) determining in the one or more target plasma the expression levels of a plurality of nucleic acid molecules, each nucleic acid molecule encoding a microRNA sequence; (b) determining the expression levels of the plurality of nucleic acid molecules in one or more healthy control plasma; and (c) identifying from the plurality of nucleic acid molecules one or more nucleic acid molecules that are differentially expressed in the target and control plasma by comparing the respective expression levels obtained in steps (a) and (b), wherein the one or more differentially expressed nucleic acid molecules together represent a nucleic acid expression signature, as defined herein, that is indicative for the presence of colorectal cancer.
  • the method comprising: (a) determining in the one or more target plasma the expression levels of a combination of nucleic acid molecules, each nucleic acid molecule encoding a microRNA sequence, and calculate with certain formula, then ; (b) determining the expression levels of the combination of nucleic acid molecules in healthy control plasma, and calculate with certain formula; and (c) identifying the difference of the combination in the one or more target and control plasma by comparing the respective calculation results obtained in steps (a) and (b), wherein the one or more differentially expressed combinations together represent a signature, as defined herein, that is indicative for the presence of colorectal cancer.
  • the method is for the further use of discriminating colorectal cancer from healthy individuals, hepatocellular carcinoma and lung cancer.
  • the present invention relates to a method for monitoring treatment of colorectal cancer, the method comprising: (a) identifying in the one or more target plasma a nucleic acid expression signature by using a method, as defined herein; and (b) monitoring in blood the expression of one or more nucleic acid molecules encoding a microRNA sequence that is/are comprised in the nucleic acid expression signature in such way that the expression of a nucleic acid molecule whose expression in plasma is up-regulated before treatment but is down-regulated after treatment and the expression of a nucleic acid molecule whose expression in plasma is down-regulated before treatment but is up-regulated after treatment.
  • the present invention relates to a method for preventing or treating colorectal cancer, the method comprising: (a) identifying in plasma a nucleic acid expression signature by using a method, as defined herein; and (b) modifying in blood the expression of one or more nucleic acid molecules encoding a microRNA sequence that is/are comprised in the nucleic acid expression signature in such way that the expression of a nucleic acid molecule whose expression is up-regulated in plasma is down-regulated and the expression of a nucleic acid molecule whose expression is down-regulated in plasma is up-regulated.
  • the present invention relates to a pharmaceutical composition for the prevention and/or treatment of colorectal cancer in blood, the composition comprising one or more nucleic acid molecules, each nucleic acid molecule encoding a sequence that is at least partially complementary to a microRNA sequence encoded by a nucleic acid molecule whose expression is up-regulated in plasma from colorectal cancer patients, as defined herein, and/or that corresponds to a microRNA sequence encoded by a nucleic acid molecule whose expression is down-regulated in plasma from colorectal cancer patients, as defined herein.
  • the present invention relates to the use of said pharmaceutical composition for the manufacture of a medicament for the prevention and/or treatment of colorectal cancer.
  • Figure 1 depicts a flow chart schematically illustrating the essential method steps for determining an expression signature according to the present invention for identifying one or more target plasma exhibiting colorectal cancer.
  • Figure 2 illustrates the human miRNAs comprised in particularly preferred expression signatures in the first aspect according to the present invention for identifying one or more target plasma exhibiting colorectal cancer. Also indicates the expression levels and accuracy (RUC) of these miRNAs in the patients with colorectal cancer as compared to healthy controls (i.e. an up- regulation or a down-regulation).
  • ROC expression levels and accuracy
  • FIG. 1 illustrates the human miRNAs comprised in particularly preferred expression signatures in the second aspect according to the present invention for further discriminating colorectal cancer from healthy controls, hepatocellular cancer and lung cancer. Also indicates the expression levels and accuracy (AUC) of these miRNAs in the patients with colorectal cancer as compared to healthy control, hepatocellular carcinoma and lung cancer (i.e. an up-regulation or a down-regulation).
  • AUC expression levels and accuracy
  • the present invention is based on the unexpected finding that colorectal cancer can be reliably identified based on particular miRNA expression signatures in plasma with high sensitivity and specificity, wherein the expression signatures as defined herein typically comprises both up- and down-regulated human miRNAs. More specifically, said miRNA expression signatures - by analyzing the overall miRNA expression pattern and/or the respective individual miRNA expression level(s) in plasma - allow the detection of colorectal cancer at an early disease state and discriminating healthy individuals, hepatocellular carcinoma and lung cancer.
  • miRNA microRNA
  • colon relates to the colon, the rectum and/or the appendix, i.e. the complete large intestine.
  • cancer also referred to as “carcinoma”
  • cancer generally denotes any type of malignant neoplasm, that is, any morphological and/or physiological alterations (based on genetic re-programming) of target cells exhibiting or having a predisposition to develop characteristics of a carcinoma as compared to unaffected (healthy) wild- type control cells.
  • alterations may relate inter alia to cell size and shape (enlargement or reduction), cell proliferation (increase in cell number), cell differentiation (change in physiological state), apoptosis (programmed cell death) or cell survival.
  • colonrectal cancer refers to cancerous growths in the colon, rectum, and appendix.
  • CRC colorectal cancer
  • Colorectal cancer may be classified according to the Dukes system (Dukes, C.E.
  • plasma is the yellow liquid component of blood, in which the blood cells in whole blood would normally be suspended. It makes up about 55% of the total blood volume. It is mostly water (90% by volume) and contains dissolved proteins, glucose, clotting factors, mineral ions, hormones and carbon dioxide
  • plasma being the main medium for excretory product transportation
  • Blood plasma is prepared by spinning a tube of fresh blood in a centrifuge until the blood cells fall to the bottom of the tube. The blood plasma is then poured or drawn off. Blood plasma has a density of approximately 1025 kg/m 3 , or 1.025 kg/1. Recent research showed that miRNA is stable in plasma.
  • the term "plasma sample” refers to plasma taken from individuals being examined or from healthy control.
  • patient refers to a human being at least supposed to have colorectal cancer
  • target plasma refers to plasma collected from patients
  • healthy individual or “healthy control” typically denotes a healthy person not having characteristics of such a cancerous phenotype.
