US20040152112A1 - Compositions and methods for cancer diagnosis and therapy - Google Patents

Compositions and methods for cancer diagnosis and therapy Download PDF

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US20040152112A1
US20040152112A1 US10/706,798 US70679803A US2004152112A1 US 20040152112 A1 US20040152112 A1 US 20040152112A1 US 70679803 A US70679803 A US 70679803A US 2004152112 A1 US2004152112 A1 US 2004152112A1
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mir15
mir16
cells
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Carlo Croce
George Calin
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Thomas Jefferson University
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Assigned to THOMAS JEFFERSON UNIVERSITY reassignment THOMAS JEFFERSON UNIVERSITY ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: CROCE, CARLO
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Priority to US11/375,650 priority patent/US7723035B2/en
Priority to US12/319,331 priority patent/US9006190B2/en
Priority to US12/727,778 priority patent/US8557515B2/en
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/10—Dispersions; Emulsions
    • A61K9/127—Synthetic bilayered vehicles, e.g. liposomes or liposomes with cholesterol as the only non-phosphatidyl surfactant
    • 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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P13/00—Drugs for disorders of the urinary system
    • A61P13/08—Drugs for disorders of the urinary system of the prostate
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/02—Antineoplastic agents specific for leukemia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
    • 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
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering nucleic acids [NA]
    • C12N2310/141—MicroRNAs, miRNAs
    • C—CHEMISTRY; METALLURGY
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/178—Oligonucleotides characterized by their use miRNA, siRNA or ncRNA

Definitions

  • the invention relates to the diagnosis of cancers, in particular to the diagnosis of chronic lymphocytic leukemias or prostate cancer by detecting miR15 and miR16 copy number, mutational status, or gene expression.
  • the invention also relates to the treatment of cancers, involving the reduction or absence of miR15 or miR16 gene expression, in particular to the treatment of chronic lymphocytic leukemias or prostate cancer by administering miR15 or miR16 gene products.
  • CLL chronic lymphocytic leukemia
  • prostate cancer are clinically important neoplastic diseases of adult humans.
  • CLL is the most common form of adult leukemia in the Western world.
  • the age-adjusted incidence of prostate cancer now surpasses that of all other cancers among men in the United States, and, after lung cancer, is the second leading cause of all male cancer deaths in the country.
  • miRNAs are found in over one hundred distinct organisms, including fruit flies, nematodes and humans. miRNAs are believed to be involved in a variety of processes that modulate development in these organisms.
  • the miRNAs are typically processed from 60- to 70-nucleotide foldback RNA precursor structures, which are transcribed from the miRNA gene.
  • the RNA precursor or processed miRNA products are easily detected, and a lack of these molecules can indicate a deletion or loss of function of the corresponding miRNA gene.
  • Prostate cancer can also be treated with external beam radiation or brachytherapy (e.g., with radioactive “seeds”), again either alone or in combination with surgery.
  • brachytherapy e.g., with radioactive “seeds”
  • Such treatments risk exposing normal tissue of the patient to the radiation, and may not be entirely effective.
  • the miR15 or miR16 genes are localized to 13q14 in humans, and that the 13q14 region is deleted in a significant portion of subjects suffering from CLL or prostate cancer. It has also been found that the RNA products of the miR15 or miR16 genes inhibit the neoplastic or tumorigenic growth of CLL and prostate cancer cells. The RNA products can be used as a therapy for cancers which involve downregulation of the miR15 or miR16 genes.
  • the miR15 and miR16 micro RNA genes are located at 13q14 within a 30 kb region of loss in CLL and prostate cancer, and both genes are deleted or down-regulated in the majority of CLL and prostate cancer cases.
  • the invention provides a diagnostic test for CLL or prostate cancer comprising detection of the gene product from these genes, detection of miR15 or miR16 gene copy number, or determination of the mutational status.
  • the diagnostic test comprises isolating RNA from a subject suspected of having CLL or prostate cancer, and detecting the levels of the miR15 or miR16 gene product by Northern blot hybridization using probes for miR15 or miR16 RNA precursor or processed miRNA, wherein a reduction in miR15 or miR16 precursor or processed microRNA as compared to a control normal sample is diagnostic of CLL or prostate cancer.
  • the diagnostic test comprises isolating DNA from a subject suspected of having an miR15 or miR16 mediated cancer such as CLL or prostate cancer, and detecting the miR15 or miR16 gene copy number by Southern blot hybridization using probes for miR15 or miR16 gene sequences, wherein a reduction in gene copy number to one or zero is diagnostic of CLL or prostate cancer.
  • the diagnostic test comprises detecting a reduction in miR15 or miR16 gene copy number by evaluating the loss of heterozygosity of the D13S273 and D13S272 markers, wherein a loss of heterozygosity at these markers is diagnostic of CLL or prostate cancer.
  • the diagnostic test comprises isolating DNA from a subject suspected of having CLL or prostate cancer, and detecting deletions or mutations in the miR15 or miR16 genes by PCR amplification of miR15 or miR16 gene fragments and comparing the amplified fragments with amplified fragments from a control normal sample, wherein the detection of a mutation in one or more copies of the miR15 or miR16 genes is diagnostic of CLL or prostate cancer.
  • the amplified fragments can be compared by the single stranded conformational polymorphism technique.
  • the mutation is a partial deletion in the miR15 or miR16 gene sequences.
  • the diagnostic test comprises isolating RNA from a subject suspected of having CLL or prostate cancer and detection of a mutation in miR15 or miR16 gene products is diagnostic of CLL or prostate cancer.
  • the diagnostic test comprises isolating RNA from a subject suspected of having CLL or prostate cancer, and detecting the levels of the miR15 or miR16 gene product by amplification of the miR15 or miR16 precursor or processed microRNA by reverse-transcriptase polymerase chain reaction, wherein a reduction in miR15 or miR16 precursor or processed microRNA as compared to an internal control amplified RNA is diagnostic of CLL or prostate cancer.
  • the invention also provides a method of treating an miR15 or miR16 mediated cancer in a subject in need of such treatment, comprising administering an effective amount of an miR15 or miR16 gene product to the subject, such that proliferation of cancer cells in inhibited.
  • the invention also provides a method of treating miR15 or miR16 mediated cancer in a subject in need of such treatment, in which cells from the subject are isolated and transfected ex vivo with an effective amount a nucleic acid comprising sequences encoding the miR15 or miR16 gene product.
  • the expression of the miR15 or miR16 gene product in the transfected cells can be confirmed.
  • the cells are then reimplanted into the subject, and proliferation of cancer cells in the subject is inhibited.
  • the invention still further provides a pharmaceutical composition for treating a subject having miR15 or miR16 mediated cancer, comprising an isolated miR15 or miR16 gene product, or a nucleic acid encoding an miR15 or miR16 gene product, and a pharmaceutically acceptable carrier.
  • FIGS. 1A and 1B are schematic representations of the predicted secondary structure of the miR15 and miR16 precursor RNA, respectively.
  • the RNA secondary structure prediction was performed using the “mfold” program, version 3.1 of Matthews et al. (1999), J. Mol. Biol. 288:911-940, and manually refined to accommodate G/U wobble base pairs in the helical segments.
  • the sequence of the processed miR15 and miR16 miRNA is underlined. Adapted from Lagos-Quintana et al. (2001), Science 294:853-858.
  • FIG. 2A is map of genes within the 13q14 tumor suppressor locus in CLL showing the localization of the miR15/16 gene cluster. The position of genetic markers and the position of genes on the map are shown.
  • FIG. 2B is a map of previously reported 13q14 deletions, marked by horizontally striped boxes.
  • FIG. 2C is a map of the locus between the D13S1150 and D13S272 markers. The orientation of each gene in this locus is marked by an arrow under the gene name, and colored vertical bars mark the position of corresponding exons for each gene.
  • FIG. 2D is a map of the locus between the Alu 18 and D13S272 markers. Bars and boxes mark the position of exons for LEU2/ALT1 and LEU1. The short vertical arrows mark the position of miR15 and miR16 genes. Circles mark the position of PCR primers used to screen somatic cell hybrid clones derived from a fusion of two independent leukemia cases (CLL-A and CLL-B). Filled boxes represent portions of chromosome 13 present in the hybrids.
  • ⁇ ⁇ 31.4 kb ⁇ indicates an approximately 31.4 kb deleted region in clone CLL-A, which was derived from a patient with CLL carrying a t(2;13)(q12;q13) translocation, bilateral retinoblastoma, and ulcerative colitis.
  • the long vertical arrow represents the position of the breakpoint in clone CLL-B carrying a t(2;13)(q32;q14) translocation
  • ⁇ ⁇ 29 kb ⁇ indicates an approximately 29 kb deleted region in this clone.
