KR101819795B1 - Genetic marker for predicting and detecting development of colorectal cancer - Google Patents

Genetic marker for predicting and detecting development of colorectal cancer Download PDF

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KR101819795B1
KR101819795B1 KR1020150108781A KR20150108781A KR101819795B1 KR 101819795 B1 KR101819795 B1 KR 101819795B1 KR 1020150108781 A KR1020150108781 A KR 1020150108781A KR 20150108781 A KR20150108781 A KR 20150108781A KR 101819795 B1 KR101819795 B1 KR 101819795B1
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김성주
지선하
박종근
이아름
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가톨릭대학교 산학협력단
연세대학교 산학협력단
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Abstract

The present invention relates to a method for identifying a specific single nucleotide polymorphism (SNP) base having a significant correlation with the risk of developing a colorectal cancer, to thereby predict a risk of developing colon cancer, a polynucleotide or cDNA And a microarray and kit comprising the same.

Description

[0002] Genetic markers for diagnosis and prediction of colorectal cancer outbreak [

The present invention relates to a method for diagnosing or predicting the onset of colorectal cancer by identifying a specific single nucleotide polymorphism (SNP) base having a significant correlation with the risk of developing colon cancer, a polynucleotide capable of identifying the SNP, DNA, A compound or cDNA, and a microarray and kit comprising the same.

In addition, the present invention relates to a composition for diagnosing or predicting the onset of colon cancer comprising microalgae corresponding to said genetic markers.

The structure of the large intestine is from the end of the small intestine to the anus, which is about 1.5m in length. The large intestine consists of ascending, traversing, descending, sigmoid colon, rectum, and anus. The main function of the colon is to digest the remaining food from the small intestine and absorb the water and electrolyte, and to discharge the remaining residue.

Colorectal cancer is a malignant tumor of the ascending colon, transverse colon, descending colon, sigmoid colon, and rectal mucosa. It is composed of adenocarcinoma, adenocarcinoma, and adenocarcinoma, including adenocarcinoma, lymphoma, sarcoma and squamous cell carcinoma. The incidence of colorectal cancer in Korea is as follows: ascending colon and s-colon are 25% and 20%, respectively.

In Korea, colorectal cancer was not a common disease before the 1970s, but it is now increasing due to changes in Westernized diet. According to the National Census of Statistics (National Approval Statistics No. 10154) and the Ministry of Health and Welfare Cancer Registration Statistics (National Approval Statistics No. 11744), among the 10 years from 2000 to 2010, the incidence of colorectal cancer was 21.8 out of 100,000 41.5, the mortality rate has almost doubled from 8.8 to 15.4 out of 100,000, and is still increasing. Colon cancer, like other gastrointestinal cancers, is the most effective treatment modality, with a 70-90% survival rate from the first stage to the third stage, but a survival rate of 15% at the last stage.

The major risk factors for colorectal cancer can be divided into two major categories. The first is an environmental factor, which is known to be a risk factor for elderly, excessive meat consumption, lack of fiber intake, lack of vitamin intake, lack of calcium intake, lack of exercise, drinking and smoking. It is known that APC, KRAS, P53, MLH1, MSH2, INK4A and SMAD4 are involved in several stages of cancer development and metastasis.

On the other hand, in humans, polymorphism, single nucleotide polymorphism (SNP), occurs once every 1000 bases. The genetic polymorphism found in more than 5% of the population is called common polymorphism, The 5% polymorphism is called rare polymorphism. Currently, studies on the diagnosis and risk prediction of multifactorial diseases that are caused by the interaction of multiple genetic mutations and environmental factors, which cause multiple gene mutations, are under way. have.

The present inventors hypothesized that "there are SNPs that can affect colon cancer" and analyzed the relationship between the SNPs in the clinical samples and the risk of colon cancer in patients with colorectal cancer and normal people in order to identify such SNPs , And found SNP biomarkers capable of predicting the risk of developing colon cancer, thereby completing the present invention.

