Name: characterization of functionally associated mirnas in glioblastoma and their engineering into artificial clusters for gene therapy
Uploaded: 2019-10-04T14:30:00
Description: Watch this Scientific Journal Video about Characterization of Functionally Associated miRNAs in Glioblastoma and their Engineering into Artificial Clusters for Gene Therapy at JoVE.com

The authors wish to thank the members of the Harvey Cushing Neuro Oncology Laboratory for support and constructive criticism. This work was supported by NINDS grants K12NS80223 and K08NS101091 to P. P.

1. Characterization of Functionally Associated miRNAs in Glioblastoma
<ol>
	<li>Analysis of broad differential miRNA expression in glioblastoma vs. brain
	<ol>
		<li>First, determine the most significantly deregulated miRNAs in the tumor. This can be achieved using at least three different methods:
		<ol>
			<li>Mine the Cancer Genome Atlas, found at https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga, for sequencing data11.</li>
			<li>Perform mi...

<ol>
	<li>Wu, Y. E., Parikshak, N. N., Belgard, T. G., Geschwind, D. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-wide,+integrative+analysis+implicates+miRNA+dysregulation+in+autism+spectrum+disorder.">Genome-wide, integrative analysis implicates miRNA dysregulation in autism spectrum disorder.</a> Nature Neuroscience. 19, 1463-1476 (2016).</li><li>Esteller, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Non-coding+RNAs+in+human+disease.">Non-coding RNAs in human disease.</a> Nature Reviews Genetics. 12, 861-874 (2011).</li><li>Moradifard, S., Hoseinbeyki, M., Ganji, S. M., Minuchehr, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+miRNA+and+Gene+Expression+Profiles+in+Alzheimer's+Disease:+A+Meta-Analysis+Approach.">Analysis of miRNA and Gene Expression Profiles in Alzheimer's Disease: A Meta-Analysis Approach.</a> Scientific Reports. 8, 4767 (2018).</li><li>Calin, G. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Frequent+deletions+and+down-regulation+of+micro-+RNA+genes+miR15+and+miR16+at+13q14+in+chronic+lymphocytic+leukemia.">Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia.</a> Proceedings of the National Academy of Sciencesof the United States of America. 99, 15524-15529 (2002).</li><li>Croce, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Causes+and+consequences+of+miRNA+dysregulation+in+cancer.">Causes and consequences of miRNA dysregulation in cancer.</a> Nature Reviews Genetics. 10, 704-714 (2009).</li><li>Ambros, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=miRNAs:+tiny+regulators+with+great+potential.">miRNAs: tiny regulators with great potential.</a> Cell. 107, 823-826 (2001).</li><li>Treiber, T., Treiber, N., Meister, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+miRNA+biogenesis+and+its+crosstalk+with+other+cellular+pathways.">Regulation of miRNA biogenesis and its crosstalk with other cellular pathways.</a> Nature Reviews Molecular Cell Biology. 20, 5-20 (2019).</li><li>He, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+miRNA+polycistron+as+a+potential+human+oncogene.">A miRNA polycistron as a potential human oncogene.</a> Nature. 435, 828-833 (2005).</li><li>Santos, M. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=miR-124,+&#8722;128,+and+&#8722;137+orchestrate+neural+differentiation+by+acting+on+overlapping+gene+sets+containing+a+highly+connected+transcription+factor+network.">miR-124, &#8722;128, and &#8722;137 orchestrate neural differentiation by acting on overlapping gene sets containing a highly connected transcription factor network.</a> Stem Cells. 34, 220-232 (2016).</li><li>Bhaskaran, V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+functional+synergism+of+miRNA+clustering+provides+therapeutically+relevant+epigenetic+interference+in+glioblastoma.">The functional synergism of miRNA clustering provides therapeutically relevant epigenetic interference in glioblastoma.</a> Nature Communications. 10 (1), 442 (2019).</li><li>Kim, T. M., Huang, W., Park, R., Park, P. J., Johnson, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+developmental+taxonomy+of+glioblastoma+defined+and+maintained+by+MiRNAs.">A developmental taxonomy of glioblastoma defined and maintained by MiRNAs.</a> Cancer Research. 71 (9), 3387-3399 (2011).</li><li>Dell'Aversana, C., Giorgio, C., Altucci, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MiRNA+Expression+Profiling+Using+Agilent+One-Color+Microarray.">MiRNA Expression Profiling Using Agilent One-Color Microarray.</a> Methods in Molecular Biology. 1509, 169-183 (2017).</li><li>Silber, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=miR-124+and+miR-137+inhibit+proliferation+of+glioblastoma+multiforme+cells+and+induce+differentiation+of+brain+tumor+stem+cells.">miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells.</a> BMC Medicine. 6 (14), (2008).</li><li>Hester, M. