Abstract
The pursuit of minimally invasive biomarkers is a challenging but exciting area of research. Clearly, such markers would need to be sensitive and specific enough to aid in the detection of breast cancer at an early stage, would monitor progression of the disease, and could predict the individual patient’s response to treatment. Unfortunately, to date, markers with such characteristics have not made it to the clinic for breast cancer. Past years, many studies indicated that the non-coding part of our genome (the so called ‘junk’ DNA), may be an ideal source for these biomarkers. In this chapter, the potential use of microRNAs and long non-coding RNAs as biomarkers will be discussed.
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References
Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843–854
Chen K, Rajewsky N (2007) The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet 8(2):93–103
Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215–233
Kusenda B et al (2006) MicroRNA biogenesis, functionality and cancer relevance. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 150(2):205–215
Homo sapiens miRNAs in the miRBase at Manchester University. http://www.mirbase.org/
Bentwich I et al (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37(7):766–770
Friedman RC et al (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19(1):92–105
Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120(1):15–20
Lagos-Quintana M et al (2001) Identification of novel genes coding for small expressed RNAs. Science 294(5543):853–858
Lau NC et al (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294(5543):858–862
Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294(5543):862–864
Lee Y et al (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23(20):4051–4060
Baskerville S, Bartel DP (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11(3):241–247
Rodriguez A et al (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14(10A):1902–1910
Lee Y et al (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 21(17):4663–4670
Cai X, Hagedorn CH, Cullen BR (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10(12):1957–1966
Denli AM et al (2004) Processing of primary microRNAs by the Microprocessor complex. Nature 432(7014):231–235
Gregory RI et al (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432(7014):235–240
Lund E et al (2004) Nuclear export of microRNA precursors. Science 303(5654):95–98
Grishok A et al (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106(1):23–34
Hutvagner G et al (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293(5531):834–838
Ketting RF et al (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 15(20):2654–2659
Gregory RI et al (2005) Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123(4):631–640
Lin SL, Chang D, Ying SY (2005) Asymmetry of intronic pre-miRNA structures in functional RISC assembly. Gene 356:32–38
Brennecke J et al (2005) Principles of microRNA-target recognition. PLoS Biol 3(3), e85
Kren BT et al (2009) MicroRNAs identified in highly purified liver-derived mitochondria may play a role in apoptosis. RNA Biol 6(1):65–72
Tanzer A, Stadler PF (2004) Molecular evolution of a microRNA cluster. J Mol Biol 339(2):327–335
Lewis BP et al (2003) Prediction of mammalian microRNA targets. Cell 115(7):787–798
Krek A et al (2005) Combinatorial microRNA target predictions. Nat Genet 37(5):495–500
Rajewsky N (2006) microRNA target predictions in animals. Nat Genet 38(Suppl):S8–S13
Brennecke J et al (2003) Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113(1):25–36
Calin GA et al (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A 101(9):2999–3004
Negrini M et al (1995) Definition and refinement of chromosome 11 regions of loss of heterozygosity in breast cancer: identification of a new region at 11q23.3. Cancer Res 55(14):3003–3007
Calin GA, Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6(11):857–866
Lu J et al (2005) MicroRNA expression profiles classify human cancers. Nature 435(7043):834–838
Gaur A et al (2007) Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res 67(6):2456–2468
Calin GA et al (2002) Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 99(24):15524–15529
Iorio MV et al (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65(16):7065–7070
Dvinge H et al (2013) The shaping and functional consequences of the microRNA landscape in breast cancer. Nature 497(7449):378–382
Piccart-Gebhart MJ (2006) Adjuvant trastuzumab therapy for HER2-overexpressing breast cancer: what we know and what we still need to learn. Eur J Cancer 42(12):1715–1719
Tang F et al (2006) MicroRNA expression profiling of single whole embryonic stem cells. Nucleic Acids Res 34(2):e9
Jiang J et al (2005) Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res 33(17):5394–5403
Perou CM et al (2000) Molecular portraits of human breast tumours. Nature 406(6797):747–752
Sorlie T et al (2003) Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A 100(14):8418–8423
Dowsett M, Dunbier AK (2008) Emerging biomarkers and new understanding of traditional markers in personalized therapy for breast cancer. Clin Cancer Res 14(24):8019–8026