It is an object of the present invention to solve the above problems and it is an object of the present invention to provide a method for detecting a SNP base having a significant correlation with a risk of colorectal cancer, Which can be diagnosed or predicted.

It is another object of the present invention to provide a composition capable of diagnosing or predicting the onset of colorectal cancer, comprising a polynucleotide, a DNA, a compound or cDNA thereof capable of identifying a specific SNP marker.

It is another object of the present invention to provide a kit capable of diagnosing or predicting the onset of colon cancer, comprising a polynucleotide, a DNA, a compound, or a cDNA thereof capable of identifying a specific SNP marker.

It is another object of the present invention to provide a composition for diagnosing or predicting the onset of colon cancer comprising microalgae corresponding to a specific SNP marker.

Colon cancer is caused by environmental factors and genetic factors, and it can effectively prevent colon cancer by predicting genetic factors.

The present inventors examined the SNP (rs8149) located in the 3'UTYR (3'UTR) portion of the SLC13A3 gene (Solute carrier family 13 member 3, sodium-dependent dicarboxylate transporter; NaDC3) ) And the SNP (rs7930) located in the 3 'util region of the TOMM20 gene (mitochondrial import receptor subunit TOM20 homolog) and the risk of colon cancer.

Further, miRNA interacting with each of the seed regions including rs8149 and rs7930 was predicted through a program, and the interaction between the predicted miRNA and each SNP was analyzed.

As a result, rs8149 and rs7930 can be used to predict the risk of colorectal cancer as a single SNP, and complementary miRNAs in the seed region, including rs8149 and rs7930, can be used to diagnose or predict the onset of colorectal cancer Respectively.

Accordingly, in one embodiment, the present invention provides a method for screening a gene sample obtained from a patient, wherein the polymorphism of the 26th base of the sequence represented by SEQ ID NO: 1 (NCBI refSNP ID: rs8149) in the SLC13A3 gene or the nucleotide sequence of SEQ ID NO: 2 refSNP ID: < RTI ID = 0.0 > rs7930). < / RTI >

Table 1 below shows the sequence of the corresponding SNP and its position in the refSNP ID of NCBI for the SNP marker provided in the present invention. Those skilled in the art can easily identify the position and sequence of the SNP using the above numbers. It will be apparent to those skilled in the art that the specific sequence corresponding to the refSNP ID of the SNPs registered in the NCBI may be varied slightly depending on the results of the study of the succeeding genes and such altered sequences are also included within the scope of the present invention.

NCBI refSNP ID order SEQ ID NO: rs8149 AGTTGAGCTCCACCTCCTTTCCAAG [T / C] GAGCACTCAGTGTTGAATCACAGTT One rs7930 CAAATGGTGCTCAGCAGGTGAGAAC [A / G] AAAAAACCCCAGATCTCAGTGAACT 2

For example, in the present invention, it can be predicted that the 26th allele of the sequence represented by SEQ ID NO: 1 (rs8149) in the SLC13A3 gene is T, and the risk of colon cancer is lower than that in the case of C. In a specific example of the present invention, it was confirmed that the rs8149: T allele genotype has a 0.548-fold lower risk than the rs8149: C allele ( p = 0.0082).

As another example, it can be predicted that the 26th allele of SEQ ID NO: 2 (rs7930) in the TOMM20 gene of the present invention is G, and the risk of colon cancer is higher than that of A. In a specific example of the present invention, the rs7930: G allele genotype was found to be 2.580 times higher than the rs7930: A allele ( p = 0.0045).

In the present invention, a sample obtained from a patient includes a tissue, a cell, a whole blood, a serum, a plasma, a saliva, a sputum, a cerebrospinal fluid or urine and obtains a gene sample from these samples. And includes cDNA to be synthesized.

