CN110512000A - Tumor markers, methylating reagent, kit and its application - Google Patents
Tumor markers, methylating reagent, kit and its application Download PDFInfo
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Abstract
The present invention relates to field of biotechnology, in particular to tumor markers, methylating reagent, kit and its application.The present invention passes through research discovery: the methylation level by detecting the gene promoter area TMEM240 can be very good to distinguish colorectal cancer sample from the stool sample of normal person.The present invention detects colorectal cancer using the methylating reagent containing the gene, and very high to the detection sensitivity of intestinal cancer and specificity.The present invention demonstrates relevant between the methylation level of the gene and Colorectal Cancer for the first time.
Description
Technical field
The present invention relates to field of biotechnology, in particular to tumor markers, methylating reagent, kit and its application.
Background technique
Colorectal cancer, also known as colorectal cancer are a kind of common malignants tumor of digestive tract.Its disease incidence China year by year
It increases, in China, coastal area, part such as Shanghai and Guangzhou, incidence of colorectal has leapt to second, has been only second to lung cancer.Mesh
Before think intestinal cancer formation be genetic defect and epigenetic defect accumulation result.Colorectal cancer early stage incidence of occult, Chang Wu
Manifest symptom, advanced stage may occur in which the symptoms such as hematochezia, abdominal pain, diarrhea.And when occur symptom it is medical when often advanced stage, this is to disease
People brings greatly pain and expensive medical expense.Therefore early discovery, early diagnosis, early treatment are to reduce Colorectal Cancer
One important measures of rate and the death rate.
Screening can be with early detection intestinal cancer and precancerous lesion, and removes lesion, to prevent the generation of intestinal cancer.It is big at present
The screening method of intestinal cancer mainly has occult blood test and enteroscopy.Occult blood test exists vulnerable to food effect or detects to adenoma
The not high problem of rate.Though colonoscopy is intestinal cancer diagnosis goldstandard, Population's compliance is not high when using as screening means.Therefore
It is badly in need of the intestinal cancer screening method that a kind of accuracy is high, compliance is high.
Excrement genetic test is increasingly taken seriously now as a kind of new intestinal cancer screening method.This methodThe intestinal cancer screening guide in the U.S. was included in 2016.This method have it is convenient, noninvasive, to intestinal cancer and cancer
The features such as recall rate of preceding lesion adenoma is high.It does pairs of intestinal cancer and detects high performance excrement gene detecting kit, mainly need
Overcome two big obstacles: the extraction of faeces DNA and marker selection.On the one hand, complicated component in excrement, to downstream reaction
Mortifier is more, and there are many more DNA of bacteria, and the target gene of people is extracted from such mixture, needs a set of Gao Min's
Gene extracts and purification process；On the other hand, there are many current and relevant marker of intestinal cancer, especially DNA methylation mark
Object, because studies have shown that, DNA methylation is the earliest events that tumour is formed.But many methylation markers are in cell, tissue
Level is done well, and when for screenings media such as excrement, blood, is just lowered to the sensibility and specificity of intestinal cancer,
For example vimentin gene, sensibility in the tissue have 83%, 46% are just fallen below in stool sample, similar goes back
There are the genes such as SFRP1, SFRP2, such marker is unable to satisfy the demand for being really used for intestinal cancer clinical detection.Therefore, it selects
Having the marker of high detection sensitivity and specificity to intestinal cancer in excrement is the key that intestinal cancer excrement genetic test, and
Such marker is expected to really be used for the clinical detection of intestinal cancer.
Summary of the invention
In view of this, the present invention provides a kind of tumor markers, methylating reagent, kit and its application.The tumour mark
Will object is very high to the sensibility of intestinal cancer in excrement.
In order to achieve the above-mentioned object of the invention, the present invention the following technical schemes are provided:
The present invention provides TMEM240 genes to prepare the application in tumor markers.
In some specific embodiments of the invention, the tumour is colorectal carcinoma.
In some specific embodiments of the invention, the tumour is colorectal cancer or adenoma.