  • control plasma denotes plasma collected from healthy individuals.
  • control when comparing different cancer types, the individual having the other cancer types and plasma collected from these individuals is typically considered the "control".
  • the plasma samples used are derived from biological specimens collected from the subjects to be diagnosed for the presence of colorectal cancer.
  • the biological samples may include body tissues and fluids, such as colorectal tissue, serum, blood cell, sputum, and urine. Furthermore, the biological sample may be obtained from individual have colorectal cancerous characteristics or suspected to be cancerous. Furthermore, the sample may be purified from the obtained body tissues and fluids if necessary, and then used as the biological sample. According to the present invention, the expression level of the nucleic acid markers of the present invention is determined in the subject-derived biological sample(s).
  • the sample used for detection in the in vitro methods of the present invention should generally be collected in a clinically acceptable manner, preferably in a way that nucleic acids (in particular RNA) or proteins are preserved.
  • the samples to be analyzed are typically from blood. Furthermore, lung tissue and other types of sample can be used as well. Samples, in particular after initial processing may be pooled. However, also non-pooled samples may be used.
  • microRNA (or “miRNA”), as used herein, is given its ordinary meaning in the art (Bartel, D.P. (2004) Cell 23, 281-292; He, L. and Hannon, G.J. (2004) Nat Rev Genet 5, 522-531). Accordingly, a "microRNA” denotes an RNA molecule derived from a genomic locus that is processed from transcripts that can form local RNA precursor miRNA structures.
  • the mature miRNA is usually 20, 21, 22, 23, 24, or 25 nucleotides in length, although other numbers of nucleotides may be present as well, for example 18, 19, 26 or 27 nucleotides.
  • the miRNA encoding sequence has the potential to pair with flanking genomic sequences, placing the mature miRNA within an imperfect RNA duplex (herein also referred to as stem-loop or hairpin structure or as pre-miRNA), which serves as an intermediate for miRNA processing from a longer precursor transcript.
  • This processing typically occurs through the consecutive action of two specific endonucleases termed Drosha and Dicer, respectively.
  • Drosha generates from the primary transcript (herein also denoted "pri-miRNA”) a miRNA precursor (herein also denoted "pre-miRNA”) that typically folds into a hairpin or stem-loop structure.
  • miRNA duplex is excised by means of Dicer that comprises the mature miRNA at one arm of the hairpin or stem-loop structure and a similar- sized segment (commonly referred to miRNA*) at the other arm.
  • the miRNA is then guided to its target mRNA to exert its function, whereas the miRNA* is degraded.
  • miRNAs are typically derived from a segment of the genome that is distinct from predicted protein-coding regions.
  • miRNA precursor refers to the portion of a miRNA primary transcript from which the mature miRNA is processed.
  • pre-miRNA folds into a stable hairpin (i.e. a duplex) or a stem-loop structure.
  • the hairpin structures typically range from 50 to 80 nucleotides in length, preferably from 60 to 70 nucleotides (counting the miRNA residues, those pairing to the miRNA, and any intervening segment(s) but excluding more distal sequences).
  • nucleic acid molecule encoding a microRNA sequence denotes any nucleic acid molecule coding for a microRNA (miRNA). Thus, the term does not only refer to mature miRNAs but also to the respective precursor miRNAs and primary miRNA transcripts as defined above. Furthermore, the present invention is not restricted to RNA molecules but also includes corresponding DNA molecules encoding a microRNA, e.g. DNA molecules generated by reverse transcribing a miRNA sequence.
  • a nucleic acid molecule encoding a microRNA sequence according to the invention typically encodes a single miRNA sequence (i.e. an individual miRNA). However, it is also possible that such nucleic acid molecule encodes two or more miRNA sequences (i.e. two or more miRNAs), for example a transcriptional unit comprising two or more miRNA sequences under the control of common regulatory sequences such as a promoter or a transcriptional terminator.
  • nucleic acid molecule encoding a microRNA sequence is also to be understood to include “sense nucleic acid molecules” (i.e. molecules whose nucleic acid sequence (5'— 3') matches or corresponds to the encoded miRNA (5' ⁇ 3') sequence) and “anti-sense nucleic acid molecules” (i.e. molecules whose nucleic acid sequence is complementary to the encoded miRNA (5'— » 3') sequence or, in other words, matches the reverse complement (3' ⁇ 5') of the encoded miRNA sequence).
  • sense nucleic acid molecules i.e. molecules whose nucleic acid sequence (5'— 3') matches or corresponds to the encoded miRNA (5' ⁇ 3') sequence
  • anti-sense nucleic acid molecules i.e. molecules whose nucleic acid sequence is complementary to the encoded miRNA (5'— » 3') sequence or, in other words, matches the reverse complement (3' ⁇ 5') of the encoded miRNA sequence.
  • complementary refers to the capability of an "anti-sense” nucleic acid molecule sequence of forming base pairs, preferably Watson-Crick base pairs, with the corresponding "sense” nucleic acid molecule sequence (having a sequence complementary to the anti-sense sequence).
  • two nucleic acid molecules may be perfectly complementary, that is, they do not contain any base mismatches and/or additional or missing nucleotides.
  • the two molecules comprise one or more base mismatches or differ in their total numbers of nucleotides (due to additions or deletions).
  • the "complementary" nucleic acid molecule comprises at least ten contiguous nucleotides showing perfect complementarity with a sequence comprised in corresponding "sense" nucleic acid molecule.
  • the plurality of nucleic acid molecules encoding a miRNA sequence that are comprised in a diagnostic kit of the present invention may include one or more "sense nucleic acid molecules" and/or one or more "anti-sense nucleic acid molecules".
  • the diagnostic kit includes one or more "sense nucleic acid molecules” (i.e. the miRNA sequences as such), said molecules are to be considered to constitute the totality or at least a subset of differentially expressed miRNAs (i.e. molecular markers) being indicative for the presence of or the disposition to develop a particular condition, here lung cancer.
  • a diagnostic kit includes one or more "anti-sense nucleic acid molecules” (i.e.