In the present invention, the term "prediction " refers to determination of whether or not a specific individual has a possibility of developing colon cancer, whether the likelihood of developing colon cancer is relatively high, or whether colon cancer has already developed. The method of the present invention can be used for predicting any individual as an individual at high risk for developing colorectal cancer and for preventing or delaying the onset of the disease through special and appropriate management thereof. In addition, the methods of the present invention can be used clinically to make treatment decisions by early diagnosis of colon cancer and by selecting the most appropriate treatment regimen.

In the present invention, the term "polymorphism" refers to a case where two or more alleles exist in one locus. Of the polymorphic sites, only a single base differs from a polymorphism region to a single base polymorphism (single nucleotide polymorphism, SNP). Preferred polymorphic markers have two or more alleles exhibiting an incidence of 1% or more, more preferably 10% or 20% or more, in the selected population.

The term "allele " in the present invention refers to various types of genes that exist on the same locus of a homologous chromosome. Alleles are also used to indicate polymorphism, for example, SNPs have two kinds of bialles.

In another aspect, the present invention provides a composition for diagnosing or predicting the risk of developing a colorectal cancer in a patient.

(NCBI refSNP ID: rs8149) in the SLC13A3 gene, or the 26th base in the SOM13A3 gene in the TOMM20 gene represented by SEQ ID NO: 2 (NCBI refSNP ID: rs7930) And a reagent for identifying the 26th base of the sequence.

For example, the reagent contained in the composition of the present invention is preferably a polynucleotide consisting of 10 or more continuous bases including the 26th base of the sequence represented by SEQ ID NO: 1 (NCBI refSNP ID: rs8149) in the SLC13A3 gene Or a complementary polynucleotide thereof.

Further, the composition is characterized by containing a reagent for identifying the 26 th base of the sequence represented by SEQ ID NO: 2 (NCBI refSNP ID: rs7930) in the TOMM20 gene, with respect to the isolated gene sample from the patient.

For example, the reagent contained in the composition of the present invention is preferably a polynucleotide consisting of 10 or more consecutive bases including the 26th base of the sequence represented by SEQ ID NO: 2 (NCBI refSNP ID: rs7930) in the TOMM20 gene Or a complementary polynucleotide thereof.

Accordingly, the present invention provides the above polynucleotide as an embodiment.

The polynucleotide or its complementary polynucleotide according to the present invention may comprise more than 10, preferably 10 to 100, more preferably 20 to 60, even more preferably 40 to 60 contiguous bases have.

The polynucleotide or its complementary polynucleotide according to the present invention is a polymorphic sequence. A polymorphic sequence refers to a sequence comprising a polymorphic site representing a single base polymorphism in a nucleotide sequence. A polymorphic site is a site in a polymorphic sequence where a single base polymorphism occurs. In the present invention, the polynucleotide may be DNA or RNA.

In another example, the reagent contained in the composition of the present invention may preferably include a polynucleotide that specifically hybridizes with the polynucleotide or a complementary polynucleotide thereof.

Accordingly, the present invention provides, as an aspect, a polynucleotide that specifically hybridizes with the polynucleotide or a complementary polynucleotide thereof.

In the present invention, a polynucleotide that specifically hybridizes with the polynucleotide or a complementary polynucleotide thereof is an allele-specific polynucleotide.

Allele-specific polynucleotides are meant to specifically hybridize to each allele. That is, hybridization refers to hybridization so that the base of the polymorphic site present in the polymorphic sequence can be specifically discriminated. Here, hybridization can usually be performed under stringent conditions, for example, a salt concentration of 1 M or less and a temperature of 25 or more.

In the present invention, the allele-specific polynucleotide may be an allele-specific probe. That is, in the present invention, a probe means a hybridization probe, and means an oligonucleotide capable of binding sequence-specifically to a complementary strand of a nucleic acid. The allele-specific probe of the present invention has a polymorphic site among nucleic acid fragments derived from two individuals of the same species, and hybridizes to a DNA fragment derived from one individual, but not to a fragment derived from another individual. In this case, the hybridization conditions show a significant difference in the hybridization intensity between the alleles, and should be sufficiently strict so that only one of the alleles hybridizes. Preferably, the probe of the present invention aligns with the polymorphic site of the polymorphic sequence. This can lead to good hybridization differences between different allelic forms. The probe of the present invention can be used for diagnostic kits or prediction methods such as microarrays for diagnosing or predicting the risk of colon cancer by detecting alleles.

