Name: a stainless protocol for high quality rna isolation from laser capture microdissected purkinje cells in the human post-mortem cerebellum
Uploaded: 2019-01-17T14:45:00
Description: Watch this Scientific Journal Video about A Stainless Protocol for High Quality RNA Isolation from Laser Capture Microdissected Purkinje Cells in the Human Post-Mortem Cerebellum at JoVE.com

The authors would like to acknowledge The New York Brain Bank, Dr. Jean Paul Vonsattel and Dr. Etty Cort&#233;s, for their assistance in cutting and preserving the frozen human brain tissue samples for these experiments. The authors would like to acknowledge the individuals who generously donated their brain for the continuing research into Essential Tremor. Dr. Faust and Dr. Martuscello would like to acknowledge Columbia University Department of Pathology and Cell Biology for their continued support and core research space. The authors would like to acknowledge NIH R01 NS088257 Louis/Faust) for research funding for this project. LCM images were performed in the Confocal and Specialized Microscopy Shared Resource of the Herbert Irving Comprehensive Cancer Center at Columbia University, supported by NIH grant #P30 CA013696 (National Cancer Institute). The authors would like to acknowledge Theresa Swayne and Laura Munteanu for their continued assistance with specialized microscopy.

All human samples utilized in this protocol have been obtained with informed consent and have been approved by the Internal Review Board (IRB) at Columbia University and Yale University.
NOTE: The entirety of this protocol should follow strict RNA handling guidelines, whereby a gloved hand is always used, all surfaces are cleaned with an RNase decontaminator and all working materials are RNA/DNA/Nuclease free.
1. Test RNA Integrity of Tissue prior to ...

