Disclosure of Invention
Technical problem to be solved
Aiming at the defects of the prior art, the invention provides a predictive marker and a kit for determining whether a liver cancer patient relapses, wherein the content of the marker is detected by adopting a mass spectrometry method to judge the risk of postoperative relapse of the liver cancer patient; the method is simple and practical, and the sensitivity and specificity of the detection method can be better improved through the detection of various small molecules.
(II) technical scheme
In order to realize the purpose, the invention is realized by the following technical scheme:
application of at least one protein of MRPL49 protein, CUTA protein, TIAL1 protein and CFL1 protein as a marker for determining whether liver cancer relapses in preparation of a liver cancer relapse determination reagent.
The application of at least one specific nucleic acid probe of MRPL49 specific nucleic acid probe, CUTA specific nucleic acid probe, TIAL1 specific nucleic acid probe and CFL1 specific nucleic acid probe in the preparation of liver cancer recurrence diagnosis kit.
A kit for diagnosing liver cancer recurrence comprises at least one of a reagent for specifically detecting MRPL49 protein, a reagent for specifically detecting CUTA protein, a reagent for specifically detecting TIAL1 protein and a reagent for specifically detecting CFL1 protein.
Preferably, the reagent for specifically detecting the MRPL49 protein is a primer or a probe which specifically recognizes the nucleic acid of the MRPL49 protein; the reagent for specifically detecting the CUTA protein is a primer or a probe for specifically recognizing the nucleic acid of the CUTA protein; the reagent for specifically detecting the TIAL1 protein is a primer or a probe which specifically recognizes the nucleic acid of the TIAL1 protein; the reagent for specifically detecting CFL1 protein is a primer or a probe which specifically recognizes CFL1 protein nucleic acid.
A prognostic method for a marker of whether a patient with liver cancer has relapsed, comprising the steps of: and detecting the protein expression quantity intensity value of MRPL49 protein, CUTA protein, TIAL1 protein or CFL1 protein in the sample to be detected by adopting an LC-MS/MS mass spectrometry.
Preferably, when the protein expression intensity value of the MRPL49 protein in the sample is less than 37923871, the patient is judged to be a relapse patient, otherwise, the patient is judged to be a non-relapse patient after operation, and the false positive rate is 8.6%.
Preferably, when the protein expression intensity value of the CUTA protein in the sample is less than 382233711.7, the patient is judged to be a relapse patient, otherwise, the patient is judged to be a non-relapse patient after operation, and the false positive rate is 22.9%.
Preferably, when the protein expression intensity value of the TIAL1 protein in the sample is less than 131017834, the patient is judged to be a relapse patient, otherwise, the patient is judged to be a non-relapse patient after operation, and the false positive rate is 22.9%.
Preferably, the CFL1 protein in the sample is judged to be a relapse patient when the protein expression intensity value is less than 6181959261, otherwise, the CFL1 protein is judged to be a relapse patient after operation, and the false positive rate is 22.9%.
(III) advantageous effects
Compared with the prior art, the invention has the following beneficial effects:
(1) The invention adopts LC-MS/MS mass spectrometry to detect the sample to be detected, after mass spectrometry is carried out on a large number of clinical samples, 4 protein molecules are determined to have good detection benefit by the difference multiple (more than 2 or less than 0.5) of the corresponding molecular contents of the cancer tissues of the patients without liver cancer recurrence and the cancer tissues of the patients with liver cancer recurrence. The 4 protein molecules (MRPL 49 protein, CUTA protein, TIAL1 protein and CFL1 protein) can be used as markers for diagnosing whether liver cancer recurs.
(2) The invention takes MRPL49 protein, CUTA protein, TIAL1 protein and CFL1 protein as biomarkers to diagnose the postoperative recurrence risk of the liver cancer of a subject, is simple and easy to implement, has safe and effective diagnosis process, is easy to be accepted by patients, has unified diagnosis standard and is less influenced by individual subjective factors.
(3) The method can provide a new treatment target and thought for the research and development of anti-liver cancer relapse drugs in the future through the biomarkers detected by mass spectrometry.
Detailed Description
In order to make the objects, technical solutions and advantages of the embodiments of the present invention clearer, the technical solutions in the embodiments of the present invention will be clearly and completely described below with reference to the embodiments of the present invention, and it is obvious that the described embodiments are some embodiments of the present invention, but not all embodiments. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention.