  • FIG. 3A is a Northern blot analysis of miR15 and miR16 gene expression in normal human kidney, prostate, liver, skeletal muscle (“Sk muscle”), testicle, CD5+ B cells (CD5+), leukemia cells (“Per B1 Leuk”), and bone marrow (“BM”).
  • FIG. 3B is a loss of heterozygosity (“LOH”) analysis of microsatellite makers D13S272 and D13S273 in 18 CLL patients.
  • DNA from normal human CD5+ cells was used as a control.
  • the LOH status for the samples is shown as “+/+ heterozygosity,” “+/ ⁇ LOH,” “ ⁇ / ⁇ homozygous deletion,” “NI” (not informative), “?” (not enough material) and “ND” (not done).
  • Ethidium bromide-stained Northern gels were used as normalization controls.
  • nucleic acid sequences herein are given in the 5′ to 3′ direction.
  • deoxyribonucleotides in a nucleic acid sequence are represented by capital letters (e.g., deoxythymidine is “T”), and ribonucleotides in a nucleic acid sequence are represented by lower case letters (e.g., uridine is “u”).
  • CLL or prostate cancer can be diagnosed by detecting a reduction in miR15 or miR16 gene copy number, or by detecting mutations in one or more copies of the miR15 or miR16 genes.
  • a reduction in miR15 or miR16 gene copy number from diploid to haploid, or to no copies, is diagnostic of CLL or prostate cancer.
  • a mutation in one or both copies of the miR15 or miR16 genes implies a loss of gene function, and is diagnostic of CLL or prostate cancer.
  • a “CLL cell” is a lymphocyte from a subject who has or is suspected of having CLL, which lymphocyte has a “CLL Score” of at least 4 as determined according to the scoring system of Matutes et al. (1994), Leukemia 8(10):1640-1645, the entire disclosure of which is herein incorporated by reference.
  • a “prostate cancer cell” is a neoplastic or tumorigenic cell of prostate origin, whether or not located in the prostate. One skilled in the art can readily identify a CLL or prostate cancer cell.
  • the miR15/miR16 gene cluster has been mapped to 13q14.
  • the nucleic acid sequences of these genes are contained within clone 317g11, the nucleotide sequence of which is given in GenBank record accession no. AC069475. The entire disclosure of that record is incorporated herein by reference.
  • a deletion or mutation in the miR15 or miR16 genes can be detected by determining the structure or sequence of these genes in tissue from a subject suspected of having CLL or prostate cancer, and comparing this with the structure or sequence of these genes in a sample of unaffected tissue from the subject, or in a sample of tissue from a normal control. Such a comparison can be made by any suitable technique.
  • tissue sample is derived from a subject. The sample is then prepared for determination of miR15 or miR16 gene product expression or deletion or mutation of miR15 or miR16 genes.
  • a tissue sample includes a biopsy of interest, as well as blood and fluid samples.
  • an “miR15 or miR16 mediated cancer” is any cancer in which the expression of the miR15 or miR16 genes is reduced or absent in at least a portion of tumorigenic or neoplastic cells associated with that cancer.
  • Examples of miR15 or miR16 mediated cancers include CLL and prostate cancer.
  • the presence of miR15 or miR16 deletions or mutations can be detected by Southern blot hybridization of the genomic DNA from a subject, using probes for miR15 or miR16 genes, e.g., as described below.
  • a sample of tissue or blood can be removed from a subject suspected of having CLL or prostate cancer by conventional biopsy techniques.
  • a blood sample can be removed from a subject suspected of having CLL or prostate cancer, and white blood cells isolated for DNA extraction.
  • the blood or tissue sample is preferably obtained from the patient prior to initiation of radiotherapy or chemotherapy.
  • a corresponding tissue or blood sample can be obtained from unaffected tissues of the subject, or from a normal human individual, for use as a control.
  • Southern blot hybridization techniques are within the skill in the art.
  • the genomic DNA isolated from tissue or blood from a subject suspected of having CLL or prostate cancer can be digested with restriction endonucleases. This digestion generates restriction fragments of the genomic DNA, which can be separated by electrophoresis, for example on an agarose gel.
  • the restriction fragments are then blotted onto a hybridization membrane (e.g., nitrocellulose or nylon), and hybridized with labeled probes specific for the miR15 or miR16 genes.
  • a deletion or mutation of these genes is indicated by an alteration of the restriction fragment patterns on the hybridization membrane, as compared to a control DNA sample which has been treated identically to the DNA sample from the subject.
  • Probe labeling and hybridization conditions suitable for detecting miR15 or miR16 gene copy number or mutations can be readily determined by one of ordinary skill in the art.
  • the term “deletion,” as used herein, refers to partial deletion of a gene or to deletion of the entire gene.
  • the miR15 and miR16 nucleic acid probes for Southern blot hybridization can be designed based upon the published sequence of the miR15 and miR16 microRNAs as described in Lagos-Quintana et al. (2001), Science 294:853-858, the entire disclosure of which is incorporated herein by reference.
  • the nucleotide sequence of the miR15 microRNA is uagcagcacauaaugguuugug (SEQ ID NO:3).
  • the nucleotide sequence of the miR16 microRNA is uagcagcacguaaauauuggcg (SEQ ID NO:4).
  • Suitable probes for detecting miR15 and miR16 DNA are, respectively: CACAAACCATTATGTGCTTGCTA (SEQ ID NO: 5) GCCAATATTTACGTGCTGCTA (SEQ ID NO: 6)
  • SEQ ID NO:5 and SEQ ID NO:6 can also be used to probe for miR15 or miR16 DNA.
  • the nucleic acid probe can be labeled with, e.g., a radionuclide such as 3 H, 32 P, 33 P, 14 C, or 35 S; a heavy metal; or a ligand capable of functioning as a specific binding pair member for a labeled ligand (e.g., biotin, avidin or an antibody), a fluorescent molecule, a chemiluminescent molecule, an enzyme or the like.
  • a radionuclide such as 3 H, 32 P, 33 P, 14 C, or 35 S
  • a heavy metal e.g., a ligand capable of functioning as a specific binding pair member for a labeled ligand (e.g., biotin, avidin or an antibody), a fluorescent molecule, a chemiluminescent molecule, an enzyme or the like.
  • Probes can be labeled to high specific activity by either the nick translation method of Rigby et al. (1977), J. Mol. Biol. 113:237-251 or by the random priming method of Fienberg et al. (1983), Anal. Biochem. 132:6-13, the entire disclosures of which are herein incorporated by reference. The latter is the method of choice for synthesizing 32 P-labeled probes of high specific activity from single-stranded DNA or from RNA templates.
  • nick translation method by replacing preexisting nucleotides with highly radioactive nucleotides according to the nick translation method, it is possible to prepare 32 P-labeled nucleic acid probes with a specific activity well in excess of 10 8 cpm/microgram. Autoradiographic detection of hybridization can then be performed by exposing hybridized filters to photographic film. Densitometric scanning of the photographic films exposed by the hybridized filters provides an accurate measurement of miR15 or miR16 gene copy number. Alternatively, miR15 or miR16 gene copy number can be quantified by computerized imaging systems, such the Molecular Dynamics 400-B 2D Phosphorimager available from Amersham Biosciences, Piscataway, N.J.
  • the random-primer method can be used to incorporate the dTTP analogue 5-(N-(N-biotinyl-epsilon-aminocaproyl)-3-aminoallyl)deoxyuridine triphosphate into the probe molecule.
  • the biotinylated probe oligonucleotide can be detected by reaction with biotin-binding proteins such as avidin, streptavidin, or anti-biotin antibodies coupled with fluorescent dyes or enzymes which produce color reactions.
  • Deletions or mutations of the miR15 or miR16 genes can also be detected by amplifying a fragment of these genes by polymerase chain reaction (PCR), and analyzing the amplified fragment by sequencing or by electrophoresis to determine if the sequence and/or length of the amplified fragment from the subject's DNA sample is different from that of the control DNA sample.
  • PCR polymerase chain reaction
  • Suitable reaction and cycling conditions for PCR amplification of DNA fragments can be readily determined by one of ordinary skill in the art. Exemplary PCR reaction and cycling conditions are given in the methods used for the Examples, below.
  • Diagnosis of an miR15 or miR16 mediated cancer can be performed by detecting deletions of 13q14 between various chromosome markers, such as the markers indicated in FIGS. 1A, 1B, and 2 A-2D.
  • a deletion in the region of 13q14 between microsatellite markers D13S272 and D13S273 comprising miR15 or miR16 indicates the presence of an miR15 or miR16 mediated cancer.
  • An alternative method of determining the number of miR15 or miR16 genes per diploid genome in a sample of tissue relies on the fact that the miR15/miR16 gene cluster is located in 13q14, and is linked to the markers D13S272 and D13S273.
