[1]龚俊杰,等.基于公共数据集的三阴性乳腺癌转录组学分析[J].深圳大学学报理工版,2021,38(5):517-527.[doi:10.3724/SP.J.1249.2021.05517]
 GONG Junjie,WANG Ping,et al.Transcriptome analysis of triple negative breast cancer based on public database[J].Journal of Shenzhen University Science and Engineering,2021,38(5):517-527.[doi:10.3724/SP.J.1249.2021.05517]
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基于公共数据集的三阴性乳腺癌转录组学分析()
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《深圳大学学报理工版》[ISSN:1000-2618/CN:44-1401/N]

卷:
第38卷
期数:
2021年第5期
页码:
517-527
栏目:
生物工程
出版日期:
2021-09-15

文章信息/Info

Title:
Transcriptome analysis of triple negative breast cancer based on public database
文章编号:
202105011
作者:
龚俊杰1 2王平1徐子金1
1)浙江工业大学药学院,浙江杭州310014
2)义乌市中心医院药剂科,浙江义乌322099
Author(s):
GONG Junjie1 2 WANG Ping1 and XU Zijin1
1) College of Pharmacy, Zhejiang University of Technology, Hangzhou 310014, Zhejiang Province, P.R.China
2) Department of Pharmacy, Yiwu Central Hospital,Yiwu 322099, Zhejiang Province, P.R.China
关键词:
转录组学三阴性乳腺癌公共数据库基因芯片生物信息学分析病理标志物
Keywords:
transcriptomics triple negative breast cancer public database gene chip bioinformatics analysis pathological marker
分类号:
Q819;Q756
DOI:
10.3724/SP.J.1249.2021.05517
文献标志码:
A
摘要:
三阴性乳腺癌(triple negative breast cancer, TNBC)是乳腺癌中恶性程度较高的一种病理分型,因其病理呈现雌激素受体、孕激素受体和人类表皮生长因子受体2均为阴性的特殊性,使得目前药物治疗效果不甚理想,探究与TNBC病变过程相关的病理标志物是当前乳腺癌研究领域的热点之一.通过高通量基因表达(gene expression omnibus, GEO)数据库获取TNBC相关的基因集,并进行主成分分析、差异基因筛选、基因功能和信号通路的富集分析、蛋白互作网络构建以及加权基因共表达网络分析等转录组学分析.结果表明,TNBC和非TNBC具有明显不同的基因表达模式,这些差异基因主要富集于表皮生长和分化、乳腺上皮细胞生长和发育等相关生物学过程,还富集于转录因子结合相关分子功能与雌激素信号转导相关通路.整合蛋白互作网络和共表达网络的结果,可以预测TFF1、 FOXA1、 AGR2和AGR3可能是涉及TNBC病理表型的关键基因.研究结果为揭示TNBC潜在的病理标志物以及由此衍生的疾病诊疗靶标或分子调控机制,提供一定的理论研究依据.
Abstract:
Triple negative breast cancer (TNBC) is a pathological type with high malignancy in breast cancer. Because the estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 appear histologically negative, the treatment effect of the existing drug is not ideal. Exploring the TNBC related pathological markers is one of hot spots in the research field of breast cancer. TNBC related gene sets are obtained from gene expression omnibus (GEO) database for transcriptome analysis, including principal component analysis, screening differentially expressed genes (DEGs), gene function enrichment analysis and signal pathway enrichment analysis, protein interaction network construction, weighted gene coexpression network analysis (WGCNA), etc. The results show that there are significantly differentially expressed genes (DEGs) between TNBC and non TNBC population. These DEGs are mainly enriched in the biological processes related to epidermal growth and differentiation, growth and development of mammary epithelial cells, and in molecular functions related to transcription factor binding and estrogen signal transduction pathways. The results of protein interaction network and weighted gene coexpression network analysis are integrated and TFF1, FOXA1, AGR2 and AGR3 are predicted as the key genes involved in the pathological phenotype of TNBC. The study of transcriptome analysis based on TNBC gene set in public database may provide certain theoretical research basis to reveal the potential biomarkers for pathogenesis of TNBC, and the derived disease diagnosis and therapeutic targets or molecular regulation mechanisms.

参考文献/References:

[1] VAGIA E, MAHALINGAM D, CRISTOFANILLI M. The landscape of targeted therapies in TNBC[J].Cancers,2020,12(4):916.
[2] NEDELJKOVIC' M, DAMJANOVIC' A. Mechanisms of chemotherapy resistance in triple-negative breast cancer: how we can rise to the challenge[J].Cells,2019,8(9):957.
[3] 周游, 王雅楠, 张堃, 等. ER阳性乳腺癌中西达本胺逆转内分泌耐药[J].深圳大学学报理工版,2018,35(4):339-344.
ZHOU You,WANG Ya’nan,ZHANG Kun,et al.Reverse effect of chidamide on endocrine resistance in estrogen receptor-positive breast cancer[J].Journal of Shenzhen University Science and Engineering,2018,35(4):339-344.(in Chinese)
[4] HRDLICKOVA R, TOLOUE M, TIAN Bin. RNA-seq methods for transcriptome analysis[J].Wiley Interdisciplinary Reviews: RNA,2017,8(1). doi:10.1002/wrna.1364.
[5] STARK R, GRZELAK M, HADFIELD J. RNA sequencing: the teenage years[J].Nature Reviews Genetics,2019,20(11):631-656.
[6] LIU Wei, LI Li, YE Hua, et al. Weighted gene co-expression network analysis in biomedicine research[J]. Chinese Journal of Biotechnology,2017,33(11):1791-1801.
[7] ZHOU Yingyao, ZHOU Bin, PACHE L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets[J].Nature Communication,2019,10(1):1523.
[8] TANG Jianning, LUO yongwen, WU Gaosong, et al. Prognostic genes of breast cancer identified by gene co-expression network analysis[J].Frontiers in Oncology,2018,8:374.
[9] YI Jie, REN Liwen, LI Dandan, et al. Trefoil factor 1 (TFF1) is a potential prognostic biomarker with functional significance in breast cancers[J].Biomedicine and Pharmacotherapy,2020,124:109827.
[10] 贾海全.乳腺癌雄激素受体研究进展[J].临床研究,2018,26(2):197-198.
JIA Haiquan. Research progress of androgen receptor in breast cancer[J]. Clinical Research,2018,26(2):197-198.(in Chinese)
[11] GUIU S, CHARON-BARRA C, VERNEREY D, et al. Coexpression of androgen receptor and FOXA1 in nonmetastatic triple-negative breast cancer: ancillary study from PACS08 trial[J].Future Oncology,2015,11(16):2283-2297.
[12] GUIU S, MOLLEVI C, CHARON-BARRA C, et al. Prognostic value of androgen receptor and FOXA1 co-expression in non-metastatic triple negative breast cancer and correlation with other biomarkers[J].British Journal of Cancer,2018,119(1):76-79.
[13] ROBINSON J L, MACARTHUR S, ROSS-INNES C S, et al. Androgen receptor driven transcription in molecular apocrine breast cancer is mediated by FoxA1[J].EMBO Journal,2011,30(15):3019-3027.
[14] WOLF I, BOSE S, WILLIAMSON E A, et al. FOXA1: growth inhibitor and a favorable prognostic factor in human breast cancer[J].International Journal of Cancer,2007,120(5):1013-1022.
[15] WU Shao, LUO Zhi, YU PengJiu, et al. Suberoylanilide hydroxamic acid (SAHA) promotes the epithelial mesenchymal transition of triple negative breast cancer cells via HDAC8/FOXA1 signals[J].Biological Chemistry,2016,397(1):75-83.
[16] LIU Yubo, WANG Xue, ZHU Tong, et al. Resistance to bortezomib in breast cancer cells that downregulate Bim through FOXA1 O-GlcNAcylation[J].Journal of Cellular Physiology,2019,234(10):17527-17537.
[17] XU Yixiang, QIN Li, SUN Tong, et al. Twist1 promotes breast cancer invasion and metastasis by silencing FOXA1 expression[J].Oncogene,2017,36(8):1157-1166.
[18] BENAYED-GUERFALI D, DABBCHE-BOURICHA E, AYADI W, et al. Association of FOXA1 and EMT markers (Twist1 and E-cadherin) in breast cancer[J].Molecular Biology Reports,2019,46(3):3247-3255.
[19] GUO Jilong, GONG Guohua, ZHANG Bin. Identification and prognostic value of anterior gradient protein 2 expression in breast cancer based on tissue microarray[J].Tumour Biology,2017,39(7):1010428317713392.
[20] OBACZ J, TAKACOVA M, BRYCHTOVA V, et al. The role of AGR2 and AGR3 in cancer: similar but not identical[J].European Journal of Cell Biology,2015,94(3/4):139-147.
[21] OBACZ J, BRYCHTOVA V, PODHOREC J, et al. Anterior gradient protein 3 is associated with less aggressive tumors and better outcome of breast cancer patients[J].OncoTargets and Therapy,2015,8:1523-1532.
[22] JIAN Lei, XIE Jian, GUO Shipeng, et al. AGR3 promotes estrogen receptor-positive breast cancer cell proliferation in an estrogen-dependent manner[J].Oncology Letters,2020,20(2):1441-1451.
[23] OBACZ J, SOMMEROVA L, SICARI D, et al. Extracellular AGR3 regulates breast cancer cells migration via Src signaling[J].Oncology Letters,2019,18(5):4449-4456.
[24] XU Qiao, SHAO Ying, ZHANG Jinman, et al. Anterior gradient 3 promotes breast cancer development and chemotherapy response[J].Cancer Research and Treatment,2020,52(1):218-245.

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备注/Memo

备注/Memo:
Received:2021-02-04;Accepted:2021-07-20;Online(CNKI):2021-09-06
Foundation:Zhejiang Science and Technology Plan (2017C04009); Key Intergovernmental Cooperation Program on International Science and Technology Innovation (2017YFE0130100)
Corresponding author:Professor WANG Ping.E-mail:cczyyxzj@163.com
Citation:GONG Junjie,WANG Ping,XU Zijin,et al.Transcriptome analysis of triple negative breast cancer based on public database[J]. Journal of Shenzhen University Science and Engineering, 2021, 38(5): 517-527.(in Chinese)
基金项目:浙江省科技计划资助项目(2017C04009);政府间国际科技创新合作重点专项资助项目(2017YFE0130100)
作者简介:龚俊杰(1995—),浙江工业大学硕士研究生.研究方向:转录组学.E-mail:2274897305@qq.com
引文:龚俊杰,王平,徐子金.基于公共数据集的三阴性乳腺癌转录组学分析[J]. 深圳大学学报理工版,2021,38(5):517-527.
更新日期/Last Update: 2021-09-30