In some specific embodiments of the invention, sample to be tested is tissue, body fluid or excreta.
In some specific embodiments of the invention, the body fluid includes extracellular fluid, tissue fluid, blood, lymph
Liquid, cerebrospinal fluid or aqueous humor.
In some specific embodiments of the invention, the excreta is sputum, urine or excrement.
The present invention also provides the methylating reagents of TMEM240 gene, obtain including the island CpG for TMEM240 gene
Capture sequence, primer and/or probe.
In some specific embodiments of the invention, methylating reagent provided by the invention includes being directed to TMEM240 base
Capture sequence, primer and/or the probe that the island CpG of the promoter region of cause or the promoter region near zone obtains.
In some specific embodiments of the invention, the tool of capture sequence described in methylating reagent provided by the invention
Have it is following shown in any one in nucleotide sequence:
I, there is nucleotide sequence shown in SEQ ID NO:1；
II, there is nucleotide sequence shown in SEQ ID NO:1 to be modified, replace, miss or add one or more alkali
The nucleotide sequence or have the function of core similar in the island the CpG acquisition of nucleotide sequence shown in SEQ ID NO:1 that base obtains
Nucleotide sequence；
III, at least sequence of 80% homology or there is SEQ with nucleotide sequence shown in SEQ ID NO:1
Nucleotide sequence similar in the function that the island CpG of nucleotide sequence shown in ID NO:1 obtains；
The complementary series of IV, the sequence as shown in I, II or III.
In some specific embodiments of the invention, the tool of upstream primer described in methylating reagent provided by the invention
Have it is following shown in any one in nucleotide sequence:
V, there is nucleotide sequence shown in SEQ ID NO:2；
VI, there is nucleotide sequence shown in SEQ ID NO:2 to be modified, replace, miss or add one or more alkali
The nucleotide sequence that base obtains；
VII, at least sequence of 80% homology or there is SEQ ID with nucleotide sequence shown in SEQ ID NO:2
Nucleotide sequence similar in the function that the island CpG of nucleotide sequence shown in NO:2 obtains；
VIII, the complementary series of the sequence as shown in V, VI or VII.
In some specific embodiments of the invention, the tool of downstream primer described in methylating reagent provided by the invention
Have it is following shown in any one in nucleotide sequence:
Ⅸ, there is nucleotide sequence shown in SEQ ID NO:3；
Ⅹ, there is nucleotide sequence shown in SEQ ID NO:3 to be modified, replace, miss or add one or more alkali
The nucleotide sequence that base obtains；
Ⅺ, at least sequence of 80% homology or there is SEQ ID with nucleotide sequence shown in SEQ ID NO:3
Nucleotide sequence similar in the function that the island CpG of nucleotide sequence shown in NO:3 obtains；
Ⅻ, the complementary series of the sequence as shown in Ⅸ, Ⅹ or Ⅺ.
In some specific embodiments of the invention, probe described in methylating reagent provided by the invention has such as
Any one in nucleotide sequence shown in lower:
XIII, there is nucleotide sequence shown in SEQ ID NO:4；
XIV, there is nucleotide sequence shown in SEQ ID NO:4 to be modified, replace, miss or add one or more
The nucleotide sequence that base obtains；
XV, at least sequence of 80% homology or there is SEQ ID with nucleotide sequence shown in SEQ ID NO:4
Nucleotide sequence similar in the function that the island CpG of nucleotide sequence shown in NO:4 obtains；
The complementary series of XVI, the sequence as shown in XIII, XIV or XV.
The present invention also provides application of the methylating reagent in the kit of preparation detection tumour.
In some specific embodiments of the invention, tumour described in the application of methylating reagent provided by the invention
For colorectal carcinoma.
In some specific embodiments of the invention, tumour described in the application of methylating reagent provided by the invention
For colorectal cancer or adenoma.
In some specific embodiments of the invention, sample to be tested in the application of methylating reagent provided by the invention
For tissue, body fluid or excreta.