<ol>
	<li>Liu, 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=Laser+capture+microdissection+for+the+investigative+pathologist.">Laser capture microdissection for the investigative pathologist.</a> Veterinary Pathology. 51 (1), 257-269 (2014).</li><li>Datta, 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=Laser+capture+microdissection:+Big+data+from+small+samples.">Laser capture microdissection: Big data from small samples.</a> Histology and Histopathology. 30 (11), 1255-1269 (2015).</li><li>Romero, I. G., Pai, A. A., Tung, J., Gilad, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA-seq:+impact+of+RNA+degradation+on+transcript+quantification.">RNA-seq: impact of RNA degradation on transcript quantification.</a> BMC Biology. 12 (42), 1-13 (2014).</li><li>Bevilacqua, C., Ducos, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laser+microdissection:+A+powerful+tool+for+genomics+at+cell+level.">Laser microdissection: A powerful tool for genomics at cell level.</a> Molecular Aspects Medicine. 59, 5-27 (2018).</li><li>Sidova, M., Tomankova, S., Abaffy, P., Kubista, M., Sindelka, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+post-mortem+and+physical+degradation+on+RNA+integrity+and+quality.">Effects of post-mortem and physical degradation on RNA integrity and quality.</a> Biomolecular Detection and Quantification. 5, 3-9 (2015).</li><li>Wang, 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=Histological+staining+methods+preparatory+to+laser+capture+microdissection+significantly+affect+the+integrity+of+the+cellular+RNA.">Histological staining methods preparatory to laser capture microdissection significantly affect the integrity of the cellular RNA.</a> BMC Genomics. 7, 97 (2006).</li><li>Mahalingam, M., Murray, G. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Laser Capture Microdissection: Methods and Protocols. , (2018).</li><li>Vandewoestyne, M., 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=Laser+capture+microdissection:+should+an+ultraviolet+or+infrared+laser+be+used.">Laser capture microdissection: should an ultraviolet or infrared laser be used.</a> Analytical Biochemistry. 439 (2), 88-98 (2013).</li><li>Graeme, M. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Laser Capture Microdissection. Third edn. , (2018).</li><li>Louis, E. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Re-thinking+the+biology+of+essential+tremor:+From+models+to+morphology.">Re-thinking the biology of essential tremor: From models to morphology.</a> Parkinsonism &amp; Related Disorders. 20, 88-93 (2014).</li><li>Choe, M., 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=Purkinje+cell+loss+in+essential+tremor:+Random+sampling+quantification+and+nearest+neighbor+analysis.">Purkinje cell loss in essential tremor: Random sampling quantification and nearest neighbor analysis.</a> Movement Disorders. 31 (3), 393-401 (2016).</li><li>Louis, E. D., 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=Neuropathological+changes+in+essential+tremor:+33+cases+compared+with+21+controls.">Neuropathological changes in essential tremor: 33 cases compared with 21 controls.</a> Brain. , 3297-3307 (2007).</li><li>Louis, E. D., 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=Neuropathologic+findings+in+essential+tremor.">Neuropathologic findings in essential tremor.</a> Neurology. 13 (66), 1756-1759 (2006).</li><li>Schroeder, 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=The+RIN:+an+RNA+integrity+number+for+assigning+integrity+values+to+RNA+measurements.">The RIN: an RNA integrity number for assigning integrity values to RNA measurements.</a> BMC Molecular Biology. 7, 3 (2006).</li><li>Jensen, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laser+Capture+Microdissection.">Laser Capture Microdissection.</a> The Anatomical Record. (296), 1683-1687 (2013).