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Journal of Applied Genetics

, Volume 60, Issue 3–4, pp 335–346 | Cite as

An integrative bioinformatics analysis identified miR-375 as a candidate key regulator of malignant breast cancer

  • Jiaxuan Liu
  • Ping Wang
  • Ping Zhang
  • Xinyu Zhang
  • Hang Du
  • Qiang Liu
  • Bo Huang
  • Caiyun Qian
  • Shuhua Zhang
  • Weifeng Zhu
  • Xiaohong Yang
  • Yingqun XiaoEmail author
  • Zhuoqi LiuEmail author
  • Daya LuoEmail author
Human Genetics • Original Paper

Abstract

MicroRNAs (miRNAs) are key regulators that play important biological roles in carcinogenesis and are promising biomarkers for cancer diagnosis and therapy. hsa-miR-375-3p (miR-375) has been suggested to serve as a tumor suppressor or oncogene in various tumor types; however, its specific expression and potential regulatory role in malignant breast cancer remain unclear. In this study, the results from noncoding RNA microarray analysis indicated that the miR-375 expression level is significantly decreased in malignant basal-like breast cancer compared with luminal-like breast cancer. A total of 1895 co-downregulated and 1645 co-upregulated genes were identified in miR-375 mimic-transfected basal-like breast cancer cell lines. Predicted miR-375 targets were obtained from the online databases TargetScan and DIANA-microT-CDS. Combined KEGG enrichment analysis for coregulated genes and predicted miR-375 targets provided information and revealed differences in potential dynamic signaling pathways regulated by miR-375 and also indicated specific regulatory pathways, such as RNA transport and processing, in basal-like breast cancer. Additionally, gene expression microarray analysis accompanied by UALCAN analysis was performed to screen upregulated genes in the basal-like subtype. Four potential key genes, including LDHB, CPNE8, QKI, and EIF5A2, were identified as candidate target genes of miR-375. Therefore, the present study demonstrated that miR-375 may be a potential key regulator and provide a promising direction for diagnostic and therapeutic developments for malignant breast cancer.

Keywords

Breast cancer miR-375 Bioinformatics Biological pathway 

Notes

Acknowledgments

The authors would like to thank Qingmei Zhong, Xianhe Yang, Wu Wang, and Di Yao at Department of Pathology, Affiliated Infectious Diseases Hospital, Nanchang University, for their technical assistance.

Author contributions

DY.L., ZQ.L., and YQ.X. designed the experiments and reviewed paper; ZQ.L., JX.L., P.W., and Q.L. performed the dataset analysis; JX.L. and P.W. wrote the manuscript; CY.Q., SH.Z., WF.Z., and XH.Y. administered the cell models, qRT-PCR; P.Z., XY.Z., H.D., and B.H. carried out the immunohistochemistry. All authors reviewed and approved the final version.

Funding

This work was partially supported by National Natural Science Foundation of China (No. 81160248, 81360313, 81560464) (to Daya Luo and Zhuoqi Liu), Natural Science Foundation of Jiangxi Province (No. 20151BAB205058, 20171BAB205055) (to Daya Luo and Zhuoqi Liu). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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ESM 1 (PDF 35 kb)
13353_2019_507_MOESM2_ESM.pdf (42 kb)
ESM 2 (PDF 41 kb)
13353_2019_507_MOESM3_ESM.xlsx (704 kb)
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References