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two+factor+reprogramming+of+human+neural+stem+cells+into+pluripotency.">Two factor reprogramming of human neural stem cells into pluripotency.</a> PLoS ONE. 4 (9), e7044 (2009).</li><li>Hsieh, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IGF-I+instructs+multipotent+adult+neural+progenitor+cells+to+become+oligodendrocytes.">IGF-I instructs multipotent adult neural progenitor cells to become oligodendrocytes.</a> Journal of Cell Biology. 164 (1), 111-122 (2004).</li><li>Agarwal, V., Bell, G. W., Nam, J., Bartel, D. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Predicting+effective+miRNA+target+sites+in+mammalian+mRNAs.">Predicting effective miRNA target sites in mammalian mRNAs.</a> eLife. 4, e05005 (2015).</li><li>Betel, D., Wilson, M., Gabow, A., Marks, D. S., Sander, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+miRNA.org+resource:+targets+and+expression.">The miRNA.org resource: targets and expression.</a> Nucleic Acids Research. 36, D149-D153 (2008).</li><li>Wong, N., Wang, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=miRD(B)+an+online+resource+for+miRNA+target+prediction+and+functional+annotations.">miRD(B) an online resource for miRNA target prediction and functional annotations.</a> Nucleic Acids Research. 43 (D1), D146-D152 (2015).</li><li>Vlachos, I. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DIANA-miRPath+v3.0:+deciphering+miRNA+function+with+experimental+support.">DIANA-miRPath v3.0: deciphering miRNA function with experimental support.</a> Nucleic Acids Research. 43 (W1), W460-W466 (2015).</li><li>Chen, J., Bardes, E. E., Aronow, B. J., Jegga, A. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ToppGene+Suite+for+gene+list+enrichment+analysis+and+candidate+gene+prioritization.">ToppGene Suite for gene list enrichment analysis and candidate gene prioritization.</a> Nucleic Acids Research. 305, W305-W311 (2009).</li><li>Aken, B. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ensembl+2017.">Ensembl 2017.</a> Nucleic Acids Research. 45, D635-D642 (2017).</li><li>Kozomara, A., Birgaoanu, M., Griffiths-Jones, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=miRBase:+from+miRNA+sequences+to+function.">miRBase: from miRNA sequences to function.</a> Nucleic Acid Research. 47, D155-D162 (2019).</li><li>Lorenz, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vienna+RNA+Package+2.0.">Vienna RNA Package 2.0.</a> Algorithms for Molecular Biology. 6 (1), 26 (2011).</li><li>Hughes, R. A., Ellington, A. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synthetic+DNA+synthesis+and+assembly:+Putting+the+synthetic+in+synthetic+biology.">Synthetic DNA synthesis and assembly: Putting the synthetic in synthetic biology.</a> Cold Spring Harbor Perspectives in Biology. 9 (1), a023812 (2017).</li><li>Crommentuijn, M. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intracranial+AAV-sTRAIL+combined+with+lanatoside+C+prolongs+survival+in+an+orthotopic+xenograft+mouse+model+of+invasive+glioblastoma.">Intracranial AAV-sTRAIL combined with lanatoside C prolongs survival in an orthotopic xenograft mouse model of invasive glioblastoma.</a> Molecular Oncology. 10 (4), 625-634 (2016).</li><li>Ivey, K. N., Srivastava, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MiRNAs+as+regulators+of+differentiation+and+cell+fate+decisions.">MiRNAs as regulators of differentiation and cell fate decisions.</a> Cell Stem Cell. 7, 36-41 (2010).</li><li>Han, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+Basis+for+the+Recognition+of+Primary+miRNAs+by+the+Drosha-DGCR8+Complex.">Molecular Basis for the Recognition of Primary miRNAs by the Drosha-DGCR8 Complex.</a> Cell. 125, 887-901 (2006).</li><li>Barroso-del Jesus, A., Lucena-Aguilar, G., Menendez, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+miR-302-367+cluster+as+a+potential+stemness+regulator+in+ESCs.">The miR-302-367 cluster as a potential stemness regulator in ESCs.</a> Cell Cycle. 8, 394-398 (2009).</li><li>Liu, Y. P., Haasnoot, J., Brake, O., Berkhout, B., Konstantinova, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inhibition+of+HIV-1+by+multiple+shRNAs+expressed+from+a+single+miRNA+polycistron.">Inhibition of HIV-1 by multiple shRNAs expressed from a single miRNA polycistron.</a> Nucleic Acid Research. 36, 2811-2824 (2008).</li><li>Chen, S. C., Stern, P., Guo, Z., Chen, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expression+of+Multiple+Artificial+MiRNAs+from+a+Chicken+miRNA126-Based+Lentiviral+Vector.">Expression of Multiple Artificial MiRNAs from a Chicken miRNA126-Based Lentiviral Vector.</a> PLoS ONE. 6 (7), e22437 (2011).</li><li>Yang, X., Marcucci, K., Anguela, X., Couto, L. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preclinical+Evaluation+of+An+Anti-HCV+miRNA+Cluster+for+Treatment+of+HCV+Infection.">Preclinical Evaluation of An Anti-HCV miRNA Cluster for Treatment of HCV Infection.</a> Molecular Therapy. 21, 588-601 (2013).</li></ol>