  • said molecules may comprise inter alia probe molecules (for performing hybridization assays) and/or oligonucleotide primers (e.g., for reverse transcription or PCR applications) that are suitable for detecting and/or quantifying one or more particular (complementary) miRNA sequences in a given sample.
  • a plurality of nucleic acid molecules as defined within the present invention may comprise at least two, at least ten, at least 50, at least 100, at least 200, at least 500, at least 1.000, at least 10.000 or at least 100.000 nucleic acid molecules, each molecule encoding a miRNA sequence.
  • the term “differentially expressed”, as used herein, denotes an altered expression level of a particular miRNA in the disease plasma as compared to the healthy controls, or as compared to other types of disease samples, which may be an up- regulation (i.e. an increased miRNA concentration in the plasma) or a down-regulation (i.e. a reduced or abolished miRNA concentration in the plasma).
  • the nucleic acid molecule is activated to a higher or lower level in the disease plasma samples than in the control plasma.
  • a nucleic acid molecule is to considered differentially expressed if the respective expression levels of this nucleic acid molecule in disease plasma samples and control samples typically differ by at least 5% or at least 10%, preferably by at least 20% or at least 25%, and most preferably by at least 30% or at least 50%.
  • the latter values correspond to an at least 1.3-fold or at least 1.5-fold up-regulation of the expression level of a given nucleic acid molecule in the disease plasma samples compared to the control plasma samples or vice versa an at least 0.7-fold or at least 0.5-fold down-regulation of the expression level in the disease plasma samples, respectively.
  • expression level refers to extent to which a particular miRNA sequence is transcribed from its genomic locus, that is, the concentration of a miRNA in the plasma sample to be analyzed.
  • control plasma typically denotes a plasma sample collected from (healthy) individual not having characteristics of a colorectal cancer phenotype.
  • the plasma collected from the patients with other cancer types is typically considered the "control plasma”.
  • determining of expression levels typically follows established standard procedures well known in the art (Sambrook, J. et al. (1989) Molecular Cloning: A Laboratory Manual. 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; Ausubel, F.M. et al. (2001) Current Protocols in Molecular Biology. Wiley & Sons, Hoboken, NJ). Determination may occur at the RNA level, for example by Northern blot analysis using miRNA-specific probes, or at the DNA level following reverse transcription (and cloning) of the RNA population, for example by quantitative PCR or real-time PCR techniques.
  • the term "determining", as used herein, includes the analysis of any nucleic acid molecules encoding a microRNA sequence as described above.
  • the standard value of the expression levels obtained in several independent measurements of a given sample for example, two, three, five or ten measurements
  • the standard value may be obtained by any method known in the art. For example, a range of mean + 2 SD (standard deviation) or mean ⁇ 3 SD may be used as standard value.
  • control nucleic acids e.g. housekeeping genes whose expression levels are known not to differ depending on the disease states of the individual from whom the sample was collected.
  • housekeeping genes include inter alia ⁇ -actin, glycerinaldehyde 3-phosphate dehydrogenase, and ribosomal protein PI .
  • the control nucleic acid is another miRNA known to be stably expressed during the various non-cancerous and (pre-)cancerous states of the individual from whom the sample was collected.
  • the expression levels for plasma sample it may also be possible to define based on experimental evidence and/or prior art data on or more cut-off values for a particular disease phenotype (i.e. a disease state).
  • the respective expression levels for the plasma sample can be determined by using a stably expressed control miRNA for normalization. If the "normalized” expression levels calculated are higher than the respective cutoff value defined, then this finding would be indicative for an up- regulation of gene expression. Vice versa, if the "normalized” expression levels calculated are lower than the respective cutoff value defined, then this finding would be indicative for a down-regulation of gene expression.
  • the term "identifying colorectal cancer and/or discriminating other cancer types” is intended to also encompass predictions and likelihood analysis (in the sense of “diagnosing”).
  • the compositions and methods disclosed herein are intended to be used clinically in making decisions concerning treatment modalities, including therapeutic intervention, diagnostic criteria such as disease stages, and disease monitoring and surveillance for the disease.
  • an intermediate result for examining the condition of a subject may be provided. Such intermediate result may be combined with additional information to assist a doctor, nurse, or other practitioner to diagnose that a subject suffers from the disease.
  • the invention may be used to detect cancerous changes through plasma sample, and provide a doctor with useful information for diagnosis.
  • the invention may also be used to discriminate between colorectal cancer and other cancer types including hepatocellular carcinoma and lung cancer.
  • one or more differentially expressed nucleic acid molecules identified together represent a nucleic acid expression signature that is indicative for colorectal cancer through plasma sample.
  • expression signature denotes a set of nucleic acid molecules (e.g., miRNAs), wherein the expression level of the individual nucleic acid molecules differs between the plasma collected from colorectal cancer patient and the healthy control.
  • a nucleic acid expression signature is also referred to as a set of markers and represents a minimum number of (different) nucleic acid molecules, each encoding a miRNA sequence that is capable for identifying a phenotypic state of an individual.
  • the present invention relates to a diagnostic kit of molecular markers in blood for identifying colorectal cancer, the kit comprising a plurality of nucleic acid molecules, each nucleic acid molecule encoding a microRNA sequence, wherein one or more of the plurality of nucleic acid molecules are differentially expressed in the target plasma as compared to healthy controls, and wherein the differentially expressed signatures are derived from tumor-related or plasma- specific signatures, and wherein the one or more differentially expressed nucleic acid molecules together represent a nucleic acid expression signature that is indicative for the presence of colorectal cancer.
  • the nucleic acid expression signature may comprise at least thirty-fivenucleic acid molecules, preferably at least twelve nucleic acid molecules, and particularly preferably at least six nucleic acid molecules.
  • the nucleic acid expression signature comprises at least one nucleic acid molecule encoding a microRNA sequence whose expression is up-regulated in the one or more target plasma compared to the one or more healthy controls and at least one nucleic acid molecule encoding a microRNA sequence whose expression is down-regulated in the one or more target plasma compared to the one or more healthy control plasma.