  • the loss of a copy of the miR15 or miR16 genes in an individual who is heterozygous at a locus linked to the D13S272 and D13S273 markers can be inferred from the loss of heterozygosity in these markers.
  • Methods for determining loss of heterozygosity of chromosomal markers are within the skill in the art. An exemplary loss of heterozygosity study is given in Example 3 below.
  • SSCP single strand conformational polymorphism
  • a deletion or mutation in one or both miR15 or miR16 genes can also cause a reduction in miR15 or miR16 gene expression.
  • CLL or prostate cancer can also be diagnosed by detecting expression levels of the RNA produced from the miR15 or miR16 genes, where a reduction in miR15 or miR16 gene expression is diagnostic of CLL or prostate cancer.
  • the miR15 and miR16 genes are each transcribed to produce a ⁇ 70 kb precursor RNA which forms a stem-loop structure.
  • the precursor RNA is not translated into a protein, but is rather processed into a “micro RNA” or “miRNA,” which is believed to be the functional gene product.
  • an “miR15 or miR16 gene product” means the processed or unprocessed RNA transcripts from the miR15 or miR16 genes, as described more fully below.
  • RNA RNA transcripts
  • gene product are used interchangeably herein in the context of miR15 or miR16 gene expression.
  • the miR15 and miR16 precursor RNAs are described in Lagos-Quintana et al. (2001), Science 294, 853-858, the entire disclosure of which is incorporated herein by reference.
  • the sequences of the miR15 and miR16 precursor RNAs are given in SEQ ID NO:1 and SEQ ID NO:2.
  • the predicted stem-loop structures of SEQ ID NO:1 and SEQ ID NO:2, are shown in FIGS. 1A and 1B, respectively.
  • the miR15 and miR16 precursor RNAs are co-expressed from the miR15/miR16 gene cluster, and are processed by the Dicer/Argonaute complex into the functional miRNA products. See, e.g., Lee et al. (2001), Science 294:862. Both functional miRNA products from these genes are single-stranded RNA molecules of 22 nucleotides in length which have a 5′ terminal monophosphate and a 3′ terminal hydroxyl group.
  • the nucleotide sequence of the processed miR15 microRNA is uagcagcacauaaugguuugug (SEQ ID NO:3).
  • the nucleotide sequence of the processed miR16 microRNA is uagcagcacguaaauauuggcg (SEQ ID NO:4).
  • the 60-70 nt RNA precursor molecules produced from the miR15 or miR16 genes can be detected.
  • the shorter miR15 and miR16 microRNA gene products which are produced through processing of the precursor RNAs by the Dicer and Argonaute proteins, can be detected.
  • RNA expression levels are within the level of skill in the art. For example, a sample of tissue or blood from a subject suspected of having CLL or prostate cancer is obtained as described above. As a control, a corresponding tissue or blood sample can be obtained from unaffected tissues of the subject, or from a normal human individual as described above. The control tissue or blood sample is then processed along with the sample from the subject. The levels of miR15 or miR16 gene expression in the subject can then be compared to those from unaffected tissue from the subject, or to the miR15 or miR16 expression levels in tissue or blood from the normal control.
  • the relative miR15 or miR16 expression level in CLL cells or cells of the sampled prostate tumor are conveniently determined with respect to one or more standards.
  • the standards may comprise, for example, a zero expression level on the one hand and the expression level of the gene in normal tissue of the same patient, or the expression level in the tissue of a normal control group on the other hand.
  • the standard may also comprise the miR15 or miR16 expression level in a standard cell line. The size of the decrement in miR15 or miR16 expression in comparison to normal expression levels is indicative of the future clinical outcome following treatment.
  • the levels of miR15 or miR16 gene expression in a subject suspected of having CLL or prostate cancer can be compared to average levels of miR15 or miR16 gene expression previously obtained for a population of normal human controls.
  • RNA transcripts of a particular gene in cells are well known to those skilled in the art. According to one such method, total cellular RNA can be purified from cells by homogenization in the presence of nucleic acid extraction buffer, followed by centrifugation. Nucleic acids are precipitated, and DNA is removed by treatment with DNase and precipitation. The RNA molecules are then separated by gel electrophoresis on agarose gels according to standard techniques, and transferred to nitrocellulose filters by, e.g., the so-called “Northern” blotting technique. The RNA is then immobilized on the filters by heating.
  • RNA Detection and quantification of specific RNA is accomplished using appropriately labeled DNA or RNA probes complementary to the RNA in question. See, for example, Molecular Cloning: A Laboratory Manual , J. Sambrook et al., eds., 2nd edition, Cold Spring Harbor Laboratory Press, 1989, Chapter 7, the entire disclosure of which is incorporated by reference.
  • Suitable probes for Northern blot hybridization of miR15 or miR16 RNA include SEQ ID NO:5 and SEQ ID NO:6.
  • RNA transcript levels can be quantified by computerized imaging of the hybridization blot, for example with the Molecular Dynamics 400-B 2D Phosphorimager available from Amersham Biosciences, Piscataway, N.J.
  • RNA transcripts can be carried out according to the technique of in situ hybridization.
  • This technique requires fewer cells than the Northern blotting technique, and involves depositing whole cells onto a microscope cover slip and probing the nucleic acid content of the cell with a solution containing radioactive or otherwise labeled cDNA or cRNA probes.
  • This technique is particularly well-suited for analyzing tissue biopsy samples from subjects suspected of having prostate cancer.
  • the practice of the in situ hybridization technique is described in more detail in U.S. Pat. No. 5,427,916, the entire disclosure of which is incorporated herein by reference.
  • Suitable probes for in situ hybridization of miR15 or miR16 RNA include SEQ ID NO:5 and SEQ ID NO:6.
  • the relative number of miR15 or miR16 transcripts can also be determined by reverse transcription of miR15 or miR16 transcripts, followed by amplification in a polymerase chain reaction (RT-PCR).
  • the levels of miR15 or miR16 transcripts can be quantified in comparison with an internal standard, for example, levels of mRNA from a “housekeeping” gene present in the same sample.
  • a suitable “housekeeping” gene for use as an internal standard includes myosin or glyceraldehyde-3-phosphate dehydrogenase (G3PDH).
  • G3PDH myosin or glyceraldehyde-3-phosphate dehydrogenase
  • An miR15 or miR16 mediated cancer can be treated by administering the isolated gene product of the miR15 or miR16 genes, either alone or in combination, to an miR15 or miR16 mediated cancer cell. Without wishing to be bound by any theory, it is believed that the miR15 or miR16 gene products suppress the neoplastic or tumorigenic growth of such cancer cells.
  • CLL or prostate cancer can be treated by administering the isolated gene product of the miR15 or miR16 genes, either alone or in combination, to a CLL or prostate cancer cell.
  • an “miR15 or miR16 mediated cancer cell” is a tumorigenic or neoplastic cell isolated from a subject suffering from an miR15 or miR16 mediated cancer.
  • An miR15 or miR16 mediated cancer cell can be identified by detecting a reduction or absence of miR15 or miR16 gene products in the cell, or by detecting a cancerous or neoplastic phenotype in the cell.
  • One skilled in the art can readily identify cells with a cancerous or neoplastic phenotype. For example, such cells are insensitive to contact-induced growth inhibition in culture, and will form foci when cultured for extended periods.
  • Cancerous or neoplastic cells also exhibit characteristic morphological changes, disorganized patterns of colony growth and acquisition of anchorage-independent growth. Cancerous or neoplastic cells also have the ability to form invasive tumors in susceptible animals, which can be evaluated by injecting the cells, for example, into athymic mice using techniques within the skill in the art.
  • an “isolated” gene product is one which is altered or removed from the natural state through human intervention.
  • an RNA naturally present in a living animal is not “isolated.”
  • a synthetic RNA, or an RNA partially or completely separated from the coexisting materials of its natural state is “isolated.”
  • An isolated RNA can exist in substantially purified form, or can exist in a cell into which the RNA has been delivered.
  • an miR15 or miR16 gene product which is deliberately delivered to or expressed in a cell such as a CLL or prostate cancer cell, is considered an “isolated” gene product.
  • the miR15 and miR16 gene products can be obtained using a number of standard techniques.
  • the gene products can be chemically synthesized or recombinantly produced using methods known in the art.
  • the RNA products are chemically synthesized using appropriately protected ribonucleoside phosphoramidites and a conventional DNA/RNA synthesizer.
  • RNA molecules or synthesis reagents Commercial suppliers of synthetic RNA molecules or synthesis reagents include Proligo (Hamburg, Germany), Dharmacon Research (Lafayette, Colo., USA), Pierce Chemical (part of Perbio Science, Rockford, Ill., USA), Glen Research (Sterling, Va., USA), ChemGenes (Ashland, Mass., USA) and Cruachem (Glasgow, UK).