This protocol is based on the notion that rather than functioning in isolation, miRNAs are biologically relevant by working in groups, and these groups are transcriptionally determined by specific cellular contexts26. To justify this approach from a translational perspective, a follow-up protocol that allows recreation of this multi-miRNA pattern in cells/tissues is introduced. This is possible by taking advantage of the relatively simple biogenesis of miRNAs, whereby the recognition of the charac...

miRNAs offer an unmatched opportunity for the development of a broad gene therapy approach to many diseases1,2,3, including cancer4,5. This is based on several unique features of these biological molecules, including their small size6, simple biogenesis7, and natural tendency to function in association8. Many diseases are characterized by specific miRNA expression patterns, which often converge on the regulation of complex biological functions9. The purpose of this method is first to define a strategy to identify groups of miRNAs that are synergistically relevant for specific cellular functions. Consequently, it provides a strategy for the re-establishment of such miRNA combinations in downstream studies and applications.
This method allows for functional analysis of multiple miRNAs at once, leveraging on their simultaneous targeting of a large number of mRNAs, thus recapitulating the complex landscapes of diseases. This approach has been recently employed to define a group of three miRNAs that 1) are simultaneously downregulated in brain cancer and 2) show a strong co-expression pattern during neural differentiation as well as in response to genotoxic stress by radiation or a DNA alkylating agent. The combinatorial re-expression of this module of three miRNAs by the clustering method described below results in profound interference with the biology of cancer cells and can be easily used as a gene therapy strategy for preclinical studies10. This protocol may be of particular interest to those involved in miRNA research and its translational applications.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.4% low melting temperature agarose&#160;</td>
			<td>IBI Scientific</td>
			<td>IB70058</td>
			<td></td>
		</tr>
		<tr>
			<td>0.45 &#181;M sterile filter unit</td>
			<td>Merck Millipore</td>
			<td>SLH033RS</td>
			<td></td>
		</tr>
		<tr>
			<td>1.5-mL Microcentrifuge tube</td>
			<td>Eppendorf</td>
			<td>22431081</td>
			<td></td>
		</tr>
		<tr>
			<td>6-Well plates&#160;</td>
			<td>Greiner Bio-One</td>
			<td>657160</td>
			<td></td>
		</tr>
		<tr>
			<td>Athymic mice (FoxN1 nu/nu)</td>
			<td>Envigo</td>
			<td>069(nu)/070(nu/+)</td>
			<td></td>
		</tr>
		<tr>
			<td>B-27 Supplement&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>12587010</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture flask</td>
			<td>Greiner Bio-One</td>
			<td>660175</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Scraper, 16cm</td>
			<td>Sarstedt</td>
			<td>83.1832</td>
			<td></td>
		</tr>
		<tr>
			<td>Cesium 137 irradiator&#160;</td>
			<td>JL Sheperd and Associates</td>
			<td>Core Facility (Harvard Medical School)</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Sigma-Aldrich</td>
			<td>439142-4L</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM, high glucose, pyruvate&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>11995040</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#8217;s phosphate-buffered saline&#160;</td>
			<td>Gibco</td>
			<td>14190144</td>
			<td></td>
		</tr>
		<tr>
			<td>Eosin Y solution&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>E4009</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>F9665</td>
			<td></td>
		</tr>
		<tr>
			<td>Formalin solution</td>
			<td>Sigma-Aldrich</td>
			<td>HT501128</td>
			<td></td>
		</tr>
		<tr>
			<td>GlutaMAX Supplement&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>35050061</td>
			<td></td>
		</tr>
		<tr>
			<td>HEK-293</td>
			<td>American Type Culture Collecti</td>
			<td>ATCC CRL-1573</td>
			<td></td>
		</tr>
		<tr>
			<td>Hematoxylin solution</td>
			<td>Sigma-Aldrich</td>
			<td>1051750500</td>
			<td></td>
		</tr>
		<tr>
			<td>Human primary glioma stem-like cells (GBM62)</td>
			<td></td>
			<td></td>
			<td>Provided by Dr. E. A. Chiocca (Brigham and Women&#8217;s Hospital, Boston, MA)</td>
		</tr>
		<tr>
			<td>Human primary glioma stem-like cells (MGG4)</td>
			<td></td>
			<td></td>