In some specific embodiments of the invention, body fluid described in the application of methylating reagent provided by the invention
Including extracellular fluid, tissue fluid, blood, lymph, cerebrospinal fluid or aqueous humor.
In some specific embodiments of the invention, drained described in the application of methylating reagent provided by the invention
Object is sputum, urine or excrement.
The present invention also provides a kind of kits for detecting tumour, including normal in the methylating reagent and kit
Reagent.
In some specific embodiments of the invention, kit tumour detected provided by the invention is Colon and rectum
Tumour.
In some specific embodiments of the invention, kit tumour detected provided by the invention is Colon and rectum
Cancer or adenoma.
In some specific embodiments of the invention, kit sample to be tested detected provided by the invention is group
It knits, body fluid or excreta.
In some specific embodiments of the invention, kit body fluid detected provided by the invention includes cell
External solution, tissue fluid, blood, lymph, cerebrospinal fluid or aqueous humor.
In some specific embodiments of the invention, kit excreta detected provided by the invention be sputum,
Urine or excrement.
The present invention also provides a kind of detection methods of tumour, by detecting the methylation level of TMEM240 gene, area
Divide normal sample and tumor sample.
In some specific embodiments of the invention, the present invention is mentioned through the detection gene promoter area TMEM240 and is opened
The methylation level of mover area near zone distinguishes normal sample and tumor sample.
In some specific embodiments of the invention, methylation level uses the methylating reagent or described
Kit detection.
In some specific embodiments of the invention, examination criteria are as follows: tumor specimen and normal mark are judged according to dividing value
This, the dividing value of the Ct value in stool sample is 32~42, it is preferable that the dividing value of the Ct value in stool sample is 35, the excrement
The dividing value that the Ct value of sample is less than the Ct value is then judged as tumor specimen, and the Ct value of the stool sample is more than or equal to described
The dividing value of Ct value is then judged as normal specimen.
The dividing value can be adjusted according to the actual situation.
The present invention passes through research discovery: the methylation level by detecting the gene promoter area TMEM240, can be fine
The stool sample from normal person in distinguish colorectal cancer sample.The present invention is exactly to be tried using the methylation containing the gene
Agent detects colorectal cancer, and to the detection sensitivity of intestinal cancer and specificity very high.The present invention demonstrates the base for the first time
It is relevant between the methylation level and Colorectal Cancer of cause.
Compared with the marker of existing detection intestinal cancer, marker provided by the invention and technical solution can be with very high
Sensibility and specificity detect colorectal cancer, specifically have the following:
1, the methylating reagent provided by the invention containing TMEM240 gene can be in specificity in stool sample
When 94%, 83% colorectal cancer is detected.
Methylating reagent provided by the invention containing TMEM240 gene and extraction detection method can be very convenient, accurate
Colorectal cancer and normal person are judged in ground, and the methylating reagent of the gene is expected to be used for excrement gene detecting kit, and services
In the clinical detection of intestinal cancer.
Detailed description of the invention
In order to more clearly explain the embodiment of the invention or the technical proposal in the existing technology, below will to embodiment or
Attached drawing needed to be used in the description of the prior art is briefly described.
During Fig. 1 shows that 1 excrement of embodiment is tested, the ROC curve of TMEM240 genetic test colorectal cancer；
During Fig. 2 shows that 1 excrement of embodiment is tested, TMEM240 gene standard curve AFLP system；
Fig. 3 shows in 19 pairs of histological examinations of comparative example 2, the ROC curve of SFRP1 genetic test colorectal cancer；
During Fig. 4 shows that 36 excrement of comparative example 2 are tested, the ROC curve of SFRP1 genetic test colorectal cancer.
Specific embodiment
The invention discloses a kind of tumor markers, methylating reagent, kit and its application, those skilled in the art
Present disclosure can be used for reference, realization of process parameters is suitably modified.In particular, it should be pointed out that all similar substitutions and modifications
Apparent to those skilled in the art, they are considered as being included in the present invention.Method and application of the invention
Be described by preferred embodiment, related personnel obviously can not depart from the content of present invention, in spirit and scope it is right
Method described herein and application are modified or appropriate changes and combinations, carry out implementation and application the technology of the present invention.
