Combined MicroRNA in situ hybridization and immunohistochemical detection of protein markers

Methods in Molecular Biology

Volumn 986, Issue , 2013, Pages 353-365

  Nielsen, Boye Schnack ^a   Holmstrøm, Kim ^a  

^a NONE

Author keywords

Fluorescence multiplexing; Immunohistochemistry; In situ hybridization; Locked nucleic acid; MicroRNA

Indexed keywords

ALPHA SMOOTH MUSCLE ACTIN; MICRORNA; MICRORNA 205; MICRORNA 21; PROTEIN; MIRN205 MICRORNA, HUMAN; MIRN21 MICRORNA, HUMAN; OLIGONUCLEOTIDE; TUMOR MARKER;

ARTICLE; DOWN REGULATION; GENE TARGETING; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; IN SITU HYBRIDIZATION; MONITORING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN TARGETING; TISSUE PREPARATION; TISSUE SECTION; 3' UNTRANSLATED REGION; CHEMISTRY; CHROMOSOME DELETION; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; PROTEIN SYNTHESIS; SINGLE NUCLEOTIDE POLYMORPHISM;

3' UNTRANSLATED REGIONS; CHROMOSOME DELETION; HUMANS; IMMUNOHISTOCHEMISTRY; IN SITU HYBRIDIZATION; MICRORNAS; OLIGONUCLEOTIDES; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN BIOSYNTHESIS; TUMOR MARKERS, BIOLOGICAL;

MLCS; MLOWN;

EID: 84881231224     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-311-4_22     Document Type: Article

References (50)

