Patent Application
20100317723
The present invention relates to improved G-rich oligonucleotide (GRO) aptamers specific to nucleolin, a method of preparing the aptamers and a use of the aptamers for diagnosing and/or treating a nucleolin-associated disease.
Nucleolin is a protein that is expressed at elevated levels in transformed cells. Tumor cells have been shown to present nucleolin on the cell surface as well as expressing it in the cytoplasm and nucleus. Nucleolin plays multiple roles in the cell and is involved in ribosome biogenesis, cell growth, and DNA replication.
Aptamers are about 60˜80mers of synthetic ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) oligonucleotides which are known to be discovered by the process called systematic evolution of ligands by exponential enrichment (SELEX) based on high affinity and specific molecular fit with their targets of interest.
Aptamer have recently preferred to be applied for diagnosing and treating cancers as imaging target agents rather than monoclonal antibodies due to the following characteristics: inexpensive, efficient and rapid for production, highly stable for long-term storage, versatile molecules that can be easily modified with imaging probe, small size (8-15 kDa) resulting low immune risk and better penetration into target tissues in vivo, and high affinity molecular probe.
A large number of aptamers targeting cancer-related proteins, such as Wilim's tumor protein 1 (WT1), transcription factor 1 (TCF-1), human epidermal growth factor receptor 3 (HER-3), prostate-specific membrane antigene (PSMA), tenascin-C, nucleolin, pigpen and vascular endothelial growth factor (VEGF), have been developed to target and image cancers.
Some chemical modifications on the ribose backbone of aptamer nucleotides using 2′-amino or 2′-fluoro pyrimidines have been in situ and in vitro studied with the existing aptamers to be resistant to nucleases, more capable of transfer across membranes or more capable of specific binding to the target of interest, but they influence the structure of aptamers, resulting in the loss of aptamer properties.
The present inventors found that chemically 5-modified deoxyuridine (dU)-containing GRO29A (SEQ ID NO: 1) and AS1411 (SEQ ID NO: 2) exhibit much higher affinity to nucloelin protein than that of non-modified AS1411 and GRO29A in various cancer cell types, to complete the present invention.
An embodiment provides a nucleolin-specific aptamer having the nucleotide sequence of SEQ ID NO: 1 or 2, wherein one or more thymidines (T) are independently substituted with a modified deoxyuridine (dU), and wherein the modified dU is a deoxyuridine having a hydrophobic group at 5′ position. The modified deoxyuridine may be 5-(N-b enzylcarboxyamide)-2′-deoxyuridine (BzdU), 5-(N-naphthylcarboxyamide)-2′-deoxyuridine (NapdU), or 5-(N-4-pyrrolebenzylcarboxyamide)-2′-deoxyuridine (4-PBdU).
Another embodiment provides a pharmaceutical composition containing the nucleolin-specific aptamer. The pharmaceutical composition may a nucleolin inhibitor or agent for inhibiting an abnormal hyper-proliferation of cell, for example an anticancer agent.
Another embodiment provides a method of diagnosing a hyper-proliferative cell disorder, such as cancer using the nucleolin-specific aptamer labeled with a detectable label.
Another embodiment provides a method of treating a nucleolin-associated cancer using the nucleolin-specific aptamer.
Another embodiment provides a method of inhibiting an abnormal hyper-proliferation of call using the nucleolin-specific aptamer.
Still another embodiment provides a method of inhibiting nucleolin using the nucleolin-specific aptamer.
The present invention relates to improved G-rich oligonucleotide (GRO) aptamers specific to nucleolin, a method of preparing the aptamers and a use of the aptamers for diagnosing and/or treating a cancer.
GRO29A (TTTGGTGGTGGTGGTTGTGGTGGTGGTGG; SEQ ID NO: 1) and AS1411 (GGTGGTGGTGGTTGTGGTGGTGGTGG; SEQ ID NO: 2) are G-rich oligonucleotide (GRO) aptamers comprising a single-strand DNA chain of 29 or 26 bases with unmodified phosphodiester linkages. G-rich oligonucleotide (GROs) are a class of non-antisense nucleic acids that exhibit potent anti-proliferative effects against almost every cancer cell type that was tested and thus, appears to have broad therapeutic potential. GRO29A and AS1411 have been known to bind to the nucleolin protein, which is expressed at elevated levels in transformed cells. Almost all tumor cells have been shown to present nucleolin on the cell surface as well as expressing it in the cytoplasm and nucleus. Nucleolin plays multiple roles in the cell and is involved in ribosome biogenesis, cell growth and DNA replication. The mechanism of GRO anti-proliferative activity appears to depend on their binding to the nucleolin protein.
GRO29A and AS1411 self-anneal to form a biomolecular quadruplex structure that is extremely stable and resistant to degradation by serum enzyme. GRO29A and AS1411 have shown activity against a wide range of solid and blood cancer cell lines in preclinical experiments and could therefore have potential against a variety of human cancers.
