Journal of Shandong University (Health Sciences) ›› 2021, Vol. 59 ›› Issue (1): 64-71.doi: 10.6040/j.issn.1671-7554.0.2020.1033

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Predicting colon cancer prognosis genes and clinical application value based on TCGA database

ZHEN Qiulai1,2, LYU Xinran3, YE Hui1, DING Xuchao3, CHAI Xiaoxue1, HU Xin1, ZHOU Ming1, CAO Lili1,3   

  1. 1. Department of Oncology, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Shandong Provincial Key Laboratory for Rheumatic Disease and Translational Medicine, Jinan 250014, Shandong, China;
    2. Department of Blood Transfusion, Central Hospital of Zibo Mining Group Co., Ltd., Zibo 255120, Shandong, China;
    3. Department of Oncology, The First Affiliated Hospital of Shandong First Medical University, Jinan 250014, Shandong, China
  • Published:2021-01-09

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Abstract: Objective To screen the prognostic genes, identify risks and predict prognosis by excavating colon cancer data from TCGA database. Methods The RNA expression data and clinical information of colon cancer patients were downloaded from TCGA database. A proportional hazard regression model was constructed and a risk scoring formula was formed after univariate Cox and multivariate Cox regression analyses. The patients were divided into high-risk and low-risk groups based on the median risk score to determine the mortality risk. The receiver operating characteristic(ROC)curve and area under the curve(AUC)were used to verify the evaluation performance of the model. Survival analysis of prognosis-related genes was performed using R language. The differentially expressed genes were analyzed using GO function and KEGG pathway enrichment. Results Of the 5 544 differentially expressed genes, 27 were associated with overall survival, and 11 were screened to construct the prognostic model, including GABRD, FAM132B, LRRN4, RP11-400N13.2, RP11-108K3.2, RNU6-403P, RP11-429J17.8, LINC01296, RP11-190J1.3, AC002076.10 and CTC-573N18.1. ROC analysis showed that the 5-year survival rate was 39.5%(95%CI: 29.5-53.0)in the high-risk group and 89.6%(95%CI: 82.2-97.7)in the low-risk group, with AUC being0.827, indicating that the model could effectively distinguish patients with high and low risks. Conclusion The risk score obtained from the Cox proportional hazard model genes combined with clinical information can be used to evaluate the prognosis and survival of patients with colon cancer.

Key words: TCGA database, Colon cancer, RNA, Cox proportional hazard model, Survival

CLC Number: 

