# Patent

## Title
Methods for reverting methylation by targeting methyltransferases

## Abstract

Methods for restoring a desired pattern of DNA methylation, inducing re-expression of methylation-silenced tumor suppressor genes (TSGs), and/or inhibiting tumorigenicity both in vitro and in vivo in a subject in need thereof by administering an effective amount of one or more miR-29s sufficient to target one or more of DNMT3A and DNMT3B are disclosed.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application No. 60/962,795 filed Jul. 31, 2007, and PCT/US2008/071532 filed Jul. 30, 2008, the entire disclosure of which is expressly incorporated herein by reference.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH
This invention was not made with any Government support and the Government has no rights in this invention.


BACKGROUND
Lung cancer is the leading cause of cancer mortality in the United States, with an incidence of approximately 213,000 new cases per year and a very high mortalityl15. Despite new drugs and therapeutic regimens, the prognosis for lung cancer patients has not changed significantly in the last 20 years, emphasizing the need for novel treatment strategies. Targeting the epigenome, represents a promising therapeutic strategy in cancer16.
Aberrant DNA methylation has been shown to play important roles in lung cancer17:
1) promoter methylation is one of the mechanisms responsible for silencing TSGs18-20, such as CDKN2A, CDH13, FHIT, WWOX, CDH1, and RASSF1A;
2) mRNA expression of the maintenance and de novo DNA methyltransferases, DNMT1 and DNMT3B, respectively, were reportedly elevated in 53% and 58% of 102 NSCLCs, respectively, and the DNMT1 mRNA level was shown to be an independent prognostic factor for survival13;
3) DNMT1, DNMT3A and DNMT3B protein expression is elevated in lung tumors relative to normal lung tissue12;
4) a specific polymorphism in the human DNMT3B promoter, which significantly increases the promoter activity, has been associated with increased lung cancer risk21;
5) inhibition of DNMT1-mediated DNA methylation reduced tobacco carcinogen-induced lung cancer in mice by >50%22.
MicroRNAs (miRNAs), non-coding RNAs of 19-25 nucleotides that regulate gene expression by inducing translational inhibition or cleavage of their target mRNAs through base pairing to partially or fully complementary sites, are involved in critical biological processes, including development, cell differentiation, apoptosis and proliferation1,2. Recently, specific miRNA expression profiles, with diagnostic and prognostic implications, have been identified for specific cancers (refs. 3-5 for review). Notably, members of the miR-29 family, previously shown to be down-regulated in NSCLC6,7, have been predicted in silico to be complementary to sites in the 3′ untranslated regions (3′UTRs) of DNMT3A and B genes, using different miRNA target gene prediction algorithms (PicTar8, TargetScan3.19, MiRanda10, and miRGen11) (FIG. 1).
Among the reported down-regulated miRNAs in lung cancer, the miR-29 family (29a, 29b, and 29c), has intriguing complementarities to the 3′ untranslated regions (UTRs) of DNMT3A and 3B (de novo methyltransferases)8-11, two key enzymes involved in DNA methylation, that are frequently up-regulated in lung cancer12 and associated with poor prognosis13.
While there is now believed that miRNAs play a role in carcinogenesis, miRNA expression is different in lung cancer versus its normal counterpart. Further, the significance of this aberrant expression is poorly understood.
Therefore, there is a need to determine whether miR-29s can target both DNMT3A and DNTM3B and whether the restoration of miR-29s can normalize aberrant patterns of methylation in lung cancers such as, for example, non-small cell lung cancer (NSCLC).
SUMMARY OF INVENTION
In one broad aspect, there is described herein a method for restoring a desired pattern of DNA methylation in a subject in need thereof, comprising administering an effective amount of one or more miR-29s sufficient to target one or more of DNMT3A and DNMT3B.
In another broad aspect, there is described herein a method for inducing re-expression of methylation-silenced tumor suppressor genes (TSGs) in a subject in need thereof, comprising administering an effective amount of one or more miR-29s sufficient to target one or more of DNMT3A and DNMT3B. In certain embodiments, the TSG comprises one or more of FHIT and WWOX.
In another broad aspect, there is described herein a method for inhibiting tumorigenicity both in vitro and in vivo in a subject in need thereof, comprising administering an effective amount of one or more miR-29s sufficient to target one or more of DNMT3A and DNMT3B.
The methods described herein are useful in subjects suffering from malignancies such as lung cancer.
In another aspect, there is described herein a method useful for epigenetic regulation of non-small cell lung cancer (NSCLC).
In certain embodiments, the endogenous miR-29b is useful as a primer to initiate the retrotranscription of DNMT3B mRNA.
In another aspect, there is described herein a method for reducing global DNA methylation comprising administering an effective amount of one or more miR-29s that target DNMT3A and DNMT3B, wherein expression of the miR-29s contribute to DNA epigenetic modifications in a cancer cell.
In another aspect, there is described herein a method for achieving DNA hypomethylation by combining at least one nucleoside analog with one or more miR-29s sufficient to block de novo and maintenance DNMT pathways. In certain embodiments, the nucleoside analog comprises decitabine.
In another aspect, there is described herein a method for increasing expression of a tumor suppression gene (TSG) comprising transfecting a cell with one or more mi-R29s. In certain embodiments, the TSG comprises one or more of FHIT and WWOX proteins.
In another aspect, there is described herein a method for inhibiting in vitro cell growth and/or inducing apoptosis with respect to scrambled controls in the cells, comprising transfecting one or more cells with one or more miR-29s.
In another aspect, there is described herein a method for down-modulating expression levels of FHIT and/or WWOX enzymes, comprising regulating the DNMT3A and/or DNMT3B by transfecting the cell with one or more miR-29 family members. In certain embodiments, the cell is a lung cancer cell.
In another aspect, there is described herein a method for reducing global DNA methylation comprising inducing expression of mi-R29s in lung cancer cells.
In another aspect, there is described herein a method for restoring expression of TSGs comprising inducing expression of mi-R29s in lung cancer cells.
In another aspect, there is described herein a method for inhibiting tumorigenicity both in vitro and in vivo comprising inducing expression of mi-R29s in lung cancer cells.
In another aspect, there is described herein a method for developing an epigenetic therapy using synthetic miR-29s, alone or in combination with other treatments, to reactivate tumor suppressors and normalize aberrant patterns of methylation in a cancer cell. In certain embodiments, the cancer cell is a lung cancer cell.
In another aspect, there is described herein a method of diagnosing whether a subject has, is at risk for developing, or has a decrease survival prognosis for, a lung cancer-related disease, comprising measuring the level of at least one miR gene product in a test sample from the subject; wherein an alteration in the level of the miR gene product in the test sample, relative to the level of a corresponding miR gene product in a control sample, is indicative of the subject either having, or being at risk for developing, the lung cancer-related disease; and wherein the at least one miR gene product is selected from the group consisting of miR29a, miR-29b, miR-29c and combinations thereof.
In still other aspects, there is described herein markers associated with a lung cancer-induced state of various cells. It has been discovered that the higher than normal level of expression of any of these markers or combination of these markers correlates with the presence of a lung cancer-related disease in a patient. Methods are provided for detecting the presence of a lung cancer-related disease in a sample; the absence of a in a sample; the stage of a lung cancer-related disease; and, other characteristics of a lung cancer-related disease that are relevant to the assessment, prevention, diagnosis, characterization and therapy of a lung cancer-related disease in a patient. Methods of treating a lung cancer-related disease are also provided.
In still other aspects, there is described herein methods for treating a patient afflicted with a lung cancer-related disease or at risk of developing a lung cancer-related disease. Such methods may comprise reducing the expression and/or interfering with the biological function of a marker. In one embodiment, the method comprises providing to the patient an antisense oligonucleotide or polynucleotide complementary to a marker nucleic acid, or a segment thereof. For example, an antisense polynucleotide may be provided to the patient through the delivery of a vector that expresses an anti-sense polynucleotide of a marker nucleic acid or a fragment thereof. In another embodiment, the method comprises providing to the patient an antibody, an antibody derivative or antibody fragment, which binds specifically with a marker protein, or a fragment of the protein.
Various objects and advantages of this invention will become apparent to those skilled in the art from the following detailed description of the preferred embodiment, when read in light of the accompanying drawings.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1. Complementarity sites for miR-29s in the 3′UTR region of DNMT3A and 3B.
Hsa-mi-R29a [SEQ ID NO: 1]
Hsa-mi-R29b [SEQ ID NO: 2]
Hsa-mi-R29c [SEQ ID NO: 3]
845-869 DNMT3A [SEQ ID NO: 4]
843-869 DNMT3A [SEQ ID NO: 5]
846-869 DNMT3A [SEQ ID NO: 6]
1184-1209 DNMT3B [SEQ ID NO: 7]
244-267 DNMT3B [SEQ ID NO: 8]
1374-1398 DNMT3B [SEQ ID NO: 9]
1182-1209 DNMT3B [SEQ ID NO: 10]
1185-1209 DNMT3B [SEQ ID NO: 11
The capital and bold letters identify perfect base matches, according to the TARGETSCAN 3.1 software. The PICTAR software identifies two additional match-regions between miR-29a and DNMT3B, indicated with an asterisk. *.
FIG. 2. MiR-29s directly target DNMT3A and B.
FIG. 2a). Results of the luciferase assay for DNMT3s expression after transfection with miR-29s in A549 cells.
FIG. 2b). Upper, assessment of expression of DNMT3A and DNMT3B mRNAs by qRT-PCR, after transfection of A549 cells with miR-29s or a negative control; lower, silencing of miR-29s with antisense molecules (AS) induces increased expression of DNMT3A and DNMT3B mRNA.
FIG. 2c). Western blot of proteins extracted from A549 cells that were co-transfected with the GFP-repression vectors for the DNMT3A and B-3′UTR plus miR29s or scrambled oligonucleotides.
FIG. 2d). miR-29b acts as an endogenous primer to retro-transcribe its predicted DNMT3B mRNA target, Black font: DNMT3B cDNA (RefSeq# NM—175848); blue font: cloned and sequenced cDNAs experimentally obtained (8 clones analyzed); red font: deduced RNA sequences and corresponding miR-29b.









3′UTR-DNMT3B 1178-1217:



[SEQ ID NO: 12]



TTTAACACCTTTTACTCTTCTTAC-TGGTGCTATTTTGTAG



 



cDNA (8):



[SEQ ID NO: 13]



TTTAACACCTTTTACTCTTCTTAA:TGGTGCTA-ADAPTER



 



RNA:



[SEQ ID NO: 14]



3′ AAAUGAGAAGAAUU:ACCACGAU 5′



 



Hsa-miR-29b:



[SEQ ID NO: 2]



3′ UUGUGACUAAAGUUUACCACGAU 5′






Upper underlined black and blue nucleotides have no homology between target and experimental cDNAs. The lower underlined red nucleotides represent RNA sequence complementary to cDNAs that lack homology to miR-29b sequence. Nucleotides in bold represent the PICTAR predicted match site.
FIG. 3. Effect of restoration of miR-29s on the cancer cell epigenome.
FIG. 3a). Global DNA methylation changes induced by miR-29s on A549 cells harvested 48 and 72 h after transfection. The results are compared to non-transfected cells (mock) and cells transfected with a scrambled oligonucleotide (Scr). Global DNA methylation status was determined by LC/MS-MS.
FIG. 3b). Determination of FHIT and WWOX mRNA levels in A549 and H1299 cells, 48 h after transfection with miR-29s or a negative control, by qRT PCR; miR-29s induced re-expression of FHIT and WWOX mRNAs.
FIG. 3c). Immunoblot of FHIT and WWOX proteins in A549 and H1299 cells, 72 h after transfection with miR-29s or negative control; by 72 h miR-29s induced increased expression of FHIT and WWOX proteins. The numbers above the immunoblot images represent the intensity of the bands relative to the GAPDH gene (upper row: FHIT; lower row: WWOX).
FIG. 3d). Graphical representation of the quantitative DNA methylation data for FHIT and WWOX promoter region using the MassARRAY system. Each square represents a single CpG or a group of CpGs analyzed, and each arrow represents a sample. Methylation frequencies are displayed for each experiment in a color code that extends from light green (lower methylation frequencies) to bright red (higher methylation frequencies).
FIG. 4. Effects of miR-29s on tumorigenicity of A549 cells.
FIG. 4a). Growth curve of A549 cells transfected in vitro with miR-29s, scrambled (Scr) oligonucleotide or mock-transfected (Mock). The curves represent the average cell number of 3 different experiments.
FIG. 4b). Percent live cells were measured in A549 cells transfected with scrambled (Scr) oligonucleotide or with miR-29s oligonucleotides (100 nM final concentration). After 24 hours, cells were harvested and suspended in binding buffer with annexin V-FITC and propidium iodide, followed by flow cytometry to assess cell death. Error bars indicate SD.
FIG. 4c). Growth curve of engrafted tumors in nude mice injected with A549 cells pre-transfected (48 h before injection) with miR-29s, scr oligonucleotides, or mock-transfected.
FIG. 4d). Comparison of tumor engraftment sizes of mock-, Scr-, and miR-29s-transfected A549 cells, 21 days post injection in nude mice. The images show average-sized tumors from among 5 of each category.
FIG. 4e). Tumor weights ±SD in nude mice.
FIG. 5. DNMT3A protein expression level in NSCLCs is inversely associated with overall survival. Kaplan-Meier curve showing survival of 172 NSCLC patients with different levels of DNMT3A expression in tumors, relative to adjacent normal lung. Patients with higher expression of DNMT3A had shorter overall survival (P=0.029). There was a trend toward a similar association of DNMT3B protein expression level with survival but no such association for DNMT1.
FIG. 6. Correlation of endogenous miR-29 levels with DNMT3A/B mRNA levels. Inverse correlation between endogenous mRNA levels of DNMT3A, 3B and endogenous levels of miR-29s, determined by qRT PCR in 14 NSCLCs. R=regression coefficient, □=regression line; ♦=actual sample correlations.