Raw materials used, auxiliary material and examination in tumor markers provided by the invention, methylating reagent, kit and its application
Agent is available on the market.
Below with reference to embodiment, the present invention is further explained:
Embodiment 1
36 stool samples (18 colorectal cancers, 18 normal, through colonoscopy or definitive pathological diagnosis) is chosen, is ground
100ul capture magnetic bead (the capture sequence containing TMEM240 gene) is added in centrifugation, and technical solution operates as described above,
DNA 15ul after finally obtaining Bisulfite conversion.Then the methylation level of qMSP detection TMEM240 is carried out.
QMSP reaction system: 25ul (nuclease-free water 8.2ul, 5 × Colorless Go Taq Flexi Buffer
5ul, MgCl2 (25mM) 5ul, dNTPs (10mM) 1ul, Go Taq Hot Start polymerase 0.5ul, Forward
Primer (100uM) 0.125ul, Reverse primer (100uM) 0.125ul, Probe (100uM) 0.05ul, DNA
5ul).Response procedures: 95 DEG C of 4min, (95 DEG C of 20s, 56 DEG C of 30s, 72 DEG C of 30s) × 45Cycles, 37 DEG C of 30s.
Copy number of the gene in sample is finally calculated according to standard curve.
The site that TMEM240 gene methylates is relative constant, is predominantly located on promoter region or the neighbouring island CpG.
Wherein one group of capture sequence, primer and probe is devised for these regions, and in TMEM240 gene methylation reagent.
The capture sequence that contains in reagent, primed probe are as follows:
The capture sequence of TMEM240: 5 '-
GGTTGTGGACTCACCGGCCACAGTTGCAGTGGCAGACGC-3’
The qMSP primed probe of TMEM240:
Forward Primer:5 '-CGCGTGTTTGATGGATATGAAC-3 '
Reverse Primer:5 '-CGACCACAATTACAATAACAAACG-3 '
Probe:5 '-CGTATTTGCGGGGCGAGGATC-3 '
In excrement experiment, the ROC curve of TMEM240 genetic test colorectal cancer is as shown in Figure 1:
For colorectal cancer, the detection sensitivity of TMEM240 gene is 83% (15/18), and specificity is 94% (17/
18), area is 0.949 (95%CI:0.883-1, p < 0.0001) under ROC curve
In excrement experiment, TMEM240 gene standard curve AFLP system is as shown in Figure 2:
Marking bent amplification efficiency is 101%, linearity R2=0.999.
The initial data of 1 excrement of table experiment
1 note of table: " no amplification " indicates no amplification curve, and no Ct data belong to the range greater than dividing value.
Comparative example 1
There is research to be mentioned with QIAamp DNA Stool Mini Kit (QIAGEN) to the DNA of stool sample at present
It takes, then qualitatively or quantitatively detects sample with methylation status of PTEN promoter (MSP) or quantitative methylation status of PTEN promoter (qMSP)
The level of middle marker.Colorectal cancer is wherein detected by MSP because needing to run electrophoresis, it is more inconvenient to operate, and has product dirty
Contaminate risk；The total DNA that the DNA in excrement is people and bacterium, real people are extracted by QIAamp DNA Stool Mini Kit
Tumour DNA it is few, be unfavorable for subsequent PCR detection.
Comparative example 2
Some researches show that SFRP1 gene methylation is related with intestinal cancer, the methylation of the gene is detected in excrement,
Colorectal cancer can be detected.53 stool samples (29 intestinal cancer, 7 adenomas, 17 it is normal) in experiment, be in specificity
When 86%, 89% colorectal carcinoma can be detected.(Zhang W, Bauer M,Croner RS,Pelz JO,Lodygin D,
Hermeking H,Sturzl M, Hohenberger W,Matzel KE.DNA stool test for colorectal
cancer: Hypermethylation of the secreted frizzled-related protein-1
gene.DISEASES OF THE COLON&RECTUM 2007；50(10):1618-26；discussion 1626-7.)