			<td>Provided by Dr. Hiroaki Wakimoto (Massachusetts General Hospital, Boston, MA)</td>
		</tr>
		<tr>
			<td>Lentiviral vector pCDH-CMV-MCS-EF1-copGFP</td>
			<td>System Biosciences</td>
			<td>CD511B-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Lipofectamine 2000&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>11668019</td>
			<td></td>
		</tr>
		<tr>
			<td>Microcentrifuge refrigerated</td>
			<td>Eppendorf</td>
			<td>model no. 5424 R, cat. no.5404000138</td>
			<td></td>
		</tr>
		<tr>
			<td>Mounting medium&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>4112APG</td>
			<td></td>
		</tr>
		<tr>
			<td>Nalgene High-Speed Polycarbonate Round Bottom Centrifuge Tubes&#160;</td>
			<td>Thermo Fisher Scientific&#160;</td>
			<td>3117-0380PK</td>
			<td></td>
		</tr>
		<tr>
			<td>NanoDrop</td>
			<td>Thermo Fisher Scientific</td>
			<td>2000c</td>
			<td></td>
		</tr>
		<tr>
			<td>Neural Progenitor cells (NPC)</td>
			<td></td>
			<td></td>
			<td>Provided by Dr. Jakub Godlewski (Brigham and Women&#8217;s Hospital, Boston, MA)</td>
		</tr>
		<tr>
			<td>Neurobasal Medium&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>21103049</td>
			<td></td>
		</tr>
		<tr>
			<td>Nikon eclipse Ti motorized fluorescent microscope system</td>
			<td>Nikon, Japan</td>
			<td>14314</td>
			<td></td>
		</tr>
		<tr>
			<td>Opti-MEM</td>
			<td>Thermo Fisher Scientific</td>
			<td>31985088</td>
			<td></td>
		</tr>
		<tr>
			<td>PCR tubes&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>CLS6571-960EA</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>Petri-Dishes 94/16&#160;</td>
			<td>Greiner Bio-One</td>
			<td>632180</td>
			<td></td>
		</tr>
		<tr>
			<td>Poly-D-Lysine&#160;</td>
			<td>Sigma- Aldrich</td>
			<td>P4707</td>
			<td></td>
		</tr>
		<tr>
			<td>Recombinant Human EGF&#160;</td>
			<td>PeproTech&#160;</td>
			<td>AF-100-15</td>
			<td></td>
		</tr>
		<tr>
			<td>Recombinant Human FGF-basic&#160;</td>
			<td>PeproTech&#160;</td>
			<td>AF-100-18B</td>
			<td></td>
		</tr>
		<tr>
			<td>Retinoic acid</td>
			<td>Gibco</td>
			<td>12587-010&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>RNA Miniprep Kit</td>
			<td>Direct-zol</td>
			<td>R2050</td>
			<td></td>
		</tr>
		<tr>
			<td>S1000 Thermal Cycler&#160;</td>
			<td>Bio-Rad</td>
			<td>1852196</td>
			<td></td>
		</tr>
		<tr>
			<td>Small Animal Image-Guided Micro Irradiator&#160;</td>
			<td>Xstrahal Life Sciences, UK</td>
			<td>Core facility (Dana-Farber Cancer Institute, Boston, MA)</td>
			<td></td>
		</tr>
		<tr>
			<td>Sorvall WX+ Ultracentrifuge&#160;</td>
			<td>Thermo Fisher Scientific&#160;</td>
			<td>75000100</td>
			<td></td>
		</tr>
		<tr>
			<td>StemPro Accutase&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>A1110501</td>
			<td></td>
		</tr>
		<tr>
			<td>StepOne Real-Time PCR System</td>
			<td>Applied Biosystems&#160;</td>
			<td>4376357</td>
			<td></td>
		</tr>
		<tr>
			<td>SterilGARD biosafety cabinet&#160;</td>
			<td>The Baker Company</td>
			<td>SG403A-HE</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Sigma-Aldrich</td>
			<td>S9378</td>
			<td></td>
		</tr>
		<tr>
			<td>T98-G</td>
			<td>American Type Culture Collecti</td>
			<td>ATCC CRL-1690</td>
			<td></td>
		</tr>
		<tr>
			<td>TaqMan MicroRNA Reverse Transcription Kit&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>4366596</td>
			<td></td>
		</tr>
		<tr>
			<td>TaqMan Universal PCR Master Mix</td>
			<td>Thermo Fisher Scientific</td>
			<td>4324018</td>
			<td></td>
		</tr>
		<tr>
			<td>Temozolomide</td>
			<td>Tocris Bioscience</td>
			<td>2706</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue-Tek optimum cutting temperature&#160;</td>
			<td>Fisher Scientific</td>
			<td>NC9636948</td>
			<td></td>
		</tr>
		<tr>
			<td>TRIzol Reagent&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>15596026</td>
			<td>Lysis reagent</td>
		</tr>
		<tr>
			<td>U251-MG</td>
			<td>American Type Culture Collecti</td>
			<td>ATCC HTB-17</td>
			<td></td>
		</tr>
		<tr>
			<td>U87-MG&#160;</td>
			<td>American Type Culture Collecti</td>
			<td>ATCC HTB-14</td>
			<td></td>
		</tr>
		<tr>
			<td>ViraPower Lentivector Expression system&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>K4970-00</td>
			<td></td>
		</tr>
		<tr>
			<td>Water, HPLC grade</td>
			<td>Fisher</td>
			<td>W54</td>
			<td></td>
		</tr>
		<tr>
			<td>Xylene&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>534056</td>
			<td></td>
		</tr>
	</tbody>
</table>