In the present invention, the allele-specific polynucleotide may be an allele-specific primer. The appropriate length of the primer may vary depending on the purpose of use, but is generally comprised of 15 to 30 bases. The primer sequence need not be completely complementary to the template, but should be sufficiently complementary to hybridize with the template. The primer hybridizes to a DNA sequence containing a polymorphic site to amplify a DNA fragment containing the polymorphic site. The primer of the present invention can be used for a diagnostic kit such as a microarray for predicting the risk of colon cancer by detecting alleles, a prediction method and the like.

Polynucleotides, polynucleotides or cDNAs thereof that specifically hybridize with the polynucleotides included in the composition of the present invention, and also for the production of microarrays or kits for diagnosing or predicting the risk of colon cancer. The microarray or kit may be prepared by conventional methods known to those skilled in the art.

In the present invention, the microarray may be a conventional microarray, except for the polynucleotide, cDNA, etc. of the present invention. The hybridization of nucleic acids on a microarray and the detection of hybridization results are well known in the art. The detection may be performed, for example, by labeling the nucleic acid sample with a labeling substance capable of generating a detectable signal including a fluorescent substance, such as Cy3 and Cy5, and then hybridizing on the microarray, The hybridization result can be detected.

In the present invention, the kit may include not only the polynucleotide, cDNA, etc. of the present invention but also one or more other component compositions, solutions or devices suitable for the assay method. In one embodiment, the kit of the present invention may be a kit containing the necessary elements necessary to perform PCR and may be a test tube or other suitable container, reaction buffer (pH and magnesium concentrations vary), deoxynucleotides (dNTPs) Enzymes such as Taq polymerase and reverse transcriptase, DNase, RNAse inhibitor, DEPC-water and sterile water. In another embodiment, the kit of the present invention may be a kit for predicting the risk of colorectal cancer including essential elements necessary for carrying out a DNA chip, and the DNA chip kit may include a polynucleotide, a primer or a probe specific for the SNP And the substrate may comprise a nucleic acid corresponding to a quantitation control gene or a fragment thereof.

The genotyping of the SNP of the present invention can be confirmed by sequencing analysis, sequencing analysis using an automatic sequencer, pyrosequencing, hybridization with a microarray, PCR-RELP (restriction fragment length polymorphism), PCR-SSCP single strand conformation polymorphism (PCR), SSO (specific sequence oligonucleotide), ASO (allele specific oligonucleotide) hybridization method using PCR-SSO method and dot hybridization method, TaqMan-PCR method, MALDI-TOF / MS method, RCA method rolling circle amplification, HRM (high resolution melting), primer extension, Southern blot hybridization, dot hybridization, and the like.

Further, the results of the SNP polymorphism can be statistically processed using statistical analysis methods commonly used in the art, such as Student's t-test, Chi- continuous variables, categorical variables, odds ratios, and 95% confidence intervals, obtained through linear regression analysis, linear regression line analysis, and multiple logistic regression analysis, % Confidence interval, and so on.

The present invention can provide information that can diagnose or predict a colorectal cancer risk early by providing a genotype susceptible to colon cancer. In addition, the present invention can provide a method for providing information for developing and predicting a diagnostic kit for early diagnosis of a composition capable of preventing colon cancer.

FIG. 1 shows miRNAs that have been experimentally verified to interact with rs8149 among miRNA predicted through a program.
Fig. 2 shows miRNAs that were experimentally verified by interaction with rs7930 among the miRNAs predicted through the program.
Figure 3 shows the results of comparing the activity of luciferase by interaction with hsa-miR-3614-5p in rs8149.
Figure 4 shows the results of comparing the activity of luciferase by interaction with hsa-miR-4273 in rs7930.
Figure 5 shows the results of comparing the expression level of SLC13A3 protein after treatment with hsa-miR-3614-5p for each allelic genotype of rs8149 and the expression level of TOMM20 protein after treatment of hsa-miR-4273 with each allelotype of rs7930 .