The methylation level of SFRP1 gene is equally had detected in 19 pairs of tissues and 36 stool samples, in stool sample
Target gene extracting method is the same as embodiment 1.In 19 pairs of histological examinations, according to Protocol, QIAamp DNA Kit is used respectively
(QIAGEN) tissue DNA is extracted, then converts DNA with EZ DNA Methylation Kit (Zymo Research).
Then the methylation level of qMSP detection SFRP1 is carried out.
QMSP reaction system and reaction step are tested with the excrement of embodiment 1.Finally gene is calculated according to standard curve to exist
Methylation value in sample: (Target/ACTB) * 100.QMSP primed probe used is the same as embodiment 1.
The ROC curve of SFRP1 genetic test colorectal cancer is as shown in Figure 3:
For Colorectal Carcinoma, the detection sensitivity of SFRP1 gene is 89%, and specificity is 95%, under ROC curve
Area is 0.972 (95%CI:0.929-1, p < 0.001).
In 36 excrement experiments, the ROC curve of SFRP1 genetic test colorectal cancer is as shown in Figure 4:
For colorectal cancer, the detection sensitivity of SFRP1 gene is 67%, and specificity is 94%, area under ROC curve
It is 0.892 (95%CI:0.790-0.994, p < 0.0001).
It can be seen that SFRP1 gene pairs Colorectal Carcinoma detection sensitivity with higher and specificity, and in excrement
Just its sensibility just significantly reduces in sample.
The above is only a preferred embodiment of the present invention, it is noted that for the ordinary skill people of the art
For member, various improvements and modifications may be made without departing from the principle of the present invention, these improvements and modifications
It should be regarded as protection scope of the present invention.
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Claims (24)
1.TMEM240 gene is preparing the application in tumor markers.
2. application as described in claim 1, which is characterized in that the tumour is colorectal carcinoma.
3. application as described in claim 1, which is characterized in that the tumour is colorectal cancer or adenoma.
4. application as described in any one of claims 1 to 3, which is characterized in that sample to be tested is tissue, body fluid or excreta.
5. application as claimed in claim 4, which is characterized in that the excreta is sputum, urine or excrement.
The methylating reagent of 6.TMEM240 gene, which is characterized in that the capture obtained including the island CpG for TMEM240 gene
Sequence, primer and/or probe.
7. methylating reagent as claimed in claim 6, which is characterized in that including for TMEM240 gene promoter region or
Capture sequence, primer and/or the probe that the island CpG of the promoter region near zone obtains.
8. methylating reagent as claimed in claims 6 or 7, which is characterized in that the capture sequence has core as follows
Any one in nucleotide sequence:
I, there is nucleotide sequence shown in SEQ ID NO:1；
II, there is nucleotide sequence shown in SEQ ID NO:1 to be modified, replace, miss or add one or more bases and obtain
Nucleotide sequence or have the function of nucleotide sequence shown in SEQ ID NO:1 the island CpG obtain similar in nucleotide
Sequence；
III, at least sequence of 80% homology or there is SEQ ID NO with nucleotide sequence shown in SEQ ID NO:1:
Nucleotide sequence similar in the function that the island CpG of nucleotide sequence shown in 1 obtains；
The complementary series of IV, the sequence as shown in I, II or III.
