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中华结直肠疾病电子杂志 ›› 2019, Vol. 08 ›› Issue (04) : 363 -369. doi: 10.3877/cma.j.issn.2095-3224.2019.04.008

所属专题: 文献

论著

基于COSMIC数据库的结直肠转移性癌的体细胞突变基因变化的研究
康争春1, 鄂继福1,(), 朱良亮1, 闫飞虎1, 于恩达1,()   
  1. 1. 200433 上海,海军军医大学附属长海医院肛肠外科
  • 收稿日期:2018-10-23 出版日期:2019-08-25
  • 通信作者: 鄂继福, 于恩达
  • 基金资助:
    上海市科学技术委员会基础研究重大重点项目(No.13JC1407201); 国家重点基础研究发展计划(973计划;No.2015CB554001); 第二军医大学精准医学转化应用研究专项项目(No.2017JZ19); 国家自然科学基金青年科学基金项目(No.81802434)

Study on the changes of somatic mutation in colorectal metastatic cancer based on COSMIC database

Zhengchun Kang1, Jifu E1,(), Liangliang Zhu1, Feihu Yan1, Enda Yu1,()   

  1. 1. Department of Colorectal Surgery, Changhai Hospital, PLA Navy Medical Uneversity, Shanghai 200433, China
  • Received:2018-10-23 Published:2019-08-25
  • Corresponding author: Jifu E, Enda Yu
  • About author:
    Corresponding author: E Jifu, Email:
    Yu Enda, Email:
引用本文:

康争春, 鄂继福, 朱良亮, 闫飞虎, 于恩达. 基于COSMIC数据库的结直肠转移性癌的体细胞突变基因变化的研究[J/OL]. 中华结直肠疾病电子杂志, 2019, 08(04): 363-369.

Zhengchun Kang, Jifu E, Liangliang Zhu, Feihu Yan, Enda Yu. Study on the changes of somatic mutation in colorectal metastatic cancer based on COSMIC database[J/OL]. Chinese Journal of Colorectal Diseases(Electronic Edition), 2019, 08(04): 363-369.

目的

利用癌症体细胞突变目录(COSMIC)数据库,筛选结直肠原发性癌和结直肠转移性癌两类癌组织之间的具有显著差异的体细胞基因突变,并分析其可能的功能及通路。

方法

从COSMIC数据库下载结直肠癌全外显子测序数据,在R 3.5.0环境下,利用卡方检验或Fisher确切概率法对结直肠原发性癌和结直肠转移性癌两类癌组织之间的差异体细胞突变基因进行挖掘,记录具有显著差异的体细胞突变基因并进行功能及通路富集分析,探索其可能生物学功能及通路。

结果

共发现120个具有显著差异的体细胞突变基因,包括RHEB、RP11-368J21.2、AGAP10等,对其进行GO和KEGG富集分析显示,这些显著性差异体细胞突变基因可能与如脱氢酶活性、还原酶活性、细胞周期停滞、代谢途径、PI3K-Akt信号通路、细胞周期、细胞粘附分子、癌症中的转录失调、铂类耐药性等功能及通路相关。

结论

挖掘结直肠原发性癌和结直肠转移性癌之间的显著差异体细胞突变基因可为研究结直肠癌的转移调控机制提供借鉴,显著差异体细胞突变基因可能作为结直肠癌转移诊断标志物或转移治疗靶点应用于临床。

Objective

To screen the significant differences in somatic gene mutations between primary colorectal cancer and colorectal metastatic cancer using the Catalogue of Somatic Mutations In Cancer Catalog (COSMIC) Database and analyze its possible functions and pathways.

Methods

The colorectal cancer whole-exome sequencing data was downloaded from the COSMIC database. In the R 3.5.0 environment, the chi-square test or Fisher′ exact test was used to analysis the primary colorectal cancer and colorectal metastatic cancer. The differences in somatic mutation genes were mined, and somatically mutated genes with significant differences were recorded and functional and pathway enrichment analysis was performed to explore their possible biological functions and pathways.

Results

A total of 120 somatic mutations, including RHEB, RP11-368J21.2, AGAP10, etc, were found. The GO and KEGG enrichment analysis showed that these significant differences in somatic mutations may be related to dehydrogenase activity, reductase activity, cell cycle arrest, metabolic pathway, PI3K-Akt signaling pathway, cell cycle, cell adhesion molecules, transcriptional disorders in cancer, platinum resistance, and other functions and pathways.

Conclusion

The significant difference in somatic mutation between primary colorectal cancer and colorectal metastatic cancer can provide a reference for studying the metastasis mechanism of colorectal cancer. Significant differences in somatic mutations may be used as clinical diagnostic markers for metastatic colorectal cancer or as targets for metastasis therapy.