The inventors directly applied chemically modified pyrimidine-based nucleoside(s) (e.g., deoxyuridine (dU), deoxycytidine (dC), uridine (U), cytidine (C), etc.) into the GRO aptamers (AS1411 and GRO29A), which binds to nucleolin protein expressed in abnormally hyperproliferative cells, such as cancer cells, to find a type of GRO aptamer more capable of specific binding to abnormally hyperproliferative cells, such as cancer cells. The modified nucleoside may be a pyrimidine nucleoside modified by a hydrophobic group, such as benzyl group, a naphthyl group, or a pyrrolebenzyl group, at its 5′ position. Modified nucleoside may be exemplified as 5-(N-benzylcarboxyamide)-2′-deoxyuridine (called BzdU), 5-(N-naphthylcarboxyamide)-2′-deoxyuridine (called NapdU), 5-(N-4-pyrrolebenzylcarboxyamide)-2′-deoxyuridine (called 4-PBdU), 5-(N-benzylcarboxyamide)-2′-deoxycytidine (called BzdC), 5-(N-naphthylcarboxyamide)-2′-deoxycytidine (called NapdC), 5-(N-4-pyrrolebenzylcarboxyamide)-2′-deoxycytidine (called 4-PBdC), 5-(N-benzylcarboxyamide)-2′-uridine (called BzU), 5-(N-naphthylcarboxyamide)-2′-uridine (called NapU), 5-(N-4-pyrrolebenzylcarboxyamide)-2′-uridine (called 4-PBU), 5-(N-benzylcarboxyamide)-2′-cytidine (called BzC), 5-(N-naphthylcarboxyamide)-2′-cytidine (called NapC), 5-(N-4-pyrrolebenzylcarboxyamide)-2′-cytidine (called 4-PBC), and the like.
In the concrete embodiment, several hundred compounds of GRO aptamer (AS1411 and GRO29A)-containing modified dU such as BzdU, NapdU and 4-PBdU (BzdU-containing-, NapdU-containing- and 4-PBdU-containing GRO aptamer) were exemplarily synthesized by randomly substituting one to twelve thymidines (T) in GRO29A (SEQ ID NO: 1) and one to nine thymidine in AS1411 (SEQ ID NO: 2) with modified dUs. The modified pyrimidine nucleoside having a hydrophobic group, such as benzyl group, a naphthyl group, or a pyrrolebenzyl group, at its 5′ position can be sufficiently exemplified by the modified dUs as described above. Several statistically quantified fluorescence measurement, qualified confocal imaging analysis, FACS analysis, and MTT assay demonstrated with replaced T by modified dUs of a particular position of GRO aptamers (AS1411 and GRO29A). The results show that the modified dU-containing GRO aptamers significantly increased the targeting affinity to various cell lines, implying that the position and number of substituents in GRO aptamers (AS1411 and GRO29A) are critical parameters to improve the aptamer function. In the present invention, it is revealed that chemical modification on the existing aptamers would enhance the binding and targeting affinity to targets of interest without additional SELEX procedure.
The inventors also found that AS1411, which is a modified form of GRO29A by deletion of ‘TTT’ present at 5′ end of GRO29A, has similar or higher affinity to nucleolin compared to GRO29A, indicating that the three bases present at 5′ end of GRO29A (SEQ ID NO: 1) play no important role in the affinity to nucleolin. Therefore, the sequence and/or presence/absence of the three bases may not matter in the present invention, and thus following SEQ ID NO: 3 can also be included in the present invention:
wherein ‘N’ may be absent or 1 to 20 nucleosides, preferably 1 to 10 nucleosides, which is independently selected from the group consisting of adenosine (A), thymidine (T)/uridine (U), cytidine (C), and guanosine (G).
Hereinafter, the present invention is described in detail.
In an aspect, a nucleolin-specific aptamer is provided. As used herein, ‘nucleolin-specific aptamer’ means an aptamer having a specifically high affinity to nucleolin protein, thereby being capable of specifically binding to nucleolin protein.
The aptamer has the nucleotide sequence of SEQ ID NO: 3, preferably SEQ ID NO: 1 or 2, wherein one or more thymidines (T) are independently substituted with a modified pyrimidine nucleoside (e.g., deoxyuridine (dU), deoxycytidine (dC), uridine (U), cytidine (C), etc.). The modified pyrimidine nucleoside may be a pyrimidine nucleoside having a hydrophobic group at 5′ position. The hydrophobic group may have a benzyl group, a naphthyl group, or a pyrrolebenzyl group. By such modification of pyrimidine nucleoside with a hydrophobic group, the affinity of the aptamer to nucleolin is considerably improved compared with that of non-modified aptamer.
In a concrete embodiment, the hydrophobic group may be benzylcarboxyamide, naphthylcarboxyamide, pyrrolebenzylcarboxyamide and the like, and accordingly, the modified pyrimidine nucleoside may be 5-(N-benzylcarboxyamide)-2′-deoxyuridine (called BzdU), 5-(N-naphthylcarboxyamide)-2′-deoxyuridine (called NapdU), 5-(N-4-pyrrolebenzylcarboxyamide)-2′-deoxyuridine (called 4-PBdU), 5-(N-benzylcarboxyamide)-2′-deoxycytidine (called BzdC), 5-(N-naphthylcarboxyamide)-2′-deoxycytidine (called NapdC), 5-(N-4-pyrrolebenzylcarboxyamide)-2′-deoxycytidine (called 4-PBdC), 5-(N-benzylcarboxyamide)-2′-uridine (called BzU), 5-(N-naphthylcarboxyamide)-2′-uridine (called NapU), 5-(N-4-pyrrolebenzylcarboxyamide)-2′-uridine (called 4-PBU), 5-(N-benzylcarboxyamide)-2′-cytidine (called BzC), 5-(N-naphthylcarboxyamide)-2′-cytidine (called NapC), 5-(N-4-pyrrolebenzylcarboxyamide)-2′-cytidine (called 4-PBC), and the like.
