Top

BMC Cancer

Published in:

Open Access 01-12-2021 | Breast Cancer | Research

MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker

Authors: Sevan Omer Majed, Suhad Asad Mustafa

Published in: BMC Cancer | Issue 1/2021

Abstract

Introduction

Disruption of cellular processes in the breast by abnormally expressed miRNA is characterized to develop cancer. We aimed to identify the differential expression of small RNAs (sRNAs) and mRNAs in formalin-fixed paraffin-embedded (FFPE) tissue of the breast cancer (BC) and normal adjacent tissue (NAT). Another aim is to determine the differential expression of miR-1275 as a novel biomarker for BC and also identify its target genes.

Methods

TrueQuant method for analysis of sRNA expression and MACE-sequencing method for analysis of gene expression were used analyzing. The RT-qPCR technique was used to confirm miR-1275 down expression. Target genes of miR-1275 were computationally identified using target prediction sites and also the expression level of them was experimentally determined among the expressed genes.

Results

TrueQuant findings showed that 1400 sRNAs were differentially expressed in the FFPE tissue of two Kurdish cases with BC, as compared to NAT. Among the sRNAs, 29 small RNAs were shown to be significantly downregulated in BC cells. The RT-qPCR results confirmed that miR-1275 was significantly down-expressed in 20 Kurdish cases with BC compared to NAT. However, Overall survival (OS) analysis revealed that the correlation between the expression level of miR-1275 and clinical significance was highly corrected in cases with BC (OS rate: P = 0.0401). The MACE-seq results revealed that 26,843 genes were differentially expressed in the BC tissue compared to NAT, but 7041 genes were displayed in a scatter plot. Furthermore, putative target genes (DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA) were computationally identified as direct targets of miR-1275 in several target predicted sites. The MACE-seq results revealed that the expression level of these targets was increased in BC tissue compared to NAT. The level of these targets was negatively associated with miR-1275 expression. Finally, the role of down-regulated miR-1275 on its targets in biological mechanisms of BC cells was identified; including cell growth, proliferation, movement, invasion, metastasis, and apoptosis.

Conclusion

Down-expressed miR-1275, a tumor suppressor, is a novel biomarker for early detection of BC. DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA are newly identified to be targeted by miR-1275.

Control, C.f.D. and Prevention. Cancer survivors--United States, 2007. MMWR Morb Mortal Wkly Rep. 2011;60(9):269.

Jiang X, Tang H, Chen T. Epidemiology of gynecologic cancers in China. J Gynecol Oncol. 2018;29(1):e7.CrossRefPubMed

Adhami M, Haghdoost AA, Sadeghi B, Malekpour Afshar R. Candidate miRNAs in human breast cancer biomarkers: a systematic review. Breast Cancer. 2018;25(2):198–205. https://doi.org/10.1007/s12282-017-0814-8.CrossRefPubMed

Toda H, Seki N, Kurozumi S, Shinden Y, Yamada Y, Nohata N, et al. RNA-sequence-based microRNA expression signature in breast cancer: tumor-suppressive miR-101-5p regulates molecular pathogenesis. Mol Oncol. 2020;14(2):426–46. https://doi.org/10.1002/1878-0261.12602.CrossRefPubMed

DeSantis C, Howlader N, Cronin KA, Jemal A. Breast cancer incidence rates in US women are no longer declining. Cancer Epidemiol Prev Biomark. 2011;20(5):733–9. https://doi.org/10.1158/1055-9965.EPI-11-0061.CrossRef

Campeau PM, Foulkes WD, Tischkowitz MD. Hereditary breast cancer: new genetic developments, new therapeutic avenues. Hum Genet. 2008;124(1):31–42. https://doi.org/10.1007/s00439-008-0529-1.CrossRefPubMed

Economopoulou P, Dimitriadis G, Psyrri A. Beyond BRCA: new hereditary breast cancer susceptibility genes. Cancer Treat Rev. 2015;41(1):1–8. https://doi.org/10.1016/j.ctrv.2014.10.008.CrossRefPubMed

Perou CM, et al. Molecular portraits of human breast tumours. Nature. 2000;406(6797):747–52.CrossRefPubMed

Rouzier R, Perou CM, Symmans WF, Ibrahim N, Cristofanilli M, Anderson K, et al. Breast cancer molecular subtypes respond differently to preoperative chemotherapy. Clin Cancer Res. 2005;11(16):5678–85. https://doi.org/10.1158/1078-0432.CCR-04-2421.CrossRefPubMed

10.