Hereinafter, the present invention will be described in detail with reference to examples. However, the following examples are illustrative of the present invention, and the present invention is not limited by the following examples.

Example 1. Overview of statistical analysis

In the present invention, the relationship between rs8149 of SLC13A3 and rs7930 of TOMM20 and polymorphism of single-nucleotide polymorphism is shown through statistical analysis.

In the present invention, information on the normal and colorectal cancer patients having no history of colon cancer was collected from Koreans. In the normal group, participants who had no previous history of colorectal cancer or who had no familial history were included in the study. The subjects who were diagnosed with colorectal cancer based on International Classification of Diseases for Oncology (ICD-O) were included.

In the present invention, the frequency of genotype / allele through the Chi square test was examined to analyze the relationship between the single nucleotide polymorphism and the risk of colon cancer. When the frequency was less than 5, (Fisher's exact test). In addition, after testing the frequency of genotype / allele, the risk of colon cancer according to the genotype / allele was basically analyzed by logistic regression to determine odds ratio ratio, and adjusted for age, sex, and body mass index (BMI).

Example 2. Correlation analysis of genotype / allele frequency of single nucleotide polymorphism rs8149 and risk of colon cancer

To determine the association of single nucleotide polymorphism rs8149 with colorectal cancer, we analyzed association and risk by analyzing genotypes in 1571 patients and 615 patients (Table 2).

Genotype / allele Normal group (%) Patient group (%) P -value The odds ratio 95% confidence interval (95% Confidence Interval) P -value CC 1451 (92) 588 (96) 0.0223 1.00
(Reference value)
- -
CT 119 (8) 27 (4) 0.544 0.346-0.855 0.0084 TT 1 (0) 0 (0) - - - CT + TT 120 (8) 27 (4) 0.0064 0.538 0.342-0.845 0.0072 C allele 3021 (96) 1203 (98) 0.0074 1.00
(Reference value)
- -
T allele 121 (4) 27 (2) 0.0060 0.542 0.348-0.845 0.0070

As shown in Table 2, the genotype of rs8149 (p = 0.0223) and the allele (p = 0.0060) were all associated with colorectal cancer.

In addition, the odds ratio analysis showed that the CT + TT genotype was lower (p = 0.0072) than the CC genotype, with a risk of colorectal cancer being 0.538 (95% confidence interval 0.342 ~ 0.845) The risk of colorectal cancer was found to be low (p = 0.0070) as 0.542 (95% confidence interval; 0.348 ~ 0.845) compared with the C allele.

Example 3. Correlation analysis between the frequency of genotype / allele of single base polymorphism rs7930 and the risk of colon cancer

In this study, 945 normal subjects and 323 patients were analyzed in Korean cancer prevention II (KCPII). The association of each genotype (AA vs. AG) and allele (A allele vs. G allele) with colorectal cancer was analyzed and the odds ratio was analyzed and shown in Table 3.

Genotype / allele Normal group (%) Patient group (%) P -value The odds ratio 95% confidence interval (95% Confidence Interval) P -value AA 915 (97) 301 (93) 0.004 1.00
(Reference value)
- -
AG 30 (3) 22 (7) 2.648 1.362-5.151 0.0041 A allele 1860 (98) 624 (97) 0.005 1.00
(Reference value)
- -
G allele 30 (2) 22 (3) 2.580 1.341-4.964 0.0045

As shown in Table 3 above, the genotype of rs7930 was associated with colorectal cancer (p = 0.004), and the risk of developing colon cancer in AG genotype was 2.648 (95% confidence interval, 1.362-5.151) (P = 0.0041), respectively. In addition, the allele of rs7930 was also associated with colorectal cancer (p = 0.005). Specifically, the risk of developing a colorectal cancer in a G allele was 2.580 (95% confidence interval, 1.341-4.964) (P = 0.0045), respectively.