The inventors found that the position of thymidine to be modified is also important to improve the affinity to nucleolin. The modification of thymidines present at central region of the aptamer considerably contributes to improve the affinity to nucleolin. The central region may be a loop site of the aptamer. More specifically, the central region may be 12th to 18th positions, preferably 15th and 16th positions of SEQ ID NO: 1, or 9th to 18th positions, preferably 12th and 13th positions of SEQ ID NO: 2 or SEQ ID NO: 3 (when the positions are counted starting from ‘G’ after ‘N’ at 5′-end). As shown in
Therefore, in a preferable embodiment, at least two thymidines present in 12th to 18th positions, preferably at 15th and 16th positions of SEQ ID NO: 1, or present in 9th to 18th positions, preferably at 12th and 13th positions of SEQ ID NO: 2 or SEQ ID NO: 3 (when the positions are counted starting from ‘G’ after ‘N’ at 5′-end) are substituted with the modified deoxyuridine. In a concrete embodiment, the aptamer has the nucleotide sequence of SEQ ID NO: 1, wherein 2 to 12 thymidines essentially comprising two thymidines present in 12th to 18th positions, preferably at 15th and 16th positions are replaced with modified deoxyuridines. In another concrete embodiment, the aptamer has the nucleotide sequence of SEQ ID NO: 2 or SEQ ID NO: 3 (when the positions are counted starting from ‘G’ after ‘N’ at 5′-end), wherein 2 to 9 thymidines essentially comprising two thymidines present in 9th to 18th positions, preferably at 12th and 13th positions are replaced with modified deoxyuridines.
In another aspect, a method of preparing the nucleolin-specific aptamer according to the present invention is provided. The method may comprise the steps of replacing one or more thymidines (T) present in the nucleotide sequence of SEQ ID NO: 1 or 2 with the modified pyrimidine nucleoside(s) (e.g., dU, dC, U, C, etc.) as described above.
Nucleolin functions as a marker of hyper-proliferative cells, such as cancer cells, since nucleolin is specifically expressed on surface of hyper-proliferative cells, such as cancer cells. Therefore, the nucleolin-specific aptamer according to the present invention can be useful in diagnosing various hyper-proliferative cell disorders.
As used herein, the hyper-proliferative cell disorder refers to excess (abnormally high) cell proliferation (abnormal hyper-proliferation of cell), relative to that occurring with the same type of cell in the general population and/or the same type of cell obtained from a patient at an earlier time. The term denotes malignant as well as non-malignant cell populations. Such disorders have an excess cell proliferation of one or more subsets of cells, which often appear to differ from the surrounding tissue both morphologically and genotypically. The excess cell proliferation can be determined by reference to the general population and/or by reference to a particular patient, e.g. at an earlier point in the individual's life. Hyper-proliferative cell disorders can occur in different types of animals and in humans, and produce different physical manifestations depending upon the affected cells. The hyper-proliferative cell disorders may include various cancers.
Therefore, in another aspect, a method of diagnosing a hyper-proliferative cell disorder, such as a cancer, using the nucleolin-specific aptamer according to the present invention is provided. The method may comprise the steps of:
contacting the nucleolin-specific aptamer with a sample from a subject, wherein the aptamer is labeled with a detectable label; and
detecting a signal from the label.
In the method, the subject is determined as having a hyper-proliferative cell disorder, such as a cancer, when the signal is detected. The nucleolin specific aptamer is as described above.
The subject to be diagnosed may be from any mammalian species, e.g. primate sp., particularly humans; rodents including mice, rats and hamsters; rabbits; equines, bovines, canines, felines; and the like. Animal models may be of interest for experimental investigations, providing a model for treatment of human disease. The sample may be any bio-sample from the subject, such as cells, tissues, blood, body fluid, and the like.
The cancer that can be diagnosed by the present invention may be any nucleolin-associated cancer including any solid cancers and blood cancers, including leukemias, lymphomas (Hodgkins and non-Hodgkins), and other myeloproliferative disorders; carcinomas of solid tissue, sarcomas, melanomas, adenomas, hypoxic tumors, squamous cell carcinomas of the mouth, throat, larynx, or lung, genitourinary cancers such as cervical and bladder cancer, hematopoietic cancers, head and neck cancers, and nervous system cancers, benign lesions such as papillomas, and the like. The nucleolin-associated cancer may be selected from the group consisting of leukemia, lymphoma, breast cancer, liver cancer, gastric cancer, ovarian carcinoma, cervical carcinoma, glioma cancer, colon cancer, lung cancer, pancreas cancer, prostate cancer, liver cancer, stomach cancer, uterine cancer, bladder cancer, thyroid cancer, ovary cancer, melanoma cancer, cervical cancer, and the like, but not be limited thereto.
The label may be any one which can be detectable by any conventional means. For example, the label may be one or more selected from the group consisting of a fluorescence material, infrared material, quantum dots, ion oxide bead, PET probe (e.g., 68gallium), T1 MR probe including iron oxide (e.g., Fe3O4), T2 MR probe (e.g., MnFe2O4, or GdFe2O4 nanoparticles), and the like, but not be limited thereto.