  1. Agarwal V, Bell G, Nam J, Bartel D (2015) Predicting effective microRNA target sites in mammalian mRNAs. Elife 4.  https://doi.org/10.7554/eLife.05005
  2. Ambros VR (2004) The functions of animal microRNAs. Nature 431:350–355CrossRefGoogle Scholar
  3. Avril N et al (2001) Glucose metabolism of breast cancer assessed by 18F-FDG PET: histologic and immunohistochemical tissue analysis. J Nucl Med 42:9–16PubMedGoogle Scholar
  4. Bar I, Merhi A, Abdelsater F, Ben AA, Sollennita S, Canon JL, Delrée P (2017) The MicroRNA miR-210 is expressed by cancer cells but also by the tumor microenvironment in triple-negative breast cancer. J Histochem Cytochem 65:22155417702849Google Scholar
  5. Barrett T et al (2013) NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res 41:991–995Google Scholar
  6. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297Google Scholar
  7. Bian Y et al (2012) Downregulation of tumor suppressor QKI in gastric cancer and its implication in cancer prognosis. Biochem Biophys Res Commun 422:187–193PubMedGoogle Scholar
  8. Blenkiron C, Goldstein LD, Thorne NP, Spiteri I, Chin SF, Dunning MJ et al (2007) MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol 8(10):R214.  https://doi.org/10.1186/gb-2007-8-10-r214 PubMedPubMedCentralGoogle Scholar
  9. Bryant RJ et al (2012) Changes in circulating microRNA levels associated with prostate cancer. Br J Cancer 106:768–774PubMedPubMedCentralGoogle Scholar
  10. Chan S et al (2017) Basal-A triple-negative breast cancer cells selectively rely on rna splicing for survival. Mol Cancer Ther 16:2849–2861.  https://doi.org/10.1158/1535-7163.mct-17-0461 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Chandrashekar DS, Bashel B, Balasubramanya SAH, Creighton CJ, Ponce-Rodriguez I, Chakravarthi B, Varambally S (2017) UALCAN: a portal for facilitating tumor subgroup gene expression and survival analyses. Neoplasia 19:649–658PubMedPubMedCentralGoogle Scholar
  12. Chen AJ et al (2012) STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA. Genes Dev 26:1459–1472PubMedPubMedCentralGoogle Scholar
  13. Choi N et al (2015) miR-93/miR-106b/miR-375-CIC-CRABP1: a novel regulatory axis in prostate cancer progression. Oncotarget 6:23533–23547PubMedPubMedCentralGoogle Scholar
  14. Corsini LR, Bronte G, Terrasi M, Amodeo V, Fanale D, Fiorentino E et al (2012) The role of microRNAs in cancer: diagnostic and prognostic biomarkers and targets of therapies. Expert Opin Ther Targets 16.  https://doi.org/10.1517/14728222.2011.650632 PubMedGoogle Scholar
  15. Ding L et al (2010) MiR-375 frequently downregulated in gastric cancer inhibits cell proliferation by targeting JAK2. Cell Res 20:784–793PubMedGoogle Scholar
  16. Drakaki A, Iliopoulos D (2009) MicroRNA gene networks in oncogenesis. Curr Genomics 10:35–41PubMedPubMedCentralGoogle Scholar
  17. Enerly E et al (2011) miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors. PLoS One 6:e16915PubMedPubMedCentralGoogle Scholar
  18. Fu D, Li J, Wei J, Zhang Z, Luo Y, Tan H, Ren C (2018) HMGB2 is associated with malignancy and regulates Warburg effect by targeting LDHB and FBP1 in breast cancer. Cell Commun Signal 16:8PubMedPubMedCentralGoogle Scholar
  19. Goldhirsch A, Wood W, Coates A, Gelber R, Thürlimann B, Senn H (2011) Strategies for subtypes--dealing with the diversity of breast cancer: highlights of the St. Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2011. Ann Oncol 22:1736–1747PubMedPubMedCentralGoogle Scholar