Example 4. miRNAs interacting with single base polymorphisms rs8149 and rs7930, respectively

4.1 Prediction of miRNA interacting with single base polymorphisms rs8149 and rs7930, respectively

The following three programs were used to predict miRNAs interacting with the single nucleotide polymorphisms rs8149 and rs7930, respectively.

end. miRNASNP v2.0 (http://www.bioguo.org/miRNASNP/search.php

I. PolymiRTS database 3.0 ( http://compbio.uthsc.edu/miRSNP/)

All. MirSNP ( http://202.38.126.151/hmdd/mirsnp/search/)

Of the predicted miRNA candidates, the miRNAs experimentally confirmed to interact with the single nucleotide polymorph rs8149 and the single nucleotide polymorph rs7930 are shown in Table 4 below.

miR3614-5p CCACUUGGAUCUGAAGGCUGCCC SEQ ID NO: 3 miR4273 CCCCUGUGUGUGUUCUCUGAUGGACAG SEQ ID NO: 4

4.2 Interaction analysis of predicted miRNA and single base polymorphisms rs8149 and rs7930, respectively

In order to analyze the interaction between the predicted miRNA and each single nucleotide polymorphism, the activity of luciferase was measured according to the allele gene in the presence of miRNA using a cell culture system.

First, a 3'-utiline (UTR) cDNA fragment containing each single nucleotide polymorphism was cloned into the psiCHECK2 vector, a dual luciferase plasmid, to prepare a plasmid as follows.

end. psiCHECK2 / h_SLC13A3_3'UTR_C alelle plasmid

I. psiCHECK2 / h_SLC13A3_3'UTR_T allele plasmid

All. psiCHECK2 / h_TOMM20_3'UTR_A alelle plasmid

la. psiCHECK2 / h_TOMM20_3'UTR_G alelle plasmid

Then, the predicted miRNA mimic was transfected into a colon cancer cell line (HCT116, SW620, DLD1, LoVo, SNUC4), and after 24 hours, 1 ug of an allele gene plasmid was transfected into the colon cancer cell line, respectively .

Proteins were extracted from cells of the colon cancer cell line using passive lysis buffer solution (promega ™) after 48 hours (after a total of 72 hours), and luciferase activity was measured using a dual luciferase assay kit (promega ™) Respectively. The activity of Firefly luciferase was used to measure the transfection efficiency, and the activity of Renilla luciferase was divided by the activity of Firefly luciferase to determine the degree of interaction between miRNA and alleles. Each of the above experiments was repeated three times, and the luciferase activity was measured by duplicate experiment under the same conditions in the first experiment. The luciferase activity by the interaction of hsa-miR-3614-5p in the single nucleotide polymorph rs8149 and the luciferase activity by the interaction with hsa-miR-4273 in the single nucleotide polymorphism rs7930 are shown in FIGS. 3 and 4, respectively.

As shown in FIG. 3, the luciferase activity of the T allele of rs8149 in all cell lines (HCT116, SW620, DLD1, LoVo) decreased to a significant level compared to the luciferase activity of the C allele (HCT116; p = 0.013, SW620 ; p = 0.013, DLD1; p = 0.002, LoVo; p = 0.036). This suggests that hsa-miR-3614-5p specifically interacts with the allele T of rs8149.

4, the luciferase activity of the A allele of rs7930 was decreased (SNUC4; p = 0.074) in the cell line SNUC4 as compared with the activity of the G allele, and in the cell lines HCT116, SW620 and DLD1, (SW620; p <0.001, DLD1; p = 0.019, HCT116; p = 0.021). This suggests that hsa-miR-4273 specifically interacts with rs7930 allele A.

Example 5: Measurement of inhibition of protein expression by miRNA

As shown in Example 4, it was found that hsa-miR-3614-5p and hsa-miR-4273 interact differentially according to alleles of rs8149 and rs7930. Based on this, And the effect on the expression of the gene containing the polymorphism was identified.