When the labeled-nucleolin specific aptamer is contacted with the sample, and then, non-reacted aptamer is removed (for example, by washing), if nucleolin is present in the sample (i.e., the subject having abnormally hyper-proliferative cells, such as cancer cells, resulted from the presence of nucleolin), the aptamer specifically binds to nucleolin on cells, and the signal from the label attached to the aptaemer is detected, allowing to diagnose a hyper-proliferative cell disease, such as a cancer, as described above.
Nucleolin is associated with cell cycle and cell division, and thus, when the nucleolin specific aptamer of the present invention binds to nucleolin, thereby interfering with the function of nucleolin, resulting in interfering with the cell cycle, arresting cell-cycle, for example at the S-phase, inhibiting DNA replication, inducing cell death, etc. Therefore, the nucleolin specific aptamer of the present invention can function as an inhibitor of nucleolin, and agent for inhibiting hyperproliferation of cell, and thereby being useful in treating a hyper-proliferative cell disease, such as cancer, as described above.
Therefore, in another aspect, a method of inhibiting nucleolin using the nucleolin-specific aptamer is provided. The method may comprise the step of administering the nucleolin-specific aptamer according to the present invention to a subject or a sample comprising nucleolin-expressing cells. In addition, a method of inhibiting hyperproliferation of cell cased by nucleolin using the nucleolin-specific aptamer is also provided. The method may comprise the step of administering the nucleolin-specific aptamer of claim 1 to a subject or a sample comprising nucleolin-expressing cells.
The nucleolin-specific aptamer is as described above. The subject may be from any mammalian species, e.g. primate sp., particularly humans; rodents including mice, rats and hamsters; rabbits; equines, bovines, canines, felines; and the like, who is in need of the inhibition of nucleolin and/or hyperpriliferation of cell caused by nucleolin. Animal models may be of interest for experimental investigations, providing a model for treatment of human disease. The sample may be any bio-sample from the subject, such as cells, tissues, blood, body fluid, and the like.
In another aspect, a method of inhibiting an abnormal hyper-proliferation of cell using the nucleolin-specific aptamer according to the present invention is provided. In addition, a method of treating a hyper-proliferative cell disorder, such as a cancer (nucleolin-associated cancer) using the nucleolin-specific aptamer according to the present invention is also provided.
The method may comprise the step of administering an effective amount of the nucleolin-specific aptamer to a subject who needs the inhibition of the abnormal hyper-proliferation of cell and/or the treatment of the abnormal hyper-proliferation of cell, for example, the treatment of a cancer. As described above, the nucleolin-specific aptamer has an excellent affinity to nucleolin to inhibit nucleolin, thereby exhibiting a treatment effect for cell hyper-proliferation, such as a cancer.
The nucleolin specific aptamer is as described above. The subject may be from any mammalian species, e.g. primate sp., particularly humans; rodents including mice, rats and hamsters; rabbits; equines, bovines, canines, felines; and the like, who needs the inhibition of the abnormal hyper-proliferation of cell and/or the treatment of the abnormal hyper-proliferation of cell, for example, the treatment of a cancer. Animal models may be of interest for experimental investigations, providing a model for treatment of human disease. The cancer that can be treated by the present invention may be any nucleolin-associated cancer including any solid cancers and blood cancers, including leukemias, lymphomas (Hodgkins and non-Hodgkins), and other myeloproliferative disorders; carcinomas of solid tissue, sarcomas, melanomas, adenomas, hypoxic tumors, squamous cell carcinomas of the mouth, throat, larynx, and lung, genitourinary cancers such as cervical and bladder cancer, hematopoietic cancers, head and neck cancers, and nervous system cancers, benign lesions such as papillomas, and the like. The nucleolin-associated cancer may be selected from the group consisting of leukemia, lymphoma, breast cancer, liver cancer, gastric cancer, ovarian carcinoma, cervical carcinoma, glioma cancer, colon cancer, lung cancer, pancreas cancer, prostate cancer, liver cancer, stomach cancer, uterine cancer, bladder cancer, thyroid cancer, ovary cancer, melanoma cancer, cervical cancer, and the like, but not be limited thereto.
The effective amount means an amount exhibiting a therapeutic effect on the inhibition of nucleolin or hyper-proliferation of cell, for example treating a cancer, and may be properly controlled depending on the condition of the subject and/or severity of disease. The effective amount can be administered in one or more administrations. The administration may be performed by oral or parenteral (e.g., intravenous, subcutaneous, intramuscular, and the like) pathway, but not limited thereto.
In still another aspect, a pharmaceutical composition containing the nucleolin-specific aptamer according to the present invention as an active ingredient is provided. The pharmaceutical composition may a nucleolin inhibitor or agent for inhibiting an abnormal hyper-proliferation of cell, for example an anticancer agent.
A better understanding of the present invention may be obtained in light of the following examples that are set forth to illustrate, but are not to be construed to limit, the present invention.
1.1: Design of Cy3-Labeled Modified dU AS1411 and GRO29A
Forty-seven different compounds of Cy3-labeled BzdU-containing GRO29A were designed and synthesized. The GRO29A oligonucleotides (TTTGGTGGTGGTGGTTGTGGTGGTGGTGG, SEQ ID NO: 1) incorporated with 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BzdU) and labeled with Cy3 were prepared according to the following synthesis procedure of Example 1.2. One to twelve thymidines in GRO29A oligonucleotides were randomly replaced with BzdU (see FIG. 1).
The designed forty-seven Cy3-labeled BzdU-containing GRO29A are summarized in Table 1.