Screening of biomarkers associated with liver cancer diagnosis
1. Experimental procedure
(1) Protein sample information
Sample preparation: samples from the liver cancer recurrent tissue were taken in 5 cases and 35 cases from the postoperative non-recurrent tissue, respectively.
(2) Sample pretreatment
Extracting protein from a sample by adopting an SDT (4% (w/v) sodium dodecyl sulfate, 100mM Tris/HCl pH7.6,0.1M dithiothreitol) cracking method, and then carrying out protein quantification by adopting a BCA method; taking a proper amount of protein from each sample, carrying out trypsin enzymolysis by using a Filter aid protein preparation (FAS) method, desalting peptide fragments by using a C18 Cartridge, adding 40 mu L of 0.1% formic acid solution for redissolution after freeze-drying the peptide fragments, and quantifying the peptide fragments (OD 280).
The BCA method is used for protein quantification, and is characterized in that the protein concentration can be calculated according to the light absorption value, and the protein binds Cu under the alkaline condition 2+ Reduction to Cu + ,Cu + Form a purple colored complex with the BCA reagent, two molecules of BCA chelate one Cu + . And comparing the absorption value of the water-soluble compound at 562nm with a standard curve to calculate the concentration of the protein to be detected.
(3) LC-MS/MS data acquisition
Each sample was separated using a nanoliter flow rate HPLC liquid phase system Easy nLC.
Wherein: the buffer solution A was 0.1% formic acid aqueous solution, and the solution B was 0.1% formic acid acetonitrile aqueous solution (acetonitrile: 84%).
The column was equilibrated with 95% solution A, and the sample was applied to a loading column (Thermo Scientific Acclaim PepMap100, 100. Mu.m. By 2cm, nanoViper C18) by an autosampler, separated by an analytical column (Thermo Scientific EASY column, 10cm, ID 75. Mu.m, 3. Mu.m, C18-A2) at a flow rate of 300nL/min.
After chromatographic separation, the sample is subjected to mass spectrometry by using a Q-exact mass spectrometer. The detection mode is positive ions, the scanning range of the parent ions is 300-1800m/z, the primary mass spectrum resolution is 70,000 at 200m/z, the AGC (Automatic gain control) target is 1e6, the Maximum IT is 50ms, and the Dynamic exclusion time (Dynamic exclusion) is 60.0s. The mass-to-charge ratio of the polypeptide and the polypeptide fragments was collected as follows: 20 fragment patterns (MS 2 scan) were collected after each full scan (full scan), with an MS2 Activation Type of HCD, an Isolation window of 2m/z, a secondary mass resolution of 17, 500 at 200m/z, a Normalized fusion Energy of 30eV, and an underfill of 0.1%.
(4) Protein identification and quantitative analysis
The RAW data of mass spectrometry is RAW file, and the software MaxQuant software (version number 1.5.3.17) is used for library checking identification and quantitative analysis.
iBAQ Intensity is the amount of protein expressed in sample X based on the iBAQ algorithm, and is approximately equal to the absolute concentration of protein in that sample. LFQ Intensity is the relative protein expression of sample X based on the LFQ algorithm, and is often used for group comparisons. One of these is generally chosen by Labelfree as a quantitative result.
IBAQ (Intensity-based absorbance quantification) and LFQ belong to two different protein quantification algorithms provided by Maxquant software.
iBAQ is generally used for absolute quantification of proteins in samples, the main algorithm being based on the ratio of the sum of the intensities of the peptides identified for the protein to the theoretical number of peptides.
LFQ is generally used for pairwise quantitative comparison among groups, and the main algorithm is pair-wise correction through peptide fragments and protein multilayers. This patent uses LFQ for protein quantification.
(5) Statistical analysis
Carrying out ratio calculation and statistical analysis on data which conform to at least two non-null values in the same group of the three-time repeated data, wherein the data comprise LFQ or iBAQ strength value ratios and P-values of all comparison groups; and (5) preliminarily screening out the difference foreign matters among the groups.
