WO2011049322A2 - Method for detecting methylation of breast cancer-specific methylation marker gene for breast cancer diagnosis - Google Patents

Abstract

The present invention relates to a method for detecting the methylation of a breast cancer-specific methylation marker gene for breast cancer diagnosis, and more particularly, to a method which involves detecting methylation of a breast cancer-specific methylation marker gene which is methylated specifically in a breast cancer cell, and provides information for the diagnosis of breast cancer or the stage of progression of breast cancer. When the methylation detection method of the present invention is used together with a diagnosis composition, a kit, and a nucleic acid chip, more accurate and quicker early diagnosis of breast cancer can be facilitated as compared to conventional methods, the stage of progression of breast cancer can be checked, and a non-invasive serum sample is made available, to thereby diagnose breast cancer in a more simple and accurate manner.

Description

Method for detecting methylation of breast cancer specific methylation marker gene for breast cancer diagnosis

The present invention relates to a methylation detection method of a breast cancer specific methylation marker gene for breast cancer diagnosis, and more particularly, to detect a methylation of a breast cancer specific marker gene that is specifically methylated in breast cancer cells to diagnose breast cancer or its advanced stage diagnosis. It relates to a method for providing information for.

Breast cancer is a malignant tumor of the breast, and it is known to be caused by a transition from cancer cells to epithelial cells, which are the outermost cells in tissues or milk tubes that make milk (milk). Breast cancer is known to occur most frequently among women in developed countries, and Korea is the second most common cancer after stomach cancer. In addition, it is the fifth highest mortality cancer after stomach cancer, liver cancer, uterine cancer, and lung cancer.

This increase in breast cancer is likely to be due to changes in lifestyle, such as changes in diet, Western lifestyles, the first menstruation, or fewer births, avoiding lactation, and using birth control pills. This phenomenon is remarkable in neighboring Japan, and the most common cancer in Japanese women has become breast cancer, and it is not difficult to predict that breast cancer will overtake uterine cancer and occupy the level in female cancer in the near future.

In particular, the characteristics of breast cancer in Korea is that the frequency of breast cancer is relatively high in the 40's, unlike the prevalence in the 50's in the West. Therefore, a breast cancer management guideline suitable for Korea, which is different from the western breast cancer management guideline, is needed.

Breast cancer is a cancer that can be diagnosed early and treated early. Therefore, early diagnosis is important. Early detection of breast cancer is known to have a 10-year survival rate of about 85% or more. It is easy to think of cancer as symptoms such as tiredness, lack of appetite, and anemia, but there are no such symptoms in the early stages of breast cancer, and no breast or core pain. Because of this, many people do not realize, and many are found to be quite large cores. Therefore, in order to increase the survival time of patients, early diagnosis is the best method when the lesion range is small. Therefore, the diagnosis method is more efficient than the conventional methods for diagnosing breast cancer. The development of breast cancer specific biomarkers with high sensitivity and specificity is urgently needed.

Recently, methods for diagnosing cancer through DNA methylation measurement have been proposed. DNA methylation mainly occurs in the cytosine of CpG island of the promoter region of a specific gene, thereby binding of transcription factors. As a result of being disturbed, the expression of a specific gene is blocked, and detection of methylation of the promoter CpG island of a tumor suppressor gene is a great help in cancer research, which is called methylation specific PCR (MSP). Attempts to diagnose cancer screening and screening by using methods such as) and automatic base analysis have been actively conducted.

Although methylation of the promoter CpG islands directly causes carcinogenesis or causes secondary changes in carcinogenesis, tumor suppressor genes, DNA repair genes, and cell cycles in many cancers are controversial. It has been confirmed that the expression of these genes is blocked due to hyper-methylation of regulatory genes. In particular, it is known that hypermethylation occurs at the promoter region of specific genes at an early stage of cancer development.

Therefore, promoter methylation of tumor-related genes is an important indicator of cancer, which can be used in many ways, such as diagnosis and early diagnosis of cancer, prediction of carcinogenic risk, prediction of cancer prognosis, follow-up treatment, and prediction of response to anticancer therapy. . Attempts have recently been made to investigate the promoter methylation of tumor-related genes in blood, sputum, saliva, feces, and urine and use them in various cancer treatments (Esteller, M. et al., Cancer Res., 59:67) . , 1999; Sanchez-Cespedez, M. et al., Cancer Res. , 60: 892, 2000; Ahlquist, DA et al., Gastroenterol ., 119: 1219, 2000).

Accordingly, the present inventors have made efforts to develop an effective breast cancer specific methylation marker capable of early diagnosis, risk of cancer, or predicting the prognosis of cancer, and as a result, the OTP (NM_032109, Orthopedia Homeobox) gene is specific to breast cancer cells. It has been methylated, and it was confirmed that breast cancer can be diagnosed by measuring the degree of methylation using this as a biomarker, thereby completing the present invention.

Summary of the Invention

It is a main object of the present invention to provide a breast cancer specific methylated biomarker that is specifically methylated in breast cancer that can be effectively used for breast cancer diagnosis, and to provide information for early diagnosis of breast cancer using the same.

Another object of the present invention is to provide a method for detecting methylation of an OTP (NM_032109, Orthopedia Homeobox) gene, which is a breast cancer specific methylation marker gene, and a kit and a nucleic acid chip for diagnosing breast cancer using the same.

In order to achieve the above object, the present invention provides a method for detecting methylation of a breast cancer specific methylation marker gene for the diagnosis of breast cancer, comprising the following steps:

(a) preparing a clinical sample containing DNA; And

(b) detecting methylation of the CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene from the DNA of the clinical sample.

