Micro RNA detection in long-term fixed tissue of cortical glutamatergic pyramidal neurons after targeted laser-capture neuroanatomical microdissection

Journal of Neuroscience Methods

Volumn 235, Issue , 2014, Pages 76-82

  Herai, Roberto R ^a,b   Stefanacci, Lisa ^c   Hrvoj Mihic, Branka ^c   Chailangkarn, Thanathom ^a,b   Hanson, Kari ^c   Semendeferi, Katerina ^c,d   Muotri, Alysson R ^a,b,c,d  

^a RADY CHILDREN'S HOSPITAL   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d San Diego   (United States)

Author keywords

Bioinformatics analysis; High throughput sequencing; Laser capture microdissection; Long term formalin fixation; Micro RNA; Small RNA

Indexed keywords

FORMALDEHYDE; FORMALDEHYDE DEHYDROGENASE; MICRORNA; MICRORNA 155; PARAFFIN; TRANSFER RNA; GLUTAMIC ACID;

ADULT; ARTICLE; BIOINFORMATICS; BRAIN; BRAIN CORTEX; CELL POPULATION; CELL SHAPE; CELL STRUCTURE; GENETIC ANALYSIS; HUMAN; HUMAN TISSUE; LASER CAPTURE MICRODISSECTION; MALE; MICRODISSECTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PYRAMIDAL NERVE CELL; RNA SEQUENCE; BIOLOGY; GENETIC PROCEDURES; METABOLISM; PROCEDURES; TISSUE FIXATION;

ADULT; CEREBRAL CORTEX; COMPUTATIONAL BIOLOGY; FORMALDEHYDE; GENETIC TECHNIQUES; GLUTAMIC ACID; HUMANS; LASER CAPTURE MICRODISSECTION; MALE; MICRORNAS; PARAFFIN; PYRAMIDAL CELLS; TISSUE FIXATION;

EID: 84904290815     PISSN: 01650270     EISSN: 1872678X     Source Type: Journal    
DOI: 10.1016/j.jneumeth.2014.06.028     Document Type: Article

References (33)

