Composition for detecting cervical cancer and application thereof

Abstract

The invention provides a composition for detecting early cervical cancer and application thereof, the composition comprises nucleic acid for detecting the methylation state of a target gene, and the target gene is one or more than two of a JAM3 gene, an EPHA7 gene and an ST6GALNAC5 gene. The invention also provides a kit comprising the composition, and application of the composition in preparation of the kit for in-vitro detection of early cervical cancer.

Description

Technical Field

[0001] The present application belongs to the field of molecular biology and relates to gene detection, and specifically to a composition for detecting cervical cancer and its use. Background Art

[0002] Since most cervical cancers are caused by HPV infection, of which HPV 16 accounts for about 50% and HPV 18 accounts for about 20%, HPV testing is often used as a means of cervical cancer screening. However, HPV testing has the disadvantage of insufficient specificity, and persistent positive results can cause panic in patients, leading to a surge in the number of colposcopy examinations in hospitals and even over-medicalization.

[0003] The occurrence of cervical cancer can be effectively controlled by examining and treating precancerous lesions. In the process of cervical intraepithelial neoplasia (CIN) developing into cervical cancer, it is accompanied by abnormal expression of specific gene methylation. Detecting the degree of gene methylation can be used as an important indicator of cervical cancer. When detecting transformed lesions (partial C1N2 and CIN3) through gene methylation, the risk of cancer progression can be known, prompting doctors whether to immediately intervene in treatment or maintain observation and tracking. Therefore, DNA methylation testing may help with early detection of cancer, risk stratification, and formulation of treatment plans.

[0004] Currently, the commonly used methods for cervical cancer detection are cervical / vaginal cytology smear examination or HPV testing. The TCT test used in the former is more dependent on the experience of the cytopathologist and is affected by the patient's personal physiological condition and the sampling location, which may cause certain difficulties in interpreting the results. In addition, some special types of cervical cancer may have false negatives. The latter HPV test is not specific enough, and persistent positivity will cause panic in patients, leading to a surge in the number of colposcopy examinations in hospitals and even over-medicalization.

[0005] The purpose of the present invention is to provide a new type of biomolecular marker with great diagnostic value for early cervical cancer, and a corresponding early screening method. Summary of the invention

[0006] Based on the problems existing in the existing cervical cancer detection, the purpose of the present application is to provide a composition for detecting cervical cancer and its use.

[0007] The specific technical solutions of this application are as follows:

[0008] 1. A composition for in vitro detection of early cervical cancer, comprising:

[0009] Nucleic acid used to detect the methylation status of the target gene,

[0010] Wherein, the methylation state of the target gene is characterized by the methylation of the target sequence of the target gene,

[0011] Wherein, the target gene is one or more of the JAM3 gene, the EPHA7 gene and the ST6GALNAC5 gene.

[0012] 2. The composition according to item 1, wherein the target gene is JAM3 gene, EPHA7 gene and ST6GALNAC5 gene.

[0013] 3. The composition according to item 1, wherein the target sequence of the JAM3 gene is as shown in any one of SEQ ID NOs: 1-12, or includes a sequence shown in any one of SEQ ID NOs: 1-12;

[0014] Preferably, the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 1-4 and any one of SEQ ID NOs: 5-8; or the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 1-4 and any one of SEQ ID NOs: 9-12; or the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 5-8 and any one of SEQ ID NOs: 9-12, or the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 1-4 and any one of SEQ ID NOs: 5-8 and any one of SEQ ID NOs: 9-12.

[0015] 4. The composition according to item 1, wherein the target sequence of the EPHA7 gene is as shown in any one of SEQ ID NOs: 13-24, or includes a sequence shown in any one of SEQ ID NOs: 13-24;

[0016] Preferably, the target sequence of the EPHA7 gene includes the sequence shown in any one of SEQ ID NOs: 13-16 and any one of SEQ ID NOs: 17-20; or the target sequence of the JAM3 gene includes the sequence shown in any one of SEQ ID NOs: 13-16 and any one of SEQ ID NOs: 21-24; or the target sequence of the EPHA7 gene includes the sequence shown in any one of SEQ ID NOs: 17-20 and any one of SEQ ID NOs: 21-24, or the target sequence of the EPHA7 gene includes the sequence shown in any one of SEQ ID NOs: 13-16 and any one of SEQ ID NOs: 17-20 and any one of SEQ ID NOs: 21-24.

[0017] 5. The composition according to item 1, wherein the target sequence of the ST6GALNAC5 gene is as shown in any one of SEQ ID NOs: 25-36, or includes a sequence shown in any one of SEQ ID NOs: 25-36;

[0018] Preferably, the target sequence of the ST6GALNAC5 gene includes a sequence as shown in any one of SEQ ID NOs: 25-28 and any one of SEQ ID NOs: 29-32, or the target sequence of the ST6GALNAC5 gene includes a sequence as shown in any one of SEQ ID NOs: 25-28 and any one of SEQ ID NOs: 33-36, or the target sequence of the VSTM2B gene includes a sequence as shown in any one of SEQ ID NOs: 29-32 and any one of SEQ ID NOs: 33-36, or the target sequence of the ST6GALNAC5 gene includes a sequence as shown in any one of SEQ ID NOs: 25-28 and any one of SEQ ID NOs: 29-32 and any one of SEQ ID NOs: 33-36.

[0019] 6. The composition according to any one of items 1 to 5, wherein the nucleic acid for detecting the methylation status of the target gene comprises:

[0020] The primer is a fragment of at least 9 nucleotides in the target sequence of the target gene, and the fragment contains at least one CpG dinucleotide sequence.

[0021] 7. The composition according to any one of items 1 to 6, wherein the nucleic acid for detecting the methylation status of the target gene comprises:

[0022] A probe, wherein the probe is a fragment of at least 15 nucleotides that hybridizes to the target sequence of the target gene under moderately stringent or stringent conditions,

[0023] The fragment comprises at least one CpG dinucleotide sequence.

[0024] 8. The composition according to any one of items 1 to 7, further comprising:

[0025] A reagent that converts unmethylated cytosine base at position 5 of the target sequence of the target gene into uracil.

[0026] 9. The composition according to any one of items 1 to 8, wherein the nucleic acid for detecting the methylation status of the target gene further comprises:

[0027] Blockers that preferentially bind to target sequences in their unmethylated state.

[0028] 10. The composition according to item 9, wherein,

[0029] The fragment of at least 9 nucleotides is a sequence of SEQ ID NO: 37 and SEQ ID NO: 38, or a sequence of SEQ ID NO: 40 and SEQ ID NO: 41, or a sequence of SEQ ID NO: 43 and SEQ ID NO: 44; or a sequence of SEQ ID NO: 46 and SEQ ID NO: 47, or a sequence of SEQ ID NO: 49 and SEQ ID NO: 50, or a sequence of SEQ ID NO: 52 and SEQ ID NO: 53; or a sequence of SEQ ID NO: 55 and SEQ ID NO: 56, or a sequence of SEQ ID NO: 58 and SEQ ID NO: 59, or a sequence of SEQ ID NO: 61 and SEQ ID NO: 62;

[0030] The fragment of at least 15 nucleotides is a sequence of SEQ ID NO: 39, or a sequence of SEQ ID NO: 42, or a sequence of SEQ ID NO: 45; or a sequence of SEQ ID NO: 48, or a sequence of SEQ ID NO: 51, or a sequence of SEQ ID NO: 54; or a sequence of SEQ ID NO: 57, or a sequence of SEQ ID NO: 60, or a sequence of SEQ ID NO: 63.

[0031] 11. An oligonucleotide for in vitro detection of cervical cancer, comprising:

[0032] A fragment of at least 9 nucleotides of a sequence as shown in any one of SEQ ID NOs: 1-12 or a complementary sequence thereof and comprising at least one CpG dinucleotide sequence; and / or

[0033] A fragment of at least 9 nucleotides of a sequence as shown in any one of SEQ ID NOs: 13-24 or a complementary sequence thereof and comprising at least one CpG dinucleotide sequence; and / or

[0034] A fragment of at least 9 nucleotides of a sequence as shown in any one of SEQ ID NOs: 25-36 or a complementary sequence thereof and comprising at least one CpG dinucleotide sequence.

[0035] 12. The oligonucleotide according to item 11, further comprising:

[0036] A fragment that hybridizes to at least 15 nucleotides of the sequence as shown in any one of SEQ ID NOs: 1-12 or its complementary sequence under moderately stringent or stringent conditions and contains at least one CpG dinucleotide sequence; and / or

[0037] A fragment that hybridizes to at least 15 nucleotides of the sequence as shown in any one of SEQ ID NOs: 13-24 or its complementary sequence under moderately stringent or stringent conditions and comprises at least one CpG dinucleotide sequence; and / or

[0038] A fragment that hybridizes to at least 15 nucleotides of the sequence shown in any one of SEQ ID NOs: 25-36 or its complementary sequence under moderately stringent or stringent conditions and contains at least one CpG dinucleotide sequence.

[0039] 13. The oligonucleotide according to item 11, further comprising:

[0040] Blockers that preferentially bind to target sequences in their unmethylated state.

[0041] 14. An oligonucleotide for in vitro detection of cervical cancer, comprising:

[0042] The sequences of SEQ ID NO:37 and SEQ ID NO:38.

[0043] 15. The oligonucleotide according to item 14, further comprising:

[0044] The sequence of SEQ ID NO:39.

[0045] 16. An oligonucleotide for in vitro detection of cervical cancer, comprising:

[0046] The sequences of SEQ ID NO:40 and SEQ ID NO:41.

[0047] 17. The oligonucleotide according to item 16, further comprising:

[0048] The sequence of SEQ ID NO:42.

[0049] 18. An oligonucleotide for in vitro detection of cervical cancer, comprising:

[0050] Sequences of SEQ ID NO:43 and SEQ ID NO:44.