表1 突变率top30的基因位点
表2 结直肠原发性癌和结直肠转移性癌top30差异突变基因结果
基因 结直肠原发性癌突变率 结直肠转移性癌突变率 χ2 P
RHEB 0.00286123 0.086206897 32.01980399 1.53×10-08
RP11-368J21.2 0.001430615 0.068965517 27.64667 1.46×10-07
AGAP10 0 0.051724138 24.37795003 7.92×10-07
PRKRIR 0.00286123 0.068965517 21.94934078 2.80×10-06
NMRAL1 0.004291845 0.068965517 17.90125811 2.33×10-05
QPCT 0.001430615 0.051724138 17.09281147 3.56×10-05
TOMM40 0.001430615 0.051724138 17.09281147 3.56×10-05
PYCR2 0.001430615 0.051724138 17.09281147 3.56×10-05
SLC18A1 0.010014306 0.086206897 15.34447432 8.96×10-05
KDR 0.038626609 0.155172414 13.59040229 0.000227345
HSD17B4 0.011444921 0.086206897 13.58267182 0.000228283
ENSG00000188912 0 0.034482759 12.85251807 0.000337025
HIST2H3D 0 0.034482759 12.85251807 0.000337025
RGPD1 0 0.034482759 12.85251807 0.000337025
MORF4L1 0 0.034482759 12.85251807 0.000337025
CSTL1 0 0.034482759 12.85251807 0.000337025
MANSC1 0 0.034482759 12.85251807 0.000337025
CDK7 0 0.034482759 12.85251807 0.000337025
AHSA1 0 0.034482759 12.85251807 0.000337025
TRAPPC6B 0 0.034482759 12.85251807 0.000337025
DGCR6L 0 0.034482759 12.85251807 0.000337025
C17orf77 0.00286123 0.051724138 12.75260599 0.000355513
NPIP 0.00286123 0.051724138 12.75260599 0.000355513
ANAPC1 0.025751073 0.120689655 12.28920299 0.000455586
RASA4 0.008583691 0.068965517 10.70535245 0.00106826
LLPH 0.008583691 0.068965517 10.70535245 0.00106826
OR5B3 0.008583691 0.068965517 10.70535245 0.00106826
PRB2 0.008583691 0.068965517 10.70535245 0.00106826
IPMK 0.008583691 0.068965517 10.70535245 0.00106826
ESCO2 0.008583691 0.068965517 10.70535245 0.00106826
图1 差异基因突变位点的manhattan图(横坐标代表染色体位置,纵坐标代表-log10 p,红线代表P值等于0.05)
表3 结直肠原发性癌和结直肠转移性癌top30差异突变基因位点结果
基因位点 结直肠原发性癌突变率 结直肠转移性癌突变率 χ2 P
RHEB|COSM5757012|c.169C>T 0 0.086206897 48.23220622 3.79×10-12
AOC3|COSM5755045|c.1634T>C 0 0.068965517 36.23003121 1.75×10-09
NMRAL1|COSM148011|c.755C>T 0 0.068965517 36.23003121 1.75×10-09
IPMK|COSM5753509|c.1096T>G 0 0.068965517 36.23003121 1.75×10-09
ESCO2|COSM150477|c.239C>T 0 0.068965517 36.23003121 1.75×10-09
TRPV2|COSM148200|c.50G>C 0 0.068965517 36.23003121 1.75×10-09
U2SURP|COSM5756177|c.769G>C 0 0.068965517 36.23003121 1.75×10-09
GCOM1|COSM147926|c.830C>T 0 0.051724138 24.37795003 7.92×10-07
AGAP10|COSM415019|c.683A>G 0 0.051724138 24.37795003 7.92×10-07
SACM1L|COSM149368|c.1301A>T 0 0.051724138 24.37795003 7.92×10-07
HMMR|COSM150009|c.1103T>C 0 0.051724138 24.37795003 7.92×10-07
PTCH2|COSM1162381|c.2963C>T 0 0.051724138 24.37795003 7.92×10-07
FSIP1|COSM147876|c.1583G>C 0 0.051724138 24.37795003 7.92×10-07
IL7R|COSM132904|c.731C>T 0 0.051724138 24.37795003 7.92×10-07
ARHGEF37|COSM149984|c.1388C>T 0 0.051724138 24.37795003 7.92×10-07
MUC7|COSM249589|c.746T>C 0 0.051724138 24.37795003 7.92×10-07
SPATA6|COSM146506|c.1433G>A 0 0.051724138 24.37795003 7.92×10-07
HSD17B4|COSM1130959|c.1675A>G 0 0.051724138 24.37795003 7.92×10-07
CD300LD|COSM148338|c.265G>A 0 0.051724138 24.37795003 7.92×10-07
SYCE1|COSM147098|c.288G>T 0 0.051724138 24.37795003 7.92×10-07
P2RX7|COSM147626|c.809G>A 0 0.051724138 24.37795003 7.92×10-07
PKD1|COSM5754804|c.6779T>C 0 0.051724138 24.37795003 7.92×10-07
C17orf77|COSM148339|c.593C>T 0 0.051724138 24.37795003 7.92×10-07
MRGPRX2|COSM147163|c.185A>G 0 0.051724138 24.37795003 7.92×10-07
OR5B3|COSM147247|c.541G>A 0 0.051724138 24.37795003 7.92×10-07
INADL|COSM1126971|c.1198A>G 0 0.051724138 24.37795003 7.92×10-07
OR10G4|COSM147352|c.883A>C 0 0.051724138 24.37795003 7.92×10-07
MYH4|COSM148193|c.2648C>T 0 0.051724138 24.37795003 7.92×10-07
ALOX15B|COSM148187|c.2026A>G 0 0.051724138 24.37795003 7.92×10-07
OR5B3|COSM147248|c.509A>G 0 0.051724138 24.37795003 7.92×10-07
图2 GO功能富集结果
图3 KEGG通路富集结果
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