  • the miR15 and miR16 gene products can be expressed from recombinant circular or linear DNA plasmids using any suitable promoter.
  • suitable promoters for expressing RNA from a plasmid include the U6 or H1 RNA pol III promoter sequences, or the cytomegalovirus promoters. Selection of other suitable promoters is within the skill in the art.
  • the recombinant plasmids of the invention can also comprise inducible or regulatable promoters for expression of the miR15 and miR16 gene products in CLL, prostate cancer, or other cells.
  • the miR15 and miR16 gene products which are expressed from recombinant plasmids can be isolated from cultured cell expression systems by standard techniques.
  • the miR15 and miR16 gene products which are expressed from recombinant plasmids can also be delivered to and expressed directly in the CLL or prostate cancer cells.
  • the use of recombinant plasmids to deliver the miR15 and miR16 gene products to CLL or prostate cancer cells is discussed in more detail below.
  • the miR15 and miR16 gene products can be expressed from a separate recombinant plasmid, or can be expressed from the same recombinant plasmid.
  • the miR15 and miR16 gene products are expressed as the RNA precursor molecules from a single plasmid, and the precursor molecules are processed into the functional miRNA molecules by a suitable processing system.
  • suitable processing systems include the in vitro Drosophila cell lysate system as described in U.S. published application 2002/0086356 of Tuschl et al., the entire disclosure of which is herein incorporated by reference.
  • a plasmid expressing the miR15 or miR16 gene products comprises a sequence encoding the miR15 or miR16 precursor RNA under the control of the CMV intermediate-early promoter.
  • “under the control” of a promoter means that the nucleic acid sequences encoding the miRNA product are located 3′ of the promoter, so that the promoter can initiate transcription of the miRNA product coding sequences.
  • the miR15 or miR16 gene products can also be expressed from recombinant viral vectors. It is contemplated that the miR15 and miR16 gene products can be expressed from two separate recombinant viral vectors, or from the same viral vector.
  • the RNA expressed from the recombinant viral vectors can either be isolated from cultured cell expression systems by standard techniques, or can be expressed directly in CLL or prostate cancer cells. The use of recombinant viral vectors to deliver the miR15 or miR16 gene products to CLL or prostate cancer cells is discussed in more detail below.
  • the recombinant viral vectors of the invention comprise sequences encoding the miR15 and miR16 gene products and any suitable promoter for expressing the RNA sequences.
  • suitable promoters include, for example, the U6 or H1 RNA pol III promoter sequences, or the cytomegalovirus promoters. Selection of other suitable promoters is within the skill in the art.
  • the recombinant viral vectors of the invention can also comprise inducible or regulatable promoters for expression of the miR15 and miR16 gene products in a CLL or prostate cancer cell.
  • Any viral vector capable of accepting the coding sequences for the miR15 and miR16 gene products can be used; for example, vectors derived from adenovirus (AV); adeno-associated virus (AAV); retroviruses (e.g., lentiviruses (LV), Rhabdoviruses, murine leukemia virus); herpes virus, and the like.
  • the tropism of the viral vectors can also be modified by pseudotyping the vectors with envelope proteins or other surface antigens from other viruses.
  • an AAV vector of the invention can be pseudotyped with surface proteins from vesicular stomatitis virus (VSV), rabies, Ebola, Mokola, and the like.
  • recombinant viral vectors suitable for use in the invention methods for inserting nucleic acid sequences for expressing RNA into the vector, methods of delivering the viral vector to the cells of interest, and recovery of the expressed RNA products are within the skill in the art. See, for example, Domburg (1995), Gene Therap. 2:301-310; Eglitis (1988), Biotechniques 6:608-614; Miller (1990), Hum. Gene Therap. 1:5-14; and Anderson (1998), Nature 392:25-30, the entire disclosures of which are herein incorporated by reference.
  • Preferred viral vectors are those derived from AV and AAV.
  • a suitable AV vector for expressing the miRNA of the invention, a method for constructing the recombinant AV vector, and a method for delivering the vector into target cells are described in Xia et al. (2002), Nat. Biotech. 20:1006-1010, the entire disclosure of which is herein incorporated by reference.
  • Suitable AAV vectors for expressing the miRNA of the invention, methods for constructing the recombinant AAV vector, and methods for delivering the vectors into target cells are described in Samulski et al. (1987), J. Virol. 61:3096-3101; Fisher et al. (1996), J.
  • the miR15 and miR16 gene products are expressed from a single recombinant AAV vector comprising the CMV intermediate early promoter.
  • a recombinant AAV viral vector of the invention comprises a nucleic acid sequence encoding the miR15 or miR16 precursor RNA in operable connection with a polyT termination sequence under the control of a human U6 RNA promoter.
  • operable connection with a polyT termination sequence means that the nucleic acid sequences encoding the sense or antisense strands are immediately adjacent to the polyT termination signal in the 5′ direction.
  • the polyT termination signals act to terminate transcription.
  • the miR15 or miR16 gene products are used to inhibit the neoplastic or tumorigenic growth of miR15 or miR16 mediated cancer cells, in particular of CLL or prostate cancer cells.
  • the processed miR15 and miR16 miRNAs bind to complementary sequences in one or more target mRNAs which are necessary to initiate and/or maintain neoplastic or tumorigenic growth in these cells.
  • the invention provides a method of treating an miR15 or miR16 mediated cancer, for example CLL or prostate cancer, in a subject in need of such treatment.
  • the method comprises administering an effective amount of an miR15 or miR16 gene product to the subject, such that proliferation of miR15 or miR16 mediated cancer cells is inhibited.
  • an miR15 or miR16 mediated cancer is a cancer in which expression of either or both the miR15 or miR16 genes is reduced or absent in at least a portion of tumor or neoplastic cells associated with the disease. Expression of the miR15 or miR16 genes is reduced or absent in tumor or neoplastic cells from CLL or prostate cancer; thus, CLL and prostate cancer are considered to be miR15 or miR16 mediated cancers. A reduction or absence of miR15 or miR16 gene expression may also be found in other cancers; such cancers would therefore also be considered miR15 or miR16 mediated cancers.
  • expression of the miR15 or miR16 genes may be reduced or absent in primary or metastatic tumor or neoplastic cells from cancers of at least the following histologic subtypes: sarcoma (cancers of the connective and other tissue of mesodermal origin); melanoma (cancers deriving from pigmented melanocytes); carcinoma (cancers of epithelial origin); adenocarcinoma (cancers of glandular epithelial origin); cancers of neural origin (glioma/glioblastoma and astrocytoma); and hematological neoplasias, such as leukemias and lymphomas (e.g., acute lymphoblastic leukemia and chronic myelocytic leukemia).
  • sarcoma cancers of the connective and other tissue of mesodermal origin
  • melanoma cancers deriving from pigmented melanocytes
  • carcinoma cancers of epithelial origin
  • Expression of the miR15 or miR16 genes may also be reduced or absent in cancers having their origin in at least the following organs or tissues, regardless of histologic subtype: breast; tissues of the male and female urogenital system (e.g. ureter, bladder, prostate, testis, ovary, cervix, uterus, vagina); lung; tissues of the gastrointestinal system (e.g., stomach, large and small intestine, colon, rectum); exocrine glands such as the pancreas and adrenals; tissues of the mouth and esophagus; brain and spinal cord; kidney (renal); pancreas; hepatobiliary system (e.g., liver, gall bladder); lymphatic system; smooth and striated muscle; bone and bone marrow; skin; and tissues of the eye.
  • urogenital system e.g. ureter, bladder, prostate, testis, ovary, cervix, uterus, vagina
  • lung tissues of the gastrointestinal system (e.
  • Expression of the miR15 or miR16 genes may also be reduced or absent in cancers or tumors in any prognostic stage of development, for example as measured by the “Overall Stage Groupings” (also called “Roman Numeral”) or the “Tumor, Nodes, and Metastases” (TNM) staging systems.
  • Appropriate prognostic staging systems and stage descriptions for a given cancer are known in the art, for example as described in the National Cancer Institute's “CancerNet” Internet website.
  • a subject in need of treatment for an miR15 or miR16 mediated cancer can be identified by obtaining a sample of tumor or neoplastic cells (or cells suspected of being tumor or neoplastic) from the subject, and determining whether the expression of miR15 or miR16 is reduced or absent in at least a portion of the cells as compared to cells from normal tissue obtained from the subject. Methods for detecting miR15 or miR16 gene expression levels in cells are within the skill in the art (see above). Alternatively, the miR15 or miR16 expression in cells obtained from a subject can be compared to average expression levels of these genes in cells obtained from a population of normal subjects. A subject in need of treatment for CLL can be readily identified by a physician using standard diagnostic techniques.
