Patent Application
20220033911
The present invention relates to a method for determining prognosis of endometrial cancer.
Endometrial cancer is a cancer that develops in endometrium, and is one of gynecological malignancies most frequently found in developed countries. Although frequently found in postmenopausal women, cases of onset of endometrial cancer have been notably increasing in recent years among younger premenopausal women aged 40 or below. Current major therapy of endometrial cancer is surgery, that is, hysterectomy, bilateral salpingo-oophorectomy, and optional lymphoidectomy. Fertility preservation therapy is, however, chosen in some cases particularly for younger patients who wish pregnancy in the future, in order to avoid surgical menopause. Hormone therapy using medroxyprogesterone acetate (MPA) and the like is one known fertility preservation therapy. Such MPA therapy reportedly showed excellent therapeutic effect on early endometrial tumor including atypical hyperplasia and early stage endometrial cancer.
In other aspect, the fertility preservation therapy has been suffering from a problem of recurrence. It has been reported that recurrence rate of early stage endometrial cancer patient who underwent the MPA therapy reached approximately 63% (Non-Patent Literature 1), meaning that the MPA therapy suffers from higher risk of recurrence as compared with the surgical therapy. Moreover, the MPA therapy is effective mostly for early stage patients who are not observed to have invasion into myometrium. Hence, the MPA therapy, when applied, needs carful observation of the patients not only regarding their wishes to preserve fertility, but also compatibility of the patients to the therapy, considering the stage and risk of recurrence of cancer.
Abnormal methylation of DNA has been found to closely correlate with malignant transformation, and has therefore been attracting attention. A characteristic epigenetic abnormality in cancer cell has been known to relate to abnormal methylation of DNA in CpG island. The CpG island is a region where a two-base sequence of cytosine (C)-guanine (G), linked by a phosphodiester bond (p), appears with high frequency, and is often found in the promoter region upstream of a gene. Abnormal methylation of DNA in the CpG island relates to carcinogenesis, typically by way of inactivation of tumor suppressor gene. Non-Patent Literature 2 describes 13 genes which the methylation level is increased in CpG islands of, in correlation with increase of DNA methylation level in endometrial cancer patients. Non-Patent Literature 3 describes DNA methylation marker that can serve as a marker for high risk group of endometrial cancer. Non-Patent Literature 4 identifies approximately 27,000 and approximately 15,700 DNA regions that cause methylation respectively in relation to endometrioid cancer and serous cancer of uterine corpus, including some regions common to both cancers. Non-Patent Literature 5 identifies 12 regions that cause methylation in relation to ovarian cancer and endometrial cancer, including CpG island in ZNF154 promoter.
Methods based on bisulfite method have already been established as methods for analyzing methylated DNA, and have been widely used. Currently applied methods for analyzing methylated DNA, based on the bisulfite method, include Methylation-Specific PCR (MSP), Combined Bisulfite Restriction Analysis (COBRA), BAC-Array based Methylated CpG island Amplification (BAMCA), sequencing using next generation sequencer (MethylCap-seq), method for detecting a single-base extension reaction by using methylated/non-methylated DNA-specific probe (Infinium (registered trademark) assay), and methylation-sensitive restriction enzyme digestion sequencing (MRE-seq).
Patent Literature 1 discloses a method for detecting risk of poor prognosis of renal cell cancer by detecting methylation level at CpG sites in specific genes by, for example, bead array method, mass spectrometry (MassARRAY method), pyrosequencing, methylation-sensitive high resolution melting curve analysis, quantitative PCR, direct sequencing of bisulfite-treated product, and COBRA method. Patent Literature 2 discloses a method for determining prognosis of renal cell cancer, by detecting methylation level at CpG sites in specific genes, on the basis of difference of retention time in ion exchange chromatography.
The present invention is to provide a method for determining status, prognosis or risk of onset of endometrial cancer on the basis of methylation level of DNA, and a method for acquiring data for the determination.
The present inventors identified gene regions in endometrial cancer tissue, having methylation levels different from that in normal endometrial tissue, and further identified, from among these gene regions, those having methylation levels different depending on malignancy of endometrial cancer. The present inventors further found that prognosis of endometrial cancer, compatibility of endometrial cancer patients to preservation therapy, and risk of onset of endometrial cancer can be determined by measuring data regarding DNA methylation levels of such gene regions.
The present invention therefore provides the following:
[1] A method for detecting a cell or tissue derived from an endometrial cancer patient with poor prognosis, the method comprising:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue comprising the cell; and
detecting a cell or tissue derived from the endometrial cancer patient with poor prognosis, on the basis of the detected DNA methylation level,
wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at or near the chromosomal positions listed in Table A.
[2] A method for detecting a cell or tissue derived from an endometrial cancer patient compatible to preservation therapy, the method comprising:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue containing the cell; and
detecting a cell or tissue derived from the endometrial cancer patient compatible to preservation therapy, on the basis of the detected DNA methylation level,
wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at or near the chromosomal positions listed in Table A.
[3] A method for determining malignant transformation risk of endometrium, the method comprising:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cell or tissue containing the cell; and
determining malignant transformation risk in the endometrium, on the basis of the detected DNA methylation level,
wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at or near the chromosomal positions listed in Table A.
[4] A method for determining prognosis of endometrial cancer, the method comprising:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue containing the cell of a subject; and
determining prognosis of endometrial cancer of the subject, on the basis of the detected DNA methylation level,
wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at or near the chromosomal positions listed in Table A.
[5] A method for determining compatibility of an endometrial cancer patient to a preservation therapy, the method comprising:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue containing the cell of the endometrial cancer patient; and
determining compatibility of the endometrial cancer patient to preservation therapy, on the basis of the detected DNA methylation level,
wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at or near the chromosomal positions listed in Table A.
[6] A method for determining risk of endometrial cancer, the method comprising:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cell or tissue containing the cell of a subject; and
determining risk of endometrial cancer of the subject, on the basis of the detected DNA methylation level,
wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at or near the chromosomal positions listed in Table A.
[7] A method for acquiring data for use in detecting a cell or tissue derived from an endometrial cancer patient with poor prognosis, or in determining prognosis of endometrial cancer, the method comprising:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue containing the cell of a subject; and
acquiring data for use in detecting a cell or tissue derived from the endometrial cancer patient with poor prognosis, or data for use in determining prognosis of endometrial cancer of the subject, on the basis of the detected DNA methylation level,
wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at or near the chromosomal positions listed in Table A.
[8] A method for acquiring data for use in detecting a cell or tissue derived from an endometrial cancer patient compatible to a preservation therapy, or for use in determining compatibility of an endometrial cancer patient to the preservation therapy, the method comprising:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue containing the cell of the endometrial cancer patient; and
acquiring data for use in detecting a cell or tissue derived from the endometrial cancer patient compatible to the preservation therapy, or data for use in determining compatibility of the endometrial cancer patient to the preservation therapy, on the basis of the detected DNA methylation level,
wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at or near the chromosomal positions listed in Table A.
[9] A method for acquiring data for use in determining malignant transformation risk of endometrium, or for use in determining risk of endometrial cancer, the method comprising:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cell or tissue containing the cell of a subject; and
acquiring data for use in determining malignant transformation risk of endometrium, or data for use in determining risk of endometrial cancer of the subject, on the basis of the detected DNA methylation level,
wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at or near the chromosomal positions listed in Table A.
[10] The method according to any one of [1] to [9], wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at chromosome 10, position 106,400,259; chromosome 8, position 56,852,290; chromosome 14, position 60,973,823; chromosome 6, position 28,226,980; chromosome 1, position 62,660,624; chromosome 6, position 10,390,919; chromosome 8, position 132,321,917; chromosome 11, position 5,346,249; chromosome 21, position 31,972,506; chromosome 2, position 1,928,480; and chromosome 1, position 248,366,399, and CpG sites located near the positions.
