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CN115786501B - Enhancer functional site related to colorectal cancer early screening and auxiliary diagnosis and application thereof - Google Patents

Enhancer functional site related to colorectal cancer early screening and auxiliary diagnosis and application thereof Download PDF

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CN115786501B
CN115786501B CN202210779427.0A CN202210779427A CN115786501B CN 115786501 B CN115786501 B CN 115786501B CN 202210779427 A CN202210779427 A CN 202210779427A CN 115786501 B CN115786501 B CN 115786501B
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colorectal cancer
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enhancer
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CN115786501A (en
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田剑波
缪小平
应聘婷
李艳敏
朱颖
鲁泽群
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Wuhan University WHU
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Abstract

本发明涉及一种与结直肠癌早期筛查和辅助诊断相关的增强子功能位点标志物及其应用,该标志物为rs4810856。经大规模人群数据以及生物功能学实验证实,rs4810856位点具有增强子功能调控活性,且携带rs4810856[C]基因型的个体更易与转录因子ZEB1结合,从而影响该区域与靶基因的启动子的染色质交互作用,促进靶基因PREX1、CSE1L及STAU1的表达水平,进而促进癌细胞增殖,导致个体结直肠癌患病风险增加。通过针对rs4810856进行巧妙的引物和探针设计,依靠荧光定量PCR,即可对正常人群进行rs4810856危险位点的检测,从而鉴别结直肠癌的高危人群,辅助结直肠癌患者的诊断。

Figure 202210779427

The present invention relates to an enhancer function site marker related to early screening and auxiliary diagnosis of colorectal cancer and its application, the marker is rs4810856. Large-scale population data and biological functional experiments have confirmed that the rs4810856 site has enhancer function regulatory activity, and individuals carrying the rs4810856[C] genotype are more likely to bind to the transcription factor ZEB1, thereby affecting the relationship between this region and the promoter of the target gene. Chromatin interaction promotes the expression levels of target genes PREX1, CSE1L and STAU1, thereby promoting the proliferation of cancer cells, resulting in an increased risk of individual colorectal cancer. Through the ingenious design of primers and probes for rs4810856, and relying on fluorescent quantitative PCR, the risk sites of rs4810856 can be detected in normal people, so as to identify high-risk groups of colorectal cancer and assist the diagnosis of colorectal cancer patients.

Figure 202210779427

Description

一种与结直肠癌早期筛查和辅助诊断相关的增强子功能位点 及其应用An enhancer functional site associated with early screening and auxiliary diagnosis of colorectal cancer and its application

技术领域technical field

本发明涉及基因工程及肿瘤医学领域,具体涉及一种与结直肠癌早期筛查有关的增强子功能位点及其应用。The invention relates to the fields of genetic engineering and tumor medicine, in particular to an enhancer functional site related to early screening of colorectal cancer and its application.

背景技术Background technique

结直肠癌是常见的消化道恶性肿瘤之一,严重威胁了人类生命健康。其发病率位列我国恶性肿瘤第三位,且随着国家经济水平的发展以及居民生活方式和饮食结构的改变,我国结直肠癌的发病率和死亡率均呈现逐年上升的趋势,结直肠癌已成为中国乃至全世界亟待解决的重大公共卫生问题。目前,针对结直肠癌最有效的筛查方法是粪便隐血检查(F I T)结合结肠镜检查。但是,这种方法也存在着检出率不高、患者接受度不高等问题。因此,如果能更为精准的针对结直肠癌的高危个体开展早期筛查和早期诊断,则可以使得患者的接受度更高,且能为国家节省大量的医疗支出。Colorectal cancer is one of the common malignant tumors of the digestive tract, which seriously threatens human life and health. Its incidence rate ranks third among malignant tumors in my country, and with the development of the country's economic level and the changes in residents' lifestyle and diet structure, the incidence and mortality of colorectal cancer in my country are showing an increasing trend year by year, colorectal cancer It has become a major public health problem to be solved urgently in China and even in the world. Currently, the most effective screening method for colorectal cancer is fecal occult blood test (FIT) combined with colonoscopy. However, this method also has problems such as low detection rate and low patient acceptance. Therefore, if early screening and early diagnosis can be carried out more accurately for high-risk individuals of colorectal cancer, it can make patients more acceptable and save a lot of medical expenses for the country.

近年来,以分子遗传学为基础的个体化筛查方案,成为结直肠癌高危人群筛查的重点。单核苷酸多态性(Single Nucleotide Polymorphism,SNP)是最常见的遗传变异,是一类已被证实与肿瘤发生风险相关的分子标志物,其反映了个体的遗传背景差异。迄今为止,GWAS已鉴定出了100多个结直肠癌遗传易感SNP,在GWAS所发现的易感SNP中,超过90%的位于基因组非编码区域可通过参与基因表达调控来影响结直肠癌风险。GWAS飞速发展的同时,在基因组高通量检测技术的支持下,研究者发现非编码区域中包含着许多顺式调控元件(Cis-Regulatory Element,CRE),比如启动子、增强子及绝缘子等,它们可在基因表达调控中发挥巨大的作用,从而影响肿瘤的发生和易感性。随着表观组学以及三维基因组学的兴起,研究者对CREs的特征以及作用机制也越来越明了。例如,通过染色质转座酶可及性测序(Assay for Transposase Accessible Chromatin with high-throughputsequencing,ATAC-seq)技术发现CREs常富集在染色质开放区域,裸露的DNA使其更容易与转录因子(Transcription Factor,TF)结合,进而参与基因表达调控。通过染色质免疫共沉淀测序(Chromatin Immunoprecipitation and high-throughput sequencing,ChIP-seq)技术发现CREs附近的核小体常具有特定的组蛋白修饰,包括H3K27ac、H3K27me3及H3K4me1。这些特殊的表观遗传标记可以帮助预测CREs的活性状态,并对不同的CREs加以区分。此外,随着高通量染色质三维构象捕获技术(High-Through Chromosome ConformationCapture,Hi-C)的不断成熟。研究者发现染色质可通过三维折叠形成环状结构(ChromatinLooping),从空间上拉近了增强子和启动子的距离,进而激活基因转录。In recent years, individualized screening programs based on molecular genetics have become the focus of screening high-risk groups for colorectal cancer. Single nucleotide polymorphism (Single Nucleotide Polymorphism, SNP) is the most common genetic variation, and it is a kind of molecular marker that has been confirmed to be associated with the risk of tumor occurrence, which reflects the differences in the genetic background of individuals. So far, GWAS has identified more than 100 colorectal cancer genetic susceptibility SNPs. Among the susceptibility SNPs discovered by GWAS, more than 90% are located in non-coding regions of the genome, which can affect the risk of colorectal cancer by participating in the regulation of gene expression . With the rapid development of GWAS, with the support of genome high-throughput detection technology, researchers found that non-coding regions contain many cis-regulatory elements (Cis-Regulatory Element, CRE), such as promoters, enhancers and insulators, etc. They can play a huge role in the regulation of gene expression, thereby affecting tumorigenesis and susceptibility. With the rise of epigenomics and three-dimensional genomics, researchers have become more and more aware of the characteristics and mechanism of action of CREs. For example, through chromatin transposase accessibility sequencing (Assay for Transposase Accessible Chromatin with high-throughput sequencing, ATAC-seq) technology found that CREs are often enriched in open regions of chromatin, and exposed DNA makes it easier to interact with transcription factors ( Transcription Factor (TF) binding, and then participate in the regulation of gene expression. Through Chromatin Immunoprecipitation and high-throughput sequencing (ChIP-seq) technology, it was found that nucleosomes near CREs often have specific histone modifications, including H3K27ac, H3K27me3 and H3K4me1. These special epigenetic marks can help predict the activity status of CREs and distinguish different CREs. In addition, with the continuous maturity of high-throughput chromatin three-dimensional conformation capture technology (High-Through Chromosome Conformation Capture, Hi-C). The researchers found that chromatin can form a ring structure (ChromatinLooping) through three-dimensional folding, which spatially shortens the distance between the enhancer and the promoter, thereby activating gene transcription.

