RNA-seq analysis identified hormone-related genes associated with prognosis of triple negative breast cancer

Chen Fei; Li Yuancheng; Qin Na; Wang Fengliang; Du Jiangbo; Wang Cheng; Du Fangzhi; Jiang Tao; Jiang Yue; Dai Juncheng; Hu Zhibin; Lu Cheng; Shen Hongbing

doi:10.7555/JBR.34.20190111

Volume 34 Issue 2

Mar. 2020

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The Journal of Biomedical Research > 2020 > 34(2): 129-138. > DOI: 10.7555/JBR.34.20190111

Chen Fei, Li Yuancheng, Qin Na, Wang Fengliang, Du Jiangbo, Wang Cheng, Du Fangzhi, Jiang Tao, Jiang Yue, Dai Juncheng, Hu Zhibin, Lu Cheng, Shen Hongbing. RNA-seq analysis identified hormone-related genes associated with prognosis of triple negative breast cancer[J]. The Journal of Biomedical Research, 2020, 34(2): 129-138. DOI: 10.7555/JBR.34.20190111

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RNA-seq analysis identified hormone-related genes associated with prognosis of triple negative breast cancer

Chen Fei^1,2,3,
Li Yuancheng^2,3,
Qin Na^2,3,
Wang Fengliang¹,
Du Jiangbo^2,3,
Wang Cheng^2,3,4,
Du Fangzhi⁵,
Jiang Tao^2,3,
Jiang Yue^2,3,
Dai Juncheng^2,3,
Hu Zhibin^2,3,
Lu Cheng^1, ,,
Shen Hongbing^2,3, ,

1.
Department of Breast Surgery, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
2.
Department of Epidemiology, Center for Global Health, School of Public Health
3.
Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine
4.
Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu 211116, China
5.
Department of Clinical Management, National Center for STD Control, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu 210042, China

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Corresponding author:
Cheng Lu, Department of Breast Surgery, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China. Tel: +86-25-52226902, E-mail: lucheng_njmu@163.com

Hongbing Shen, Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China. Tel: +86-25-86868409, Email: hbshen@njmu.edu.cn
Received Date: August 01, 2019
Revised Date: October 21, 2019
Accepted Date: November 13, 2019
Available Online: January 28, 2020

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Abstract

Abstract

Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer that currently lacks effective biomarkers and therapeutic targets required to investigate the diagnosis and treatment of TNBC. Here we performed a comprehensive differential analysis of 165 TNBC samples by integrating RNA-seq data of breast tumor tissues and adjacent normal tissues from both our cohort and The Cancer Genome Atlas (TCGA). Pathway enrichment analysis was conducted to evaluate the biological function of TNBC-specific expressed genes. Further multivariate Cox proportional hazard regression was performed to evaluate the effect of these genes on TNBC prognosis. In this report, we identified a total of 148 TNBC-specific expressed genes that were primarily enriched in mammary gland morphogenesis and hormone levels related pathways, suggesting that mammary gland morphogenesis might play a unique role in TNBC patients differing from other breast cancer types. Further survival analysis revealed that nine genes (FSIP1, ADCY5, FSD1, HMSD, CMTM5, AFF3, CYP2A7, ATP1A2, and C11orf86) were significantly associated with the prognosis of TNBC patients, while three of them (ADCY5, CYP2A7, and ATP1A2) were involved in the hormone-related pathways. These findings indicated the vital role of the hormone-related genes in TNBC tumorigenesis and may provide some independent prognostic markers as well as novel therapeutic targets for TNBC.
- RNA-seq,
- triple negative breast cancer,
- prognosis,
- differential expression