Cy3-labeled BzdU-containing GRO29A derivatives contained 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BzdU) in Z. CRO29A indicated the control form of GRO29A, wherein all ‘G’s in GRO29A are substituted with ‘C’.
The GRO29A oligonucleotides incorporated with 5-(N-napthylcarboxyamide)-2′-deoxyuridine (NapdU) instead of BzdU and labeled with Cy3 were also designed (see Table 2), and prepared according to the following synthesis procedure of Example 1.2.
ZZTGGTGGTGGTGGTTGTGGTGGTGGZGG
ZTTGGTGGTGGTGGZZGTGGTGGTGGTGG
ZTZGGTGGTGGTGGZZGTGGTGGTGGTGG
ZZZGGTGGTGGTGGZZGTGGTGGTGGTGG
Cy3-labeled NapdU-containing GRO29A derivatives contained 5-(N-napthylcarboxyamide)-2′-deoxyuridine (NapdU) in Z. CRO29A indicated the control form of GRO29A, wherein all ‘G’s in GRO29A are substituted with ‘C’.
Modified dU-containing AS1411 derivatives were also designed and synthesized by randomly substituting one to nine thymidine (T) in AS1411 (GGTGGTGGTGGTTGTGGTGGTGGTGG, SEQ ID NO: 2). Modified dU inserting on AS1411 is independently selected from 5-(N-benzylcorboxyamide)-2′-deoxyuridine[BzdU] and 5-(N-naphthylcarboxyamide)-2′-deoxyuridine[NapdU] and 5-(N-4-pyrrimidylbenzylcarboxyamide)-2′-deoxyuridine[4-PBdU]. The modified dU-containing AS1411 derivatives were summarized in Tables 3-5.
Cy3-labeled BzdU-containing AS1411 derivatives contained 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BzdU) in Z. Control AS1411 indicated the control form of AS1411, wherein all ‘G’s in AS1411 are substituted with ‘C’.
1.2: Synthesis of Cy3-Labeled Modified dU AS1411 and GRO29A
Cy3-labeled AS1411 (GGTGGTGGTGGTTGTGGTGGTGGTGG, SEQ ID NO: 2) and GRO29A (TTTGGTGGTGGTGGTTGTGGTGGTGGTGG, SEQ ID NO: 1), and Cy3-labeled modified dU-containing AS1411 and GRO29A were synthesized using a Mermade 12 DNA synthesizer (BioAutomation Manufacturing, Irging, Tex.) with standard solid phase phosphoramidite chemistry. 5-(N-benzylcarboxyamide)-2′-deoxyuridine (BzdU), 5-(N-naphthylcarboxyamide)-2′-deoxyuridine (NapdU), and 5-(N-4-Pyrrolebenzylcarboxyamide)-2′-deoxyuridine (4-PBdU)-phosphoramidite were offered by Samchully Pharmaceutical (Seoul, Korea). All oligonucleotide syntheses were performed in house.
All oligonucleotides were synthesized on functionalized controlled pore glass (CPG) synthesized using a Mermade 12 DNA synthesizer (BioAutomation Manufacturing, Irging, Tex.) with 0.067 M solution of the modified dU (BzdU, NapdU or 4-PBdU)-amidite in anhydrous acetonitrile. For incorporation of dA, dG, dC and dT residues standard phosphoramidites with excyclic amino groups protected with benzoyl group (for dA and dC) and isobutyryl group (for G) were used. For incorporation of modified dU-amidite, phosphoramidite solution was delivered in two portions, each followed by a 5 min coupling wait time. Oxidation of the internucleotide phosphate to phosphate was carried out using an oxidizer [tetrahydrofuran (THF), pyridine, 0.02 M iodine and water] with waiting time. All other steps in the protocol supplied by the manufacturer were used without modification. The coupling efficiencies were >97%. After completion of the synthesis, the next step is treatment with the cleavage solution (t-butylamine:methanol:water, 1:1:2) at 70° C. for 5 hours to hydrolyze the ester linking the DNA to the support and to remove protecting groups from the purine and pyrimidine bases and followed by freezing, filtration, and speed-vac evaporation to dryness.
Crude oligonucleotides were purified by high performance liquid chromatography (AKTA basic HPLC, XBridge OST C18 10×50 mm, A=100 mM buffer triethylammoniumbiocarbonate (TEAB), pH=7, B=acetonitrile, 8% to 40% B in 20 min, flow 5 mL min-1, at 65° C., 1=254 and 290 nm). Purified aptamers were precipitated by ethanol and desalted by Centricon (Millipore Bedford, Mass.). Finally, desalted aptamers were resuspened in water or phosphate buffered saline and sterilized by filtration through a 0.2-μm syringe filter. Molecular weight and purity of each aptamer was checked by Q-TRAP 2000 ESI-MS spectroscopy (Applied Biosystems foster city, CA) and P/ACE™ 2000 capillary gel electrophoresis (Beckman coulter. fullerton, CA).
2.1: Cell Culture
C6 cells (American type culture collection), which are a rat glioma cell lines, were maintained in DMEM (Gibco, Grand Island, N.Y.) supplemented with 10% fetal bovine serum (FBS, Invitrogen, Grand Island, N.Y.), 10 U/ml penicillin (Invitrogen, Grand Island, N.Y.), and 10 μg/ml streptomycin in a 5% CO2-humidified chamber at 37° C. The cells were cultured in multiwell chamber slides overnight or 2 days till they reach about 50-80% confluence. After confluent of cells 90-100%, cells were aspirated off media with transfer pipettes and washed with PBS (1× Phosphate Buffered Saline) briefly. After trypsinization, cells were collected by standard culture media and ⅕ cells that were centrifuged 1000 rpm for 5 min were transferred into T75 flask holding 10 ml media.