[0051] 19. The oligonucleotide according to item 18, further comprising:

[0052] The sequence of SEQ ID NO:45.

[0053] 20. An oligonucleotide for in vitro detection of cervical cancer, comprising:

[0054] Sequences of SEQ ID NO:46 and SEQ ID NO:47.

[0055] 21. The oligonucleotide according to item 20, further comprising:

[0056] The sequence of SEQ ID NO:48.

[0057] 22. An oligonucleotide for in vitro detection of cervical cancer, comprising:

[0058] The sequences of SEQ ID NO:49 and SEQ ID NO:50.

[0059] 23. The oligonucleotide according to item 22, further comprising:

[0060] The sequence of SEQ ID NO:51.

[0061] 24. An oligonucleotide for in vitro detection of cervical cancer, comprising:

[0062] Sequences of SEQ ID NO:52 and SEQ ID NO:53.

[0063] 25. The oligonucleotide according to item 24, further comprising:

[0064] The sequence of SEQ ID NO:54.

[0065] 26. An oligonucleotide for in vitro detection of cervical cancer, comprising:

[0066] Sequences of SEQ ID NO:55 and SEQ ID NO:56.

[0067] 27. The oligonucleotide according to item 26, further comprising:

[0068] The sequence of SEQ ID NO:57.

[0069] 28. An oligonucleotide for in vitro detection of cervical cancer, comprising:

[0070] Sequences of SEQ ID NO:58 and SEQ ID NO:59.

[0071] 29. The oligonucleotide according to item 28, further comprising:

[0072] The sequence of SEQ ID NO:60.

[0073] 30. An oligonucleotide for in vitro detection of cervical cancer, comprising:

[0074] Sequences of SEQ ID NO:61 and SEQ ID NO:62.

[0075] 31. An oligonucleotide according to item 30, further comprising:

[0076] The sequence of SEQ ID NO:63.

[0077] 32. A kit comprising the composition according to any one of items 1 to 10 or the oligonucleotide according to any one of items 11 to 31.

[0078] 33. A kit according to item 32, further comprising at least one other component selected from the group consisting of:

[0079] Nucleoside triphosphates, DNA polymerase and buffer required for the function of the DNA polymerase.

[0080] 34. A kit according to item 32 or 33, wherein the samples used for detection in the kit include: cell lines, histological sections, tissue biopsy / paraffin-embedded tissue, body fluids, feces, colon effluent, urine, plasma, serum, whole blood, separated blood cells, cells separated from blood, or a combination thereof.

[0081] 35. The kit according to any one of items 32 to 34, further comprising: instructions.

[0082] 36. Use of the composition according to any one of Items 1 to 10 or the oligonucleotide according to any one of Items 11 to 31 in the preparation of a kit for in vitro detection of cervical cancer.

[0083] 37. The use according to item 36, wherein the kit for in vitro detection of cervical cancer detects cervical cancer by a method comprising the following steps:

[0084] 1) separating a DNA sample including a target sequence of a target gene or a fragment thereof from a biological sample to be tested;

[0085] 2) determining the methylation status of the target sequence of the target gene;

[0086] 3) The state of the biological sample is judged by the detection result of the methylation state of the target sequence of the target gene, thereby realizing in vitro detection of cervical cancer.

[0087] 38. The use according to item 37, wherein the method comprises the steps of:

[0088] Extracting genomic DNA from the biological sample to be tested;

[0089] Treat the extracted genomic DNA with a reagent to convert the unmethylated cytosine base at position 5 into uracil or other bases;

[0090] contacting the DNA sample treated with the reagent with a DNA polymerase and a primer of a target sequence of a target gene to perform a DNA polymerization reaction;

[0091] detecting the amplified product with a probe; and

[0092] Based on the presence or absence of the amplification product, the methylation status of at least one CpG dinucleotide of the target sequence of the target gene is determined.

[0093] 39. The use according to item 38, wherein the reagent is a bisulfite reagent.

[0094] 40. Use of JAM3 gene, EPHA7 gene and ST6GALNAC5 gene in preparing a kit for in vitro detection of early cervical cancer.

[0095] 41. The use according to item 40, wherein the target sequence of the JAM3 gene is as shown in any one of SEQ ID NOs: 1-12, or the target sequence of the JAM3 gene comprises a sequence as shown in any one of SEQ ID NOs: 1-12,

[0096] Preferably, the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 1-4 and any one of SEQ ID NOs: 5-8, or the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 1-4 and any one of SEQ ID NOs: 9-12, or the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 5-8 and any one of SEQ ID NOs: 9-12, or the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 1-4 and any one of SEQ ID NOs: 5-8 and any one of SEQ ID NOs: 9-12.

[0097] 42. The use according to item 40, wherein the target sequence of the EPHA7 gene is as shown in any one of SEQ ID NOs: 13-24, and the target sequence of the EPHA7 gene comprises a sequence as shown in any one of SEQ ID NOs: 13-24,

[0098] Preferably, the target sequence of the EPHA7 gene includes a sequence as shown in any one of SEQ ID NOs: 13-16 and any one of SEQ ID NOs: 17-20, or the target sequence of the EPHA7 gene includes a sequence as shown in any one of SEQ ID NOs: 13-16 and any one of SEQ ID NOs: 21-24, or the target sequence of the KCNK12 gene includes a sequence as shown in any one of SEQ ID NOs: 17-20 and any one of SEQ ID NOs: 21-24, or the target sequence of the EPHA7 gene includes a sequence as shown in any one of SEQ ID NOs: 13-16 and any one of SEQ ID NOs: 17-20 and any one of SEQ ID NOs: 21-24.

[0099] 43. The use according to item 40, wherein the target sequence of the ST6GALNAC5 gene is as shown in any one of SEQ ID NOs: 25-36, or the target sequence of the ST6GALNAC5 gene includes a sequence as shown in any one of SEQ ID NOs: 25-36,

[0100] Preferably, the target sequence of the VSTM2B gene includes a sequence as shown in any one of SEQ ID NOs: 25-28 and any one of SEQ ID NOs: 29-32, or the target sequence of the VSTM2B gene includes a sequence as shown in any one of SEQ ID NOs: 25-28 and any one of SEQ ID NOs: 33-36, or the target sequence of the VSTM2B gene includes a sequence as shown in any one of SEQ ID NOs: 29-32 and any one of SEQ ID NOs: 33-36, or the target sequence of the VSTM2B gene includes a sequence as shown in any one of SEQ ID NOs: 25-28 and any one of SEQ ID NOs: 29-32 and any one of SEQ ID NOs: 33-36.

[0101] This application has the following beneficial effects:

[0102] The present application has screened out the JAM3 gene, EPHA7 gene and ST6GALNAC5 gene that can sensitively and specifically detect the cervical cancer related markers, and determined the target sequence of abnormal methylation of the related markers, which can sensitively and specifically detect the methylation state of the gene. The marker can be used for auxiliary diagnosis of high-grade cervical lesions or cervical cancer and HPV positive shunt management, and has high sensitivity and specificity for late transformed CIN2 / 3 and cervical cancer, which is more accurate and efficient. At the same time, the composition described in the present application is used for screening of asymptomatic people in a non-invasive manner, has the characteristics of non-invasiveness, and can achieve real-time monitoring.

[0103] The composition described in the present application is used for screening asymptomatic people in a non-invasive manner, reducing the harm caused by invasive testing. The composition has higher sensitivity and accuracy and can achieve real-time monitoring. DETAILED DESCRIPTION

[0104] The present application is described in detail below. Although specific embodiments of the present application are shown, it should be understood that the present application can be implemented in various forms and should not be limited by the embodiments described herein. On the contrary, these embodiments are provided to enable a more thorough understanding of the present application and to fully convey the scope of the present application to those skilled in the art.

[0105] Unless otherwise indicated, the implementation of this application will use conventional molecular biology (including recombinant technology), microbiology, cell biology, biochemistry and genetics techniques, which are all within the scope of conventional technical means in the art. Such techniques are described in detail in the literature, such as Molecular Cloning: A Laboratory Manual, Second Edition (Sambrook et al., 1989); Oligonucleotide Synthesis (MJ Gait, 1984 Edition); Animal Cell Culture (RI Freshney, 1987 Edition); Methods in Enzymology Series (American Academic Press, Inc.); Current Protocols in Molecular Biology (FM Ausubel et al., 1987 Edition, and regularly updated); PCR: The Polymerase Chain Reaction (Mullis et al., 1994 Edition). The primers, probes, blockers and kits used in this application can be prepared using standard techniques known in the art.

[0106] Unless otherwise defined, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this application belongs.

[0107] definition

[0108] The term "precancerous cell" as used herein refers to a cell that is in the early stages of transformation into a cancer cell or that is prone to transformation into a cancer cell. Such a cell may exhibit one or more phenotypic traits characteristic of a cancer cell.

[0109] "Stringent hybridization conditions" and "stringency" in this application refer to the conditions under which a probe hybridizes to its target sequence, typically in a complex mixture of nucleic acids. Stringent conditions are sequence dependent and are different in different environments. Longer sequences hybridize specifically at higher temperatures. For detailed guidance on nucleic acid hybridization, refer to Tijssen, Biochemistry and Molecular Biology Techniques - Nucleic Acid Probe Hybridization, "A Review of Hybridization Principles and Nucleic Acid Assay Strategies". Generally, stringent conditions are about 5-10°C below the melting point (Tm) of the specific nucleic acid at a defined ionic strength pH. At the temperature of Tm (at a defined ionic strength, pH and nucleic acid concentration), 50% of the probes complementary to the target hybridize to the target sequence in a balanced manner. Stringent conditions can also be achieved by adding destabilizers. For selective or specific hybridization, the positive signal is twice the background hybridization, preferably 10 times. Exemplary stringent hybridization conditions are as follows: hybridization in a solution of 50% formamide, 5x SSC and 1% SDS at 42°C, or hybridization in a solution of 5x SSC and 1% SDS at 65°C, followed by washing in a solution of 0.2x SSC and 0.1% SDS at 65°C.