然而,如何有效地整合这些多组学数据,从而在全基因组范围内寻找CREs并确定它们的靶基因,始终是一个巨大的挑战。近期,为优化对CREs及其靶基因的预测,研究者们开发了接触活动模型(Activity-by-Contact Model,ABC model),通过整合代表调控元件活性状态(Activity)的ATAC-seq和H3K27ac ChIP-seq信号峰及代表染色质接触频率(Contact)的Hi-C数据,在全基因组范围内鉴定出活性增强子元件并确定其所调控的靶基因。ABC模型基于简单的生化概念,即远端候选调控元件对靶基因表达的定量影响应该取决于它作为增强子的活性(Activity),加权于它与靶基因启动子的染色质接触频率(Contact);而一个候选调控元件对靶基因表达的相对贡献值取决于该元件的定量影响除以靶基因所在区域内所有候选调控元件的总定量影响。该模型最终得到每个增强子-靶基因对应的ABC分数,以评估增强子对基因表达调控效应的强弱。However, how to effectively integrate these multi-omics data to search for CREs and identify their target genes on a genome-wide scale remains a great challenge. Recently, in order to optimize the prediction of CREs and their target genes, researchers developed the Activity-by-Contact Model (ABC model), by integrating ATAC-seq and H3K27ac ChIP representing the activity status of regulatory elements (Activity) -seq signal peaks and Hi-C data representing chromatin contact frequency (Contact), identify active enhancer elements genome-wide and determine the target genes they regulate. The ABC model is based on the simple biochemical concept that the quantitative impact of a distal candidate regulatory element on target gene expression should depend on its activity as an enhancer, weighted by its chromatin contact frequency with the target gene promoter (Contact) ; while the relative contribution of a candidate regulatory element to the expression of a target gene is determined by dividing the quantitative impact of that element by the total quantitative impact of all candidate regulatory elements within the region of the target gene. The model finally obtains the ABC score corresponding to each enhancer-target gene to evaluate the strength of the enhancer's regulatory effect on gene expression.

发明内容Contents of the invention

本发明的目的在于克服现有技术的不足,提供一种结直肠癌早期筛查和辅助诊断的增强子功能SNP位点标志物及其应用。The purpose of the present invention is to overcome the deficiencies of the prior art, and provide an enhancer function SNP site marker for early screening and auxiliary diagnosis of colorectal cancer and its application.

本发明解决上述技术问题的技术方案如下:The technical scheme that the present invention solves the problems of the technologies described above is as follows:

一种与结直肠癌早期筛查和辅助诊断相关的增强子功能位点标志物,该标志物为rs4810856。An enhancer functional site marker related to early screening and auxiliary diagnosis of colorectal cancer, the marker is rs4810856.

所述的与结直肠癌早期筛查和辅助诊断相关的增强子功能位点标志物的特异性扩增引物,所述rs4810856的特异性扩增引物序列为SEQ ID NO:1和SEQ ID NO:2。The specific amplification primers for the enhancer function site markers related to the early screening and auxiliary diagnosis of colorectal cancer, the specific amplification primer sequences for rs4810856 are SEQ ID NO: 1 and SEQ ID NO: 2.

所述的与结直肠癌早期筛查和辅助诊断相关的增强子功能位点标志物的特异性探针,所述rs4810856的探针序列为SEQ ID NO:3和SEQ ID NO:4。The specific probe of the enhancer function site marker related to the early screening and auxiliary diagnosis of colorectal cancer, the probe sequence of rs4810856 is SEQ ID NO: 3 and SEQ ID NO: 4.

所述的与结直肠癌早期筛查和辅助诊断相关的增强子功能位点标志物的检测试剂在制备结直肠癌辅助诊断试剂盒中的应用。The application of the detection reagent of the enhancer function site marker related to early screening and auxiliary diagnosis of colorectal cancer in the preparation of colorectal cancer auxiliary diagnosis kit.

一种结直肠癌早期筛查和辅助诊断试剂盒,用于检测外周血DNA中的rs4810856。A colorectal cancer early screening and auxiliary diagnostic kit for detecting rs4810856 in peripheral blood DNA.

所述的结直肠癌早期筛查和辅助诊断试剂盒,包括上述SNP标志物的特异性扩增引物和SNP标志物的特异性探针。The kit for early screening and auxiliary diagnosis of colorectal cancer includes the above-mentioned specific amplification primers for SNP markers and specific probes for SNP markers.