  20. Guodong Y et al (2010) RNA-binding protein quaking, a critical regulator of colon epithelial differentiation and a suppressor of colon cancer. Gastroenterology 138:231–240.e235Google Scholar
  21. Hall MP et al (2013) Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation. RNA 19:627–638PubMedPubMedCentralGoogle Scholar
  22. Harris TM et al (2012) Low-level expression of miR-375 correlates with poor outcome and metastasis while altering the invasive properties of head and neck squamous cell carcinomas. Am J Pathol 180:917–928PubMedPubMedCentralGoogle Scholar
  23. He XX et al (2012) MicroRNA-375 targets AEG-1 in hepatocellular carcinoma and suppresses liver cancer cell growth in vitro and in vivo. Oncogene 31:3357–3369PubMedGoogle Scholar
  24. He S, Shi J, Mao J, Luo X, Liu W, Liu R, Yang F (2019) The expression of miR-375 in prostate cancer: a study based on GEO, TCGA data and bioinformatics analysis. Pathol Res Pract 152375.  https://doi.org/10.1016/j.prp.2019.03.004 Google Scholar
  25. Hong S et al (2014) SHOX2 is a direct miR-375 target and a novel epithelial-to-mesenchymal transition inducer in breast cancer cells. Neoplasia 16:279–290PubMedPubMedCentralGoogle Scholar
  26. Iorio MV et al (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65:7065–7070Google Scholar
  27. Isozaki Y et al (2012) Identification of novel molecular targets regulated by tumor suppressive miR-375 induced by histone acetylation in esophageal squamous cell carcinoma. Int J Oncol 41:985PubMedGoogle Scholar
  28. Karamboulas C, Ailles L (2013) Developmental signaling pathways in cancer stem cells of solid tumors. Biochim Biophys Acta 1830:2481–2495PubMedGoogle Scholar
  29. Karamitehrani F, Fallahian F, Atri M (2012) Expression of cGMP-dependent protein kinase, PKGIα, PKGIβ, and PKGII in malignant and benign breast tumors. Tumor Biol 33:1927–1932Google Scholar
  30. Kinoshita T et al (2012) Abstract 137: molecular networks regulated by tumor suppressive microRNA-375 in head and neck squamous cell carcinoma. Cancer Res 72:137Google Scholar
  31. Komatsu S et al (2011) Circulating microRNAs in plasma of patients with oesophageal squamous cell carcinoma. Br J Cancer 105:104–111PubMedPubMedCentralGoogle Scholar
  32. Komatsu S, Ichikawa D, Takeshita H, Konishi H, Nagata H, Hirajima S et al (2012) Prognostic impact of circulating miR-21 and miR-375 in plasma of patients with esophageal squamous cell carcinoma. Expert Opin Biol Ther 12.  https://doi.org/10.1517/14712598.2012.681373 PubMedGoogle Scholar
  33. Larocque D, Galarneau A, Liu HN, Scott M, Almazan G, Richard S (2004) Protection of p27(Kip1) mRNA by quaking RNA binding proteins promotes oligodendrocyte differentiation. Nat Neurosci 8:27–33PubMedGoogle Scholar
  34. Li L et al (2010) Serum microRNA profiles serve as novel biomarkers for hbv infection and diagnosis of hbv-positive hepatocarcinoma. Cancer Res 70:9798–9807PubMedGoogle Scholar
  35. Li X, Lin R, Li J (2011) Epigenetic silencing of microRNA-375 regulates PDK1 expression in esophageal cancer. Dig Dis Sci 56:2849–2856PubMedGoogle Scholar
  36. Li J, Li X, Li Y, Yang H, Wang L, Qin Y et al (2013) Cell-specific detection of miR-375 downregulation for predicting the prognosis of esophageal squamous cell carcinoma by miRNA in situ hybridization. PLoS One 8(1).  https://doi.org/10.1371/journal.pone.0053582 PubMedPubMedCentralGoogle Scholar
  37. Lin HC, Yeh CC, Chao LY, Tsai MH, Chen HH, Chuang EY, Lai LC (2018) The hypoxia-responsive lncRNA NDRG-OT1 promotes NDRG1 degradation via ubiquitin-mediated proteolysis in breast cancer cells. Oncotarget 9:10470–10482.  https://doi.org/10.18632/oncotarget.23732 CrossRefPubMedGoogle Scholar