DESCRIPTION OF EMBODIMENTS
Throughout this disclosure, various publications, patents and published patent specifications are referenced by an identifying citation. The disclosures of these publications, patents and published patent specifications are hereby incorporated by reference into the present disclosure to more fully describe the state of the art to which this invention pertains.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art (e.g., in cell culture, molecular genetics, nucleic acid chemistry, hybridization techniques and biochemistry). Standard techniques are used for molecular, genetic and biochemical methods which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (Glover ed., 1985); Oligonucleotide Synthesis (Gait ed., 1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid Hybridization (Hames & Higgins eds., 1984); Transcription And Translation (Hames & Higgins eds., 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells (Miller and Calos eds., 1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols. 154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (Weir and Blackwell, eds., 1986); The Laboratory Rat, editor in chief: Mark A. Suckow; authors: Sharp and LaRegina. CRC Press, Boston, 1988, which are incorporated herein by reference) and chemical methods.
As used in the specification and claims, the singular form “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a cell” includes a plurality of cells, including mixtures thereof.
As used herein interchangeably, a “miR gene product,” “microRNA,” “miR,” or “miRNA” refers to the unprocessed (e.g., precursor) or processed (e.g., mature) RNA transcript from a miR gene. As the miR gene products are not translated into protein, the term “miR gene products” does not include proteins. The unprocessed miR gene transcript is also called a “miR precursor” or “miR prec” and typically comprises an RNA transcript of about 70-100 nucleotides in length. The miR precursor can be processed by digestion with an RNAse (for example, Dicer, Argonaut, or RNAse III (e.g., E. coli RNAse III)) into an active 19-25 nucleotide RNA molecule. This active 19-25 nucleotide RNA molecule is also called the “processed” miR gene transcript or “mature” miRNA.
A “marker” is a gene or protein whose altered level of expression in a tissue or cell from its expression level in normal or healthy tissue or cell is associated with a disease state.
The “normal” level of expression of a marker is the level of expression of the marker in lung cells of a human subject or patient not afflicted with a lung cancer-related disease.
An “over-expression” or “significantly higher level of expression” of a marker refers to an expression level in a test sample that is greater than the standard error of the assay employed to assess expression, and in certain embodiments, at least twice, and in other embodiments, three, four, five or ten times the expression level of the marker in a control sample (e.g., sample from a healthy subject not having the marker associated disease) and in certain embodiments, the average expression level of the marker in several control samples.
A “significantly lower level of expression” of a marker refers to an expression level in a test sample that is at least twice, and in certain embodiments, three, four, five or ten times lower than the expression level of the marker in a control sample (e.g., sample from a healthy subject not having the marker associated disease) and in certain embodiments, the average expression level of the marker in several control samples.
A “kit” is any manufacture (e.g. a package or container) comprising at least one reagent, e.g., a probe, for specifically detecting the expression of a marker. The kit may be promoted, distributed or sold as a unit for performing the methods of the present invention.
“Proteins” encompass marker proteins and their fragments; variant marker proteins and their fragments; peptides and polypeptides comprising an at least 15 amino acid segment of a marker or variant marker protein; and fusion proteins comprising a marker or variant marker protein, or an at least 15 amino acid segment of a marker or variant marker protein.
In a first broad aspect, there is provided herein the identification of particular microRNAs whose expression is altered in cancer cells associated with different lung cancers, relative to normal control cells.
The active 19-25 nucleotide RNA molecule can be obtained from the miR precursor through natural processing routes (e.g., using intact cells or cell lysates) or by synthetic processing routes (e.g., using isolated processing enzymes, such as isolated Dicer. Argonaut, or RNAse III). It is understood that the active 19-25 nucleotide RNA molecule can also be produced directly by biological or chemical synthesis, without having been processed from the miR precursor. When a microRNA is referred to herein by name, the name corresponds to both the precursor and mature forms, unless otherwise indicated.
In one aspect, there is provided herein methods of diagnosing whether a subject has, or is at risk for developing, a lung cancer, comprising measuring the level of at least one miR gene product in a test sample from the subject and comparing the level of the miR gene product in the test sample to the level of a corresponding miR gene product in a control sample. As used herein, a “subject” can be any mammal that has, or is suspected of having, a lung cancer. In a preferred embodiment, the subject is a human who has, or is suspected of having, a lung cancer.
In one embodiment, the at least one miR gene product measured in the test sample is selected from the group consisting of miR29a, miR-29b, miR-29c, and combinations thereof. In a particular embodiment, the miR gene product is miR-29b.
The lung cancer-related disease can be any disorder or cancer that arises from the lung tissues. Such cancers are typically associated with the formation and/or presence of tumor masses and can be, for example, any form of lung cancer, for example, lung cancers of differing histology (e.g., adenocarcinoma, squamous cell carcinoma). Furthermore, the lung cancer may be associated with a particular prognosis (e.g., low survival rate, fast progression).
The level of at least one miR gene product can be measured in a biological sample (e.g.; cells, tissues) obtained from the subject. For example, a tissue sample (e.g., from a tumor) can be removed from a subject suspected of having a lung cancer-related disease by conventional biopsy techniques. In another embodiment, a blood sample can be removed from the subject, and blood cells (e.g., white blood cells) can be isolated for DNA extraction by standard techniques. The blood or tissue sample is preferably obtained from the subject prior to initiation of radiotherapy, chemotherapy or other therapeutic treatment. A corresponding control tissue or blood sample can be obtained from unaffected tissues of the subject, from a normal human individual or population of normal individuals, or from cultured cells corresponding to the majority of cells in the subject's sample. The control tissue or blood sample is then processed along with the sample from the subject, so that the levels of miR gene product produced from a given miR gene in cells from the subject's sample can be compared to the corresponding miR gene product levels from cells of the control sample. A reference miR expression standard for the biological sample can also be used as a control.
An alteration (e.g., an increase or decrease) in the level of a miR gene product in the sample obtained from the subject, relative to the level of a corresponding miR gene product in a control sample, is indicative of the presence of a lung cancer-related disease in the subject.
In one embodiment, the level of the at least one miR gene product in the test sample is greater than the level of the corresponding miR gene product in the control sample (i.e., expression of the miR gene product is “up-regulated”). As used herein, expression of a miR gene product is “up-regulated” when the amount of miR gene product in a cell or tissue sample from a subject is greater than the amount of the same gene product in a control cell or tissue sample.
In another embodiment, the level of the at least one miR gene product in the test sample is less than the level of the corresponding miR gene product in the control sample (i.e., expression of the miR gene product is “down-regulated”). As used herein, expression of a miR gene is “down-regulated” when the amount of miR gene product produced from that gene in a cell or tissue sample from a subject is less than the amount produced from the same gene in a control cell or tissue sample.
The relative miR gene expression in the control and normal samples can be determined with respect to one or more RNA expression standards. The standards can comprise, for example, a zero miR gene expression level, the miR gene expression level in a standard cell line, the miR gene expression level in unaffected tissues of the subject, or the average level of miR gene expression previously obtained for a population of normal human controls.
The level of a miR gene product in a sample can be measured using any technique that is suitable for detecting RNA expression levels in a biological sample. Suitable techniques (e.g., Northern blot analysis, RT-PCR, in situ hybridization) for determining RNA expression levels in a biological sample (e.g., cells, tissues) are well known to those of skill in the art. In a particular embodiment, the level of at least one miR gene product is detected using Northern blot analysis. For example, 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. The RNA is then immobilized on the filters by heating. 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 a given miR gene product can be produced from the nucleic acid sequences and include, but are not limited to, probes having at least about 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or complete complementarity to a miR gene product of interest. Methods for preparation of labeled DNA and RNA probes, and the conditions for hybridization thereof to target nucleotide sequences, are described in Molecular Cloning: A Laboratory Manual, J. Sambrook et al., eds., 2nd edition, Cold Spring Harbor Laboratory Press, 1989, Chapters 10 and 11, the disclosures of which are incorporated herein by reference.
In one non-limiting example, the nucleic acid probe can be labeled with, e.g., a radionuclide, such as 3H, 32P, 33P, 14C, or 35S; a heavy metal; 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 incorporated herein by reference. The latter is the method of choice for synthesizing 32P-labeled probes of high specific activity from single-stranded DNA or from RNA templates. For example, by replacing preexisting nucleotides with highly radioactive nucleotides according to the nick translation method, it is possible to prepare 32P-labeled nucleic acid probes with a specific activity well in excess of 108 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 miR gene transcript levels. Using another approach, miR gene transcript levels can be quantified by computerized imaging systems, such as the Molecular Dynamics 400-B 2D Phosphorimager available from Amersham Biosciences, Piscataway, N.J.
Where radionuclide labeling of DNA or RNA probes is not practical, the random-primer method can be used to incorporate an analogue, for example, 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, and antibodies (e.g., anti-biotin antibodies) coupled to fluorescent dyes or enzymes that produce color reactions.
In addition to Northern and other RNA hybridization techniques, determining the levels of RNA transcripts can be accomplished using 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 nucleic acid (e.g., cDNA or RNA) probes. This technique is particularly well-suited for analyzing tissue biopsy samples from subjects. 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.
In one non-limiting example, suitable probes for in situ hybridization of a given miR gene product can be produced from the nucleic acid sequences, and include, but are not limited to, probes having at least about 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or complete complementarity to a miR gene product of interest, as described above.
The relative number of miR gene transcripts in cells can also be determined by reverse transcription of miR gene transcripts, followed by amplification of the reverse-transcribed transcripts by polymerase chain reaction (RT-PCR). The levels of miR gene transcripts can be quantified in comparison with an internal standard, for example, the level of mRNA from a “housekeeping” gene present in the same sample. A suitable “housekeeping” gene for use as an internal standard includes, e.g., myosin or glyceraldehyde-3-phosphate dehydrogenase (G3PDH). Methods for performing quantitative and semi-quantitative RT-PCR, and variations thereof, are well known to those of skill in the art.
In some instances, it may be desirable to simultaneously determine the expression level of a plurality of different miR gene products in a sample. In other instances, it may be desirable to determine the expression level of the transcripts of all known miR genes correlated with a cancer. Assessing cancer-specific expression levels for hundreds of miR genes or gene products is time consuming and requires a large amount of total RNA (e.g., at least 20 μg for each Northern blot) and autoradiographic techniques that require radioactive isotopes.
To overcome these limitations, an oligolibrary, in microchip format (i.e., a microarray), may be constructed containing a set of oligonucleotide (e.g., oligodeoxynucleotides) probes that are specific for a set of miR genes. Using such a microarray, the expression level of multiple microRNAs in a biological sample can be determined by reverse transcribing the RNAs to generate a set of target oligodeoxynucleotides, and hybridizing them to probe the oligonucleotides on the microarray to generate a hybridization, or expression, profile. The hybridization profile of the test sample can then be compared to that of a control sample to determine which microRNAs have an altered expression level in lung cancer cells.
As used herein, “probe oligonucleotide” or “probe oligodeoxynucleotide” refers to an oligonucleotide that is capable of hybridizing to a target oligonucleotide. “Target oligonucleotide” or “target oligodeoxynucleotide” refers to a molecule to be detected (e.g., via hybridization). By “miR-specific probe oligonucleotide” or “probe oligonucleotide specific for a miR” is meant a probe oligonucleotide that has a sequence selected to hybridize to a specific miR gene product, or to a reverse transcript of the specific miR gene product.
An “expression profile” or “hybridization profile” of a particular sample is essentially a fingerprint of the state of the sample; while two states may have any particular gene similarly expressed, the evaluation of a number of genes simultaneously allows the generation of a gene expression profile that is unique to the state of the cell. That is, normal tissue may be distinguished from cancerous (e.g., tumor) tissue, and within cancerous tissue, different prognosis states (for example, good or poor long term survival prospects) may be determined. By comparing expression profiles of the cancer tissue in different states, information regarding which genes are important (including both up- and down-regulation of genes) in each of these states is obtained. The identification of sequences that are differentially expressed in cancer tissue, as well as differential expression resulting in different prognostic outcomes, allows the use of this information in a number of ways.
In one non-limiting example, a particular treatment regime may be evaluated (e.g., to determine whether a chemotherapeutic drug acts to improve the long-term prognosis in a particular patient). Similarly, diagnosis may be done or confirmed by comparing patient samples with known expression profiles. Furthermore, these gene expression profiles (or individual genes) allow screening of drug candidates that suppress the lung cancer expression profile or convert a poor prognosis profile to a better prognosis profile.
Accordingly, there is also provided herein methods of diagnosing whether a subject has, or is at risk for developing, a lung cancer, comprising reverse transcribing RNA from a test sample obtained from the subject to provide a set of target oligodeoxynucleotides, hybridizing the target oligodeoxynucleotides to a microarray comprising miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample, and comparing the test sample hybridization profile to a hybridization profile generated from a control sample or reference standard, wherein an alteration in the signal of at least one miRNA is indicative of the subject either having, or being at risk for developing, lung cancer.
In one embodiment, the microarray comprises miRNA-specific probe oligonucleotides for a substantial portion of all known human miRNAs. In a particular embodiment, the microarray comprises miRNA-specific probe oligonucleotides for one or more miRNAs selected from the group consisting of miR29a, miR-29b, miR-29c and combinations thereof.
The microarray can be prepared from gene-specific oligonucleotide probes generated from known miRNA sequences. The array may contain two different oligonucleotide probes for each miRNA, one containing the active, mature sequence and the other being specific for the precursor of the miRNA. The array may also contain controls, such as one or more mouse sequences differing from human orthologs by only a few bases, which can serve as controls for hybridization stringency conditions, tRNAs or other RNAs (e.g., rRNAs, mRNAs) from both species may also be printed on the microchip, providing an internal, relatively stable, positive control for specific hybridization. One or more appropriate controls for non-specific hybridization may also be included on the microchip. For this purpose, sequences are selected based upon the absence of any homology with any known miRNAs.
The microarray may be fabricated using techniques known in the art. For example, probe oligonucleotides of an appropriate length, e.g., 40 nucleotides, are 5′-amine modified at position C6 and printed using commercially available microarray systems, e.g., the GeneMachine OmniGridTM 100 Microarrayer and Amersham CodeLinkTM activated slides. Labeled cDNA oligomer corresponding to the target RNAs is prepared by reverse transcribing the target RNA with labeled primer. Following first strand synthesis, the RNA/DNA hybrids are denatured to degrade the RNA templates. The labeled target cDNAs thus prepared are then hybridized to the microarray chip under hybridizing conditions, e.g., 6×SSPE/30% formamide at 25° C. for 18 hours, followed by washing in 0.75×TNT (Tris HCl/NaCl/Tween 20) at 37° C. for 40 minutes. At positions on the array where the immobilized probe DNA recognizes a complementary target cDNA in the sample, hybridization occurs. The labeled target cDNA marks the exact position on the array where binding occurs, allowing automatic detection and quantification. The output consists of a list of hybridization events, indicating the relative abundance of specific cDNA sequences, and therefore the relative abundance of the corresponding complementary miRs, in the patient sample.
According to one embodiment, the labeled cDNA oligomer is a biotin-labeled cDNA, prepared from a biotin-labeled primer. The microarray is then processed by direct detection of the biotin-containing transcripts using, e.g., Streptavidin-Alexa647 conjugate, and scanned utilizing conventional scanning methods. Image intensities of each spot on the array are proportional to the abundance of the corresponding miR in the patient sample.
The use of the array has several advantages for miRNA expression detection. First, the global expression of several hundred genes can be identified in the same sample at one time point. Second, through careful design of the oligonucleotide probes, expression of both mature and precursor molecules can be identified. Third, in comparison with Northern blot analysis, the chip requires a small amount of RNA, and provides reproducible results using 2.5 μg of total RNA. The relatively limited number of miRNAs (a few hundred per species) allows the construction of a common microarray for several species, with distinct oligonucleotide probes for each. Such a tool allows for analysis of trans-species expression for each known miR under various conditions.
In addition to use for quantitative expression level assays of specific miR5, a microchip containing miRNA-specific probe oligonucleotides corresponding to a substantial portion of the miRNome, preferably the entire miRNome, may be employed to carry out miR gene expression profiling, for analysis of miR expression patterns. Distinct miR signatures can be associated with established disease markers, or directly with a disease state.
According to the expression profiling methods described herein, total RNA from a sample from a subject suspected of having a lung cancer-related disease quantitatively reverse transcribed to provide a set of labeled target oligodeoxynucleotides complementary to the RNA in the sample. The target oligodeoxynucleotides are then hybridized to a microarray comprising miRNA-specific probe oligonucleotides to provide a hybridization profile for the sample. The result is a hybridization profile for the sample representing the expression pattern of miRNA in the sample. The hybridization profile comprises the signal from the binding of the target oligodeoxynucleotides from the sample to the miRNA-specific probe oligonucleotides in the microarray. The profile may be recorded as the presence or absence of binding (signal vs. zero signal).
More preferably, the profile recorded includes the intensity of the signal from each hybridization. The profile is compared to the hybridization profile generated from a normal, i.e., noncancerous, control sample. An alteration in the signal is indicative of the presence of, or propensity to develop, cancer in the subject.
Other techniques for measuring miR gene expression are also within the skill in the art, and include various techniques for measuring rates of RNA transcription and degradation.
There is also provided herein methods of determining the prognosis of a subject with a lung cancer, comprising measuring the level of at least one miR gene product, which is associated with a particular prognosis in a lung cancer-related disease (e.g., a good or positive prognosis, a poor or adverse prognosis), in a test sample from the subject.
According to these methods, an alteration in the level of a miR gene product that is associated with a particular prognosis in the test sample, as compared to the level of a corresponding miR gene product in a control sample, is indicative of the subject having a lung cancer with a particular prognosis. In one embodiment, the miR gene product is associated with an adverse (i.e., poor) prognosis. Examples of an adverse prognosis include, but are not limited to, low survival rate and rapid disease progression. In certain embodiments, the level of the at least one miR gene product is measured by reverse transcribing RNA from a test sample obtained from the subject to provide a set of target oligodeoxynucleotides, hybridizing the target oligodeoxynucleotides to a microarray that comprises miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample, and comparing the test sample hybridization profile to a hybridization profile generated from a control sample.
Without wishing to be bound by any one theory, it is believed that alterations in the level of one or more miR gene products in cells can result in the deregulation of one or more intended targets for these miRs, which can lead to the formation of lung cancers. Therefore, altering the level of the miR gene product (e.g., by decreasing the level of a miR gene product that is up-regulated in lung cancer cells, by increasing the level of a miR gene product that is down-regulated in lung cancer cells) may successfully treat the lung cancer.
Accordingly, there is further provided herein methods of inhibiting tumorigenesis in a subject who has, or is suspected of having, a lung cancer wherein at least one miR gene product is deregulated (e.g., down-regulated, up-regulated) in the cancer cells of the subject. When the at least one isolated miR gene product is down-regulated in the cancer cells (e.g., miR-29 family), the method comprises administering an effective amount of the at least one isolated miR gene product, or an isolated variant or biologically-active fragment thereof, such that proliferation of cancer cells in the subject is inhibited.
For example, when a miR gene product is down-regulated in a cancer cell in a subject, administering an effective amount of an isolated miR gene product to the subject can inhibit proliferation of the cancer cell. The isolated miR gene product that is administered to the subject can be identical to the endogenous wild-type miR gene product (e.g., a miR gene product) that is down-regulated in the cancer cell or it can be a variant or biologically-active fragment thereof.
As defined herein, a “variant” of a miR gene product refers to a miRNA that has less than 100% identity to a corresponding wild-type miR gene product and possesses one or more biological activities of the corresponding wild-type miR gene product. Examples of such biological activities include, but are not limited to, inhibition of expression of a target RNA molecule (e.g., inhibiting translation of a target RNA molecule, modulating the stability of a target RNA molecule, inhibiting processing of a target RNA molecule) and inhibition of a cellular process associated with lung cancer (e.g., cell differentiation, cell growth, cell death). These variants include species variants and variants that are the consequence of one or more mutations (e.g., a substitution, a deletion, an insertion) in a miR gene. In certain embodiments, the variant is at least about 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identical to a corresponding wild-type miR gene product.
As defined herein, a “biologically-active fragment” of a miR gene product refers to an RNA fragment of a miR gene product that possesses one or more biological activities of a corresponding wild-type miR gene product. As described above, examples of such biological activities include, but are not limited to, inhibition of expression of a target RNA molecule and inhibition of a cellular process associated with a lung cancer. In certain embodiments, the biologically-active fragment is at least about 5, 7, 10, 12, 15, or 17 nucleotides in length.
In a particular embodiment, an isolated miR gene product can be administered to a subject in combination with one or more additional anti-cancer treatments. Suitable anti-cancer treatments include, but are not limited to, chemotherapy, radiation therapy and combinations thereof (e.g. chemoradiation).
When the at least one isolated miR gene product is up-regulated in the cancer cells, the method comprises administering to the subject an effective amount of at least one compound for inhibiting expression of the at least one miR gene product, referred to herein as miR gene expression-inhibition compounds, such that proliferation of the cancer cells is inhibited. In a particular embodiment, the at least one miR expression-inhibition compound is specific for a miR gene product selected from the group consisting miR29 family, including miR-29a, miR-29b, miR-29c, and combinations thereof.
The terms “treat”, “treating” and “treatment”, as used herein, refer to ameliorating symptoms associated with a disease or condition, for example, a lung cancer, including preventing or delaying the onset of the disease symptoms, and/or lessening the severity or frequency of symptoms of the disease or condition. The terms “subject”, “patient” and “individual” are defined herein to include animals, such as mammals, including, but not limited to, primates, cows, sheep, goats, horses, dogs, cats, rabbits, guinea pigs, rats, mice or other bovine, ovine, equine, canine, feline, rodent, or murine species. In a preferred embodiment, the animal is a human.
As used herein, an “effective amount” of an isolated miR gene product is an amount sufficient to inhibit proliferation of a cancer cell in a subject suffering from a lung cancer. One skilled in the art can readily determine an effective amount of a miR gene product 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.
For example, an effective amount of an isolated miR gene product 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 isolated miR gene product based on the weight of a tumor mass can be in the range of about 10-500 micrograms/gram of tumor mass. In certain embodiments, the tumor mass can be at least about 10 micrograms/gram of tumor mass, at least about 60 micrograms/gram of tumor mass or at least about 100 micrograms/gram of tumor mass.
An effective amount of an isolated miR gene product 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 herein. For example, an effective amount of the isolated miR gene product is administered to a subject can range from about 5 to about 3000 micrograms/kg of body weight, from about 700-1000 micrograms/kg of body weight, or greater than about 1000 micrograms/kg of body weight.
One skilled in the art can also readily determine an appropriate dosage regimen for the administration of an isolated miR gene product to a given subject. For example, a miR gene product can be administered to the subject once (e.g., as a single injection or deposition). Alternatively, a miR gene product can be administered once or twice daily to a subject for a period of from about three to about twenty-eight days, more particularly from about seven to about ten days. In a particular dosage regimen, a miR gene product is administered once a day for seven days. Where a dosage regimen comprises multiple administrations, it is understood that the effective amount of the miR gene product administered to the subject can comprise the total amount of gene product administered over the entire dosage regimen.
As used herein, an “isolated” miR gene product is one that is synthesized, or altered or removed from the natural state through human intervention. For example, a synthetic miR gene product, or a miR gene product partially or completely separated from the coexisting materials of its natural state, is considered to be “isolated.” An isolated miR gene product can exist in substantially-purified form, or can exist in a cell into which the miR gene product has been delivered. Thus, a miR gene product that is deliberately delivered to, or expressed in, a cell is considered an “isolated” miR gene product. A miR gene product produced inside a cell from a miR precursor molecule is also considered to be an “isolated” molecule. According to one particular embodiment, the isolated miR gene products described herein can be used for the manufacture of a medicament for treating a lung cancer in a subject (e.g., a human).
Isolated miR gene products can be obtained using a number of standard techniques. For example, the miR gene products can be chemically synthesized or recombinantly produced using methods known in the art. In one embodiment, miR gene products are chemically synthesized using appropriately protected ribonucleoside phosphoramidites and a conventional DNA/RNA synthesizer. Commercial suppliers of synthetic RNA molecules or synthesis reagents include, e.g., Proligo (Hamburg, Germany), Dharmacon Research (Lafayette, Colo., U.S.A.), Pierce Chemical (part of Perbio Science, Rockford, Ill., U.S.A.), Glen Research (Sterling, Va., U.S.A.), ChemGenes (Ashland, Mass., U.S.A.) and Cruachem (Glasgow, UK).
Alternatively, the miR 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, e.g., 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 miR gene products in cancer cells.
The miR gene products that are expressed from recombinant plasmids can be isolated from cultured cell expression systems by standard techniques. The miR gene products that are expressed from recombinant plasmids can also be delivered to, and expressed directly in, the cancer cells. The use of recombinant plasmids to deliver the miR gene products to cancer cells is discussed in more detail below.
The miR gene products can be expressed from a separate recombinant plasmid, or they can be expressed from the same recombinant plasmid. In one embodiment, the miR gene products are expressed as RNA precursor molecules from a single plasmid, and the precursor molecules are processed into the functional miR gene product by a suitable processing system, including, but not limited to, processing systems extant within a cancer cell. Other suitable processing systems include, e.g., the in vitro Drosophila cell lysate system (e.g., as described in U.S. Published Patent Application No. 2002/0086356 to Tuschl et al., the entire disclosure of which is incorporated herein by reference) and the E. coli RNAse III system (e.g., as described in U.S. Published Patent Application No. 2004/0014113 to Yang et al., the entire disclosure of which is incorporated herein by reference).
Selection of plasmids suitable for expressing the miR gene products, methods for inserting nucleic acid sequences into the plasmid to express the gene products, and methods of delivering the recombinant plasmid to the cells of interest are within the skill in the art. See, for example, Zeng et al. (2002), Molecular Cell 9:1327-1333; Tuschl (2002), Nat. Biotechnol, 20:446-448; Brummelkamp et al. (2002), Science 296:550-553; Miyagishi et al. (2002), Nat. Biotechnol. 20:497-500; Paddison et al. (2002), Genes Dev. 16:948-958; Lee et al. (2002), Nat. Biotechnol. 20:500-505; and Paul et al. (2002), Nat. Biotechnol. 20:505-508, the entire disclosures of which are incorporated herein by reference.
In one embodiment, a plasmid expressing the miR gene products comprises a sequence encoding a miR precursor RNA under the control of the CMV intermediate-early promoter. As used herein, “under the control” of a promoter means that the nucleic acid sequences encoding the miR gene product are located 3′ of the promoter, so that the promoter can initiate transcription of the miR gene product coding sequences.
The miR gene products can also be expressed from recombinant viral vectors. It is contemplated that the miR 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 cancer cells. The use of recombinant viral vectors to deliver the miR gene products to cancer cells is discussed in more detail below.
The recombinant viral vectors of the invention comprise sequences encoding the miR gene products and any suitable promoter for expressing the RNA sequences. Suitable promoters include, but are not limited to, 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 miR gene products in a cancer cell.
Any viral vector capable of accepting the coding sequences for the miR 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 be modified by pseudotyping the vectors with envelope proteins or other surface antigens from other viruses, or by substituting different viral capsid proteins, as appropriate.
For example, lentiviral vectors of the invention can be pseudotyped with surface proteins from vesicular stomatitis virus (VSV), rabies, Ebola, Mokola, and the like. AAV vectors of the invention can be made to target different cells by engineering the vectors to express different capsid protein serotypes. For example, an AAV vector expressing a serotype 2 capsid on a serotype 2 genome is called AAV 2/2. This serotype 2 capsid gene in the AAV 2/2 vector can be replaced by a serotype 5 capsid gene to produce an AAV 2/5 vector. Techniques for constructing AAV vectors that express different capsid protein serotypes are within the skill in the art; see, e.g., Rabinowitz, J. E., et al. (2002), J. Virol. 76:791-801, the entire disclosure of which is incorporated herein by reference.
Selection of 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, Dornburg (1995), Gene Therapy 2:301-310; Eglitis (1988), Biotechniques 6:608-614; Miller (1990), Hum. Gene Therapy 1:5-14; and Anderson (1998), Nature 392:25-30, the entire disclosures of which are incorporated herein by reference.