[11] The method according to any one of [1] to [9], wherein the target CpG site is at least one CpG site selected from the group consisting of:
CpG site contained in the DNA region of chromosome 10, from position 106,400,199 to position 106,400,320;
CpG site contained in the region of chromosome 8, from position 56,852,230 to position 56,852,351;
CpG site contained in the region of chromosome 14, from position 60,973,763 to position 60,973,884;
CpG site contained in the region of chromosome 6, from position 28,226,920 to position 28,227,041;
CpG site contained in the region of chromosome 1, from position 62,660,564 to position 62,660,685;
CpG site contained in the region of chromosome 6, from position 10,390,859 to position 10,390,980;
CpG site contained in the region of chromosome 8, from position 132,321,857 to position 132,321,978;
CpG site contained in the region of chromosome 11, from position 5,346,189 to position 5,346,310;
CpG site contained in the region of chromosome 21, from position 31,972,446 to position 31,972,567;
CpG site contained in the region of chromosome 2, from position 1,928,420 to position 1,928,541; and
CpG site contained in the region of chromosome 1, from position 248,366,339 to position 248,366,460.
[12] The method according to any one of [1] to [9], wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites contained in a DNA region consisting of any one of nucleotide sequences represented by SEQ ID NOs 1 to 11 or complementary sequences thereof.
[13] The method according to any one of [1] to [12], wherein the detection of the DNA methylation level comprises detecting the DNA methylation level at the target CpG site, by using the genomic DNA which has been treated with bisulfite.
[14] The method according to [13], wherein the DNA methylation level is detected by pyrosequencing, mass spectrometry, bead array method, or ion exchange chromatography.
[15] A primer or a probe for use in determining prognosis of endometrial cancer, endometrial cancer patient compatible to preservation therapy, or risk of endometrial cancer,
wherein the primer or the probe has at least 12 base long, and is hybridizable with a target CpG site which has been treated with bisulfite, and
the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at or near the chromosomal positions listed in Table A.
[16] The primer or the probe according to [15], wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites located at chromosome 10, position 106,400,259; chromosome 8, position 56,852,290; chromosome 14, position 60,973,823; chromosome 6, position 28,226,980; chromosome 1, position 62,660,624; chromosome 6, position 10,390,919; chromosome 8, position 132,321,917; chromosome 11, position 5,346,249; chromosome 21, position 31,972,506; chromosome 2, position 1,928,480; and chromosome 1, position 248,366,399, and CpG sites located near the positions.
[17] The primer or the probe according to [15], wherein the target CpG site is at least one CpG site selected from the group consisting of the following CpG sites:
CpG site contained in the region of chromosome 10, from position 106,400,199 to position 106,400,320;
CpG site contained in the region of chromosome 8, from position 56,852,230 to position 56,852,351;
CpG site contained in the region of chromosome 14, from position 60,973,763 to position 60,973,884;
CpG site contained in the region of chromosome 6, from position 28,226,920 to position 28,227,041;
CpG site contained in the region of chromosome 1, from position 62,660,564 to position 62,660,685;
CpG site contained in the region of chromosome 6, from position 10,390,859 to position 10,390,980;
CpG site contained in the region of chromosome 8, from position 132,321,857 to position 132,321,978;
CpG site contained in the region of chromosome 11, from position 5,346,189 to position 5,346,310;
CpG site contained in the region of chromosome 21, from position 31,972,446 to position 31,972,567;
CpG site contained in the region of chromosome 2, from position 1,928,420 to position 1,928,541; and
CpG site contained in the region of chromosome 1, from position 248,366,339 to position 248,366,460.
[18] The primer or the probe according to [15], wherein the target CpG site is at least one CpG site selected from the group consisting of CpG sites contained in a DNA region consisting of any one of nucleotide sequences represented by SEQ ID NOs 1 to 11 or complementary sequences thereof.
The present invention makes it possible to determine prognosis (including malignancy and risk of recurrence) of endometrial cancer, compatibility of endometrial cancer patients to preservation therapy, and risk of onset of endometrial cancer, with high sensitivity and specificity. The present invention enables early diagnosis of endometrial cancer. The present invention also provides a guideline for determining treatment policy for endometrial cancer patients, such as determine whether surgery or preservation therapy should be chosen. The present invention can provide information on benefit of preservation therapy, and risk of recurrence after preservation therapy, for younger endometrial cancer patients who wish future pregnancy, and to improve QOL and survival rate of the patients. The present invention can also provide data for use in determining or diagnosing these events.
“Endometrial cancer” in the present specification is referred to as cancer that develops in endometrium, and more specifically to endometrioid cancer. The “endometrial cancer” in the present specification includes primary cancer and recurrent cancer. “Juvenile endometrial cancer” in the present specification is referred to as endometrial cancer in premenopausal women, more specifically in women of reproductive age, and more specifically in women aged 40 or under. Meanwhile, “senile endometrial cancer” in the present specification is referred to as endometrial cancer other than juvenile endometrial cancer, and more specifically endometrial cancer in women aged over 40 years, or women over reproductive age.
“Risk of cancer” in the present specification is referred to as current onset of cancer, or risk of future onset. “Malignant transformation risk” of cell or tissue in the present specification means that the cell or tissue currently has cancer, or risk of having cancer in the future. “Risk of recurrence” of cancer in the present specification is referred to as current recurrence of cancer, or risk of future recurrence. “Risk of recurrence” of endometrial cancer in the present specification is specifically referred to as risk of recurrence of endometrial cancer after preservation therapy.
“Malignancy” in the present specification is referred to as stage or grade of cancer. The stage of endometrial cancer may be determined according to surgical staging prepared by the International Federation of Gynecology and Obstetrics (FIGO), or tumor node metastasis (TNM) classification prepared by the Union for International Cancer Control (UICC). “High malignancy” cancer in the present specification is referred to as cancer at more advanced stage or at higher grade.
“Prognosis” of cancer in the present specification is referred to as future status of cancer. It is understood that, for example, the higher the possibility of improvement of cancer, the “better” (or non-poorer) the prognosis would be, whereas the lower the possibility of improvement, the “worse” (or poorer) the prognosis would be. “Prognosis” of cancer reflects malignancy and risk of recurrence of the cancers. It is understood that the higher the malignancy or risk of recurrence of cancer, the “worse” (or poorer) the prognosis would be. For example, poorer prognosis of cancer can mean that the cancer has higher malignancy or higher risk of recurrence, meanwhile better prognosis of cancer can mean that the cancer has lower malignancy or lower risk of recurrence.
“Preservation therapy” of endometrial cancer in the present specification is referred to as a method of cancer therapy that preserves uterus of the patient, and more specifically means fertility preservation therapy, that is, a method for treating cancer so as to preserve fertility of the patient. Examples of the preservation therapy include non-surgical treatments such as chemical therapy, radiation therapy, hormone therapy, and combinations of them. Examples of the hormone therapy include progesterone therapy by, for example, administration of medroxyprogesterone acetate (MPA). The preservation therapy may alternatively be any combination of the aforementioned non-surgical treatments and surgical treatment (such as partial endometrial resection), so long as fertility of the patient can be preserved. The “preservation therapy” in the present specification is more specifically referred to as progesterone therapy by, for example, administration of medroxyprogesterone acetate (MPA), or a combination of the progesterone therapy and surgical treatment that can preserve fertility of the patient.
“CpG site” in the present specification means a site where cytosine (C) and guanine (G) are linked by a phosphodiester bond (p) in DNA. A region where the CpG sites appear with high frequency is referred to as CpG island. The CpG island is often found at a position close to the coding region of gene, for example, in the promoter region, so that the CpG site of gene is often found in the CpG island that resides closer to the coding region of gene, or in the promoter region of gene. “CpG site of (a certain) gene” in the present specification, when not specifically defined, preferably means a CpG site contained in the CpG island that resides closer to the coding region of such gene, and more preferably means a CpG site that resides in the promoter region of such gene.
“DNA methylation” in the present specification means a status where the carbon atom at the 5-position of cytosine in DNA is methylated. “DNA methylation level” at a certain CpG site in the present specification means ratio of methylation of DNA at the CpG site. Highness and lowness of the DNA methylation level in the present specification respectively mean highness and lowness of the ratio of methylation of DNA.