characterization of functionally associated mirnas in glioblastoma and their engineering into artificial clusters for gene therapy

The biological relevance of microRNAs (miRNAs) in health and disease significantly relies on specific combinations of many simultaneously deregulated miRNAs rather than the action of a single miRNA. The characterization of these specific miRNAs modules is a fundamental step in maximizing their use in therapy. This is extremely relevant because their combinatorial attributes can be practically exploited. Described here is a method to define a specific miRNA signature relevant to the control of oncogenic chromatin repressors in glioblastoma. The approach first defines a general group of miRNAs that are deregulated in tumors in comparison to normal tissue. The analysis is further refined by differential culture conditions, underscoring a subgroup of miRNAs that are co-expressed simultaneously during specific cellular states. Finally, the miRNAs that satisfy these filters are combined into an artificial polycistronic transgenes, which is based on a scaffold of naturally existing miRNA clusters genes, then used for overexpression of these miRNA modules into receiving cells.

This method allowed characterization of a module of three miRNAs that are consistently downregulated in brain tumors, which are co-expressed specifically during neuronal differentiation (Figure 1) and involved in the tumor survival response after therapy (Figure 2). This is accomplished by regulating a complex oncogenic chromatin repressive pathway. This co-expression pattern suggested a strong synergistic activity among these th...

Watch this Scientific Journal Video about Characterization of Functionally Associated miRNAs in Glioblastoma and their Engineering into Artificial Clusters for Gene Therapy at JoVE.com

Characterization of Functionally Associated miRNAs in Glioblastoma and their Engineering into Artificial Clusters for Gene Therapy

Described here is a protocol for characterizing modules of biologically synergistic miRNAs and their assembly into short transgenes, which allows simultaneous overexpression for gene therapy applications.