Particularly suitable viral vectors are those derived from AV and AAV. A suitable AV vector for expressing the miR gene products, 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 incorporated herein by reference. Suitable AAV vectors for expressing the miR gene products, 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. Virol., 70:520-532; Samulski et al. (1989), J. Virol. 63:3822-3826; U.S. Pat. No. 5,252,479; U.S. Pat. No. 5,139,941; International Patent Application No. WO 94/13788; and International Patent Application No. WO 93/24641, the entire disclosures of which are incorporated herein by reference. In one embodiment, the miR gene products are expressed from a single recombinant AAV vector comprising the CMV intermediate early promoter.
In a certain embodiment, a recombinant AAV viral vector of the invention comprises a nucleic acid sequence encoding a miR precursor RNA in operable connection with a polyT termination sequence under the control of a human U6 RNA promoter. As used herein, “in 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. During transcription of the miR sequences from the vector, the polyT termination signals act to terminate transcription.
In other embodiments of the treatment methods of the invention, an effective amount of at least one compound that inhibits miR expression can be administered to the subject. As used herein, “inhibiting miR expression” means that the production of the precursor and/or active, mature form of miR gene product after treatment is less than the amount produced prior to treatment. One skilled in the art can readily determine whether miR expression has been inhibited in a cancer cell, using, for example, the techniques for determining miR transcript level discussed above for the diagnostic method. Inhibition can occur at the level of gene expression (i.e., by inhibiting transcription of a miR gene encoding the miR gene product) or at the level of processing (e.g., by inhibiting processing of a miR precursor into a mature, active miR).
As used herein, an “effective amount” of a compound that inhibits miR expression is an amount sufficient to inhibit proliferation of a cancer cell in a subject suffering from a cancer (e.g., a lung cancer). One skilled in the art can readily determine an effective amount of a miR expression-inhibition compound 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.
For example, an effective amount of the expression-inhibition compound can be based on the approximate weight of a tumor mass to be treated, as described herein. An effective amount of a compound that inhibits miR expression can also be based on the approximate or estimated body weight of a subject to be treated, as described herein.
One skilled in the art can also readily determine an appropriate dosage regimen for administering a compound that inhibits miR expression to a given subject.
Suitable compounds for inhibiting miR gene expression include double-stranded RNA (such as short- or small-interfering RNA or “siRNA”), antisense nucleic acids, and enzymatic RNA molecules, such as ribozymes. Each of these compounds can be targeted to a given miR gene product and interfere with the expression of (e.g., inhibit translation of, induce cleavage or destruction of) the target miR gene product.
For example, expression of a given miR gene can be inhibited by inducing RNA interference of the miR gene with an isolated double-stranded RNA (“dsRNA”) molecule which has at least 90%, for example at least 95%, at least 98%, at least 99%, or 100%, sequence homology with at least a portion of the miR gene product. In a particular embodiment, the dsRNA molecule is a “short or small interfering RNA” or “siRNA.”
siRNA useful in the present methods comprise short double-stranded RNA from about 17 nucleotides to about 29 nucleotides in length, preferably from about 19 to about 25 nucleotides in length. The siRNA comprise a sense RNA strand and a complementary antisense RNA strand annealed together by standard Watson-Crick base-pairing interactions (hereinafter “base-paired”). The sense strand comprises a nucleic acid sequence that is substantially identical to a nucleic acid sequence contained within the target miR gene product.
As used herein, a nucleic acid sequence in an siRNA which is “substantially identical” to a target sequence contained within the target mRNA is a nucleic acid sequence that is identical to the target sequence, or that differs from the target sequence by one or two nucleotides. The sense and antisense strands of the siRNA can comprise two complementary, single-stranded RNA molecules, or can comprise a single molecule in which two complementary portions are base-paired and are covalently linked by a single-stranded “hairpin” area.
The siRNA can also be altered RNA that differs from naturally-occurring RNA by the addition, deletion, substitution and/or alteration of one or more nucleotides. Such alterations can include addition of non-nucleotide material, such as to the end(s) of the siRNA or to one or more internal nucleotides of the siRNA, or modifications that make the siRNA resistant to nuclease digestion, or the substitution of one or more nucleotides in the siRNA with deoxyribonucleotides.
One or both strands of the siRNA can also comprise a 3′ overhang. As used herein, a “3′ overhang” refers to at least one unpaired nucleotide extending from the 3′-end of a duplexed RNA strand. Thus, in certain embodiments, the siRNA comprises at least one 3′ overhang of from 1 to about 6 nucleotides (which includes ribonucleotides or deoxyribonucleotides) in length, from 1 to about 5 nucleotides in length, from 1 to about 4 nucleotides in length, or from about 2 to about 4 nucleotides in length. In a particular embodiment, the 3′ overhang is present on both strands of the siRNA, and is 2 nucleotides in length. For example, each strand of the siRNA can comprise 3′ overhangs of dithymidylic acid (“Ti”) or diuridylic acid (“uu”).
The siRNA can be produced chemically or biologically, or can be expressed from a recombinant plasmid or viral vector, as described above for the isolated miR gene products. Exemplary methods for producing and testing dsRNA or siRNA molecules are described in U.S. Published Patent Application No. 2002/0173478 to Gewirtz and in U.S. Published Patent Application No. 2004/0018176 to Reich et al., the entire disclosures of both of which are incorporated herein by reference.
Expression of a given miR gene can also be inhibited by an antisense nucleic acid. As used herein, an “antisense nucleic acid” refers to a nucleic acid molecule that binds to target RNA by means of RNA-RNA, RNA-DNA or RNA-peptide nucleic acid interactions, which alters the activity of the target RNA. Antisense nucleic acids suitable for use in the present methods are single-stranded nucleic acids (e.g., RNA, DNA, RNA-DNA chimeras, peptide nucleic acid (PNA)) that generally comprise a nucleic acid sequence complementary to a contiguous nucleic acid sequence in a miR gene product. The antisense nucleic acid can comprise a nucleic acid sequence that is 50-100% complementary, 75-100% complementary, or 95-100% complementary to a contiguous nucleic acid sequence in a miR gene product.
Without wishing to be bound by any theory, it is believed that the antisense nucleic acids activate RNase H or another cellular nuclease that digests the miR gene product/antisense nucleic acid duplex.
Antisense nucleic acids can also contain modifications to the nucleic acid backbone or to the sugar and base moieties (or their equivalent) to enhance target specificity, nuclease resistance, delivery or other properties related to efficacy of the molecule. Such modifications include cholesterol moieties, duplex intercalators, such as acridine, or one or more nuclease-resistant groups.
Antisense nucleic acids can be produced chemically or biologically, or can be expressed from a recombinant plasmid or viral vector, as described above for the isolated miR gene products. Exemplary methods for producing and testing are within the skill in the art; see, e.g., Stein and Cheng (1993), Science 261:1004 and U.S. Pat. No. 5,849,902 to Woolf et al., the entire disclosures of which are incorporated herein by reference.
Expression of a given miR gene can also be inhibited by an enzymatic nucleic acid. As used herein, an “enzymatic nucleic acid” refers to a nucleic acid comprising a substrate binding region that has complementarity to a contiguous nucleic acid sequence of a miR gene product, and which is able to specifically cleave the miR gene product. The enzymatic nucleic acid substrate binding region can be, for example, 50-100% complementary, 75-100% complementary, or 95-100% complementary to a contiguous nucleic acid sequence in a miR gene product. The enzymatic nucleic acids can also comprise modifications at the base, sugar, and/or phosphate groups.
Exemplary enzymatic nucleic acids for use in the present methods include de novo methyltransferases, including DNMT3A and DNMT3B, as described in the Examples herein.
The enzymatic nucleic acids can be produced chemically or biologically, or can be expressed from a recombinant plasmid or viral vector, as described above for the isolated miR gene products. Exemplary methods for producing and testing dsRNA or siRNA molecules are described in Werner and Uhlenbeck (1995), Nucl. Acids Res. 23:2092-96; Hammann et al. (1999), Antisense and Nucleic Acid Drug Dev. 9:25-31; and U.S. Pat. No. 4,987,071 to Cech et al, the entire disclosures of which are incorporated herein by reference.
Administration of at least one miR gene product, or at least one compound for inhibiting miR expression, will inhibit the proliferation of cancer cells in a subject who has a lung cancer.
As used herein, to “inhibit the proliferation of a cancer cell” means to kill the cell, or permanently or temporarily arrest or slow the growth of the cell. Inhibition of cancer cell proliferation can be inferred if the number of such cells in the subject remains constant or decreases after administration of the miR gene products or miR gene expression-inhibition compounds. An inhibition of 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 cancer cells in the body of a subject can be determined by direct measurement, or by estimation from the size of primary or metastatic tumor masses. For example, the number of cancer cells in a subject can be measured by immunohistological methods, flow cytometry, or other techniques designed to detect characteristic surface markers of cancer cells.
The size of 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.
The miR gene products or miR gene expression-inhibition compounds can be administered to a subject by any means suitable for delivering these compounds to cancer cells of the subject. For example, the miR gene products or miR expression-inhibition compounds can be administered by methods suitable to transfect cells of the subject with these compounds, or with nucleic acids comprising sequences encoding these compounds.
In one embodiment, the cells are transfected with a plasmid or viral vector comprising sequences encoding at least one miR gene product or miR gene expression-inhibition compound.
Transfection methods for eukaryotic cells are well known in the art, and include, e.g., 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.
For example, 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. The amount of nucleic acid used is not critical to the practice of the invention; acceptable results may be achieved with 0.1-100 micrograms of nucleic acid/105 cells. For example, a ratio of about 0.5 micrograms of plasmid vector in 3 micrograms of DOTAP per 105 cells can be used.
A miR gene product or miR gene expression-inhibition compound can also be administered to a subject by any suitable enteral or parenteral administration route. Suitable enteral administration routes for the present methods include, e.g., oral, rectal, or intranasal delivery. Suitable parenteral administration routes include, e.g., 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. Particularly suitable administration routes are injection, infusion and direct injection into the tumor.
In the present methods, a miR gene product or miR gene product expression-inhibition compound can be administered to the subject either as naked RNA, in combination with a delivery reagent, or as a nucleic acid (e.g., a recombinant plasmid or viral vector) comprising sequences that express the miR gene product or miR gene product expression-inhibition compound. Suitable delivery reagents include, e.g., the Mirus Transit TKO lipophilic reagent; lipofectin; lipofectamine; cellfectin; polycations (e.g., polylysine), and liposomes.
Recombinant plasmids and viral vectors comprising sequences that express the miR gene products or miR gene expression-inhibition compounds, and techniques for delivering such plasmids and vectors to cancer cells, are discussed herein and/or are well known in the art.
In a particular embodiment, liposomes are used to deliver a miR gene product or miR gene expression-inhibition compound (or nucleic acids comprising sequences encoding them) to a subject. Liposomes can also increase the blood half-life of the gene products or nucleic acids. Suitable liposomes 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 incorporated herein by reference.
The liposomes for use in the present methods can comprise a ligand molecule that targets the liposome to cancer cells. Ligands that bind to receptors prevalent in cancer cells, such as monoclonal antibodies that bind to tumor cell antigens, are preferred.
The liposomes for use in the present methods can also be modified so as to avoid clearance by the mononuclear macrophage system (“MMS”) and reticuloendothelial system (“RES”). Such modified liposomes have opsonization-inhibition moieties on the surface or incorporated into the liposome structure. In a particularly preferred embodiment, a liposome of the invention can comprise both an opsonization-inhibition moiety 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. As used herein, 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 that 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 incorporated herein 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 GM1. Copolymers of PEG, methoxy PEG, or methoxy PPG, or derivatives thereof, are also suitable. In addition, 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. Preferably, the opsonization-inhibiting moiety is a PEG, PPG, or a derivative thereof. Liposomes modified with PEG or PEG-derivatives are sometimes called “PEGylated liposomes.”
The opsonization-inhibiting moiety can be bound to the liposome membrane by any one of numerous well-known techniques. For example, an N-hydroxysuccinimide ester of PEG can be bound to a phosphatidyl-ethanolamine lipid-soluble anchor, and then bound to a membrane. Similarly, a dextran polymer can be derivatized with a stearylamine lipid-soluble anchor via reductive amination using Na(CN)BH3 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, lung tumors, will efficiently accumulate these liposomes; see Gabizon, et al. (1988), Proc. Natl. Acad. Sci., U.S.A., 18:6949-53. In addition, the reduced uptake by the RES lowers the toxicity of stealth liposomes by preventing significant accumulation of the liposomes in the liver and spleen. Thus, liposomes that are modified with opsonization-inhibition moieties are particularly suited to deliver the miR gene products or miR gene expression-inhibition compounds (or nucleic acids comprising sequences encoding them) to tumor cells.
The miR gene products or miR gene expression-inhibition compounds can be formulated as pharmaceutical compositions, sometimes called “medicaments,” prior to administering them to a subject, according to techniques known in the art. Accordingly, the invention encompasses pharmaceutical compositions for treating a lung cancer.
In one embodiment, the pharmaceutical composition comprises at least one isolated miR gene product, or an isolated variant or biologically-active fragment thereof, and a pharmaceutically-acceptable carrier. In a particular embodiment, the at least one miR gene product corresponds to a miR gene product that has a decreased level of expression in lung cancer cells relative to suitable control cells. In certain embodiments the isolated miR gene product is selected from the group consisting of miR29a, miR-29b, miR-29c, and combinations thereof.
In other embodiments, the pharmaceutical compositions of the invention comprise at least one miR expression-inhibition compound. In a particular embodiment, the at least one miR gene expression-inhibition compound is specific for a miR gene whose expression is greater in lung cancer cells than control cells. In certain embodiments, the miR gene expression-inhibition compound is specific for one or more miR gene products selected from the group consisting miR29a, miR-29b, miR-29c, and combinations thereof.
Pharmaceutical compositions of the present invention are characterized as being at least sterile and pyrogen-free. As used herein, “pharmaceutical compositions” 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 incorporated herein by reference.
The present pharmaceutical compositions comprise at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them) (e.g., 0.1 to 90% by weight), or a physiologically-acceptable salt thereof, mixed with a pharmaceutically-acceptable carrier. In certain embodiments, the pharmaceutical compositions of the invention additionally comprise one or more anti-cancer agents (e.g., chemotherapeutic agents). The pharmaceutical formulations of the invention can also comprise at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them), which are encapsulated by liposomes and a pharmaceutically-acceptable carrier. In one embodiment, the pharmaceutical composition comprises a miR gene or gene product that is one or more of miR29a, miR-29b and miR-29c.
Especially suitable pharmaceutically-acceptable carriers are water, buffered water, normal saline, 0.4% saline, 0.3% glycine, hyaluronic acid and the like.
In a particular embodiment, the pharmaceutical compositions of the invention comprise at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them) that is resistant to degradation by nucleases.
One skilled in the art can readily synthesize nucleic acids that are nuclease resistant, for example, by incorporating one or more ribonucleotides that is modified at the 2′-position into the miR gene product. Suitable 2′-modified ribonucleotides include those modified at the 2′-position with fluoro, amino, alkyl, alkoxy, and O-allyl.
Pharmaceutical 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, e.g., physiologically biocompatible buffers (e.g., tromethamine hydrochloride), additions of chelants (such as, for example, DTPA or DTPA-bisamide) or calcium chelate complexes (such 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.
For solid pharmaceutical compositions of the invention, conventional nontoxic solid pharmaceutically-acceptable carriers can be used; for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like.
For example, 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 at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them). A pharmaceutical composition for aerosol (inhalational) administration can comprise 0.01-20% by weight, preferably 1%-10% by weight, of the at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them) encapsulated in a liposome as described above, and a propellant. A carrier can also be included as desired; e.g., lecithin for intranasal delivery.
The pharmaceutical compositions of the invention can further comprise one or more anti-cancer agents. In a particular embodiment, the compositions comprise at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them) and at least one chemotherapeutic agent. Chemotherapeutic agents that are suitable for the methods of the invention include, but are not limited to, DNA-alkylating agents, anti-tumor antibiotic agents, anti-metabolic agents, tubulin stabilizing agents, tubulin destabilizing agents, hormone antagonist agents, topoisomerase inhibitors, protein kinase inhibitors, HMG-CoA inhibitors, CDK inhibitors, cyclin inhibitors, caspase inhibitors, metalloproteinase inhibitors, antisense nucleic acids, triple-helix DNAs, nucleic acids aptamers, and molecularly-modified viral, bacterial and exotoxic agents. Examples of suitable agents for the compositions of the present invention include, but are not limited to, cytidine arabinoside, methotrexate, vincristine, etoposide (VP-16), doxorubicin (adriamycin), cisplatin (CDDP), dexamethasone, arglabin, cyclophosphamide, sarcolysin, methylnitrosourea, fluorouracil, 5-fluorouracil (5FU), vinblastine, camptothecin, actinomycin-D, mitomycin C, hydrogen peroxide, oxaliplatin, irinotecan, topotecan, leucovorin, carmustine, streptozocin, CPT-11, taxol, tamoxifen, dacarbazine, rituximab, daunorubicin, 1-β-D-arabinofuranosylcytosine, imatinib, fludarabine, docetaxel, FOLFOX4.
There is also provided herein methods of identifying an inhibitor of tumorigenesis, comprising providing a test agent to a cell and measuring the level of at least one miR gene product in the cell. In one embodiment, the method comprises providing a test agent to a cell and measuring the level of at least one miR gene product associated with decreased expression levels in cancer cells. An increase in the level of the miR gene product in the cell after the agent is provided, relative to a suitable control cell (e.g., agent is not provided), is indicative of the test agent being an inhibitor of tumorigenesis. In a particular embodiment, at least one miR gene product associated with decreased expression levels in cancer cells is selected from the group consisting of miR29a, miR-29b, miR-29c, and combinations thereof.
In other embodiments, the method comprises providing a test agent to a cell and measuring the level of at least one miR gene product associated with increased expression levels in cancer cells. A decrease in the level of the miR gene product in the cell after the agent is provided, relative to a suitable control cell (e.g., agent is not provided), is indicative of the test agent being an inhibitor of tumorigenesis. In a particular embodiment, at least one miR gene product associated with increased expression levels in cancer cells is selected from the group consisting of miR29a, miR-29b, miR-29c, and combinations thereof.
Suitable agents include, but are not limited to drugs (e.g., small molecules, peptides), and biological macromolecules (e.g., proteins, nucleic acids). The agent can be produced recombinantly, synthetically, or it may be isolated (i.e., purified) from a natural source. Various methods for providing such agents to a cell (e.g., transfection) are well known in the art, and several of such methods are described hereinabove. Methods for detecting the expression of at least one miR gene product (e.g., Northern blotting, in situ hybridization. RT-PCR, expression profiling) are also well known in the art. Several of these methods are also described hereinabove.
The invention will now be illustrated by the following non-limiting examples.
EXAMPLE 1
MiR-29s expression is inversely correlated to DNMT3A and 3B in lung cancer patients. In addition, miR-29s directly target both DNMT3A and 3B. The enforced expression of miR-29s in lung cancer cell lines restores normal patterns of DNA methylation, induces re-expression of methylation-silenced tumor suppressor genes (TSGs), such as FHIT, and WWOX and inhibits tumorigenicity both in vitro and in vivo.
These findings support a role of miR-29s in the epigenetic regulation of NSCLC, providing a rationale for the development of miR-based strategies for the treatment of lung cancer.
172 matched non-neoplastic/primary NSCLC tissue pairs were analyzed by immunohistochemical analysis of tissue microarrays (TMAs). As shown in FIG. 5, higher expression of DNMT3A protein was significantly associated with lower overall survival (P=0.029). Statistically significant correlations with survival were not observed for DNMT1 and DNTM3B in this patient population.
To validate these miRNA-target interactions in vivo, the DNMT3A and DNTM3B complementary sites were cloned into the 3′UTR of the firefly luciferase gene and co-transfected with miR-29a, mi-R29b or miR-29c in A459 (NSCLC) cells.
As shown in FIG. 2a, all three miRNAs (miR-29a, mi-R29b or miR-29c) significantly reduced the luciferase activity with respect to the scrambled oligonucleotide. To assess whether ectopic expression of individual miR-29 sequences induces down-regulation of endogenous DNMT3A and DNTM3B mRNA levels, we also performed quantitative RT-PCR (qRT-PCR) in A549 and H1299 lung cancer-derived cells, transfected with scrambled RNA or with miR-29s.
Overexpression of individual miR-29s induced marked reduction of DNMT3A and DNMT3B mRNA levels (FIG. 2b, upper), whereas silencing of miR-29s with antisense molecules, induced up-regulation of DNMT3A and DNMT3B mRNA levels (FIG. 2b, lower) (results shown only for A549 cells).
To demonstrate that overexpression of miR-29s could downmodulate Dnmt3A and 3B protein expression, we used a GFP-reporter vector, QBI-GFP25.
Briefly, we cloned the 3′UTRs of DNMT3A and DNMT3B downstream of the GFP encoding sequence of the QBI-GFP25 vector, allowing expression of a fusion GFP protein containing the 3′UTR of DNMT3A or DNMT3B. A549 cells were cotransfected with the GFP-3A/3B-3′UTR-vector plus miR-29a, 29b, 29c, or scrambled oligonucleotide. Marked reduction in GFP protein expression was observed in cells transfected with miR-29s (FIG. 2c), especially GFP-3B-3′UTR protein; the protein expression results were consistent with those obtained by qRT-PCR, in which endogenous DNMT3B 11mRNA was more significantly reduced by expression of miR-29s (FIG. 2b).
While not wishing to be bound by theory, it is now believed that that the preferential downregulation of DNMT3B compared to DNMT3A may be possibly due to an overall higher number of predicted matching “seeds” of miR-29s with 3B 3′-UTR (3 for 29a, 1 for 29b, 1 for 29c) than with 3A 3′-UTR (1 for each miR-29).
In addition, the DNMT3B 3′UTR presents matching sites differing for no more than 1 nucleotide for miR-29a and for 29b/c matches. Thus, the transfection with any member of the miR-29 family may result in more robust silencing of DNMT3B than DNMT3A, according to the “coordinate principle” that miRNAs may act cooperatively through multiple target sites in one gene10,23.
To show a direct, functional interaction of the DNMT3B 3′UTR with miR-29b, a recently described detection method was used to detect miRNA-mRNA complexes in eukaryotic cells by synthesizing cDNA on a mRNA template using miRNAs as the endogenous cytoplasmic primer24. The endogenous miR-29b, at the Pictar-predicted site of interaction with 3′ UTR8, is able to function as a “natural” primer to initiate the retrotranscription of DNMT3B 11mRNA (FIG. 2d).
It was then determined whether DNMT3A and DNMT3B mRNA expression is inversely correlated to the levels of miR-29s in primary NSCLC tissues. Fourteen (14) NSCLCs were analyzed for expression levels of DNMT3A and DNMT3B mRNAs and for miR-29a, 29b, and 29c expression by qRT-PCR25. A statistically significant inverse correlation (FIG. 6) was observed between DNMT3A mRNA and miR-29a (P=0.02) and miR-29c (P=0.02).
A similar inverse correlation was observed for DNMT3B mRNA levels and miR-29a (P=0.02) and miR-29c (P=0.04). Although there was a trend toward inverse correlation of DNMT3A and DNMT3B mRNA levels with miR-29b level, the association was not statistically significant (DNMT3A P=0.14, DNMT3B P=0.09), this may be due either to the small number of cancers analyzed or to the fact that while miR-29a and 29c are transcribed from only one chromosomal location, on chromosome 7 and 1 respectively, mature miR-29b is transcribed from two different primary transcripts on different chromosomes, the miR-29b-1/miR-29a cluster on 7q32.3 and the miR-29b-2/miR-29c cluster on 1q32.2. The probe used in qRT-PCR to determine the mature product of miR-29b is unable to distinguish between the 29b-1 or 29b-2 gene products.
The discovery that miR-29s target DNMT3A and DNMT3B shows that expression of these miRNAs contributes to the DNA epigenetic modifications in cancer. To address this issue, A549 cells were transfected with miR-29a, miR-29b, miR-29c or scrambled oligonucleotides and analyzed global DNA methylation 48 and 72 h later, using an LC-MS/MS method.26.
As shown in FIG. 3a, all three miR-29s reduced global DNA methylation, with respect to the control. The effect appeared more robust for miR-29b, with reduction of 30% after 48 h and 40% after 72 h. The percentage of global methylation reduction observed in cells treated with miR-29b is comparable to that observed with DNMT1 inhibitors such as decitabine26, and is partial with either approach. While not wishing to be bound by theory, the inventor herein now believes that a more robust global DNA hypomethylation can be achieved combining decitabine (or other nucleoside analogs) with miR-29s thereby blocking both de novo and maintenance DNMT pathways.
To characterize effects of the methylation changes on gene expression, the mRNA expression levels of two TSGs, FHIT and WWOX, which are frequently silenced by promoter methylation in lung cancer14 were analyzed.
As shown in FIG. 3b upper, 48 h after transfection of A549 cells, FHIT expression was increased by miR-29a, 29b and 29c expression by  ̃65%, 89%, and 74%, respectively, and the WWOX mRNA level was increased by  ̃40%, and 60% by miR-29a and 29b respectively; a similar trend was observed in H1299 cells (FIG. 3b, lower).
Increased expression of both FHIT and WWOX proteins was also observed in both cell lines (FIG. 3c).
To determine if miR-29s regulate expression of FHIT and WWOX by altering promoter methylation of these genes, the methylation status of the regulatory region of FHIT and WWOX was examined using the MassARRAY system27 (quantitative high-throughput DNA methylation analysis) in A549 and H1299 cells transfected with miR-29b. Two bisulfite reactions (one for each gene CpG island) were designed, which covered 7 CpGs and 11 CpGs for FHIT and WWOX respectively. In miR-29b transfected H1299 and A549 cells, the MassARRAY analysis for FHIT showed an average reduction of 19.1% and 54.3% methylation, respectively, whereas for WWOX in H1299 showed an average reduction of 32.1% compared with the scrambled oligonucleotide (FIG. 3d).
The effects of re-expression of miR-29s on tumorigenicity of A549 cells were also assessed. The ectopic expression of miR-29s in A549 inhibited in vitro cell growth (FIG. 4a), and induced apoptosis with respect to the scrambled control transfection (FIG. 4b).
The inhibitory effect of miR-29s on A549 tumorigenicity was also observed in vivo. Transfection with miR-29s inhibited the growth of A549 engrafted tumors, with respect to mock and scrambled oligo transfected cells (FIG. 4c, 4d, 4e), thus illustrating a likely antineoplastic effect of these miRNAs.
Thus, this example shows that expression of miR-29 family members is inversely correlated with DNMT3A and DNMT3B expression in lung cancers and these miRNAs down-modulate expression levels of both enzymes.
Furthermore, enforced expression of these miRNAs in lung cancer cells leads to reduced global DNA methylation, restores expression of TSGs and inhibits tumorigenicity both in vitro and in vivo. These results are useful for developing novel epigenetic therapies using synthetic miR-29s, alone or in combination with other treatments, to reactivate tumor suppressors and normalize aberrant patterns of methylation in lung cancer. Since loss of expression of miR-29 family members is observed in other common human malignancies, this approach may be extended to the treatment of other human malignancies.
Methods.
Samples
We obtained 172 lung cancer samples, including squamous cell, adeno-, large cell and neuroendocrine large cell carcinomas, collectively referred to as non small cell lung carcinomas (NSCLCs) from the Pathology Core Facility at The Ohio State University to perform tissue microarrays (TMAs) for DNMTs expression. Clinical features (histological diagnosis, sex, age, TNM status and survival time) were available for these patients.
Primary lung cancer tissues (8 squamous carcinomas and 6 adenocarcinomas) were purchased from the Cooperative Human Tissue Network-Midwestern Division, Columbus, Ohio, to perform qRT-PCR analysis. Total RNAs were isolated by TRIzol (Invitrogen, Carlsbad, Calif.) extraction, according to the manufacturer's instructions.
Tissue Microarrays
Tissue micro arrays (TMAs): each array contained 4 samples of each lung cancer along with multiple appropriate lung and other normal tissue spots. The TMAs, usually two for each antiserum, were stained with antisera against DNMT1, DNTM3A and DNMT3B proteins, and expression of each of these enzymes in lung cancer was compared with clinical features to seek significant correlations. DNMT1, DNMT3A and DNMT3B protein expression were assessed on the lung cancer TMAs, using DNMT1 antiserum from GeneTex (GTX13537, San Antonio, Tex.) at a dilution of 1:150; DNMT3A antiserum from Novus Biologicals (ab-4897, Littleton, Colo.) at a dilution of 1:25 and DNTM3B antiserum from Abgent (AP1035a, San Diego, Calif.) at a dilution of 1:32. 4 micron sections from TMA blocks were placed on positively charged slides, placed in a 60° C. oven for 1 h, cooled, deparaffinized and rehydrated through xylene and graded ethanol solutions to water. Slides were quenched for 5 min in 3% hydrogen peroxide to block endogenous peroxidase. Antigens were retrieved in TRS (Dako, Carpinteria, Calif.) solution at. 95 C, 25 min. Slides were exposed to primary antisera for 1 h at room temperature and to secondary antisera (1:200) for 20 min, room temperature; secondary antisera were goat anti-mouse for DNMT1 and goat anti-rabbit for DNMT3A and DMT3B. All slides were blocked for endogenous biotin prior to application of the biotinylated secondary antisera. Chromogen detection was with Vectastain Elite (Vector, cat# PK-6100) for 30 min. The substrate chromogen was DAB+(Dako, cat# K3468). Slides were counterstained with hematoxylin, dehydrated through graded ethanol solutions and cover-slipped.
TMAs were read and scored by a pathologist who was blinded to clinical features; expression scores were determined by multiplying the percent of positive cells in an individual sample by the intensity of staining; the intensity of staining was assessed on a scale from 1 to 3, where 1 was the least intense staining and 3 was the most intense. For example, a sample with 10% positive cells with intensity 3 was assigned a score of 30, the same score as a sample with 30% positive cells with intensity 1.
Quantitative RT-PCR. Quantitative RT-PCR (qRT-PCR) analysis for miRNA s was performed in triplicate with the TaqMan MicroRNA assays kit (Applied Biosystems, Foster City, Calif.), according to the manufacturer's instructions. 18S RNA was used for normalization; qRT-PCR analyses for other genes of interest were performed as previously described. RNA was reverse transcribed to cDNA with gene-specific primers and IQ SYBR Green Supermix (Biorad, Hercules, Calif.). GAPDH served as normalization control. For the silencing of miR-29s, A549 and H1299 cells were transfected in 6-well plates by using Lipofectamine 2000 reagent (Invitrogen), according to the manufacturer's protocol, with 100 nM (final) of antisense miR-29a, 29b-1, 29c or scrambled antisense miR (Fidelity Systems, Gaithersburg, Md.).
Cell culture. A549 and H 1299 lung cancer cells from the American Type Culture Collection (Manassas, Va.) were maintained in RPMI medium 1640 with 10% FBS and antibiotics (100 U/ml penicillin, and 100 μg/ml streptomycin).
Luciferase reporter assay for targeting DNMT 3′UTRs. For luciferase reporter experiments a DNMT3A 3′UTR segment of 979 bp and a DNMT3B 3′UTR segment of 978 bp were amplified by PCR from human genomic DNA and inserted into the pGL3-control vector with SV40 promoter (Promega), using the XbaI site immediately upstream from the stop codon of luciferase. The following sets of primers were used to generate specific fragments:









DNMT3A-UTR Fw:



[SEQ ID NO: 15]



5′-GCTCTAGAGCCGAAAAGGGTTGGACATCAT-3′,



 



DNMT3A-UTR Rv:



[SEQ ID NO: 16]



5′-GCTCTAGAGCGCCGAGGGAGTCTCCTTTTA-3′;



 



DNMT3B-UTR Fw:



[SEQ ID NO: 17]



5′-GCTCTAGAGCTAGGTAGCAACGTGGCTTTT-3′,



 



 



DNMT3B-UTR Rv:



[SEQ ID NO: 18]



5′-GCTCTAGAGCGCCCCACAAAACTTGTCAAC-3′.






The amplified 3′UTR of DNMT3A contains an XbaI restriction site in position 583, so we cloned separately the upstream 3′UTR (DNMT3A 3′-UTRup=583 bp) and the downstream fragment (DNMT3A 3′-UTRdown=396 bp) into the pGL3 vectors. The predicted match seed of miR-29s is located in the DNMT3A 3′-UTR down fragment, which was used to perform the luciferase assay.
A549 cells were co-transfected in 12-well plates by using Lipofectamine 2000 reagent (Invitrogen), according to the manufacturer's protocol, with 0.4 μg of the firefly luciferase report vector and 0.08 μg of the control vector containing Renilla luciferase pRL-TK vector (Promega). For each well, 100 nM (final) of precursor miR-29a, 29b-1, 29c or scrambled miR (Ambion) was used. Firefly and Renilla luciferase activities were measured consecutively by using dual-luciferase assays (Promega), 24 h after the transfection. The experiments were performed in triplicate.
GFP-repression constructs to assess effect of DNMT 3′UTRs on protein expression. For GFP-repression, a DNMT3A 3′UTR segment of 1472 bp and a DNMT3B 3′UTR segment of 1566 bp (corresponding to the whole length of the 3′UTRs) were amplified by PCR from human genomic DNA and inserted into the QBI-GFP25 vector (Autofluorescent Proteins, Canada), using the BamHI-EcoRI cloning sites located 3′ of the GFP encoding sequence of the vector (which has no stop codon at the end of the GFP coding sequence). The following primer sets were used to generate specific fragments:









DNMT3A-GFP Fw:



[SEQ ID NO: 19]



5′-CGGGATCCGCAGGATAGCCAAGTTCAGC-3′,



 



DNMT3A-GFP Rv:



[SEQ ID NO: 20]



5′-CCCAAGCTTAAGTGAGAAACTGGGCCTGA-3′;



 



DNMT3B-GFP Fw:



[SEQ ID NO: 21]



5′-CGGGATCCCTCGATCAAACAGGGGAAAA-3′,



 



DNMT3B-GFP Rv:



[SEQ ID NO: 22]



5′-CCCAAGCTTGTTACGTCGTGGCTCCAGTT-3′.



 






A549 cells were co-transfected in 12-well plates using Lipofectamine 2000 reagent (Invitrogen) according to the manufacturer's protocol with 2 μg of the GFP repression vector containing the 3′UTR of DNMT3A (QBI-GFP25-DNMT3A) or the 3′UTR of DNMT3B (QBI-GFP25-DNMT3B) and with 100 nM (final) of precursor miR29a, 29b-1, 29c, or scrambled oligonucleotide (Ambion). As an additional control, a group of cells was also transfected with the GFP vector (no miR). Cells were harvested after 24 h. Protein extraction and immunoblot analysis were performed as previously described2. The following primary antisera were used: rabbit polyclonal anti-GFP, 1:1000 (Novus Biologicals, Littleton, Colo.).
Detection of miR29b—DNMT3B RNA complexes. To detect miR-29b-DNMT3B RNA complexes, we used the method described by Vatolin S. et al.3 to determine if endogenous miR-29b was able to serve as primer for retrotranscription of DNMT3B mRNA in A549 cells. The cDNAs were cloned in pCR2.1-TOPO Vector (Invitrogen). The following sets of primers and adapter sequence were used (GSP meaning gene specific primer):







GSP-DNMT3B:


[SEQ ID NO: 23]


5′-GAGATGACAGGGAAAACTGC-3′;


 


GSP-DNMT3B 5N:


[SEQ ID NO: 24]


5′-ACAGGGAAAACTGCAAAGCT-3′;


 


Adapter:


[SEQ ID NO: 25]


5′-CGACTGGAGCACGAGGACACTGACATGGACTGAAGGAGTAGAAA-3′;


 


Adapter 5N:


[SEQ ID NO: 26]


5′-CTGAAGGAGTAGAAA-3′.






Primers 5N represent nested primers from the adapter and GSP sequence used to sensitize the detection of the PCR bands.
Global methylation studies. The global methylation status of A549 cells after transfection with scrambled miRNA and with miR-29s, was determined as previously described. For this assay, 2×106 A549 cells were transfected as described above for the luciferase assay, and collected 48 and 72 h later.
Quantitative DNA methylation. Quantitative DNA methylation analysis of the regulatory regions of FHIT and WWOX was done using the EpiTYPER methylation analysis assay (Sequenom, San Diego, Calif.). Two bisulfite reactions (one for each gene CpG island) were designed, which covered 7 CpGs and 11 CpGs for FHIT and WWOX respectively. The DNA of scrambled-, or miR-29b-transfected A549/H1299 was extracted 48 h after the transfection and 1 μg of DNA was bisulfite treated, in vitro transcribed, cleaved by Rnase A, and subjected to matrix-assisted laser desorption ionization-time of flight (MALD1-TOF) mass spectrometry analysis to determine methylation patterns, as described5. The following primers were used to amplify the regulatory regions of the FHIT and WWOX genes:







[SEQ ID NO: 27]








FHIT Fw:
5′-GGGGAGGTAAGTTTAAGTGGAATATTGTT-3′


 







[SEQ ID NO: 28]








FHIT Rv:
5′-CACCCCCAAAACCAAAAACTATAAC-3′


 







[SEQ ID NO: 29]








WWOX Fw:
5′-TTGAAAGAAAGTTTTTTAAAATTAGGAAAT-3′


 







[SEQ ID NO: 30]








WWOX Rv:
5′-TCAAAAAAACAAAACCTAAAAAAAA-3′.