Eroles P, Bosch A, Alejandro Pérez-Fidalgo J, Lluch A. Molecular biology in breast cancer: intrinsic subtypes and signaling pathways. Cancer Treat Rev. 2012;38(6):698–707. https://doi.org/10.1016/j.ctrv.2011.11.005.CrossRefPubMed

11.

Park S, Koo JS, Kim MS, Park HS, Lee JS, Lee JS, et al. Characteristics and outcomes according to molecular subtypes of breast cancer as classified by a panel of four biomarkers using immunohistochemistry. Breast. 2012;21(1):50–7. https://doi.org/10.1016/j.breast.2011.07.008.CrossRefPubMed

12.

Prat A, Pineda E, Adamo B, Galván P, Fernández A, Gaba L, et al. Clinical implications of the intrinsic molecular subtypes of breast cancer. Breast. 2015;24:S26–35. https://doi.org/10.1016/j.breast.2015.07.008.CrossRefPubMed

13.

Duttagupta R, Jiang R, Gollub J, Getts RC, Jones KW. Impact of cellular miRNAs on circulating miRNA biomarker signatures. PLoS One. 2011;6(6):e20769. https://doi.org/10.1371/journal.pone.0020769.CrossRefPubMedPubMedCentral

14.

Tomimaru Y, Eguchi H, Nagano H, Wada H, Kobayashi S, Marubashi S, et al. Circulating microRNA-21 as a novel biomarker for hepatocellular carcinoma. J Hepatol. 2012;56(1):167–75. https://doi.org/10.1016/j.jhep.2011.04.026.CrossRefPubMed

15.

Gebert LF, MacRae IJ. Regulation of microRNA function in animals. Nat Rev Mol Cell Biol. 2019;20(1):21–37. https://doi.org/10.1038/s41580-018-0045-7.CrossRefPubMedPubMedCentral

16.

Treiber T, Treiber N, Meister G. Regulation of microRNA biogenesis and its crosstalk with other cellular pathways. Nat Rev Mol Cell Biol. 2019;20(1):5–20. https://doi.org/10.1038/s41580-018-0059-1.CrossRefPubMed

17.

Zhang B, Pan X, Cobb GP, Anderson TA. microRNAs as oncogenes and tumor suppressors. Dev Biol. 2007;302(1):1–12. https://doi.org/10.1016/j.ydbio.2006.08.028.CrossRefPubMed

18.

Rufino-Palomares EE, et al. MicroRNAs as oncogenes and tumor suppressors. MicroRNAs Med. 2014:223–43.

19.

Cheng AM, Byrom MW, Shelton J, Ford LP. Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis. Nucleic Acids Res. 2005;33(4):1290–7. https://doi.org/10.1093/nar/gki200.CrossRefPubMedPubMedCentral

20.

Toda H, Kurozumi S, Kijima Y, Idichi T, Shinden Y, Yamada Y, et al. Molecular pathogenesis of triple-negative breast cancer based on microRNA expression signatures: antitumor miR-204-5p targets AP1S3. J Hum Genet. 2018;63(12):1197–210. https://doi.org/10.1038/s10038-018-0510-3.CrossRefPubMed

21.

Iorio MV, Ferracin M, Liu CG, Veronese A, Spizzo R, Sabbioni S, et al. MicroRNA gene expression deregulation in human breast cancer. Cancer Res. 2005;65(16):7065–70. https://doi.org/10.1158/0008-5472.CAN-05-1783.CrossRefPubMed

22.

Kwon MJ. Emerging roles of claudins in human cancer. Int J Mol Sci. 2013;14(9):18148–80. https://doi.org/10.3390/ijms140918148.CrossRefPubMedPubMedCentral

23.

Peña-Chilet M, Martínez MT, Pérez-Fidalgo JA, Peiró-Chova L, Oltra SS, Tormo E, et al. MicroRNA profile in very young women with breast cancer. BMC Cancer. 2014;14(1):529. https://doi.org/10.1186/1471-2407-14-529.CrossRefPubMedPubMedCentral

24.

Liu D, Hu X, Zhou H, Shi G, Wu J. Identification of aberrantly expressed miRNAs in gastric cancer. Gastroenterol Res Pract. 2014;2014:1–9. https://doi.org/10.1155/2014/473817.CrossRef

25.

Parafioriti A, et al. Ewing’s sarcoma: an analysis of miRNA expression profiles and target genes in paraffin-embedded primary tumor tissue. Int J Mol Sci. 2016;17(5):656.CrossRefPubMedCentral

26.

Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C, et al. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods. 2008;44(1):3–12. https://doi.org/10.1016/j.ymeth.2007.09.009.CrossRefPubMedPubMedCentral

27.

Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9. https://doi.org/10.1038/nmeth.1923.CrossRefPubMedPubMedCentral

28.

Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–9. https://doi.org/10.1093/bioinformatics/btu638.CrossRefPubMed

29.

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. https://doi.org/10.1186/s13059-014-0550-8.CrossRefPubMedPubMedCentral

30.

Kurozumi S, Yamaguchi Y, Kurosumi M, Ohira M, Matsumoto H, Horiguchi J. Recent trends in microRNA research into breast cancer with particular focus on the associations between microRNAs and intrinsic subtypes. J Hum Genet. 2017;62(1):15–24. https://doi.org/10.1038/jhg.2016.89.CrossRefPubMed

31.

Gupta I, Sareyeldin R, al-Hashimi I, al-Thawadi HA, al Farsi H, Vranic S, et al. Triple negative breast cancer profile, from gene to microRNA, in relation to ethnicity. Cancers. 2019;11(3):363. https://doi.org/10.3390/cancers11030363.CrossRefPubMedCentral

32.

Khordadmehr M, Shahbazi R, Ezzati H, Jigari-Asl F, Sadreddini S, Baradaran B. Key microRNAs in the biology of breast cancer; emerging evidence in the last decade. J Cell Physiol. 2019;234(6):8316–26. https://doi.org/10.1002/jcp.27716.CrossRefPubMed

33.

Gebeshuber CA, Martinez J. miR-100 suppresses IGF2 and inhibits breast tumorigenesis by interfering with proliferation and survival signaling. Oncogene. 2013;32(27):3306–10. https://doi.org/10.1038/onc.2012.372.CrossRefPubMed

34.

Li XY, Luo QF, Wei CK, Li DF, Li J, Fang L. MiRNA-107 inhibits proliferation and migration by targeting CDK8 in breast cancer. Int J Clin Exp Med. 2014;7(1):32–40.PubMedPubMedCentral

35.

Wang B, Wang H, Yang Z. MiR-122 inhibits cell proliferation and tumorigenesis of breast cancer by targeting IGF1R. PLoS One. 2012;7(10):e47053. https://doi.org/10.1371/journal.pone.0047053.CrossRefPubMedPubMedCentral

36.

Wang Y-W, Zhang W, Ma R. Bioinformatic identification of chemoresistance-associated microRNAs in breast cancer based on microarray data. Oncol Rep. 2018;39(3):1003–10. https://doi.org/10.3892/or.2018.6205.CrossRefPubMedPubMedCentral

37.

Mei JW, Yang ZY, Xiang HG, Bao R, Ye YY, Ren T, et al. MicroRNA-1275 inhibits cell migration and invasion in gastric cancer by regulating vimentin and E-cadherin via JAZF1. BMC Cancer. 2019;19(1):740. https://doi.org/10.1186/s12885-019-5929-1.CrossRefPubMedPubMedCentral

38.

Sun KY, Peng T, Chen Z, Huang J, Zhou XH. MicroRNA-1275 suppresses cell growth, and retards G1/S transition in human nasopharyngeal carcinoma by down-regulation of HOXB5. J Cell Commun Signal. 2016;10(4):305–14. https://doi.org/10.1007/s12079-016-0351-9.CrossRefPubMedPubMedCentral

39.

He J, Yu L, Wang CM, Zhou XF. MiR-1275 promotes non-small cell lung cancer cell proliferation and metastasis by regulating LZTS3 expression. Eur Rev Med Pharmacol Sci. 2018;22(9):2680–7. https://doi.org/10.26355/eurrev_201805_14964.CrossRefPubMed

40.

Liu MD, Wu H, Wang S, Pang P, Jin S, Sun CF, et al. MiR-1275 promotes cell migration, invasion and proliferation in squamous cell carcinoma of head and neck via up-regulating IGF-1R and CCR7. Gene. 2018;646:1–7. https://doi.org/10.1016/j.gene.2017.12.049.CrossRefPubMed

41.

Yang JR, Shi MX, Zeng Y. LncRNA HAND2-AS1 inhibits proliferation and promotes apoptosis of chronic myeloid leukemia cells by sponging with micRNA-1275. Eur Rev Med Pharmacol Sci. 2019;23(5):2103–11. https://doi.org/10.26355/eurrev_201903_17254.CrossRefPubMed

42.