5.1 Experimental Method

First, the rs8149 genotype and rs7930 genotype of each cell line were determined by sequencing method after genomic DNA PCR. First, PCR was performed using the DNA of each cell line as a template using a pair of primers amplifying regions containing a single nucleotide polymorphism. Subsequently, the nucleotide sequence was determined by capillary sequencing method and the genotype of each cell line was typed. Genotypes of rs8149 and rs7930 of colon cancer cell lines are shown in Table 5 below.

Rs8149 (SLC13A3) Rs7930 (TOMM20) CC CT TT AA AG CCD18co O O SW620 O O SNUC5 O O SNUC4 O O SNUC2b O O CoLo320DM O O HCT116 O O HT29 O O DLD1 O O LoVo O O

Iii) 25 nM of hsa-miR-3614-5p mimic or hsa-miR-4273 mimic, respectively; and iii) a control group transfected with 25 nM control miRNA, Were transfected and the expression level of the protein was identified.

72 hours after the miRNA was transfected, the cells were harvested and the protein was extracted with RIPA lysis buffer solution. The proteins were quantified by Bradford assay. Western blotting was performed after electrophoresis of proteins of 50 ((SLC13A3) or 30 ((TOMM20) by polyacrylamide gel electrophoresis (PAGE).

Anti-rabbit SLC13A3 (abcam, 1: 2250 dilution, 61kDa) and anti-mouse TOMM20 (abcam, 16kDa, 1: 5000 dilution) were used as primary antibodies and loading control was beta-actin -mouse beta-actin, abm, 43 kDa, 1: 5000 dilution) was used. Anti-rabbit IgG-HRP (santacruz, 1: 5000 dilution) and anti-mouse IgG-HRP (santacruz, 1: 5000 dilution) were used as secondary antibodies.

Western blot bands were then identified using the ECL solution and the detected bands were analyzed using ImageJ (http://imagej.nih.gov/ij/) to compare the band intensity of the beta-actin versus the target protein The intensity is quantified and is shown in FIG.

5.2 Differences in Expression of SLC13A3 Protein by Interaction of rs8149 Allele with hsa-miR-3614-5p

As shown in Fig. 5, the expression of SLC13A3 protein in the cells treated with hsa-miR3614-5p mimic was not different from that of the control group (SW620; p = 0.368, DLD1; p = 0.650 ). However, in the case of DLD1 and HT29, which are CT genotypes of rs8149, the expression of SLC13A3 protein in cells treated with hsa-miR3614-5p mimic was significantly decreased (DLD1; 16.4%, p = 0.012, HT29; 22.8% Decrease, p = 0.049). In addition, in the case of LoVo, which is a TT genotype, rs8149 decreased more than in CT genotype cells (48.6% decrease, p = 0.042).

Thus, hsa-miR-3614-5p interacts with the T allele of rs8149 and inhibits the expression of SLC13A3 in cells.

5.3 Differences in Expression of TOMM20 Protein by Interaction of hs-miR-4273 with rs7930 Allele

As shown in Fig. 5, the expression of TOMM20 protein in hsa-miR-4273 mimic treated cells was decreased in DLD1, HCT116, and LoVo cell lines, in which rs7930 was the AG genotype (DLD1; 32.2% decrease p = 0.038, HCT116, 32.3% decrease p = 0.029, LoVo 32.3% decrease p = 0.022).

In addition, in the SNUC4, SNUC5, and SW620 cell lines, in which rs7930 was the AA genotype, the expression of TOMM20 protein in hsa-miR-4273 mimic-treated cells was further decreased (SNUC4; 51.9% 0.01, SNUC5; 51.9% decrease, p = 0.002, SW620; 51.9% decrease, p = 0.059).

Thus, hsa-miR-4273 acts on the A allele of rs7930 and inhibits TOMM20 expression.