One aspect of the present invention relates to a method for determining prognosis of endometrial cancer. An embodiment of this aspect relates to a method for determining prognosis of endometrial cancer, the method includes:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue containing the cell of a subject; and
determining prognosis of endometrial cancer of the subject, on the basis of the detected DNA methylation level. Another embodiment of this aspect relates to a method for detecting a cell or tissue derived from an endometrial cancer patient with poor prognosis, the method includes:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue containing the cell of a subject; and
detecting a cell or tissue derived from the endometrial cancer patient with poor prognosis, on the basis of the detected DNA methylation level. Examples of the subject in this aspect include subjects in need of determination of prognosis of endometrial cancer, such as endometrial cancer patients including those before treatment, during treatment or after treatment of endometrial cancer. The endometrial cancer patient is preferably a juvenile endometrial cancer patient. Preferred example of the subject includes patients who currently, or wish to, undergo preservation therapy of endometrial cancer, and more preferred example includes juvenile endometrial cancer patients currently, or wish to, undergo fertility preservation therapy.
Another aspect of the present invention relates to a method for determining compatibility of an endometrial cancer patient to a preservation therapy. An embodiment of this aspect relates to a method for determining compatibility of an endometrial cancer patient to a preservation therapy, the method includes:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue containing the cell of an endometrial cancer patient; and
determining compatibility of the endometrial cancer patient to the preservation therapy, on the basis of the detected DNA methylation level. Another embodiment of this aspect relates to a method for detecting a cell or tissue derived from an endometrial cancer patient compatible to a preservation therapy, the method includes:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue containing the cell of an endometrial cancer patient; and
detecting a cell or tissue derived from the endometrial cancer patient compatible to the preservation therapy, on the basis of the detected DNA methylation level. Examples of the endometrial cancer patient in this aspect include patients in need of determination of compatibility to the preservation therapy. Preferred example of the endometrial cancer patient includes patients who currently, or wish to, undergo preservation therapy of endometrial cancer, and more preferred example includes juvenile endometrial cancer patients who currently, or wish to, undergo fertility preservation therapy.
Still another aspect of the present invention relates to a method for determining risk of endometrial cancer. An embodiment of this aspect relates to a method for determining risk of endometrial cancer in a subject, the method includes:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cell or tissue containing the cell of a subject; and
determining risk of endometrial cancer of the subject, on the basis of the detected DNA methylation level. Another embodiment of this aspect relates to a method for determining malignant transformation risk of endometrium, the method includes:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cell or tissue containing the cell of a subject; and
determining malignant transformation risk of endometrium of the subject, on the basis of the detected DNA methylation level. Examples of the subject in this aspect include subjects in need of determination of risk of endometrial cancer, such as medical examinees and suspected patients of endometrial cancer.
Examples of the genomic DNA derived from an endometrial cell, endometrial cancer cell, or tissue containing them, used in the method of the present invention include genomic DNA prepared from endometrial cell, endometrial cancer cells, or tissue containing the cell of the subject. Examples of the endometrial cell, endometrial cancer cell or tissue containing the cell include a fresh endometrial cell, endometrial cancer cell or tissue containing the cell, which are sampled by surgery or biopsy; a frozen endometrial cell, frozen endometrial cancer cell or frozen tissue containing the cell, which are frozen after sampled; and an endometrial cell, endometrial cancer cell or tissue containing the cell, which are formalin-fixed and embedded in paraffin after sampled. Among them, a frozen endometrial cell, frozen endometrial cancer cell or tissue containing the cell are preferred, from the viewpoint of suppressing decomposition of the genomic DNA in the cell or the tissue, and of detecting the DNA methylation level more efficiently.
The technique for preparing a sample DNA from the tissue or the cell may suitably be selected from among known methods, without special limitation. Examples of known methods for preparing DNA are exemplified by phenol-chloroform method, and DNA extraction methods with use of commercially available DNA extraction kit such as QIAamp DNA Mini kit (from Qiagen), Clean Columns (from Nextec Inc.), AquaPure (from Bio-Rad Laboratories, Inc.), ZR Plant/Seed DNA Kit (from Zymo Research), prepGEM (from ZyGEM Co., Ltd.), and BuccalQuick (from TrimGen Corp.).
The prepared genomic DNA is preferably treated with bisulfite. The method for treating DNA with bisulfite may suitably be selected from among known methods, without special limitation. Examples of known methods for the bisulfite treatment include methods with use of commercially available kit such as EZ DNA Methylation-Gold™ kit (from Zymo Research), EpiTect Bisulfite Kit (48) (from Qiagen), MethylEasy (from Human Genetic Signatures Pty), Cells-to-CpG Bisulfite Conversion Kit (from Applied Biosystems), and CpGenome Turbo Bisulfite Modification Kit (from MERCK MILLIPORE).
The bisulfite-treated DNA is further preferably amplified. The method of amplification is preferably PCR, although not specifically limited. The method and condition for amplification may suitably be selected from known methods and conditions, depending on sequence, length and quantity of DNA to be amplified.
As detailed later in Examples, the present inventors found that the DNA methylation level at the CpG sites listed in Tables 1 to 3 are different between a patient group with high malignancy of endometrial cancer, and a patient group with low malignancy of endometrial cancer. In particular, the DNA methylation level at the CpG sites listed in Table 1 made it possible, in Examples descried later, to discriminate the patients with high malignancy and the patients with low malignancy, with 100% sensitivity and specificity. The DNA methylation level at the CpG sites listed in Tables 1 to 3 reflect progression (malignancy) of endometrial cancer, and can therefore be used as a marker that represents prognosis (including malignancy and risk of recurrence) and risk of endometrial cancer.
Hence, examples of the target CpG sites for which the DNA methylation level is detected in the method of the present invention include CpG sites located at or near the chromosomal positions listed in Tables 1 to 3. The method of the present invention may therefore only detect the DNA methylation level for at least one CpG site selected from the group consisting of the CpG sites located at or near the chromosomal positions listed in Tables 1 to 3.
In the present specification, the chromosomal positions of the CpG sites are denoted, on the basis of positions on the NCBI Database Genome Reference Consortium Human Build (GRCh37), which is a reference human genomic sequence. In the present specification, gene names are based on those registered in the NCBI database ([www.ncbi.nlm.nih.gov/gene]).
“Near” the chromosomal position in the present specification means a region ranges from 500-bases upstream (5′-side of DNA) to 500-bases downstream (3′-side of DNA), preferably from 200-bases upstream to 200-bases downstream, more preferably 100-bases upstream to 100-bases downstream, and even more preferably 60-bases upstream to 60-bases downstream on both sides of such chromosomal position.
Examples of the CpG sites located at or near the chromosomal positions listed in Tables 1, 2 and 3 respectively include CpG sites contained in the DNA regions listed in Tables 4, 5 and 6.
In other words, examples of the target CpG sites for which the DNA methylation level is detected include CpG sites contained in the DNA regions consisting of any nucleotide sequences represented by SEQ ID NOs 1 to 68 or complementary sequences thereof.
In the method of the present invention, it suffices to detect the DNA methylation level for at least one CpG site from among the aforementioned target CpG sites. For example in the method of the present invention, it suffices to detect the DNA methylation level for at least one CpG site selected from the group consisting of the CpG sites contained in the DNA regions listed in Tables 4, 5 and 6. In the present specification, it alternatively suffices to detect the DNA methylation level for at least one CpG site selected from the group consisting of CpG sites contained in the DNA regions consisting of nucleotide sequences represented by SEQ ID NOs 1 to 68 or complementary sequences thereof.
The target CpG sites used in the method of the present invention is preferably at least one CpG site selected from the group consisting of CpG sites located at chromosome 10, position 106,400,259; chromosome 8, position 56,852,290; chromosome 14, position 60,973,823; chromosome 6, position 28,226,980; chromosome 1, position 62,660,624; chromosome 6, position 10,390,919; chromosome 8, position 132,321,917; chromosome 11, position 5,346,249; chromosome 21, position 31,972,506; chromosome 2, position 1,928,480; and chromosome 1, position 248,366,399, and CpG sites located near the positions.
