Fully automated fluorescence-based four-color multiplex assay for co-detection of microRNA and protein biomarkers in clinical tissue specimens

Methods in Molecular Biology

Volumn 1211, Issue , 2014, Pages 151-170

  Sempere, Lorenzo F ^a  

^a NONE

Author keywords

Biomarker; Breast cancer; Diagnostics; Formalin fixed paraffin embedded tissue (FFPE); Immunohistochemistry (IHC); In situ hybridization (ISH); Locked nucleic acid (LNA); MicroRNA (miRNA, miR); Molecular pathology

Indexed keywords

BIOLOGICAL MARKER; CD11B ANTIGEN; CD20 ANTIGEN; CD45 ANTIGEN; COLLAGEN TYPE 1; CYTOKERATIN 19; CYTOKERATIN 7; MICRORNA; MICRORNA 10B; MICRORNA 126; MICRORNA 145; MICRORNA 155; MICRORNA 205; MICRORNA 21; MICRORNA 210; MICRORNA 34A; RNA 18S; SMALL NUCLEAR RNA; SMOOTH MUSCLE ACTIN; TUBULIN; U6 SMALL NUCLEAR RNA; UNCLASSIFIED DRUG; VIMENTIN; LOCKED NUCLEIC ACID; OLIGONUCLEOTIDE; PARAFFIN; PROTEIN; TUMOR MARKER;

ARTICLE; BREAST CANCER; BREAST EPITHELIUM CELL; CARCINOMA CELL; CONTROLLED STUDY; FIBROBLAST; FLUORESCENCE ANALYSIS; FLUORESCENCE MICROSCOPY; FULLY AUTOMATED FLUORESCENCE BASED FOUR COLOR MULTIPLEX ASSAY; GENE EXPRESSION; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; IN SITU HYBRIDIZATION; LABORATORY AUTOMATION; LEUKOCYTE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; RNA ANALYSIS; TUMOR MICROENVIRONMENT; BREAST; BREAST TUMOR; FEMALE; FLUORESCENCE IMAGING; FLUORESCENCE IN SITU HYBRIDIZATION; PATHOLOGY; PROCEDURES; TISSUE FIXATION;

BREAST; BREAST NEOPLASMS; FEMALE; HUMANS; IMMUNOHISTOCHEMISTRY; IN SITU HYBRIDIZATION, FLUORESCENCE; MICRORNAS; MICROSCOPY, FLUORESCENCE; OLIGONUCLEOTIDES; OPTICAL IMAGING; PARAFFIN EMBEDDING; PROTEINS; TISSUE FIXATION; TUMOR MARKERS, BIOLOGICAL;

EID: 84921801026     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1459-3_13     Document Type: Article

References (79)

1. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294:862–864
2. Lau NC, Lim LP, Weinstein EG et al (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858–862
3. Lagos-Quintana M, Rauhut R, Lendeckel W et al (2001) Identification of novel genes coding for small expressed RNAs. Science 294:853–858
4. Ambros V (2004) The functions of animal microRNAs. Nature 431:350–355
5. Mendell JT, Olson EN (2012) MicroRNAs in stress signaling and human disease. Cell 148: 1172–1187
6. Krol J, Loedige I, Filipowicz W (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11:597–610
7. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215–233
8. Ketting RF (2011) MicroRNA biogenesis and function: an overview. Adv Exp Med Biol 700:1–14
9. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39:D152–D157
10. Garzon R, Fabbri M, Cimmino A et al (2006) MicroRNA expression and function in cancer. Trends Mol Med 12:580–587
11. Plasterk RH (2006) Micro RNAs in animal development. Cell 124:877–881
12. Kloosterman WP, Plasterk RH (2006) The diverse functions of microRNAs in animal development and disease. Dev Cell 11: 441–450
13. Curtis C, Shah SP, Chin SF et al (2012) The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486:346–352
14. Yuan Y, Failmezger H, Rueda OM et al (2012) Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling. Sci Transl Med 4:157ra143
15. Martinez P, Birkbak NJ, Gerlinger M et al (2013) Parallel evolution of tumour subclones mimics diversity between tumours. J Pathol 230:356–364
16. Gerlinger M, Rowan AJ, Horswell S et al (2012) Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 366:883–892
17. Heppner GH (1984) Tumor heterogeneity. Cancer Res 44:2259–2265
18. Klein CA (2013) Selection and adaptation during metastatic cancer progression. Nature 501:365–372
19. Bedard PL, Hansen AR, Ratain MJ et al (2013) Tumour heterogeneity in the clinic. Nature 501:355–364
20. Junttila MR, de Sauvage FJ (2013) Influence of tumour micro-environment heterogeneity on therapeutic response. Nature 501:346–354
21. Burrell RA, McGranahan N, Bartek J et al (2013) The causes and consequences of genetic heterogeneity in cancer evolution. Nature 501:338–345
22. Meacham CE, Morrison SJ (2013) Tumour heterogeneity and cancer cell plasticity. Nature 501:328–337
23. Marte B (2013) Tumour heterogeneity. Nature 501:327
24. Almendro V, Marusyk A, Polyak K (2013) Cellular heterogeneity and molecular evolution in cancer. Annu Rev Pathol 8:277–302
25. Marusyk A, Almendro V, Polyak K (2012) Intra-tumour heterogeneity: a looking glass for cancer? Nat Rev Cancer 12:323–334
26. Wood LD, Parsons DW, Jones S et al (2007) The genomic landscapes of human breast and colorectal cancers. Science 318:1108–1113
27. Jones S, Zhang X, Parsons DW et al (2008) Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321:1801–1806
28. Nelson PT, Wilfred BR (2009) In situ hybridization is a necessary experimental complement to microRNA (miRNA) expression profiling in the human brain. Neurosci Lett 466:69–72
29. Sempere LF (2011) Integrating contextual miRNA and protein signatures for diagnostic and treatment decisions in cancer. Expert Rev Mol Diagn 11:813–827
30. Sempere LF, Kauppinen S (2009) Translational implications of microRNAs in clinical diagnostics and therapeutics. In: Bradshaw RA, Dennis EA (eds) Handbook of cell signaling, 2nd edn. Academic, Oxford, pp 2965–2981
31. Zhang X, Lu X, Lopez-Berestein G et al (2013) In situ hybridization-based detection of microRNAs in human diseases. MicroRNA Diagn Ther 1:12–23
32. Nana-Sinkam SP, Croce CM (2013) Clinical applications for microRNAs in cancer. Clin Pharmacol Ther 93:98–104
33. Ventura A, Jacks T (2009) MicroRNAs and cancer: short RNAs go a long way. Cell 136: 586–591
34. Kloosterman WP, Wienholds E, de BE et al (2006) In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nat Methods 3:27–29
35. Wienholds E, Kloosterman WP, Miska E et al (2005) MicroRNA expression in zebrafish embryonic development. Science 309:310–311
36. Valoczi A, Hornyik C, Varga N et al (2004) Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res 32:e175
37. Koshkin AA, Wengel J (1998) Synthesis of novel 2′, 3′-linked bicyclic thymine ribonucleosides. J Org Chem 63:2778–2781
38. Castoldi M, Schmidt S, Benes V et al (2006) A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA 12:913–920
39. Nelson PT, Baldwin DA, Kloosterman WP et al (2006) RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA 12:187–191
40. Sempere LF, Christensen M, Silahtaroglu A et al (2007) Altered microRNA expression confined to specific epithelial cell subpopulations in breast cancer. Cancer Res 67: 11612–11620
41. Sempere LF, Preis M, Yezefski T et al (2010) Fluorescence-based codetection with protein markers reveals distinct cellular compartments for altered MicroRNA expression in solid tumors. Clin Cancer Res 16:4246–4255
42. Sempere LF, Korc M (2013) A method for conducting highly sensitive microRNA in situ hybridization and immunohistochemical analysis in pancreatic cancer. Methods Mol Biol 980:43–59
43. Speel EJ, Hopman AH, Komminoth P (2006) Tyramide signal amplification for DNA and mRNA in situ hybridization. Methods Mol Biol 326:33–60
44. Bobrow MN, Moen PT Jr (2001) Tyramide signal amplification (TSA) systems for the enhancement of ISH signals in cytogenetics. Curr Protoc Cytom Chapter 8, Unit
45. Jorgensen S, Baker A, Moller S et al (2010) Robust one-day in situ hybridization protocol for detection of microRNAs in paraffin samples using LNA probes. Methods 52:375–381
46. Mardin WA, Mees ST (2009) MicroRNAs: novel diagnostic and therapeutic tools for pancreatic ductal adenocarcinoma? Ann Surg Oncol 16:3183–3189