[0110] Furthermore, nucleic acids that do not hybridize under stringent conditions are still substantially similar if the polypeptides encoded by the nucleic acids are substantially similar. In this case, the nucleic acids are typically hybridized under moderately stringent hybridization conditions. As an example, "moderately stringent hybridization conditions" include hybridization in a solution of 40% formamide, 1M sodium chloride and 1% SDS at 37°C, and washing in a solution of 1xSSC at 45°C. Guidance for achieving conditions that achieve the same stringency is readily apparent to one of ordinary skill in the art. For PCR, a temperature of around 36°C is typically suitable for low stringency amplification, while the annealing temperature ranges from 32°C to 48°C based on the length of the primers. For highly stringent PCR amplification, it is generally at 62°C, while the annealing temperature for highly stringent hybridization ranges from 50°C to 65°C based on the length and specificity of the primers. Cycling conditions for high stringency and low stringency amplifications typically include a denaturation phase at 90-95° C. for 30 seconds to 2 minutes, an annealing phase for 30 seconds to 2 minutes, and an extension phase for 1 to 2 minutes at about 72° C. Tools and guidance for low and high stringency amplification reactions are available in the art.

[0111] " oligonucleotide " in the present application refers to the molecule consisting of two or more nucleotides, preferably the molecule consisting of more than three nucleotides, and its accurate size can rely on many factors, and these factors in turn are determined by the final function and purpose of the oligonucleotide. In some embodiments, oligonucleotide can include a length of 10 nucleotides to 100 nucleotides. In some embodiments, oligonucleotide can include a length of 10 nucleotides to 30 nucleotides, or can have a length of 20 and 25 nucleotides. In some specific embodiments, oligonucleotides shorter than these lengths are also suitable.

[0112] The application's "primer" means an oligonucleotide that can be used as a starting point for synthesis when placed under conditions that induce the synthesis of a primer extension product complementary to a nucleic acid chain, i.e., in the presence of nucleotides and an inducer such as a DNA or RNA polymerase and at a suitable temperature and pH, whether it is naturally occurring or synthetically produced in a purified restriction digest. Primers can be single-stranded or double-stranded, and must be long enough to induce the synthesis of a desired extension product in the presence of an inducer. The exact length of a primer depends on a variety of factors, including temperature, primer source, and the method used. For example, for diagnostic and prognostic applications, an oligonucleotide primer typically contains at least or more than about 9, 10, or 15, or 20, or 25 or more nucleotides, but it can contain fewer nucleotides or more nucleotides. Factors involved in determining the appropriate length of a primer are well known to those skilled in the art.

[0113] The "primer pair" of the present application refers to a primer pair that hybridizes to opposite strands of a target DNA molecule or to a target DNA region flanking a nucleotide sequence to be amplified.

[0114] As used herein, a "primer site" refers to a region of a target DNA or other nucleic acid to which a primer hybridizes.

[0115] The "probe" of the present application, when referring to a nucleic acid sequence, is used in its usual sense to refer to a selected nucleic acid sequence that can hybridize with a target sequence under specified conditions and can be used to detect the presence of the target sequence. The probe is a single-stranded or double-stranded DNA with a length ranging from tens to hundreds or even thousands of base pairs, which can utilize the high accuracy of molecular denaturation, renaturation and complementary base pairing to hydrogen bond (hybridize) with complementary non-labeled single-stranded DNA or RNA in the sample to be tested to form a double-stranded complex (hybrid). It should be understood by those skilled in the art that in some cases, the probe can also be used as a primer, and the primer can be used as a probe.

[0116] "DNA methylation" of the present application refers to the addition of a methyl group to the 5th position of cytosine (C), which is usually (but not necessarily) in the case of a CpG (cytosine followed by guanine) dinucleotide. As a stable modification state, DNA methylation can be inherited to newborn daughter DNA during the DNA replication process under the action of DNA methyltransferase, and is an important epigenetic mechanism. When DNA is methylated, methylation of the gene promoter region can lead to transcriptional silencing of tumor suppressor genes, so it is closely related to the occurrence of tumors. Abnormal methylation includes hypermethylation of tumor suppressor genes and DNA repair genes, hypomethylation of repetitive sequence DNA, and loss of imprinting of certain genes, which are related to the occurrence of various tumors. As used herein, "increased methylation level" or "significant methylation level" refers to the presence of at least one methylated cytosine nucleotide in a DNA sequence, wherein the corresponding C in a normal control sample (e.g., a DNA sample extracted from a non-cancerous cell or tissue sample or a DNA sample treated for methylation of DNA residues) is unmethylated, and in certain embodiments, at least 2, 3, 4, 5, 6, 7, 8, 9, 10 or more Cs may be methylated, wherein the Cs at these positions in the control DNA sample are unmethylated.

[0117] In embodiments, a variety of different methods can be used to detect DNA methylation changes. The method for detecting DNA methylation includes, for example, utilizing southern or polymerase chain reaction (PCR) analysis of methylation-sensitive restriction endonuclease (MSRE) assay, methylation-specific or methylation-sensitive PCR (MS-PCR), methylation-sensitive single nucleotide primer extension (Ms-SnuPE), high resolution melting (HRM) analysis, bisulfite sequencing, pyrophosphate sequencing, methylation-specific single-stranded conformation analysis (MS-SSCA), combined bisulfite restriction analysis (COBRA), methylation-specific denaturing gradient gel electrophoresis (MS-DGGE), methylation-specific melting curve analysis (MS-MCA), methylation-specific denaturing high performance liquid chromatography (MS-DHPLC), methylation-specific microarray (MSO). These determinations can be PCR analysis, quantitative analysis using fluorescent labels or southern imprint analysis.

[0118] A "methylation assay" as used herein refers to any assay that determines the methylation status of one or more CpG dinucleotide sequences within a DNA sequence.

[0119] "Detection" as used herein refers to any process of observing a marker or marker change in a sample (e.g., a change in the methylation state of a marker or the expression level of a nucleic acid or protein sequence), regardless of whether the marker or marker change is actually detected. In other words, the act of detecting a marker or marker change in a sample is "detection", even if the marker is determined to be absent or below a sensitivity level. Detection can be a quantitative, semi-quantitative, or non-quantitative observation, and can be based on comparison with one or more control samples. It should be understood that detecting cervical cancer disclosed herein includes detecting precancerous cells that are beginning to develop into cervical cancer cells or are about to develop into cervical cancer cells, or have an increased tendency to develop into cervical cancer cells. Detecting cervical cancer can also include detecting a possible probability of death or a possible prognosis of a disease condition.

[0120] "Homology", "identity" and "similarity" of the present application refer to the sequence similarity between two nucleic acid molecules. "Homology", "identity" or "similarity" can be determined by comparing the positions in each sequence, and the sequences can be aligned for the purpose of comparison. When equivalent positions in the compared sequences are occupied by the same base, the molecules are identical at that position; when equivalent sites are occupied by the same or similar amino acid (for example, similar in spatial properties or charged properties) residues, the molecules can be said to be homologous (similar) at that position. The expression of homology / similarity or identity percentage refers to the function of the number of identical or similar amino acids at the positions shared by the compared sequences. "Unrelated" or "non-homologous" sequences share less than 40% identity, preferably less than 25% identity with the sequences of the present application. When comparing two sequences, the absence of residues (amino acids or nucleic acids) or the presence of extra residues also reduces identity and homology / similarity. In a specific embodiment, two or more sequences or subsequences are considered to be substantially or significantly homologous, similar or identical if their sequences are about 60%, or about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical over a specified region, as determined using the BLAST or BLAST 2.0 sequence comparison algorithm with the default parameters described below or by manual alignment and visual inspection provided online by, for example, the National Center for Biotechnology Information (NCBI). This definition also relates to or can be used to test the complement of a sequence. Thus, to the extent permitted by the context of the present invention, for example, if the nucleotide sequence can be predicted to occur naturally in a DNA duplex, or can occur naturally in the form of one or both of the complementary strands, then the nucleotide sequence that is complementary to a specified target sequence or a variant thereof is itself considered to be "similar" to the target sequence, and when referring to "similar" nucleic acid sequences, single-stranded sequences, their complementary sequences, double-stranded strand complexes, sequences that can encode the same or similar polypeptide products, and any allowed variants of any of the above. Circumstances in which similarity must be limited to the analysis of a single nucleic acid strand sequence can include, for example, the detection and quantification of the expression of a specific RNA sequence or coding sequence in a cell. This definition also includes sequences with deletions and / or additions, as well as sequences with substitutions.In embodiments, the identity or similarity can be over a region that is at least about 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 10, 21, 22, 23, 24, 25, or more nucleotides in length, or over a region that is more than about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or more than about 100 nucleotides in length.

[0121] "Amplification" herein refers to the process of obtaining multiple copies of a specific locus of a nucleic acid, such as genomic DNA or cDNA. Amplification can be achieved using any of a variety of known means, including but not limited to polymerase chain reaction (PCR), transcription-based amplification, and strand displacement amplification (SDA).

[0122] The "fluorescence-based real-time PCR" or "real-time fluorescence quantitative PCR" in this application refers to a method in which a fluorescent group is added to the PCR reaction system, the entire PCR process is monitored in real time using the accumulation of fluorescent signals, and finally the unknown template is quantitatively analyzed using a standard curve. In this PCR technology, there is a very important concept, the cycle threshold, also known as the Ct value. C stands for Cycle, t stands for threshold, and the meaning of the Ct value is: the number of cycles experienced when the fluorescent signal in each reaction tube reaches the set threshold. For example, the method for setting the fluorescence threshold is as follows: the fluorescent signal of the first 15 cycles of the PCR reaction is used as the fluorescent background signal, and the default (default) setting of the fluorescence threshold is 10 times the standard deviation of the fluorescent signal of 3-15 cycles.