The biological relevance of microRNAs (miRNAs) in health and disease significantly relies on specific combinations of many simultaneously deregulated ...

This protocol allows the simultaneous modulation of many micro RNAs in eukaryotic cells and is based on a very simple and flexible method which minimizes molecular cloning steps. This technique has implications for the study of micro RNA functional interactions in vitro, but more importantly it provides a platform for a more effective use of micro RNAs in therapy. We have mainly developed and used it in the context of brain cancer, but it applies to any diseases where multiple alterations of gene expression are involved.We have tested our artificial trans genes in other models such as breast and thyroid cancer lines showing the reproducibility of this technique. Basic knowledge of bioinformatics and micro RNA biology is helpful for this protocol, but not indispensable. A bioinformatics approach is important to define relevant micro RNA combinations and the TRK-11, while familiarity with the micro RNA processing measurably is important to understand how these different micro RNAs can be assembled into artificial DNA clusters that can be successfully processed once stable to the specific cells.To coat dish, first dissolve poly-D-lysine in water at a concentration of 100 micrograms per milliliter. Pour the solution into the dish at the amount of one milliliter of solution per 25 square centimeters surface. Swirl the dish to make sure of coverage of the whole dish.After six hours aspirate the poly-D-lysine solution and rinse twice with PBS. Plate human neural stem cells in the amount of 100, 000 cells per five milliliter of the medium, either in stem cell medium, astrocytic differentiation medium or neuronal differentiation medium. After cell plating, place the dish in an incubator at 37 degrees Celsius and five percent carbon dioxide for one week and proceed to perform micro RNA expression analysis according to the manuscript.To culture GBM-34 glioblastoma stem-like cells, start with one times ten to the fifth cells and five milliliter of neurobasal medium in a 25 square centimeter low attachment flask. Place the flask into an incubator at 37 degrees Celsius and five percent carbon dioxide. 48 hours after plating, add doubling concentrations of DNA alkylating agent temozolomide every seven days.Start with addition of five micromolar TMZ supplemented in five milliliters medium for five days. After five days, remove the medium and replace with fresh medium without temozolomide to allow the surviving cells to recover. After 48 hours, add 10 micromolar temozolomide and incubate for another five days.Repeat the doubling temozolomide treatment until concentration of at least 100 micromolar is reached and cells become resistant to the drug. After the induction of resistance, lie cells using 1 milliliter of Lysis reagent. Extract total RNA and analyze the expression of the specific micro RNAs according to the manuscript.To obtain the predicted targetome of each micro RNA previously defined, use micro RNA targeting prediction tools. From the front page of TargetScan, select the micro RNA of interest from the pre-populated drop down menu. Click the submit button.Download the resulting list of targets as a spreadsheet using the download table link. To decrease the chances of false positive predictions, include only targets within the conserved sites column and downstream analysis. Additional micro RNA prediction programs obtain further stringency and only include targets that are common to all algorithms.Then, open ToppGene suite 20. To evaluate for the enrichment of pathways that are common to each micro RNA, paste the list of targets obtained in the training gene sets window. Click on HGNC Symbol as the entry type.Click submit and start. The program provides an output table showing the most significant GO categories for the entered list of genes. To finally establish the contribution of each micro RNA to the regulation of a common pathway or cellular process, open the venn-diagram function provided in the Bioinformatics and Evolutionary Genomics website.Check each obtained targetome against the full list of genes involved in the specific cellular process. If target messenger RNAs for each micro RNAs of interest are in the respective windows, upload of copy-paste the list. Name each list with a unique identifier.Click submit. The program provides a visual output of a venn-diagram with numbers of genes in each sector as well as a full list of messenger RNAs for each subset and intersection combinations. To group the selected micro RNAs into a functional trans gene, obtain a transgenic scaffold based on the miR-17-92 cluster locus.Obtain the nucleotide sequence from the ensembled genome browser. Select the approximately 800 base pair core sequence encompassing all six encoded micro RNA hairpins of the locus and at least 200 nucleotide flanking sequences both upstream and downstream of the core sequence. Paste the sequence into any word editing program.Define the sequence of each one of the six native hair pins by retrieving them in miR base. Mark each one of these sequences within the span of previously identified core sequence. Any sequences between each hairpin represent spacer sequences.Next, obtain the hairpin sequences of micro RNAs intended to be over expressed in the trans gene from miR base. Carefully note the specific nucleotides that are at the sites of micro processor cleavage. Delete the native hairpin sequences from the core sequence with the exception of three to five nucleotides at both the five and thee ends of each hairpin which will serve as an acceptor for the new hairpins.Paste the hairpin sequences of the desired micro RNAs to replace the previously deleted hairpins. Add desired restriction sequences at both flanking regions of the trans gene to facilitate sub-cloning into delivery vectors of choice. Verify that the chosen restriction sequences are not present within the sequence itself.To verify the two dimensional structure of the trans gene, copy the full transgenic sequence into the RNA structure prediction software program RNA Webfold. Select standard program settings and click proceed. Analyze the graphical output, particularly for the presence of well defined hairpins in presence of double stranded stem structures that are at least 11 nucleotides proximal to the micro processor cleavage site.Also, look for the absence of branching points within the hairpin sequences. At this point, the trans gene is ready to be produced by gene synthesis and cloned into the desired delivery vectors. This method allowed characterization of a module of three micro RNAs that are consistently down regulated in brain tumors, which are co-expressed specifically during neuronal differentiation.Co-expression patterns of micro RNA modules during genotoxic stress were confirmed and suggested a strong synergistic activity among these three micro RNAs. The designed trans gene could simultaneously recapitulate the expression of the three micro RNAs in glioblastoma cells, both in vitro and in vivo, with significant interference in tumor biology and promising translational applicability. Additionally, the transgenic cluster was also functional in a breast cancer model.The crucial requirements of this protocol are maintaining the original size of processor cleavage in the trans gene. And make sure that the stem loop structure of chimeric micro RNA hairpins is preserved. With this method, we can concentrate multiple biologically active micro RNA genes into very short DNA sequences which can literally be vitroly be fitted into any delivery vectors for gene therapy use.This method is ideal to study the functional interaction among different micro RNAs and to interfere with complex multifactorial cellular pathways which will otherwise require multiple drug combinations.