The heat map in FIG. 3d was created using Heatmap builder version 1.0 by Stanford University.
Western Blot. Analysis for the FHIT and WWOX proteins. Protein extraction and immunoblot analysis were performed as previously described2. The following primary antisera were used: rabbit polyclonal anti-FHIT, 1:1000 (Zymed, San Francisco, Calif.); mouse monoclonal anti-WWOX, 1:500 (as in ref. 2). Quantitation of the signal for FHIT, WWOX and Gapdh was performed by using a Molecular Dynamics Personal Densitometer SI and IMAGEQUANT 5.2 software (Image Products International, Chantilly, Va.).
Cell growth curve. A549 cells (5×104) were plated in 6× multi-well plates and transfected, after 24 hours, with scrambled oligonucleotides or miR-29s oligonucleotides from Ambion at a final concentration of 100 nM, with Lipofectamine 2000 (Invitrogen), according to manufacturer's protocol. As a control also not transfected (mock) cells were included. Cells were harvested and counted at 24 h intervals using a ViCell counter (Beckman Coulter, Fullerton, Calif.). Each sample was run in triplicate.
Apoptosis and Flow Cytometric Studies. A549 cells (2×105) were transfected with scrambled oligonucleotides or miR-29s oligonucleotides from Ambion at a final concentration of 100 nM, with Lipofectamine 2000 (Invitrogen), according to manufacturer's protocol. After 24 h cells were resuspended in binding buffer containing annexin V-fluorescein isothiocyanate (FITC) and propidium iodide according to the supplier's instructions (BD Biosciences, San Diego, Calif.), and assessed by flow cytometry using a Beckman-Coulter model EPICS XL cytometer (Beckman-Coulter). Each sample was run in triplicate.
In vivo studies. Animal studies were performed according to institutional guidelines. A549 cells were transfected in vitro with 100 nM (final concentration) of scrambled (Scr) oligonucleotides, or miR-29a, -29b, or -29c, or were mock-transfected by using Lipofectamine 2000 reagent (Invitrogen), according to the manufacturer's protocol. At 48 h after transfection, 3×106 viable cells were injected subcutaneously into the left flanks of 6-wk-old female nude mice (Charles River Breeding Laboratories, Wilmington, Mass.), five mice per group. Tumor diameters were measured after 7 days from injection and then every 5 days. At 21 days after injection, mice were sacrificed and tumors were weighted after necropsy. Tumor volumes were determined by using the equation V (in mm3)=A×B2/2, where A is the largest diameter and B is the perpendicular diameter.
Statistical Analysis. P values were two-sided and obtained using the SPSS software package (SPSS10.0). Overall survival was calculated from the time of diagnosis until the date of last follow-up. Data were censored for patients who were alive at the time of last follow-up. To perform the survival analysis and generate a Kaplan-Meier (KM) plot, DNMT1, DNMT3A and DNMT3B levels measured by immunohistochemical staining, were converted into discrete variables by splitting the samples into two classes (high and low expression, according to the DNMT score <10 (low) or >10 (high)). Survival curves were obtained for each group and compared by using the log-rank test. To assess correlation between miRNA expression and DNMT expression we used Pearson correlation and linear regression analysis (SPSS package). These functions examine each pair of measurements (one from the miRNA and the other from DNMTs) to determine if the two variables tend to move together or in the opposite direction, that is if the larger values from the miRNA (high expression) are associated with the lower values from DNMT expression.
EXAMPLE 2
Methods, Reagents and Kits for Diagnosing, Staging, Prognosing, Monitoring and Treating Lung Cancer-Related Diseases.
It is to be understood that all examples herein are to be considered non-limiting in their scope. Various aspects are described in further detail in the following subsections.
Diagnostic Methods
In one embodiment, there is provided a diagnostic method of assessing whether a patient has a lung cancer-related disease or has higher than normal risk for developing a lung cancer-related disease, comprising the steps of comparing the level of expression of a marker in a patient sample and the normal level of expression of the marker in a control, e.g., a sample from a patient without a lung cancer-related disease.
A significantly higher level of expression of the marker in the patient sample as compared to the normal level is an indication that the patient is afflicted with a lung cancer-related disease or has higher than normal risk for developing a lung cancer-related disease.
The markers are selected such that the positive predictive value of the methods is at least about 10%, and in certain non-limiting embodiments, about 25%, about 50% or about 90%. Also preferred for use in the methods are markers that are differentially expressed, as compared to normal cells, by at least two-fold in at least about 20%, and in certain non-limiting embodiments, about 50% or about 75%.
In one diagnostic method of assessing whether a patient is afflicted with a lung cancer-related disease (e.g., new detection (“screening”), detection of recurrence, reflex testing), the method comprises comparing: a) the level of expression of a marker in a patient sample, and b) the normal level of expression of the marker in a control non-lung cancer-related disease sample. A significantly higher level of expression of the marker in the patient sample as compared to the normal level is an indication that the patient is afflicted with a lung cancer-related disease.
There is also provided diagnostic methods for assessing the efficacy of a therapy for inhibiting a lung cancer-related disease in a patient. Such methods comprise comparing: a) expression of a marker in a first sample obtained from the patient prior to providing at least a portion of the therapy to the patient, and b) expression of the marker in a second sample obtained from the patient following provision of the portion of the therapy. A significantly lower level of expression of the marker in the second sample relative to that in the first sample is an indication that the therapy is efficacious for inhibiting a lung cancer-related disease in the patient.
It will be appreciated that in these methods the “therapy” may be any therapy for treating a lung cancer-related disease including, but not limited to, pharmaceutical compositions, gene therapy and biologic therapy such as the administering of antibodies and chemokines. Thus, the methods described herein may be used to evaluate a patient before, during and after therapy, for example, to evaluate the reduction in disease state.
In certain aspects, the diagnostic methods are directed to therapy using a chemical or biologic agent. These methods comprise comparing: a) expression of a marker in a first sample obtained from the patient and maintained in the presence of the chemical or biologic agent, and b) expression of the marker in a second sample obtained from the patient and maintained in the absence of the agent. A significantly lower level of expression of the marker in the second sample relative to that in the first sample is an indication that the agent is efficacious for inhibiting a lung cancer-related disease in the patient. In one embodiment, the first and second samples can be portions of a single sample obtained from the patient or portions of pooled samples obtained from the patient.
Methods for Assessing Prognosis
There is also provided a monitoring method for assessing the progression of a lung cancer-related disease in a patient, the method comprising: a) detecting in a patient sample at a first time point, the expression of a marker; b) repeating step a) at a subsequent time point in time; and c) comparing the level of expression detected in steps a) and b), and therefrom monitoring the progression of a lung cancer-related disease in the patient. A significantly higher level of expression of the marker in the sample at the subsequent time point from that of the sample at the first time point is an indication that the lung cancer-related disease has progressed, whereas a significantly lower level of expression is an indication that the lung cancer-related disease has regressed.
There is further provided a diagnostic method for determining whether a lung cancer-related disease has worsened or is likely to worsen in the future, the method comprising comparing: a) the level of expression of a marker in a patient sample, and b) the normal level of expression of the marker in a control sample. A significantly higher level of expression in the patient sample as compared to the normal level is an indication that the lung cancer-related disease has worsened or is likely to worsen in the future.
Methods for Assessing Inhibitory, Therapeutic and/or Harmful Compositions
There is also provided a test method for selecting a composition for inhibiting a lung cancer-related disease in a patient. This method comprises the steps of: a) obtaining a sample comprising cells from the patient; b) separately maintaining aliquots of the sample in the presence of a plurality of test compositions; c) comparing expression of a marker in each of the aliquots; and d) selecting one of the test compositions which significantly reduces the level of expression of the marker in the aliquot containing that test composition, relative to the levels of expression of the marker in the presence of the other test compositions.
There is additionally provided a test method of assessing the harmful potential of a compound in causing a lung cancer-related disease. This method comprises the steps of: a) maintaining separate aliquots of cells in the presence and absence of the compound; and b) comparing expression of a marker in each of the aliquots. A significantly higher level of expression of the marker in the aliquot maintained in the presence of the compound, relative to that of the aliquot maintained in the absence of the compound, is an indication that the compound possesses such harmful potential.
In addition, there is further provided a method of inhibiting a lung cancer-related disease in a patient. This method comprises the steps of: a) obtaining a sample comprising cells from the patient; b) separately maintaining aliquots of the sample in the presence of a plurality of compositions; c) comparing expression of a marker in each of the aliquots; and d) administering to the patient at least one of the compositions which significantly lowers the level of expression of the marker in the aliquot containing that composition, relative to the levels of expression of the marker in the presence of the other compositions.
The level of expression of a marker in a sample can be assessed, for example, by detecting the presence in the sample of: the corresponding marker protein or a fragment of the protein (e.g. by using a reagent, such as an antibody, an antibody derivative, an antibody fragment or single-chain antibody, which binds specifically with the protein or protein fragment) the corresponding marker nucleic acid (e.g. a nucleotide transcript, or a complement thereof), or a fragment of the nucleic acid (e.g. by contacting transcribed polynucleotides obtained from the sample with a substrate having affixed thereto one or more nucleic acids having the entire or a segment of the nucleic acid sequence or a complement thereof) a metabolite which is produced directly (i.e., catalyzed) or indirectly by the corresponding marker protein.
Any of the aforementioned methods may be performed using at least one or a plurality (e.g., 2, 3, 5, or 10 or more) of lung cancer-related disease markers. In such methods, the level of expression in the sample of each of a plurality of markers, at least one of which is a marker, is compared with the normal level of expression of each of the plurality of markers in samples of the same type obtained from control humans not afflicted with a lung cancer-related disease. A significantly altered (i.e., increased or decreased as specified in the above-described methods using a single marker) level of expression in the sample of one or more markers, or some combination thereof, relative to that marker's corresponding normal or control level, is an indication that the patient is afflicted with a lung cancer-related disease. For all of the aforementioned methods, the marker(s) are selected such that the positive predictive value of the method is at least about 10%.
Examples of Candidate Agents
The candidate agents may be pharmacologic agents already known in the art or may be agents previously unknown to have any pharmacological activity. The agents may be naturally arising or designed in the laboratory. They may be isolated from microorganisms, animals or plants, or may be produced recombinantly, or synthesized by any suitable chemical method. They may be small molecules, nucleic acids, proteins, peptides or peptidomimetics. In certain embodiments, candidate agents are small organic compounds having a molecular weight of more than 50 and less than about 2,500 daltons. Candidate agents comprise functional groups necessary for structural interaction with proteins. Candidate agents are also found among biomolecules including, but not limited to: peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof.
Candidate agents are obtained from a wide variety of sources including libraries of synthetic or natural compounds. There are, for example, numerous means available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides and oligopeptides. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced. Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries. In certain embodiments, the candidate agents can be obtained using any of the numerous approaches in combinatorial library methods art, including, by non-limiting example: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the “one-bead one-compound” library method; and synthetic library methods using affinity chromatography selection.
In certain further embodiments, certain pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, etc. to produce structural analogs.
The same methods for identifying therapeutic agents for treating a lung cancer-related disease can also be used to validate lead compounds/agents generated from in vitro studies.
The candidate agent may be an agent that up- or down-regulates one or more lung cancer-related disease response pathways. In certain embodiments, the candidate agent may be an antagonist that affects such pathway.
Methods for Treating a Lung Cancer-Related Disease
There is provided herein methods for treating, inhibiting, relieving or reversing a lung cancer-related disease response. In the methods described herein, an agent that interferes with a signaling cascade is administered to an individual in need thereof, such as, but not limited to, lung cancer-related disease patients in whom such complications are not yet evident and those who already have at least one lung cancer-related disease response.
In the former instance, such treatment is useful to prevent the occurrence of such lung cancer-related disease response and/or reduce the extent to which they occur. In the latter instance, such treatment is useful to reduce the extent to which such lung cancer-related disease response occurs, prevent their further development or reverse the lung cancer-related disease response.
In certain embodiments, the agent that interferes with the lung cancer-related disease response cascade may be an antibody specific for such response.
Expression of a Marker
Expression of a marker can be inhibited in a number of ways, including, by way of a non-limiting example, an antisense oligonucleotide can be provided to the lung cancer-related disease cells in order to inhibit transcription, translation, or both, of the marker(s). Alternately, a polynucleotide encoding an antibody, an antibody derivative, or an antibody fragment which specifically binds a marker protein, and operably linked with an appropriate promoter/regulator region, can be provided to the cell in order to generate intracellular antibodies which will inhibit the function or activity of the protein. The expression and/or function of a marker may also be inhibited by treating the lung cancer-related disease cell with an antibody, antibody derivative or antibody fragment that specifically binds a marker protein. Using the methods described herein, a variety of molecules, particularly including molecules sufficiently small that they are able to cross the cell membrane, can be screened in order to identify molecules which inhibit expression of a marker or inhibit the function of a marker protein. The compound so identified can be provided to the patient in order to inhibit lung cancer-related disease cells of the patient.
Any marker or combination of markers, as well as any certain markers in combination with the markers, may be used in the compositions, kits and methods described herein. In general, it is desirable to use markers for which the difference between the level of expression of the marker in lung cancer-related disease cells and the level of expression of the same marker in normal lung cells is as great as possible. Although this difference can be as small as the limit of detection of the method for assessing expression of the marker, it is desirable that the difference be at least greater than the standard error of the assessment method, and, in certain embodiments, a difference of at least 2-, 3-, 4-, 5-, 6-, 7-, 8-, 9-, 10-, 15-, 20-, 100-, 500-, 1000-fold or greater than the level of expression of the same marker in normal tissue.
It is recognized that certain marker proteins are secreted to the extracellular space surrounding the cells. These markers are used in certain embodiments of the compositions, kits and methods, owing to the fact that such marker proteins can be detected in a lung cancer-associated body fluid sample, which may be more easily collected from a human patient than a tissue biopsy sample. In addition, in vivo techniques for detection of a marker protein include introducing into a subject a labeled antibody directed against the protein. For example, the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.
In order to determine whether any particular marker protein is a secreted protein, the marker protein is expressed in, for example, a mammalian cell, such as a human lung line, extracellular fluid is collected, and the presence or absence of the protein in the extracellular fluid is assessed (e.g. using a labeled antibody which binds specifically with the protein).
It will be appreciated that patient samples containing lung cells may be used in the methods described herein. In these embodiments, the level of expression of the marker can be assessed by assessing the amount (e.g., absolute amount or concentration) of the marker in a sample. The cell sample can, of course, be subjected to a variety of post-collection preparative and storage techniques (e.g., nucleic acid and/or protein extraction, fixation, storage, freezing, ultrafiltration, concentration, evaporation, centrifugation, etc.) prior to assessing the amount of the marker in the sample.
It will also be appreciated that the markers may be shed from the cells into the digestive system, the blood stream and/or interstitial spaces. The shed markers can be tested, for example, by examining the serum or plasma.
The compositions, kits and methods can be used to detect expression of marker proteins having at least one portion which is displayed on the surface of cells which express it. For example, immunological methods may be used to detect such proteins on whole cells, or computer-based sequence analysis methods may be used to predict the presence of at least one extracellular domain (i.e., including both secreted proteins and proteins having at least one cell-surface domain). Expression of a marker protein having at least one portion which is displayed on the surface of a cell which expresses it may be detected without necessarily lysing the cell (e.g., using a labeled antibody which binds specifically with a cell-surface domain of the protein).
Expression of a marker may be assessed by any of a wide variety of methods for detecting expression of a transcribed nucleic acid or protein. Non-limiting examples of such methods include immunological methods for detection of secreted, cell-surface, cytoplasmic or nuclear proteins, protein purification methods, protein function or activity assays, nucleic acid hybridization methods, nucleic acid reverse transcription methods and nucleic acid amplification methods.
In a particular embodiment, expression of a marker is assessed using an antibody (e.g., a radio-labeled, chromophore-labeled, fluorophore-labeled or enzyme-labeled antibody), an antibody derivative (e.g., an antibody conjugated with a substrate or with the protein or ligand of a protein-ligand pair), or an antibody fragment (e.g., a single-chain antibody, an isolated antibody hypervariable domain, etc.) which binds specifically with a marker protein or fragment thereof, including a marker protein which has undergone all or a portion of its normal post-translational modification.
In another particular embodiment, expression of a marker is assessed by preparing mRNA/cDNA (i.e., a transcribed polynucleotide) from cells in a patient sample, and by hybridizing the mRNA/cDNA with a reference polynucleotide which is a complement of a marker nucleic acid, or a fragment thereof, cDNA can, optionally, be amplified using any of a variety of polymerase chain reaction methods prior to hybridization with the reference polynucleotide; preferably, it is not amplified. Expression of one or more markers can likewise be detected using quantitative PCR to assess the level of expression of the marker(s). Alternatively, any of the many methods of detecting mutations or variants (e.g. single nucleotide polymorphisms, deletions, etc.) of a marker may be used to detect occurrence of a marker in a patient.
In a related embodiment, a mixture of transcribed polynucleotides obtained from the sample is contacted with a substrate having fixed thereto a polynucleotide complementary to or homologous with at least a portion (e.g., at least 7, 10, 15, 20, 25, 30, 40, 50, 100, 500, or more nucleotide residues) of a marker nucleic acid. If polynucleotides complementary to or homologous with are differentially detectable on the substrate (e.g., detectable using different chromophores or fluorophores, or fixed to different selected positions), then the levels of expression of a plurality of markers can be assessed simultaneously using a single substrate (e.g., a “gene chip” microarray of polynucleotides fixed at selected positions). When a method of assessing marker expression is used which involves hybridization of one nucleic acid with another, it is desired that the hybridization be performed under stringent hybridization conditions.
In certain embodiments, the biomarker assays can be performed using mass spectrometry or surface plasmon resonance. In various embodiment, the method of identifying an agent active against a lung cancer-related disease can include a) providing a sample of cells containing one or more markers or derivative thereof; b) preparing an extract from said cells; c) mixing said extract with a labeled nucleic acid probe containing a marker binding site; and, d) determining the formation of a complex between the marker and the nucleic acid probe in the presence or absence of the test agent. The determining step can include subjecting said extract/nucleic acid probe mixture to an electrophoretic mobility shift assay.
In certain embodiments, the determining step comprises an assay selected from an enzyme linked immunoabsorption assay (ELISA), fluorescence based assays and ultra high throughput assays, for example surface plasmon resonance (SPR) or fluorescence correlation spectroscopy (FCS) assays. In such embodiments, the SPR sensor is useful for direct real-time observation of biomolecular interactions since SPR is sensitive to minute refractive index changes at a metal-dielectric surface. SPR is a surface technique that is sensitive to changes of 105 to 10−6 refractive index (RI) units within approximately 200 nm of the SPR sensor/sample interface. Thus, SPR spectroscopy is useful for monitoring the growth of thin organic films deposited on the sensing layer.
Because the compositions, kits, and methods rely on detection of a difference in expression levels of one or more markers, it is desired that the level of expression of the marker is significantly greater than the minimum detection limit of the method used to assess expression in at least one of normal cells and lung cancer-affected cells.
It is understood that by routine screening of additional patient samples using one or more of the markers, it will be realized that certain of the markers are over-expressed in cells of various types, including specific lung cancer-related diseases.
In addition, as a greater number of patient samples are assessed for expression of the markers and the outcomes of the individual patients from whom the samples were obtained are correlated, it will also be confirmed that altered expression of certain of the markers are strongly correlated with a lung cancer-related disease and that altered expression of other markers are strongly correlated with other diseases. The compositions, kits, and methods are thus useful for characterizing one or more of the stage, grade, histological type, and nature of a lung cancer-related disease in patients.
When the compositions, kits, and methods are used for characterizing one or more of the stage, grade, histological type, and nature of a lung cancer-related disease in a patient, it is desired that the marker or panel of markers is selected such that a positive result is obtained in at least about 20%, and in certain embodiments, at least about 40%, 60%, or 80%, and in substantially all patients afflicted with a lung cancer-related disease of the corresponding stage, grade, histological type, or nature. The marker or panel of markers invention can be selected such that a positive predictive value of greater than about 10% is obtained for the general population (in a non-limiting example, coupled with an assay specificity greater than 80%).
When a plurality of markers are used in the compositions, kits, and methods, the level of expression of each marker in a patient sample can be compared with the normal level of expression of each of the plurality of markers in non-lung cancer samples of the same type, either in a single reaction mixture (i.e. using reagents, such as different fluorescent probes, for each marker) or in individual reaction mixtures corresponding to one or more of the markers. In one embodiment, a significantly increased level of expression of more than one of the plurality of markers in the sample, relative to the corresponding normal levels, is an indication that the patient is afflicted with a lung cancer-related disease. When a plurality of markers is used, 2, 3, 4, 5, 8, 10, 12, 15, 20, 30, or 50 or more individual markers can be used; in certain embodiments, the use of fewer markers may be desired.