  38. Lisa AC et al (2006) Race, breast cancer subtypes, and survival in the Carolina Breast Cancer Study. J Am Med Assoc 295:2492–2502Google Scholar
  39. Liu P, Cheng H, Roberts TM, Zhao JJ (2009) Targeting the phosphoinositide 3-kinase pathway in cancer. Nat Rev Drug Discov 8:627–644.  https://doi.org/10.1038/nrd2926 CrossRefPubMedPubMedCentralGoogle Scholar
  40. Lu J et al (2005) MicroRNA expression profiles classify human cancers. Nature 435:834–838PubMedGoogle Scholar
  41. Lu W et al (2014) QKI impairs self-renewal and tumorigenicity of oral cancer cells via repression of SOX2. Cancer Biol Ther 15:1174–1184PubMedPubMedCentralGoogle Scholar
  42. Luo D et al (2013) A systematic evaluation of miRNA:mRNA interactions involved in the migration and invasion of breast cancer cells. J Transl Med 11:57PubMedPubMedCentralGoogle Scholar
  43. Mathé EA et al (2009) MicroRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus: associations with survival. Clin Cancer Res 15:6192–6200PubMedPubMedCentralGoogle Scholar
  44. Mathews MB, Hershey JW (2015) The translation factor eIF5A and human cancer. Biochim Biophys Acta 1849:836–844PubMedPubMedCentralGoogle Scholar
  45. Matsui WH (2016) Cancer stem cell signaling pathways. Medicine 95:S8–S19.  https://doi.org/10.1097/md.0000000000004765 CrossRefPubMedPubMedCentralGoogle Scholar
  46. Mccleland ML et al (2012) An integrated genomic screen identifies LDHB as an essential gene for triple-negative breast cancer. Cancer Res 72:5812PubMedGoogle Scholar
  47. Munagala R, Aqil F, Vadhanam MV, Gupta RC (2013) MicroRNA ‘signature’ during estrogen-mediated mammary carcinogenesis and its reversal by ellagic acid intervention. Cancer Lett 339:175–184PubMedPubMedCentralGoogle Scholar
  48. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27:29–34PubMedPubMedCentralGoogle Scholar
  49. Oliveros JC (2007-2015) Venny. An interactive tool for comparing lists with Venn’s diagrams. http://bioinfogp.cnb.csic.es/tools/venny/index.html
  50. Ouaamari AE, Baroukh N, Martens GA, Lebrun P, Pipeleers D, Obberghen aE (2008) miR-375 targets 3'-phosphoinositide-dependent protein kinase-1 and regulates glucose-induced biological responses in pancreatic β-cells. Diabetes 57:2708PubMedPubMedCentralGoogle Scholar
  51. Paraskevopoulou M et al (2013) DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res 41:W169–W173PubMedPubMedCentralGoogle Scholar
  52. Parker J et al (2009) Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 27:1160–1167PubMedPubMedCentralGoogle Scholar
  53. Poy MN et al (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432:226–230PubMedGoogle Scholar
  54. Reis-Filho JS, Tutt AN (2010) Triple negative tumours: a critical review. Histopathology 52:108–118Google Scholar
  55. Saccomanno L, Loushin C, Jan E, Punkay E, Artzt K, Goodwin EB (1999) The STAR protein QKI-6 is a translational repressor. Proc Natl Acad Sci U S A 96:12605–12610PubMedPubMedCentralGoogle Scholar
  56. Schieber MS, Chandel NS (2013) ROS links glucose metabolism to breast cancer stem cell and EMT phenotype. Cancer Cell 23:265–267.  https://doi.org/10.1016/j.ccr.2013.02.021 CrossRefPubMedGoogle Scholar
  57. Silva JM et al (2002) Expression of thyroid hormone receptor/erbA genes is altered in human breast cancer. Oncogene 21:4307–4316PubMedGoogle Scholar
  58. Simonini PDSR et al (2010) Epigenetically deregulated microRNA-375 is involved in a positive feedback loop with estrogen receptor α in breast cancer cells. Cancer Res 70:9175–9184Google Scholar