2.2: Protein Assay
To normalize fluorescence signals of forty-seven Cy3-labeled BzdU-containing GRO29A and eighteen Cy3-labeled NapdU-containing GRO29A compounds, cells treated with each compound were collected with 120 μl PBS buffer after trypsinization and followed with BCA protein assay (Thermo Fisher Scientific Inc. Waltham, Mass.). Then, the collected cells were moved into 96-microplate well and treated mixture of reagent A and B (1:50 (v/v)) and incubated at 37° C. for 30 min. After the buret reaction, the absorbance at or near 562 nm reader measured on a plate.
2.3: Fluorescence Intensity
To determine the targeting efficiency of the cancers, fluorescence intensities of forty-seven Cy3-labeled BzdU-containing GRO29A and eighteen Cy3-labeled NapdU-containing GRO29A compounds were quantified to evaluate their targeting efficiency at C6 cells by the Varioskan Flash spectral scanning multimode reader (Thermo Fisher Scientific Inc. Waltham, Mass.; excitation: 535 nm, scanning wavelength: 570 nm with a band width: 12 nm). C6 cells were seeded 1×105 cell density onto Magne to FACTION 24 plate (Chemicell, GmbH, Germany) and caring at a 5% CO2-humidified chamber. After 24 hours of grown, these seeded cells were incubated in DMEM (Dubelocos' modified essential media) with 20 nM of Cy3-labeled GRO29A or AS1411, or 20 nM of each of the Cy3-labeled modified dU-containing GRO29A or AS1411 compounds at for 30 minute at 4° C. for decreasing non-specific binding during 30 min and rinsed by PBS (1×), then replaced to 200 μl Tris buffer, and then treated with each of 47 different compounds (20 pmole). Then, seeded cells was washed with PBS (phosphate buffered saline) two times each for 10 min at RT using shaking incubation (30 rpm) to remove the unbound Cy3-labeled modified dU-containing GRO29A or AS1411 compounds, and subjected to trypsinization to detach from the plate surface. These cells were collected by PBS (1×) (120 μl) and transferred into 96-well plate (Chemicell, GmbH, Germany) for measurement of fluorescence intensity (100 μl).
The fluorescence intensities of the Cy3-labeled modified dU-containing GRO29A or AS1411 compounds, targeting the nucleolin proteins expressed in the cellular membrane of the C6 cells, were quantified and normalized by units of the cells measured by the Bradford protein assay using Varioskan Flash spectral scanning multimode reader.
2.4: Confocal Laser Microscopy Assay
To further validate the increased binding affinity of modified dU-containing GRO29A or AS1411 by confocal microscopy analysis. Confocal microscopy imaging a laser scanning microscope (Carl Zeiss, Inc., Weimer, Germany; HFT 405/488 nm, DAPI imaging: 420-480 nm, Cy3-labeled compounds: 488/543) was used and each C6 cell was seeded 1×105 cells onto 12 mm sterile coverslip in 24-well plate. After 24 hr, C6 cells were incubated in PBS for 30 min at 4° C. with Cy3-GRO29A or AS1411, or Cy3-(5-BzdU)-modified GRO29A or AS1411 compounds (respectively, 20 nM).
To remove the unbound conjugates, the cells were washed three times during 10 min using shaking incubation (30 rpm) in PBS (1×) and fixed with 200 ul of 3.7% formaldehyde solution (Sigma, Saint Louis, Mo.) that was treated 200 μl into cells and incubated at shaking incubation (20 rpm) each for 20 min. After washed three times with PBS for 10 min into shaking incubation, this was followed by staining of the nucleus with a 4′,6-diamidino-2-phenylindole dihydrochloride (DAPI; emission: 460 nm, blue color) using the mounting solution (Vector Laboratories, Inc., Burlingame, Calif.). Fluorescent imaging of targeting C6 cells was visualized by red color. All fluorescence data were acquired at an excitation of 535 nm and emission of 570 nm. The side of fixed cells onto coverslip was put on 10 μl of mountain solution (Vector Resources Inc, Torrance, Calif. USA). The confocal images were acquired at low magnifications (200×).
2.5: Statistical Analysis
Fold ratio of fluorescence activity for 47 different compounds of Cy3-labeled BzdU-containing GRO29A and eighteen Cy3-labeled NapdU-containing GRO29A and the Cy3-labeled CRO29A was normalized to the fluorescence signals of Cy3-AS1411 and p-values were calculated using the Student's t-test.