In order to maximize the sensitivity of the compositions, kits, and methods (i.e. by interference attributable to cells of non-lung origin in a patient sample), it is desirable that the marker used therein be a marker which has a restricted tissue distribution. e.g., normally not expressed in a non-lung tissue.
It is recognized that the compositions, kits, and methods will be of particular utility to patients having an enhanced risk of developing a lung cancer-related disease and their medical advisors. Patients recognized as having an enhanced risk of developing a lung cancer-related disease include, for example, patients having a familial history of a lung cancer-related disease.
The level of expression of a marker in normal human lung tissue can be assessed in a variety of ways. In one embodiment, this normal level of expression is assessed by assessing the level of expression of the marker in a portion of lung cells which appear to be normal and by comparing this normal level of expression with the level of expression in a portion of the lung cells which is suspected of being abnormal. Alternately, and particularly as further information becomes available as a result of routine performance of the methods described herein, population-average values for normal expression of the markers may be used. In other embodiments, the ‘normal’ level of expression of a marker may be determined by assessing expression of the marker in a patient sample obtained from a non-lung cancer-afflicted patient, from a patient sample obtained from a patient before the suspected onset of a lung cancer-related disease in the patient, from archived patient samples, and the like.
There is also provided herein compositions, kits, and methods for assessing the presence of lung cancer-related disease cells in a sample (e.g. an archived tissue sample or a sample obtained from a patient). These compositions, kits, and methods are substantially the same as those described above, except that, where necessary, the compositions, kits, and methods are adapted for use with samples other than patient samples. For example, when the sample to be used is a parafinized, archived human tissue sample, it can be necessary to adjust the ratio of compounds in the compositions, in the kits, or the methods used to assess levels of marker expression in the sample.
Methods of Producing Antibodies
There is also provided herein a method of making an isolated hybridoma which produces an antibody useful for assessing whether a patient is afflicted with a lung cancer-related disease. In this method, a protein or peptide comprising the entirety or a segment of a marker protein is synthesized or isolated (e.g. by purification from a cell in which it is expressed or by transcription and translation of a nucleic acid encoding the protein or peptide in vivo or in vitro). A vertebrate, for example, a mammal such as a mouse, rat, rabbit, or sheep, is immunized using the protein or peptide. The vertebrate may optionally (and preferably) be immunized at least one additional time with the protein or peptide, so that the vertebrate exhibits a robust immune response to the protein or peptide. Splenocytes are isolated from the immunized vertebrate and fused with an immortalized cell line to form hybridomas, using any of a variety of methods. Hybridomas formed in this manner are then screened using standard methods to identify one or more hybridomas which produce an antibody which specifically binds with the marker protein or a fragment thereof. There is also provided herein hybridomas made by this method and antibodies made using such hybridomas.
Methods of Assessing Efficacy
There is also provided herein a method of assessing the efficacy of a test compound for inhibiting lung cancer-related disease cells. As described above, differences in the level of expression of the markers correlate with the abnormal state of lung cells. Although it is recognized that changes in the levels of expression of certain of the markers likely result from the abnormal state of lung cells, it is likewise recognized that changes in the levels of expression of other of the markers induce, maintain, and promote the abnormal state of those cells. Thus, compounds which inhibit a lung cancer-related disease in a patient will cause the level of expression of one or more of the markers to change to a level nearer the normal level of expression for that marker (i.e. the level of expression for the marker in normal lung cells).
This method thus comprises comparing expression of a marker in a first lung cell sample and maintained in the presence of the test compound and expression of the marker in a second lung cell sample and maintained in the absence of the test compound. A significantly reduced expression of a marker in the presence of the test compound is an indication that the test compound inhibits a lung cancer-related disease. The lung cell samples may, for example, be aliquots of a single sample of normal lung cells obtained from a patient, pooled samples of normal lung cells obtained from a patient, cells of a normal lung cell line, aliquots of a single sample of lung cancer-related disease cells obtained from a patient, pooled samples of lung cancer-related disease cells obtained from a patient, cells of a lung cancer-related disease cell line, or the like.
In one embodiment, the samples are lung cancer-related disease cells obtained from a patient and a plurality of compounds believed to be effective for inhibiting various lung cancer-related diseases are tested in order to identify the compound which is likely to best inhibit the lung cancer-related disease in the patient.
This method may likewise be used to assess the efficacy of a therapy for inhibiting a lung cancer-related disease in a patient. In this method, the level of expression of one or more markers in a pair of samples (one subjected to the therapy, the other not subjected to the therapy) is assessed. As with the method of assessing the efficacy of test compounds, if the therapy induces a significantly lower level of expression of a marker then the therapy is efficacious for inhibiting a lung cancer-related disease. As above, if samples from a selected patient are used in this method, then alternative therapies can be assessed in vitro in order to select a therapy most likely to be efficacious for inhibiting a lung cancer-related disease in the patient.
As described herein, the abnormal state of human lung cells is correlated with changes in the levels of expression of the markers. There is also provided a method for assessing the harmful potential of a test compound. This method comprises maintaining separate aliquots of human lung cells in the presence and absence of the test compound. Expression of a marker in each of the aliquots is compared. A significantly higher level of expression of a marker in the aliquot maintained in the presence of the test compound (relative to the aliquot maintained in the absence of the test compound) is an indication that the test compound possesses a harmful potential. The relative harmful potential of various test compounds can be assessed by comparing the degree of enhancement or inhibition of the level of expression of the relevant markers, by comparing the number of markers for which the level of expression is enhanced or inhibited, or by comparing both.
Isolated Proteins and Antibodies
One aspect pertains to isolated marker proteins and biologically active portions thereof, as well as polypeptide fragments suitable for use as immunogens to raise antibodies directed against a marker protein or a fragment thereof. In one embodiment, the native marker protein can be isolated from cells or tissue sources by an appropriate purification scheme using standard protein purification techniques. In another embodiment, a protein or peptide comprising the whole or a segment of the marker protein is produced by recombinant DNA techniques. Alternative to recombinant expression, such protein or peptide can be synthesized chemically using standard peptide synthesis techniques.
An “isolated” or “purified” protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the protein is derived, or substantially free of chemical precursors or other chemicals when chemically synthesized. The language “substantially free of cellular material” includes preparations of protein in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced. Thus, protein that is substantially free of cellular material includes preparations of protein having less than about 30%, 20%, 10%, or 5% (by dry weight) of heterologous protein (also referred to herein as a “contaminating protein”).
When the protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, 10%, or 5% of the volume of the protein preparation. When the protein is produced by chemical synthesis, it is preferably substantially free of chemical precursors or other chemicals, i.e., it is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein. Accordingly such preparations of the protein have less than about 30%, 20%, 10%, 5% (by dry weight) of chemical precursors or compounds other than the polypeptide of interest.
Biologically active portions of a marker protein include polypeptides comprising amino acid sequences sufficiently identical to or derived from the amino acid sequence of the marker protein, which include fewer amino acids than the full length protein, and exhibit at least one activity of the corresponding full-length protein. Typically, biologically active portions comprise a domain or motif with at least one activity of the corresponding full-length protein. A biologically active portion of a marker protein can be a polypeptide which is, for example, 10, 25, 50, 100 or more amino acids in length. Moreover, other biologically active portions, in which other regions of the marker protein are deleted, can be prepared by recombinant techniques and evaluated for one or more of the functional activities of the native form of the marker protein. In certain embodiments, useful proteins are substantially identical (e.g., at least about 40%, and in certain embodiments, 50%, 60%, 70%, 80%, 90%, 95%, or 99%) to one of these sequences and retain the functional activity of the corresponding naturally-occurring marker protein yet differ in amino acid sequence due to natural allelic variation or mutagenesis.
In addition, libraries of segments of a marker protein can be used to generate a variegated population of polypeptides for screening and subsequent selection of variant marker proteins or segments thereof.
Predictive Medicine
There is also provided herein uses of the animal models and markers in the field of predictive medicine in which diagnostic assays, prognostic assays, pharmacogenomics, and monitoring clinical trials are used for prognostic (predictive) purposes to thereby treat an individual prophylactically. Accordingly, there is also provided herein diagnostic assays for determining the level of expression of one or more marker proteins or nucleic acids, in order to determine whether an individual is at risk of developing a lung cancer-related disease. Such assays can be used for prognostic or predictive purposes to thereby prophylactically treat an individual prior to the onset of the lung cancer-related disease.
In another aspect, the methods are useful for at least periodic screening of the same individual to see if that individual has been exposed to chemicals or toxins that change his/her expression patterns.
Yet another aspect pertains to monitoring the influence of agents (e.g., drugs or other compounds administered either to inhibit a lung cancer-related disease or to treat or prevent any other disorder (e.g., in order to understand any system effects that such treatment may have) on the expression or activity of a marker in clinical trials.
Pharmacogenomics
The markers are also useful as pharmacogenomic markers. As used herein, a “pharmacogenomic marker” is an objective biochemical marker whose expression level correlates with a specific clinical drug response or susceptibility in a patient. The presence or quantity of the pharmacogenomic marker expression is related to the predicted response of the patient and more particularly the patient's tumor to therapy with a specific drug or class of drugs. By assessing the presence or quantity of the expression of one or more pharmacogenomic markers in a patient, a drug therapy which is most appropriate for the patient, or which is predicted to have a greater degree of success, may be selected.
Monitoring Clinical Trials
Monitoring the influence of agents (e.g., drug compounds) on the level of expression of a marker can be applied not only in basic drug screening, but also in clinical trials. For example, the effectiveness of an agent to affect marker expression can be monitored in clinical trials of subjects receiving treatment for a lung cancer-related disease.
In one non-limiting embodiment, the present invention provides a method for monitoring the effectiveness of treatment of a subject with an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) comprising the steps of (i) obtaining a pre-administration sample from a subject prior to administration of the agent; (ii) detecting the level of expression of one or more selected markers in the pre-administration sample; (iii) obtaining one or more post-administration samples from the subject; (iv) detecting the level of expression of the marker(s) in the post-administration samples; (v) comparing the level of expression of the marker(s) in the pre-administration sample with the level of expression of the marker(s) in the post-administration sample or samples; and (vi) altering the administration of the agent to the subject accordingly.
For example, increased expression of the marker gene(s) during the course of treatment may indicate ineffective dosage and the desirability of increasing the dosage. Conversely, decreased expression of the marker gene(s) may indicate efficacious treatment and no need to change dosage.
Electronic Apparatus Readable Media, Systems, Arrays and Methods of Using Same
As used herein, “electronic apparatus readable media” refers to any suitable medium for storing, holding or containing data or information that can be read and accessed directly by an electronic apparatus. Such media can include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as compact disc; electronic storage media such as RAM, ROM, EPROM, EEPROM and the like; and general hard disks and hybrids of these categories such as magnetic/optical storage media. The medium is adapted or configured for having recorded thereon a marker as described herein.
As used herein, the term “electronic apparatus” is intended to include any suitable computing or processing apparatus or other device configured or adapted for storing data or information. Examples of electronic apparatus suitable for use with the present invention include stand-alone computing apparatus; networks, including a local area network (LAN), a wide area network (WAN) Internet, Intranet, and Extranet; electronic appliances such as personal digital assistants (PDAs), cellular phone, pager and the like; and local and distributed processing systems.
As used herein, “recorded” refers to a process for storing or encoding information on the electronic apparatus readable medium. Those skilled in the art can readily adopt any method for recording information on media to generate materials comprising the markers described herein.
A variety of software programs and formats can be used to store the marker information of the present invention on the electronic apparatus readable medium. Any number of data processor structuring formats (e.g., text file or database) may be employed in order to obtain or create a medium having recorded thereon the markers. By providing the markers in readable form, one can routinely access the marker sequence information for a variety of purposes. For example, one skilled in the art can use the nucleotide or amino acid sequences in readable form to compare a target sequence or target structural motif with the sequence information stored within the data storage means. Search means are used to identify fragments or regions of the sequences which match a particular target sequence or target motif.
Thus, there is also provided herein a medium for holding instructions for performing a method for determining whether a subject has a lung cancer-related disease or a pre-disposition to a lung cancer-related disease, wherein the method comprises the steps of determining the presence or absence of a marker and based on the presence or absence of the marker, determining whether the subject has a lung cancer-related disease or a pre-disposition to a lung cancer-related disease and/or recommending a particular treatment for a lung cancer-related disease or pre-lung cancer-related disease condition.
There is also provided herein an electronic system and/or in a network, a method for determining whether a subject has a lung cancer-related disease or a pre-disposition to a lung cancer-related disease associated with a marker wherein the method comprises the steps of determining the presence or absence of the marker, and based on the presence or absence of the marker, determining whether the subject has a lung cancer-related disease or a pre-disposition to a lung cancer-related disease, and/or recommending a particular treatment for the lung cancer-related disease or pre-lung cancer-related disease condition. The method may further comprise the step of receiving phenotypic information associated with the subject and/or acquiring from a network phenotypic information associated with the subject.
Also provided herein is a network, a method for determining whether a subject has a lung cancer-related disease or a pre-disposition to a lung cancer-related disease associated with a marker, the method comprising the steps of receiving information associated with the marker, receiving phenotypic information associated with the subject, acquiring information from the network corresponding to the marker and/or a lung cancer-related disease, and based on one or more of the phenotypic information, the marker, and the acquired information, determining whether the subject has a lung cancer-related disease or a pre-disposition to a lung cancer-related disease. The method may further comprise the step of recommending a particular treatment, for the lung cancer-related disease or pre-lung cancer-related disease condition.
There is also provided herein a business method for determining whether a subject has a lung cancer-related disease or a pre-disposition to a lung cancer-related disease, the method comprising the steps of receiving information associated with the marker, receiving phenotypic information associated with the subject, acquiring information from the network corresponding to the marker and/or a lung cancer-related disease, and based on one or more of the phenotypic information, the marker, and the acquired information, determining whether the subject has a lung cancer-related disease or a pre-disposition to a lung cancer-related disease. The method may further comprise the step of recommending a particular treatment for the lung cancer-related disease or pre-lung cancer-related disease condition.
There is also provided herein an array that can be used to assay expression of one or more genes in the array. In one embodiment, the array can be used to assay gene expression in a tissue to ascertain tissue specificity of genes in the array. In this manner, up to about 7000 or more genes can be simultaneously assayed for expression. This allows a profile to be developed showing a battery of genes specifically expressed in one or more tissues.
In addition to such qualitative determination, there is provided herein the quantitation of gene expression. Thus, not only tissue specificity, but also the level of expression of a battery of genes in the tissue is ascertainable. Thus, genes can be grouped on the basis of their tissue expression per se and level of expression in that tissue. This is useful, for example, in ascertaining the relationship of gene expression between or among tissues. Thus, one tissue can be perturbed and the effect on gene expression in a second tissue can be determined. In this context, the effect of one cell type on another cell type in response to a biological stimulus can be determined.
Such a determination is useful, for example, to know the effect of cell-cell interaction at the level of gene expression. If an agent is administered therapeutically to treat one cell type but has an undesirable effect on another cell type, the method provides an assay to determine the molecular basis of the undesirable effect and thus provides the opportunity to co-administer a counteracting agent or otherwise treat the undesired effect. Similarly, even within a single cell type, undesirable biological effects can be determined at the molecular level. Thus, the effects of an agent on expression of other than the target gene can be ascertained and counteracted.
In another embodiment, the array can be used to monitor the time course of expression of one or more genes in the array. This can occur in various biological contexts, as disclosed herein, for example development of a lung cancer-related disease, progression of a lung cancer-related disease, and processes, such as cellular transformation associated with a lung cancer-related disease.
The array is also useful for ascertaining the effect of the expression of a gene or the expression of other genes in the same cell or in different cells. This provides, for example, for a selection of alternate molecular targets for therapeutic intervention if the ultimate or downstream target cannot be regulated.
The array is also useful for ascertaining differential expression patterns of one or more genes in normal and abnormal cells. This provides a battery of genes that could serve as a molecular target for diagnosis or therapeutic intervention.
Surrogate Markers
The markers may serve as surrogate markers for one or more disorders or disease states or for conditions leading up to a lung cancer-related disease state. As used herein, a “surrogate marker” is an objective biochemical marker which correlates with the absence or presence of a disease or disorder, or with the progression of a disease or disorder. The presence or quantity of such markers is independent of the disease. Therefore, these markers may serve to indicate whether a particular course of treatment is effective in lessening a disease state or disorder. Surrogate markers are of particular use when the presence or extent of a disease state or disorder is difficult to assess through standard methodologies, or when an assessment of disease progression is desired before a potentially dangerous clinical endpoint is reached.
The markers are also useful as pharmacodynamic markers. As used herein, a “pharmacodynamic marker” is an objective biochemical marker which correlates specifically with drug effects. The presence or quantity of a pharmacodynamic marker is not related to the disease state or disorder for which the drug is being administered; therefore, the presence or quantity of the marker is indicative of the presence or activity of the drug in a subject. For example, a pharmacodynamic marker may be indicative of the concentration of the drug in a biological tissue, in that the marker is either expressed or transcribed or not expressed or transcribed in that tissue in relationship to the level of the drug. In this fashion, the distribution or uptake of the drug may be monitored by the pharmacodynamic marker. Similarly, the presence or quantity of the pharmacodynamic marker may be related to the presence or quantity of the metabolic product of a drug, such that the presence or quantity of the marker is indicative of the relative breakdown rate of the drug in vivo.
Pharmacodynamic markers are of particular use in increasing the sensitivity of detection of drug effects, particularly when the drug is administered in low doses. Since even a small amount of a drug may be sufficient to activate multiple rounds of marker transcription or expression, the amplified marker may be in a quantity which is more readily detectable than the drug itself. Also, the marker may be more easily detected due to the nature of the marker itself; for example, using the methods described herein, antibodies may be employed in an immune-based detection system for a protein marker, or marker-specific radiolabeled probes may be used to detect a mRNA marker. Furthermore, the use of a pharmacodynamic marker may offer mechanism-based prediction of risk due to drug treatment beyond the range of possible direct observations.
Protocols for Testing
The method of testing for lung cancer-related diseases comprises, for example measuring the expression level of each marker gene in a biological sample from a subject over time and comparing the level with that of the marker gene in a control biological sample.
When the marker gene is one of the genes described herein and the expression level is differentially expressed (for examples, higher or lower than that in the control), the subject is judged to be affected with a lung cancer-related disease. When the expression level of the marker gene falls within the permissible range, the subject is unlikely to be affected with a lung cancer-related disease.
The standard value for the control may be pre-determined by measuring the expression level of the marker gene in the control, in order to compare the expression levels. For example, the standard value can be determined based on the expression level of the above-mentioned marker gene in the control. For example, in certain embodiments, the permissible range is taken as ±2S.D, based on the standard value. Once the standard value is determined, the testing method may be performed by measuring only the expression level in a biological sample from a subject and comparing the value with the determined standard value for the control.
Expression levels of marker genes include transcription of the marker genes to mRNA, and translation into proteins. Therefore, one method of testing for a lung cancer-related disease is performed based on a comparison of the intensity of expression of mRNA corresponding to the marker genes, or the expression level of proteins encoded by the marker genes.