Kuo Y-C, Huang KY, Yang CH, Yang YS, Lee WY, Chiang CW. Regulation of phosphorylation of Thr-308 of Akt, cell proliferation, and survival by the B55α regulatory subunit targeting of the protein phosphatase 2A holoenzyme to Akt. J Biol Chem. 2008;283(4):1882–92. https://doi.org/10.1074/jbc.M709585200.CrossRefPubMed

43.

Kiely PA, O'Gorman D, Luong K, Ron D, O'Connor R. Insulin-like growth factor I controls a mutually exclusive association of RACK1 with protein phosphatase 2A and β1 integrin to promote cell migration. Mol Cell Biol. 2006;26(11):4041–51. https://doi.org/10.1128/MCB.01868-05.CrossRefPubMedPubMedCentral

44.

Jiang H, Cheng L, Hu P, Liu R. MicroRNA-663b mediates TAM resistance in breast cancer by modulating TP73 expression. Mol Med Rep. 2018;18(1):1120–6. https://doi.org/10.3892/mmr.2018.9064.CrossRefPubMed

45.

Friedrich M, Heimer N, Stoehr C, Steven A, Wach S, Taubert H, et al. CREB1 is affected by the microRNAs miR-22-3p, miR-26a-5p, miR-27a-3p, and miR-221-3p and correlates with adverse clinicopathological features in renal cell carcinoma. Sci Rep. 2020;10(1):6499. https://doi.org/10.1038/s41598-020-63403-y.CrossRefPubMedPubMedCentral

46.

Tang W, Li GS, Li JD, Pan WY, Shi Q, Xiong DD, et al. The role of upregulated miR-375 expression in breast cancer: an in vitro and in silico study. Pathol Res Pract. 2020;216(1):152754. https://doi.org/10.1016/j.prp.2019.152754.CrossRefPubMed

47.

Cohen H, Ben-Hamo R, Gidoni M, Yitzhaki I, Kozol R, Zilberberg A, et al. Shift in GATA3 functions, and GATA3 mutations, control progression and clinical presentation in breast cancer. Breast Cancer Res. 2014;16(6):464. https://doi.org/10.1186/s13058-014-0464-0.CrossRefPubMedPubMedCentral

48.

Liu X, Li C, Yang Y, Liu X, Li R, Zhang M, et al. Synaptotagmin 7 in twist-related protein 1-mediated epithelial – Mesenchymal transition of non-small cell lung cancer. EBioMedicine. 2019;46:42–53. https://doi.org/10.1016/j.ebiom.2019.07.071.CrossRefPubMedPubMedCentral

Title: MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker
Authors: Sevan Omer Majed
Suhad Asad Mustafa
Publication date: 01-12-2021
Publisher: BioMed Central
Keywords: Breast Cancer
Breast Cancer
Published in: BMC Cancer / Issue 1/2021
Electronic ISSN: 1471-2407
DOI: https://doi.org/10.1186/s12885-021-08218-4

Webinar | 19-02-2024 | 17:30 (CET)

Keynote webinar | Spotlight on antibody–drug conjugates in cancer

Watch now

Antibody–drug conjugates (ADCs) are novel agents that have shown promise across multiple tumor types. Explore the current landscape of ADCs in breast and lung cancer with our experts, and gain insights into the mechanism of action, key clinical trials data, existing challenges, and future directions.

Dr. Véronique Diéras

Prof. Fabrice Barlesi

Developed by: Springer Medicine

At a glance: The STEP trials

Springer Medicine

Abstract

Introduction

Methods

Results

Conclusion

Please log in to get access to this content

Other articles of this Issue 1/2021

Olaparib-mediated enhancement of 5-fluorouracil cytotoxicity in mismatch repair deficient colorectal cancer cells

Mapping the EORTC QLQ-C30 to EQ-5D-3L in patients with breast cancer

The association between cognitive impairment and breast and colorectal cancer screening utilization

Comprehensive analyses of competing endogenous RNA networks reveal potential biomarkers for predicting hepatocellular carcinoma recurrence

Carnitine palmitoyl transferase 1A is a novel diagnostic and predictive biomarker for breast cancer

pERK-mediated IL8 secretion can enhance the migration, invasion, and cisplatin resistance of CD10-positive oral cancer cells

Keynote webinar | Spotlight on antibody–drug conjugates in cancer