And further verifying whether the differential protein has significance according to P-value. Selecting a protein substance which has multidimensional statistical analysis Fold change >2 or <0.5 and is considered that the content of the protein substance has obvious Fold difference between cancer tissues and tissues beside the cancer, and screening out the protein substance with univariate statistical analysis P value <0.05 as a protein with significant difference; thereby obtaining the differential protein molecules. Then, SPSS software is used for making a ROC curve of the differential protein, and the area under the curve (AUC) is calculated, so that the diagnostic value of the differential protein is judged. The specific judgment method is that the area under the AUC line is more than 0.7, P is less than 0.05, and the threshold standard (cut off value) when the John's index is maximum is used as the threshold standard for judging whether the tumor is present or not (if the multiple is more than 2, the tumor detection is positive if the multiple is more than the threshold, and if the multiple is less than 0.5, the liver cancer detection is positive if the multiple is less than the threshold), thereby obtaining higher sensitivity and specificity.
(6) Bioinformatics analysis
(1) GO functional notes
The GO Annotation is carried out on a target protein set by using Blast2GO, and the process can be roughly summarized into four steps of sequence alignment (Blast), GO entry extraction (Mapping), GO Annotation (Annotation), interProScan supplementary Annotation (Annotation), and the like.
(2) KEGG pathway annotation
KEGG pathway Annotation was performed on a set of target proteins using KAAS (KEGG automated Annotation Server) software.
(3) Enrichment analysis with GO annotation and KEGG annotation
And comparing the distribution conditions of each GO classification or KEGG channel in the target protein set and the total protein set by adopting Fisher's Exact Test, and performing GO annotation or KEGG channel annotation enrichment analysis on the target protein set.
(4) Protein clustering analysis
First, the quantitative information of the target protein set is normalized (normalized to the (-1,1) interval). Then, two dimensions of the expression amounts of the sample and the protein were simultaneously classified using a Complexheatmap R package (R Version 3.4) (distance algorithm: euclidean, ligation: average linkage), and a hierarchical clustering heat map was generated.
(5) Protein interaction network analysis
The interaction relationship between the target proteins was found based on the information in the STRING database, and the interaction network was generated and analyzed using the Cytoscape software (version number: 3.2.1).
(7) Differentially expressed protein screening
Differentially expressed proteins were screened for numbers of differentially expressed proteins for each comparative group using criteria with fold change greater than 2.0 fold (up-regulation greater than 2 fold or down-regulation less than 0.5) and P value less than 0.05.
(8) Basic principle of experiment
Unlabeled quantitative proteomics (Label-free) technology has become an important method of mass spectrometry in recent years. There are two main quantitative principles of the Label-free technology: firstly, the development of non-labeled quantitative methods of spectrum counts is earlier, and a plurality of quantitative algorithms are formed, but the core principle is that the identification result of MS2 is taken as the basis of quantification, and the difference of various methods lies in the correction of high-throughput data by a later algorithm; the principle of the second unlabeled quantification method is based on MS1 and the integration of each peptide fragment signal on the LCMS chromatogram is calculated. The Maxquant algorithm adopted by the invention is based on the second principle.
2. Results of the experiment
By mass spectrum data analysis and comparison of protein micromolecules of the liver cancer recurrent tissue and the non-recurrent tissue (non-recurrent after operation), 4 protein molecules are obtained and can be used as biomarkers related to liver cancer recurrence.
In order to evaluate the diagnosis efficiency of the protein expression intensity value of the protein molecule on liver cancer, the invention adopts ROC curve analysis, and AUC is the area under the ROC curve, is the most commonly used parameter for evaluating the characteristics of the ROC curve, and is also an important test accuracy index. If the AUC is less than 0.7, the diagnosis accuracy is low; the AUC is more than 0.7, so that the requirement of clinical diagnosis can be met.
Specific results and analyses were as follows:
(1) And detecting that the MRPL49 protein has difference between the liver cancer recurrent tissue and the postoperative non-recurrent tissue by adopting an LC-MS/MS mass spectrometry.
The research shows that MRPL49 protein is significantly down-regulated by 0.24 times in the liver cancer recurrence sample, and the p value is less than 0.05.
As can be seen from FIG. 1, the AUC of MRPL49 protein was 0.943>, 0.7, indicating that MRPL49 protein has a good effect of determining whether or not there is a recurrence of liver cancer after surgery.
When the cut off value of MRPL49 protein is 37923871, the sensitivity is 100% and the specificity is 91.4%. When the individual detection is carried out, the protein expression intensity value of MRPL49 protein is less than 37923871, the patient is judged as a patient with liver cancer relapse, otherwise, the patient is judged as a patient without relapse after operation (the false positive rate is 8.6%).