Research

JoVE Journal

Genetics

In Vitro Transcription Assays and Their Application in Drug Discovery

In Vitro Transcription Assays and Their Application in Drug Discovery

In vitro transcription assays have been developed and widely used for many years to study the molecular mechanisms involved in transcription. This process ...

Perturbations of Circulating miRNAs in Irritable Bowel Syndrome Detected Using a Multiplexed High-throughput Gene Expression Platform

The gene expression platform assay allows for robust and highly reproducible quantification of the expression of up to 800 transcripts (mRNA or miRNAs) in ...

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

The processing of most eukaryotic RNAs is mediated by RNA Binding Proteins (RBPs) with modular configurations, including an RNA recognition module, which ...

Rearing and Double-stranded RNA-mediated Gene Knockdown in the Hide Beetle, Dermestes maculatus

Rearing and Double-stranded RNA-mediated Gene Knockdown in the Hide Beetle, Dermestes maculatus

Advances in genomics have raised the possibility of probing biodiversity at an unprecedented scale. However, sequence alone will not be informative ...

Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples

Chromatin Immunoprecipitation ChIP Protocol for Low-abundance Embryonic Samples

Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, ...

Microinjection of CRISPR/Cas9 Protein into Channel Catfish, Ictalurus punctatus, Embryos for Gene Editing

Microinjection of CRISPR/Cas9 Protein into Channel Catfish, Ictalurus punctatus, Embryos for Gene Editing

The complete genome of the channel catfish, Ictalurus punctatus, has been sequenced, leading to greater opportunities for studying channel catfish gene ...

Production and Purification of Baculovirus for Gene Therapy Application

Baculovirus has traditionally been used for the production of recombinant protein and vaccine. However, more recently, baculovirus is emerging as a ...

Highly Efficient Gene Disruption of Murine and Human Hematopoietic Progenitor Cells by CRISPR/Cas9

Advances in the hematopoietic stem cell (HSCs) field have been aided by methods to genetically engineer primary progenitor cells as well as animal models. ...

Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs

MicroRNAs (miRNAs) are a class of small noncoding RNAs that post-transcriptionally regulate cellular gene expression. MiRNAs bind to the 3&#39; ...

Isolation, Characterization and MicroRNA-based Genetic Modification of Human Dental Follicle Stem Cells

To date, several stem cell types at different developmental stages are in the focus for the treatment of degenerative diseases. Yet, certain aspects, such ...