[0123] The "cut-off value of real-time PCR" of the present application refers to a critical Ct value for judging the positive or negative of a sample for a certain biomarker. According to certain specific real-time methods of the present application, "the critical Ct value (CutOff value) is obtained based on a certain amount of sample data and statistical processing", and the critical Ct value may vary according to the required sensitivity or specificity requirements.

[0124] The "sensitivity" in this application refers to the proportion of cancer detected from a certain cancer sample, and its calculation formula is: Sensitivity = (detected cancer / all cancers), while "specificity" refers to the proportion of normal detected in a certain normal human sample, and its calculation formula is: Specificity = (detected negative / total negative).

[0125] The "label" or "detectable part" of the present application is a component that can be detected by spectroscopic, photochemical, biochemical, immunochemical, chemical or other physical means. For example, useful labels include 32P, fluorescent dyes, electron-dense reagents, enzymes (e.g., enzymes commonly used in ELISA), biotin, digoxigenin or haptens and proteins that can be prepared to be detectable, for example, by incorporating a radioactive label into a peptide or for detecting antibodies that specifically react with a peptide.

[0126] Nucleic acid molecules can be detected using a variety of different methods. Nucleic acid detection methods include, for example, PCR and nucleic acid hybridization (e.g., Southern blot, Northern blot or in situ hybridization). Specifically, oligonucleotides (e.g., oligonucleotide primers) capable of amplifying target nucleic acids can be used for PCR reactions. PCR methods generally include the following steps: obtaining a sample, separating nucleic acids (e.g., DNA, RNA or both) from the sample, and contacting the nucleic acid with one or more oligonucleotide primers, which specifically hybridize with the template nucleic acid under conditions that enable template nucleic acid amplification to occur. In the presence of template nucleic acid, an amplification product is produced. The conditions for nucleic acid amplification and amplification product detection are known to those skilled in the art. A variety of improvements to basic PCR techniques have been developed, including, but not limited to, anchored PCR, RACE PCR, RT-PCR and ligase chain reaction (LCR). The primer pairs in the amplification reaction must anneal to the relative strands of the template nucleic acid, and should be kept at a suitable distance from each other so that the polymerase can effectively polymerize across the region and make it possible to easily detect the amplification product, for example, using electrophoresis. For example, a computer program such as OLIGO (Molecular Biology Insights Inc., Cascade, Colo.) can be used to design oligonucleotide primers to assist in designing primers with similar melting temperatures. Typically, oligonucleotide primers are 9-30 or 40 or 50 nucleotides in length (e.g., 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides in length), but oligonucleotide primers can be longer or shorter, as long as appropriate amplification conditions are used.

[0127] Detection of the amplification product or hybridization complex is usually achieved using a detectable label. The term "label", when referring to nucleic acids, is intended to include direct labeling of nucleic acids by coupling (i.e., physically linking) a detectable substance to the nucleic acid, and indirect labeling of nucleic acids by reacting with another reagent directly labeled with a detectable substance. Detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include avidin streptavidin / biotin and avidin / biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride, or phycoerythrin; examples of luminescent materials include luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin. Examples of indirect labeling include end-labeling of a nucleic acid with biotin, such that the nucleic acid can be detected using fluorescently labeled streptavidin.

[0128] Overview

[0129] On the one hand, the present application provides a composition for in vitro detection of cervical cancer, the composition comprising a nucleic acid for detecting the methylation state within a target sequence of a target gene, wherein the methylation state of the target gene is characterized by the methylation of the target sequence of the target gene, wherein the target gene is one, two or three of the JAM3 gene, EPHA7 gene and ST6GALNAC5 gene.

[0130] The present application provides a group of target sequences of target genes that are abnormally methylated in cervical cancer, including target sequences of JAM3 gene, EPHA7 gene and ST6GALNAC5 gene. Among them, the target sequence of JAM3 gene is shown in any one of SEQ ID NO: 1-12, or includes the sequence shown in any one of SEQ ID NO: 1-12. The target sequence of EPHA7 gene is shown in any one of SEQ ID NO: 13-24, or includes the sequence shown in any one of SEQ ID NO: 13-24. The target sequence of ST6GALNAC5 gene is shown in any one of SEQ ID NO: 25-36, or includes the sequence shown in any one of SEQ ID NO: 25-36.

[0131] Those skilled in the art can also understand that the target sequences of the JAM3 gene, EPHA7 gene and ST6GALNAC5 gene are not limited to the specific sequences listed above. The target sequence of the JAM3 gene should include a sequence that contains one or two or three or more nucleotide mutations compared to the sequence shown in any one of SEQ ID NOs: 1-12, but is still substantially functionally the same, and also includes a sequence that has 95%, 96%, 97%, 98% or 99% sequence identity compared to the sequence shown in any one of SEQ ID NOs: 1-12, and also includes a sequence that deletes one or more nucleotides, adds one or more nucleotides, or replaces one or more nucleotides based on the nucleotide sequence shown in any one of SEQ ID NOs: 1-12 but has 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity with the nucleotide sequence shown in any one of SEQ ID NOs: 1-12. The target sequence of the EPHA7 gene should include a sequence comprising one, two or three or more nucleotide mutations compared to the sequence shown in any one of SEQ ID NOs: 13-24, but having substantially the same essential function as the sequence, and also includes a sequence having 95%, 96%, 97%, 98% or 99% sequence identity compared to the sequence shown in any one of SEQ ID NOs: 13-24, and also includes a sequence having 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to the nucleotide sequence shown in any one of SEQ ID NOs: 13-24 by deleting one or more nucleotides, adding one or more nucleotides, or replacing one or more nucleotides. The target sequence of the ST6GALNAC5 gene should include a sequence that contains one, two or three or more nucleotide mutations compared to the sequence shown in any one of SEQ ID NOs: 25-36, but is still substantially functionally the same, and also includes a sequence with 95%, 96%, 97%, 98% or 99% sequence identity compared to the sequence shown in any one of SEQ ID NOs: 25-36. It also includes a sequence that deletes one or more nucleotides, adds one or more nucleotides, or replaces one or more nucleotides based on the nucleotide sequence shown in any one of SEQ ID NOs: 25-36 but has 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity with the nucleotide sequence shown in any one of SEQ ID NOs: 25-36.

[0132] The target sequence (5'-3') of the JAM3-1 gene is as follows:

[0133] SEQ ID NO: 1

[0134] GGCAGGCTGGGCGCATGCGCGCGGGGACTACAAGCCGCGCCGCGCTGCCGCTGGCCCCTCAGCAACCCTCGAC

[0135] The target sequence of the JAM3-1 gene after bisulfite treatment (5'-3') is as follows:

[0136] SEQ ID NO: 2

[0137] GGTAGGTTGGGCGTATGCGCGCGGGGATTATAAGTCGCGTCGCGTTGTCGTTGGTTTTTTAGTAATTTTCGAT

[0138] The reverse complementary sequence (5'-3') of the target sequence of the JAM3-1 gene is as follows:

[0139] SEQ ID NO: 3

[0140] GTCGAGGGTTGCTGAGGGGCCAGCGGCAGCGCGGCGCGGCTTGTAGTCCCCGCGCGCATGCGCCCAGCCTGCC

[0141] The reverse complementary sequence of the target sequence of the JAM3-1 gene after bisulfite treatment (5'-3') is as follows:

[0142] SEQ ID NO: 4

[0143] GTCGAGGGTTGTTGAGGGGTTAGCGGTAGCGCGGCGCGGTTTGTAGTTTTCGCGCGTATGCGTTTAGTTTGTT

[0144] The target sequence (5'-3') of the JAM3-2 gene is as follows:

[0145] SEQ ID NO: 5

[0146] CCTCGACATGGCGCTGAGGCGGCCACCGCGACTCCGGCTCTGCGCTCGGCTGCCTGACTTCTTCC

[0147] The target sequence of the JAM3-2 gene after bisulfite treatment (5'-3') is as follows:

[0148] SEQ ID NO: 6

[0149] TTTCGATATGGCGTTGAGGCGGTTATCGCGATTTCGGTTTTGCGTTCGGTTGTTTGATTTTTTTT

[0150] The reverse complementary sequence (5'-3') of the target sequence of the JAM3-2 gene is as follows:

[0151] SEQ ID NO: 7

[0152] GGAAGAAGTCAGGCAGCCGAGCGCAGAGCCGGAGTCGCGGTGGCCGCCTCAGCGCCATGTCGAGG

[0153] The reverse complementary sequence of the target sequence of the JAM3-2 gene after bisulfite treatment (5'-3') is as follows:

[0154] SEQ ID NO: 8

[0155] GGAAGAAGTTAGGTAGTCGAGCGTAGAGTCGGAGTCGCGGTGGTCGTTTTAGCGTTATGTCGAGG

[0156] The target sequence (5'-3') of the JAM3-3 gene is as follows:

[0157] SEQ ID NO: 9

[0158] CTCGGCTGCCTGACTTCTTCCTGCTGCTGCTTTTCAGGGGTGAGTTTGCGCGTTTCCGCTGTTGGGAGACTAGGGTCTGGGGGCG

[0159] The target sequence of the JAM3-3 gene after bisulfite treatment (5'-3') is as follows:

[0160] SEQ ID NO: 10

[0161] TTCGGTTGTTTGATTTTTTTTTGTTGTTGTTTTTTAGGGGTGAGTTTGCGCGTTTTCGTTGTTGGGAGATTAGGGTTTGGGGGCG

[0162] The reverse complementary sequence (5'-3') of the target sequence of the JAM3-3 gene is as follows:

[0163] SEQ ID NO: 11

[0164] CGCCCCAGACCCTAGTCTCCCAACAGCGGAAACGCGCAAACTCACCCCTGAAAAGCAGCAGCAGGAAGAAGTCAGGCAGCCGAG

[0165] The reverse complementary sequence of the target sequence of the JAM3-3 gene after bisulfite treatment (5'-3') is as follows:

[0166] SEQ ID NO: 12

[0167] CGTTTTTAGATTTTAGTTTTTAATAGCGGAAACGCGTAAATTTATTTTTGAAAAGTAGTAGTAGGAAGAAGTTAGGTAGTCGAG

[0168] The target sequence (5'-3') of the EPHA7-1 gene is as follows:

[0169] SEQ ID NO: 13

[0170] CATCGATTCCCCTTCTCGGTCCCCGATCGGCTGCTCCACGTTTAGCTTTTTTTAATTTCCCCCCCACTCCTGTTCGCTCGCACCGTGTTTGC

[0171] The sequence (5'-3') of the target sequence of the EPHA7-1 gene after bisulfite treatment is as follows:

[0172] SEQ ID NO: 14

[0173] TATCGATTTTTTTTTTCGGTTTTCGATCGGTTGTTTTACGTTTAGTTTTTTTTAATTTTTTTTTTATTTTTGTTCGTTCGTATCGTGTTTGT

[0174] The reverse complementary sequence (5'-3') of the target sequence of the EPHA7-1 gene is as follows:

[0175] SEQ ID NO: 15

[0176] GCAAACACGGTGCGAGCGAACAGGAGTGGGGGGGAAATTAAAAAAAGCTAAACGTGGAGCAGCCGATCGGGGACCGAGAAGGGGAATCGATG

[0177] The reverse complementary sequence of the target sequence of the EPHA7-1 gene after bisulfite treatment (5'-3') is as follows:

[0178] SEQ ID NO: 16

[0179] GTAAATACGGTGCGAGCGAATAGGAGTGGGGGGGAAATTAAAAAAAGTTAAACGTGGAGTAGTCGATCGGGGATCGAGAAGGGGAATCGATG

[0180] The target sequence (5'-3') of the EPHA7-2 gene is as follows:

[0181] SEQ ID NO: 17

[0182] CACTCCTGTTCGCTCGCACCGTGTTTGCTGCCTGCAAGTCTCCGACTGCAGACCGGCCGCTTGCTCCACAC

[0183] The sequence (5'-3') of the target sequence of the EPHA7-2 gene after bisulfite treatment is as follows:

[0184] SEQ ID NO: 18

[0185] TATTTTTGTTCGTTCGTATCGTGTTTGTTGTTTGTAAGTTTTCGATTGTAGATCGGTCGTTTGTTTTATAT

[0186] The reverse complementary sequence (5'-3') of the target sequence of the EPHA7-2 gene is as follows:

[0187] SEQ ID NO: 19

[0188] GTGTGGAGCAAGCGGCCGGTCTGCAGTCGGAGACTTGCAGGCAGCAAACACGGTGCGAGCGAACAGGAGTG

[0189] The reverse complementary sequence of the target sequence of the EPHA7-2 gene after bisulfite treatment (5'-3') is as follows:

[0190] SEQ ID NO: 20

[0191] GTGTGGAGTAAGCGGTCGGTTTGTAGTCGGAGATTTGTAGGTAGTAAATACGGTGCGAGCGAATAGGAGTG

[0192] The target sequence (5'-3') of the EPHA7-3 gene is as follows:

[0193] SEQ ID NO: 21

[0194] ACCGGCCGCTTGCTCCACACTCCAATAATATCAATTAGGGGGGGAGGGGGCGGGGCTCCGAGCTGAGAGCCTCCGCCACTCGGGCTGAGT

[0195] The sequence (5'-3') of the target sequence of the EPHA7-3 gene after bisulfite treatment is as follows:

[0196] SEQ ID NO: 22

[0197] ATCGGTCGTTTGTTTTATATTTTAATAATATTAATTAGGGGGGGGAGGGGGCGGGGTTTCGAGTTGAGAGTTTTCGTTATTCGGGTTGAGT

[0198] The reverse complementary sequence (5'-3') of the target sequence of the EPHA7-3 gene is as follows:

[0199] SEQ ID NO: 23

[0200] ACTCAGCCCGAGTGGCGGAGGCTCTCAGCTCGGAGCCCCGCCCTCCCCCCCTAATTGATATTATTGGAGTGTGGAGCAAGCGGCCGGT

[0201] The reverse complementary sequence of the target sequence of the EPHA7-3 gene after bisulfite treatment (5'-3') is as follows:

[0202] SEQ ID NO: 24

[0203] ATTTAGTTCGAGTGGCGGAGGTTTTTAGTTCGGAGTTTCGTTTTTTTTTTTTTTAATTGATATTATTGGAGTGTGGAGTAAGCGGTCGGT

[0204] The target sequence (5'-3') of the ST6GALNAC5-1 gene is as follows:

[0205] SEQ ID NO: 25

[0206] GCCGAAAGCAGCGACGCGCCCGGAGCATCCCTTGCGATACGCTAGGGGACGGTGCTTTCTCTGTCCCAGTTGCGTGCGGCG

[0207] The target sequence of the ST6GALNAC5-1 gene after bisulfite treatment (5'-3') is as follows:

[0208] SEQ ID NO: 26

[0209] GTCGAAAGTAGCGACGCGTTCGGAGTATTTTTTGCGATACGTTAGGGGACGGTGTTTTTTTTGTTTTAGTTGCGTGCGGCG

[0210] The reverse complementary sequence (5'-3') of the target sequence of the ST6GALNAC5-1 gene is as follows:

[0211] SEQ ID NO: 27

[0212] CGCCGCACGCAACTGGGACAGAGAAAGCACCGTCCCCTAGCGTATCGCAAGGGATGCTCCGGGCGCGTCGCTGCTTTCGGC

[0213] The reverse complementary sequence of the target sequence of the ST6GALNAC5-1 gene after bisulfite treatment (5'-3') is as follows:

[0214] SEQ ID NO: 28

[0215] CGTCGTACGTAATTGGGATAGAGAAAGTATCGTTTTTTAGCGTATCGTAAGGGATGTTTCGGGCGCGTCGTTGTTTTCGGT

[0216] The target sequence (5'-3') of the ST6GALNAC5-2 gene is as follows:

[0217] SEQ ID NO: 29

[0218] GTTGCGTGCGGCGGGGCTGGGGCCCAGGCCGCCCCAAATCTCCCCACTAGAGTGAC

[0219] The target sequence of the ST6GALNAC5-2 gene after bisulfite treatment (5'-3') is as follows:

[0220] SEQ ID NO: 30

[0221] GTTGCGTGCGGCGGGGTTGGGGTTTAGGTCGTTTTAAATTTTTTTTATTAGAGTGAT

[0222] The reverse complementary sequence (5'-3') of the target sequence of the ST6GALNAC5-2 gene is as follows:

[0223] SEQ ID NO: 31

[0224] GTCACTCTAGTGGGGGAGATTTGGGGCGGCCTGGGCCCCAGCCCCGCCGCACGCAAC

[0225] The reverse complementary sequence of the target sequence of the ST6GALNAC5-2 gene after bisulfite treatment (5'-3') is as follows:

[0226] SEQ ID NO: 32

[0227] GTTATTTTAGTGGGGGAGATTTGGGGCGGTTTGGGTTTTAGTTTCGTCGTACGTAAT

[0228] The target sequence (5'-3') of the ST6GALNAC5-3 gene is as follows:

[0229] SEQ ID NO: 33

[0230] CCACTAGAGTGACCACCGCACAGTTGTCCCCGCTGGGCGCGCTCCTCCGGTGTCTGCGCTCAGCCGCTCTCCTCTTCTCTCCCGCC

[0231] The target sequence of the ST6GALNAC5-3 gene after bisulfite treatment (5'-3') is as follows:

[0232] SEQ ID NO: 34

[0233] TTATTAGAGTGATTATCGTATAGTTGTTTTCGTTGGGCGCGTTTTTTCGGTGTTTGCGTTTAGTCGTTTTTTTTTTTTTTTTCGTT

[0234] The reverse complementary sequence (5'-3') of the target sequence of the ST6GALNAC5-3 gene is as follows:

[0235] SEQ ID NO: 35

[0236] GGCGGGAGAGAGAAGAGGAGAGCGGCTGAGCGCAGACACCGGAGGAGCGCGCCCAGCGGGGACAACTGTGCGGTGGTCACTCTAGTGG

[0237] The reverse complementary sequence of the target sequence of the ST6GALNAC5-3 gene after bisulfite treatment (5'-3') is as follows:

[0238] SEQ ID NO: 36

[0239] GGCGGGAGAGAGAAGAGGAGAGCGGTTGAGCGTAGATATCGGAGGAGCGCGTTTAGCGGGGATAATTGTGCGGTGGTTATTTTAGTGG

[0240] The target sequences and related sequences of JAM3 gene, EPHA7 gene and ST6GALNAC5 gene are shown in Table 1:

[0241] Table 1 Target sequences and related sequences of JAM3 gene, EPHA7 gene and ST6GALNAC5 gene

[0242]

[0243]

[0244] Preferably, the nucleic acid used to detect the methylation state of the target gene includes a fragment of at least 9 nucleotides in the target sequence of the target gene, wherein the fragment contains at least one CpG dinucleotide sequence. In certain preferred embodiments, if the sample DNA to be tested is converted using bisulfite, the nucleic acid used to detect the methylation state of the target gene includes a fragment of at least 9 nucleotides in the sequence after bisulfite conversion of the target sequence of the target gene, preferably a fragment of at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides, wherein the nucleotide fragment contains at least one CpG dinucleotide sequence.