  • CLL Chronic lymphocytic leukemia: recommendations for diagnosis, staging, and response criteria. International Workshop on Chronic Lymphocytic Leukemia,” (1989) Annals of Internal Medicine 110(3):236-238, the entire disclosure of which is herein incorporated by reference.
  • subjects with CLL exhibit circulating CLL cells, lymphocytosis (i.e., lymphocyte counts in the blood equal to or higher than 10,000 cells per cubic millimeter), and a progressive accumulation of CLL cells in the bone marrow and lymphatic tissues.
  • CLL cells in a subject's blood or other tissue can be confirmed by direct visual observation of a blood sample, and/or by determining the “CLL Score” of lymphocytes.
  • the CLL Score indicates the presence or absence of five lymphocyte surface markers characteristic of CLL cells: CD5+, CD23+, FMC7 ⁇ , and weak expression (+/ ⁇ ) of surface immunoglobulin (SmIg) and CD22. This scoring system gives a value of 1 or 0 for each of these five markers according to whether it is typical or a typical for CLL.
  • CLL cells have a CLL Score 4 or 5, while lymphocytes from other leukemias have a CLL Score of ⁇ 1 to 3. See Matutes et al.
  • CLL cells also have relatively low levels of surface-membrane immunoglobulin as compared with normal peripheral blood B cells. Surface-membrane immunoglobulin levels on lymphocytes can be readily detected according to standard techniques; see, e.g., Rozman et al. (1995), New England Journal of Medicine 333:1052-1057, the entire disclosure of which is herein incorporated by reference.
  • a subject in need of treatment for prostate cancer can also be readily identified by a physician according to standard diagnostic techniques, using criteria such as patient age, detection of an enlarged prostate by digital rectal exam, prostate-specific antigen (“PSA”) level, Gleason score of biopsy material, and the presence of immunohistochemically detectable genetic markers such as p53, p21, and cyclins on cells from prostate tissue.
  • PSA prostate-specific antigen
  • Gleason score of biopsy material
  • immunohistochemically detectable genetic markers such as p53, p21, and cyclins on cells from prostate tissue.
  • a serum PSA level of 20 ng/ml or greater and a poorly differentiated prostate tissue histology (e.g., Gleason score 8 or higher) is indicative of prostate cancer.
  • the presence of prostate tumors in a subject can also be confirmed by non-invasive imaging techniques, such as CT scan, transrectal ultrasound of the prostate (“TRUSP”), and magnetic resonance imaging (“MRI”), as are known in the art.
  • an “effective amount” of miR15 or miR16 gene products is an amount sufficient to inhibit proliferation of an miR15 or miR16 mediated cancer cell in a subject suffering from an miR15 or miR16 mediated cancer.
  • an effective amount of miR15 or miR16 gene products can be an amount sufficient to inhibit proliferation of CLL cells in a subject suffering from CLL, or inhibit proliferation of prostate cancer cells in a subject suffering from prostate cancer.
  • a “prostate tumor cell” is not necessarily located in the prostate, but includes cells from metastatic tumors of prostate origin.
  • to “inhibit the proliferation of an miR15 or miR16 mediated cancer cell” means to kill the cell, or permanently or temporarily arrest the growth of the cell. Inhibition of miR15 or miR16 mediated cancer cell proliferation can be inferred if the number of such cells in the subject remains constant or decreases after administration of the miR15 or miR16 gene products. An inhibition of miR15 or miR16 mediated cancer cell proliferation can also be inferred if the absolute number of such cells increases, but the rate of tumor growth decreases.
  • the number of miR15 or miR16 mediated cancer cells in a subject's body can be determined by direct measurement, or by estimation from the size of primary or metastatic tumor masses.
  • the number of CLL cells in a subject can be readily determined, for example by a whole blood or white blood cell count.
  • the number of CLL cells can also be readily determined by immunohistological methods, flow cytometry, or other techniques designed to detect the characteristic surface markers of CLL cells.
  • the size of a prostate tumor mass or a tumor mass can be ascertained by direct visual observation, or by diagnostic imaging methods such as X-ray, magnetic resonance imaging, ultrasound, and scintigraphy. Diagnostic imaging methods used to ascertain size of the tumor mass can be employed with or without contrast agents, as is known in the art.
  • the size of a tumor mass can also be ascertained by physical means, such as palpation of the tissue mass or measurement of the tissue mass with a measuring instrument such as a caliper.
  • a preferred physical means for determining the size of a tumor mass is the digital rectal exam.
  • One skilled in the art can readily determine an effective amount of the miR15 or miR16 gene products to be administered to a given subject, by taking into account factors such as the size and weight of the subject; the extent of disease penetration; the age, health and sex of the subject; the route of administration; and whether the administration is regional or systemic.
  • an effective amount of the compounds of the invention can be based on the approximate weight of a tumor mass to be treated.
  • the approximate weight of a tumor mass can be determined by calculating the approximate volume of the mass, wherein one cubic centimeter of volume is roughly equivalent to one gram.
  • An effective amount of the miR15 or miR16 gene products based on the weight of a tumor mass can be at least about 10 micrograms/gram of tumor mass, and is preferably between about 10-500 micrograms/gram of tumor mass. More preferably, the effective amount is at least about 60 micrograms/gram of tumor mass. Particularly preferably, the effective amount is at least about 100 micrograms/gram of tumor mass. It is preferred that an effective amount based on the weight of the tumor mass be injected directly into the tumor.
  • an effective amount of the miR15 or miR16 gene products can also be based on the approximate or estimated body weight of a subject to be treated. Preferably, such effective amounts are administered parenterally or enterally, as described below.
  • an effective amount of the miR15 or miR16 gene products administered to a subject can range from about 5-3000 micrograms/kg of body weight, and is preferably between about 700-1000 micrograms/kg of body weight, and is more preferably greater than about 1000 micrograms/kg of body weight.
  • the miR15 and miR16 gene products can be administered to the subject once (e.g., as a single injection or deposition).
  • the gene products can be administered once or twice daily to a subject for a period of from about three to about twenty-eight days, more preferably from about seven to about ten days.
  • the miR15 and miR16 gene products are administered once a day for seven days.
  • a dosage regimen comprises multiple administrations, it is understood that the effective amount of the miR15 and miR16 gene products administered to the subject can comprise the total amount of gene product administered over the entire dosage regimen.
  • the miR15 and miR16 gene products can be administered to a subject by any means suitable for delivering the gene products to cells of the subject, such as hematopoietic stem cells (HSCs), CLL cells or prostate cancer cells.
  • the miR15 and miR16 gene products can be administered by methods suitable to transfect cells of the subject with miR15 or miR16 gene products, or with nucleic acids comprising sequences encoding the miR15 or miR16 gene products.
  • the cells can be transfected directly with the miR15 or miR16 gene products (as these are nucleic acids), or can be transfected with nucleic acids comprising sequences encoding the miR15 or miR16 gene products.
  • the cells are transfected with a plasmid or viral vector comprising sequences encoding the miR15 or miR16 gene products, as described above.
  • Transfection methods for eukaryotic cells include direct injection of the nucleic acid into the nucleus or pronucleus of a cell; electroporation; liposome transfer or transfer mediated by lipophilic materials; receptor mediated nucleic acid delivery, bioballistic or particle acceleration; calcium phosphate precipitation, and transfection mediated by viral vectors.
  • cells can be transfected with a liposomal transfer compound, e.g., DOTAP (N-[1-(2,3-dioleoyloxy)propyl]-N,N,N-trimethyl-ammonium methylsulfate, Boehringer-Mannheim) or an equivalent, such as LIPOFECTIN.
  • DOTAP N-[1-(2,3-dioleoyloxy)propyl]-N,N,N-trimethyl-ammonium methylsulfate, Boehringer-Mannheim
  • LIPOFECTIN LIPOFECTIN
  • miR15 or miR16 mediated cancer cells are isolated from the subject, transfected with nucleic acids encoding the miR15 and miR16 gene products, and reintroduced into the subject.
  • the transfected and reimplanted cells are CLL cells.
  • the transfected and reimplanted cells are HSCs from a subject who has been diagnosed with CLL.
  • Suitable purging techniques include, for example, leukopheresis of mobilized peripheral blood cells, immunoaffinity-based selection or killing of tumor cells, or the use of cytotoxic or photosensitizing agents to selectively kill tumor cells, as are known in the art. See, for example, Bone Marrow Processing and Purging, Part 5 (A. Gee, ed.), CRC Press, Boca Raton, Fla., 1991; Lydaki et al. (1996) J. Photochem. and Photobiol. 32:27-32; and Gazitt et al. (1995), Blood, 86:381-389, the entire disclosures of which are herein incorporated by reference.