本发明的有益效果为:从分子生物学及基因诊断水平上,提供了筛选结直肠癌高危人群的技术方法。此方法基于我们前期通过ABC模型整合多组学技术显示,rs4810856位点与中国人群的结直肠癌易感性相关。通过针对rs4810856位点进行巧妙的引物和探针设计,能够依靠荧光定量PCR,即可对正常人群进行rs4810856危险位点的检测,从而鉴别结直肠癌的高危人群,辅助结直肠癌早期筛查及诊断,该技术方法设计巧妙、简易可行、结果准确可靠,可在各级医院进行推广,对于评估结直肠癌的患病风险提供了帮助,有助于临床上对该类人群进行结直肠癌筛查和早期干预。The beneficial effects of the invention are: from the molecular biology and gene diagnosis level, it provides a technical method for screening high-risk groups of colorectal cancer. This method is based on our previous integration of multi-omics technology through the ABC model, showing that the rs4810856 locus is associated with the susceptibility of colorectal cancer in the Chinese population. Through the ingenious design of primers and probes for the rs4810856 site, it is possible to detect the risk site of rs4810856 in the normal population by means of fluorescent quantitative PCR, thereby identifying high-risk groups of colorectal cancer, assisting early screening and monitoring of colorectal cancer. Diagnosis, this technical method is ingeniously designed, simple and feasible, and the results are accurate and reliable. It can be promoted in hospitals at all levels. It provides help in assessing the risk of colorectal cancer and is helpful for clinical colorectal cancer screening for this group of people. investigation and early intervention.

附图说明Description of drawings

图1ABC图谱法鉴定结直肠癌易感位点rs4810856的流程图;Fig. 1 Flowchart of identification of colorectal cancer susceptibility locus rs4810856 by ABC map method;

图2增强子位点rs4810856人群筛选及潜在调控效果示意图;Figure 2 Schematic diagram of population screening and potential regulatory effects of enhancer site rs4810856;

图3基于SNP位点rs4810856的结直肠癌风险预测模型AUC曲线图;Figure 3 AUC curve of colorectal cancer risk prediction model based on SNP rs4810856;

图4为rs4810856双荧光素酶报告基因实验结果示意图;Figure 4 is a schematic diagram of the results of the rs4810856 dual luciferase reporter gene experiment;

图5为rs4810856基因型对靶基因PREX1、CSE1L和STAU1表达水平的调控示意图;Figure 5 is a schematic diagram of the regulation of the expression levels of the target genes PREX1, CSE1L and STAU1 by the rs4810856 genotype;

图6 CRISPR/Cas9构建SW480和HCT116细胞中rs4810856单核苷酸突变示意图;Fig. 6 Schematic diagram of rs4810856 single nucleotide mutation constructed by CRISPR/Cas9 in SW480 and HCT116 cells;

图7 rs4810856位点影响结直肠癌细胞增殖能力示意图;Figure 7 Schematic diagram of rs4810856 site affecting the proliferation ability of colorectal cancer cells;

图8靶基因PREX1、CSE1L及STAU1过表达对结直肠癌细胞系增殖能力的影响示意图;Figure 8 Schematic diagram of the effect of overexpression of target genes PREX1, CSE1L and STAU1 on the proliferation ability of colorectal cancer cell lines;

图9靶基因PREX1、CSE1L及STAU1过表达对裸鼠皮下成瘤的影响示意图。Fig. 9 Schematic diagram of the effect of overexpression of target genes PREX1, CSE1L and STAU1 on subcutaneous tumor formation in nude mice.

具体实施方式Detailed ways

以下对本发明的原理和特征进行描述,所举实例只用于解释本发明,并非用于限定本发明的范围。The principles and features of the present invention are described below, and the examples given are only used to explain the present invention, and are not intended to limit the scope of the present invention.

本发明解决上述技术问题的技术方案如下:The technical scheme that the present invention solves the problems of the technologies described above is as follows:

一种与结直肠癌早期筛查和辅助诊断相关的增强子功能位点标志物,该标志物为rs4810856。An enhancer functional site marker related to early screening and auxiliary diagnosis of colorectal cancer, the marker is rs4810856.

所述rs4810856的特异性扩增引物序列为SEQ ID NO:1和SEQ ID NO:2。The specific amplification primer sequences of rs4810856 are SEQ ID NO: 1 and SEQ ID NO: 2.

所述与结直肠癌早期筛查和辅助诊断相关的增强子功能位点标志物的特异性探针,所述rs4810856的探针序列为SEQ ID NO:3和SEQ ID NO:4。The specific probe of the enhancer function site marker related to early screening and auxiliary diagnosis of colorectal cancer, the probe sequence of rs4810856 is SEQ ID NO: 3 and SEQ ID NO: 4.

所述与结直肠癌早期筛查和辅助诊断相关的增强子功能位点标志物的检测试剂在制备结直肠癌辅助诊断试剂盒中的应用。The application of the detection reagent of the enhancer functional site marker related to early screening and auxiliary diagnosis of colorectal cancer in the preparation of colorectal cancer auxiliary diagnosis kit.

一种结直肠癌早期筛查和辅助诊断试剂盒,该试剂盒用于检测外周血DNA中的rs4810856。A kit for early screening and auxiliary diagnosis of colorectal cancer, which is used to detect rs4810856 in peripheral blood DNA.

所述试剂盒包括上述SNP标志物的特异性扩增引物和上述SNP标志物的特异性探针。The kit includes specific amplification primers for the above-mentioned SNP markers and specific probes for the above-mentioned SNP markers.

