Background
Statistically, about 90% of cancer patients die from secondary tumors, and metastasis of the primary tumor or release of Circulating Tumor Cells (CTCs) is often responsible for the formation of secondary tumors. As early as 1869, the scientist Ashworth first proposed the concept of CTCs. CTCs are currently defined as tumor cells released into the peripheral blood circulation from solid tumors or metastases, either spontaneously or as a result of a diagnostic procedure. Tumor cells which enter the circulation and are not cleared form tiny cancer emboli through migration, adhesion and mutual aggregation, and develop into metastases under certain conditions. Therefore, the detection of the CTCs in the peripheral blood indicates that the tumor metastasis is likely to occur, and the detection of the CTCs in the peripheral blood has important clinical application value and has great significance for clinical early screening and diagnosis, curative effect and prognosis. The U.S. Food and Drug Administration (FDA) has also approved a CTCs detection system for predicting progression-free survival (PFS) and total survival (OS) of metastatic breast, colorectal or prostate cancer.
For hundreds of millions of peripheral blood cells, the number of CTCs in the peripheral blood is rare, approximately every 105~107Only one CTCs is present in a single monocyte. The existing detection technologies for CTCs mainly include Immunocytochemistry (ICC), Flow Cytometry (FCM), and reverse transcription polymerase chain reaction (RT-PCR). The immunocytochemistry method has the defects that the sensitivity is low, and factors such as target antigen non-expression of poorly differentiated tumor cells, lymphocyte cross reaction and the like influence the detection specificity; flow cytometry is expensive, time consuming and low in sensitivity; the RT-PCR method is complicated in steps, time-consuming, long in time-consuming, easy to pollute and brings great inconvenience to clinical detection, and false positive and false negative can be caused by epithelial cell pollution, illegal transcription of markers, expression difference among individuals and the like during sampling.
Although there is a precedent of using fluorescence PCR to detect CTCs (see, for example, Jinxiangfeng, etc. non-small cell lung cancer patients peripheral blood CK19mRNA expression and significance, Qilu journal of medicine, 23 rd volume 3 th phase), it still suffers from false positive and false negative (especially false negative) results, and the interpretation results are not intuitive, and it is difficult to perform semi-quantitative analysis, so the sensitivity is very low, and it has to be judged by dividing "1 copy number per microliter is greater than or equal to the positive result, and 1 copy number per microliter is negative" (i.e. 1000 copy/ml), which has little value for popularization and use in the case that each milliliter of samples is only 1-100 copy in many practical patients, resulting in a lot of false negative results, so that doctors have no sense.
For this reason, the present inventors have made diligent and long-term efforts to find that the final detection results are not good using conventional RNA extraction kits, and thus improvement is required from the time of processing a sample (e.g., peripheral blood); it is also found that the improvement of partial primers and probes and their PCR amplification steps can make the interpretation result intuitive and can perform semi-quantitative analysis in a larger range; more surprisingly, the inventor abandons the research miszone of the prior art which pursues quantitative or semi-quantitative analysis, designs a primer pair and a probe which do not interfere with each other, and greatly increases the sensitivity and the reliability of qualitative analysis while keeping certain semi-quantitative analysis capability. Moreover, the method is easy to automate and scale, can reduce manual operation errors and pollution, saves operation time and cost, can be widely used for grading and prognosticating the diseases of patients with breast cancer, colon cancer, prostate cancer, lung cancer and gastric cancer, and provides a basis for selecting a treatment scheme and monitoring the treatment effect.
Disclosure of Invention
The invention aims to provide the application of reagents used in the novel detection method in the preparation of a kit for detecting circulating tumor cell molecule-specific markers. In addition, the invention also provides a reagent, a kit and the like which can be used in the application.
In particular, in a first aspect, the present invention provides the use of reagents used in a detection method for the manufacture of a kit for the detection of a marker specific for a cellular molecule of a circulating tumour (e.g. breast, colon, prostate, lung and/or stomach cancer, preferably breast cancer), wherein the detection method comprises:
(1) processing a sample (e.g., peripheral blood);
(2) extracting nucleic acid from the treated product obtained in the step (1); and,
(3) and (3) carrying out fluorescence PCR detection on the nucleic acid extract obtained in the step (2).
Preferably in the use of the first aspect of the invention, the detection of the circulating tumour cell molecule specific marker is also carried out by said detection method, although the circulating tumour cell molecule specific marker may be detected by other methods.