[0245] More preferably, the nucleic acid used to detect the methylation status of the target gene includes a fragment of at least 15 nucleotides in the target sequence of the target gene that hybridizes under moderate stringency or stringent conditions, wherein the fragment of the nucleotide contains at least one CpG dinucleotide sequence. In certain preferred embodiments, if the test sample DNA is converted using bisulfite, the nucleic acid used to detect the methylation status of the target gene includes a fragment of at least 15 nucleotides in the sequence after bisulfite conversion, preferably at least 16, 17, 18, 19, 20 or more nucleotides, hybridized to the target sequence of the target gene under moderate stringency or stringent conditions, wherein the fragment of the nucleotide contains at least one CpG dinucleotide sequence.

[0246] Preferably, the composition further comprises a reagent for converting the unmethylated cytosine base at position 5 of the target sequence of the target gene into uracil. More preferably, the reagent is bisulfite.

[0247] The nucleic acid used to detect the methylation status of the target gene may also include a blocker that preferentially binds to DNA in an unmethylated state.

[0248] Preferably, the composition comprises one or more of the primers and probes shown in Table 2:

[0249] Table 2 Primer and probe sequences used in this application

[0250]

[0251]

[0252] In Table 2, "F" indicates a forward primer; "R" indicates a reverse primer; and "P" indicates a probe.

[0253] Preferably, the fluorescent labeling method of the probe sequence used in the present application is as shown in Table 3.

[0254] Table 3 A fluorescent labeling method for the probe sequences used in this application

[0255] Sequence number sequence name 5' labeling 3' labeling SEQ ID NO: 39 JAM3-1P FAM BHQ1 SEQ ID NO: 48 EPHA7-1P Cy5 BHQ3 SEQ ID NO: 57 ST6GALNAC5-1P VIC BHQ1

[0256] In certain embodiments, the composition further comprises an agent for converting the unmethylated cytosine base at position 5 of the gene into uracil. Preferably, the agent is bisulfite. Bisulfite modification of DNA is a known tool for assessing the methylation status of CpGs. In the DNA of eukaryotic cells, 5-methylcytosine is the most common covalent base modification. 5-methylcytosine cannot be identified by sequencing because 5-methylcytosine has the same base pairing behavior as cytosine. In addition, during PCR amplification, the epigenetic information carried by 5-methylcytosine is completely lost. The method most commonly used to analyze the presence of 5-methylcytosine in DNA is based on the specific reaction of bisulfite with cytosine; after subsequent alkaline hydrolysis, unmethylated cytosine is converted into uracil, which corresponds to thymine in pairing behavior; but under these conditions, 5-methylcytosine remains unmodified. Thus the original DNA is transformed in this way, so that the 5-methylcytosine, which was originally indistinguishable from cytosine in its hybridization behavior, can now be detected as the only remaining cytosine by conventional known molecular biology techniques, such as by amplification and hybridization. All these techniques are based on different base pairing characteristics and can now be fully utilized. Therefore, typically, the present application provides the combined use of bisulfite technology and one or more methylation assays to determine the methylation state of the CpG dinucleotide sequence in the target sequence of the target gene. In addition, the method of the present application is suitable for analyzing heterogeneous samples, such as low-concentration tumor cells in blood or feces. Therefore, when analyzing the methylation state of the CpG dinucleotide sequence in this sample, those skilled in the art can use quantitative determination methods to determine the methylation level (such as percentage, number, ratio, proportion or degree) of a specific CpG dinucleotide sequence, rather than the methylation state. Accordingly, the term methylation status or methylation state should also be considered to refer to the value reflecting the methylation state of the CpG dinucleotide sequence.

[0257] On the other hand, the present application provides oligonucleotides for in vitro detection of cervical cancer, comprising: a fragment of at least 9 nucleotides of a sequence shown in any one of SEQ ID NOs: 1-12 or its complementary sequence and containing at least one CpG dinucleotide sequence; and / or a fragment of at least 9 nucleotides of a sequence shown in any one of SEQ ID NOs: 13-24 or its complementary sequence and containing at least one CpG dinucleotide sequence; and / or a fragment of at least 9 nucleotides of a sequence shown in any one of SEQ ID NOs: 25-36 or its complementary sequence and containing at least one CpG dinucleotide sequence.

[0258] Preferably, the oligonucleotide for in vitro detection of cervical cancer comprises: a fragment of at least 9 nucleotides in a sequence after bisulfite conversion of a sequence shown in any one of SEQ ID NOs: 1-12 or a complementary sequence thereof; and / or a fragment of at least 9 nucleotides in a sequence after bisulfite conversion of a sequence shown in any one of SEQ ID NOs: 13-24 or a complementary sequence thereof and containing at least one CpG dinucleotide sequence; and / or a fragment of at least 9 nucleotides in a sequence after bisulfite conversion of a sequence shown in any one of SEQ ID NOs: 25-36 or a complementary sequence thereof and containing at least one CpG dinucleotide sequence.

[0259] The oligonucleotides for in vitro detection of cervical cancer of the present application also include: a fragment that hybridizes to at least 15 nucleotides in a sequence shown in any one of SEQ ID NOs: 1-12 or its complementary sequence under moderately stringent or stringent conditions and contains at least one CpG dinucleotide sequence; and / or a fragment that hybridizes to at least 15 nucleotides in a sequence shown in any one of SEQ ID NOs: 13-24 or its complementary sequence under moderately stringent or stringent conditions and contains at least one CpG dinucleotide sequence; and / or a fragment that hybridizes to at least 15 nucleotides in a sequence shown in any one of SEQ ID NOs: 25-36 or its complementary sequence under moderately stringent or stringent conditions and contains at least one CpG dinucleotide sequence.

[0260] Preferably, the oligonucleotide for in vitro detection of cervical cancer comprises: a fragment of at least 15 nucleotides in a sequence after bisulfite conversion of a sequence shown in any one of SEQ ID NOs: 1-12 or its complementary sequence, which hybridizes under moderately stringent or stringent conditions and comprises at least one CpG dinucleotide sequence; and / or a fragment of at least 15 nucleotides in a sequence after bisulfite conversion of a sequence shown in any one of SEQ ID NOs: 13-24 or its complementary sequence, which hybridizes under moderately stringent or stringent conditions and comprises at least one CpG dinucleotide sequence; and / or a fragment of at least 15 nucleotides in a sequence after bisulfite conversion of a sequence shown in any one of SEQ ID NOs: 25-36 or its complementary sequence, which hybridizes under moderately stringent or stringent conditions and comprises at least one CpG dinucleotide sequence.

[0261] The oligonucleotide for in vitro detection of cervical cancer of the present application may also include: a blocker that preferentially binds to DNA in a non-methylated state.

[0262] In a specific embodiment, the oligonucleotide for detecting cervical cancer in vitro comprises the sequences of SEQ ID NO: 37 and SEQ ID NO: 38. It also comprises the sequence of SEQ ID NO: 39.

[0263] In another specific embodiment, the oligonucleotide for detecting cervical cancer in vitro comprises the sequences of SEQ ID NO: 40 and SEQ ID NO: 41. It also comprises the sequence of SEQ ID NO: 42.

[0264] In another specific embodiment, the oligonucleotide for detecting cervical cancer in vitro comprises the sequences of SEQ ID NO: 43 and SEQ ID NO: 44. It also comprises the sequence of SEQ ID NO: 45.

[0265] In another specific embodiment, the oligonucleotide for detecting cervical cancer in vitro comprises the sequences of SEQ ID NO: 46 and SEQ ID NO: 47. It also comprises the sequence of SEQ ID NO: 48.

[0266] In another specific embodiment, the oligonucleotide for detecting cervical cancer in vitro comprises the sequences of SEQ ID NO: 49 and SEQ ID NO: 50 and also comprises the sequence of SEQ ID NO: 51.

[0267] In another specific embodiment, the oligonucleotide for detecting cervical cancer in vitro comprises the sequences of SEQ ID NO: 52 and SEQ ID NO: 53. It also comprises the sequence of SEQ ID NO: 54.

[0268] In another specific embodiment, the oligonucleotide for detecting cervical cancer in vitro comprises the sequences of SEQ ID NO: 55 and SEQ ID NO: 56. It also comprises the sequence of SEQ ID NO: 57.

[0269] In another specific embodiment, the oligonucleotide for detecting cervical cancer in vitro comprises the sequences of SEQ ID NO: 58 and SEQ ID NO: 59 and also comprises the sequence of SEQ ID NO: 60.

[0270] In another specific embodiment, the oligonucleotide for detecting cervical cancer in vitro comprises the sequences of SEQ ID NO: 61 and SEQ ID NO: 62, and further comprises the sequence of SEQ ID NO: 63.

[0271] In another aspect, the present application provides a kit comprising the composition, which further comprises at least one other component selected from the following: nucleoside triphosphates, DNA polymerase, and a buffer required for the function of the DNA polymerase.

[0272] Typically, the kit also includes a container for holding a patient sample. In addition, the kit also includes instructions for use and interpretation of the test results.

[0273] The present application also relates to the use of the above-mentioned composition and oligonucleotide in preparing a kit for in vitro detection of cervical cancer.

[0274] The present application also relates to the use of one or more of the JAM3 gene, the EPHA7 gene and the ST6GALNAC5 gene in preparing a kit for in vitro detection of cervical cancer.

[0275] The protein encoded by the JAM3 gene is a member of the junctional adhesion molecule protein family. Junctional adhesion molecule proteins are proteins on the cell surface that are responsible for the interaction between cells and / or between cells and the extracellular matrix (ECM).

[0276] The EPHA7 gene refers to Ephrin receptor A7 (EphA7), which is a member of the Eph receptor family. It is widely involved in intercellular signal transduction and regulates cell proliferation and differentiation.

[0277] The ST6GALNAC5 gene, which encodes an α2,6-sialyltransferase involved in the biosynthesis of α-series gangliosides, was previously identified as one of the genes mediating breast cancer metastasis to the brain.

[0278] In another aspect, the present application provides a method for detecting cervical cancer in vitro, the method comprising the following steps:

[0279] 1) Isolating the target sequence or fragment thereof of the target gene in the sample to be tested;

[0280] 2) determining the methylation status of the target sequence of the target gene;

[0281] 3) The state of the sample is determined by the detection result of the methylation state of the target sequence of the target gene, thereby realizing in vitro detection of cervical cancer.