In a preferred embodiment, the target CpG site used in the method of the present invention is at least one CpG site selected from the group consisting of:
CpG site contained in the region of chromosome 10, from position 106,400,199 to position 106,400,320;
CpG site contained in the region of chromosome 8, position 56,852,230 to position 56,852,351;
CpG site contained in the region of chromosome 14, from position 60,973,763 to position 60,973,884;
CpG site contained in the region of chromosome 6, from position 28,226,920 to position 28,227,041;
CpG site contained in the region of chromosome 1, from position 62,660,564 to position 62,660,685;
CpG site contained in the region of chromosome 6, from position 10,390,859 to position 10,390,980;
CpG site contained in the region of chromosome 8, from position 132,321,857 to position 132,321,978;
CpG site contained in the region of chromosome 11, from position 5,346,189 to position 5,346,310;
CpG site contained in the region of chromosome 21, from position 31,972,446 to position 31,972,567;
CpG site contained in the region of chromosome 2, from position 1,928,420 to position 1,928,541; and
CpG site contained in the region of chromosome 1, from position 248,366,339 to position 248,366,460.
In a preferred embodiment, the target CpG site used in the method of the present invention is at least one CpG site selected from the group consisting of CpG sites contained in the DNA regions consisting of nucleotide sequences represented by SEQ ID NOs 1 to 11 or complementary sequences thereof.
In a more preferred embodiment, the target CpG sites for which the DNA methylation level is detected in the method of the present invention is preferably at least one CpG site selected from the group consisting of CpG sites located at chromosome 10, position 106,400,259; chromosome 8, position 56,852,290; chromosome 14, position 60,973,823; chromosome 6, position 28,226,980; chromosome 1, position 62,660,624; chromosome 6, position 10,390,919; chromosome 8, position 132,321,917; chromosome 11, position 5,346,249; chromosome 21, position 31,972,506; chromosome 2, position 1,928,480; and chromosome 1, position 248,366,399.
The aforementioned CpG sites may be combined for use as the target, from the viewpoint of improving sensitivity or specificity in detection of the DNA methylation level. Examples of the combination include a combination of any one of CpG sites listed in Table 1 with a CpG site located near them; a combination of any two or more of the CpG sites listed in Table 1; a combination of all CpG sites listed in Table 1; and a combination of any one or more CpG sites listed in Table 1 with any one or more CpG sites listed in Table 2 or 3. Among them, a combination of any one of CpG sites listed in Table 1 with a CpG site near them; a combination of any two or more of the CpG sites listed in Table 1; and a combination of all CpG sites listed in Table 1 are preferred.
Hence in a case where the bisulfite-treated DNA is amplified by, for example, PCR in the method of the present invention as described above, the DNA region containing the target CpG site is amplified. Preferably, the DNA region containing the target CpG site is amplified.
More preferably, in a case where the bisulfite-treated DNA is amplified by, for example, PCR in the method of the present invention, a part of, or the entirety of any of the DNA regions listed in Tables 4 to 6 is amplified. Even more preferably, a part of, or the entirety of any of the DNA regions listed in Table 4 is amplified. Size of the DNA region to be amplified is not specifically limited, so long as the target CpG site is contained therein.
In the method of the present invention, a technique for detection of the DNA methylation level at the CpG site may only be a technique capable of quantifying the DNA methylation level at the given CpG site, and may suitably be selected from known techniques. Examples of such known techniques include first to eight techniques enumerated below.
The first technique is a method of quantifying the DNA methylation at the CpG site by using a single base extension reaction with a probe prepared to have a base complementary to methylated cytosine or non-methylated cytosine at the 3′-terminal. The first technique is, for example, based on the principle below. First, the genomic DNA is subjected to the bisulfite treatment. The bisulfite treatment converts the non-methylated cytosine residue into uracil, whereas the methylated cytosine residue remains unconverted (see Clark S J, et al., Nucleic Acids Res., 1994, vol. 22, p. 2990-7). Next, whole genome amplification is conducted using the thus bisulfite-treated genomic DNA as a template, the product is then fragmented by using an enzyme (typically fragmented into approximately 300 to 600 bp), and allowed to dissociate into a single strand.
In the first technique, a probe which is hybridizable with the genomic DNA converted by the bisulfite treatment, and in which the base at the 3′-terminal is a base complementary to cytosine in the CpG site is prepared. That is, when such CpG site is methylated, the 3′-terminal base of the probe is guanine, whereas when such CpG site remains unmethylated, the 3′ terminal base of the probe is adenine.
Such two kinds of probes different from each other only in the 3′-terminal base complementary to the CpG site, are then hybridized with the aforementioned single-strand DNA fragment, and the product is subjected to the single base extension reaction in the presence of a fluorescence-labeled base. As a consequence, in a case where the CpG site in the single-strand fragment is methylated, the probe having guanine as the 3′-terminal base (methylation detecting probe) has the fluorescence-labeled base incorporated by the single base extension reaction, whereas the probe having adenine as the 3′-terminal base (non-methylation detecting probe) does not cause the single base extension reaction due to mismatching of the 3′-terminal base, and does not have the fluorescence-labeled base incorporated therein. On the other hand, in a case where the CpG site in the single-strand fragment is not methylated, the non-methylation detecting probe has the fluorescence-labeled base incorporated therein, whereas the methylation detecting probe does not have the fluorescence-labeled base incorporated therein. The DNA methylation level may therefore be calculated from intensity of fluorescence emitted from the methylation detecting probe and/or the non-methylation detecting probe.
In another aspect, the first technique may employ a probe hybridizable with the genomic DNA converted by the bisulfite treatment, in which the 3′-terminal base is a base complementary to guanine in the CpG site, in place of employing the aforementioned methylation detecting probe or the non-methylation detecting probe. Such probe is then hybridized with the aforementioned single-strand DNA fragment, and the product is subjected to the single base extension reaction in the presence of guanine labeled with a fluorescent substance, and/or adenine labeled with a fluorescent dye different from the fluorescent substance. As a consequence, in a case where the CpG site is methylated, the probe has fluorescence-labeled guanine incorporated therein, whereas in a case where the CpG site is not methylated, the probe has fluorescence-labeled adenine incorporated therein, so that the DNA methylation level can therefore be calculated from intensity of fluorescence emitted from the individual fluorescent substances incorporated into the probes.
Examples of such first technique preferably include bead array method (Infinium (registered trademark) assay, for example).
The second technique is a method of quantifying the methylated DNA by mass spectrometry. The second technique is, for example, based on the principle below. First, the genomic DNA is subjected to the bisulfite treatment. Next, a DNA containing at least one of the aforementioned CpG sites is amplified with a T7 promoter-added primer using the bisulfite-treated genomic DNA as a template. Next, the amplified DNA is transcribed into RNA, and then subjected to a base-specific cleavage reaction with RNase. The cleavage reaction products are then analyzed by using a mass spectrometer for mass spectrometry.
Mass of the product derived from methylated cytosine residue (mass of cytosine) and mass of the product derived from non-methylated cytosine residue (mass of uracil), obtained by the mass spectrometry, are compared to calculate the DNA methylation level at the CpG site.
Preferred examples of such second technique include DNA methylation analysis with a mass spectrometer (MassARRAY (registered trademark), see Jurinke C, et al., Mutat. Res., 2005, 573, p. 83-95, and Patent Literature 2, for example).
MassARRAY (registered trademark) amplifies the bisulfite-treated DNA that contains the CpG site, transcribes it into RNA, and specifically cleaves the product at uracil with an RNAase. This produces RNA fragments having different lengths depending on presence or absence of DNA methylation. The obtained RNA fragments are subjected to mass spectrometry, and thereby the fragments having methylated CpG site and the non-methylated fragments are separately detected according to difference of molecular weight. The primer used for amplifying the DNA containing the CpG site may be designed by using, for example, EpiDesigner (software for designing primer for use in MassARRAY, from SEQUENOM). Mass spectrometry of the RNA fragments employs a MALDI-TOF MAS (for example, MassARRAY Analyzer 4 from SEQUENOM), capable of detecting a mass difference of a single base. The DNA methylation level is calculated from a mass ratio of the RNA fragment derived from methylated DNA and the RNA fragment derived from non-methylated DNA.
The third technique is based on the principle below. First, the genomic DNA is subjected to the bisulfite treatment. Although the non-methylated cytosine residue is converted to uracil by the bisulfite treatment, uracil is represented by thymine in the extension reaction (sequencing reaction) below. Next, a DNA containing at least one of the aforementioned CpG sites is amplified, using the bisulfite-treated genomic DNA as a template. The amplified DNA is then dissociated into single strands. Next, one strand is isolated from the thus dissociated single strand DNAs. The strand is then extended base by base, from the vicinity of a base in the CpG site, during which pyrophosphoric acid produced therein is enzymatically allowed to cause luminescence, and luminescence intensity is measured. Luminescence intensity ascribed to methylated cytosine residues (luminescence intensity of cytosine) and luminescence intensity ascribed to non-methylated cytosine residues (luminescence intensity of thymine) are compared, and the DNA methylation level (%) at the CpG site is then calculated by, for example, using the equation below.