In the kit, different reagents may be separately contained in different containers, or several reagents which are stored for a long period of time without chemical reaction may be selected and stored in the same container. The container may be a bottle, a cartridge, a syringe, or the like capable of containing the above-mentioned reagents, such as containers conventionally used for containing PCR, enzyme, or nucleic acid reagents. Since some reagents are readily available, these reagents may not be included, e.g., only a portion of the reagents may be included in the kit. In addition, the kit may also contain a label or instructions indicating that the assay according to the first aspect of the invention is to be carried out. The label may be affixed to the container or printed directly onto the container, or separate instructions may be provided. The kit may be further packaged in a larger package as desired, such as for ease of transport and storage, and such products are also within the scope of the present invention. A preferred kit is the kit of the fourth aspect of the invention hereinafter.
As used herein, the term "sample" or "specimen" is used interchangeably to refer to an ex vivo sample, such as blood, blood product, urine or saliva, which potentially contains a target nucleic acid. Detection methods in the application of the present invention may be considered as an independent aspect of the present invention. The detection method is a double detection method, and aims at two CTCs markers respectively, so that the false positive of a qualitative result can be eliminated. Since whether the detected small amount or trace amount of CTCs can cause the secondary disease of the tumor or not can be judged by an experienced doctor according to the comprehensive conditions of the constitution, medical history, clinical symptoms, etc. of the corresponding person, the detection method in the application of the present invention is preferably a non-diagnostic method, i.e., a method in which the diagnosis result or health condition of the disease cannot be directly obtained.
Preferably, in the application of the first aspect of the present invention, the method for detecting fluorescence PCR in step (3) comprises: (3-1) mixing a nucleic acid extract, a reverse transcriptase, an RNase inhibitor, a DNA polymerase, dNTPs, a target nucleic acid primer pair and a probe labeled with a fluorophore and a quencher and having a detection wavelength different from that of the fluorophore labeled with the two probes in a single PCR reaction tube, wherein,
the target nucleic acid primer pair comprises:
AACGAGCCAGCCTATCTTGAATC,
TTCTGACTTGATCTGTGACCGGAG,
CTGAATCCAATCTTTGCTCACC, and
ATGCTTGAAGGCCAATATGA,
the target nucleic acid probe comprises:
CCGACATCGCCGCTCCGTAACAT, and
CCTCTATTCAGATCCAGCGGATA
(3-2) carrying out reverse transcription and PCR reaction, and detecting fluorescence with different wavelengths in real time; and,
(3-3) judging whether the marker target nucleic acid exists in the sample according to the Ct value calculated by the fluorescence detection result.
In this context, "single PCR reaction vessel" means that the reverse transcription and real-time PCR processes are technically carried out in the same vessel, without having to replace the vessel. In the real-time PCR method of the first aspect of the invention, the steps of cDNA synthesis, PCR amplification and real-time fluorescence detection can be completed in the same container, and the container does not need to be replaced in the whole process, so that the operation is convenient, the time is saved, and the error is reduced. The operator only needs to add the sample and the reaction reagent into the container, and the whole process is automatically completed by a common real-time fluorescence PCR instrument sold in the market.
Typically, each probe is labeled with a fluorescent group at the 5 'end and a quencher group at the 3' end of the nucleotide sequence. Preferably wherein each probe is labelled with a different fluorophore. Preferably, fluorescent groups and quenching groups thereof are commercially available, e.g., those which can be used And conventional products, which have different detection wavelengths, and can also be used to synthesize probes labeled with fluorescent labels, with purity meeting HPLC standard and without impurity bands, wherein the concentration of each target nucleic acid probe in the single PCR reaction vessel is greater than 5pmol/ml, preferably 6-12 pmol/ml, more preferably 7-10 pmol/ml, and most preferably 8 pmol/ml. In the embodiment of the present invention, the fluorescent-labeled probes labeled with different detection wavelengths used therein are synthesized by Shanghai Biotechnology engineering services Co., Ltd, and the preferred fluorescent group is any combination of two of FAM, VIC, NED, TexasRed and CY 5. Therefore, it may be further preferred that in the method of fluorescence PCR detection in step (3), each probe is labeled with a different fluorescent group, preferably a fluorescent group selected from FAM, VIC, NED, Texas Red and CY 5.
In the present invention, in order to balance the amplification conditions of different primer pairs and to expand the range capable of semiquantitation as much as possible, experiments have found that the optimal conditions are as follows: the conditions for each cycle of the PCR reaction were 94 ℃ for 10 seconds and 60 ℃ for 30 seconds. In a specific embodiment of the present invention, the PCR reaction is preceded by reverse transcription, i.e., denaturation at 42 ℃ for 30min and preferably at 94 ℃ for 10min, and then 45 cycles of the above conditions are performed.