  • tumor-related refers to signatures that differentially expressed in plasma from colorectal cancer patients and in control plasma and are also differentially expressed in colorectal cancer tissues cells and non-cancer tissue cells.
  • the colorectal cancer tissue cells refer to cancerous colorectal cells collected from dissections derived from the subjects to be diagnosed for the presence of colorectal cancer.
  • the non-cancer tissue cells typically denotes a (healthy) wild- type cell not having characteristics of such a cancerous phenotype.
  • plasma-specific refers to signatures that are that differentially expressed in plasma from colorectal cancer patients and in control plasma are not found significantly differentially expressed in colorectal cancer tissues cells and non-cancer tissue cells.
  • nucleic acid molecules comprised in the nucleic acid expression signature are human sequences (hereinafter designated “hsa” (Homo sapiens).
  • the nucleic acid expression signature comprises any one or more of the nucleic acid molecules encoding tumor-related signatures: hsa-miR-409-3p (SEQ ID NO:l), hsa-miR-25 (SEQ ID NO:2), hsa-miR-93 (SEQ ID NO:3), hsa-miR-96 (SEQ ID NO:4), hsa-miR-301a (SEQ ID NO:5), hsa-miR- 342-3p (SEQ ID NO:6), hsa-miR-19b (SEQ ID NO:7), hsa-miR-451 (SEQ ID NO:8), hsa-miR-486-5p (SEQ ID NO:9), hsa-miR-187* (SEQ ID NO:10), hsa-miR- 92a (SEQ ID NO:l l), hsa-miR-19a (SEQ ID NO:
  • the miRNA hsa-miR-1238 (SEQ ID NO: 44) and hsa-miR- 1228 (SEQ ID NO: 45) may be preferably used, which is stably expressed in colorectal cancer plasma.
  • nucleic acid sequences of the above-referenced miRNAs are listed in Table 1.
  • the expression of any one or more of the nucleic acid molecules encoding hsa-miR-409-3p and hsa-mir-671-3p is up- regulated and the expression of any one or more of the nucleic acid molecules encoding hsa-miR-25, hsa-miR-93, hsa-miR-96, hsa-miR-301a, hsa-miR-342-3p, hsa-miR-19b, hsa-miR-451, hsa-miR-486-5p, hsa-miR-187*, hsa-miR-92a, hsa- miR-1 a, hsa-miR-20b, hsa-miR-20a, hsa-miR-139-3p, hsa-miR-107, hsa-miR-17, hs
  • any one or more of the plurality of nucleic acid molecules or “any one or more of the plurality of nucleic acid molecules” as used herein, may relate to any subgroup of the plurality of nucleic acid molecules, e.g., any one, any two, any three, any four, any five, any six, any seven, any eight, any nine, any ten, and so forth nucleic acid molecules, each encoding a microRNA sequence that are comprised in the nucleic acid expression signature, as defined herein.
  • the nucleic acid expression signature comprises any one or more nucleic acid combinations encoding hsa-miR-409- 3p/hsa-miR-16-2*, hsa-miR-409-3p/hsa-miR-96, hsa-miR-671-3p/hsa-miR-548c-5p, hsa-miR-671-3p/hsa-miR-16-2 :
  • the present invention relates to a diagnostic kit of molecular markers for discriminating colorectal cancer from healthy controls and other cancer types, the kit comprising a plurality of nucleic acid molecules, each nucleic acid molecule encoding a microRNA sequence, wherein one or more of the plurality of nucleic acid molecules are differentially expressed in the target plasma and in one or more healthy control plasma as well as other cancer types, and wherein the one or more differentially expressed nucleic acid molecules together represent a nucleic acid expression signature that is indicative for the presence of colorectal cancer, and wherein the other cancer types include hepatocellular carcinoma and lung cancer.
  • the nucleic acid expression signature may comprise at least twenty- threenucleic acid molecules, preferably at least eighteen nucleic acid molecules, and particularly preferably at least sixnucleic acid molecules.
  • the nucleic acid expression signature comprises at least one nucleic acid molecule encoding a microRNA sequence whose expression is up-regulated in the one or more target plasma compared to the one or more healthy individuals, hepatocellular carcinoma and lung cancer, and at least one nucleic acid molecule encoding a microRNA sequence whose expression is down- regulated in the one or more target plasma compared to the one or more healthy individuals, hepatocellular carcinoma and lung cancer.
  • the nucleic acid expression signature comprises any one or more of the nucleic acid molecules encoding tumor-related signatures: hsa-miR-409-3p (SEQ ID NO: 1), hsa-miR-129-3p (SEQ ID NO: 34), hsa-miR-33b* (SEQ ID NO: 35), hsa-miR-7 (SEQ ID NO: 36), hsa-miR-196b (SEQ ID NO: 37), hsa-miR-93 (SEQ ID NO: 3), hsa-miR-486-5p (SEQ ID NO: 9), hsa- miR-25 (SEQ ID NO: 2), hsa-miR-92a (SEQ ID NO: 11), hsa-miR-19b (SEQ ID NO: 7); plasma- specific signatures: hsa-miR-671-3p (SEQ ID NO: 21), hsa-miR
  • the expression of any one or more of the nucleic acid molecules encoding hsa-miR-409-3p, hsa-mir-671-3p, hsa-miR-33b*, hsa-miR-92b, hsa-miR-149, hsa-miR-129*, hsa-miR-563, hsa-miR-129-3p, hsa- miR-634, hsa-let-7b*, hsa-miR-602 and hsa-miR-1227 is up-regulated and the expression of any one or more of the nucleic acid molecules encoding hsa-miR-16- 2*, hsa-miR-7, hsa-miR-196a, hsa-miR-196b, hsa-miR-486-5p, hsa-miR-93, h
  • the nucleic acid expression signature comprises any one or more nucleic acid combinations encoding hsa-miR-33b*/hsa- miR-196a, hsa-miR-92b/hsa-miR-196a, hsa-miR-563/hsa-miR-196a, hsa-miR- 1227/hsa-miR- 196a, hsa-miR- 129-3p/hsa-miR- 16-2*, hsa-miR- 129*/hsa-miR- 16- 2*, hsa-miR-92b/hsa-miR-16-2*, hsa-miR-129*/hsa-miR-196a, hsa-miR-1227/hsa- miR-16-2*, hsa-miR-129-3p/hsa-m
  • the present invention relates to a method for identifying one or more target plasma exhibiting colorectal cancer, the method comprising: (a) determining in the one or more target plasma the expression levels of a plurality of nucleic acid molecules, each nucleic acid molecule encoding a microRNA sequence; (b) determining the expression levels of the plurality of nucleic acid molecules in one or more healthy control plasma; and (c) identifying from the plurality of nucleic acid molecules one or more nucleic acid molecules that are differentially expressed in the target and control plasma by comparing the respective expression levels obtained in steps (a) and (b), wherein the one or more differentially expressed nucleic acid molecules together represent a nucleic acid expression signature, as defined herein, that is indicative for the presence of colorectal cancer.