2.6: Results
The results of fluorescence analysis for several Cy3-labeled BzdU-containing GRO29A compounds are shown in
The fold ratio of which the fluorescence signals for 47 different compounds of Cy3-labeled BzdU-containing GRO29A was normalized to that of Cy3-labeled GRO29A showed that seven different compounds, Compound No. 1642-11, 1642-13, 1642-19, 1642-30, 1642-39, 1642-49, and 1642-51 had about a 1.5 fold or more binding affinity to C6 cells as shown in
To further validate the increased binding affinity of Cy3-labeled BzdU-containing GRO29A by confocal microscopy analysis, compounds No. 1642-19, 1642-39 and 1642-51 were incubated and visualized in C6 cells with Cy3-labeled GRO29A and Cy3-labeled CRO29A (negative control). Twenty 20 nM of each compound was targeted in the C6 cells. The results of confocal microscopy analysis for compounds No. 1642-19, 1642-39, and 1642-51 were shown in
To test functional activity of BzdU-containing GRO29A, the compounds numbers 1642-39, 1642-51 and 1642-19, in other cancer cells, the inventors first extended cancer targeting assay by selecting another cancer cells, HeLa (human cervix cancer cell line, ATCC), and a normal healthy cell line, CHO (chinese hamster ovary cell line, ATCC). The measurement of fluorescence intensity was performed as described above for C6 cells. The obtained results are shown in
As shown in
The results for Cy3-labeled NapdU-containing GRO29A compounds are shown in
3.1: Cell Culture
All cultures were grown in a humidified incubator maintained at 37° C. with 95% air/5% CO2. C6 (Glioma cancer), MDA-MB231 (Breast cancer), MG63 (osteosarcoma), U87MG (Glioma cancer), OVCAR-3 (Ovarian carcinoma), and HeLa (Cervical Carcinoma) human cancerous cells were obtained from the American Type Culture Collection (ATCC) and were propagated in DMEM medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 IUmmL−1), and streptomycine (100 IUmmL−1). AGS (Gastric cancer, ATCC) and HepG2 (Liver cancer, ATCC) cells were grown in RPMI1640 and MEM (Invitrogen, Carlsbad, Calif.), respectively. NIH3T3 cells (Normal, ATCC) were cultured in DMEM supplemented with 10% FBS and antibiotics (100 IUmmL−1 penicillin, 100 IUmmL−1 streptomycin, Invitrogen, Carlsbad, Calif.). The modified aptamer was dissolved in culture media before addition to the cell cultures for the cell proliferation assay.
3.2: FACS (Fluorescence Activated Cell Sorter) Analysis
Cells monolayers were detached by 2 mM EDTA, filtered with 40 μm Cell strainer (BD Falcon), and then washed with HBSS solution (Gibco). The each Cy3-labeled aptamer (AS1411 or modified dU containing AS1411, 100 pmol) was incubated with cells respectively in 200 μL of HBSS solution on ice for 60 min. Cells were washed three times with 500 μL of HBSS solution and suspended in 1 mL of 1% paraformaldehyde solution. The fluorescence was determined with FACSCalibur (BD Biosciences) by counting 10,000 events.
The obtained results in various cell lines are shown in
In particular, both of central double modified dU-containing and a more modified dU-containing AS1411 have been shown same or similar binding to various cancer cell lines. The activity between central double modification and a more modification of AS1411 were measured through the FACS analysis as described above, and the obtained results are shown in
C6 rat glioma cells (ATCC) were cultured in Dulbecco's modified Eagle's medium (Invitrogen), supplemented with 10% heat-inactivated (65° C. for 20 min) fetal bovine serum (Invitrogen) with 1% antibiotics (Invitrogen), in a standard incubator (5% CO2 atmosphere at 37° C.). 5×106 cells of the cultured C6 cells were transplanted into subcutaneous tissue of both thigh of nude mice (male, BALB/c, 7-weeks old, Chalsriver).
T2 axial images were obtained using 1.5-T MR imager (GE Medical Systems, Milwaukee, Wis., USA) in animal coil box. During the experimentation, the tumor-bearing nude mice were intraperitoneal injections of 50 mL of a ketamine and xylazine (2:1) solution for anesthesia. The temperature and respirations of the tumor-bearing nude mice were monitored by a rectal thermistor. The sequence parameters for repetitive time (TR) and echo time (TE) were 1400 and 55.8 ms, respectively.
MNP@SiO2(RITC)-(PEG)/COOH/pro-N/NH2 nanoparticles (MF, 2 mg/mL) were purchased from Biterials (Seoul, Korea) and prepared as previously described (17). Carboxyl moieties (1.1×104/nanoparticle) of the MF particles (size; 50 nm; hydrodynamic diameter; 58.1 nm) were covalently linked to a 5′—NH2-modified AS1411 aptamer (SEQ ID NO: 2) or the modified dU containing AS1411 aptamer using N-(3-dimethylaminopropyl)-N-ethylcarbodiimide (EDC) (MF:aptamer molar ratio in conjugation reaction, 1:3, Sigma) for 1 h at room temperature. The AS1411-MF conjugates were washed off by centrifugation at 22,250 g for 10 min and resuspended in selection buffer solution (50 mM Tris-HCl, pH 7.4). Amine groups (6.4×104/nanoparticle) protected by the Fmoc group were released by 20% piperidine (Sigma) in an N,N-dimethylformamide solution (Sigma). After 1 h of incubation, the AS1411-MF particles were washed off twice with Tris buffer (pH 7.4) and briefly sonicated.
The AS1411-MF particle and modified dU containing AS1411 (central double NapdU-containing AS1411(1642-161))-MF particle were suspended in PBS, and injected into the tumor-bearing nude mice through tail-vein injection in the amount of 5 mg/kg of body weight. T2-weighted MR images were obtained from the both thigh of the tumor-bearing nude mice before and 24 hr after intravenous injection of AS1411-MF or AS1411(1642-161)-MF, and shown in
To test another functional activity of the chemically modified nucleolin aptamer on tumor cell death, cell proliferation test was performed by MTT assay, based on the fact that nucleolin aptamer has antiproliferative effects by specifically binding to the nucleolin transmembrane protein in cancer cells.