</li><li>Waller, 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=Isolation+of+enriched+glial+populations+from+post-mortem+human+CNS+material+by+immuno-laser+capture+microdissection.">Isolation of enriched glial populations from post-mortem human CNS material by immuno-laser capture microdissection.</a> Journal of Neuroscience Methods. 208 (2), 108-113 (2012).</li><li>Lee, 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=Laser-capture+microdissection+and+transcriptional+profiling+of+the+dorsomedial+nucleus+of+the+hypothalamus.">Laser-capture microdissection and transcriptional profiling of the dorsomedial nucleus of the hypothalamus.</a> Journal of Comparative Neurology. 520 (16), 3617-3632 (2012).</li><li>Cummings, M., 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+robust+RNA+integrity-preserving+staining+protocol+for+laser+capture+microdissection+of+endometrial+cancer+tissue.">A robust RNA integrity-preserving staining protocol for laser capture microdissection of endometrial cancer tissue.</a> Analytical Biochemistry. 416 (1), 123-125 (2011).</li><li>Sonne, S. B., 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=Optimizing+staining+protocols+for+laser+microdissection+of+specific+cell+types+from+the+testis+including+carcinoma+in+situ.">Optimizing staining protocols for laser microdissection of specific cell types from the testis including carcinoma in situ.</a> PLoS One. 4 (5), 5536 (2009).</li><li>Butler, A. 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=Recovery+of+high-quality+RNA+from+laser+capture+microdissected+human+and+rodent+pancreas.">Recovery of high-quality RNA from laser capture microdissected human and rodent pancreas.</a> Journal of Histotechnology. 39 (2), 59-65 (2016).</li><li>Schuierer, 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=A+comprehensive+assessment+of+RNA-seq+protocols+for+degraded+and+low-quantity+samples.">A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples.</a> BMC Genomics. 18 (1), 442 (2017).</li><li>Kumar, 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=Age-associated+changes+in+gene+expression+in+human+brain+and+isolated+neurons.">Age-associated changes in gene expression in human brain and isolated neurons.</a> Neurobiology of Aging. 34 (4), 1199-1209 (2013).</li><li>Sampaio-Silva, F., Magalhaes, T., Carvalho, F., Dinis-Oliveira, R. J., Silvestre, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Profiling+of+RNA+degradation+for+estimation+of+post+mortem+[corrected]+interval.">Profiling of RNA degradation for estimation of post mortem [corrected] interval.</a> PLoS One. 8 (2), 56507 (2013).</li><li>Walker, D. G., 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=Characterization+of+RNA+isolated+from+eighteen+different+human+tissues:+results+from+a+rapid+human+autopsy+program.">Characterization of RNA isolated from eighteen different human tissues: results from a rapid human autopsy program.</a> Cell Tissue Bank. 17 (3), 361-375 (2016).</li><li>Birdsill, A. C., Walker, D. G., Lue, L., Sue, L. I., Beach, T. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Postmortem+interval+effect+on+RNA+and+gene+expression+in+human+brain+tissue.">Postmortem interval effect on RNA and gene expression in human brain tissue.</a> Cell Tissue Bank. 12 (4), 311-318 (2011).</li><li>Adiconis, X., 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=Comparative+analysis+of+RNA+sequencing+methods+for+degraded+or+low-input+samples.">Comparative analysis of RNA sequencing methods for degraded or low-input samples.</a> Nature Methods. 10 (7), 623-629 (2013).</li><li>Parekh, S., Ziegenhain, C., Vieth, B., Enard, W., Hellmann, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+impact+of+amplification+on+differential+expression+analyses+by+RNA-seq.">The impact of amplification on differential expression analyses by RNA-seq.</a> Scientific Reports. 6, 25533 (2016).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Carl Zeiss Microscopy. , (2012).</li></ol>