  • the method comprising: (a) determining in the one or more target plasma the expression levels of a combination of nucleic acid molecules, each nucleic acid molecule encoding a microRNA sequence, and calculate with certain formula, then ; (b) determining the expression levels of the combination of nucleic acid molecules in healthy control plasma, and calculate with certain formula; and (c) identifying the difference of the combination in the one or more target and control plasma by comparing the respective calculation results obtained in steps (a) and (b), wherein the one or more differentially expressed combinations together represent a signature, as defined herein, that is indicative for the presence of colorectal cancer.
  • the method is for the further use of discriminating colorectal cancer from healthy individuals, hepatocellular carcinoma and lung cancer.
  • the present invention relates to a method for monitoring treatment of colorectal cancer, the method comprising: (a) identifying in the one or more target plasma a nucleic acid expression signature by using a method, as defined herein; and (b) monitoring in blood the expression of one or more nucleic acid molecules encoding a microRNA sequence that is/are comprised in the nucleic acid expression signature in such way that the expression of a nucleic acid molecule whose expression in plasma is up-regulated before treatment but is down-regulated after treatment and the expression of a nucleic acid molecule whose expression in plasma is down-regulated before treatment but is up-regulated after treatment.
  • modifying the expression of a nucleic acid molecule encoding a miRNA sequence denotes any manipulation of a particular nucleic acid molecule resulting in an altered expression level of said molecule, that is, the production of a different amount of corresponding miRNA as compared to the expression of the "wild-type" (i.e. the unmodified control).
  • the term "different amount”, as used herein, includes both a higher amount and a lower amount than determined in the unmodified control.
  • a manipulation, as defined herein may either up-regulate (i.e. activate) or down-regulate (i.e. inhibit) the expression (i.e. particularly transcription) of a nucleic acid molecule.
  • the present invention relates to a method for preventing or treating colorectal cancer, the method comprising: (a) identifying in plasma a nucleic acid expression signature by using a method, as defined herein; and (b) modifying in blood the expression of one or more nucleic acid molecules encoding a microRNA sequence that is/are comprised in the nucleic acid expression signature in such way that the expression of a nucleic acid molecule whose expression is up- regulated in plasma is down-regulated and the expression of a nucleic acid molecule whose expression is down-regulated in plasma is up-regulated.
  • expression of one or more nucleic acid molecules encoding a microRNA sequence comprised in the nucleic acid expression signature is modified in such way that the expression of a nucleic acid molecule whose expression is up-regulated in plasma is down-regulated and the expression of a nucleic acid molecule whose expression is down-regulated in plasma is up- regulated.
  • the modification of expression of a particular nucleic acid molecule encoding a miRNA sequence occurs in an anti-cyclical pattern to the regulation of said molecule in plasma of cancer patients in order to interfere with the "excess activity" of an up-regulated molecule and/or to restore the "deficient activity" of a down-regulated molecule in plasma.
  • down-regulating the expression of a nucleic acid molecule comprises introducing into the patient a nucleic acid molecule encoding a sequence that is complementary to the microRNA sequence encoded by nucleic acid molecule to be down-regulated.
  • introducing into blood refers to any manipulation allowing the transfer of one or more nucleic acid molecules into blood. Examples of such techniques include injection, digestion or any other techniques may be involved.
  • complementary sequence is to be understood that the "complementary" nucleic acid molecule (herein also referred to as an "anti-sense nucleic acid molecule”) introduced into blood is capable of forming base pairs, preferably Watson-Crick base pairs, with the up-regulated endogenous "sense" nucleic acid molecule.
  • nucleic acid molecules may be perfectly complementary, that is, they do not contain any base mismatches and/or additional or missing nucleotides.
  • the two molecules comprise one or more base mismatches or differ in their total numbers of nucleotides (due to additions or deletions).
  • the "complementary" nucleic acid molecule comprises a stretch of at least ten contiguous nucleotides showing perfect complementarity with a sequence comprised in the up-regulated "sense" nucleic acid molecule.
  • the "complementary" nucleic acid molecule i.e. the nucleic acid molecule encoding a nucleic acid sequence that is complementary to the microRNA sequence encoded by nucleic acid molecule to be down-regulated
  • the "complementary" nucleic acid molecule may be a naturally occurring DNA- or RNA molecule or a synthetic nucleic acid molecule comprising in its sequence one or more modified nucleotides which may be of the same type or of one or more different types.
  • nucleic acid molecule comprises at least one ribonucleotide backbone unit and at least one deoxyribonucleotide backbone unit.
  • the nucleic acid molecule may contain one or more modifications of the RNA backbone into 2'-0-methyl group or 2'-0-mefhoxyefhyl group (also referred to as "2'-( -methylation"), which prevented nuclease degradation in the culture media and, importantly, also prevented endonucleolytic cleavage by the RNA-induced silencing complex nuclease, leading to irreversible inhibition of the miRNA.
  • LNAs locked nucleic acids
  • RNA inhibitors that can be expressed in cells, as RNAs produced from transgenes, were generated as well.