As can be seen from FIG. 2, the liver cancer recurrent tissue samples are mainly distributed below the detection threshold (solid line in FIG. 2), and the postoperative non-recurrent tissue samples are mainly distributed above the detection threshold, indicating that the difference between the protein expression level intensity values of the liver cancer recurrent tissue and the postoperative non-recurrent tissue is large, and the detection threshold has a good detection effect.
In conclusion, the MRPL49 protein can be used as a predictive marker for recurrence after liver cancer surgery.
(2) The difference of the CUTA protein in the liver cancer recurrent tissue and the postoperative non-recurrent tissue is detected by adopting an LC-MS/MS mass spectrometry.
The research finds that the significant down-regulation of the CUTA protein is 0.34 times in the liver cancer recurrence sample, and the p value is less than 0.05.
As can be seen from FIG. 3, the AUC of the CUTA protein is 0.863 > -0.7, which indicates that the CUTA protein has a good judgment effect, i.e., can be used as a marker for the recurrence of the liver cancer after the operation.
When the protein expression level of the CUTA protein was 382233711.7, the sensitivity was 100% and the specificity was 77.1%. When the individual detection is carried out, the protein expression intensity value of the CUTA protein is less than 382233711.7, the patient is judged to be a recurrent patient, otherwise, the patient is judged to be a non-recurrent patient after the operation (the false positive rate is 22.9%).
As can be seen from fig. 4, the liver cancer recurrent tissue samples are mainly distributed below the detection threshold (solid line in fig. 4), and the postoperative non-recurrent tissue samples are mainly distributed above the detection threshold, which indicates that the difference between the protein expression level intensity values of the liver cancer recurrent tissue and the postoperative non-recurrent tissue is large, and the detection threshold has a good detection effect.
In summary, the CUTA protein can be used as a predictive marker for recurrence after liver cancer operation.
(3) By adopting LC-MS/MS mass spectrometry, the TIAL1 protein is detected to have difference between the liver cancer recurrent tissue and the postoperative non-recurrent tissue.
Research shows that the TIAL1 protein is significantly down-regulated by 0.49 times in a liver cancer recurrence sample, and the p value is less than 0.05.
As can be seen from FIG. 5, the AUC of TIAL1 protein was 0.869>0.7, which indicates that the protein was effective in determining whether or not the recurrence of cancer was observed after surgery.
When the protein expression level of TIAL1 protein was 131017834, the sensitivity was 100% and the specificity was 77.1%. When the individual detection is carried out, the protein expression intensity value of the TIAL1 protein is less than 131017834, the patient is judged to be a relapse patient, otherwise, the patient is judged to be a non-relapse patient after the operation (the false positive rate is 22.9%).
As can be seen from fig. 6, the liver cancer recurrent tissue samples are mainly distributed below the detection threshold (solid line in fig. 6), and the postoperative non-recurrent tissue samples are mainly distributed above the detection threshold, indicating that the difference between the protein expression level intensity values of the liver cancer recurrent tissue and the postoperative non-recurrent tissue is large, and the detection threshold has a good detection effect.
In summary, the TIAL1 protein can be used as a predictive marker for recurrence after liver cancer operation.
(4) And detecting that the CFL1 protein has difference between the liver cancer recurrent tissue and the postoperative non-recurrent tissue by adopting an LC-MS/MS mass spectrometry.
Research shows that CFL1 protein is down-regulated by 0.49 times in the significance of a liver cancer recurrence sample, and the p value is less than 0.05.
As can be seen from FIG. 7, the AUC of CFL1 protein is 0.886 >0.7, which indicates that CFL1 protein has a good judging effect, i.e., can be used as a marker for the recurrence of liver cancer after surgery.
When the protein expression level intensity value of CFL1 protein was 6181959261, the sensitivity was 80% and the specificity was 77.1%. When the individual detection is carried out, the CFL1 protein expression quantity intensity value is less than 6181959261, the patient is judged to be a relapse patient, otherwise, the patient is judged to be a non-relapse patient after the operation (the false positive rate is 22.9%).
As can be seen from FIG. 8, the samples of the liver cancer recurrent tissue were mainly distributed below the detection threshold (solid line in FIG. 8), and the samples of the non-recurrent tissue were mainly distributed above the detection threshold, indicating that the intensity values of the protein expression levels of the liver cancer recurrent tissue and the post-operative non-recurrent tissue are greatly different, and the detection threshold has a good detection effect.
In conclusion, the protein of CFL1 can be used as a predictive marker for recurrence after liver cancer surgery.