The present invention also provides a composition for diagnosing breast cancer containing the CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene.

The present invention also provides a method for diagnosing breast cancer through methylation detection of a breast cancer specific methylation marker gene comprising the following steps:

(a) preparing a clinical sample containing DNA; And

(b) diagnosing breast cancer or its progression if the CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene is detected as methylated from the DNA of the clinical sample.

The present invention also provides the use of the CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene for the diagnosis of breast cancer.

The present invention also provides PCR primer pairs for amplifying fragments comprising CpG islands of the OTP (NM_032109, Orthopedia Homeobox) gene and sequencing for pyro sequencing the PCR products amplified by the primer pairs. Provided are a kit for diagnosing breast cancer containing a primer.

The present invention also provides a nucleic acid chip for diagnosing breast cancer in which a fragment comprising a CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene and a probe capable of hybridizing under strict conditions are immobilized.

Other features and embodiments of the present invention will become more apparent from the following detailed description and the appended claims.

1 is a schematic diagram showing a process of discovering a methylated biomarker for diagnosing breast cancer through CpG microarray analysis and comparative selection of genes that are re-expressed by dimethylation.

Figure 2 shows the degree of quantitative methylation through pyro sequencing of one methylation gene in breast cancer cell lines and normal breast tissue.

Figure 3 is a measure of the degree of methylation of OTP gene in breast cancer tissue and normal finding tissue connected to it.

4 is a measure of breast cancer diagnosis ability by performing ROC curve analysis.

Detailed Description of the Invention and Preferred Embodiments

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In general, the nomenclature used herein is well known and commonly used in the art.

The present invention uses the CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene, which is a gene whose expression is increased by dimethylation, is a biomarker. The present invention relates to a composition for diagnosing breast cancer containing the CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene, which is a breast cancer specific methylation marker gene.

In the present invention, the CpG island may be characterized in that the intron (intron) region of the OTP gene is present, wherein the intron region from + 2001nt to + 2200nt based on the transcription start point As a sequence, it may be characterized by including the nucleotide sequence of SEQ ID NO: 1.

In the present invention, among genes hypermethylated in breast cancer tissue and genes reactivated by dimethylation, the OTP gene (NM_032109, Orthopedia Homeobox) gene was found to be useful for diagnosing breast cancer. The method for screening a methylated marker gene according to comprises the steps of: (a) separating genomic DNA from transformed and non-transformed cells; (b) separating the methylated DNA from the separated genomic DNA by reacting with a protein that binds to the methylated DNA; And (c) amplifying the methylated DNA, hybridizing to a CpG microarray, and then selecting a gene having a greatest difference in methylation degree between normal cells and cancer cells as a methylation marker gene; (d) treating the breast cancer cell line with a dimethylating agent to select genes with increased expression; (e) comparing the gene lists of (c) and (d) to determine common genes as methylated biomarker candidate genes.

As a screening method of the methylated biomarker gene, not only breast cancer but also various methylated genes can be found in various stages of dysplasia progressing to breast cancer, and the selected genes can be screened for breast cancer, risk assessment, prediction, disease identification, and disease stage. It can also be used to select diagnostic and therapeutic targets.

Identifying genes methylated in breast cancer and at various stages of abnormality enables early and accurate diagnosis of breast cancer and can identify new targets for establishing and treating methylation lists using multiple genes. In addition, methylation data according to the present invention will be able to establish a more accurate breast cancer diagnosis system in conjunction with other non-methylated associated biomarker detection methods.

With the methods of the present invention, one can diagnose breast cancer progression at various stages or stages, including determining the methylation stage of one or more nucleic acid biomarkers obtained from a sample. The methylation of nucleic acid isolated from a sample of each stage of breast cancer can be compared to the methylation of one or more nucleic acids obtained from a sample that does not have cell proliferative abnormalities of breast tissue, thereby identifying the specific stage of breast cancer of the sample, wherein the methylation The step may be hypermethylation.

In one example of the invention, the nucleic acid may be methylated at the regulatory site of a gene. As another example, since methylation starts from the outside of the regulatory region of the gene and proceeds to the inside, detection of methylation at the outside of the regulatory region enables early diagnosis of genes involved in cellular transformation.

In another embodiment of the present invention, the methylation gene marker can be used for early diagnosis of cells likely to form breast cancer. When a gene identified to be methylated in cancer cells is methylated in cells that appear clinically or morphologically normal, the cells that appear to be normal are in progress of cancer. Therefore, breast cancer specific genes in cells that appear to be normal confirm methylation, thereby allowing early diagnosis of breast cancer.

By using the methylation marker gene of the present invention, it is possible to detect cell growth abnormality (heterogeneous progression) of breast tissue in a specimen. The method includes contacting a sample comprising one or more nucleic acids isolated from a sample with an agent capable of determining one or more methylation states. The method includes identifying the methylation status of one or more sites in one or more nucleic acids, wherein the methylation status of the nucleic acid is determined by the methylation status of the same site in the nucleic acid of the sample that does not have cell growth abnormalities (progressive dysplasia) of breast tissue. It may be characterized by a difference.

In another embodiment of the present invention, by examining the methylation frequency of the gene specifically methylated in breast cancer, and by determining the methylation frequency of the tissue having the possibility of breast cancer progression, the possibility of tissue development into breast cancer can be evaluated.

Thus, in another aspect, the present invention relates to a method for detecting methylation of a breast cancer specific methylation marker gene for diagnosing breast cancer comprising the following steps:

(a) preparing a clinical sample containing DNA; And

(b) detecting methylation of the CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene from the DNA of the clinical sample.