Harvey JM et al (1999) Estrogen receptor status by immunohistochemistry is superior to the ligand-binding assay for predicting response to adjuvant endocrine therapy in breast cancer. J Clin Oncol 17(5):1474–1481
Yamashita H et al (2006) Immunohistochemical evaluation of hormone receptor status for predicting response to endocrine therapy in metastatic breast cancer. Breast Cancer 13(1):74–83
Adams BD, Furneaux H, White BA (2007) The micro-ribonucleic acid (miRNA) miR-206 targets the human estrogen receptor-alpha (ERalpha) and represses ERalpha messenger RNA and protein expression in breast cancer cell lines. Mol Endocrinol 21(5):1132–1147
Boyerinas B et al (2010) The role of let-7 in cell differentiation and cancer. Endocr Relat Cancer 17(1):F19–F36
Griffiths-Jones S et al (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36(Database issue):D154–D158
Blenkiron C et al (2007) MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol 8(10):R214
Mattie MD et al (2006) Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Mol Cancer 5:24
Harris L et al (2007) American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer. J Clin Oncol 25(33):5287–5312
O’Hanlon DM et al (1995) An evaluation of preoperative CA 15–3 measurement in primary breast carcinoma. Br J Cancer 71(6):1288–1291
Uehara M et al (2008) Long-term prognostic study of carcinoembryonic antigen (CEA) and carbohydrate antigen 15–3 (CA 15–3) in breast cancer. Int J Clin Oncol 13(5):447–451
Taplin S et al (2008) Mammography facility characteristics associated with interpretive accuracy of screening mammography. J Natl Cancer Inst 100(12):876–887
Lawrie CH et al (2008) Detection of elevated levels of tumour-associated microRNAs in serum of patients with diffuse large B-cell lymphoma. Br J Haematol 141(5):672–675
Chen X et al (2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18(10):997–1006
Gilad S et al (2008) Serum microRNAs are promising novel biomarkers. PLoS One 3(9), e3148
Corsten MF et al (2010) Circulating microRNA-208b and microRNA-499 reflect myocardial damage in cardiovascular disease. Circ Cardiovasc Genet 3(6):499–506
Etheridge A et al (2011) Extracellular microRNA: a new source of biomarkers. Mutat Res 717(1–2):85–90
Huang Z et al (2010) Plasma microRNAs are promising novel biomarkers for early detection of colorectal cancer. Int J Cancer 127(1):118–126
Park NJ et al (2009) Salivary microRNA: discovery, characterization, and clinical utility for oral cancer detection. Clin Cancer Res 15(17):5473–5477
Hanson EK, Lubenow H, Ballantyne J (2009) Identification of forensically relevant body fluids using a panel of differentially expressed microRNAs. Anal Biochem 387(2):303–314
Wang K et al (2010) Export of microRNAs and microRNA-protective protein by mammalian cells. Nucleic Acids Res 38(20):7248–7259
Weber JA et al (2010) The microRNA spectrum in 12 body fluids. Clin Chem 56(11):1733–1741
Zen K, Zhang CY (2012) Circulating microRNAs: a novel class of biomarkers to diagnose and monitor human cancers. Med Res Rev 32(2):326–48
Zubakov D et al (2010) MicroRNA markers for forensic body fluid identification obtained from microarray screening and quantitative RT-PCR confirmation. Int J Legal Med 124(3):217–226
Weickmann JL, Glitz DG (1982) Human ribonucleases. Quantitation of pancreatic-like enzymes in serum, urine, and organ preparations. J Biol Chem 257(15):8705–8710
Mitchell PS et al (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 105(30):10513–10518
Kroh EM et al (2010) Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR). Methods 50(4):298–301
Wu Q et al (2011) Next-generation sequencing of microRNAs for breast cancer detection. J Biomed Biotechnol 2011:597145
Asaga S et al (2011) Direct serum assay for microRNA-21 concentrations in early and advanced breast cancer. Clin Chem 57(1):84–91
Heneghan HM et al (2010) Systemic miRNA-195 differentiates breast cancer from other malignancies and is a potential biomarker for detecting noninvasive and early stage disease. Oncologist 15(7):673–682
Zhao H et al (2010) A pilot study of circulating miRNAs as potential biomarkers of early stage breast cancer. PLoS One 5(10), e13735
Ng EK et al (2013) Circulating microRNAs as specific biomarkers for breast cancer detection. PLoS One 8(1), e53141
Gupta GP, Massague J (2006) Cancer metastasis: building a framework. Cell 127(4):679–695
Nguyen DX, Bos PD, Massague J (2009) Metastasis: from dissemination to organ-specific colonization. Nat Rev Cancer 9(4):274–284
Sawan C et al (2008) Epigenetic drivers and genetic passengers on the road to cancer. Mutat Res 642(1–2):1–13
Ma L, Weinberg RA (2008) Micromanagers of malignancy: role of microRNAs in regulating metastasis. Trends Genet 24(9):448–456
Nicoloso MS et al (2009) MicroRNAs–the micro steering wheel of tumour metastases. Nat Rev Cancer 9(4):293–302
Ma L, Teruya-Feldstein J, Weinberg RA (2007) Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature 449(7163):682–688
Gee HE et al (2008) MicroRNA-10b and breast cancer metastasis. Nature 455(7216):E8–E9, author reply E9
Huang GL et al (2009) Clinical significance of miR-21 expression in breast cancer: SYBR-Green I-based real-time RT-PCR study of invasive ductal carcinoma. Oncol Rep 21(3):673–679