[0282] According to certain preferred embodiments, the method further comprises the following steps:

[0283] 1) Extracting genomic DNA from the sample to be tested;

[0284] 2) treating the DNA sample obtained in step 1) with a reagent to convert the unmethylated cytosine base at position 5 into uracil or other bases, that is, the unmethylated cytosine base at position 5 of the target sequence of the target gene is converted into uracil or other bases, and the converted base is different from the unmethylated cytosine base at position 5 in terms of hybridization performance and is detectable;

[0285] 3) contacting the DNA sample treated in step 2) with a DNA polymerase and a primer of the target sequence of the target gene, so that the treated target sequence of the target gene is amplified to produce an amplification product or is not amplified; if the treated target sequence of the target gene undergoes a DNA polymerization reaction, an amplification product will be produced; if the treated target sequence of the target gene does not undergo a DNA polymerization reaction, it will not be amplified;

[0286] 4) detecting the amplified product with a probe; and

[0287] 5) determining the methylation status of at least one CpG dinucleotide of the target sequence of the target gene based on the presence or absence of the amplification product.

[0288] Preferably, a typical primer includes a fragment of the target sequence of the target gene, and the fragment of the target sequence of the target gene contains a fragment of at least 9 nucleotides that is identical, complementary, or hybridizes under moderately stringent or stringent conditions to any one of SEQ ID NOs: 1-12, any one of SEQ ID NOs: 13-24, and any one of SEQ ID NOs: 25-36.

[0289] Preferably, a typical probe comprises a fragment of the target sequence of the target gene, wherein the fragment of the target sequence of the target gene comprises a fragment of at least 15 nucleotides that are respectively identical, complementary to, or hybridize under moderately stringent or stringent conditions to any one of SEQ ID NOs: 1-12, any one of SEQ ID NOs: 13-24, and any one of SEQ ID NOs: 25-36.

[0290] Preferably, one or more of the primers and probes are as shown in Table 2 above.

[0291] Furthermore, the contacting or amplifying comprises using at least one of the following methods: using a thermostable DNA polymerase as the amplification enzyme, using a polymerase lacking 5'-3' exonuclease activity, using polymerase chain reaction (PCR), and generating amplification product nucleic acid molecules with detectable labels.

[0292] Preferably, the methylation state is determined by PCR, such as "fluorescence-based real-time PCR technology", methylation-sensitive single nucleotide primer extension reaction (Ms-SNuPE), methylation-specific PCR (MSP), and methylated CpG island amplification (MCA) and other determination methods are used to determine the methylation state of at least one CpG dinucleotide of the target sequence of the target gene. Among them, the "fluorescence-based real-time PCR" determination is a high-throughput quantitative methylation determination, which uses fluorescence-based real-time PCR (TaqMan) technology and does not require further operation after the PCR step. In short, the "fluorescence-based real-time PCR" method starts with a mixed sample of genomic DNA, which is converted into a mixed pool of methylation-dependent sequence differences in a sodium bisulfite reaction according to standard operations. Subsequently, fluorescence-based PCR is performed in a "biased" reaction (using PCR primers that overlap known CpG dinucleotides). Sequence differences can be generated at the amplification level and at the fluorescence detection amplification level. The "fluorescence-based real-time PCR" determination can be used as a quantitative test of methylation state in genomic DNA samples, wherein sequence differentiation occurs at the probe hybridization level. In this quantitative mode, in the presence of a fluorescent probe that overlaps a specific CpG dinucleotide, the PCR reaction provides a methylation-specific amplification. The non-biased control for the initial DNA amount is provided by the following reaction: neither the primer nor the probe covers any CpG dinucleotide. The "fluorescence-based real-time PCR" method can be used with any suitable probe, such as "TaqMan", "Lightcycler", etc. The TaqMan probe is a fluorescent reporter (RCHFRrter) and a quencher molecule (Quencher) double-labeled, and is designed to be specific to a relatively high GC content region, so that it melts at a temperature of about 10°C higher than the forward or reverse primer in the PCR cycle. This allows the TaqMan probe to remain fully hybridized in the PCR annealing / extension step. When the Taq polymerase synthesizes a new chain in the PCR, it will eventually encounter the annealed TaqMan probe. The Taq polymerase 5' to 3' endonuclease activity will then replace the TaqMan probe by digesting it, thereby releasing the fluorescent reporter molecule for quantitative detection of its now unquenched signal using a real-time fluorescence detection system. Typical reagents for "fluorescence-based real-time PCR" analysis may include, but are not limited to: target sequence PCR primers for target genes; non-specific amplification blockers; TaqMan or Lightcycler probes; optimized PCR buffer and deoxynucleotides; and Taq polymerase, etc.

[0293] In certain preferred embodiments, the methylation state of at least one CpG dinucleotide in the target sequence of the target gene is determined by the critical Ct value of the real-time PCR reaction. By using the method of analyzing DNA in a biological sample by real-time PCR reaction, the methylation state of the target sequence of the target gene can be conveniently detected, and the critical Ct value of the PCR reaction can be used to quickly and conveniently determine whether the sample is positive, thereby providing a non-invasive and convenient in vitro detection method for cervical cancer.

[0294] The sample is selected from cell lines, histological sections, tissue biopsies / paraffin-embedded tissues, body fluids, feces, colon effluent, urine, plasma, serum, whole blood, isolated blood cells, cells isolated from blood, or a combination thereof. Preferred samples are plasma and tissues.

[0295] The inventors of the present application have found that there are significant differences between the methylation states of the target sequences of the JAM3 gene, EPHA7 gene and ST6GALNAC5 gene in cervical cancer tissues and the methylation states of the target sequences of the genes in normal tissues: in cervical cancer tissues, the target sequences of the JAM3 gene, EPHA7 gene and ST6GALNAC5 gene are methylated, while in normal tissues, the target sequences of the JAM3 gene, EPHA7 gene and ST6GALNAC5 gene are not methylated. Therefore, the present application provides a method for in vitro detection of cervical cancer by detecting the methylation state of one or more gene target sequences of the JAM3 gene, EPHA7 gene and ST6GALNAC5 gene in a sample. The method provided by the present application can detect cervical cancer non-invasively and rapidly.

[0296] Example

[0297] The present application provides a general and / or specific description of the materials and test methods used in the experiments. In the following examples, unless otherwise specified, % means wt%, i.e., weight percentage. The reagents or instruments used without indicating the manufacturer are all conventional reagent products that can be obtained commercially.

[0298] Example 1 Primer and probe test

[0299] First, the low methylation level sites were screened in the second-generation sequencing information of 340 healthy WBC and 102 healthy plasma cfDNA samples. Secondly, the low methylation level sites screened were analyzed in plasma and cervical cancer tissues, and the sites that were different in 103 cervical cancer plasma and 102 normal plasma, and in 56 cervical cancer tissues and 56 adjacent tissues were screened as candidate markers. Then, the candidate markers were traced back to plasma. Finally, the sensitivity and specificity of cervical cancer tissues and normal plasma were verified, and three specific markers, JAM3 gene, EPHA7 gene, and ST6GALNAC5 gene, were identified.

[0300] Primers and probes were designed according to the target sequences of the above three genes. The designed primer and probe sequences are shown in Table 2 above.

[0301] Normal human leukocyte cell line DNA is usually in a low / non-methylated state and can be used as a negative control. The amount of DNA used in this embodiment is 15.75 ng / reaction; fully methylated DNA is in a high / fully methylated state and can be used as a positive control. The amount of DNA used in this embodiment is 200 pg / reaction. The DNA sample is first subjected to bisulfite conversion, and the converted BisDNA is used as a template to perform real-time PCR amplification using the above-mentioned primer probe. The β-actin (ACTB) gene is used as an internal reference, and a β-actin gene amplicon is created by using primers complementary to the β-actin gene sequence, and the β-actin gene amplicon is detected with a specific probe. Each sample is subjected to at least one real-time PCR, and in some specific embodiments, two or three real-time PCR tests are performed. The PCR system for the primer probe test is shown in Table 4 below.

[0302] Table 4 PCR system for primer probe test

[0303]

[0304]

[0305] Note: “F” stands for forward primer; “R” stands for reverse primer; “P” stands for probe.

[0306] The PCR amplification program used was: 94°C, 20 min; (93°C, 30 s; 57°C, 35 s-reading fluorescence signal) 45 cycles; 40°C, 5 s.

[0307] The results are shown in Table 5. When BisDNA of fully methylated DNA was used as a template, JAM3 gene, EPHA7 gene and ST6GALNAC5 gene were all effectively amplified; while when BisDNA of WBC was used as a template, except for the internal reference gene ACTB, the other target genes were not amplified.

[0308] Table 5 Test results of primers and probes for each gene

[0309]

[0310]

[0311] “No Ct” means no Ct value was detected.

[0312] Example 2

[0313] According to the results of cytology (TCT) tests, cervical precancerous lesions can be divided into low-grade squamous intraepithelial lesions (LSIL) and high-grade squamous intraepithelial lesions (HSIL). According to the results of histological biopsy, cervical intraepithelial neoplasia includes CIN1, CIN2 and CIN3. CIN 1 is a low-grade lesion, which refers to mild atypical cytological changes in the subepithelial 1 / 3 layer. CIN 2 is a high-grade lesion, which refers to moderate atypical cytological changes limited to the subepithelial 2 / 3 layer, with normal epithelial maturity. CIN 3 is a high-grade lesion, which refers to severe atypical cytological changes in which the lesion range exceeds the subepithelial 2 / 3 layer and even involves the entire layer.