47. Nielsen BS (2012) MicroRNA in situ hybridization. Methods Mol Biol 822:67–84
48. Singh U, Keirstead N, Wolujczyk A et al (2013) General principles and methods for routine automated microRNA in situ hybridization and double labeling with immunohistochemistry. Biotechonl Histochem 89:259–266
49. Pena JT, Sohn-Lee C, Rouhanifard SH et al (2009) miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nat Methods 6:139–141
50. Liu X, Sempere LF, Guo Y et al (2011) Involvement of microRNAs in lung cancer biology and therapy. Transl Res 157:200–208
51. Nielsen BS, Holmstrom K (2013) Combined microRNA in situ hybridization and immunohistochemical detection of protein markers. Methods Mol Biol 986:353–365
52. Chaudhuri AD, Yelamanchili SV, Fox HS (2013) Combined fluorescent in situ hybridization for detection of microRNAs and immunofluorescent labeling for cell-type markers. Front Cell Neurosci 7:160
53. de Planell-Saguer M, Rodicio MC, Mourelatos Z (2010) Rapid in situ codetection of noncoding RNAs and proteins in cells and formalinfixed paraffin-embedded tissue sections without protease treatment. Nat Protoc 5:1061–1073
54. Nuovo GJ (2010) In situ detection of microRNAs in paraffin embedded, formalin fixed tissues and the co-localization of their putative targets. Methods 52:307–315
55. Nuovo GJ, Elton TS, Nana-Sinkam P et al (2009) A methodology for the combined in situ analyses of the precursor and mature forms of microRNAs and correlation with their putative targets. Nat Protoc 4:107–115
56. Nuovo GJ (2008) In situ detection of precursor and mature microRNAs in paraffin embedded, formalin fixed tissues and cell preparations. Methods 44:39–46
57. Hermansen SK, Dahlrot RH, Nielsen BS et al (2013) MiR-21 expression in the tumor cell compartment holds unfavorable prognostic value in gliomas. J Neurooncol 111:71–81
58. Yamamichi N, Shimomura R, Inada K et al (2009) Locked nucleic acid in situ hybridization analysis of miR-21 expression during colorectal cancer development. Clin Cancer Res 15: 4009–4016
59. Habbe N, Koorstra JB, Mendell JT et al (2009) MicroRNA miR-155 is a biomarker of early pancreatic neoplasia. Cancer Biol Ther 8:340–346
60. Preis M, Gardner TB, Gordon SR et al (2011) MicroRNA-10b Expression correlates with response to neoadjuvant therapy and survival in pancreatic ductal adenocarcinoma. Clin Cancer Res 17:5812–5821
61. Rask L, Balslev E, Jorgensen S et al (2011) High expression of miR-21 in tumor stroma correlates with increased cancer cell proliferation in human breast cancer. APMIS 119:663–673
62. Quesne JL, Jones J, Warren J et al (2012) Biological and prognostic associations of miR- 205 and let-7b in breast cancer revealed by in situ hybridization analysis of micro-RNA expression in arrays of archival tumour tissue. J Pathol 227:306–314
63. Kjaer-Frifeldt S, Hansen TF, Nielsen BS et al (2012) The prognostic importance of miR- 21 in stage II colon cancer: a population-based study. Br J Cancer 107:1169–1174
64. Nielsen BS, Jorgensen S, Fog JU et al (2011) High levels of microRNA-21 in the stroma of colorectal cancers predict short disease-free survival in stage II colon cancer patients. Clin Exp Metastasis 28:27–38
65. Liu X, Sempere LF, Ouyang H et al (2010) MicroRNA-31 functions as an oncogenic microRNA in mouse and human lung cancer cells by repressing specific tumor suppressors. J Clin Invest 120:1298–1309
66. Hansen TF, Andersen CL, Nielsen BS et al (2011) Elevated microRNA-126 is associated with high vascular endothelial growth factor receptor 2 expression levels and high microvessel density in colorectal cancer. Oncol Lett 2:1101–1106
67. Gravgaard KH, Lyng MB, Laenkholm AV et al (2012) The miRNA-200 family and miRNA-9 exhibit differential expression in primary versus corresponding metastatic tissue in breast cancer. Breast Cancer Res Treat 134:207–217
68. Qian P, Zuo Z, Wu Z et al (2011) Pivotal role of reduced let-7g expression in breast cancer invasion and metastasis. Cancer Res 71: 6463–6474
69. Hanna JA, Wimberly H, Kumar S et al (2012) Quantitative analysis of microRNAs in tissue microarrays by in situ hybridization. Biotechniques 52:235–245
70. Hanna JA, Hahn L, Agarwal S et al (2012) In situ measurement of miR-205 in malignant melanoma tissue supports its role as a tumor suppressor microRNA. Lab Invest 92:1390–1397
71. Jia Z, Wang K, Zhang A et al (2013) miR-19a and miR-19b overexpression in gliomas. Pathol Oncol Res 19:847–853
72. Farrell JJ, Toste P, Wu N et al (2013) Endoscopically acquired pancreatic cyst fluid microRNA 21 and 221 are associated with invasive cancer. Am J Gastroenterol 108:1352–1359
73. Wang K, Jia Z, Zou J et al (2013) Analysis of hsa-miR-30a-5p expression in human gliomas. Pathol Oncol Res 19:405–411
74. Ma Y, Zhang P, Wang F et al (2012) miR-150 as a potential biomarker associated with prognosis and therapeutic outcome in colorectal cancer. Gut 61:1447–1453
75. Tang W, Zhu J, Su S et al (2012) MiR-27 as a prognostic marker for breast cancer progression and patient survival. PLoS One 7:e51702
76. Donnem T, Eklo K, Berg T et al (2011) Prognostic impact of MiR-155 in non-small cell lung cancer evaluated by in situ hybridization. J Transl Med 9:6
77. Kadera BE, Li L, Toste PA et al (2013) MicroRNA-21 in pancreatic ductal adenocarcinoma tumor-associated fibroblasts promotes metastasis. PLoS One 8:e71978
78. Dillhoff M, Liu J, Frankel W et al (2008) MicroRNA-21 is overexpressed in pancreatic cancer and a potential predictor of survival. J Gastrointest Surg 12:2171–2176
79. Renwick N, Cekan P, Masry PA et al (2013) Multicolor microRNA FISH effectively differentiates tumor types. J Clin Invest 123: 2694–2702