具体地说,本发明解决问题的技术方案包括:(1)建立统一标准的标本库和数据库:以标准操作程序(SOP)采集符合标准的受试者血液样本,系统收集完整的人口学资料和临床资料。(2)基因型检测:选择结直肠癌病例和健康对照,利用ABC模型结合ATAC-seq、CHIP-seq、RNA-se、Hi-C等多组学,更精准的找到与结直肠癌发病相关的SNP标志物rs4810856(3)对筛选出的阳性关联标志物,在独立的大人群样本中进行验证,以判断其关联的稳定性。(4)结直肠癌辅助诊断试剂盒的研制:根据结直肠癌病例和健康对照中基因型分布频率有显著差异的遗传标志物开发早期筛查及辅助诊断试剂盒。Specifically, the technical solution to the problem of the present invention includes: (1) establishing a unified standard specimen library and database: collecting standard operating procedures (SOPs) to collect standard blood samples from subjects, systematically collecting complete demographic data and clinical information. (2) Genotype detection: Select colorectal cancer cases and healthy controls, and use the ABC model combined with ATAC-seq, CHIP-seq, RNA-se, Hi-C and other multi-omics to more accurately find the correlation with the incidence of colorectal cancer The SNP marker rs4810856(3) of the screened positive association markers was verified in an independent large population sample to judge the stability of the association. (4) Development of auxiliary diagnostic kits for colorectal cancer: develop early screening and auxiliary diagnostic kits based on genetic markers with significant differences in genotype distribution frequencies between colorectal cancer cases and healthy controls.

具体来说本发明的研究的实验方法主要包括以下内容:Specifically the experimental method of the research of the present invention mainly comprises the following contents:

首先,我们从华中科技大学附属同济医院收集由结直肠癌外科手术切除的10例新鲜结直肠癌组织样本。10例样本均分别进行了ATAC-seq、H3K27ac ChIP-seq以及RNA-seq实验。我们利用ABC模型系统整合ATAC-seq、H3K27acChIP-seq、RNA-seq及Hi-C组学数据,Hi-C实验数据由ENCODE数据库下载获得,综合考虑增强子活性以及与靶基因启动子的染色质交互作用对基因表达的影响,进而在全基因组范围内鉴定增强子元件及其调控的靶基因,绘制出增强子-靶基因映射图谱。以ABC分数≥0.02作为显著性阈值,共鉴定出26,877个显著性的ABC增强子SNPs位点,具体流程如图1所示。First, we collected 10 fresh colorectal cancer tissue samples from Tongji Hospital affiliated to Huazhong University of Science and Technology, which were resected by colorectal cancer surgery. All 10 samples were subjected to ATAC-seq, H3K27ac ChIP-seq and RNA-seq experiments. We use the ABC model system to integrate ATAC-seq, H3K27acChIP-seq, RNA-seq and Hi-C omics data. The Hi-C experimental data is downloaded from the ENCODE database, considering enhancer activity and chromatin with the target gene promoter The effect of interaction on gene expression, and then identify enhancer elements and their regulated target genes on a genome-wide scale, and draw an enhancer-target gene mapping map. With the ABC score ≥ 0.02 as the significance threshold, a total of 26,877 significant ABC enhancer SNPs were identified. The specific process is shown in Figure 1.

接着,我们从dbGaP数据库中下载了欧洲人群三个结直肠癌GWAS数据集,合并数据后共包含17,789名结直肠癌病例和19,951名对照样本。基本人口学特征如表1所示。基于非条件Logistic回归模型,并在校正年龄和性别混杂因素后,我们计算鉴定出的ABC增强子SNPs与结直肠癌易感性的关联,并由此绘制曼哈顿图,结果如图2中A图所示。在计算过程中,我们以P值<0.05作为显著性阈值,共鉴定出4,847个与结直肠癌风险相关的ABC增强子SNPs。其中,我们发现rs4810856所在的增强子区域:chr20:48682097-48683408,具有最强的基因表达调控效应,并可同时调控三个靶基因:PREX1、CSE1L及STAU1,结果如图2中B图所示。病例对照研究结果表明,携带rs4810856风险基因型的个体,在欧洲人群样本中,结直肠癌的患病风险分别较正常人增加4%(OR=1.04,95%CI:1.01-1.08,P=3.68×10-5)。Next, we downloaded three colorectal cancer GWAS datasets for European populations from the dbGaP database, and the combined data contained a total of 17,789 colorectal cancer cases and 19,951 control samples. The basic demographic characteristics are shown in Table 1. Based on the unconditional Logistic regression model, and after adjusting the confounding factors of age and sex, we calculated the association between the identified ABC enhancer SNPs and the susceptibility to colorectal cancer, and then drew the Manhattan plot. The results are shown in panel A of Figure 2 Show. In the calculation process, we identified a total of 4,847 ABC enhancer SNPs associated with colorectal cancer risk using P-value <0.05 as the significance threshold. Among them, we found that the enhancer region where rs4810856 is located: chr20:48682097-48683408, has the strongest gene expression regulation effect, and can simultaneously regulate three target genes: PREX1, CSE1L and STAU1, the results are shown in Figure 2 B . The results of the case-control study showed that individuals carrying the rs4810856 risk genotype had an increased risk of colorectal cancer by 4% compared with normal individuals in European population samples (OR=1.04, 95% CI: 1.01-1.08, P=3.68 ×10 -5 ).

表1.研究中采用的欧洲人群和中国人群结直肠癌患者和正常对照的基本资料Table 1. Basic information of colorectal cancer patients and normal controls in the European and Chinese populations used in the study

Figure BDA0003727232980000061
Figure BDA0003727232980000061

表2.欧洲人群样本rs4810856结直肠癌风险关联分析结果Table 2. Results of risk association analysis of rs4810856 colorectal cancer in European population samples

Figure BDA0003727232980000062
Figure BDA0003727232980000062

同时,从中国北京武汉两地区共募集了具有完整病历资料的6,024例结直肠癌患者和10,022例无肿瘤病史的正常对照,对这些人进行了基因分型。患者经组织病理学确诊,无年龄限制;正常对照无肿瘤病史,经体检无肿瘤体征。同时收集了研究对象的性别、年龄、吸烟和饮酒等信息。每个研究对象均知情同意参加本研究并捐献2ml外周静脉血,用于分离制备淋巴细胞基因组DNA。基本人口学特征如表1所示。At the same time, a total of 6,024 colorectal cancer patients with complete medical records and 10,022 normal controls without tumor history were recruited from Beijing and Wuhan, China, and genotyped these individuals. The patients were diagnosed by histopathology, and there was no age limit; the normal controls had no history of tumor, and no signs of tumor after physical examination. At the same time, information such as gender, age, smoking and drinking of the research subjects was collected. Each research subject gave informed consent to participate in this study and donated 2ml of peripheral venous blood for the separation and preparation of lymphocyte genomic DNA. The basic demographic characteristics are shown in Table 1.