  • the isolated CLL cells or HSCs can be transfected by any suitable technique, as discussed above. After transfection, a portion of the CLL cells or HSCs can be examined to confirm the presence of appropriate expression levels of the gene products. Once appropriate expression of miR15 or miR16 gene products has been confirmed, the remaining transfected cells can then be reintroduced into the subject. Transfected CLL cells or HSCs can be reintroduced into the subject by parenteral methods, including intravenous infusion or direct injection into the bone marrow. The transfected cells are preferably reintroduced into the subject in a saline solution or other pharmaceutically acceptable carrier. A suitable number of transfected cells for reintroduction is from about 10 5 to about 10 8 cells per kilogram of subject body weight. The number of transfected cells available for re-introduction can be increased by expanding the cells in culture prior to transfection.
  • the CLL cells or HSCs are transfected with a nucleic acid comprising sequences which encode an miR15 or miR16 gene product, e.g. a plasmid expression vector, that stably integrates into the CLL cell or HSC genome to provide long-term expression of the compound.
  • a nucleic acid comprising sequences which encode an miR15 or miR16 gene product, e.g. a plasmid expression vector, that stably integrates into the CLL cell or HSC genome to provide long-term expression of the compound.
  • Stable integration and expression can be confirmed by techniques known in the art, such as a Southern blot of genomic DNA using miR15 or miR16 cDNA (or fragments thereof) as a probe. Expression of miR15 or miR16 gene products can also be detected by standard Northern blot techniques.
  • the CLL cells or HSCs stably transfected with sequences encoding the miR15 or miR16 gene products continue to express the compound once they are re-implanted into the subject.
  • An exemplary method of isolating HSC from a subject, transfecting them with plasmids expressing miR15 and miR16 gene products, and reimplanting the transfected HSC into the subject is given in Example 8 below.
  • the miR15 and miR16 gene products can also be administered to a subject by any suitable enteral or parenteral administration route.
  • Suitable enteral administration routes for the present methods include oral, rectal, or intranasal delivery.
  • Suitable parenteral administration routes include intravascular administration (e.g.
  • intravenous bolus injection intravenous infusion, intra-arterial bolus injection, intra-arterial infusion and catheter instillation into the vasculature
  • peri- and intra-tissue injection e.g., peri-tumoral and intra-tumoral injection, intra-retinal injection, or subretinal injection
  • subcutaneous injection or deposition including subcutaneous infusion (such as by osmotic pumps); direct application to the tissue of interest, for example by a catheter or other placement device (e.g., a retinal pellet or a suppository or an implant comprising a porous, non-porous, or gelatinous material); and inhalation.
  • a catheter or other placement device e.g., a retinal pellet or a suppository or an implant comprising a porous, non-porous, or gelatinous material
  • the miR15 and miR16 gene products are administered by injection or infusion.
  • the miR15 and miR16 gene products are preferably administered by direct injection into the tumor.
  • the miR15 and miR16 gene products can be administered to the subject either as naked RNA, in conjunction with a delivery reagent, or as a nucleic acid (e.g., a recombinant plasmid or viral vector) comprising sequences which expresses the gene product.
  • a delivery reagent e.g., a recombinant plasmid or viral vector
  • Suitable delivery reagents for administration of the miR15 and miR16 gene products include the Mirus Transit TKO lipophilic reagent; lipofectin; lipofectamine; cellfectin; or polycations (e.g., polylysine), or liposomes.
  • Recombinant plasmids comprising sequences which express the miR15 or miR16 gene products are discussed above.
  • Recombinant viral vectors comprising sequences which expresses the miR15 or miR16 gene products are also discussed above, and methods for delivering such vectors to CLL or prostate cancer cells of a subject are within the skill in the art.
  • liposomes are used to deliver the miR15 or miR16 gene products, or nucleic acids comprising sequences encoding the gene products, to a subject. Liposomes can also increase the blood half-life of the gene products or nucleic acids.
  • the miR15 or miR16 gene products, or nucleic acids comprising sequences encoding the gene products are encapsulated in liposomes prior to administration to the subject.
  • Liposomes suitable for use in the invention can be formed from standard vesicle-forming lipids, which generally include neutral or negatively charged phospholipids and a sterol such as cholesterol.
  • the selection of lipids is generally guided by consideration of factors such as the desired liposome size and half-life of the liposomes in the blood stream.
  • a variety of methods are known for preparing liposomes, for example as described in Szoka et al. (1980), Ann. Rev. Biophys. Bioeng. 9:467; and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369, the entire disclosures of which are herein incorporated by reference.
  • the liposomes encapsulating the miR15 or miR16 gene products, or nucleic-acids comprising sequences encoding the gene products can comprise a ligand molecule that targets the liposome to an miR15 or miR16 mediated cancer cell, such as a CLL or prostate cancer cell.
  • a ligand molecule that targets the liposome to an miR15 or miR16 mediated cancer cell, such as a CLL or prostate cancer cell.
  • Ligands which bind to receptors prevalent in such cancer cells such as monoclonal antibodies that bind to tumor cell antigens or CLL cell surface markers, are preferred.
  • the liposomes encapsulating the miR15 or miR16 gene products, or nucleic acids comprising sequences encoding the gene products can also be modified so as to avoid clearance by the mononuclear macrophage system (“MMS”) and reticuloendothelial system (“RES”).
  • MMS mononuclear macrophage system
  • RES reticuloendothelial system
  • modified liposomes have opsonization-inhibition moieties on the surface or incorporated into the liposome structure.
  • a liposome of the invention can comprise both opsonization-inhibition moieties and a ligand.
  • Opsonization-inhibiting moieties for use in preparing the liposomes of the invention are typically large hydrophilic polymers that are bound to the liposome membrane.
  • an opsonization inhibiting moiety is “bound” to a liposome membrane when it is chemically or physically attached to the membrane, e.g., by the intercalation of a lipid-soluble anchor into the membrane itself, or by binding directly to active groups of membrane lipids.
  • These opsonization-inhibiting hydrophilic polymers form a protective surface layer which significantly decreases the uptake of the liposomes by the MMS and RES; e.g., as described in U.S. Pat. No. 4,920,016, the entire disclosure of which is herein incorporated by reference.
  • Opsonization inhibiting moieties suitable for modifying liposomes are preferably water-soluble polymers with a number-average molecular weight from about 500 to about 40,000 daltons, and more preferably from about 2,000 to about 20,000 daltons.
  • Such polymers include polyethylene glycol (PEG) or polypropylene glycol (PPG) derivatives; e.g., methoxy PEG or PPG, and PEG or PPG stearate; synthetic polymers such as polyacrylamide or poly N-vinyl pyrrolidone; linear, branched, or dendrimeric polyamidoamines; polyacrylic acids; polyalcohols, e.g., polyvinylalcohol and polyxylitol to which carboxylic or amino groups are chemically linked, as well as gangliosides, such as ganglioside GM 1 .
  • Copolymers of PEG, methoxy PEG, or methoxy PPG, or derivatives thereof, are also suitable.
  • the opsonization inhibiting polymer can be a block copolymer of PEG and either a polyamino acid, polysaccharide, polyamidoamine, polyethyleneamine, or polynucleotide.
  • the opsonization inhibiting polymers can also be natural polysaccharides containing amino acids or carboxylic acids, e.g., galacturonic acid, glucuronic acid, mannuronic acid, hyaluronic acid, pectic acid, neuraminic acid, alginic acid, carrageenan; aminated polysaccharides or oligosaccharides (linear or branched); or carboxylated polysaccharides or oligosaccharides, e.g., reacted with derivatives of carbonic acids with resultant linking of carboxylic groups.
  • the opsonization-inhibiting moiety is a PEG, PPG, or derivatives thereof. Liposomes modified with PEG or PEG-derivatives
  • the opsonization inhibiting moiety can be bound to the liposome membrane by any one of numerous well-known techniques.
  • an N-hydroxysuccinimide ester of PEG can be bound to a phosphatidyl-ethanolamine lipid-soluble anchor, and then bound to a membrane.
  • a dextran polymer can be derivatized with a stearylamine lipid-soluble anchor via reductive amination using Na(CN)BH 3 and a solvent mixture such as tetrahydrofuran and water in a 30:12 ratio at 60° C.
  • Liposomes modified with opsonization-inhibition moieties remain in the circulation much longer than unmodified liposomes. For this reason, such liposomes are sometimes called “stealth” liposomes. Stealth liposomes are known to accumulate in tissues fed by porous or “leaky” microvasculature. Thus, tissue characterized by such microvasculature defects, for example solid tumors, will efficiently accumulate these liposomes; see Gabizon, et al. (1988), Proc. Natl. Acad. Sci., USA, 18: 6949-53.
  • liposomes that are modified with opsonization-inhibition moieties are particularly suited to deliver the miR15 or miR16 gene products, or nucleic acids comprising sequences encoding the gene products, to tumor cells.