1. Barger N., Stefanacci L., Schumann C.M., Sherwood C.C., Annese J., Allman J.M., et al. Neuronal populations in the basolateral nuclei of the amygdala are differentially increased in humans compared with apes: a stereological study. J Comp Neurol 2012, 520(13):3035-3054.
2. Bedewi A.EL., Miller L. Discrimination between paraffin-embedded and frozen skin sections using synchrotron infrared microspectroscopy. Int J Pept Res Ther 2014, 20(1):13-17.
3. Bjartmar L., Huberman A.D., Ullian E.M., Rentería R.C., Liu X., Xu W., et al. Neuronal pentraxins mediate synaptic refinement in the developing visual system. J Neurosci 2006, 26(June (23)):6269-6281.
4. Cardoso A.L., Guedes J.R., Pereira de Almeida L., Pedroso de Lima M.C. miR-155 modulates microglia-mediated immune response by down-regulating SOCS-1 and promoting cytokine and nitric oxide production. Immunology 2012, 135(January (1)):73-88.
5. Chen A., Xiong L-J., Tong Y., Mao M. Neuroprotective effect of brain-derived neurotrophic factor mediated by autophagy through the PI3K/Akt/mTOR pathway. Mol Med Rep 2013, 8(October (4)):1011-1016.
6. Culpin R.E., Sieniawski M., Proctor S.J., Menon G., Mainou-Fowler T. MicroRNAs are suitable for assessment as biomarkers from formalin-fixed paraffin-embedded tissue, and miR-24 represents an appropriate reference microRNA for diffuse large B-cell lymphoma studies. J Clin Pathol 2013, 66(March (3)):249-252.
7. Dent E.W., Gupton S.L., Gertler F.B. The growth cone cytoskeleton in axon outgrowth and guidance. Cold Spring Harb Perspect Biol 2011, 3(March (3)).
8. Gantier M.P., McCoy C.E., Rusinova I., Saulep D., Wang D., Xu D., et al. Analysis of microRNA turnover in mammalian cells following Dicer1 ablation. Nucleic Acids Res 2011, 39(July (13)):5692-5703.
9. Gascon E., Gao F.-B. Cause or effect: misregulation of microRNA pathways in neurodegeneration. Front Neurosci 2012, 9(January (6)):48.
10. Hsu J., Hanna P., Van Wagoner D.R., Barnard J., Serre D., Chung M.K., et al. Whole genome expression differences in human left and right atria ascertained by RNA sequencing. Circ Cardiovasc Genet 2012, 5(June (3)):327-335.
11. Jin L., Majerus J., Oliveira A., Inwards C.Y., Nascimento A.G., Burgart L.J., et al. Detection of fusion gene transcripts in fresh-frozen and formalin-fixed paraffin-embedded tissue sections of soft-tissue sarcomas after laser capture microdissection and RT-PCR. Diagn Mol Pathol 2003, 12(4):224-230.
12. Kai Z.S., Pasquinelli A.E. MicroRNA assassins: factors that regulate the disappearance of miRNAs. Nat Struct Mol Biol 2010, 17(January (1)):5-10.
13. Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(May (4)):357-359.
14. Li J., Smyth P., Flavin R., Cahill S., Denning K., Aherne S., et al. Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells. BMC Biotechnol 2007, 7(January (1)):36.
15. Li X., Lu Y., Chen Y., Lu W., Xie X. MicroRNA profile of paclitaxel-resistant serous ovarian carcinoma based on formalin-fixed paraffin-embedded samples. BMC Cancer 2013, 13(January (1)):216.
16. Li Y., Li Z., Zhou S., Wen J., Geng B., Yang J., et al. Genome-wide analysis of human microRNA stability. Biomed Res Int 2013, 2013(January):368975.
17. Liu D.-Z., Tian Y., Ander B.P., Xu H., Stamova B.S., Zhan X., et al. Brain and blood microRNA expression profiling of ischemic stroke, intracerebral hemorrhage, and kainate seizures. J Cereb Blood Flow Metab 2010, 30(January (1)):92-101.
18. Van Maldegem F., de Wit M., Morsink F., Musler A., Weegenaar J., van Noesel C.J.M. Effects of processing delay, formalin fixation, and immunohistochemistry on RNA recovery from formalin-fixed paraffin-embedded tissue sections. Diagn Mol Pathol 2008, 17(March (1)):51-58.
19. Marchetto M.C.N., Narvaiza I., Denli A.M., Benner C., Lazzarini T.A., Nathanson J.L., et al. Differential L1 regulation in pluripotent stem cells of humans and apes. Nature 2013, 503(November (7477)):525-529.
20. Mattick J.S., Makunin I.V. Non-coding RNA. Hum Mol Genet 2006, 15(April (Spec No. 1)):R17-R29.
21. Muotri A.R., Gage F.H. Generation of neuronal variability and complexity. Nature 2006, 441(June (7097)):1087-1093.
22. Patel R.K., Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 2012, 7(January (2)):e30619.
23. Ravo M., Mutarelli M., Ferraro L., Grober O.M.V., Paris O., Tarallo R., et al. Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays. Lab Invest 2008, 88(April (4)):430-440.
24. Ribeiro-Silva A., Zhang H., Jeffrey S.S. RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies. BMC Mol Biol 2007, 8(January):118.
25. Sherwood C.C., Stimpson C.D., Raghanti M.A., Wildman D.E., Uddin M., Grossman L.I., et al. Evolution of increased glia-neuron ratios in the human frontal cortex. Proc Natl Acad Sci USA 2006, 103(September (37)):13606-13611.
26. Smirnova L., Gräfe A., Seiler A., Schumacher S., Nitsch R., Wulczyn F.G. Regulation of miRNA expression during neural cell specification. Eur J Neurosci 2005, 21(March (6)):1469-1477.
27. Tarassishin L., Loudig O., Bauman A., Shafit-Zagardo B., Suh H-S., Lee S.C. Interferon regulatory factor 3 inhibits astrocyte inflammatory gene expression through suppression of the proinflammatory miR-155 and miR-155*. Glia 2011, 59(December (12)):1911-1922.
28. Tuddenham L., Jung J.S., Chane-Woon-Ming B., Dölken L., Pfeffer S. Small RNA deep sequencing identifies microRNAs and other small noncoding RNAs from human herpesvirus 6B. J Virol 2012, 86(February (3)):1638-1649.
29. Walters Z.S., Villarejo-Balcells B., Olmos D., Buist T.W.S., Missiaglia E., Allen R., et al. JARID2 is a direct target of the PAX3-FOXO1 fusion protein and inhibits myogenic differentiation of rhabdomyosarcoma cells. Oncogene 2014, 33(9):1148-1157.
30. Wu Y-Q., Lin X., Liu C-M., Jamrich M., Shaffer L.G. Identification of a human brain-specific gene, calneuron 1, a new member of the calmodulin superfamily. Mol Genet Metab 2001, 72(4):343-350.
31. Xu X-L., Zong R., Li Z., Biswas M.H.U., Fang Z., Nelson D.L., et al. FXR1P but not FMRP regulates the levels of mammalian brain-specific microRNA-9 and microRNA-124. J Neurosci 2011, 31(September (39)):13705-13709.
32. Yamakawa N., Okuyama K., Ogata J., Kanai A., Helwak A., Takamatsu M., et al. Novel functional small RNAs are selectively loaded onto mammalian Ago1. Nucleic Acids Res 2014, (March).
33. Yost S.E., Smith E.N., Schwab R.B., Bao L., Jung H., Wang X., et al. Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic Acids Res 2012, 40(August (14)):e107.