Bandyopadhyay S et al (2004) PTEN up-regulates the tumor metastasis suppressor gene Drg-1 in prostate and breast cancer. Cancer Res 64(21):7655–7660
Varga AE et al (2005) Silencing of the Tropomyosin-1 gene by DNA methylation alters tumor suppressor function of TGF-beta. Oncogene 24(32):5043–5052
Qian B et al (2009) High miR-21 expression in breast cancer associated with poor disease-free survival in early stage disease and high TGF-beta1. Breast Cancer Res Treat 117(1):131–140
Yan LX et al (2008) MicroRNA miR-21 overexpression in human breast cancer is associated with advanced clinical stage, lymph node metastasis and patient poor prognosis. RNA 14(11):2348–2360
Zhu Q et al (2012) miR-21 promotes migration and invasion by the miR-21-PDCD4-AP-1 feedback loop in human hepatocellular carcinoma. Oncol Rep 27(5):1660–1668
Gibbons DL et al (2009) Contextual extracellular cues promote tumor cell EMT and metastasis by regulating miR-200 family expression. Genes Dev 23(18):2140–2151
Adams BD, Guttilla IK, White BA (2008) Involvement of microRNAs in breast cancer. Semin Reprod Med 26(6):522–536
Liu C, Tang DG (2011) MicroRNA regulation of cancer stem cells. Cancer Res 71(18):5950–5954
Ahmad A et al (2011) Phosphoglucose isomerase/autocrine motility factor mediates epithelial-mesenchymal transition regulated by miR-200 in breast cancer cells. Cancer Res 71(9):3400–3409
Gregory PA et al (2008) The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nat Cell Biol 10(5):593–601
Corcoran C et al (2011) Intracellular and extracellular microRNAs in breast cancer. Clin Chem 57(1):18–32
Maitah MY et al (2011) Up-regulation of sonic hedgehog contributes to TGF-beta1-induced epithelial to mesenchymal transition in NSCLC cells. PLoS One 6(1), e16068
Zavadil J, Bottinger EP (2005) TGF-beta and epithelial-to-mesenchymal transitions. Oncogene 24(37):5764–5774
Tryndyak VP, Beland FA, Pogribny IP (2010) E-cadherin transcriptional down-regulation by epigenetic and microRNA-200 family alterations is related to mesenchymal and drug-resistant phenotypes in human breast cancer cells. Int J Cancer 126(11):2575–2583
Burk U et al (2008) A reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells. EMBO Rep 9(6):582–589
Valastyan S et al (2011) Activation of miR-31 function in already-established metastases elicits metastatic regression. Genes Dev 25(6):646–659
Valastyan S et al (2009) A pleiotropically acting microRNA, miR-31, inhibits breast cancer metastasis. Cell 137(6):1032–1046
Stuelten CH, Salomon DS (2010) miR-31 in cancer: location matters. Cell Cycle 9(23):4608–4609
Valastyan S, Weinberg RA (2010) miR-31: a crucial overseer of tumor metastasis and other emerging roles. Cell Cycle 9(11):2124–2129
Tavazoie SF et al (2008) Endogenous human microRNAs that suppress breast cancer metastasis. Nature 451(7175):147–152
Png KJ et al (2011) MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer. Genes Dev 25(3):226–231
Yu F et al (2007) Let-7 regulates self renewal and tumorigenicity of breast cancer cells. Cell 131(6):1109–1123
Ma L et al (2010) miR-9, a MYC/MYCN-activated microRNA, regulates E-cadherin and cancer metastasis. Nat Cell Biol 12(3):247–256
Zhou X et al (2012) MicroRNA-9 as potential biomarker for breast cancer local recurrence and tumor estrogen receptor status. PLoS One 7(6):e39011
Katayama S et al (2005) Antisense transcription in the mammalian transcriptome. Science 309(5740):1564–1566
Cabili MN et al (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25(18):1915–1927
Derrien T, Guigo R, Johnson R (2011) The long non-coding RNAs: a new (P)layer in the “Dark Matter”. Front Genet 2:107
Guttman M et al (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28(5):503–510
Caretti G et al (2006) The RNA helicases p68/p72 and the noncoding RNA SRA are coregulators of MyoD and skeletal muscle differentiation. Dev Cell 11(4):547–560
Feng J et al (2006) The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 20(11):1470–1484
Lanz RB et al (1999) A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell 97(1):17–27
Mazo A et al (2007) Transcriptional interference: an unexpected layer of complexity in gene regulation. J Cell Sci 120(Pt 16):2755–2761
Willingham AT et al (2005) A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309(5740):1570–1573
Orom UA et al (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143(1):46–58
Gupta RA et al (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464(7291):1071–1076
Rinn JL et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7):1311–1323
Chisholm KM et al (2012) Detection of long non-coding RNA in archival tissue: correlation with polycomb protein expression in primary and metastatic breast carcinoma. PLoS One 7(10):e47998
Chen W et al (1997) Expression of neural BC200 RNA in human tumours. J Pathol 183(3):345–351
Iacoangeli A et al (2004) BC200 RNA in invasive and preinvasive breast cancer. Carcinogenesis 25(11):2125–2133
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De Leeneer, K., Claes, K. (2015). Non Coding RNA Molecules as Potential Biomarkers in Breast Cancer. In: Scatena, R. (eds) Advances in Cancer Biomarkers. Advances in Experimental Medicine and Biology, vol 867. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-7215-0_16
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