DNA methylation level (%)=luminescence intensity of cytosine×100/(luminescence intensity of cytosine+luminescence intensity of thymine).
The third technique is, for example, Pyrosequencing (registered trademark) (see Anal. Biochem., (2000) 10:103-110).
The fourth technique is, for example, based on the principle below. First, the genomic DNA is subjected to the bisulfite treatment. Next, in a reaction system containing an intercalator that causes fluorescence upon being intercalated into the double strand of DNA, a nucleotide that contains at least one CpG site is amplified using the bisulfite-treated genomic DNA as a template. Next, temperature of the reaction system is changed, and change of fluorescence intensity of the intercalator is detected. A melting curve of the nucleotide containing at least one CpG site is compared with a melting curve of a product amplified by using a methylated or non-methylated control sample as a template, and the DNA methylation level at the CpG site is calculated.
Examples of the fourth technique include methylation-sensitive high resolution melting curve analysis (MS-HRM) (see Wojdacz T K, et al., Nat. Protoc., 2008, 3, p. 1903-8).
The fifth technique is based on the principle below. First, the genomic DNA is subjected to the bisulfite treatment. Next, a primer set that enables amplification when the CpG site is methylated, and a primer set that enables amplification when the CpG site is not methylated are prepared. Next, a nucleotide containing at least one of the aforementioned CpG sites is amplified by using each of these primer sets and the bisulfite-treated genomic DNA as a template. The amount of the thus obtained amplified product, that is, the amount of amplified product specific to the methylated CpG site and the amount of amplified product specific to the non-methylated CpG site are compared, to thereby calculate the DNA methylation level at the CpG site.
In another aspect of the fifth technique, first the genomic DNA is subjected to the bisulfite treatment. Next, an oligonucleotide probe that contains a nucleotide hybridizable when the CpG site is methylated and that is labeled with a reporter fluorescent dye and a quencher fluorescent dye is prepared. Next, an oligonucleotide probe that contains a nucleotide hybridizable when the CpG site is not methylated and that is labeled with a reporter fluorescent dye different from the aforementioned reporter fluorescent dye, and with the quencher fluorescent dye is also prepared. The bisulfite-treated genomic DNA is then hybridized with each of the oligonucleotide probes, and a nucleotide that contains the CpG site is then amplified using, as a template, such genomic DNA hybridized with the oligonucleotide probe. Fluorescence emitted from the reporter fluorescent dye, upon decomposition of the oligonucleotide probe during amplification, is then detected. Intensity of the thus detected fluorescence emitted from the reporter fluorescent dye which is specific to the methylated cytosine CpG site is compared with intensity of fluorescence emitted from the reporter fluorescent dye which is specific to the non-methylated cytosine CpG site, to thereby calculate the DNA methylation level at the CpG site.
Examples of the fifth technique include methylation-specific polymerase chain reaction (MS-PCR) using real-time quantitative PCR, such as MethyLight method using TaqMan probe (registered trademark).
The sixth technique is based on the principle below. First, the genomic DNA is subjected to the bisulfite treatment. Next, a direct sequencing reaction is allowed to proceed using, as a template, a nucleotide that contains the bisulfite-converted CpG site. Fluorescence intensity ascribed to a determined base sequence, that is, fluorescence intensity ascribed to the methylated cytosine residue (fluorescence intensity of cytosine) is then compared with fluorescence intensity ascribed to the non-methylated cytosine residue (luminescence intensity of thymine), to thereby calculate the DNA methylation level at the CpG site.
In another aspect of the sixth technique, first the genomic DNA is subjected to the bisulfite treatment. Next, a nucleotide that contains the bisulfite-treated CpG site is cloned by, for example, a PCR reaction. Base sequences of the thus obtained individual cloned products are then determined, and the number of the cloned products having the base sequence specific to the methylated cytosine CpG site is compared with the number of the cloned products having the base sequence specific to the non-methylated cytosine CpG site, to thereby calculate the DNA methylation level at the CpG site.
Examples of the sixth technique include bisulfite direct sequencing, and bisulfite cloning sequencing (see Kristensen L S, et al., Clin. Chem., 2009, 55, p. 1471-83).
The seventh technique is based on the principle below. First, the genomic DNA is subjected to the bisulfite treatment. Next, a region that contains the CpG site is amplified by PCR using, as a template, a nucleotide that contains the bisulfite-treated CpG site. The amplified DNA fragment is then treated with a restriction enzyme that can recognize a site having different sequences depending on whether the CpG site is methylated or not methylated. Restriction enzyme fragment derived from the methylated CpG site and restriction enzyme fragment derived from the non-methylated CpG site are then fractionated by electrophoresis, and the band density is quantitatively analyzed to thereby calculate the DNA methylation level at the CpG site.
Examples of the seventh technique include combined bisulfite restriction analysis (COBRA).
The eighth technique is a method using ion exchange chromatography. The eighth technique is based on the principle below. First, the genomic DNA is subjected to the bisulfite treatment. The product is then fragmented to obtain a DNA fragment that contains the CpG site. A region containing the CpG site is then amplified by PCR using the obtained DNA fragment as a template. The amplified DNA fragment is then subjected to ion exchange chromatography, to thereby separate DNA having the methylated CpG site and DNA having the non-methylated CpG site.
Chain length of the PCR-amplified product in the eighth technique may suitably be selected in view of factors including shortening of PCR amplification time, shortening of analysis time by ion exchange chromatography, and keeping of separation performance. The chain length of the PCR-amplified product, in case of using a CpG site-rich sample DNA, is preferably 1000 bp or shorter, more preferably 700 bp or shorter, and even more preferably 500 bp or shorter. Meanwhile, the chain length of the PCR-amplified product, in case of using a CpG site-poor sample DNA, is 30 to 40 bp at the shortest, which is the chain length of PCR-amplified product in case of using a primer of approximately 15 mer long at which non-specific hybridization in PCR is avoidable. On the other hand, the primer is preferably designed so as to enrich the CpG site. For example, the content of cytosine at the CpG site preferably accounts for 2% or more, more preferably 5% or more relative to the chain length of the PCR-amplified product.
According to the eighth technique, the non-methylated cytosine residue is converted into uracil during the bisulfite treatment of the genomic DNA, and then converted into thymine by PCR. On the other hand, the methylated cytosine residue remains unchanged even after the bisulfite treatment and PCR. Due to such difference of the bases, a fragment that contains methylated cytosine (methylated fragment) and a non-methylated fragment are detectable as separate peaks with different retention times in ion exchange chromatography. More specifically, the methylated fragment is detectable as a peak whose retention time is shorter than that of the non-methylated fragment. Whether DNA at the CpG site is methylated or not can therefore be determined on the basis of the retention time of the peaks in ion exchange chromatography. In a case where a plurality of CpG sites are contained in DNA to be subjected to ion exchange chromatography, the more the CpG sites are methylated, the shorter the retention time of the peak is. The DNA methylation level at the CpG site can therefore be calculated on the basis of the retention time of the peak. It may alternatively be possible to calculate abundance or abundance ratio of each of the methylated fragment and the non-methylated fragment, on the basis of area or height of the peaks.
Whether the DNA at the CpG site is methylated or not, or, the DNA methylation level at the CpG site is preferably determined by comparing the DNA methylation level at the CpG site with a known sample (control), or by using a calibration curve preliminarily prepared by using samples with known DNA methylation levels. Still alternatively, one can preliminarily determine, by using samples with known DNA methylation levels, a retention time at which the retention time of peak of the methylated fragment having highly methylated CpG site is discriminable from the retention time of peak of the fragment having a low methylation level (also referred to as reference retention time in the present specification). For example, any fragment detected earlier than the reference retention time is determined to be highly-methylated DNA.