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References

[1]	Torre LA, Bray F, Siegel RL, et al. Global cancer statistics, 2012[J]. CA Cancer J Clin, 2015, 65(2): 87–108. doi: 10.3322/caac.21262
[2]	Chen WQ, Zheng RS, Baade PD, et al. Cancer statistics in China, 2015[J]. CA Cancer J Clin, 2016, 66(2): 115–132. doi: 10.3322/caac.21338
[3]	Fan L, Strasser-Weippl K, Li JJ, et al. Breast cancer in China[J]. Lancet Oncol, 2014, 15(7): E279–E289. doi: 10.1016/S1470-2045(13)70567-9
[4]	Weigelt B, Reis-Filho JS. Histological and molecular types of breast cancer: is there a unifying taxonomy?[J]. Nat Rev Clin Oncol, 2009, 6(12): 718–730. doi: 10.1038/nrclinonc.2009.166
[5]	Ni XJ, Zhao YC, Ma JJ, et al. Hypoxia-induced factor-1 alpha upregulates vascular endothelial growth factor C to promote lymphangiogenesis and angiogenesis in breast cancer patients[J]. J Biomed Res, 2013, 27(6): 478–485.
[6]	Carey LA, Dees EC, Sawyer L, et al. The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes[J]. Clin Cancer Res, 2007, 13(8): 2329–2334. doi: 10.1158/1078-0432.CCR-06-1109
[7]	Foulkes WD, Smith IE, Reis-Filho JS. Triple-negative breast cancer[J]. N Engl J Med, 2010, 363(20): 1938–1948. doi: 10.1056/NEJMra1001389
[8]	Pogoda K, Niwińska A, Murawska M, et al. Analysis of pattern, time and risk factors influencing recurrence in triple-negative breast cancer patients[J]. Med Oncol, 2013, 30(1): 388. doi: 10.1007/s12032-012-0388-4
[9]	Perou CM, Sørlie T, Eisen MB, et al. Molecular portraits of human breast tumours[J]. Nature, 2000, 406(6797): 747–752. doi: 10.1038/35021093
[10]	Sørlie T, Perou CM, Tibshirani R, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications[J]. Proc Natl Acad Sci USA, 2001, 98(19): 10869–10874. doi: 10.1073/pnas.191367098
[11]	Cardoso F, van't Veer LJ, Bogaerts J, et al. 70-gene signature as an aid to treatment decisions in early-stage breast cancer[J]. N Engl J Med, 2016, 375(8): 717–729. doi: 10.1056/NEJMoa1602253
[12]	Paik S, Shak S, Tang G, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer[J]. N Engl J Med, 2004, 351(27): 2817–2826. doi: 10.1056/NEJMoa041588
[13]	Reis-Filho JS, Pusztai L. Gene expression profiling in breast cancer: classification, prognostication, and prediction[J]. Lancet, 2011, 378(9805): 1812–1823. doi: 10.1016/S0140-6736(11)61539-0
[14]	Kwa M, Makris A, Esteva FJ. Clinical utility of gene-expression signatures in early stage breast cancer[J]. Nat Rev Clin Oncol, 2017, 14(10): 595–610. doi: 10.1038/nrclinonc.2017.74
[15]	Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics[J]. Nat Rev Genet, 2009, 10(1): 57–63. doi: 10.1038/nrg2484
[16]	Eswaran J, Cyanam D, Mudvari P, et al. Transcriptomic landscape of breast cancers through mRNA sequencing[J]. Sci Rep, 2012, 2: 264. doi: 10.1038/srep00264
[17]	Horvath A, Pakala SB, Mudvari P, et al. Novel insights into breast cancer genetic variance through RNA sequencing[J]. Sci Rep, 2013, 3: 2256. doi: 10.1038/srep02256
[18]	Hammond MEH, Hayes DF, Dowsett M, et al. American Society of Clinical Oncology/College Of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer[J]. J Clin Oncol, 2010, 28(16): 2784–2795. doi: 10.1200/JCO.2009.25.6529
[19]	Wolff AC, Hammond MEH, Hicks DG, et al. Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update[J]. J Clin Oncol, 2013, 31(31): 3997–4013. doi: 10.1200/JCO.2013.50.9984
[20]	Webb ES, Liu P, Baleeiro R, et al. Immune checkpoint inhibitors in cancer therapy[J]. J Biomed Res, 2018, 32(5): 317–326.
[21]	Denkert C, Liedtke C, Tutt A, et al. Molecular alterations in triple-negative breast cancer-the road to new treatment strategies[J]. Lancet, 2017, 389(10087): 2430–2442. doi: 10.1016/S0140-6736(16)32454-0