我们将两地募集到的人群样本用于两阶段人群验证,通过运用非条件logistic回归模型对两个阶段人群样本分别计算SNP位点rs4810856与结直肠癌易感性的关联,并校正性别、年龄、吸烟和饮酒情况。中国人群两阶段病例对照分析结果显示,携带rs4810856[C]风险基因型的个体,结直肠癌的患病风险分别增加30%和14%(OR=1.30,95%CI:1.12-1.49,P=2.72×10-4;OR=1.14,95%CI:1.05-1.22,P=3.76×10-4)。为加强病例对照研究的检验效能,合并两阶段的样本,检验rs4810856与结直肠癌易感性的关联。发现中国人群病例对照研究结果与欧洲人群结直肠癌样本的结果一致,携带rs4810856[C]风险基因型的个体罹患结直肠癌的风险增加16%(OR=1.16,95%CI:1.10-1.23,P=9.74×10-7),详细结果见表3。We used the population samples recruited from the two places for the two-stage population verification, and calculated the association between the SNP site rs4810856 and the susceptibility to colorectal cancer by using the unconditional logistic regression model for the two-stage population samples, and adjusted the gender, age, Smoking and alcohol use. The results of the two-stage case-control analysis of the Chinese population showed that individuals carrying the rs4810856[C] risk genotype had an increased risk of colorectal cancer by 30% and 14%, respectively (OR=1.30, 95%CI: 1.12-1.49, P= 2.72×10 -4 ; OR=1.14, 95% CI: 1.05-1.22, P=3.76×10 -4 ). In order to strengthen the testing power of the case-control study, the two-stage samples were combined to test the association between rs4810856 and colorectal cancer susceptibility. It was found that the results of the case-control study in the Chinese population were consistent with the results of colorectal cancer samples in the European population. Individuals carrying the rs4810856[C] risk genotype had an increased risk of colorectal cancer by 16% (OR=1.16, 95% CI: 1.10-1.23, P=9.74×10 -7 ), see Table 3 for detailed results.

表3.中国人群样本rs4810856结直肠癌风险关联分析结果Table 3. Results of risk association analysis of rs4810856 colorectal cancer in Chinese population samples

Figure BDA0003727232980000071
Figure BDA0003727232980000071

*采用Logistic回归模型计算,校正性别、年龄、吸烟和饮酒情况。*Calculated using Logistic regression model, adjusted for gender, age, smoking and alcohol consumption.

前期大样本人群关联分析结果显示该位点是结直肠癌风险位点,因此我们用这一风险SNP位点建立了结直肠癌的风险预测模型。我们构建了一个公式,综合考虑SNP的三种基因型和性别、年龄、吸烟及饮酒情况。其中,对于SNP基因分型,野生纯合型=“1”,杂合型=“2”,突变纯合型=“3”;对于性别,男性为“1”,女性为“0”;对于年龄,大于或等于60岁为“1”,小于60岁为“0”。分析时以多因素logistic回归系数β为权重,得到基于rs4810856分型危险评分的公式如下:The previous large-sample population association analysis showed that this locus is a risk locus for colorectal cancer, so we used this risk SNP locus to establish a risk prediction model for colorectal cancer. We constructed a formula that considered the three genotypes of SNPs and sex, age, smoking and drinking. Among them, for SNP genotyping, wild homozygous = "1", heterozygous = "2", mutant homozygous = "3"; for gender, male is "1", female is "0"; for Age, greater than or equal to 60 years old is "1", less than 60 years old is "0". In the analysis, the multivariate logistic regression coefficient β was used as the weight, and the formula of risk score based on rs4810856 classification was obtained as follows:

中国人群危险评分=(0.1064×性别的评分)+(-0.0121×年龄的评分)+(0.2015×吸烟评分)+(-0.1129×饮酒评分)+(-0.0648×rs8100241分型的评分)。Chinese population risk score=(0.1064×score of gender)+(-0.0121×score of age)+(0.2015×score of smoking)+(-0.1129×score of drinking)+(-0.0648×score of rs8100241 type).

欧洲人群危险评分=(-0.1889×性别的评分)+(-0.0296×年龄的评分)+(-0.0437×rs8100241分型的评分)European population risk score = (-0.1889×score of sex)+(-0.0296×score of age)+(-0.0437×score of rs8100241 type)

通过绘制AUC曲线,可得该模型曲线下面积在欧洲人群和中国人群分别为0.591和0.561,结果如图3所示。By drawing the AUC curve, the area under the curve of the model can be obtained as 0.591 and 0.561 for the European population and the Chinese population, respectively, and the results are shown in Figure 3.

为在功能上解析rs4810856标志物的结直肠癌风险关联,探索了该SNP位点影响结直肠癌发生发展的作用机制。In order to functionally analyze the colorectal cancer risk association of rs4810856 marker, the mechanism of action of this SNP site on the occurrence and development of colorectal cancer was explored.

首先,我们通过报告基因试验,验证了rs4810856所在区域的增强子功能调控功能。将包含rs4810856不同等位基因的DNA片段正向或反向构建于报告基因质粒载体,并分别与内部对照质粒pRL-SV40共转染SW480和HCT116两种人结直肠癌细胞系,随后检测双荧光素酶基因表达情况,并比较不同组别间的相对荧光素酶活性差异。我们发现无论DNA片段插入方向如何,含有rs4810856[C]等位基因的重组质粒的报告基因活性均显著高于pGL3-Promoter空载组,表明目的位点所在DNA片段具有增强子活性。相较于rs4810856[C]基因型组,rs4810856[T]基因型组的报告基因活性显著下降。以上实验结果表明rs4810856所在区域具有增强子活性,且该位点rs4810856[C]的增强子的转录激活效应比rs4810856[T]更强,结果如图4所示。eQTL分析结果显示,具有增强子活性的rs4810856位点在人群样本CRC组织中与靶基因PREX1、CSE1L和STAU1表达水平的密切相关,结果如图5所示。First, we verified the enhancer function regulation function of the region where rs4810856 is located by reporter gene assay. The DNA fragments containing different alleles of rs4810856 were constructed in the reporter gene plasmid vector forward or reverse, and were co-transfected with the internal control plasmid pRL-SV40 into two human colorectal cancer cell lines, SW480 and HCT116, and then the double fluorescence was detected The expression of luciferase gene was compared, and the relative luciferase activity difference among different groups was compared. We found that regardless of the insertion direction of the DNA fragment, the reporter gene activity of the recombinant plasmid containing the rs4810856[C] allele was significantly higher than that of the pGL3-Promoter empty group, indicating that the DNA fragment at the target site has enhancer activity. Compared with the rs4810856[C] genotype group, the reporter gene activity was significantly decreased in the rs4810856[T] genotype group. The above experimental results show that the region where rs4810856 is located has enhancer activity, and the enhancer of rs4810856[C] has a stronger transcriptional activation effect than rs4810856[T]. The results are shown in Figure 4. The results of eQTL analysis showed that the rs4810856 locus with enhancer activity was closely related to the expression levels of target genes PREX1, CSE1L and STAU1 in CRC tissues of population samples, the results are shown in Figure 5.