In the present invention, the step (b) may be characterized by detecting the methylation of the CpG of the intron region of the OTP gene, wherein the intron region of the OTP gene from + 2001nt + based on the transcription start point In sequence up to 2200nt, the intron may be characterized by including the nucleotide sequence of SEQ ID NO: 1.

In the present invention, the methylation detection step of step (b) includes PCR, methylation specific PCR, real time methylation specific PCR, PCR using methylated DNA specific binding protein, quantitative PCR , DNA chip, pyro sequencing and bisulfite sequencing may be performed by a method selected from the group consisting of. In addition, the clinical sample may be characterized in that selected from the group consisting of tissue, cells, milk, blood, plasma and urine suspected cancer or a diagnosis target, but is not limited thereto.

In the present invention, as an example, the method for detecting whether the intron portion of the gene is methylated may include the following steps: (a) preparing a clinical sample containing DNA; (b) isolating DNA from the clinical sample; (c) amplifying the separated DNA using a primer capable of amplifying a fragment comprising a CpG island of an intron of an OTP (NM_032109, Orthopedia Homeobox) gene; And (d) determining whether the intron is methylated based on the presence or absence of the amplified product produced in step (c).

As another example, in the present invention, by detecting the methylation status of the OTP (NM_032109, Orthopedia Homeobox) gene using a kit, it is possible to diagnose abnormalities in cell growth (dysplasia) of breast tissue present in a specimen. have.

Accordingly, in another aspect, the present invention provides a method for sequencing a PCR primer pair for amplifying a fragment containing a CpG island of an OTP (NM_032109, Orthopedia Homeobox) gene and a PCR product amplified by the primer pair. The present invention relates to a kit for diagnosing breast cancer containing a sequencing primer for sequencing.

In the present invention, the PCR primer pair may be characterized in that the base sequence represented by SEQ ID NO: 2 and 3.

In the present invention, the sequencing primer may be characterized in that the nucleotide sequence represented by SEQ ID NO: 4.

In another embodiment, in the present invention, by detecting the methylation status of the OTP (NM_032109, Orthopedia Homeobox) gene using a nucleic acid chip, a cell growth abnormality (dysplasia) of breast tissue present in a specimen may be diagnosed. Can be.

Accordingly, in another aspect, the present invention provides a nucleic acid chip for diagnosing breast cancer in which a fragment including a CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene and a probe capable of hybridizing under stringent conditions are immobilized. It is about.

In the present invention, the OTP gene may be characterized in that it contains at least one methylated CpG dinucleotide, the CpG island may be characterized in that in the intron region of the OTP gene. In this case, the intron region of the OTP gene may be a sequence from + 2001nt to + 2200nt, based on a transcription start point, and the intron may include a nucleotide sequence of SEQ ID NO: 1.

In the present invention, the probe may be characterized in that it is selected from the group consisting of nucleotide sequences represented by SEQ ID NO: 5 to 9, the specific sequence is as follows.

Probe 1: 5’-ctgtatcgag ttatctcctt ctctacccgg-3 ’(SEQ ID NO: 5)

Probe 2: 5’-acacgcaagg cccgtctccg gccag-3 ’(SEQ ID NO: 6)

Probe 3: 5’-acacgcaagg cccgtctccg gccagtatag cgacatcccg gaagaagctc-3 ’(SEQ ID NO: 7)

Probe 4: 5’-aagcccggcg ttgtcgggct acagggttcg cctcctccgc ctgagaaggc aacctcagcg-3 ’(SEQ ID NO: 8)

Probe 5: 5'-ctgtatcgag ttatctcctt ctctacccgg aaactggtcc ccatcgccat cccccaatgg acacgcaagg cccgtctccg gccagtatag cgacatcccg gaagaagctc ctcaaaatcg aagcccggcg ttgtcgggct acagggttcg cctctccccc cc accgaga

Using the diagnostic kit or nucleic acid chip of the present invention, it is possible to determine the cell growth abnormality propensity (dysplasia progression) of the breast tissue of the specimen. The method includes determining the methylation status of one or more nucleic acids isolated from the sample, wherein the methylation step of the one or more nucleic acids is compared to the methylation step of the nucleic acid isolated from the sample without cell growth abnormality (dysplasia) of breast tissue. It can be characterized by.

In another embodiment of the present invention, transformed breast cancer cells can be identified by examining methylation of the marker gene using the kit or nucleic acid chip.

In another embodiment of the present invention, breast cancer may be diagnosed by examining methylation of a marker gene using the kit or nucleic acid chip.

In another embodiment of the present invention, the possibility of progression to breast cancer can be diagnosed by examining methylation of the marker gene using the kit or nucleic acid chip using a sample showing a normal phenotype. The sample may use solid or liquid tissue, cells, milk, urine, serum or plasma.

Definitions of main terms used in the detailed description of the present invention are as follows.

As used herein, "cell transformation" refers to the alteration of a cell's characteristics from one form to another, such as from normal to abnormal, from non-tumor to tumorous, from undifferentiated to differentiation, from stem cells to non-stem cells. Means that. Additionally, the transformation can be recognized by the morphology, phenotype, biochemical properties, etc. of the cell.

“Early identification” of cancer herein refers to finding the possibility of cancer before metastasis, preferably before morphological changes are observed in sample tissue or cells. In addition, “early identification” of cell transformation refers to the possibility of transformation occurring at an early stage before the cell is transformed.

By “hypermethylation” herein is meant methylation of CpG islands.