  • microRNA sponges these competitive inhibitors are transcripts expressed from strong promoters, containing multiple, tandem binding sites to a microRNA of interest (Ebert, M.S. et al. (2007) Nat. Methods 4, 721-726).
  • the one or more nucleic acid molecules whose expression is to be down-regulated encode microRNA sequences selected from the group consisting of hsa-miR-25, hsa-miR- 93, hsa-miR-96, hsa-miR-301a, hsa-miR-342-3p, hsa-miR-19b, hsa-miR-451, hsa- miR-486-5p, hsa-miR-187*, hsa-miR-92a, hsa-miR-19a, hsa-miR-20b, hsa-miR- 20a, hsa-miR-139-3p, hsa-miR-107, hsa-miR-17, hsa-miR-140-3p, hsa-miR-30e, hsa-miR
  • up-regulating the expression of a nucleic acid molecule comprises introducing into blood a nucleic acid molecule encoding the microRNA sequence encoded by nucleic acid molecule to be up-regulated.
  • the up-regulation of the expression of a nucleic acid molecule encoding a miRNA sequence is accomplished by introducing into the one or more cells another copy of said miRNA sequence (i.e. an additional "sense" nucleic acid molecule).
  • the "sense" nucleic acid molecule to be introduced into blood may comprise the same modification as the "anti-sense" nucleic acid molecules described above.
  • the one or more nucleic acid molecules whose expression is to be up-regulated encode microRNA sequences selected from the group consisting of hsa-miR-409-3p, hsa-miR-671-3p, hsa-miR- 129-3p, hsa-miR-33b*, hsa-miR-92b, hsa-miR-129*, hsa-miR-563, hsa-miR-602 and hsa-miR-1227 with respect to the expression signature, presumably indicative for colorectal cancer as defined above.
  • the "sense” and/or the “anti-sense” nucleic acid molecules to be introduced into blood in order to modify the expression of one or more nucleic acid molecules encoding a microRNA sequence that is/are comprised in the nucleic acid expression signature may be operably linked to a regulatory sequence in order to allow expression of the nucleotide sequence.
  • a nucleic acid molecule is referred to as "capable of expressing a nucleic acid molecule" or capable “to allow expression of a nucleotide sequence” if it comprises sequence elements which contain information regarding to transcriptional and/or translational regulation, and such sequences are “operably linked” to the nucleotide sequence encoding the polypeptide.
  • An operable linkage is a linkage in which the regulatory sequence elements and the sequence to be expressed (and/or the sequences to be expressed among each other) are connected in a way that enables gene expression.
  • promoter regions necessary for gene expression may vary among species, but in general these regions comprise a promoter which, in prokaryotes, contains both the promoter per se, i.e. DNA elements directing the initiation of transcription, as well as DNA elements which, when transcribed into RNA, will signal the initiation of translation.
  • promoter regions normally include 5' non-coding sequences involved in initiation of transcription and translation, such as the -35/- 10 boxes and the Shine-Dalgarno element in prokaryotes or the TATA box, CAAT sequences, and 5'-capping elements in eukaryotes.
  • These regions can also include enhancer or repressor elements as well as translated signal and leader sequences for targeting the native polypeptide to a specific compartment of a host cell.
  • the 3' non-coding sequences may contain regulatory elements involved in transcriptional termination, polyadenylation or the like. If, however, these termination sequences are not satisfactory functional in a particular host environment, then they may be substituted with signals functional in that environment.
  • the expression of the nucleic molecules may also be influenced by the presence, e.g., of modified nucleotides (cf. the discussion above).
  • modified nucleotides cf. the discussion above.
  • LNA locked nucleic acid
  • LNA monomers are thought to increase the functional half-life of miRNAs in vivo by enhancing the resistance to degradation and by stabilizing the miRNA-target duplex structure that is crucial for silencing activity (Naguibneva, I. et al. (2006) Biomed Pharmacother 60, 633-638).
  • a nucleic acid molecule of the invention to be introduced into blood may include a regulatory sequence, preferably a promoter sequence, and optionally also a transcriptional termination sequence.
  • the promoters may allow for either a constitutive or an inducible gene expression. Suitable promoters include inter alia the E. coli ZacUV5 and tet (tetracycline-responsive) promoters, the T7 promoter as well as the SV40 promoter or the CMV promoter.
  • the nucleic acid molecules of the invention may also be comprised in a vector or other cloning vehicles, such as plasmids, phagemids, phages, cosmids or artificial chromosomes.
  • the nucleic acid molecule is comprised in a vector, particularly in an expression vector.
  • Such an expression vector can include, aside from the regulatory sequences described above and a nucleic acid sequence encoding a genetic construct as defined in the invention, replication and control sequences derived from a species compatible with the host that is used for expression as well as selection markers conferring a selectable phenotype on host. Large numbers of suitable vectors such as pSUPER and pSUPERIOR are known in the art, and are commercially available.
  • the present invention relates to a pharmaceutical composition for the prevention and/or treatment of colorectal cancer in blood, the composition comprising one or more nucleic acid molecules, each nucleic acid molecule encoding a sequence that is at least partially complementary to a microRNA sequence encoded by a nucleic acid molecule whose expression is up- regulated in plasma from colorectal cancer patients, as defined herein, and/or that corresponds to a microRNA sequence encoded by a nucleic acid molecule whose expression is down-regulated in plasma from colorectal cancer patients, as defined herein.
  • the present invention relates to the use of said pharmaceutical composition for the manufacture of a medicament for the prevention and/or treatment of colorectal cancer.
  • suitable pharmaceutical compositions include inter alia those compositions suitable for oral, rectal, nasal, topical (including buccal and sub-lingual), peritoneal and parenteral (including intramuscular, subcutaneous and intravenous) administration, or for administration by inhalation or insufflation. Administration may be local or systemic. Preferably, administration is accomplished via the oral or intravenous routes.
  • the formulations may also be packaged in discrete dosage units.
  • compositions according to the present invention include any pharmaceutical dosage forms established in the art, such as inter alia capsules, microcapsules, cachets, pills, tablets, powders, pellets, multi-p articulate formulations (e.g., beads, granules or crystals), aerosols, sprays, foams, solutions, dispersions, tinctures, syrups, elixirs, suspensions, water-in-oil emulsions such as ointments, and oil-in water emulsions such as creams, lotions, and balms.