  • the miR15 or miR16 gene products are preferably formulated as pharmaceutical compositions prior to administering to a subject, according to techniques known in the art.
  • Pharmaceutical compositions of the present invention are characterized as being at least sterile and pyrogen-free.
  • pharmaceutical formulations include formulations for human and veterinary use. Methods for preparing pharmaceutical compositions of the invention are within the skill in the art, for example as described in Remington's Pharmaceutical Science, 17th ed., Mack Publishing Company, Easton, Pa. (1985), the entire disclosure of which is herein incorporated by reference.
  • the present pharmaceutical formulations comprise the miR15 or miR16 gene products, or a nucleic acid comprising sequences encoding the gene products (e.g., 0.1 to 90% by weight), or a physiologically acceptable salt thereof, mixed with a pharmaceutically-acceptable carrier.
  • the pharmaceutical formulations of the invention can also comprise the miR15 or miR16 gene products, or nucleic acids comprising gene products encoding the gene products, which are encapsulated by liposomes and a pharmaceutically-acceptable carrier.
  • Preferred pharmaceutically-acceptable carriers are water, buffered water, normal saline, 0.4% saline, 0.3% glycine, hyaluronic acid and the like.
  • the pharmaceutical compositions of the invention comprise miR15 or miR16 gene products which are resistant to degradation by nucleases.
  • miR15 and miR16 gene products which are nuclease resistant, for example by incorporating one or more ribonucleotides which are modified at the 2′ position into the miR15 and miR16 gene products.
  • Suitable 2′-modified ribonucleotides include those modified at the 2′-position with fluoro, amino, alkyl, alkoxy, and O-allyl.
  • compositions of the invention comprise miR15 or miR16 gene products incorporating one or more 2′-modified ribonucleotides of the formulae 2′AR-nucleotide, wherein:
  • A is oxygen or a halogen (preferably fluorine, chlorine or bromine).
  • R is hydrogen or straight or branched chain C 1-6 alkyl
  • compositions of the invention comprise miR15 or miR16 gene products in which each ribonucleotide is a 2′-modified ribonucleotide.
  • compositions of the invention can also comprise conventional pharmaceutical excipients and/or additives.
  • Suitable pharmaceutical excipients include stabilizers, antioxidants, osmolality adjusting agents, buffers, and pH adjusting agents.
  • Suitable additives include physiologically biocompatible buffers (e.g., tromethamine hydrochloride), additions of chelants (such as, for example, DTPA or DTPA-bisamide) or calcium chelate complexes (as for example calcium DTPA, CaNaDTPA-bisamide), or, optionally, additions of calcium or sodium salts (for example, calcium chloride, calcium ascorbate, calcium gluconate or calcium lactate).
  • Pharmaceutical compositions of the invention can be packaged for use in liquid form, or can be lyophilized.
  • solid pharmaceutically-acceptable carriers for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like.
  • a solid pharmaceutical composition for oral administration can comprise any of the carriers and excipients listed above and 10-95%, preferably 25%-75%, of the miR15 or miR16 gene products.
  • a pharmaceutical composition for aerosol (inhalational) administration can comprise 0.01-20% by weight, preferably 1%-10% by weight, of the miR15 or miR16 gene products encapsulated in a liposome as described above, and a propellant.
  • a carrier can also be included as desired; e.g., lecithin for intranasal delivery.
  • CD5+ B-cell separation Tonsils were obtained from patients in the pediatric age group (3-9 years) undergoing routine tonsillectomies. Purified B cells were obtained by rosetting the mononuclear cells with neuraminidase treated sheep erythrocytes. The B cells were further fractionated by discontinuous Percoll gradients (Pharmacia Biotech, Uppsala, Sweden) as described in Dono M et al. (2000), J. Immunol. 164:5596-5604, the entire disclosure of which is herein incorporated by reference. The B cells collected from the 50% Percoll fraction were incubated with anti CD5 mAb followed by goat anti mouse Ig conjugated with magnetic microbeads. CD5+ B cells were obtained by positive selection by collecting the cells retained on the magnetic column MS using the MiniMACS system (Miltenyi Biotec).
  • Somatic cell hybrids were generated following conventional methods and selected in hypoxanthine-aminopterin-thymidine (HAT) medium as described in Negrini M et al. (1994), Cancer Res. 54:1818-1824, the entire disclosure of which is herein incorporated by reference.
  • DNA derived from single cell clones and subclones was isolated with the DNeasy tissue kit (Qiagen) and screened by PCR for the presence or absence of chromosome 13 and chromosome 2 markers (see Table 1 below for primer sequences).
  • CLL-B CLL case
  • CLL-A CLL case
  • RNA samples (30 ⁇ g each) were run on 15% acrylamide denaturing (urea) Criterion precast gels (Bio-Rad Laboratories, Hercules, Calif.) and then transferred onto Hybond-N+ membrane (Amersham Pharmacia Biotech). The hybridization with ⁇ - 32 P ATP was performed at 42° C. in 7% SDS, 0.2M Na2PO4 pH 7.0 overnight. Membranes were washed at 42° C., twice in 2 ⁇ SSPE, 0.1% SDS and twice with 0.5 ⁇ SSPE, 0.1% SDS. The probes used to detect miR15 and miR16 RNA were, respectively: CACAAACCATTATGTGCTTGCTA (SEQ ID NO: 5) GCCAATATTTACGTGCTGCTA (SEQ ID NO: 6)
  • Blots were stripped by boiling in 0.1% aqueous SDS/0.1 ⁇ SSC for 10 minutes, and were reprobed several times. As loading control, 5S rRNA stained with ethidium bromide was used.
  • RT-PCR Reverse Transcriptase Polymerase Chain Reaction
  • somatic cell hybrids of mouse LM-TK ⁇ and CLL cells carrying 13q14 translocations and/or deletions were generated.
  • PCR screening of resulting hybrid clones allowed the segregation of the two copies of chromosome 13 present in the tumors. In this manner, a 31.4 kb deletion was identified in one case, and the chromosomal breakpoint was precisely localized in the other (FIG. 2D).
  • the primers used to screen the somatic cell hybrids are given in Table 1.
  • LEU2 has been excluded as a likely candidate tumor suppressor gene for B-CLL (see Bullrich et al. (2001), Cancer Res. 61:6640-6648; Migliazza et al. (2001), Blood 97:2098-2104; Wolf et al. (2001), Hum. Mol. Genet. 10:1275-1285; and Mertens et al. (2002) Blood 99:4116-4121).
  • the miR15 and miR16 Genes are Localized in the Minimally Deleted Region of Chromosome 13 and Are Highly Expressed in CD5+ Cells
  • the miR15 and miR16 Genes are Frequently Deleted or Downregulated in CLL Samples with Deletions at 13q14
  • miR15 and miR16 are Also Involved in CLL Pathogenesis in Mice
  • Comparative gene hybridization also showed a loss of a region of mouse chromosome 14 (51.6-78.5 Mb) which corresponds to region 13q14 in humans.
  • cDNA sequences encoding the entire 70 nucleotide miR15 and miR16 RNA precursors are separately cloned into the context of an irrelevant mRNA expressed under the control of the cytomegalovirus immediate early (CMV-IE) promoter, according to the procedure of Zeng et al. (2002), Mol. Cell 9:1327-1333, the entire disclosure of which is herein incorporated by reference.
  • CMV-IE cytomegalovirus immediate early
  • Xho I linkers are placed on the end of double-stranded cDNA sequences encoding the miR15 and miR16 RNA precursors, and these constructs are separately cloned into the Xho I site present in the pBC12/CMV plasmid.
  • the pBC12/CMV plasmid is described in Cullen, (1986), Cell 46: 973-982, the entire disclosure of which is herein incorporated by reference.
  • the plasmid containing the miR15 precursor RNA sequences is called pCMV-miR15
  • the plasmid containing the miR16 precursor RNA sequences is called pCMV-miR16.
  • pCMV-miR15 and pCMV-miR16 are separately transfected into cultured human 293T cells by standard techniques using the FuGene 6 reagent (Roche). Total RNA is extracted as described above, and the presence of processed miR15 or miR16 RNA is detected by Northern blot analysis with miR15 and miR16 specific probes.
  • pCMV-miR15 and pCMV-miR16 are also separately transfected into cultured human prostate carcinoma cell lines 2220, 2221, 11609, 11611, LNCAP, TSUR. Total RNA is extracted as described above, and the presence of processed miR15 or miR16 RNA in the prostate carcinoma cells is detected by Northern blot analysis with miR15 and miR16 specific probes. The transfected prostate carcinoma cells are also evaluated for changes in morphology, the ability to overcome contact inhibition, and other markers indicative of a transformed phenotype.
  • CLL cells from a subject diagnosed with CLL are isolated and transfected with plasmids encoding miR15 and miR16 micro RNAs as follows.