As used herein, "sample" or "sample sample" refers to a wide range of body fluids, including all biological fluids obtained from an individual, body fluid, cell line, tissue culture, etc., depending on the type of assay being performed. Methods of obtaining bodily fluids and tissue biopsies from mammals are commonly known. Preferred source is biopsy of the breast.

Use of cancer cells for comparison with biomarker-normal cells for breast cancer

In this example, “normal” cells refers to cells that do not exhibit abnormal cell morphology or changes in cytological properties. "Tumor" cells refer to cancer cells, and "non-tumor" cells refer to cells that are part of the diseased tissue but are not considered tumor sites.

In one aspect, the present invention is based on the discovery of the relationship between breast cancer and hypermethylation of the OTP (NM_032109, Orthopedia Homeobox) gene.

For other uses of the diagnostic kits and nucleic acid chips of the present invention, the methylation stage of one or more nucleic acids isolated from a sample can be determined to early diagnose cell growth abnormalities of the sample's breast tissue. The methylation step of the one or more nucleic acids may be compared with the methylation status of one or more nucleic acids isolated from a sample that does not have cell growth potential of breast tissue. The nucleic acid is preferably a CpG-containing nucleic acid such as a CpG island.

For other uses of the diagnostic kits and nucleic acid chips of the present invention, one can diagnose abnormalities in cell growth of breast tissue of a sample comprising determining methylation of one or more nucleic acids isolated from the sample. The nucleic acid may be characterized as an OTP (NM_032109, Orthopedia Homeobox) gene, wherein the methylation step of the one or more nucleic acids is isolated from a sample that does not have the ability to cell growth abnormalities of breast tissue. Compared to the methylation status of one or more nucleic acids.

The term “prescription” means a property that is susceptible to abnormal cell growth. A virulent sample is a sample that does not yet have cell growth abnormalities, but has or has increased cell growth abnormalities.

In another aspect, the present invention provides a method for cell growth of breast tissue of a sample comprising contacting a sample comprising the nucleic acid of the sample with an agent capable of determining the methylation state of the sample and confirming methylation of one or more sites of the one or more nucleic acids. It provides a method for diagnosing abnormalities. Here, the methylation of one or more sites of one or more nucleic acids can be characterized as different from the methylation step of the same site of the same nucleic acid of a sample having no cell growth potential.

The methods of the present invention comprise determining methylation of one or more sites of one or more nucleic acids isolated from a sample. Here, the term “nucleic acid” or “nucleic acid sequence” means oligonucleotides, nucleotides, polynucleotides or fragments, single stranded or double stranded genomic origins or synthetic genomic origins or synthetic origins of DNA or RNA, sense or antisense strands. Refers to DNA or RNA of origin, peptide nucleic acid (PNA) or DNA amount or RNA quantity material of natural or synthetic origin. If the nucleic acid is RNA, it is apparent to those skilled in the art that, instead of deoxynucleotides A, G, C, and T, it is replaced with ribonucleotides A, G, C, and U, respectively.

Any nucleic acid capable of detecting the presence of differently methylated CpG islands can be used. The CpG island is a CpG rich site in the nucleic acid sequence.

Methylation

Any nucleic acid in the purified or unpurified form of the present invention may be used, and any nucleic acid containing or suspected of containing a nucleic acid sequence containing a target site (eg, a CpG-containing nucleic acid) may be used. . A nucleic acid site that can be differentially methylated is a CpG island, which is a nucleic acid sequence having a high CpG density compared to other dinucleotide CpG nucleic acid sites. Doublet CpG is only 20% probable in vertebrate DNA as predicted by the ratio of G * C base pairs. At certain sites, the density of double CpG is ten times higher than at other sites in the genome. CpG islands have an average G * C ratio of about 60%, with an average G * C ratio of normal DNA of 40%. CpG islands are typically about 1 to 2 kb in length and there are about 45,000 CpG islands in the human genome.

In many genes, CpG islands start upstream of the promoter and extend to the transcriptional site downstream. Methylation of CpG islands in promoters usually inhibits expression of genes. The CpG islands may also surround the 3 'region of the gene coding region, as well as the 5' region of the gene coding region. Therefore, CpG islands are found at several sites, including upstream of a coding sequence of a regulatory region comprising a promoter region, a coding region (eg exon region), downstream of a coding region, eg, an enhancer region and an intron. do.

Typically, the CpG-containing nucleic acid is DNA. However, the method of the present invention may apply for example a sample containing DNA or RNA containing DNA and mRNA, wherein the DNA or RNA may be single stranded or double stranded, or DNA-RNA hybrids. It may be characterized by the contained sample.

Nucleic acid mixtures may also be used. The specific nucleic acid sequence to be detected may be a fraction of a large molecule, and from the outset the specific sequence may exist in the form of isolated molecules that make up the entire nucleic acid sequence. The nucleic acid sequence need not be nucleic acid present in pure form, and the nucleic acid may be a small fraction in a complex mixture, such as containing whole human DNA. Nucleic acids included in the sample used to measure the degree of methylation of nucleic acids contained in the sample or used to detect methylated CpG islands are described in Sambrook et al. (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, NY., 1989). It can be extracted by various methods described in.

The nucleic acid isolated from the sample is obtained by biological sample of the sample. If one wants to diagnose breast cancer or the stage of its progression, the nucleic acid must be separated from the breast tissue by scrap or biopsy. Such samples may be obtained by various medical procedures known in the art.

In one embodiment of the invention, the degree of methylation of the nucleic acid of the sample obtained from the sample is measured in comparison to the same nucleic acid portion of the sample having no cell growth abnormality of the breast tissue. Hypermethylation refers to the presence of methylated alleles in one or more nucleic acids. Samples without cell growth abnormalities of breast tissue do not show methylation alleles when the same nucleic acid is tested.