  • pharmaceutical dosage forms established in the art, such as inter alia capsules, microcapsules, cachets, pills, tablets, powders, pellets, multi-p articulate formulations (e.g., beads, granules or crystals), aerosols, sprays, foams, solutions, dispersions, tinctures, syrups, elixirs, suspensions, water-in-oil emulsions such as ointments,
  • the ("sense” and "anti-sense”) nucleic acid molecules described above can be formulated into pharmaceutical compositions using pharmacologically acceptable ingredients as well as established methods of preparation (Gennaro, A.L. and Gennaro, A.R. (2000) Remington: The Science and Practice of Pharmacy, 20th Ed., Lippincott Williams & Wilkins, Philadelphia, PA; Crowder, T.M. et al. (2003 ) A Guide to Pharmaceutical Particulate Science. Interpharm/CRC, Boca Raton, FL; Niazi, S.K. (2004) Handbook of Pharmaceutical Manufacturing Formulations, CRC Press, Boca Raton, FL).
  • pharmaceutically inert inorganic or organic excipients i.e. carriers
  • pharmaceutically inert inorganic or organic excipients i.e. carriers
  • a suitable excipient for the production of solutions, suspensions, emulsions, aerosol mixtures or powders for reconstitution into solutions or aerosol mixtures prior to use include water, alcohols, glycerol, polyols, and suitable mixtures thereof as well as vegetable oils.
  • the pharmaceutical composition may also contain additives, such as, for example, fillers, binders, wetting agents, glidants, stabilizers, preservatives, emulsifiers, and furthermore solvents or solubilizers or agents for achieving a depot effect.
  • additives such as, for example, fillers, binders, wetting agents, glidants, stabilizers, preservatives, emulsifiers, and furthermore solvents or solubilizers or agents for achieving a depot effect.
  • additives such as, for example, fillers, binders, wetting agents, glidants, stabilizers, preservatives, emulsifiers, and furthermore solvents or solubilizers or agents for achieving a depot effect.
  • the nucleic acid molecules may be incorporated into slow or sustained release or targeted delivery systems, such as liposomes, nanoparticles, and microcapsules.
  • One approach involves covalently coupling the passenger strand (miRNA* strand) of the miRNA to cholesterol or derivatives/conjugates thereof to facilitate uptake through ubiquitously expressed cell-surface LDL receptors (Soutschek, J. et al. (2004) Nature 432, 173-178).
  • unconjugated, PBS-formulated locked-nucleic-acid-modified oligonucleotides (LNA-antimiR) may be used for systemic delivery (Elmen, J. et al. (2008) Nature 452, 896-899).
  • Another strategy for delivering miRNAs involves encapsulating the miRNAs into specialized liposomes formed using polyethylene glycol to reduce uptake by scavenger cells and enhance time spent in the circulation.
  • lipidoids synthesis scheme based upon the conjugate addition of alkylacrylates or alkyl- acrylamides to primary or secondary amines
  • RNAi therapeutics Akinc, A. et al. (2008) Nat Biotechnol 26, 561-569.
  • a further targeting strategy involves the mixing of miRNAs with a fusion protein composed of a targeting antibody fragment linked to protamine, the basic protein that nucleates DNA in sperm and binds miRNAs by charge (Song, E. et al. (2005) Nat. Biotechnol. 23, 709-717).
  • a fusion protein composed of a targeting antibody fragment linked to protamine, the basic protein that nucleates DNA in sperm and binds miRNAs by charge
  • a fusion protein composed of a targeting antibody fragment linked to protamine, the basic protein that nucleates DNA in sperm and binds miRNAs by charge
  • Example 1 Tissue sample collection and preparation
  • Patient data (age, sex, imaging data, therapy, other medical conditions, family history, and the like) were derived from the hospital databases for matching the various samples collected.
  • Pathologic follow-up (for example, histological analysis via hematoxylin and eosin (H&E) staining) was used for evidently determining the disease state (i.e. control, pre -cancerous stage (e.g., colorectal adenoma), primary malignancy (e.g., colorectal carcinoma) of a given sample as well as to ensure a consistent classification of the specimens.
  • H&E histological analysis via hematoxylin and eosin
  • Laser-capture micro-dissection was optionally performed for each cancerous sample in order to specifically isolate tumor cell populations (about 200.000 cells).
  • a transparent transfer film is applied to the surface of a tissue section or specimen. Under a microscope, the thin tissue section is viewed through the glass slide on which it is mounted and clusters of cells are identified for isolation.
  • a near IR laser diode integral with the microscope optics is activated. The pulsed laser beam activates a spot on the transfer film, fusing the film with the underlying cells of choice. The transfer film with the bonded cells is then lifted off the thin tissue section (Emmert- Buck, M.R. et al. (1996).
  • Example 2 Analysis of the miRNA expression profile in the tissue samples
  • a qualitative analysis of the miRNAs (differentially) expressed in a particular sample may optionally be performed using the Agilent miRNA microarray platform (Agilent Technologies, Santa Clara, CA, USA).
  • the microarray contains probes for 723 human miRNAs from the Sanger database v.10.1. Total RNA (100 ng) derived from each of 138 LCM-selected colorectal samples were used as inputs for labeling via Cy3 incorporation.
  • Microarray slides were scanned by XDR Scan (PMTIOO, PMT5). The labeling and hybridization were performed according to the protocols in the Agilent miRNA microarray system.
  • the raw data obtained for single-color (CY3) hybridization were normalized by applying a Quantile method and using GeneSpring GX10 software (Agilent Technologies, Santa Clara, CA, USA) known in the art. Unpaired t-test (p value ⁇ 0.01) after Fisher test (F-test) was used to identify differentially expressed miRNAs between colorectal cancer and matched normal control tissues.