[0314] In this example, 23 samples of CIN2 / 3 and cervical cancer exfoliated cells (10 ng / reaction), 22 samples of benign cervical diseases and CIN1 (10 ng / reaction) were selected, DNA was extracted, and after conversion to BisDNA by bisulfite, methylation of each site of JAM3, EPHA7 and ST6GALNAC5 genes was detected according to the PCR reaction system in Tables 6-8. The PCR amplification program is: 94°C, 20min; (93°C, 30S; 60°C, 35s-reading fluorescence signal) 45 cycles; 40°C, 5s.

[0315] Table 6 JAM3 PCR reaction system

[0316] Volume (μL) Final concentration Taq DNA Polymerase(Biochain) 1.2 / 4×buffer(Biochain) 11.9 1× JAM3_1F (10 μM) 1.0 250nM JAM3_1R (10 μM) 1.0 250nM JAM3_1P (10 μM) 1.0 100nM JAM3_2F (10 μM) 1.0 250nM JAM3_2R (10 μM) 1.0 250nM JAM3_2P (10 μM) 1.0 100nM JAM3_3F (10 μM) 1.0 250nM JAM3_3R (10 μM) 1.0 250nM JAM3_3P (10 μM) 1.0 100nM ACTB_F (10μM) 0.5 100nM ACTB_R(10μM) 0.5 100nM ACTB_P (10μM) 0.375 75nM BisDNA 4.0 / <![CDATA[H2O]]> 22.525 / Total 50.0 /

[0317] Table 7 EPHA7 PCR reaction system

[0318]

[0319]

[0320] Table 8 ST6GALNAC5 PCR reaction system

[0321]

[0322]

[0323] Note: In Table 6-8, “F” represents forward primer; “R” represents reverse primer; and “P” represents probe.

[0324] Finally, the Ct values ​​of real-time PCR for the target gene sequence of 23 cervical cancer samples and 22 normal benign samples were measured. The Ct values ​​of methylation detection at each site of JAM3, EPHA7 and ST6GALNAC5 genes were calculated and interpreted. The results are shown in Tables 9 and 10.

[0325] Table 9 Sensitivity of each gene in cervical cancer samples

[0326]

[0327]

[0328] Table 10 Specific detection of each gene in benign samples

[0329]

[0330] The results of Table 9 and Table 10 show that the detection of cervical cancer tissue and benign samples using JAM3 gene, EPHA7 gene and ST6GALNAC5 gene can achieve good sensitivity and specificity. When judging, firstly judge whether the gene detection result is positive according to the amplification of the three marker sites of the gene (it is considered that when the Ct value of at least one of the three markers, preferably at least two markers is less than 41, the sample is judged to be positive in the gene detection result); then judge whether the sample is positive according to the three gene results. The sensitivity of the three genes alone is 69.57%, 56.52% and 91.30% respectively; and the final sensitivity of the judgment reaches 86.96% when any one of the three genes is positive. The specificity of using JAM3, EPHA7 and ST6GALNAC5 genes alone to detect cervical cancer TCT samples and healthy TCT samples is 86.36%, 90.91% and 81.82% respectively, and the specificity of all three genes being negative is 90.91%.

[0331] Among the above three markers related to cervical cancer, judging from the test results of tissues, their tissue sensitivity is above 55%, and the sensitivity of the combined interpretation of the three genes can reach above 85%. Judging from the test results of benign tissues, the tissue specificity of single genes is above 80%, and the combined interpretation of three genes can reach above 90%. Under the conditions of small sample size verification, a tissue specificity of 80% is a relatively reasonable and high indicator level. Therefore, the above experimental results show that the three target genes selected in this application are potential markers for detecting methylation of cervical cancer.

[0332] Example 3

[0333] Two cervical exfoliated cell samples (S1 is a CIN1 sample, and S2 is a cervical cancer patient sample) were selected, and the methylation marker detection method of the present application was used. According to the PCR reaction system of Example 2, DNA was extracted, and after being converted into BisDNA by bisulfite, PCR detection was performed on the methylation of JAM3, EPHA7 and ST6GALNAC5 genes. According to the Ct value of each marker (≥41 is negative), the disease condition of the patient to whom the sample belongs was determined. When one or more of the three genes are positive, it is finally determined to be positive. The experimental results are shown in Tables 11 and 12.

[0334] Table 11 Judgment example of sample S1

[0335]

[0336] Table 12 Judgment example of sample S2

[0337]

[0338] The above experimental results show that the methylated DNA of the target gene target sequence is a marker for cervical cancer. Through the target gene target sequence methylated DNA detection of the present application, non-invasive detection of cervical cancer in vitro can be achieved, and the detection rate of cervical cancer in the nodule population can be improved.

[0339] In summary, the present application utilizes the above-mentioned compositions, nucleic acid sequences, kits and their uses, as well as the above-mentioned detection methods, to detect the methylated nucleic acid sequences of the target sequences of the target genes and their fragments, thereby realizing the in vitro detection of cervical cancer using the target sequence methylation biomarkers of the target genes, thereby effectively improving the sensitivity and specificity of in vitro detection of cervical cancer.

[0340] The above is only the preferred embodiment of the present application, and does not limit the present application in other forms. Any technician familiar with the profession may use the above disclosed technical content to change or modify it into an equivalent embodiment with equivalent changes. However, any simple modification, equivalent change and modification made to the above embodiment based on the technical essence of the present application without departing from the technical solution of the present application still falls within the protection scope of the technical solution of the present application.

Claims

1. A composition for in vitro detection of early cervical cancer, comprising: Nucleic acid used to detect the methylation status of the target gene, Wherein, the methylation state of the target gene is characterized by the methylation of the target sequence of the target gene, Wherein, the target gene is one or more of the JAM3 gene, the EPHA7 gene and the ST6GALNAC5 gene.

2. The composition according to claim 1, wherein The target genes are JAM3 gene, EPHA7 gene and ST6GALNAC5 gene.

3. The composition according to claim 1, wherein The target sequence of the JAM3 gene is as shown in any one of SEQ ID NOs: 1-12, or includes the sequence shown in any one of SEQ ID NOs: 1-12; Preferably, the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 1-4 and any one of SEQ ID NOs: 5-8; or the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 1-4 and any one of SEQ ID NOs: 9-12; or the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 5-8 and any one of SEQ ID NOs: 9-12, or the target sequence of the JAM3 gene includes a sequence as shown in any one of SEQ ID NOs: 1-4 and any one of SEQ ID NOs: 5-8 and any one of SEQ ID NOs: 9-12.

4. The composition according to claim 1, wherein The target sequence of the EPHA7 gene is as shown in any one of SEQ ID NOs: 13-24, or includes the sequence shown in any one of SEQ ID NOs: 13-24; Preferably, the target sequence of the EPHA7 gene includes the sequence shown in any one of SEQ ID NOs: 13-16 and any one of SEQ ID NOs: 17-20; or the target sequence of the JAM3 gene includes the sequence shown in any one of SEQ ID NOs: 13-16 and any one of SEQ ID NOs: 21-24; or the target sequence of the EPHA7 gene includes the sequence shown in any one of SEQ ID NOs: 17-20 and any one of SEQ ID NOs: 21-24, or the target sequence of the EPHA7 gene includes the sequence shown in any one of SEQ ID NOs: 13-16 and any one of SEQ ID NOs: 17-20 and any one of SEQ ID NOs: 21-24.

5. The composition according to claim 1, wherein The target sequence of the ST6GALNAC5 gene is as shown in any one of SEQ ID NOs: 25-36, or includes the sequence shown in any one of SEQ ID NOs: 25-36; Preferably, the target sequence of the ST6GALNAC5 gene includes a sequence as shown in any one of SEQ ID NOs: 25-28 and any one of SEQ ID NOs: 29-32, or the target sequence of the ST6GALNAC5 gene includes a sequence as shown in any one of SEQ ID NOs: 25-28 and any one of SEQ ID NOs: 33-36, or the target sequence of the VSTM2B gene includes a sequence as shown in any one of SEQ ID NOs: 29-32 and any one of SEQ ID NOs: 33-36, or the target sequence of the ST6GALNAC5 gene includes a sequence as shown in any one of SEQ ID NOs: 25-28 and any one of SEQ ID NOs: 29-32 and any one of SEQ ID NOs: 33-36.

6. An oligonucleotide for in vitro detection of cervical cancer, comprising: A fragment of at least 9 nucleotides of a sequence as shown in any one of SEQ ID NOs: 1-12 or a complementary sequence thereof and comprising at least one CpG dinucleotide sequence; and / or A fragment of at least 9 nucleotides of a sequence as shown in any one of SEQ ID NOs: 13-24 or a complementary sequence thereof and comprising at least one CpG dinucleotide sequence; and / or A fragment of at least 9 nucleotides of a sequence as shown in any one of SEQ ID NOs: 25-36 or a complementary sequence thereof and comprising at least one CpG dinucleotide sequence.

7. The oligonucleotide according to claim 6, further comprising: A fragment that hybridizes to at least 15 nucleotides of the sequence as shown in any one of SEQ ID NOs: 1-12 or its complementary sequence under moderately stringent or stringent conditions and comprises at least one CpG dinucleotide sequence; and / or A fragment that hybridizes to at least 15 nucleotides of the sequence as shown in any one of SEQ ID NOs: 13-24 or its complementary sequence under moderately stringent or stringent conditions and contains at least one CpG dinucleotide sequence; and / or A fragment that hybridizes to at least 15 nucleotides of the sequence as shown in any one of SEQ ID NOs: 25-36 or its complementary sequence under moderately stringent or stringent conditions and contains at least one CpG dinucleotide sequence.

8. A kit comprising the composition according to any one of claims 1 to 5 or the oligonucleotide according to claim 6 or 7.

9. Use of the composition according to any one of claims 1 to 5 or the oligonucleotide according to claim 6 or 7 in the preparation of a kit for in vitro detection of cervical cancer.

10. Use of JAM3 gene, EPHA7 gene and ST6GALNAC5 gene in preparing a kit for in vitro detection of early cervical cancer.

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