Individual genes and panels

The present invention can be used individually as a diagnostic or predictive marker, or a combination of several marker genes in the form of a panel display, and several marker genes can be used to improve reliability and efficiency through an overall pattern or a list of methylated genes. It can confirm that it improves. The genes identified in the present invention can be used individually or as a set of genes in which the genes mentioned in this example are combined. Alternatively, genes can be ranked, weighted, and selected for the level of likelihood of developing cancer, depending on the number and importance of the genes methylated together. Such algorithms belong to the present invention.

Methylation Detection Method

Methylation specific PCR

When bisulfite is treated with genomic DNA, cytosine at the 5′-CpG′-3 site remains cytosine when methylated, and uracil when unmethylated. Therefore, PCR primers corresponding to the sites where the 5'-CpG-3 'nucleotide sequence exists were prepared for the converted nucleotide sequence after bisulfite treatment. In this case, PCR primers corresponding to methylation and two types of primers corresponding to unmethylated were prepared. After converting the genomic DNA to bisulfite and PCR using the two kinds of primers, the PCR product is made by using the primer corresponding to the methylated sequence when methylated. In the PCR product is produced by using a primer corresponding to unmethylation. Methylation can be qualitatively confirmed by agarose gel electrophoresis.

Real time methylation specific PCR

Real-time methylation-specific PCR converts methylation-specific PCR into a real-time measurement method. After treating bisulfite with genomic DNA, design PCR primers corresponding to methylated cases, and perform real-time PCR using these primers. To do. At this time, there are two methods of detection using a TanMan probe complementary to the amplified base sequence and a method of detection using Sybergreen. Thus, real-time methylation specific PCR can selectively quantitate only methylated DNA. At this time, a standard curve was prepared using an in vitro methylated DNA sample, and amplification of the gene without the 5'-CpG-3 'sequence in the nucleotide sequence by a negative control group was quantitatively analyzed.

Pyro Sequencing

The pyro sequencing method is a method of converting the bisulfite sequencing method into quantitative real-time sequencing. Similar to bisulfite sequencing, the genomic DNA was converted by bisulfite treatment, and PCR primers corresponding to sites without the 5'-CpG-3 'sequencing were prepared. After treating genomic DNA with bisulfite, it was amplified by the PCR primers, and real-time sequencing was performed using the sequencing primers. Quantitative analysis of cytosine and thymine at the 5′-CpG-3 ′ site indicated the methylation degree as the methylation index.

PCR or quantitative PCR and DNA chips using methylated DNA specific binding proteins

In the PCR or DNA chip method using methylated DNA-specific binding proteins, when a protein that specifically binds to methylated DNA is mixed with DNA, only methylated DNA can be selectively separated because the protein specifically binds to methylated DNA. . After genomic DNA was mixed with methylated DNA specific binding proteins, only methylated DNA was selectively isolated. These isolated DNAs were amplified using PCR primers corresponding to intron sites, and then subjected to agarose electrophoresis to determine methylation.

In addition, methylation can also be determined by quantitative PCR.Methylated DNA separated by methylated DNA-specific binding proteins can be labeled with a fluorescent dye and hybridized to DNA chips having complementary probes to measure methylation. Can be. Wherein the methylated DNA specific binding protein is not limited to MBD2bt.

Detection of Differential Methylation—Methylation Sensitivity Restriction Endonuclease

Detection of differential methylation can be accomplished by contacting the nucleic acid sample with a methylation sensitive restriction endonuclease that cleaves only unmethylated CpG sites.

In a separate reaction, the samples were contacted with isochimers of methylation sensitive restriction endonucleases that cleave both methylated and unmethylated CpG sites, thereby cleaving the methylated nucleic acids.

Specific primers were added to the nucleic acid sample and the nucleic acid was amplified by conventional methods. If there is an amplification product in the sample treated with the methylation sensitive restriction endonuclease, and there is no amplification product in the isomerized sample of the methylation sensitive restriction endonuclease that cleaves both methylated and unmethylated CpG sites , Methylation occurred in the analyzed nucleic acid site. However, no amplification products were present in the samples treated with methylation sensitive restriction endonucleases, and the amplification products were also found in the samples treated with isosomeomers of methylation sensitive restriction endonucleases that cleave both methylated and unmethylated CpG sites. Existence means that no methylation occurs in the analyzed nucleic acid site.

Here, “methylation sensitive restriction endonuclease” is a restriction enzyme that contains CG at the recognition site and has activity when C is methylated compared to when C is not methylated (eg, Sma I). Non-limiting examples of methylation sensitivity limiting endonucleases include Msp I, Hpa II, Bss HII, Bst UI and Not I. The enzymes may be used alone or in combination. Other methylation sensitivity limiting endonucleotides include, but are not limited to, for example, Sac II and Eag I.

Isochimers of methylation sensitive restriction endonucleases are restriction endonucleases that have the same recognition site as methylation sensitive restriction endonucleases, but cleave both methylated and unmethylated CGs, e.g., Msp. I can be mentioned.

Primers of the invention are constructed to have “alternatively” complementarities with each strand of the locus to be amplified and, as described above, include the appropriate G or C nucleotides. This means that the primers have sufficient complementarity to hybridize with the corresponding nucleic acid strands under the conditions for carrying out the polymerization. The primer of the present invention is used in the amplification process, which is an enzymatic continuous reaction in which the target locus, such as PCR, increases to an exponential number through many reaction steps. Typically, one primer (antisense primer) has homology to the negative (-) strand of the locus and the other primer (sense primer) has homology to the positive (+) strand. When primers are annealed to the denatured nucleic acid, the chain is stretched by enzymes and reactants such as DNA polymerase I (Klenow) and nucleotides, resulting in newly synthesized + and-strands containing the target locus sequence. The newly synthesized target locus is also used as a template, and the cycle of denaturation, primer annealing and chain extension repeats exponential synthesis of the target locus sequence. The product of the continuous reaction is an independent double stranded nucleic acid having an end corresponding to the end of the specific primer used in the reaction.