Example 1
The MRPL49 protein is used as a marker for determining whether liver cancer recurs and is applied to the preparation of a liver cancer recurrence judgment reagent.
The application of the MRPL49 specific nucleic acid probe in the preparation of a liver cancer recurrence diagnosis kit.
A kit for diagnosing liver cancer recurrence comprises a reagent for specifically detecting MRPL49 protein; the agent for specifically detecting MRPL49 protein is a probe that specifically recognizes MRPL49 protein nucleic acid.
A prognostic method for a marker of whether a patient with liver cancer has relapsed, comprising the steps of: detecting the protein expression quantity intensity value of MRPL49 protein in the sample to be detected by adopting an LC-MS/MS mass spectrometry; when the protein expression intensity value of the MRPL49 protein in the sample is less than 37923871, the patient is judged to be a relapse patient, otherwise, the patient is judged to be a non-relapse patient after operation, and the false positive rate is 8.6%.
Example 2
The CUTA protein is used as a marker for determining whether liver cancer recurs and is applied to the preparation of a liver cancer recurs determination reagent.
The CUTA specific nucleic acid probe is applied to the preparation of a liver cancer recurrence diagnosis kit.
A kit for diagnosing liver cancer recurrence comprises a reagent for specifically detecting a CUTA protein; the reagent for specifically detecting the CUTA protein is a probe for specifically recognizing the nucleic acid of the CUTA protein.
A prognostic method for a marker of whether a patient with liver cancer has relapsed, comprising the steps of: detecting the protein expression quantity intensity value of the CUTA protein in the sample to be detected by adopting an LC-MS/MS mass spectrometry; when the protein expression intensity value of the CUTA protein in the sample is less than 382233711.7, the patient is judged to be a relapse patient, otherwise, the patient is judged to be a non-relapse patient after operation, and the false positive rate is 22.9%.
Example 3
The application of the TIAL1 protein as a marker for judging whether liver cancer recurs in the preparation of a reagent for judging liver cancer recurrences.
The application of the TIAL1 specific nucleic acid probe in preparing a kit for diagnosing liver cancer recurrence.
A kit for diagnosing liver cancer recurrence comprises a reagent for specifically detecting TIAL1 protein; the reagent for specifically detecting the TIAL1 protein is a probe that specifically recognizes the nucleic acid of the TIAL1 protein.
A prognostic method for a marker of whether a patient with liver cancer has relapsed, comprising the steps of: detecting the protein expression quantity intensity value of the TIAL1 protein in the sample to be detected by adopting an LC-MS/MS mass spectrometry; when the protein expression intensity value of the TIAL1 protein in the sample is less than 131017834, the patient is judged to be a relapse patient, otherwise, the patient is judged to be a non-relapse patient after operation, and the false positive rate is 22.9%.
Example 4
The CFL1 protein is used as a marker for determining whether the liver cancer is recurrent and is applied to the preparation of a liver cancer recurrence judgment reagent.
Application of the CFL1 specific nucleic acid probe in preparing a kit for diagnosing liver cancer recurrence.
A kit for diagnosing liver cancer recurrence comprises a reagent for specifically detecting CFL1 protein; the reagent for specifically detecting CFL1 protein is a probe which specifically recognizes CFL1 protein nucleic acid.
A prognostic method for a marker of whether a patient with liver cancer has relapsed, comprising the steps of: detecting the protein expression quantity intensity value of the CFL1 protein in the sample to be detected by adopting an LC-MS/MS mass spectrometry; when the protein expression intensity value of the CFL1 protein in the sample is less than 6181959261, the patient is judged to be a relapse patient, otherwise, the patient is judged to be a non-relapse patient after operation, and the false positive rate is 22.9%.
The invention takes MRPL49 protein, CUTA protein, TIAL1 protein and CFL1 protein as biomarkers to diagnose liver cancer of a testee, is simple and easy to implement, has safe and effective diagnosis process, is easy to be accepted by patients, has unified diagnosis standard and has little influence by subjective factors.
The above examples are only intended to illustrate the technical solution of the present invention, but not to limit it; although the present invention has been described in detail with reference to the foregoing embodiments, it should be understood by those of ordinary skill in the art that: the technical solutions described in the foregoing embodiments may still be modified, or some technical features may be equivalently replaced; and such modifications or substitutions do not depart from the spirit and scope of the corresponding technical solutions of the embodiments of the present invention.