The protocol presented here is specifically modified to be a stainless approach in visualizing morphologically distinct tissues for UV-LCM. This method is designed to maximize RNA integrity for subsequent direct RNA sequencing, while maintaining an enhanced level of tissue visualization. The ability to distinguish different cell types for capture, to create the purest population of cells possible, is essential for understanding different molecular profiles in human tissues15. Within the context of...

Laser capture microdissection (LCM) is a valuable research tool that allows the separation of pathologically relevant cells for subsequent molecularly driven evaluation. The use of molecular analyses in these heterogeneous tissue specimens and the correlation with pathological and clinical data is a necessary step in evaluating the translational significance of biological research1. When analyzing gene expression data from RNA, the use of frozen tissue sections is highly recommended as it allows for excellent quality of RNA as well as maximized quantity2. It has been well established that high quality and quantity of RNA are essential for meaningful data from RNA sequencing3. However, when using RNA from fresh frozen post-mortem tissue for LCM, RNA degradation is a major challenge, as it occurs immediately upon death and its extent is mediated by various factors associated with the tissue collection method4,5. Furthermore, RNA degradation is exacerbated when staining techniques are needed to recognize histologic details and cell identification. Specialized staining techniques, such as hematoxylin &#38; eosin, Nissl stain, immunofluorescence and immunohistochemistry are helpful in differentiating cells from surrounding stroma but have been shown to degrade RNA and alter transcript expression profiles6. Therefore, our laboratory has created a stainless protocol specifically designed to preserve RNA in post-mortem human cerebellum for the purposes of RNA sequencing after LCM isolation of Purkinje neurons.
In processing fresh frozen tissue for LCM, the fixation method can variably affect both RNA and tissue integrity. Formalin fixation is standard for morphological preservation, but causes cross-linking that may fragment RNA and interfere with RNA amplification7. Ethanol fixation is a better alternative for RNA isolation, as it is a coagulative fixative that does not induce cross-linking1. To enhance the visualization of tissue morphology, xylene is the best choice, as it removes lipids from the tissue. However, there are known limitations when utilizing xylene in LCM, as the tissues can dry out and become brittle causing tissue fragmentation upon laser capture7. Xylene is also a volatile toxin and must be handled properly in a fume hood. Nevertheless, xylene has been shown to enhance tissue visualization while also preserving RNA integrity8. Therefore, our protocol centers around the use of 70% ethanol fixation and ethanol dehydration, followed by xylene incubation for morphological clarity.
It is important to note the different types of laser-based microdissection systems, as they have been shown to differ in speed, precision, and RNA quality. The infrared (IR) laser capture microdissection and the ultraviolet (UV) laser microbeam microdissection systems were both novel LCM platforms that emerged almost concurrently8. The IR-LCM system employs a &#34;contact system&#34; using a transparent thermoplastic film placed directly on the tissue section, and cells of interest selectively adhere to the film by focused pulses from an IR laser. Alternatively, the UV-LCM system is a &#34;non-contact system&#34; whereby a focused laser beam cuts away the cells or regions of interest in the tissue; depending on the configuration in two currently available commercial platforms that use either an inverted or upright microscope design, tissue is acquired into a collection device by a laser-induced pressure wave that catapults it against gravity or tissue is collected by gravity, respectively. Significant advantages of the UV-LCM system include faster cell acquisition, contamination-free collection with the non-contact approach and more precise dissection due to a much smaller laser beam diameter9. This protocol was specifically designed for a UV-LCM system and has not been tested in an IR-LCM system. In either UV-LCM system design, when accumulating cells into the collection cap, the use of a coverslip that enhances cellular clarity during microscopy is not suitable, as the cells would be unable to enter into the collection cap. Therefore, to enhance tissue visualization, we tested the use of Opaque collection caps, which are designed to act as a coverslip for microscopic visualization in UV-LCM systems, against liquid filled collection caps. Liquid filled collection caps can be challenging, as the liquid is subject to evaporation and must be replaced frequently while working at the microscope. Time becomes an important factor for RNA stability, as the captured tissue dissolves immediately7.
Our laboratory studies the postmortem neuropathologic changes in the cerebellum of patients with essential tremor (ET) and related neurodegenerative disorders of the cerebellum. We have demonstrated morphologic changes centered on Purkinje cells that distinguish ET cases versus controls, including a reduced number of Purkinje cells, increased dendritic regression and a variety of axonal changes, leading us to postulate that Purkinje cell degeneration is a core biologic feature in ET pathogenesis10,11,12,13. Transcriptional profiling has been used in many neurologic diseases to explore the underlying molecular basis of degenerative cellular changes. However, transcriptional profiles from heterogeneous samples, such as brain tissue regions, can effectually mask the expression of low abundance transcripts and/or diminish the detection of molecular changes that occur only in a small population of affected cells, such as Purkinje cells in the cerebellar cortex. For instance, Purkinje cells are vastly outnumbered by the abundant granule cells in the cerebellar cortex by approximately 1:3000; thus, to effectively target their transcriptome requires specific isolation of these neurons. The cerebellar cortex is delineated by distinct layers that differ in cell density and cell size. This cellular architecture is ideal to visualize in a fresh-frozen tissue sample without dye-containing staining reagents. In theory, this protocol could also be applied to other tissue types that have similar distinctive tissue organization.
This protocol was designed to work specifically for Purkinje cell visualization in the human post-mortem cerebellum. Numerous protocols exist for the fixation, staining visualization and RNA preservation of many types of tissues for the purposes of both IR- and UV-LCM. When contemplating an experimental design for UV-LCM, individuals should tailor their protocol to best fit the needs and requirements of starting and ending materials. Here, we combine many aspects of different LCM protocols to provide an enhanced method for visualizing Purkinje cells in the post-mortem human cerebellum without the need of dye containing staining reagents to prepare high-quality RNA for transcriptome sequencing.