  59. The Gene Ontology (GO) project in 2006 (2006) Nucleic Acids Res 3434(Database issue):D322–326Google Scholar
  60. Tsukamoto Y et al (2010) MicroRNA-375 is downregulated in gastric carcinomas and regulates cell survival by targeting PDK1 and 14-3-3zeta. Cancer Res 70:2339–2349PubMedGoogle Scholar
  61. Van Schooneveld E, Wildiers H, Vergote I, Vermeulen PB, Dirix LY, Van Laere S (2015) Dysregulation of microRNAs in breast cancer and their potential role as prognostic and predictive biomarkers in patient management. Breast Cancer Res 17:21–21PubMedPubMedCentralGoogle Scholar
  62. Vasudevan S, Tong Y, Steitz JA (2007) Switching from repression to activation: microRNAs can up-regulate translation. Science (New York, NY) 318:1931–1934.  https://doi.org/10.1126/science.1149460 CrossRefGoogle Scholar
  63. Volinia S et al (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 103:2257–2261.  https://doi.org/10.1073/pnas.0510565103 CrossRefPubMedPubMedCentralGoogle Scholar
  64. Wang S et al (2013) A microRNA panel to discriminate carcinomas from high-grade intraepithelial neoplasms in colonoscopy biopsy tissue. Gut 62:280–289PubMedPubMedCentralGoogle Scholar
  65. Ward A et al (2013) Re-expression of microRNA-375 reverses both tamoxifen resistance and accompanying EMT-like properties in breast cancer. Oncogene 32:1173–1182PubMedGoogle Scholar
  66. Wei dong LI, Cai ZH, Tan YK, Dong Y, Liu MY, Jin XJ et al (2011) Expression of EIF-5A2 in breast cancer and its clinical significance. Anatomy ResearchGoogle Scholar
  67. Wong NW, Chen Y, Chen S, Wang X (2017) OncomiR: an online resource for exploring pan-cancer microRNA dysregulation. Bioinformatics 34(4).  https://doi.org/10.1093/bioinformatics/btx627 PubMedCentralGoogle Scholar
  68. Xu L, Li M, Wang M, Yan D, Feng G, An G (2014) The expression of microRNA-375 in plasma and tissue is matched in human colorectal cancer. BMC Cancer 14:714PubMedPubMedCentralGoogle Scholar
  69. Yan J, Lin J, He X (2014) The emerging role of miR-375 in cancer. Int J Cancer 135:1011–1018PubMedGoogle Scholar
  70. Yu JL, Rak JW (2003) Host microenvironment in breast cancer development: inflammatory and immune cells in tumour angiogenesis and arteriogenesis. Breast Cancer Res 5:83–88PubMedPubMedCentralGoogle Scholar
  71. Yu L et al (2010) Early detection of lung adenocarcinoma in sputum by a panel of microRNA markers. Int J Cancer 127:2870–2878PubMedPubMedCentralGoogle Scholar
  72. Yu F, Jin L, Yang G, Ji L, Wang F, Lu Z (2014) Post-transcriptional repression of FOXO1 by QKI results in low levels of FOXO1 expression in breast cancer cells. Oncol Rep 31:1459–1465PubMedGoogle Scholar
  73. Zhao B, Li L, Lei Q, Guan KL (2010) The Hippo-YAP pathway in organ size control and tumorigenesis: an updated version. Genes Dev 24:862–874.  https://doi.org/10.1101/gad.1909210 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2019

Authors and Affiliations

  1. 1.Queen Mary SchoolNanchang UniversityNanchangChina
  2. 2.Department of Pathology, The Affiliated Infectious Diseases HospitalNanchang UniversityNanchangChina
  3. 3.National Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
  4. 4.Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesNanchang UniversityNanchangChina
  5. 5.Jiangxi Cardiovascular Research InstituteJiangxi Provincial People’s HospitalNanchangChina
  6. 6.Jiangxi Province Key Laboratory of Tumor Pathogens and Molecular PathologyNanchang UniversityNanchangChina

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