The amplification reaction is preferably a PCR that is commonly used in the art. However, alternative methods such as real-time PCR or linear amplification with isothermal enzymes can also be used, and multiplex amplification reactions can also be used.

Detection of Differential Methylation-Bisulfite Sequencing Method

Other methods of detecting nucleic acids containing methylated CpG include contacting a sample containing nucleic acid with an agent that modifies unmethylated cytosine and amplifying the CpG-containing nucleic acid of the sample using CpG-specific oligonucleotide primers. It includes. Here, the oligonucleotide primer may be characterized by detecting the methylated nucleic acid by distinguishing the modified methylated and unmethylated nucleic acid. The amplification step is optional and desirable but not necessary. The method relies on a PCR reaction that distinguishes between modified (eg, chemically modified) methylated and unmethylated DNA. Such methods are disclosed in US Pat. No. 5,786,146, which is described in connection with bisulfite sequencing for the detection of methylated nucleic acids.

Kit

According to the present invention, there is provided a kit useful for detecting cell growth abnormality of a specimen. The kit of the invention comprises a compartment containing carrier means for holding a sample, a second container containing a pair of PCR primers capable of amplifying a 5'-CpG-3 'sequencing site for pyrosequencing the sample, and an amplified PCR product. One or more containers including a third container containing sequencing primers for pyrosequencing.

The carrier means is suitable for containing one or more containers, such as bottles, tubes, each container containing independent components used in the method of the invention. In the context of the present invention, one of ordinary skill in the art can readily dispense the required formulation in the container.

temperament

Once the target nucleic acid site is amplified, the nucleic acid amplification product can be hybridized with a known gene probe immobilized on a solid support (substrate) to detect the presence of the nucleic acid sequence.

Here, a "substrate" is a mixture means comprising a substance, structure, surface or material, abiotic, synthetic, inanimate, planar, spherical or specific binding, flat surface material, hybridization or enzyme recognition site Or many other recognition sites beyond the vast majority of other recognition sites or numerous other molecular species composed of surfaces, structures or materials. Such substrates include, for example, semiconductors, (organic) synthetic metals, synthetic semiconductors, insulators and dopants; Metals, alloys, elements, compounds and minerals; Synthesized, degraded, etched, lithographic, printed and microfabricated slides, devices, structures and surfaces; Industrial, polymers, plastics, membranes, silicones, silicates, glass, metals and ceramics; Wood, paper, cardboard, cotton, wool, cloth, woven and non-woven fibers, materials and fabrics, but are not limited thereto.

Some types of membranes are known in the art to have adhesion to nucleic acid sequences. Specific and non-limiting examples of such membranes are membranes for gene expression detection, such as nitrocellulose or polyvinylchloride, diaotized paper and commercially available membranes such as GENESCREEN ™, ZETAPROBE ™ (Biorad) and NYTRAN ™. Can be mentioned. Beads, glass, wafers and metal substrates are also included. Methods of attaching nucleic acids to such objects are well known in the art. Alternatively, screening can also be performed in the liquid phase.

Hybridization conditions

In nucleic acid hybridization reactions, the conditions used to achieve stringent specific levels vary depending on the nature of the nucleic acid being hybridized. For example, the length of the nucleic acid region to be hybridized, degree of homology, nucleotide sequence composition (eg, GC / AT composition ratio), and nucleic acid type (eg, RNA, DNA) select hybridization conditions. Is considered. Further considerations are whether the nucleic acid is immobilized, for example, in a filter or the like.

Examples of very stringent conditions are as follows: 2X SSC / 0.1% SDS at room temperature (hybridization conditions); 0.2X SSC / 0.1% SDS at room temperature (low stringency conditions); 0.2X SSC / 0.1% SDS at 42 ° C. (conditions with moderate stringency); 0.1X SSC at 68 ° C. conditions with high stringency. The washing process can be carried out using one of these conditions, for example a condition with high stringency, or each of the above conditions, each of 10-15 minutes in the order described above, all or all of the conditions described above. Some iterations can be done. However, as described above, the optimum conditions vary with the particular hybridization reaction involved and can be determined experimentally. In general, conditions of high stringency are used for hybridization of critical probes.

Label

Important probes are labeled so that they can be detected, for example, with radioisotopes, fluorescent compounds, bioluminescent compounds, chemiluminescent compounds, metal chelates or enzymes. Proper labeling of such probes is a technique well known in the art and can be carried out by conventional methods.

Example

Hereinafter, the present invention will be described in more detail with reference to Examples. These examples are only for illustrating the present invention, it will be apparent to those skilled in the art that the scope of the present invention is not to be construed as being limited by these examples.

Example 1 Selection of Breast Cancer Specific Methylation Marker Genes

1-1: Screening Genes Hypermethylated in Breast Cancer Tissue Samples

To screen for hypermethylated genes in breast cancer, we received breast cancer tissues and normal findings from the tissue bank of Chungnam National University Hospital and selected hypermethylated genes as follows.