  • Example 3 Plasma sample collection and preparation
  • Peripheral blood (2 ml) was drawn into EDTA tubes. Within two hours, the tubes were subjected to centrifuge at 820g for 10 min. Then, 1-ml aliquots of the plasma was transferred to 1.5-ml tubes and centrifuged at 16,000g for 10 min to pellet any remaining cellular debris. Subsequently, the supernatant was transferred to fresh tubes and stored them at -80 °C.
  • a qualitative analysis of the miRNAs (differentially) expressed in a particular plasma sample may optionally be performed using the Agilent miRNA microarray platform (Agilent Technologies, Santa Clara, CA, USA).
  • the microarray contains probes for 723 human miRNAs from the Sanger database v.10.1. Total RNA (100 ng) derived from each of 114 plasma samples were used as inputs for labeling via Cy3 incorporation.
  • Microarray slides were scanned by XDR Scan (PMT100, PMT5). The labeling and hybridization were performed according to the protocols in the Agilent miRNA microarray system.
  • the raw data obtained for single-color (CY3) hybridization were normalized by applying a stable internal miRNA control (has-miR-1238).
  • Unpaired t-test after Fisher test (F-test) was used to identify differentially expressed miRNAs between colorectal cancer patients vs. healthy individuals, and/or colorectal cancer patients vs. controls (healthy individuals, hepatocellular carcinoma and lung cancer), respectively.
  • ROC receiver operating characteristic
  • the miRNA was considered to be differentially expressed in colorectal cancer patients as compared to healthy individuals, and/or controls, respectively.
  • Tables 4-6 The experimental data in the differential miRNA expression analysis between CRC vs. healthy controls are summarized in Tables 4-6 below.
  • Table 4 lists the miRNAs exhibiting significantly differential expressions in both tissue and plasma of CRC patients as compared to control tissues and healthy control plasma, respectively.
  • Table 5 summarizes the miRNAs exhibiting a differential expression only in plasma of colorectal cancer patients as compared to healthy individuals, whereas Table 6 lists the ' best combinations of the miRNA signatures in plasma of CRC patients.
  • t denotes the colorectal cancer tissue
  • n denotes match normal control tissue
  • p denotes the patients
  • “h” denotes healthy controls.
  • Particularly preferred miRNAs SEQ ID NO: 1 to SEQ ID NO: 8 in Table 4; SEQ ID NO: 21 to SEQ ID NO: 24 in Table 5, respectively.
  • Table 7 lists tumor-related miRNA signatures for colorectal cancer; Table 8 shows plasma-specific miRNA signatures, whereas Table 9 displays the best combinations of the miRNA signatures for colorectal cancer.
  • the top combination (hsa- miR-33b* hsa-rniR-196a) had 85% accuracy as diagnostic biomarkers in differentiating CRC from healthy individuals, hepatocellular carcinoma and lung cancer.
  • t denotes the colorectal cancer tissue
  • n denotes match normal control tissue
  • CRC denotes the colorectal cancer plasma
  • control denotes plasma derived from healthy individuals, hepatocellular carcinoma and lung cancer patients.
  • Particularly preferred miRNAs are shown in bold.
  • Tumor-related miRNA signatures for colorectal cancer in discriminating healthy control are Tumor-related miRNA signatures for colorectal cancer in discriminating healthy control.
  • RT solutions were performed by using the thermal program of 16°C, 30min; 42°C, 30min; 85°C, 5min on the PCR machine (Thermal cycler alpha engine, Bio-rad). Quantitative PCR was performed with TaqMan Universal PCR Master Mix kit and and Taqman microRNA assays kits according to the instruction from Applied Biosystem. 2ul RT products were PCR amplified in IX TaqMan Universal PCR Master Mix, No AmpErase UNG, IX TaqMan MicroRNA Assay mix. Each reaction was duplicated in triple. The real-time PCR was performed in Roch Light Cycling 480 machine with the program of 96°C, 5min initial heating; then 45 or 50 cycles of 95°C, 15s; 60°C, 60s. Cp value was calculated with 2nd derivative method in LC480 software. Then miRNAs were absolutely quantified with the standard samples CP values. For the CP value for each miRNA was normalized one internal stable control hsa-miR- 1228.
  • the results obtained demonstrate a global highly specific regulation of miRNA 10 expression in colorectal cancer.
  • the respective subsets of miRNAs specified herein represent unique miRNA expression signatures for expression profiling of colorectal cancer that do not only allow the identification of a cancerogenous state as such but also enables the discrimination of hepatocellular carcinoma and lung cancer
  • the identification of the miRNA expression signatures of the present invention 15 provides a unique molecular marker that allows screening, detection, diagnosing colorectal cancer in blood. Furthermore, the expression signatures can be used to monitor the therapy response and guide the treatment decision in colorectal cancer patients. Additionally, the expression signatures may be also used for development of anti-colorectal cancer drugs.

Abstract

La présente invention concerne des compositions et des procédés de profilage de l'expression de micro-ARN (mi-ARN) dans un plasma d'un cancer colorectal. L'invention concerne notamment un kit de diagnostic de marqueurs moléculaires dans le sang pour le diagnostic du cancer colorectal, le suivi du traitement du cancer et/ou le traitement du cancer colorectal. Selon l'invention, le kit comprend une pluralité de molécules d'acide nucléique, chaque molécule d'acide nucléique codant pour une séquence de micro-ARN, une ou plusieurs molécules parmi la pluralité de molécules d'acide nucléique étant exprimées différemment dans un plasma d'un cancer colorectal et dans un plasma témoin sain, et la ou les molécules d'acide nucléique exprimées différemment représentant ensemble une signature d'expression d'acides nucléiques qui est indicatrice de la présence d'un cancer colorectal. L'invention concerne également des procédés correspondants d'utilisation de telles signatures d'expression d'acides nucléiques pour identifier un cancer colorectal et pour la prévention ou le traitement d'une telle maladie. L'invention concerne enfin une composition pharmaceutique pour la prévention et/ou le traitement du cancer colorectal.
PCT/CN2010/080233 2009-12-24 2010-12-24 Compositions et procédés pour le profilage de l'expression de micro-arn dans un plasma d'un cancer colorectal WO2011076142A1 (fr)

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