The measurement of the expression levels of marker genes in the testing for a lung cancer-related disease can be carried out according to various gene analysis methods. Specifically, one can use, for example, a hybridization technique using nucleic acids that hybridize to these genes as probes, or a gene amplification technique using DNA that hybridize to the marker genes as primers.
The probes or primers used for the testing can be designed based on the nucleotide sequences of the marker genes. The identification numbers for the nucleotide sequences of the respective marker genes are describer herein.
Further, it is to be understood that genes of higher animals generally accompany polymorphism in a high frequency. There are also many molecules that produce isoforms comprising mutually different amino acid sequences during the splicing process. Any gene associated with a lung cancer-related disease that has an activity similar to that of a marker gene is included in the marker genes, even if it has nucleotide sequence differences due to polymorphism or being an isoform.
It is also to be understood that the marker genes can include homologs of other species in addition to humans. Thus, unless otherwise specified, the expression “marker gene” refers to a homolog of the marker gene unique to the species or a foreign marker gene which has been introduced into an individual.
Also, it is to be understood that a “homolog of a marker gene” refers to a gene derived from a species other than a human, which can hybridize to the human marker gene as a probe under stringent conditions. Such stringent conditions are known to one skilled in the art who can select an appropriate condition to produce an equal stringency experimentally or empirically.
A polynucleotide comprising the nucleotide sequence of a marker gene or a nucleotide sequence that is complementary to the complementary strand of the nucleotide sequence of a marker gene and has at least 15 nucleotides, can be used as a primer or probe. Thus, a “complementary strand” means one strand of a double stranded DNA with respect to the other strand and which is composed of A:T (U for RNA) and G:C base pairs.
In addition, “complementary” means not only those that are completely complementary to a region of at least 15 continuous nucleotides, but also those that have a nucleotide sequence homology of at least 40% in certain instances, 50% in certain instances, 60% in certain instances, 70% in certain instances, at least 80%, 90%, and 95% or higher. The degree of homology between nucleotide sequences can be determined by an algorithm, BLAST, etc.
Such polynucleotides are useful as a probe to detect a marker gene, or as a primer to amplify a marker gene. When used as a primer, the polynucleotide comprises usually 15 bp to 100 bp, and in certain embodiments 15 bp to 35 bp of nucleotides. When used as a probe, a DNA comprises the whole nucleotide sequence of the marker gene (or the complementary strand thereof), or a partial sequence thereof that has at least 15 bp nucleotides. When used as a primer, the 3′ region must be complementary to the marker gene, while the 5′ region can be linked to a restriction enzyme-recognition sequence or a tag.
“Polynucleotides” may be either DNA or RNA. These polynucleotides may be either synthetic or naturally-occurring. Also, DNA used as a probe for hybridization is usually labeled. Those skilled in the art readily understand such labeling methods. Herein, the term “oligonucleotide” means a polynucleotide with a relatively low degree of polymerization. Oligonucleotides are included in polynucleotides.
Tests for a lung cancer-related disease using hybridization techniques can be performed using, for example, Northern hybridization, dot blot hybridization, or the DNA microarray technique. Furthermore, gene amplification techniques, such as the RT-PCR method may be used. By using the PCR amplification monitoring method during the gene amplification step in RT-PCR, one can achieve a more quantitative analysis of the expression of a marker gene.
In the PCR gene amplification monitoring method, the detection target (DNA or reverse transcript of RNA) is hybridized to probes that are labeled with a fluorescent dye and a quencher which absorbs the fluorescence. When the PCR proceeds and Taq polymerase degrades the probe with its 5′-3′ exonuclease activity, the fluorescent dye and the quencher draw away from each other and the fluorescence is detected. The fluorescence is detected in real time. By simultaneously measuring a standard sample in which the copy number of a target is known, it is possible to determine the copy number of the target in the subject sample with the cycle number where PCR amplification is linear. Also, one skilled in the art recognizes that the PCR amplification monitoring method can be carried out using any suitable method.
The method of testing for a lung cancer-related disease can be also carried out by detecting a protein encoded by a marker gene. Hereinafter, a protein encoded by a marker gene is described as a “marker protein.” For such test methods, for example, the Western blotting method, the immunoprecipitation method, and the ELISA method may be employed using an antibody that binds to each marker protein.
Antibodies used in the detection that bind to the marker protein may be produced by any suitable technique. Also, in order to detect a marker protein, such an antibody may be appropriately labeled. Alternatively, instead of labeling the antibody, a substance that specifically binds to the antibody, for example, protein A or protein G, may be labeled to detect the marker protein indirectly. More specifically, such a detection method can include the ELISA method.
A protein or a partial peptide thereof used as an antigen may be obtained, for example, by inserting a marker gene or a portion thereof into an expression vector, introducing the construct into an appropriate host cell to produce a transformant, culturing the transformant to express the recombinant protein, and purifying the expressed recombinant protein from the culture or the culture supernatant. Alternatively, the amino acid sequence encoded by a gene or an oligopeptide comprising a portion of the amino acid sequence encoded by a full-length cDNA are chemically synthesized to be used as an immunogen.
Furthermore, a test for a lung cancer-related disease can be performed using as an index not only the expression level of a marker gene but also the activity of a marker protein in a biological sample. Activity of a marker protein means the biological activity intrinsic to the protein. Various methods can be used for measuring the activity of each protein.
Even if a patient is not diagnosed as being affected with a lung cancer-related disease in a routine test in spite of symptoms suggesting these diseases, whether or not such a patient is suffering from a lung cancer-related disease can be easily determined by performing a test according to the methods described herein.
More specifically, in certain embodiments, when the marker gene is one of the genes described herein, an increase or decrease in the expression level of the marker gene in a patient whose symptoms suggest at least a susceptibility to a lung cancer-related disease indicates that the symptoms are primarily caused by a lung cancer-related disease.
In addition, the tests are useful to determine whether a lung cancer-related disease is improving in a patient. In other words, the methods described herein can be used to judge the therapeutic effect of a treatment for a lung cancer-related disease. Furthermore, when the marker gene is one of the genes described herein, an increase or decrease in the expression level of the marker gene in a patient, who has been diagnosed as being affected by a lung cancer-related disease, implies that the disease has progressed more.
The severity and/or susceptibility to a lung cancer-related disease may also be determined based on the difference in expression levels. For example, when the marker gene is one of the genes described herein, the degree of increase in the expression level of the marker gene is correlated with the presence and/or severity of a lung cancer-related disease.
In addition, the expression itself of a marker gene can be controlled by introducing a mutation(s) into the transcriptional regulatory region of the gene. Those skilled in the art understand such amino acid substitutions. Also, the number of amino acids that are mutated is not particularly restricted, as long as the activity is maintained. Normally, it is within 50 amino acids, in certain non-limiting embodiments, within 30 amino acids, within 10 amino acids, or within 3 amino acids. The site of mutation may be any site, as long as the activity is maintained.
In yet another aspect, there is provided herein screening methods for candidate compounds for therapeutic agents to treat a lung cancer-related disease. One or more marker genes are selected from the group of genes described herein. A therapeutic agent for a lung cancer-related disease can be obtained by selecting a compound capable of increasing or decreasing the expression level of the marker gene(s).
It is to be understood that the expression “a compound that increases the expression level of a gene” refers to a compound that promotes any one of the steps of gene transcription, gene translation, or expression of a protein activity. On the other hand, the expression “a compound that decreases the expression level of a gene”, as used herein, refers to a compound that inhibits any one of these steps.
In particular aspects, the method of screening for a therapeutic agent for a lung cancer-related disease can be carried out either in vivo or in vitro. This screening method can be performed, for example, by (1) administering a candidate compound to an animal subject; (2) measuring the expression level of a marker gene(s) in a biological sample from the animal subject; or (3) selecting a compound that increases or decreases the expression level of a marker gene(s) as compared to that in a control with which the candidate compound has not been contacted.
In still another aspect, there is provided herein a method to assess the efficacy of a candidate compound for a pharmaceutical agent on the expression level of a marker gene(s) by contacting an animal subject with the candidate compound and monitoring the effect of the compound on the expression level of the marker gene(s) in a biological sample derived from the animal subject. The variation in the expression level of the marker gene(s) in a biological sample derived from the animal subject can be monitored using the same technique as used in the testing method described above. Furthermore, based on the evaluation, a candidate compound for a pharmaceutical agent can be selected by screening.
Kits
In another aspect, there is provided various diagnostic and test kits. In one embodiment, a kit is useful for assessing whether a patient is afflicted with a lung cancer-related disease. The kit comprises a reagent for assessing expression of a marker. In another embodiment, a kit is useful for assessing the suitability of a chemical or biologic agent for inhibiting a lung cancer-related disease in a patient. Such a kit comprises a reagent for assessing expression of a marker, and may also comprise one or more of such agents.
In a further embodiment, the kits are useful for assessing the presence of lung cancer-related disease cells or treating lung cancer-related diseases. Such kits comprise an antibody, an antibody derivative or an antibody fragment, which binds specifically with a marker protein or a fragment of the protein. Such kits may also comprise a plurality of antibodies, antibody derivatives or antibody fragments wherein the plurality of such antibody agents binds specifically with a marker protein or a fragment of the protein.
In an additional embodiment, the kits are useful for assessing the presence of lung cancer-related disease cells, wherein the kit comprises a nucleic acid probe that binds specifically with a marker nucleic acid or a fragment of the nucleic acid. The kit may also comprise a plurality of probes, wherein each of the probes binds specifically with a marker nucleic acid, or a fragment of the nucleic acid.
The compositions, kits and methods described herein can have the following uses, among others: 1) assessing whether a patient is afflicted with a lung cancer-related disease; 2) assessing the stage of a lung cancer-related disease in a human patient; 3) assessing the grade of a lung cancer-related disease in a patient; 4) assessing the nature of a lung cancer-related disease in a patient; 5) assessing the potential to develop a lung cancer-related disease in a patient; 6) assessing the histological type of cells associated with a lung cancer-related disease in a patient; 7) making antibodies, antibody fragments or antibody derivatives that are useful for treating a lung cancer-related disease and/or assessing whether a patient is afflicted with a lung cancer-related disease; 8) assessing the presence of lung cancer-related disease cells; 9) assessing the efficacy of one or more test compounds for inhibiting a lung cancer-related disease in a patient; 10) assessing the efficacy of a therapy for inhibiting a lung cancer-related disease in a patient; 11) monitoring the progression of a lung cancer-related disease in a patient; 12) selecting a composition or therapy for inhibiting a lung cancer-related disease in a patient; 13) treating a patient afflicted with a lung cancer-related disease; 14) inhibiting a lung cancer-related disease in a patient; 15) assessing the harmful potential of a test compound; and 16) preventing the onset of a lung cancer-related disease in a patient at risk for developing a lung cancer-related disease.
The kits are useful for assessing the presence of lung cancer-related disease cells (e.g. in a sample such as a patient sample). The kit comprises a plurality of reagents, each of which is capable of binding specifically with a marker nucleic acid or protein. Suitable reagents for binding with a marker protein include antibodies, antibody derivatives, antibody fragments, and the like. Suitable reagents for binding with a marker nucleic acid (e.g. a genomic DNA, an mRNA, a spliced mRNA, a cDNA, or the like) include complementary nucleic acids. For example, the nucleic acid reagents may include oligonucleotides (labeled or non-labeled) fixed to a substrate, labeled oligonucleotides not bound with a substrate, pairs of PCR primers, molecular beacon probes, and the like.
The kits may optionally comprise additional components useful for performing the methods described herein. By way of example, the kit may comprise fluids (e.g. SSC buffer) suitable for annealing complementary nucleic acids or for binding an antibody with a protein with which it specifically binds, one or more sample compartments, an instructional material which describes performance of the method, a sample of normal lung cells, a sample of lung cancer-related disease cells, and the like.
Animal Model
In a broad aspect, there is provided a method for producing a non-human animal model for assessment of at least one lung cancer-related disease. The method includes exposing the animal to repeated doses of at least one chemical believed to cause lung cancer. In certain aspects, the method further includes collecting one or more selected samples from the animal; and comparing the collected sample to one or more indicia of potential lung cancer initiation or development.
In a broad aspect, there is provides a method of producing the animal model that includes: maintaining the animal in a specific chemical-free environment and sensitizing the animal with at least one chemical believed to cause lung cancer. In certain embodiments, at least a part of the animal's lung is sensitized by multiple sequential exposures. In another broad aspect, there is provided a method of screening for an agent for effectiveness against at least one lung cancer-related disease. The method generally includes: administering at least one agent to a test animal, determining whether the agent reduces or aggravates one or more symptoms of the lung cancer-related disease; correlating a reduction in one or more symptoms with effectiveness of the agent against the lung cancer-related disease; or correlating a lack of reduction in one or more symptoms with ineffectiveness of the agent. The animal model is useful for assessing one or more metabolic pathways that contribute to at least one of initiation, progression, severity, pathology, aggressiveness, grade, activity, disability, mortality, morbidity, disease sub-classification or other underlying pathogenic or pathological feature of at least one lung cancer-related disease. The analysis can be by one or more of: hierarchical clustering, signature network construction, mass spectroscopy proteomic analysis, surface plasmon resonance, linear statistical modeling, partial least squares discriminant analysis, and multiple linear regression analysis.
In a particular aspect, the animal model is assessed for at least one lung cancer-related disease, by examining an expression level of one or more markers, or a functional equivalent thereto.
The animal models created by the methods described herein will enable screening of therapeutic agents useful for treating or preventing a lung cancer-related disease. Accordingly, the methods are useful for identifying therapeutic agents for treating or preventing a lung cancer-related disease. The methods comprise administering a candidate agent to an animal model made by the methods described herein, assessing at least one lung cancer-related disease response in the animal model as compared to a control animal model to which the candidate agent has not been administered. If at least one lung cancer-related disease response is reduced in symptoms or delayed in onset, the candidate agent is an agent for treating or preventing the lung cancer-related disease.
In another aspect, there is provided herein animal models for a lung cancer-related disease where the expression level of one or more marker genes or a gene functionally equivalent to the marker gene has been elevated in the animal model. A “functionally equivalent gene” as used herein generally is a gene that encodes a protein having an activity similar to a known activity of a protein encoded by the marker gene. A representative example of a functionally equivalent gene includes a counterpart of a marker gene of a subject animal, which is intrinsic to the animal.
The animal model for a lung cancer-related disease is useful for detecting physiological changes due to a lung cancer-related disease. In certain embodiments, the animal model is useful to reveal additional functions of marker genes and to evaluate drugs whose targets are the marker genes.
In one embodiment, an animal model for a lung cancer-related disease can be created by controlling the expression level of a counterpart gene or administering a counterpart gene. The method can include creating an animal model for a lung cancer-related disease by controlling the expression level of a gene selected from the group of genes described herein. In another embodiment, the method can include creating an animal model for a lung cancer-related disease by administering the protein encoded by a gene described herein, or administering an antibody against the protein. It is to be also understood, that in certain other embodiments, the marker can be over-expressed such that the marker can then be measured using appropriate methods.
In another embodiment, an animal model for a lung cancer-related disease can be created by introducing a gene selected from such groups of genes, or by administering a protein encoded by such a gene.
In another embodiment, a lung cancer-related disease can be induced by suppressing the expression of a gene selected from such groups of genes or the activity of a protein encoded by such a gene. An antisense nucleic acid, a ribozyme, or an RNAi can be used to suppress the expression. The activity of a protein can be controlled effectively by administering a substance that inhibits the activity, such as an antibody.
The animal model is useful to elucidate the mechanism underlying a lung cancer-related disease and also to test the safety of compounds obtained by screening. For example, when an animal model develops the symptoms of lung cancer-related disease, or when a measured value involved in a certain a lung cancer-related disease alters in the animal, a screening system can be constructed to explore compounds having activity to alleviate the disease.
As used herein, the expression “an increase in the expression level” refers to any one of the following: where a marker gene introduced as a foreign gene is expressed artificially; where the transcription of a marker gene intrinsic to the subject animal and the translation thereof into the protein are enhanced; or where the hydrolysis of the protein, which is the translation product, is suppressed. As used herein, the expression “a decrease in the expression level” refers to either the state in which the transcription of a marker gene of the subject animal and the translation thereof into the protein are inhibited, or the state in which the hydrolysis of the protein, which is the translation product, is enhanced. The expression level of a gene can be determined, for example, by a difference in signal intensity on a DNA chip. Furthermore, the activity of the translation product—the protein—can be determined by comparing with that in the normal state.
It is also within the contemplated scope that the animal model can include transgenic animals, including, for example animals where a marker gene has been introduced and expressed artificially; marker gene knockout animals; and knock-in animals in which another gene has been substituted for a marker gene. A transgenic animal, into which an antisense nucleic acid of a marker gene, a ribozyme, a polynucleotide having an RNAi effect, or a DNA functioning as a decoy nucleic acid or such has been introduced, can be used as the transgenic animal. Such transgenic animals also include, for example, animals in which the activity of a marker protein has been enhanced or suppressed by introducing a mutation(s) into the coding region of the gene, or the amino acid sequence has been modified to become resistant or susceptible to hydrolysis. Mutations in an amino acid sequence include substitutions, deletions, insertions, and additions.
All patents, patent applications and references cited herein are incorporated in their entirety by reference. While the invention has been described and exemplified in sufficient detail for those skilled in this art to make and use it, various alternatives, modifications and improvements should be apparent without departing from the spirit and scope of the invention. One skilled in the art readily appreciates that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein.
The methods and reagents described herein are representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Modifications therein and other uses will occur to those skilled in the art. These modifications are encompassed within the spirit of the invention and are defined by the scope of the claims. It will also be readily apparent to a person skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention.
It should be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modifications and variations of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the appended claims.
While the invention has been described with reference to various and preferred embodiments, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted for elements thereof without departing from the essential scope of the invention. In addition, many modifications may be made to adapt a particular situation or material to the teachings of the invention without departing from the essential scope thereof.
Therefore, it is intended that the invention not be limited to the particular embodiment disclosed herein contemplated for carrying out this invention, but that the invention will include all embodiments falling within the scope of the claims.
The publication and other material used herein to illuminate the invention or provide additional details respecting the practice of the invention, are incorporated be reference herein, and for convenience are provided in the following bibliography.
Citation of the any of the documents recited herein is not intended as an admission that any of the foregoing is pertinent prior art. All statements as to the date or representation as to the contents of these documents is based on the information available to the applicant and does not constitute any admission as to the correctness of the dates or contents of these documents.
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    13. Kim, H. et al. Elevated mRNA levels of DNA methyltransferase-1 as an independent prognostic factor in primary nonsmall cell lung cancer. Cancer 107, 1042-1049 (2006).
    14. Iliopoulos, D. et al. Fragile genes as biomarkers: epigenetic control of WWOX and FHIT in lung, breast and bladder cancer. Oncogene 24, 1625-1633 (2005).
    15. Jenal, A. et al. Cancer Statistics. 2007. CA Cancer J Clin. 57, 43-66 (2007).
    16. Yoo, C. B., and Jones, P. A. Epigenetic therapy of cancer: past, present and future. Nat. Rev. Drug Discov. 5, 37-50 (2006).
    17. Schrump, D. S. & Nguyen, D. M. Targeting the epigenome for the treatment and prevention of lung cancer. Semin. Oncol. 32, 488-502 (2005).
    18. Ulivi, P. et al. P16(INK4A) and CDH13 hypermethylation in tumor and serum of non-small cell lung cancer patients. J. Cell Physiol. 206, 611-615 (2006).
    19, Fabbri, M. et al. WWOX gene restoration prevents lung cancer growth in vitro and in vivo. Proc. Natl. Acad. Sci. USA 102, 15611-15616 (2005).
    20. Suzuki, M. et al. RNA interference-mediated knockdown of DNA methyltransferase 1 leads to promoter demethylation and gene re-expression in human lung and breast cancer cells. Cancer Res. 64, 3137-3143 (2004).
    21. Shen, H. et al. A novel polymorphism in human cytosine DNA-methyltransferase-3B promoter is associated with an increased risk of lung cancer. Cancer Res. 62, 4992-4995 (2002).
    22. Belinsky, S. A. et al. Inhibition of DNA methylation and histone deacetylation prevents murine lung cancer. Cancer Res. 63, 7089-7093 (2003).
    23. Krek. A. et al. Combinatorial microRNA target predictions. Nat. Genet. 37, 495-500 (2005). 24, Vatolin, S., Navaratne, K., Weil, R. J. A novel method to detect functional microRNA targets. J. Mol. Biol. 358, 983-996 (2006).
    25. Chen, C. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 33,e179 (2005).
    26. Liu, Z. et al. Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method. Nucleic Acids Res. 35, e31 (2007).
    27. Ehrich, M. et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc. Natl. Acad. Sci. USA 102, 15785-15790 (2005).