为深入探究rs4810856单碱基基因编辑以及靶基因对结直肠癌细胞增殖的影响,我们分别进行了细胞增殖实验、克隆形成实验和体内裸鼠皮下成瘤等实验。细胞增殖实验中,我们用CRISPR/Cas9构建SW480和HCT116细胞中rs4810856单核苷酸突变型细胞系作为实验模型,研究rs4810856位点对结直肠癌细胞恶性表型的影响,构建过程见图6所示。与rs4810856[T]细胞系相比,携带rs4810856[C]细胞系的细胞增殖能力明显更强,结果如图7所示。然后,我们以PREX1、CSE1L及STAU1分别过表达和联合过表达的稳转细胞系作为实验模型,检测靶基因对结直肠癌细胞增殖能力的影响。实验发现与空白对照组细胞相比,靶基因分别过表达的细胞系克隆形成能力明显增强,并且靶基因联合过表达细胞系的克隆形成能力最强,结果如图8所示。在体内裸鼠皮下成瘤实验中,我们用稳转细胞系注射至裸鼠的皮下,定期测量不同组别间裸鼠皮下荷瘤的体积大小,并绘制皮下成瘤生长曲线。我们发现与注射空白对照细胞系的裸鼠相比,注射PREX1、CSE1L及STAU1分别过表达细胞系的裸鼠,其皮下肿瘤的体积明显增大,而注射靶基因联合过表达细胞系的裸鼠,其皮下肿瘤的体积最大,结果如图9所示。细胞表型和体内裸鼠皮下成瘤实验结果均显示PREX1、CSE1L及STAU1可发挥一定的协同效应促进结直肠癌细胞的增殖。In order to further explore the effects of rs4810856 single-base gene editing and target genes on the proliferation of colorectal cancer cells, we conducted cell proliferation experiments, colony formation experiments, and subcutaneous tumor formation experiments in nude mice. In the cell proliferation experiment, we used CRISPR/Cas9 to construct rs4810856 single nucleotide mutant cell lines in SW480 and HCT116 cells as an experimental model to study the effect of rs4810856 on the malignant phenotype of colorectal cancer cells. The construction process is shown in Figure 6. Show. Compared with the rs4810856[T] cell line, the proliferation ability of the cells carrying the rs4810856[C] cell line was significantly stronger, and the results are shown in Figure 7. Then, we used the stably transfected cell lines with overexpression of PREX1, CSE1L and STAU1 respectively and combined overexpression as experimental models to detect the effect of target genes on the proliferation ability of colorectal cancer cells. The experiment found that compared with the cells of the blank control group, the clone formation ability of the cell lines overexpressing the target genes was significantly enhanced, and the clone formation ability of the cell lines overexpressing the target genes was the strongest. The results are shown in Figure 8. In the subcutaneous tumor formation experiment in nude mice in vivo, we injected the stable cell line into the subcutaneous of nude mice, regularly measured the volume of subcutaneous tumors in different groups of nude mice, and drew the growth curve of subcutaneous tumor formation. We found that compared with the nude mice injected with blank control cell lines, the nude mice injected with PREX1, CSE1L and STAU1 overexpressed cell lines respectively had significantly larger subcutaneous tumor volume, while the nude mice injected with target gene combined with overexpressed cell lines , the subcutaneous tumor had the largest volume, and the results are shown in Figure 9. The results of cell phenotype and subcutaneous tumor formation in nude mice showed that PREX1, CSE1L and STAU1 could exert a certain synergistic effect to promote the proliferation of colorectal cancer cells.

结合上述大规模人群分析、生物信息学分析以及严谨的实验设计,结果显示位于染色质20q13.13增强子区域的rs4810856风险位点,使得相对于携带rs4810856[T]的个体,携带[C]等位基因变异的个体显著增加结直肠癌患病风险。且其作用机制是通过影响rs4810856与转录因子ZEB1的结合能力,从而抑制其所在区域与靶基因的启动子的染色质交互作用,进而降低靶基因PREX1、CSE1L及STAU1的表达水平,抑制AKT信号通路激活,降低结直肠癌发病风险。因此,位于非编码区的rs4810856风险位点与结直肠癌患病风险存在着密切的关系,有望在临床上应用,辅助结直肠癌的早期诊断,早期发现结直肠癌高危人群。Combining the above-mentioned large-scale population analysis, bioinformatics analysis and rigorous experimental design, the results show that the rs4810856 risk locus located in the chromatin 20q13. Individuals with genetic variants significantly increase the risk of colorectal cancer. And its mechanism of action is to inhibit the chromatin interaction between its region and the promoter of the target gene by affecting the binding ability of rs4810856 and the transcription factor ZEB1, thereby reducing the expression levels of the target genes PREX1, CSE1L and STAU1, and inhibiting the AKT signaling pathway Activated to reduce the risk of colorectal cancer. Therefore, the rs4810856 risk locus located in the non-coding region is closely related to the risk of colorectal cancer, and it is expected to be clinically applied to assist in the early diagnosis of colorectal cancer and early detection of high-risk groups of colorectal cancer.