  • CD5+ B cells are isolated as described above and CLL cells are identified by visual inspection or by determining the CLL Score according to the scoring system of Matutes et al. (1994), Leukemia 8(10):1640-1645, the entire disclosure of which is herein incorporated by reference. CD5+ B cells with a CLL Score of at least 4 are considered CLL cells. Deletions in the 13q14 region which remove the miR15/miR16 gene cluster are confirmed in the isolated CLL cells.
  • the isolated CLL cells are transfected with pCMV-miR15 and pCMV-miR16 by standard techniques. Total RNA is extracted as described above, and the presence of processed miR15 or miR16 RNA detected by Northern blot analysis with miR15 and miR16 specific probes. Stable integration of miR15 and miR16 gene sequences is also confirmed by Southern blot hybridization using probes specific for miR15 and miR16 gene sequences.
  • HSC Hematopoietic stem cells
  • Bone marrow is harvested from the iliac bones of a subject under general anesthesia in an operating room using standard techniques. Multiple aspirations are taken into heparinized syringes for a total of about 750 to 1000 ml bone marrow. The aspirated marrow is transferred immediately into a transport medium (TC-199, Gibco, Grand Island, N.Y.) containing 10,000 units of preservative-free heparin per 100 ml of medium. The aspirated marrow is filtered through three progressively finer meshes to obtain a cell suspension devoid of cellular aggregates, debris and bone particles. The filtered marrow is then processed further into an automated cell separator (e.g., Cobe 2991 Cell Processor) to obtain the “buffy coat” (i.e., leukocytes devoid of red cells and platelets).
  • an automated cell separator e.g., Cobe 2991 Cell Processor
  • the buffy coat preparation is partially enriched for hematopoietic stem cells (HSC) by positively selecting for CD34 + cells with immunomagnetic beads (Dynal A. S., Oslo, Norway) as follows.
  • the buffy coat preparation is suspended in supplemented alpha medium and incubated with mouse anti-HPCA-I antibody in 1:20 dilution, 45 minutes, at 4° C. with gentle inverting of tubes.
  • the cells are washed 3 ⁇ in supplemented alpha medium, and then incubated with beads coated with the Fc fragment of goat anti-mouse IgG 1 (75 ⁇ l of immunobeads/10 7 CD34 + cells). After 45 minutes of incubation at 4° C., cells adherent to the beads are positively selected using a magnetic particle concentrator, as directed by the manufacturer.
  • ⁇ 10 4 cells from the preparation enriched for HSC are incubated in 5 ml polypropylene tubes (Fisher Scientific, Pittsburgh, Pa.) in a total volume of 0.4 ml of Iscove's modified Dulbecco's medium (IMDM) containing 2% human AB serum and 10 mM Hepes buffer, and are transfected with pCMV-miR15 and pCMV-miR16 by standard techniques. Expression of miR15 or miR16 RNA is confirmed in a portion of the transfected HSC by Northern blot analysis, and stable integration of miR15 or miR16 gene sequences in a portion of the HSC is confirmed by Southern blot analysis. Approximately 4 ⁇ 10 8 /kg body weight to about 8 ⁇ 10 8 /kg body weight of the remaining transfected cells are reimplanted into the subject according to standard bone marrow transplant techniques.
  • IMDM Iscove's modified Dulbecco's medium
  • the experiment is repeated, but the bone marrow is purged of neoplastic cells with ionizing radiation prior to transfection and reimplantation, as follows.
  • Cells in the buffy coat preparation are adjusted to a cell concentration of about 2 ⁇ 10 7 /ml in TC-199 containing about 20% autologous plasma.
  • Recombinant human hematopoietic growth factors rH IL-3 or rH GM-CSF are added to the cell suspension to stimulate growth of hematopoietic neoplasms and thereby increase their sensitivity to ionizing radiation.
  • the cells are then exposed to 5-10 Gy ionizing radiation, washed once at 4° C. in TC-199 containing about 20% autologous plasma, and transfected with pCMV-miR15 and pCMV-miR16 as above.
  • Liposome Preparation 1 Liposomes composed of lactosyl cerebroside, phosphatidylglycerol, phosphatidylcholine and cholesterol in molar ratios of 1:1:4:5 are prepared by the reverse phase evaporation method described in U.S. Pat. No. 4,235,871, the entire disclosure of which is herein incorporated by reference.
  • the liposomes are prepared in an aqueous solution of 100 ⁇ g/ml processed miR15 or miR16 RNA or 500 ⁇ g/ml pCMV-miR15 or pCMV-miR16.
  • the liposomes thus prepared encapsulate either the processed miR15 or miR16 RNA, or the pCMV-miR15 or pCMV-miR16 plasmids.
  • the liposomes are then passed through a 0.4 polycarbonate membrane and suspended in saline, and are separated from non-encapsulated material by column chromatography in 135 mM sodium chloride, 10 mM sodium phosphate pH 7.4.
  • the liposomes are used without further modification, or are modified as described below.
  • a quantity of the liposomes prepared above are charged to an appropriate reaction vessel to which is added, with stirring, a solution of 20 mM sodium metaperiodate, 135 mM sodium chloride and 10 mM sodium phosphate (pH 7.4).
  • the resulting mixture is allowed to stand in darkness for 90 minutes at a temperature of about 20° C. Excess periodate is removed by dialysis of the reaction mixture against 250 ml of buffered saline (135 mM sodium chloride, 10 mM sodium phosphate, pH 7.4) for 2 hours.
  • the product is a liposome having a surface modified by oxidation of carbohydrate hydroxyl groups to aldehyde groups. Targeting groups or opsonization inhibiting moieties are conjugated to the liposome surface via these aldehyde groups.
  • Liposome Preparation 2 A second liposome preparation composed of maleimidobenzoyl-phosphatidylethanolamine (MBPE), phosphatidylcholine and cholesterol is obtained as follows.
  • MBPE is an activated phospholipid for coupling sulfhydryl-containing compounds, including proteins, to the liposomes.
  • DMPE dimyristoylphosphatidylethanolamine
  • Methanol is removed under reduced pressure and the products re-dissolved in chloroform.
  • the chloroform phase is extracted twice with 1% sodium chloride and the maleimidobenzoyl-phosphatidylethanolamine (MBPE) purified by silicic acid chromatography with chloroform/methanol (4/1) as the solvent. Following purification, thin-layer chromatography indicates a single phosphate containing spot that is ninhydrin negative.
  • MBPE maleimidobenzoyl-phosphatidylethanolamine
  • Liposomes are prepared with MBPE, phosphatidylcholine and cholesterol in molar ratios of 1:9:8 by the reverse phase evaporation method of U.S. Pat. No. 4,235,871, supra, in an aqueous solution of 100 ⁇ g/ml processed miR15 or miR16 RNA or a solution of 500 ⁇ g/ml pCMV-miR15 or pCMV-miR16. Liposomes are separated from non-encapsulated material by column chromatography in 100 mM sodium chloride-2 mM sodium phosphate (pH 6.0).
  • An appropriate vessel is charged with 1.1 ml (containing about 10 mmoles) of Liposome Preparation 1 carrying reactive aldehyde groups, or Liposome Preparation 2 above.
  • 0.2 ml of a 200 mM sodium cyanoborohydride solution and 1.0 ml of a 3 mg/ml solution of a monoclonal antibody directed against the CD5+ cell surface marker or a prostate tumor cell antigen is added to the preparation, with stirring.
  • the resulting reaction mixture is allowed to stand overnight while maintained at a temperature of 4° C.
  • the reaction mixture is separated on a Biogel A5M agarose column (Biorad, Richmond, Calif.; 1.5 ⁇ 37 cm).
  • a hormone refractory human prostate adenocarcinoma cell line (PC-3) is inoculated into nude mice, and the mice are divided into treatment and control groups.
  • PC-3 human prostate adenocarcinoma cell line
  • processed miR15 and miR16 encapsulated in liposomes are injected directly into the tumors of the control group.
  • the tumors of the control group are injected with liposomes encapsulating carrier solution only. Tumor volume is measured throughout the study.
  • the efficacy of miR15 and miR16 gene products to inhibit prostate tumor growth in the Dunning R-3327 rat prostate adenocarcinoma model is also evaluated, as follows.
  • a highly metastatic and malignant clone (RT-3.1) of Dunning R-3327 prostate adenocarcinoma cells is inoculated into Copenhagen rats, which are then divided into treatment and control groups. Both groups form solid tumor masses in approximately one week.
  • the tumors of rats in the treatment group are then injected with processed miR15 and miR16 encapsulated in liposomes twice a week for 5 weeks.
  • the tumors of the control group are injected with liposomes encapsulating carrier solution only. Tumor volume is measured throughout the study.

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