Additional References (As Listed in Methods Section)

    1. Chen, C. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 33,e179 (2005).
    2. Fabbri, M. et al. WWOX gene restoration prevents lung cancer growth in vitro and in vivo. Proc. Natl. Acad. Sci. USA 102, 15611-15616 (2005).
    3. Vatolin, S., Navaratne, K., Weil, R. J. A novel method to detect functional microRNA targets. J. Mol. Biol. 358, 983-996 (2006).
    4. Liu, Z. et al. Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method. Nucleic Acids Res. doi:10.1093/nar/gkl1156 (2007).
    5. Ehrich, M. et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc. Natl. Acad. Sci. USA 102, 15785-15790 (2005).

## Claims

1. A method for restoring a desired pattern of DNA methylation in a subject in need thereof, wherein the method comprises:
administering to the subject an effective amount of one or more miR-29s sufficient to target at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
restoring the desired pattern of DNA methylation in the subject,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the subject has a lung cancer.

2. The method of claim 1, wherein the lung cancer is a non-small cell lung cancer (NSCLC).

3. A method for restoring a desired pattern of DNA methylation in a cell in need thereof, wherein the method comprises:
transfecting the cell with an effective amount of one or more miR-29s sufficient to target at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
restoring the desired pattern of DNA methylation in the cell,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the cell is a lung cancer cell.

4. The method of claim 3, wherein the lung cancer cell is a non-small cell lung cancer (NSCLC) cell.

5. A method for inducing re-expression of at least one methylation-silenced tumor suppressor gene (TSG) in a subject in need thereof, wherein the method comprises:
administering to the subject an effective amount of one or more miR-29s sufficient to target at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
inducing re-expression of the at least one methylation-silenced TSG in the subject,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the subject has a lung cancer.

6. The method of claim 5, wherein the lung cancer is a non-small cell lung cancer (NSCLC).

7. The method of claim 5, wherein the at least one methylation-silenced TSG comprises FHIT and/or WWOX.

8. A method for inducing re-expression of at least one methylation-silenced tumor suppressor gene (TSG) in a cell in need thereof, wherein the method comprises:
transfecting the cell with an effective amount of one or more miR-29s sufficient to target at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
inducing re-expression of the at least one methylation-silenced TSG in the cell,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the cell is a lung cancer cell.

9. The method of claim 8, wherein the lung cancer cell is a non-small cell lung cancer (NSCLC) cell.

10. The method of claim 8, wherein the at least one methylation-silenced TSG comprises FHIT and/or WWOX.

11. A method for inhibiting tumorigenicity in a subject in need thereof, wherein the method comprises:
administering to the subject an effective amount of one or more miR-29s sufficient to target at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
inhibiting tumorigenicity in the subject,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the subject has a lung cancer.

12. The method of claim 11, wherein the lung cancer is a non-small cell lung cancer (NSCLC).

13. The method of claim 12, wherein the inhibiting tumorigenicity includes epigenetic regulation of the non-small cell lung cancer (NSCLC).

14. A method for inhibiting tumorigenicity in a cell in need thereof, wherein the method comprises:
transfecting the cell with an effective amount of one or more miR-29s sufficient to target at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
inhibiting tumorigenicity in the cell,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the cell is a lung cancer cell.

15. The method of claim 14, wherein the lung cancer cell is a non-small cell lung cancer (NSCLC) cell.

16. The method of claim 15, wherein the inhibiting tumorigenicity includes epigenetic modification of the non-small cell lung cancer (NSCLC) cell.

17. A method for reducing global DNA methylation in a subject in need thereof, wherein the method comprises:
administering to the subject an effective amount of one or more miR-29s sufficient to target at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
reducing global DNA methylation in the subject,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the subject has a lung cancer.

18. The method of claim 17, wherein the lung cancer is a non-small cell lung cancer (NSCLC).

19. The method of claim 18, wherein the reducing global DNA methylation includes DNA epigenetic regulation of the non-small cell lung cancer (NSCLC) by up-regulating expression of the one or more miR-29s in the subject.

20. The method of claim 17, wherein the administering includes combining the one or more miR-29s with an effective amount of one or more nucleoside analogs sufficient to block at least one de novo and maintenance methyltransferase (DNMT) pathway.

21. The method of claim 20, wherein the one or more nucleoside analogs comprise decitabine.

22. A method for reducing global DNA methylation in a cell in need thereof, wherein the method comprises:
transfecting the cell with an effective amount of one or more miR-29s sufficient to target at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
reducing global DNA methylation in the cell,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the cell is a lung cancer cell.

23. The method of claim 22, wherein the lung cancer cell is a non-small cell lung cancer (NSCLC) cell.

24. The method of claim 23, wherein the reducing global DNA methylation includes DNA epigenetic modification of the non-small cell lung cancer (NSCLC) cell by up-regulating expression of the one or more miR-29s in the non-small cell lung cancer (NSCLC) cell.

25. The method of claim 22, wherein the transfecting includes combining the one or more miR-29s with an effective amount of one or more nucleoside analogs sufficient to block at least one de novo and maintenance methyltransferase (DNMT) pathway.

26. The method of claim 25, wherein the one or more nucleoside analogs comprise decitabine.

27. A method for increasing expression of at least one tumor suppression gene (TSG) in a subject in need thereof, wherein the method comprises:
administering to the subject an effective amount of one or more miR-29s sufficient to target at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
increasing expression of the at least one TSG in the subject,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the subject has a lung cancer.

28. The method of claim 27, wherein the lung cancer is a non-small cell lung cancer (NSCLC).

29. The method of claim 27, wherein the at least one TSG comprises FHIT and/or WWOX.

30. A method for increasing expression of at least one tumor suppression gene (TSG) in a cell in need thereof, wherein the method comprises:
transfecting the cell with an effective amount of one or more miR-29s sufficient to target at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
increasing expression of the at least one TSG in the cell,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the cell is a lung cancer cell.

31. The method of claim 30, wherein the lung cancer cell is a non-small cell lung cancer (NSCLC) cell.

32. The method of claim 30, wherein the at least one TSG comprises FHIT and/or WWOX.

33. A method for increasing expression of at least one FHIT and/or WWOX enzyme in a subject in need thereof, wherein the method comprises:
administering to the subject an effective amount of one or more miR-29s sufficient to decrease expression of at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
increasing expression of the at least one FHIT and/or WWOX enzyme in the subject,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the subject has a lung cancer.

34. The method of claim 33, wherein the lung cancer is a non-small cell lung cancer (NSCLC).

35. A method for increasing expression of at least one FHIT and/or WWOX enzyme in a cell in need thereof, wherein the method comprises:
transfecting the cell with an effective amount of one or more miR-29s sufficient to decrease expression of at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
increasing expression of at least one FHIT and/or WWOX enzyme in the cell,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the cell is a lung cancer cell.

36. The method of claim 35, wherein the lung cancer cell is a non-small cell lung cancer (NSCLC) cell.

37. A method for reducing global DNA methylation in a subject in need thereof, wherein the method comprises:
administering to the subject an effective amount of one or more miR-29s sufficient to decrease expression of at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
reducing global DNA methylation in the subject,
wherein the reducing global DNA methylation includes inducing expression of the one or more miR-29s in the subject, wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the subject has a lung cancer.

38. The method of claim 37, wherein the lung cancer is a non-small cell lung cancer (NSCLC).

39. A method for reducing global DNA methylation in a cell in need thereof, wherein the method comprises:
transfecting the cell with an effective amount of one or more miR-29s sufficient to decrease expression of at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
reducing global DNA methylation in the cell,
wherein the reducing global DNA methylation includes inducing expression of the one or more miR-29s in the cell, wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the cell is a lung cancer cell.

40. The method of claim 39, wherein the lung cancer cell is a non-small cell lung cancer (NSCLC) cell.

41. A method for restoring expression of at least one tumor suppressor gene (TSG) in a subject in need thereof, wherein the method comprises:
administering to the subject an effective amount of one or more miR-29s sufficient to decrease expression of at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
restoring expression of the at least one TSG in the subject,
wherein the restoring expression of the at least one TSG includes inducing expression of the one or more miR-29s in the subject, wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the subject has a lung cancer.

42. The method of claim 41, wherein the lung cancer is a non-small cell lung cancer (NSCLC).

43. The method of claim 41, wherein the at least one TSG comprises FHIT and/or WWOX.

44. A method for restoring expression of at least one tumor suppression gene (TSG) in a cell in need thereof, wherein the method comprises:
transfecting the cell with an effective amount of one or more miR-29s sufficient to decrease expression of at least one methyltransferase comprising DNMT1, DNMT3A, and/or DNMT3B; and
restoring expression of the at least one TSG in the cell,
wherein the restoring expression of the at least one TSG includes inducing expression of the one or more miR-29s in the cell, wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the cell is a lung cancer cell.

45. The method of claim 44, wherein the lung cancer cell is a non-small cell lung cancer (NSCLC) cell.

46. The method of claim 44, wherein the at least one TSG comprises FHIT and/or WWOX.

47. A method for developing an epigenetic therapy in a subject in need thereof, wherein the method comprises:
administering to the subject an effective amount of one or more miR-29s sufficient to normalize an aberrant pattern of methylation and reactivate expression of at least one tumor suppressor gene (TSG); and
developing the epigenetic therapy in the subject,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the subject has a lung cancer.

48. The method of claim 47, wherein the lung cancer is a non-small cell lung cancer (NSCLC).

49. A method for developing an epigenetic therapy in a cell in need thereof, wherein the method comprises:
transfecting the cell with an effective amount of one or more miR-29s sufficient to normalize an aberrant pattern of methylation and reactivate expression of at least one tumor suppressor gene (TSG); and
developing the epigenetic therapy in the cell,
wherein the one or more miR-29s comprise at least one isolated or synthetic miR-29 selected from the group consisting of miR-29a, miR-29b, and miR-29c, and wherein the cell is a lung cancer cell.

50. The method of claim 49, wherein the lung cancer cell is a non-small cell lung cancer (NSCLC) cell.