To determine cell survival after exposure to the chemically modified aptamer for 5 days, measurement of cell proliferation was preformed colorimetrically by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulphophenyl)-2H-tetrazolium (MTS) assay, using the CellTiter96 Aqueous One Solution Reasgent (Promega). Cells were seeded onto 96-well plates at 4×105 cells well−1 in 100 μL of medium, and the tested modified aptamer was added to allow to attach for 24 hr. The cell monolayer was washed with phosphate buffered saline (PBS) to remove unattached cells, and the cells were maintained in serum-free medium (SFM) for 24 h, and then washed with PBS. Fresh SFM with the modified aptamer was added, and the cells were incubated for an additional 5 days. Subsequently, the cells were exposed to MTS for 15 min and absorbance was measured using a microplate reader (Dynex Technology, Chantilly, Va., USA) at an optical density (OD) of 490 nm. OD values from the control cells were designated 100% as a standard.
For test the activity CRO29A on cell proliferation, 4M of each compound, numbers 1642-39, 1642-51 and 1642-19, Cy3-labeled CRO29A, and Cy3-labeled GRO29A were added directly to MDA-MB231 cells (Breast cancer, ATCC) and incubated for 1 day. The cell viability (%) was measured based on that of control (100%). The control is a cell group without treatment of aptamer, and the results are shown in
To confirm that the central double modification of the aptamer is also critical in treating cancer, the effect of central double NapdU-containing AS1411 (4 μM) on the viability of MDA-MB231 breast cancer cells (ATCC) were measured by the method as described above, and the results are shown in
The inventors synthesized various compounds of Cy3-labeled modified dU-containing AS1411 (or GRO29A) with single or multiple modified dUs to increase their binding affinity to nucleolin proteins in the cell membranes of cancer cells. The quantification of fluorescent signals demonstrated that a variety of chemically modified AS1411 compounds using modified dU had varied binding affinity to cancer cells. The number and position of substituents in the AS1411 (or GRO29A) nucleotides were compared with the original sequences of AS1411 (or GRO29A). Our statistical analysis and confocal microscopy imaging showed that at least three compounds, numbers 1642-(TTTGGTGGTGGTGGTTGTGGTGGTGGZGG, Z=BzdU), 1642-39 (TTTGGTGGTGGTGGZZGTGGTGGTGGTGG, Z=BzdU), and 1642-51 (ZTZGGTGGTGGTGGZZGTGGTGGTGGTGG, Z=BzdU) out of 47 different Cy3-labeled BzdU-containing GRO29A, resulted in a significant increase in targeting the C6 cells. To assess whether the number and position of the BzdU incorporated into GRO29A had the influence of targeting and binding the C6 cells, the chemically modified sequences of the 47 different compounds of Cy3-labeled BzdU-containing GRO29A were compared with regard to their fluorescent activity in targeting of the C6 cells. For incorporation of NapdU into GRO29A, some central double modification, No. 1642-70 (ZTTGGTGGTGGTGGZZGTGGTGGTGGTGG), 1642-71 TZZGGTGGTGGTGGZZGTGGTGGTGGTGG), 1642-72 (ZTZGGTGGTGGTGGZZGTGGTGGTGGTGG) and 1642-73 (ZZGGTGGTGGTGGZZGTGGTGGTGGTGG) had extensively and better binding affinity to the plasma membrane of the C6 cells than the Cy3-labeled GRO29A. There are 12 thymidine nucleotides in the GRO29A sequence that can be substituted with modified dU such as BzdU and NapdU. One fixed incorporation of BzdU at the 12th thymidine, resulted in the highest binding affinity to the cancer cells and showed increased targeting affinity. In addition, most of the double incorporated BzdU or NapdU at the 7th and 8th thymidine, in the GRO29A compound, produced either a slight improvement or a significant improvement in the binding affinity for the C6 cells. Other random heavy modification of AS1411 did not result in a significant increase in the binding affinity for the C6 cells. These findings imply that chemical modification of thymidines at the central double region of GRO29A with modified dU such as BzdU or NapdU forms a more stable G-quadruplex structure via hydrophobic cavities and enhances the potential binding affinity of GRO29A for cancer cells. At the results of FACS analysis with modified dU-containing AS1411, central double modified dU-containing AS1411 (GGTGGTGGTGGZZGTGGTGGTGGTGG, Z=BzdU, NapdU and 4-PBdU) had extensively and better binding affinity to the nucleolin of cancer cell lines than AS1411. (see
The results of the examples highlight the fact that chemical modifications can directly applied to alter existing aptamers thereby increasing their binding affinity for targets without a significant increase in time or labor for the SELEX procedure. Such chemically modified aptamers could be used as a valuable clinical tool for identifying serious cancer disease, in a very early stage, and evaluation of cancer therapy. However, further analysis including the study of diverse existing aptamers and their targets as well as study of resistance to enzymatic degradation, biostability in vivo, and optimization of the number and positioning of the modified dU such as BzdU, NapdU and 4-PBdU compounds in the sequence of the existing aptamers must be studied before in vivo application is considered for the detection and treatment of cancers.
This application claims the benefit of U.S. Provisional Application No. 61/169,348, filed Apr. 15, 2009, which is incorporated by reference herein in its entirety for any purpose.
| Number | Date | Country | |
|---|---|---|---|
| 61169348 | Apr 2009 | US |