First, genomic DNA was isolated from each tissue sample. 500 ng of the genomic DNA was fragmented into 300-400 bp by ultrasonic disruption (Vibra Cell, SONICS), and methylated DNA was selectively isolated from each tissue using Methylcapture ™ (Genomictree, South Korea). After amplifying the isolated methylated DNA using GenomePlexComplete Whole Genome Amplification Kit (Sigma, USA), amplified DNA from breast cancer tissue was labeled with Cy5-dUTP, and amplified DNA from adjacent normal-tissue tissue was labeled with Cy3-dUTP and mixed. Next, hybridization was performed using a CpG microarray (Agilent, USA) in which probes for CpG present in about 27,800 CpG islands present in the human genome were integrated. After the hybridization, a series of washing procedures were performed, followed by scanning using an Agilent scanner. The calculation of signal values from microarray images can be found in the Feature Extraction Program v. 9.5.3.1 (Agilent) was used to calculate the relative difference in signal intensity between adjacent normal-tissue tissue and breast cancer tissue samples, and the difference in methylation level between adjacent normal and breast cancer tissues was analyzed using GeneSpringGX (Agilent). Large genes were selected. Statistical techniques were used to select 3,969 hypermethylated candidate genes from breast cancer tissues (FIG. 1).

1-2: Gene Selection Reactivated by Dimethylation

To confirm that the genes selected in Example 1-1 are regulated by methylation, 5-aza, which is a dimethylating agent, is applied to breast cancer cell lines MCF-7 (KCLB (Korea Cell Line Bank) 30022) and MDA-MB231 (KCLB 30026). 2-deoxycytidine (DAC, Sigma, USA) was treated for 5 days at 200 nM concentration. Untreated cell lines and treated cell lines were treated with Tri reagent to separate total RNA.

By directly comparing transcription levels between the DAC untreated cell line and the DAC treated cell line, changes in gene expression by DAC treatment were measured. As a result, it was confirmed that the expression of 1,085 genes was increased when the DAC was treated, compared to the control without the DAC. A list of 3,969 breast cancer-specific hypermethylated genes obtained in Example 1-1 and genes re-expressed more than two times by 1,085 dimethylation were compared, and 144 common genes were selected (FIG. 1). Of these 144 genes, we excluded genes whose genetic information was unclear, and among the remaining genes, 13 biomarker candidate genes related to cancer were selected. From this, one gene of high significance (OTP) was selected as a biomarker candidate for final breast cancer diagnosis (Table 1).

Table 1 List of Genes

Gene Symbol	GenBank No.	Description	Chromosome location
OTP	NM_032109	Orthopedia homeobox	5q13.3

Example 2: Measurement of Methylation of Biomarker Genes in Cancer Cell Lines

In order to further confirm the methylation status of the gene selected in Example 1-2, the bisulfite pi to a site containing a probe identified as hypermethylated in breast cancer tissues as a result of the CpG microarray experiment in Example 1-1 above Ross sequencing was performed.

To transform unmethylated cytosine to uracil using bisulfite, whole genomic DNA was isolated from breast cancer cell lines MDAMB-231 (KCLB 30026) and HCC1428 (ATCC CRL-2327) and added to 200 ng of genomic DNA. Bisulfite was treated using the EZ DNA methylation-Gold kit (Zymo Research, USA). Treatment of DNA with bisulfite leaves unmethylated cytosine modified with uracil and methylated cytosine remains unchanged. The bisulfite-treated DNA was eluted with 20 µl of sterile distilled water to perform pyrosequencing.

PCR and sequencing primers for performing pyro sequencing for the gene were designed using the PSQ assay design program (Biotage, USA). PCR and sequencing primers for methylation determination of genes are shown in Tables 2 and 3.

TABLE 2 PCR primers and conditions

gene	primer	Sequence (5 '→ 3')	SEQ ID NO:	CpG position a	Amplicon Size (bp)
OTP	Forward	TATTYGGAAATTGGTTTTTA		2	+2064, +2073, +2079, +2091, +2099	98
	Reverse	biotin- TCRATTTTAAAAAACTTCTT	3

^a nucleotide from transcription initiation point (+1): position on genomic DNA of CpG site used for methylation measurement

TABLE 3 Sequencing Primer Sequences of Methylation Marker Genes

gene	Sequence (5 '→ 3')	SEQ ID NO:
OTP	TTATYGTTATTTTTTAATGG		4

20 ng of genomic DNA converted to bisulfite was amplified by PCR. PCR reaction solution (20 ng genomic DNA converted to bisulfite, 5 μl of 10X PCR buffer (Enzynomics, Korea), 5 units of Taq polymerase (Enzynomics, Korea), 4 μl of 2.5 mM dNTP (Solgent, Korea), 2 μl of PCR primer ( 10 pmole / μl)) was treated at 95 ° C. for 5 minutes, followed by a total of 45 times of 40 seconds at 95 ° C., 45 seconds at 60 ° C., and 40 seconds at 72 ° C., followed by reaction at 72 ° C. for 5 minutes. Amplification of the PCR product was confirmed by electrophoresis using 2.0% agarose gel.

That is, after the PyroGold reagent (Biotage, USA) was treated to the amplified PCR product, pyro sequencing was performed using the PSQ96MA system (Biotage, USA). After the pyro sequencing, the degree of methylation was measured by calculating the methylation index. The methylation index was calculated by calculating the average rate of cytosine binding at each CpG site.

As a result of quantitatively expressing the degree of methylation of the biomarker in the breast cancer cell line using a pyro sequencing method, it was confirmed that the biomarker gene was methylated at high levels in both cell lines.

Meanwhile, in order for the gene to be useful as a biomarker, the gene should not be methylated in normal breast tissue. In order to confirm this, breast tissue genomic DNA (Biochain Co., USA) of non-breast cancer patients was purchased and methylation was measured by the same pyro sequencing method as described above.