9. such as the described in any item methylating reagents of claim 6 to 8, which is characterized in that the upstream primer has following institute
Any one in nucleotide sequence shown:
V, there is nucleotide sequence shown in SEQ ID NO:2；
VI, there is nucleotide sequence shown in SEQ ID NO:2 to be modified, replace, miss or add one or more bases and obtain
The nucleotide sequence obtained；
VII, at least sequence of 80% homology or there is SEQ ID NO:2 with nucleotide sequence shown in SEQ ID NO:2
Shown in nucleotide sequence the island CpG obtain function similar in nucleotide sequence；
VIII, the complementary series of the sequence as shown in V, VI or VII；
The downstream primer has any one in nucleotide sequence as follows:
Ⅸ, there is nucleotide sequence shown in SEQ ID NO:3；
Ⅹ, there is nucleotide sequence shown in SEQ ID NO:3 to be modified, replace, miss or add one or more bases and obtain
The nucleotide sequence obtained；
Ⅺ, at least sequence of 80% homology or there is SEQ ID NO:3 with nucleotide sequence shown in SEQ ID NO:3
Shown in nucleotide sequence the island CpG obtain function similar in nucleotide sequence；
Ⅻ, the complementary series of the sequence as shown in Ⅸ, Ⅹ or Ⅺ.
10. such as the described in any item methylating reagents of claim 6 to 9, which is characterized in that the probe has as follows
Any one in nucleotide sequence:
XIII, there is nucleotide sequence shown in SEQ ID NO:4；
XIV, there is nucleotide sequence shown in SEQ ID NO:4 to be modified, replace, miss or add one or more bases and obtain
The nucleotide sequence obtained；
XV, at least sequence of 80% homology or there is SEQ ID NO:4 with nucleotide sequence shown in SEQ ID NO:4
Shown in nucleotide sequence the island CpG obtain function similar in nucleotide sequence；
The complementary series of XVI, the sequence as shown in XIII, XIV or XV.
11. such as application of the described in any item methylating reagents of claim 6 to 10 in the kit of preparation detection tumour.
12. application as claimed in claim 11, which is characterized in that the tumour is intestinal cancer.
13. application as claimed in claim 11, which is characterized in that the tumour is colorectal cancer.
14. such as the described in any item applications of claim 11 to 13, which is characterized in that sample to be tested is body fluid or excreta.
15. application as claimed in claim 14, which is characterized in that the excreta is sputum, urine or excrement.
16. a kind of kit for detecting tumour, which is characterized in that including the described in any item methylations of such as claim 6 to 10
Common reagent in reagent and kit.
17. kit as claimed in claim 16, which is characterized in that the tumour is colorectal carcinoma.
18. kit as claimed in claim 16, which is characterized in that the tumour is colorectal cancer or adenoma.
19. such as the described in any item kits of claim 16 to 18, which is characterized in that sample to be tested is tissue, body fluid or row
Let out object.
20. kit as claimed in claim 19, which is characterized in that the excreta is sputum, urine or excrement.
21. a kind of detection method of tumour, which is characterized in that by detecting the methylation level of TMEM240 gene, distinguish normal
Sample and tumor sample.
22. detection method as claimed in claim 21, which is characterized in that by the detection gene promoter area TMEM240 and open
The methylation level of mover area near zone distinguishes normal sample and tumor sample.
23. the detection method as described in claim 21 or 22, which is characterized in that methylation level use as claim 6 to
The described in any item kits detections of 10 described in any item methylating reagents or such as claim 16 to 18.
24. the detection method as described in claim 21 or 22, which is characterized in that examination criteria are as follows: judge tumour according to dividing value
Sample and normal specimen, the dividing value of the Ct value in stool sample are 32~42, and the Ct value of the stool sample is less than the Ct value
Dividing value be then judged as tumor specimen, the dividing value that the Ct value of the stool sample is more than or equal to the Ct value is then judged as normal mark
This.
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| WO2021222621A1 (en) * | 2020-04-29 | 2021-11-04 | Taipei Medical University | Method for early detection, prediction of treatment response and prognosis of colorectal cancer |
| CN115917010A (en) * | 2020-04-29 | 2023-04-04 | 台北医学大学 | Method for early detection, prediction of treatment response and prognosis of colorectal cancer |
| TWI804857B (en) * | 2020-04-29 | 2023-06-11 | 臺北醫學大學 | Method for early detection, prediction of treatment response and prognosis of colorectal cancer |
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| TW202003546A (en) | 2020-01-16 |
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