Ion exchange chromatography employed in the eighth technique is preferably anion exchange chromatography. Column filler may only be a base particle having a strong cationic group on the surface thereof, and is preferably a base particle having both of strong cationic group and a weak cationic group on the surface thereof, as described in WO 2012/108516. The base particle more preferably includes a coated polymer particle that contains a hydrophobic crosslinked polymer particle and a hydrophilic polymer layer containing the strong cationic group (preferably quaternary ammonium salt) and copolymerized on the surface of the hydrophobic crosslinked polymer particle, and the weak cationic group (preferably tertiary amino group) introduced on the surface of the coated polymer particle. Column temperature during the chromatographic analysis is preferably 30° C. or higher, and lower than 90° C.
The techniques suitably applicable to the “techniques for detecting DNA methylation level” in the present invention have been described, to which the techniques are however not limited. In the aforementioned first to eighth techniques, the genomic DNA prepared from an endometrial cell, endometrial cancer cell or tissue containing the cell are further subjected to the bisulfite treatment as described above. Hence in the method of the present invention, the genomic DNA used for detecting the DNA methylation level at the CpG site is preferably a bisulfite-treated genomic DNA derived from an endometrial cell, endometrial cancer cell, or tissue containing the cell.
According to the method of the present invention, prognosis of endometrial cancer (including malignancy and risk of recurrence), compatibility of a subject to the preservation therapy, or risk of endometrial cancer (malignant transformation risk of endometrium) can be determined on the basis of detected DNA methylation level at the CpG site.
In the determination of prognosis of endometrial cancer of the present invention, whether the prognosis of endometrial cancer of the subject is good or poor; whether or not endometrial cancer of the subject is high malignancy; or whether or not the risk of recurrence of endometrial cancer of the subject is high, is determined. Also, preferably, whether or not the cell or tissue used for detecting the DNA methylation level is derived from an endometrial cancer patient with poor prognosis, or from an endometrial cancer patient with high malignancy or high risk of recurrence is determined.
In the determination of compatibility of the subject to the preservation therapy of the present invention, preferably whether or not the subject is compatible to the preservation therapy of endometrial cancer. Also, preferably, whether or not the cell or tissue used for detecting the DNA methylation level is derived from the patient compatible to the preservation therapy of endometrial cancer is determined.
In the determination of risk of endometrial cancer of the present invention, preferably whether or not the endometrium of the subject has high malignant transformation risk, or whether or not the subject has high risk of endometrial cancer. More preferably, whether or not the endometrium of the subject has high risk of having endometrial cancer in the future, or whether or not the subject has high risk of onset of endometrial cancer in the future is determined. Alternatively, whether or not the cell or tissue used for detecting the DNA methylation level is derived from the subject with high risk of endometrial cancer is determined.
A skilled person in the art may suitably set specific indices (threshold values) for the aforementioned determination, depending on the techniques for detecting the DNA methylation level. Embodiments of determination procedures will be described below.
In a first embodiment for the determination, first, receiver operating characteristic (ROC) analysis is performed on each of the CpG sites for each of the techniques for detecting the DNA methylation level, to determine sensitivity (positive rate) and specificity (negative rate). The DNA methylation level at which the sum of sensitivity and specificity reaches maximum may be set as a cutoff value. The cutoff value may be set on, for example, the basis of Youden's index.
In the first embodiment, for the CpG site where the methylation level is increased with progress of endometrial cancer (for example, CpG sites at or near the chromosomal positions listed in Table 1(A) and Table 2), when the DNA methylation level detected by the method of the present invention is higher than the cutoff value, the DNA methylation level is determined to exceed a diagnostic threshold value, and the subject is then determined to belong to a poor prognosis group of endometrial cancer or belong to a high risk group of endometrial cancer, or not to belong to a compatible group to preservation therapy. In contrast, when the detected methylation level is equal to or below the cutoff value, the subject is then determined not to belong to the poor prognosis group of endometrial cancer, or not to belong to the high risk group of endometrial cancer, or to belong to the compatible group to preservation therapy.
On the other hand, for the CpG site where the methylation level is decreased with progress of endometrial cancer (for example, CpG sites at or near the chromosomal positions listed in Table 1(B) and Table 3), when the DNA methylation level detected by the method of the present invention is lower than the cutoff value, the DNA methylation level is determined to exceed a diagnostic threshold value, and the subject is then determined to belong to the poor prognosis group of endometrial cancer, or to belong to the high risk group of endometrial cancer, or not to belong to the compatible group to preservation therapy. In contrast, when the detected methylation level is equal to or higher than the cutoff value, the subject is then determined not to belong to the poor prognosis group of endometrial cancer, or not to belong to the high risk group of endometrial cancer, or to belong to the compatible group to preservation therapy.
In a second embodiment for the determination, retention time of a peak obtained by ion exchange chromatographic analysis (the eighth technique) on DNA that contains the target CpG site derived from a subject (sample) is compared with retention time of DNA that contains the non-methylated target CpG site (negative control) or DNA that contains the methylated target CpG site (positive control), to thereby determine the methylation level of the CpG site, prognosis of cancer regarding endometrial cancer, risk, or compatibility to the preservation therapy.
In the second embodiment, for the CpG site where the methylation level is increased with progress of endometrial cancer (for example, CpG sites at or near the chromosomal positions listed in Table 1(A) and Table 2), when a peak is detected at a predetermined retention time shorter than that of a peak of the negative control from the sample, the DNA methylation level is determined to exceed a diagnostic threshold value, and the subject is then determined to belong to the poor prognosis group of endometrial cancer, or belong to the high risk group of endometrial cancer, or not to belong to the compatible group to preservation therapy. Preferably, when a peak is detected at a retention time equivalent to that of the positive control from the sample, the DNA methylation level is determined to exceed a diagnostic threshold value, and the subject is then determined to belong to the poor prognosis group of endometrial cancer, or to belong to the high risk group of endometrial cancer, or not to belong to the compatible group to preservation therapy. In contrast, when the DNA methylation level does not exceed the diagnostic threshold value, the subject is then determined not to belong to the poor prognosis group of endometrial cancer, or not to belong to the high risk group of endometrial cancer, or to belong to the compatible group to preservation therapy.
On the other hand, for the CpG site where the methylation level is decreased with progress of endometrial cancer (for example, CpG sites at or near the chromosomal positions listed in Table 1(B) and Table 3), when a peak is detected at a predetermined retention time longer than that of a peak of the positive control from the sample, the DNA methylation level is determined to exceed a diagnostic threshold value, and the subject is then determined to belong to the poor prognosis group of endometrial cancer, or to belong to the high risk group of endometrial cancer, or not to belong to the compatible group for preservation therapy. Alternatively, when a peak is detected at a retention time equivalent to that of the negative control from the sample, the DNA methylation level is determined to exceed a diagnostic threshold value, and the subject is then determined to belong to the poor prognosis group of endometrial cancer, or to belong to a high risk group of endometrial cancer, or not to belong to a compatible group to preservation therapy. In contrast, when the DNA methylation level does not exceed the diagnostic threshold value, the subject is then determined not to belong to the poor prognosis group of endometrial cancer, or not to belong to the high risk group of endometrial cancer, or to belong to the compatible group to preservation therapy.
In a case where the methylation level is detected at a plurality of CpG sites in the first and second embodiments, the number or ratio of the CpG sites at which the DNA methylation level exceeds the diagnostic threshold value may be used as an index for determination. For example, the subject may be determined to belong to the poor prognosis group of endometrial cancer, or to belong to the high risk group of endometrial cancer, or not to belong to the compatible group for preservation therapy, when the methylation level exceeds the diagnostic threshold value at all of the examined CpG sites. Alternatively, the subject may be determined to belong to the poor prognosis group of endometrial cancer, or to belong to the high risk group of endometrial cancer, or not to belong to the compatible group to preservation therapy, when the methylation level exceeds the diagnostic threshold value at a certain percentage or more of the examined CpG sites. Still alternatively, the subject may be determined to belong to the poor prognosis group of endometrial cancer, or to belong to the high risk group of endometrial cancer, or not to belong to the compatible group to preservation therapy, when the methylation level exceeds the diagnostic threshold value at a certain number of the examined CpG sites. In contrast, any subject not satisfying these criteria can be determined not to belong to the poor prognosis group of endometrial cancer, or not to belong to the high risk group of endometrial cancer, or to belong to the compatible group to preservation therapy.