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			<td height="42" style="height:42px;width:216px;">MembraneSlide NF 1.0 PEN</td>
			<td style="width:147px;">Zeiss</td>
			<td style="width:119px;">415190-9081-000</td>
			<td style="width:488px;">Membrane slides for tissue. We do not recommend using glass slides.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">AdhesiveCap 500 Opaque</td>
			<td style="width:147px;">Zeiss</td>
			<td style="width:119px;">415190-9201-000</td>
			<td style="width:488px;">Opaque caps are used to enhance visualization on inverted scopes only</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">RNase Away</td>
			<td style="width:147px;">Molecular BioProducts</td>
			<td style="width:119px;">7005-11</td>
			<td style="width:488px;">Other RNase decontamination products are also suitable. Use to clean all surfaces prior to work.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">200 Proof Ethanol</td>
			<td style="width:147px;">Decon Laboratories</td>
			<td style="width:119px;">2701</td>
			<td style="width:488px;">If using alternative Ethanol, ensure high quality. Essential for tissue fixation.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Xylenes (Certified ACS)</td>
			<td style="width:147px;">Fisher Scientific</td>
			<td style="width:119px;">X5P-1GAL</td>
			<td style="width:488px;">If using alternative xylene, ensure high quality. Essential for tissue visualization.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">UltraPure Distilled Water</td>
			<td style="width:147px;">Invitrogen</td>
			<td style="width:119px;">10977-015</td>
			<td style="width:488px;">Other RNA/DNA/Nuclease free water also suitable. Utilized in ethanol dilution only.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Slide-Fix Slide Jars</td>
			<td style="width:147px;">Evergreen</td>
			<td style="width:119px;">240-5440-G8K</td>
			<td style="width:488px;">Any slide holder/jar is also suitable. Must be cleaned prior to use. Used for fixation following sectioning.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Anti-Roll Plate, Assy. 70mm 100um</td>
			<td style="width:147px;">Leica Biosystems</td>
			<td style="width:119px;">14041933980</td>
			<td style="width:488px;">Anti-roll plate type is determined by type of cryostat and attachment location on stage. All cryostats have differing requirements.&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Diethyl pyrocarbonate (DEPC)</td>
			<td style="width:147px;">Sigma Aldrich</td>
			<td style="width:119px;">D5758-50mL</td>
			<td style="width:488px;">DEPC from any vendor will do. Follow directions for water treatment.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Kimwipes</td>
			<td style="width:147px;">Fisher Scientific</td>
			<td style="width:119px;">06-666A</td>
			<td style="width:488px;">Kimwipes can be ordered from any vendor and used at any size. Kimwipes are to be used to clean microscope and cryostat.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Tissue-Plus O.C.T. Compound</td>
			<td style="width:147px;">Fisher Scientific</td>
			<td style="width:119px;">23-730-571</td>
			<td style="width:488px;">Any brand of OCT is acceptable. No tissue will be embedded in the OCT, it is strickly to attach tissue to &#39;chuck&#39;.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Edge-Rite Low-Profile Microtome Blades</td>
			<td style="width:147px;">Thermo Scientific</td>
			<td style="width:119px;">4280L</td>
			<td style="width:488px;">Blade type is determined by type of cryostat. All cryostats have differing requirements.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Leica Microsystems 3P&#160;25 + 30MM CRYOSTAT CHUCKS</td>
			<td style="width:147px;">Fisher Scientific</td>
			<td style="width:119px;">NC0558768</td>
			<td style="width:488px;">Chuck type is determined by type of cryostat. All cryostats have different requirements. Either size is suitable.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">RNeasy Micro Kit (50)</td>
			<td style="width:147px;">Qiagen</td>
			<td style="width:119px;">74004</td>
			<td style="width:488px;">Required for RNA extraction post LCM. RLT Lysis buffer essential to gather captured cells from opaque cap.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">RNeasy Mini Kit (50)</td>
			<td style="width:147px;">Qiagen</td>
			<td style="width:119px;">74104</td>
			<td style="width:488px;">Required for RNA extraction of section preps, which are performed prior to LCM to test RNA integrity of starting tissues.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">RNase-Free DNase Set</td>
			<td style="width:147px;">Qiagen</td>
			<td style="width:119px;">79254</td>
			<td style="width:488px;">Dnase will remove any DNA to allow for a pure RNA population. Ensure Dnase is made fresh.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">2-Mercaptoethanol</td>
			<td style="width:147px;">Sigma Aldrich</td>
			<td style="width:119px;">M6250-100ML</td>
			<td style="width:488px;">Purchased volume at user discretion. Necessary for addition to RLT buffer for cell lysis. Prevents RNase activity.&#160;</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Globe Scientific&#160;Lot Certified Graduated Microcentrifuge Tube (2 mL)</td>
			<td style="width:147px;">Fisher Scientific</td>
			<td style="width:119px;">22-010-092</td>
			<td style="width:488px;">Any 2 mL tube that is RNase free, DNase free, human DNA free, and Pyrogen free will do.&#160;</td>
		</tr>
	</tbody>
</table>