As a result, as shown in Figure 2B, OTP gene showed a low methylation level of 20% or less, it was confirmed that it has the potential as a biomarker.

Example 3: Determination of Hypermethylation of Biomarker Genes in Breast Cancer Tissues

From Examples 1 and 2, (a) hypermethylated in breast cancer tissue, (b) reactivation of marker expression under dimethylation conditions, (c) contains CpG islands in the intron site, and in breast cancer cell lines The following experiment was performed to verify whether the OTP gene, which was methylated but not methylated in normal tissues, could be used as a biomarker for diagnosing breast cancer. In other words, methylation assay was performed on the biomarker using clinical tissue specimens (Chungnam University Hospital Tissue Bank) of 39 breast cancer patients. Methylation assay was performed by the pyro sequencing method described in Example 2.

As a result, as shown in FIG. 3, the OTP gene exhibited a very high level of methylation in breast cancer tissues compared to normal-breasted breast tissues in contact with normal persons and cancer tissues. The OTP gene showed hypermethylation in breast cancer tissues compared to adjacent normal findings in all 39 breast cancer tissues tested. Also, according to stage, hypermethylation was observed from stage 1, indicating the usefulness of early diagnosis of breast cancer, and the normal findings of some patients showed higher methylation than breast tissues of non-patients. Confirmed. In general, the field defect phenomenon represents the occurrence of cancer at the molecular level, even in normal tissues that are connected to cancer tissues, and suggests the high usefulness of early diagnosis.

Example 4 Evaluation of Sensitivity and Specificity of Breast Cancer Diagnosis of OTP Biomarker Genes

ROC (receiver operating calculation) curve analysis was performed to determine the methylation index cut-off for diagnosing breast cancer patients, and to determine the sensitivity and specificity.

As a result of comparing the methylation measurement results of the breast cancer tissues and the normal finding tissues connected thereto, it was confirmed that the OTP gene is an excellent biomarker for diagnosing breast cancer by showing an sensitivity of 82.1% and a specificity of 92.3% as shown in Table 4 and FIG. 4. .

Table 4 Sensitivity and Specificity of <i> OTP </ i> genes for Tissue Samples

Marker	AUC a	95% CI b	Cut-off (%)	Sensitivity (%, 95% CI)	Specificity (%, 95% CI)
OTP	0.914	0.828-0.965	31.11	82.1 (66.5-92.4)	92.3 (79.1-98.3)

^a : Area Under ROC Curve; ^b : 95% Confidence Interval

As described above, by using the methylation detection method, the diagnostic composition, the kit and the nucleic acid chip according to the present invention, early diagnosis of breast cancer can be performed more accurately and faster than the conventional method, and the progression of breast cancer can be confirmed. Serum, which is an invasive sample, can be used as a sample, which is useful because it can diagnose breast cancer more simply and accurately.

As described above in detail a specific part of the content of the present invention, for those of ordinary skill in the art, such a specific description is only a preferred embodiment, which is not limited by the scope of the present invention Will be obvious. Thus, the substantial scope of the present invention will be defined by the appended claims and their equivalents.

Electronic file attached.

Claims (15)

1. Method for detecting methylation of breast cancer specific methylation marker gene for breast cancer diagnosis comprising the following steps:

   (a) preparing a clinical sample containing DNA; And

   (b) detecting methylation of the CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene from the DNA of the clinical sample.
2. The method of claim 1, wherein step (b) detects methylation of the CpG island of the intron region of the OTP gene.
3. The method according to claim 2, wherein the intron of the OTP gene comprises the nucleotide sequence of SEQ ID NO: 1.
4. The method of claim 1, wherein step (b) comprises: PCR, methylation specific PCR, real time methylation specific PCR, PCR using methylated DNA specific binding protein, quantitative PCR, DNA chip , Pyro sequencing and bisulfite sequencing.
5. The method of claim 1, wherein the clinical sample is selected from the group consisting of tissue, cells, blood, milk, plasma, and urine from a suspected cancer patient or a diagnostic subject.
6. A composition for diagnosing breast cancer containing the CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene.
7. The composition for diagnosing breast cancer according to claim 6, wherein the CpG island is located at an intron region of the OTP gene.
8. According to claim 7, wherein the intron of the OTP gene breast cancer diagnostic composition, characterized in that it comprises a nucleotide sequence of SEQ ID NO: 1.
9. Breast cancer containing PCR primer pairs for amplifying fragments containing CpG islands of the OTP (NM_032109, Orthopedia Homeobox) gene and sequencing primers for pyro sequencing PCR products amplified by the primer pairs Diagnostic kit.
10. The diagnostic kit according to claim 9, wherein the PCR primer pair is a nucleotide sequence represented by SEQ ID NOs: 2 and 3.
11. The diagnostic kit according to claim 9, wherein the sequencing primer is a nucleotide sequence represented by the sequence of SEQ ID NO.
12. A nucleic acid chip for breast cancer diagnosis in which a fragment containing a CpG island of the OTP (NM_032109, Orthopedia Homeobox) gene and a probe capable of hybridizing under strict conditions are immobilized.
13. The diagnostic nucleic acid chip according to claim 12, wherein the CpG island is located at an intron portion of the OTP gene.
14. The diagnostic nucleic acid chip according to claim 13, wherein the intron of the OTP gene comprises the nucleotide sequence of SEQ ID NO: 1.
15. The diagnostic nucleic acid chip according to claim 12, wherein the probe is selected from the group consisting of nucleotide sequences represented by SEQ ID NOs: 5 to 9.

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