1. Ambros V (2001) microRNAs: tiny regulators with great potential. Cell 107:823-826
2. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843-854
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. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297
5. Pillai RS, Bhattacharyya SN, Artus CG et al (2005) Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 309:1573-1576
6. Liu J, Rivas FV, Wohlschlegel J et al (2005) A role for the P-body component GW182 in microRNA function. Nat Cell Biol 7: 1261-1266
7. Ambros V (2011) MicroRNAs and developmental timing. Curr Opin Genet Dev 21: 511-517
8. Cordes KR, Sheehy NT, White MP et al (2009) miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 460:705-710
9. Makeyev EV, Zhang J, Carrasco MA et al (2007) The MicroRNA miR-124 promotes neuronal differentiation by triggering brainspecific alternative pre-mRNA splicing. Mol Cell 27:435-448
10. Yao Q, Cao S, Li C et al (2011) Micro-RNA-21 regulates TGF-beta-induced myofibroblast differentiation by targeting PDCD4 in tumor-stroma interaction. Int J Cancer 128: 1783-1792
11. Madhyastha R, Madhyastha H, Nakajima Y et al (2011) MicroRNA signature in diabetic wound healing: promotive role of miR-21 infibroblast migration. Int Wound J 9:355-361
12. Medina PP, Slack FJ (2008) microRNAs and cancer: an overview. Cell Cycle 7:2485-2492
13. Winter J, Jung S, Keller S et al (2009) Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 11:228-234
14. Betel D, Wilson M, Gabow A et al (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36:D149-D153
15. Thomson DW, Bracken CP, Goodall GJ (2011) Experimental strategies for microRNA target identification. Nucleic Acids Res 39:6845-6853
16. Ferdin J, Kunej T, Calin GA (2010) Noncoding RNAs: identification of cancer-associated microRNAs by gene profiling. Technol Cancer Res Treat 9:123-138
17. Sorensen KD, Orntoft TF (2010) Discovery of prostate cancer biomarkers by microarray gene expression profiling. Expert Rev Mol Diagn 10:49-64
18. Jensen SG, Lamy P, Rasmussen MH et al (2011) Evaluation of two commercial global miRNA expression profiling platforms for detection of less abundant miRNAs. BMC Genomics 12:435
19. Burnside J, Ouyang M, Anderson A et al (2008) Deep sequencing of chicken microRNAs. BMC Genomics 9:185
20. Joyce CE, Zhou X, Xia J et al (2011) Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome. Hum Mol Genet 20:4025-4040
21. Schetter AJ, Leung SY, Sohn JJ et al (2008) MicroRNA expression profiles associated with prognosis and therapeutic outcome in colon adenocarcinoma. JAMA 299:425-436
22. Ralfkiaer U, Hagedorn PH, Bangsgaard N et al (2011) Diagnostic microRNA profiling in cutaneous T-cell lymphoma (CTCL). Blood 118:5891-5900
23. Clop A, Marcq F, Takeda H et al (2006) A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 38:813-818
24. Richardson K, Lai CQ, Parnell LD et al (2011) A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS. BMC Genomics 12:504
25. Permuth-Wey J, Thompson RC, Burton NL et al (2011) A functional polymorphism in the pre-miR-146a gene is associated with risk and prognosis in adult glioma. J Neurooncol 105:639-646
26. Lei B, Gao S, Luo LF et al (2011) A SNP in the miR-27a gene is associated with litter size in pigs. Mol Biol Rep 38:3725-3729
27. Nossent AY, Hansen JL, Doggen C et al (2011) SNPs in microRNA binding sites in 3′ -UTRs of RAAS genes in fluence arterial blood pressure and risk of myocardial infarction. Am J Hypertens 24:999-1006
28. Zhang L, Liu Y, Song F et al (2011) Functional SNP in the microRNA-367 binding site in the 3′ UTR of the calcium channel ryanodine receptor gene 3 (RYR3) affects breast cancer risk and calcification. Proc Natl Acad Sci USA 108:13653-13658
29. Lodygin D, Tarasov V, Epanchintsev A et al (2008) Inactivation of miR-34a by aberrant CpG methylation in multiple types of cancer. Cell Cycle 7:2591-2600
30. Calin GA, Ferracin M, Cimmino A et al (2005) A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 353:1793-1801
31. Trang P, Wiggins JF, Daige CL et al (2011) Systemic delivery of tumor suppressor microRNA mimics using a neutral lipid emulsion inhibits lung tumors in mice. Mol Ther 19:1116-1122
32. Sioud M (2011) Promises and challenges in developing RNAi as a research tool and therapy. Methods Mol Biol 703:173-187
33. Wang Z, Rao DD, Senzer N et al (2011) RNA interference and cancer therapy. Pharm Res 28:2983-2995
34. Garofalo M, Croce CM (2011) microRNAs: master regulators as potential therapeutics in cancer. Annu Rev Pharmacol Toxicol 51:25-43
35. Gambari R, Fabbri E, Borgatti M et al (2011) Targeting microRNAs involved in human diseases: a novel approach for modification of gene expression and drug development. Biochem Pharmacol 82:1416-1429
36. Kasinski AL, Slack FJ (2010) Potential microRNA therapies targeting Ras, NFkappaB and p53 signaling. Curr Opin Mol Ther 12:147-157
37. Stenvang J, Silahtaroglu AN, Lindow M et al (2008) The utility of LNA in microRNA-based cancer diagnostics and therapeutics. Semin Cancer Biol 18:89-102
38. 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
39. Soe MJ, Moller T, Dufva M et al (2011) A sensitive alternative for microRNA in situ hybridizations using probes of 2′ -O-methyl RNA + LNA. J Histochem Cytochem 59:661-672
40. Nielsen BS (2012) MicroRNA in situ hybridization. Methods Mol Biol 822:67-84
41. Kloosterman WP, Wienholds E, de Brujin E et al (2006) In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nat Methods 3:27-29
42. 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
43. Nuovo GJ (2010) In situ detection of microRNAs in paraffin embedded, formalinfixed tissues and the co-localization of their putative targets. Methods 52:307-315
44. 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
45. Greene SB, Herschkowitz JI, Rosen JM (2010) The ups and downs of miR-205: identifying the roles of miR-205 in mammary gland development and breast cancer. RNA Biol 7:300-304
46. 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
47. Young MR, Santhanam AN, Yoshikawa N et al (2010) Have tumor suppressor PDCD4 and its counteragent oncogenic miR-21 gone rogue? Mol Interv 10:76-79
48. Ruan Q, Wang T, Kameswaran V et al (2011) The microRNA-21-PDCD4 axis prevents type 1 diabetes by blocking pancreatic beta cell death. Proc Natl Acad Sci USA 108:12030-12035
49. Sempere LF (2011) Integrating contextual miRNA and protein signatures for diagnostic and treatment decisions in cancer. Expert Rev Mol Diagn 11:813-827
50. Soe MJ, Okkels F, Sabourin D et al (2011) HistoFlex-a micro fluidic device providing uniform flow conditions enabling highly sensitive, reproducible and quantitative in situ hybridizations. Lab Chip 11:3896-3907