As described above, the present invention can determine risk and prognosis of endometrial cancer. When early detection of the patients of high risk group regarding onset of endometrial cancer is enabled by the method of the present invention, it can provide preventive intervention to avoid onset of endometrial cancer, and can provide early treatment to improve vital prognosis of the patient. In particular, discrimination of endometrial cancer with low malignancy or small possibility of recurrence by the method of the present invention makes it possible to predict effectiveness of the preservation therapy to the patient. Prediction of effectiveness of the preservation therapy is especially beneficial to the patient of juvenile endometrial cancer who may become pregnant in the future. Although fertility preservation therapy such as MPA therapy is an important choice of therapy for a patient who wishes to become pregnant, it is effective only for early cancer patients, and suffers from higher risk of recurrence as compared with surgery. Hence, the preservation therapy, when applied, needs to be closely examined regarding compatibility of the patient to the therapy. The present invention can provide the patient who wishes the preservation therapy, with information on effectiveness of the preservation therapy to such patient, thereby contributing to improve QOL and vital prognosis of the patient.
The present invention therefore also relates to preventive intervention to the subject classified into the high risk group of endometrial cancer, using the method of risk determination of the present invention. This aspect of the present invention enables prevention, early diagnosis and early treatment of endometrial cancer in the subject of the high risk group.
The present invention also provides a therapeutic method for endometrial cancer, including treating the subject determined to have endometrial cancer by the method of determining risk of the present invention. The present invention still also provides a therapeutic method for endometrial cancer, including treating the subject classified into the poor prognosis group of endometrial cancer by the method of determining prognosis of the present invention. These aspects of the present invention enable to provide the subject having endometrial cancer, with suitable therapy further earlier. Examples of means for therapy include, but not limited to, surgery, chemical therapy, radiation therapy and hormone therapy such as MPA therapy.
In still further aspect, the present invention relates to provision of data for use in determination of the aforementioned risk and prognosis of endometrial cancer, or determination of compatibility of the patient to the preservation therapy. An embodiment of this aspect relates to a method for acquiring data for use in detecting a cell or tissue derived from an endometrial cancer patient with poor prognosis, or for determining prognosis of endometrial cancer, the method includes:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue containing the cell of a subject; and
acquiring data for use in detecting a cell or tissue derived from the endometrial cancer patient with poor prognosis, or data for use in determining prognosis of endometrial cancer of the subject, on the basis of the detected DNA methylation level. Another embodiment of this aspect relates to a method for acquiring data for use in detecting a cell or tissue derived from an endometrial cancer patient compatible to a preservation therapy, or for use in determining compatibility of an endometrial cancer patient to the preservation therapy, the method includes:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cancer cell or tissue containing the cell of the endometrial cancer patient; and
acquiring data for use in detecting a cell or tissue derived from the endometrial cancer patient compatible to the preservation therapy, or data for use in determining compatibility of the endometrial cancer patient to the preservation therapy, on the basis of the detected DNA methylation level. A still another embodiment of this aspect relates to a method for acquiring data for use in determining malignant transformation risk of endometrium, or for use in determining risk of endometrial cancer, the method includes:
detecting DNA methylation level at a target CpG site in a genomic DNA derived from an endometrial cell or tissue containing the cell of a subject; and
acquiring data for use in determining malignant transformation risk of endometrium, or data for use in determining risk of endometrial cancer of the subject, on the basis of the detected DNA methylation level. Examples of the subject, procedures for preparing the genomic DNA and for detecting the DNA methylation level, and the target CpG sites at which the methylation level needs to be detected are same as those described above. As descried previously, the DNA methylation level at the CpG sites listed in Tables 1 to 3 can be used as a marker that represents prognosis and risk of endometrial cancer or compatibility to the preservation therapy.
The method for acquiring data of the present invention is a method that does not include diagnoses by any doctor or other persons on prognosis and risk of endometrial cancer or compatibility to the preservation therapy. For example, the method is conducted at, for example, research laboratories, clinical inspection laboratories and so forth, in order to acquire data necessary for diagnoses given by doctors or other persons.
The present invention also provides a primer or a probe for use in determining prognosis of endometrial cancer (including malignancy and risk of recurrence), determining compatibility of the subject to the preservation therapy of endometrial cancer, or determining risk of endometrial cancer (malignant transformation risk of endometrium). The primer or the probe has at least 12 base long, and is hybridizable with a target CpG site which has been treated with bisulfite.
An example of the primer or the probe of the present invention is a primer or a probe hybridizable with a CpG site contained in any of the DNA regions listed in Tables 4 to 6 (for example, a DNA region consisting of any of the nucleotide sequences represented by SEQ ID NOs 1 to 68, or a complementary sequence thereof). The primer or the probe is preferably is a primer or a probe hybridizable with a CpG site contained in any of the DNA regions listed in Table 4 (for example, a DNA region consisting of any of the nucleotide sequences represented by SEQ ID NOs 1 to 11, or a complementary sequence thereof).
A preferred example of the primer or the probe of the present invention is a primer or a probe consisting of any of the nucleotide sequences represented by SEQ ID NOs 1 to 68, or a complementary sequence thereof. Another preferred example of the primer or the probe of the present invention is a primer or a probe that has 95% or larger identity to any of the nucleotide sequences represented by SEQ ID NOs 1 to 68, or to a complementary sequence thereof, and can hybridize with the same CpG site as the CpG site with which the sequence can hybridize. Also, a fragment of the primer or the probe hybridizable with the same CpG site as the CpG site with which the primer or the probe can hybridize, can be used as the primer or the probe of the present invention.
More preferred example of the primer or the probe of the present invention is a primer or a probe consisting of any of the nucleotide sequences represented by SEQ ID NOs 1 to 11, or a complementary sequence thereof. Another further preferred example of the primer or the probe of the present invention is a primer or a probe that has 95% or larger identity to any of the nucleotide sequences represented by SEQ ID NOs 1 to 11, or to a complementary sequence thereof, and can hybridize with the same CpG site as the CpG site with which the sequence can hybridize. Also, a fragment of the primer or the probe hybridizable with the same CpG site as the CpG site with which the primer or the probe can hybridize, can be used as the primer or the probe of the present invention.
Another preferred example of the primer or the probe of the present invention is a primer or a probe that is hybridizable with a DNA fragment containing the target CpG site which has been treated with bisulfite (for example, a fragment that contains any one of nucleotide sequences represented by SEQ ID NOs 1 to 68, or a complementary strand thereof), and is constructed to have, at the 3′-terminal, a base complementary to methylated cytosine or non-methylated cytosine (for example, the primer or the probe applicable to the aforementioned first technique).
Another preferred example of the primer or the probe of the present invention is a primer (sequencing primer) that can cause base-by-base extension reaction from the vicinity of a base in the target CpG site which has been treated with bisulfite (for example, the primer or the probe applicable to the aforementioned third technique). Another preferred example is a probe hybridizable with a nucleotide that contains the target CpG site which has been treated with bisulfite (for example, the primer or the probe applicable to the aforementioned fourth technique).
Another preferred example of the primer or the probe of the present invention is a primer set that can specifically amplify a region that contains the methylated or non-methylated target CpG site, in a DNA fragment containing the target CpG site (for example, a fragment that contains any one of nucleotide sequences represented by SEQ ID NOs 1 to 68, or a complementary strand thereof) which has been treated with bisulfite (for example, the primer set applicable to PCR amplification in the aforementioned fifth technique or the eighth technique).
The primer or the probe of the present invention may only be at least 12 base long, preferably at least 15 base long, more preferably at least 20 base long, and even more preferably 15 to 200 base long. In case of the probe, it is preferably 100 to 200 base long, and more preferably 100 to 150 base long. In case of the PCR primer, it is preferably 12 to 60 base long, and more preferably 15 to 40 base long. The primer or the probe of the present invention may be labeled (fluorescent-labeled, for example). The primer or the probe of the present invention is preferably a primer or a probe applicable to any one of the aforementioned first to eighth techniques.