实验方法:experimental method:

1.外周血DNA提取:1. DNA extraction from peripheral blood:

我们用常规酚-氯仿法提取DNA,具体步骤如下:We used conventional phenol-chloroform method to extract DNA, the specific steps are as follows:

1)取约3ml抗凝血,室温下5,000×g离心15min,弃去上层,留约0.3ml血细胞。加入0.5ml新鲜配制的终浓度为20μg/ml RNA酶的抽提缓冲液,混匀后37℃孵育1h。1) Take about 3ml of anticoagulated blood, centrifuge at 5,000×g for 15min at room temperature, discard the upper layer, and keep about 0.3ml of blood cells. Add 0.5ml freshly prepared extraction buffer with a final concentration of 20μg/ml RNase, mix well and incubate at 37°C for 1h.

2)加入终浓度为100μg/ml的蛋白酶K,混匀后37℃孵育过夜。2) Add proteinase K at a final concentration of 100 μg/ml, mix well and incubate overnight at 37°C.

3)每管加入Tris缓冲液平衡的酚(pH=7.0)0.7ml,充分混匀,室温下8,000×g离心15min。3) Add 0.7 ml of phenol (pH=7.0) equilibrated with Tris buffer solution to each tube, mix well, and centrifuge at 8,000×g for 15 min at room temperature.

4)将上层液体转移到另一1.5ml离心管中,加入等体积酚–氯仿(1:1)0.7ml,充分混匀15min;室温8,000×g离心15min。4) Transfer the upper layer liquid to another 1.5ml centrifuge tube, add an equal volume of phenol-chloroform (1:1) 0.7ml, mix well for 15min; centrifuge at 8,000×g for 15min at room temperature.

5)将上层液体转移到另一干净1.5ml离心管中,加入10%体积的10M乙酸铵溶液,加入2倍体积预冷的无水乙醇,–20℃静置2h以沉淀DNA。5) Transfer the upper layer liquid to another clean 1.5ml centrifuge tube, add 10% volume of 10M ammonium acetate solution, add 2 times the volume of pre-cooled absolute ethanol, and stand at -20°C for 2h to precipitate DNA.

6)沉淀出的DNA用75%乙醇洗涤,12,000×g离心15min后弃上层液体;再用75%乙醇洗涤,12,000×g离心15min后弃上层液体。6) The precipitated DNA was washed with 75% ethanol, centrifuged at 12,000×g for 15 minutes, and the upper layer was discarded; then washed with 75% ethanol, centrifuged at 12,000×g for 15 minutes, and the upper layer was discarded.

7)将管倒立在吸水纸上,待乙醇挥发干净后,每管加适当TE缓冲液,4℃放置一周后保存于–20℃备用。7) Place the tubes upside down on absorbent paper. After the ethanol has evaporated, add appropriate TE buffer solution to each tube, place at 4°C for a week, and store at -20°C for later use.

2.基因分型2. Genotyping

采用的分型平台为TaqMan基因分型技术(ABI 7900HT Real Time PCR system,Applied Biosystems),5μl PCR反应体系如表4所示:The genotyping platform used was TaqMan genotyping technology (ABI 7900HT Real Time PCR system, Applied Biosystems), and the 5 μl PCR reaction system is shown in Table 4:

表4.TaqMan基因分型体系配制Table 4. TaqMan Genotyping System Preparation

Figure BDA0003727232980000101
Figure BDA0003727232980000101

反应条件为:95℃预变性10min,然后95℃15sec和60℃1min共45个循环,降温到4℃。The reaction conditions are: pre-denaturation at 95°C for 10 min, followed by 45 cycles of 95°C for 15 sec and 60°C for 1 min, and cooling to 4°C.

反应所用的引物和探针如下:The primers and probes used in the reaction are as follows:

rs4810856引物:rs4810856 primer:

正向引物:caatacctctcattagttatgcctaagc(SEQ ID NO:1)Forward primer: caatacctctcattagttatgcctaagc (SEQ ID NO: 1)

反向引物:cagggaggagtctggtattttttaata(SEQ ID NO:2)Reverse primer: cagggaggagtctggtattttttaata (SEQ ID NO: 2)

rs4810856探针:rs4810856 probe:

正向探针:fam-acctaccatctttc-mgb(SEQ ID NO:3)Forward probe: fam-acctaccatctttc-mgb (SEQ ID NO: 3)

反向探针:vic-acctaccacctttc-mgb(SEQ ID NO:4)Reverse probe: vic-acctaccacctttc-mgb (SEQ ID NO: 4)

3.细胞增殖实验3. Cell Proliferation Experiment

1)细胞计数1) Cell count

在进行CCK-8增殖实验和克隆形成实验前,需要进行细胞计数,保证不同组别孔板中接种数量合适的细胞。本实验使用血球计数板进行细胞计数,该计数板由两个大小相同的计数池组成,每个计数池又由九个1mm×1mm方格组成,每个方格可容纳0.1mm3液体体积。具体计数步骤如下:Before conducting CCK-8 proliferation experiments and colony formation experiments, cell counting is required to ensure that an appropriate number of cells are inoculated in different groups of well plates. In this experiment, a hemocytometer is used for cell counting. The counting plate is composed of two counting pools of the same size, and each counting pool is composed of nine 1mm×1mm squares, and each square can hold a liquid volume of 0.1mm3. The specific counting steps are as follows:

①将已培养一段时间后的细胞孔板进行消化,获得细胞悬液,尽量充分混匀打散细胞。① Digest the cell plate that has been cultured for a period of time to obtain a cell suspension, mix as much as possible to disperse the cells.

②对计数板进行消毒后盖上盖玻片。② After sterilizing the counting plate, cover it with a coverslip.

③吸取10mL细胞悬液,沿玻片边缘缓慢滴入计数板中,保证盖玻片和计数板中间无气泡产生)。③Pipe 10mL of cell suspension and slowly drop it into the counting plate along the edge of the slide to ensure that there are no air bubbles between the cover glass and the counting plate).

④放置1min,于显微镜下观察计数板,并按如下原则对四角的方格进行计数:a.对于压住方格边线的细胞,只对上边和左边的细胞进行计数,b.若细胞成团块状,则计为一个细胞。④Stay for 1 min, observe the counting plate under a microscope, and count the squares at the four corners according to the following principles: a. For the cells that press the edge of the square, only count the cells on the upper and left sides; b. If the cells are clustered block, it is counted as one cell.