[22]	Louie MC, Sevigny MB. Steroid hormone receptors as prognostic markers in breast cancer[J]. Am J Cancer Res, 2017, 7(8): 1617–1636.
[23]	Bleach R, McIlroy M. The divergent function of androgen receptor in breast cancer; analysis of steroid mediators and tumor intracrinology[J]. Front Endocrinol (Lausanne), 2018, 9: 594. doi: 10.3389/fendo.2018.00594
[24]	The Endogenous Hormones and Breast Cancer Collaborative Group. Endogenous sex hormones and breast cancer in postmenopausal women: reanalysis of nine prospective studies[J]. J Natl Cancer Inst, 2002, 94(8): 606–616. doi: 10.1093/jnci/94.8.606
[25]	McNamara KM, Oguro S, Omata F, et al. The presence and impact of estrogen metabolism on the biology of triple-negative breast cancer[J]. Breast Cancer Res Treat, 2017, 161(2): 213–227. doi: 10.1007/s10549-016-4050-2
[26]	Song XZ, Zhang CW, Zhao MK, et al. Steroid Receptor Coactivator-3(SRC-3/AIB1) as a novel therapeutic target in triple negative breast cancer and its inhibition with a phospho-bufalin prodrug[J]. PLoS One, 2015, 10(10): e0140011. doi: 10.1371/journal.pone.0140011
[27]	Liu T, Zhang H, Sun L, et al. FSIP1 binds HER2 directly to regulate breast cancer growth and invasiveness[J]. Proc Natl Acad Sci USA, 2017, 114(29): 7683–7688. doi: 10.1073/pnas.1621486114
[28]	Chapman KB, Prendes MJ, Kidd JL, et al. Elevated expression of cancer/testis antigen FSIP1 in ER-positive breast tumors[J]. Biomark Med, 2013, 7(4): 601–611. doi: 10.2217/bmm.13.58
[29]	Zhang H, Luo MN, Jin ZN, et al. Expression and clinicopathological significance of FSIP1 in breast cancer[J]. Oncotarget, 2015, 6(12): 10658–10666.
[30]	Xu G, Dang CX. CMTM5 is downregulated and suppresses tumour growth in hepatocellular carcinoma through regulating PI3K-AKT signalling[J]. Cancer Cell Int, 2017, 17: 113. doi: 10.1186/s12935-017-0485-8
[31]	Li H, Li J, Su Y, et al. A novel 3p22.3 gene CMTM7 represses oncogenic EGFR signaling and inhibits cancer cell growth[J]. Oncogene, 2014, 33(24): 3109–3118. doi: 10.1038/onc.2013.282
[32]	Lefèvre L, Omeiri H, Drougat L, et al. Combined transcriptome studies identify AFF3 as a mediator of the oncogenic effects of β-catenin in adrenocortical carcinoma[J]. Oncogenesis, 2015, 4(7): e161. doi: 10.1038/oncsis.2015.20
[33]	Shi YW, Zhao Y, Zhang YJ, et al. AFF3 upregulation mediates tamoxifen resistance in breast cancers[J]. J Exp Clin Cancer Res, 2018, 37(1): 254. doi: 10.1186/s13046-018-0928-7
[34]	Prassas I, Diamandis EP. Novel therapeutic applications of cardiac glycosides[J]. Nat Rev Drug Discov, 2008, 7(11): 926–935. doi: 10.1038/nrd2682
[35]	Bogdanov A, Moiseenko FV, Dubina M. Abnormal expression of ATP1A1 and ATP1A2 in breast cancer[J]. F1000Res, 2017, 6: 10. doi: 10.12688/f1000research.10481.1
[36]	Dupuis J, Langenberg C, Prokopenko I, et al. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk[J]. Nat Genet, 2010, 42(2): 105–116. doi: 10.1038/ng.520
[37]	Okada T, Nakamura M, Nishikawa J, et al. Identification of genes specifically methylated in Epstein-Barr virus-associated gastric carcinomas[J]. Cancer Sci, 2013, 104(10): 1309–1314. doi: 10.1111/cas.12228
[38]	Modugno F, Knoll C, Kanbour-Shakir A, et al. A potential role for the estrogen-metabolizing cytochrome P450 enzymes in human breast carcinogenesis[J]. Breast Cancer Res Treat, 2003, 82(3): 191–197. doi: 10.1023/B:BREA.0000004376.21491.44

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RNA-seq analysis identified hormone-related genes associated with prognosis of triple negative breast cancer