The nucleic acid extraction may be performed by a conventional boiling method, a phenol-chloroform extraction method, a TRIzol method, a column method, or the like, and preferably the optimized magnetic bead extraction method of the present invention, that is, the method for nucleic acid extraction in step (2) is preferably a method for extracting RNA by a magnetic bead method. Such a method, in combination with the method of sample processing below, can effectively ameliorate the impact of processing/extraction failure present in the prior art. Preferred methods of nucleic acid extraction include:
adding a nucleic acid extract (preferably, the nucleic acid extract contains guanidinium isothiocyanate, sodium ethylenediaminetetraacetate, tween-20, sodium perchlorate, ethanol, and a pH buffer (e.g., Tris-HCl) to the treated product, incubating, adding magnetic beads (e.g.,magnetic beads), mixed well, magnetically separated, the supernatant discarded, washed (preferably twice, more preferably wherein the wash used for the first wash comprises sodium perchlorate and ethanol, and still more preferably wherein the wash used for the second wash comprises ethanol), and eluted (preferably wherein the eluent used for the elution comprises a pH buffer (e.g., Tris-HCl).
Although the sample can be directly subjected to nucleic acid extraction and/or fluorescence PCR detection, the present inventors have found that the final detection result can be effectively improved by performing a preliminary treatment before the nucleic acid extraction. The use of claim 1, wherein the method of treatment in step (1) comprises,
removing plasma from peripheral blood, lysing with cell lysate (e.g., ammonium chloride red blood cell lysate), adding anti-CD 45 immunomagnetic beads, mixing, incubating, magnetically separating, discarding supernatant, and washing (preferably with pH buffer (e.g., PBS)).
The invention also provides reagents and preferably reagents for use in the first aspect of the invention. For example, in a second aspect, the present invention provides a reagent for use in the first aspect of the present invention, which is the reagent for use in step (3) of the use, characterized in that it comprises a target nucleic acid primer pair and a probe, wherein the probe is labeled with a fluorophore and a quencher, and the detection wavelengths of the fluorophore labeled with the two probes are different, wherein,
the target nucleic acid primer pair comprises:
AACGAGCCAGCCTATCTTGAATC,
TTCTGACTTGATCTGTGACCGGAG,
CTGAATCCAATCTTTGCTCACC, and
ATGCTTGAAGGCCAATATGA,
the target nucleic acid probe comprises:
CCGACATCGCCGCTCCGTAACAT, and
CCTCTATTCAGATCCAGCGGATA。
preferably the reagent of the second aspect of the invention further comprises a reverse transcriptase, an RNase inhibitor, a DNA polymerase and dNTPs (including dATP, dCTP, dGTP and dTTP). Thus, a complete fluorescent PCR kit can be constructed.
Also preferably in the reagent of the second aspect of the present invention, each probe is labeled with a different fluorescent group, preferably a fluorescent group selected from FAM, VIC, NED, Texas Red and CY 5.
As another example, in a third aspect, the invention provides a reagent for use in the first aspect of the invention, which is the reagent used in steps (1) and (2) of the use, characterized in that it comprises a cell lysate (e.g., ammonium chloride red cell lysate), anti-CD 45 immunomagnetic beads and a wash solution (preferably the wash solution is a pH buffer (e.g., PBS)), and a nucleic acid extract (preferably the nucleic acid extract comprises guanidinium isothiocyanate, sodium edetate, tween-20, sodium perchlorate, ethanol and a pH buffer (e.g., Tris-HCl)), magnetic beads (e.g.,D-Beads magnetic Beads), a wash solution (preferably two wash solutions, more preferably one of the wash solutions comprises sodium perchlorate and ethanol, and even more preferably the other wash solution comprises ethanol), and an eluent (preferably the eluent comprises a pH buffer (e.g., Tris-HCl)). Thus, a kit for peripheral blood treatment and nucleic acid extraction can be constituted. The inventors have found that it is possible to obtain,the treatment of peripheral blood and nucleic acid extraction are beneficial to the detection result of fluorescence PCR.
In a fourth aspect, the invention provides a kit for detecting a marker specific for a cellular molecule of a circulating tumour (e.g. breast, colon, prostate, lung and/or stomach cancer, preferably breast cancer) comprising an agent of the second aspect of the invention and/or an agent of the third aspect of the invention. Preferably, it does not contain an internal control nucleic acid.
Preferably the kit of the fourth aspect of the invention comprises reagents according to the second aspect of the invention.
It is also preferred that the kit of the fourth aspect of the invention comprises the reagents of the third aspect of the invention.
It is also preferred that the kit of the fourth aspect of the invention comprises a reagent of the second aspect of the invention and a reagent of the third aspect of the invention.