<110> CATHOLIC UNIVERSITY INDUSTRY ACADEMIC COOPERATION FOUNDATION <120> Genetic marker for predicting and detecting development          경구암 <130> PB15-12599 <160> 4 <170> Kopatentin 2.0 <210> 1 <211> 51 <212> DNA <213> Homo sapiens <400> 1 agttgagctc cacctccttt ccaagtgagc actcagtgtt gaatcacagt t 51 <210> 2 <211> 51 <212> DNA <213> Homo sapiens <400> 2 caaatggtgc tcagcaggtg agaacaaaaa aaccccagat ctcagtgaac t 51 <210> 3 <211> 23 <212> RNA <213> Homo sapiens (miR3614-5p) <400> 3 ccacuuggau cugaaggcug ccc 23 <210> 4 <211> 27 <212> RNA <213> Homo sapiens (miR4273) <400> 4 ccccugugug uguucucuga uggacag 27

Claims (13)

Identifying the polymorphism of the 26th base of the sequence represented by SEQ ID NO: 1 (NCBI refSNP ID: rs8149) in the SLC13A3 gene for the gene sample obtained from the subject provides information for predicting the risk of developing colon cancer How to.
Identifying the polymorphism of the 26th base of the sequence represented by SEQ ID NO: 2 (NCBI refSNP ID: rs7930) in the TOMM20 gene for the gene sample obtained from the subject, to provide information for predicting the risk of developing colon cancer How to.
2. The method according to claim 1, wherein the allele of the 26 th base of SEQ ID NO: 1 is C or the allele of the 26 th base of the complementary nucleotide sequence is G, Or the risk of developing a colorectal cancer is higher than that of the allele of the 26th base of the complementary nucleotide sequence thereof.
3. The method according to claim 2, wherein the allele of the 26 th base of SEQ ID NO: 2 is G or the allele of the 26 th base of the complementary nucleotide sequence is C, Or a risk of developing a colorectal cancer is higher than when the allele of the 26 th base of the complementary nucleotide sequence is T.
The method according to claim 1, wherein, when the 26th base of SEQ ID NO: 1 is CC (complementary genotype GG), the risk of developing colon cancer is high.
3. The method according to claim 2, wherein, when the 26th base of SEQ ID NO: 2 has a genotype of GG (complementary genotype CC) or AG (complementary genotype CT), it is predicted that the risk of colon cancer is high.
A polynucleotide consisting of 12 or more consecutive bases comprising the 26th base of the sequence represented by SEQ ID NO: 1 (NCBI refSNP ID: rs8149) in the SLC13A3 gene, or a complementary polynucleotide thereof, A composition for predicting.
A polynucleotide consisting of 12 or more consecutive bases comprising the 26th base of the sequence represented by SEQ ID NO: 2 (NCBI refSNP ID: rs7930) in the TOMM20 gene, or a complementary polynucleotide thereof, A composition for predicting.
8. A composition for diagnosing or predicting the onset of colorectal cancer, comprising a polynucleotide that specifically hybridizes with the polynucleotide of claim 7 or 8.
8. A microarray for diagnosing or predicting the onset of colon cancer, comprising the polynucleotide of claim 7 or 8, and a polynucleotide that hybridizes therewith.
A kit for diagnosing or predicting the onset of colon cancer, comprising the polynucleotide of claim 7 or 8, and a polynucleotide that hybridizes therewith.
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Citations (1)

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Publication number Priority date Publication date Assignee Title
WO2012174282A2 (en) 2011-06-16 2012-12-20 Caris Life Sciences Luxembourg Holdings, S.A.R.L. Biomarker compositions and methods

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012174282A2 (en) 2011-06-16 2012-12-20 Caris Life Sciences Luxembourg Holdings, S.A.R.L. Biomarker compositions and methods

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* Cited by examiner, † Cited by third party
Title
지선하, '유전위험점수(Genetic Risk Score, GRS)를 이용한 전체 암 및 대장암 발생 예측 모형 개발' 보건복지부 암정복추진연구개발사업 최종보고서 (2012.04.30)

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