The present invention also provides a kit for use in determining prognosis of endometrial cancer, determining compatibility of the subject to the preservation therapy of endometrial cancer, or determining risk of endometrial cancer, which contains the primer or the probe of the present invention. The kit of the present invention is preferably used for determination of prognosis of endometrial cancer, determination of compatibility of the subject to the preservation therapy of endometrial cancer, determination of risk of endometrial cancer, or acquisition of data for use in determination of these events, according to any one of the aforementioned first to eighth techniques.
The kit of the present invention may contain components other than the primer or the probe of the present invention. Examples of such components include, but not limited to, reagents necessary for the bisulfite treatment (for example, a sodium bisulfite solution, etc.); reagents necessary for the PCR reaction (for example, deoxyribonucleotide, heat-resistant DNA polymerase, etc.); reagents necessary for Infinium (registered trademark) assay (for example, nucleotide labeled with fluorescent substance); reagents necessary for MassARRAY (registered trademark) (for example, RNase for use in base-specific cleavage); reagents necessary for pyrosequencing (for example, ATP sulfurylase for use in detecting pyrophosphoric acid, adenosine-5′-phosphosulfate, luciferase, luciferin, streptavidin for separating single-strand DNA, etc.); reagents necessary for MS-HRM (for example, intercalator that causes fluorescence when intercalated in double-strand DNA, etc.); and reagents necessary for detecting the label (for example, substrate and enzyme, positive control and negative control samples, buffer for use in dilution or washing of samples (tissue-derived genomic DNA, etc.), etc.). The kit may include the user's manual.
The present invention will be detailed below referring to Examples, to which the present invention is not limited.
The Example was conducted with the approval of the Ethics Committee of Keio University Hospital, in compliance with the Declaration of Helsinki. The tissue samples were obtained from the patients who underwent surgery at Keio University Hospital. Written informed consent was obtained from all patients.
Endometrial cancer tissue samples (n=74) were obtained from group (E) of endometrial cancer patients with endometrioid cancer (aged 23 to 77). Endometrial tissue samples (n=31) were obtained from group (C) of patients without endometrial cancer (aged 33 to 55). In group (E) of the endometrial cancer patients, 34 patients aged 40 or under were classified into juvenile endometrial cancer patient group (YE), and 40 patients aged over 40 years were classified into senile endometrial cancer patient group (OE).
Histological diagnosis and grade diagnosis of cancer for group (E) were conducted according to WHO classification (2003) and TNM classification. Clinical stage was diagnosed according to FIGO Staging. Recurrence of cancer was diagnosed by a clinician on the basis of medical examination and image diagnosis.
Clinicopathological factors for group (E) are listed in Table V.
Sampled tissues were freeze-preserved. Each of the obtained fresh frozen tissue samples was treated with phenol-chloroform, and then dialyzed to extract a genomic DNA. Five hundred nanograms of the extracted DNA was then subjected to the bisulfite treatment, by using EZ DNA Methylation-Gold™ kit (from Zymo Research).
DNA methylation status at 866,895 CpG sites was analyzed by using Infinium (registered trademark) MethylationEPIC BeadChip (from Illumina, Inc.), at a resolution of 1 CpG site. According to a specification available from Illumina, Inc., the seller, objects to be analyzed by MethylationEPIC BeadChip include promoter region, 5′ untranslated region, first exon, gene body and 3′ untranslated region, and covers 99% of RefSeq genes and 96% of CpG islands.
The bisulfite-treated DNA was subjected to whole genome amplification, by using Infinium (registered trademark) assay kit (from Illumina, Inc.). The amplified DNA fragment was hybridized with a probe on the chip, and the hybridized DNA was then subjected to the single base extension reaction so as to incorporate a fluorescent-labeled base therein. In this way, each of the methylation detecting probe hybridized with the DNA fragment containing the methylated CpG and the non-methylation detecting probe hybridized with a DNA fragment containing the non-methylated CpG was fluorescent-labeled. Next, fluorescent signal was measured by using iScan Reader (from Illumina, Inc.), according to the manufacturer's protocol. The obtained data was analyzed by using GenomeStudio methylation software (from Illumina, Inc.). For each CpG site, a relative ratio of signal from the methylation detecting probe, to the total of signals from the methylation detecting probe and the non-methylation detecting probe was calculated. That is, the methylation level obtained from each CpG site was represented by so-called 13 value (range: 0.00 to 1.00).
The obtained data of methylation level was subjected to Welch's t test and Bonferroni correction, to thereby detect the CpG sites that demonstrate significant difference of methylation level between group (C) and group (E) (p<0.01, and |group E average−group C average|≥0.25). As a consequence, 63,033 CpG sites, demonstrating abnormal methylation in group (E) as compared with group (C), were identified.
The juvenile endometrial cancer patient group (YE) was subjected to Infinium (registered trademark) assay according to the same procedures as in Example 1, to thereby detect the CpG sites where the DNA methylation level changes with progress of cancer. As a consequence, 40,589 CpG sites, demonstrating abnormal methylation in group (YE) as compared with group (C), were identified.
Hierarchical clustering (Euclidean distance, Ward's method, Canberra distance, complete linkage method) was carried for 63,033 CpG sites found in Example 1 on the basis of the DNA methylation level, to thereby classify group (E) into cluster A (group (E-A), n=58) and cluster B (group (E-B), n=16) (
Hierarchical clustering was carried according to the same procedures as in Example 3 on the basis of the DNA methylation level, for 40,589 CpG sites found in Example 2, to thereby classify group (YE) into cluster A (group (YE-A), n=22) and cluster B (group (YE-B), n=12) (
A marker for discriminating high-malignancy group (YE-A) and low-malignancy group (YE-B) was explored. One hundred CpG sites, having the largest differences of the DNA methylation level between group (YE-A) and group (YE-B), were subjected to ROC analysis. ROC curve was drawn for the methylation level at each site, by plotting sensitivity versus specificity regarding discrimination between group (YE-A) and group (YE-B), and the area under the curve (AUC) was calculated.
From results of the ROC analysis, 68 CpG sites with an AUC of 0.95 or larger were found. Of these, 31 CpG sites were found to show increased methylation level in group (YE-A), whereas 37 CpG sites were found to show increased methylation level in group (YE-B) (Tables 10 and 11). Of such 68 CpG sites, 11 CpG sites were found to have an AUC of unity (100% sensitivity and specificity). Of 11 CpG sites, six sites were found to show increased methylation level in group (YE-A), whereas five CpG sites were found to show increased methylation level in group (YE-B). The methylation level at these 68 CpG sites was suggested to be useful as a marker that indicates risk and prognosis of juvenile endometrial cancer, and in particular to discriminate low malignancy (that is, non-poor prognosis) group. Since the patients with the low malignancy of juvenile endometrial cancer are expectable subjects for the preservation therapy, so that the methylation level at these CpG sites is also beneficial as a marker for discriminating endometrial cancer patients compatible to the preservation therapy.
For each of eleven CpG sites identified in Example 5 to have an AUC of unity, the methylation level at which the sum of sensitivity and specificity becomes maximum (approaching closest to the upper left corner on the graph of ROC curve) was determined to be a provisional diagnostic threshold value (cutoff value), on the basis of Youden's index. As illustrated in
Moreover, since group (YE-A) and group (YE-B) of juvenile endometrial cancer patients are respectively contained in group (E-A) and group (E-B) of the whole endometrial cancer patients as demonstrated in Example 4, the DNA methylation marker identified in Example 5 was suggested to be usable as a marker that indicates risk or prognosis of cancer, not only for juvenile endometrial cancer patients but also for various types of endometrial cancer patients including senile endometrial cancer patients. Hence, for each of the DNA methylation level at eleven CpG sites identified in Example 5 to have an AUC of unity, an ROC curve was drawn by plotting sensitivity versus specificity regarding discrimination between high-malignancy group (E-A) and low-malignancy group (E-B), and the area under the curve (AUC) was calculated. Results are summarized in Table 12. Eleven CpG sites were found to have an AUC of approximately 0.94 to 0.99 or above, and half or more than half of them showed a specificity of 100°. Hence, these CpG sites were demonstrated to be useful as a marker that indicates risk or prognosis of cancer, for various types of endometrial cancer patients including juvenile endometrial cancer patients and senile endometrial cancer patients.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2018-228276 | Dec 2018 | JP | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/JP2019/047656 | 12/5/2019 | WO | 00 |