In a fifth aspect, the invention provides a primer, probe mixture, which is a mixture of primers or probes selected from the group consisting of
AACGAGCCAGCCTATCTTGAATC,
TTCTGACTTGATCTGTGACCGGAG,
CTGAATCCAATCTTTGCTCACC,
ATGCTTGAAGGCCAATATGA,
CCGACATCGCCGCTCCGTAACAT, and
CCTCTATTCAGATCCAGCGGATA。
the mixture may be used in the application of the first aspect of the invention and may also be used to constitute a reagent according to the second aspect of the invention and/or a kit according to the fourth aspect of the invention.
The invention has the beneficial effects that: the rapid and hypersensitive CTCs detection is established, can be used for detecting whether CTCs exist in peripheral blood of patients with breast cancer, colon cancer, prostate cancer, lung cancer and gastric cancer, has high accuracy, greatly reduces the possibility of false positive and false negative, particularly almost eliminates the false negative result, and is suitable for practical popularization and use; the sensitivity is high, the lowest detection limit can detect 1 copy tumor cell in 7.5mL blood, and is improved by several orders of magnitude compared with the prior art; moreover, the method is convenient and quick to operate, easy to automate and scale, capable of shortening the detection time, reducing errors caused by manual operation, free of adding internal control primers and probes and capable of saving the detection cost.
Example 3 fluorescent real-time quantitative PCR amplification
1, primer and Probe sequences
The following primer pairs and probes were synthesized, 6 nucleic acid sequences in total:
wherein the primer pair is as follows:
AACGAGCCAGCCTATCTTGAATC
TTCTGACTTGATCTGTGACCGGAG
CTGAATCCAATCTTTGCTCACC
ATGCTTGAAGGCCAATATGA
wherein the probe is
CCGACATCGCCGCTCCGTAACAT
CCTCTATTCAGATCCAGCGGATA
2, fluorescent labeling
The 5 'end of the probe is respectively marked with fluorescence labeling FAM and CY5, and the 3' end is marked with corresponding quenching groups.
3, PCR reaction conditions
The reverse transcription and the PCR amplification are carried out in the same reaction system, the total volume of the system is 60uL, and the final concentration of each component is as follows: 40uL of the nucleic acid extract obtained in example 2 or the CK19 gene positive standard at various dilutions, 15pmol/ml for each of the above 2 primer pairs, 8pmol/ml for each of the above 2 probes, 0.2mmol/ml for each of dNTP concentrations, and 10 XPCR buffer (available from TaKaRa, pH8.3, containing Mg2+) 6uL of Taq DNA polymerase, 5U of M-MLV reverse transcriptase, 20U of Rnasin5U and the balance of deionized water.
The steps of reverse transcription and PCR reaction are as follows: 30min at 42 ℃, 10min at 94 ℃ (10 s at 94 ℃, 30s at 60 ℃) for 45 cycles, and finally, using an ABI7500 real-time fluorescence PCR instrument to collect FAM and CY5 detection wavelengths by fluorescence.
4, interpretation of results criteria
Both the baseline and threshold values were automatically set by default for the ABI7500 fluorometer. If the Ct value of each fluorescence (FAM and/or CY 5) is less than or equal to 45, the CTCs exist in the sample and are judged to be positive; if the Ct value calculated by the fluorescence detection result is more than 45, the CTCs do not exist in the sample, and the sample is judged to be negative. Furthermore, if one primer pair is detected as positive by the corresponding probe, the amplification is qualitatively judged as positive regardless of whether or not the semi-quantitative analysis can be performed.
5, results
The amplification results of CK19 gene positive standard (as a control) at different dilutions are shown in FIG. 1, which indicates that the standard samples with different copy numbers can reflect accurate results and have very good readability of the results, which is 102To 105The linear relation of logarithm in the concentration range is good, and the semi-quantitative analysis can be carried out on the sample with the content of 100copy/ml or more, and the semi-quantitative range is suitable for carrying out the semi-quantitative analysisThe enclosure has advantages over the prior art.
The detection pattern for the actual patients is shown in FIG. 2, not only all can show the correct qualitative result of amplification, but also the two primer pairs and the probes do not interfere with each other, and CK19 with high copy number can be used for comparing with a control to obtain a semi-quantitative result.
In conclusion, the kit provided by the invention is rapid and high in sensitivity, the interpretation of the result is very clear and intuitive, and particularly, the (qualitative) result is accurate when repeatedly detecting samples of a large number of different actual patients, which shows that the reliability of the kit is high and internal control is not needed.
Sequence listing
<110> Huayimei Biotechnology Ltd, Suzhou
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