  • R574.62
[1] Bray F, Ferlay J, Soerjomataram I, et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries [J]. CA: A Cancer J Clin, 2018, 68(6): 394-424.
[2] Banskota S, Dahal S, Kwon E, et al. Β-Catenin gene promoter hypermethylation by reactive oxygen species correlates with the migratory and invasive potentials of colon cancer cells [J]. Cell Oncol(Dordr), 2018, 41(5): 569-580.
[3] Park SY, Wilkens LR, Setiawan VW, et al. Alcohol intake and colorectal cancer risk in the multiethnic cohort study [J]. Am J Epidemiol, 2019, 188(1): 67-76.
[4] Vanella G, Archibugi L, Stigliano S, et al. Alcohol and gastrointestinal cancers [J]. Curr Opin Gastroenterol, 2019, 35(2): 107-113.
[5] Fagunwa IO, Loughrey MB, Coleman HG. Alcohol, smoking and the risk of premalignant and malignant colorectal neoplasms [J]. Best Pract Res Clin Gastroenterol, 2017, 31(5): 561-568.
[6] Zhang J, Guo S, Li J, et al. Effects of high-fat diet-induced adipokines and cytokines on colorectal cancer development [J]. FEBS Open Bio, 2019, 9(12): 2117-2125.
[7] Triff K, McLean MW, Callaway E, et al. Dietary fat and fiber interact to uniquely modify global histone post-translational epigenetic programming in a rat colon cancer progression model [J]. Int J Cancer, 2018, 143(6): 1402-1415.
[8] Nadella S, Burks J, Al-Sabban A, et al. Dietary fat stimulates pancreatic cancer growth and promotes fibrosis of the tumor microenvironment through the cholecystokinin receptor [J]. Am J Physiol - Gastrointest Liver Physiol, 2018, 315(5): G699-G712.
[9] Bhatlekar S, Fields JZ, Boman BM. HOX genes and their role in the development of human cancers [J]. J Mol Med, 2014, 92(8): 811-823.
[10] Hong SN. Genetic and epigenetic alterations of colorectal cancer [J]. Intest Res, 2018, 16(3): 327.
[11] Mc Donald RA, Hata A, MacLean MR, et al. Micro RNA and vascular remodelling in acute vascular injury and pulmonary vascular remodelling [J]. Cardiovasc Res, 2012, 93(4): 594-604.
[12] Davis-Dusenbery BN, Wu C, Hata A. Micromanaging vascular smooth muscle cell differentiation and phenotypic modulation [J]. Arterioscler Thromb Vasc Biol, 2011, 31(11): 2370-2377.
[13] Xu G, Zhang M, Zhu H, et al. A 15-gene signature for prediction of colon cancer recurrence and prognosis based on SVM [J]. Gene, 2017, 604: 33-40. doi: 10.1016/j.gene.2016.12.016.
[14] Sun D, Chen J, Liu L, et al. Establishment of a 12-gene expression signature to predict colon cancer prognosis [J]. PeerJ, 2018, 6: e4942. doi:10.7717/peerj.4942.
[15] Zuo SG, Dai GP, Ren XQ. Identification of a 6-gene signature predicting prognosis for colorectal cancer [J]. Cancer Cell Int, 2019, 19: 6. doi: 10.1186/s12935-018-0724-7.
[16] Wang Z, Jensen MA, Zenklusen JC. A practical guide to the cancer genome atlas(TCGA)[J]. Methods Mol Biol, 2016, 1418: 111-141. doi: 10.1007/978-1-4939-3578-9_6.
[17] Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources [J]. Nat Protoc, 2009, 4(1): 44-57.
[18] Wong MCS, Huang JJ, Lok V, et al. Differences in incidence and mortality trends of colorectal cancer worldwide based on sex, age, and anatomic location [J]. Clin Gastroenterol Hepatol, 2020(20): 30196-30198. doi: 10.1016/j.cgh.2020.02.026.
[19] Araghi M, Soerjomataram I, Jenkins M, et al. Global trends in colorectal cancer mortality: projections to the year 2035 [J]. Int J Cancer, 2019, 144(12): 2992-3000.
[20] Kim EK, Song MJ, Jung Y, et al. Proteomic analysis of primary colon cancer and synchronous solitary liver metastasis[J]. Cancer Genomics Proteomics, 2019, 16(6): 583-592.
[21] Kumamoto K, Nakachi Y, Mizuno Y, et al. Expressions of 10 genes as candidate predictors of recurrence in stage III colon cancer patients receiving adjuvant oxaliplatinbased chemotherapy[J]. Oncol Lett, 2019, 18(2): 1388-1394.
[22] Zhao ZW, Fan XX, Yang LL, et al. The identification of a common different gene expression signature in patients with colorectal cancer [J]. Math Biosci Eng, 2019, 16(4): 2942-2958.
[23] Mo SB, Dai WX, Xiang WQ, et al. Prognostic and predictive value of an autophagy-related signature for early relapse in stages I-III colon cancer [J]. Carcinogenesis, 2019, 40(7): 861-870.
[24] Wang XJ, Zeng B, Lin S, et al. An integrated miRNA-lncRNA signature predicts the survival of stage II colon cancer [J]. Ann Clin Lab Sci, 2019, 49(6): 730-739.
[25] Yang H, Liu H, Lin HC, et al. Association of a novel seven-gene expression signature with the disease prognosis in colon cancer patients [J]. Aging(Albany NY), 2019, 11(19): 8710-8727.
[26] Lauss M, Kriegner A, Vierlinger K, et al. Characterization of the drugged human genome [J]. Pharmacogenomics, 2007, 8(8): 1063-1073.
[27] Nguyen TT, Ung TT, Kim NH, et al. Role of bile acids in colon carcinogenesis [J]. World J Clin Cases, 2018, 6(13): 577-588.
[28] Yan L, Gong YZ, Shao MN, et al. Distinct diagnostic and prognostic values of γ-aminobutyric acid type A receptor family genes in patients with colon adenocarcinoma [J]. Oncol Lett, 2020, 20(1): 275-291.
[29] Liu B, Pan SM, Xiao Y, et al. LINC01296/miR-26a/GALNT3 axis contributes to colorectal cancer progression by regulating O-glycosylated MUC1 via PI3K/AKT pathway [J]. J Exp Clin Cancer Res, 2018, 37: 316. doi:10.1186/s13046-018-0994-x.
[30] Jiang D, Jin M, Ye D, et al. Polymorphisms of a novel long non-coding RNA RP11-108K3.2 with colorectal cancer susceptibility and their effects on its expression [J]. Int J Biol Markers, 2020, 35(1): 3-9.
[31] Zhou W, Pan B, Liu L. Integrated bioinformatics analysis revealing independent prognostic long non-coding RNAs DNAH17-AS1 and RP11-400N13.2 and their potential oncogenic roles in colorectal cancer [J]. Oncol Lett, 2019, 18(4): 3705-3715.
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