⑤细胞悬液浓度=四角方格内细胞总数/4×104个/mL。⑤Concentration of cell suspension = total number of cells in the four-corner square/4×104 cells/mL.

2)CCK-8细胞增殖实验2) CCK-8 cell proliferation assay

本研究采用CCK-8试剂盒(Dojindo,日本)检测结直肠癌细胞增殖能力。In this study, CCK-8 kit (Dojindo, Japan) was used to detect the proliferation ability of colorectal cancer cells.

①吸取细胞悬液100mL并按计数浓度稀释至细胞量为2,000左右,接种于96孔板中。① Aspirate 100mL of cell suspension and dilute it according to the counting concentration to about 2,000 cells, and inoculate it in a 96-well plate.

②在24h、48h、72h和96h四个时间点进行细胞活性检测。向每个孔内加入10mLCCK-8试剂,上下左右摇晃以轻柔混匀,放回细胞培养箱继续培养1.5h。② Cell viability was detected at four time points of 24h, 48h, 72h and 96h. Add 10mL of CCK-8 reagent to each well, shake it up and down, left and right to mix gently, and put it back into the cell culture incubator to continue culturing for 1.5h.

③使用酶标仪进行吸光度测定,波长设定为450nm,根据四个时间点的吸光度值绘制不同实验组别的细胞增殖曲线以比较其差异。③ Use a microplate reader to measure the absorbance, the wavelength is set to 450nm, draw the cell proliferation curves of different experimental groups according to the absorbance values at four time points to compare the differences.

3)克隆形成实验3) Colony formation experiment

①在转染细胞36h后,进行细胞计数并稀释至合适浓度。在6孔板的每孔中加入2mL细胞悬液使得细胞量为1,000左右,继续培养2周左右。① After 36 hours of transfection, cells were counted and diluted to an appropriate concentration. Add 2 mL of cell suspension to each well of the 6-well plate to make the cell volume about 1,000, and continue to culture for about 2 weeks.

②期间每2~3天观察细胞形态并更换新鲜培养基。若显微镜下观察到细胞克隆时,可进行固定染色。② During the period, observe the cell morphology and replace the fresh medium every 2-3 days. If cell clones are observed under the microscope, fixation staining can be performed.

③从培养箱中取出6孔板,吸去废液并缓慢加入PBS清洗2次。吸净每孔PBS后加入2mL甲醇溶液,于室温放置30min。③Take out the 6-well plate from the incubator, suck off the waste liquid and slowly add PBS to wash it twice. After aspirating the PBS in each well, add 2mL of methanol solution and let it stand at room temperature for 30min.

④吸去甲醇后加入0.25%结晶紫溶液,避光放置30min进行染色。④ After absorbing the methanol, add 0.25% crystal violet solution, and place it in the dark for 30 minutes for staining.

⑤染色完成后,吸去孔中废液,并用双蒸水清洗孔板直至视野清晰,进行拍照保存。⑤ After the staining is completed, suck off the waste liquid in the well, and wash the orifice plate with double distilled water until the field of view is clear, and take pictures for preservation.

综上,我们通过运用ABC模型,系统的整合了ATAC-seq、CHIP-seq、RNA-seq以及Hi-C在内的多组学数据,由此构建了结直肠癌增强子-靶基因映射图谱。进一步地,结合欧洲人群和中国人群大样本的病例对照研究、生物学实验等技术方法。发现,位于20q13.13区域的rs4810856具有最强的基因表达调控效应,相比于rs4810856[T]个体,携带[C]等位基因的个体结直肠癌患病风险显著增加。机制上,我们发现位于染色质20q13.13区域的rs4810856可同时调控三个靶基因:PREX1、CSE1L及STAU1。且rs4810856[C]与转录因子ZEB1的结合能力比rs4810856[T]携带者强,从而影响其所在区域与靶基因的启动子的染色质交互作用,进而促进靶基因PREX1、CSE1L及STAU1的表达水平,且影响AKT信号通路激活,从而促进结直肠癌发病风险。因此,位于非编码区的rs4810856变异与结直肠癌患病风险有着密切的关系,有望在临床上应用,辅助结直肠癌的早期诊断,早期发现结直肠癌患者。In summary, we systematically integrated multi-omics data including ATAC-seq, CHIP-seq, RNA-seq, and Hi-C by using the ABC model, thereby constructing a colorectal cancer enhancer-target gene mapping map. Further, combined with large-scale case-control studies of European populations and Chinese populations, biological experiments and other technical methods. It was found that rs4810856 located in the 20q13.13 region had the strongest gene expression regulation effect, and individuals carrying the [C] allele had a significantly increased risk of colorectal cancer compared with rs4810856[T] individuals. Mechanistically, we found that rs4810856 located in the chromatin 20q13.13 region can simultaneously regulate three target genes: PREX1, CSE1L and STAU1. Moreover, the binding ability of rs4810856[C] to the transcription factor ZEB1 is stronger than that of rs4810856[T] carriers, which affects the chromatin interaction between its region and the promoter of the target gene, thereby promoting the expression levels of the target genes PREX1, CSE1L and STAU1 , and affect the activation of the AKT signaling pathway, thereby promoting the risk of colorectal cancer. Therefore, the rs4810856 mutation located in the non-coding region is closely related to the risk of colorectal cancer, and it is expected to be clinically applied to assist in the early diagnosis of colorectal cancer and early detection of colorectal cancer patients.

以上所述仅为本发明的较佳实施例,并不用以限制本发明,凡在本发明的精神和原则之内,所作的任何修改、等同替换、改进等,均应包含在本发明的保护范围之内。The above descriptions are only preferred embodiments of the present invention, and are not intended to limit the present invention. Any modifications, equivalent replacements, improvements, etc. made within the spirit and principles of the present invention shall be included in the protection of the present invention. within range.

Figure IDA0003727236040000011
Figure IDA0003727236040000011

Claims (1)

1.增强子功能位点rs4810856的检测试剂在制备结直肠癌辅助诊断试剂盒中的应用。1. The application of the detection reagent of enhancer functional site rs4810856 in the preparation of colorectal cancer auxiliary diagnosis kit.
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