a stainless protocol for high quality rna isolation from laser capture microdissected purkinje cells in the human post-mortem cerebellum

Laser capture microdissection (LCM) is an advantageous tool that allows for the collection of cytologically and/or phenotypically relevant cells or regions from heterogenous tissues. Captured product can be used in a variety of molecular methods for protein, DNA or RNA isolation. However, preservation of RNA from postmortem human brain tissue is especially challenging. Standard visualization techniques for LCM require histologic or immunohistochemical staining procedures that can further degrade RNA. Therefore, we designed a stainless protocol for visualization in LCM with the intended purpose of preserving RNA integrity in post-mortem human brain tissue. The Purkinje cell of the cerebellum is a good candidate for stainless visualization, due to its size and characteristic location. The cerebellar cortex has distinct layers that differ in cell density, making them a good archetype to identify under high magnification microscopy. Purkinje cells are large neurons situated between the granule cell layer, which is a densely cellular network of small neurons, and the molecular layer, which is sparse in cell bodies. Because of this architecture, the use of stainless visualization is feasible. Other organ or cell systems that mimic this phenotype would also be suitable. The stainless protocol is designed to fix fresh-frozen tissue with ethanol and remove lipids with xylene for improved morphological visualization under high magnification light microscopy. This protocol does not account for other fixation methods and is specifically designed for fresh-frozen tissue samples captured using an ultraviolet (UV)-LCM system. Here, we present a full protocol for sectioning and fixing fresh frozen post-mortem human cerebellar tissue and purification of RNA from Purkinje cells isolated by UV-LCM, while preserving RNA quality for subsequent RNA-sequencing. In our hands, this protocol produces exceptional levels of cellular visualization without the need for staining reagents and yields RNA with high RNA integrity numbers (&#8805;8) as needed for transcriptional profiling experiments.

This protocol details the steps for preparing fresh frozen post-mortem human brain tissue for UV-LCM. Thorough specifications and annotations are given for cryostat cutting, as it can be difficult to cut fresh frozen brain tissue with a high degree of precision. The most important point to consider is that fresh frozen tissue is extremely cold and requires a significant amount of time to acclimate to the warmer temperature of a cryostat. This step cannot be rushed, and it cannot be overst...

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A Stainless Protocol for High Quality RNA Isolation from Laser Capture Microdissected Purkinje Cells in the Human Post-Mortem Cerebellum

This protocol uses a stain-free approach to visualize and isolate Purkinje cells in fresh-frozen tissue from human post-mortem cerebellum via laser capture microdissection. The purpose of this protocol is to generate sufficient amounts of high-quality RNA for RNA-sequencing.

Laser capture microdissection (LCM) is an advantageous tool that allows for the collection of cytologically and/or phenotypically relevant cells or ...

This protocol is significant, because it utilizes a stain-free visualization method instead of dye-based visualization on post-mortem human brain tissue, which helps preserve RNA integrity. The preservation of RNA is a big advantage in this protocol, as it is useful, not only in post-mortem human brain tissue, but also other tissue types, with high RNase activity. To begin, remove the tissue from the freezer and place it on dry ice for transport to the cryostat.Place the clean brushes, the chuck, and the tissue into the cryostat for at least 20 minutes, to allow them to reach the optimal temperature. For cryostats with dual chambers and specimen-holding temperatures, set the object temperature to minus 16 degrees Celsius and the chamber temperature to minus 18 degrees Celsius. Set the cryostat's section thickness to 14 micrometers and the trim thickness to 30 micrometers.Next, clean the stage with a one-to-one mixture of RNase decontaminator and 70%ethanol, to prevent freezing. Obtain a new, disposable cryostat blade and clean it with RNase decontaminator. Place the cleaned blade in the blade holder on the stage.Then, clean the anti-roll plate with the RNase decontaminator. Attach the cleaned plate to the stage and wait at least 20 minutes for the blade and anti-roll plate to come down to the temperature of the cryostat. First, cut a small piece of tissue for sectioning, making sure that the section is approximately 95%cerebellar cortex.Return the remaining tissue either to dry ice, or a to a freezer, at minus 80 degrees Celsius. Next, begin slowly adding OCT on top of the chuck with a slow, circular motion. Build up layers of OTC until there is a mount approximately three millimeters high covering the chuck.When the OCT is partially frozen, but still has some liquid in the center, place the tissues on top of the mount. Let the tissue sit on top of the OCT for one to two minutes until it is completely frozen. Then, transfer the chuck with the frozen OCT and tissue into the cryostat cutting arm.Adjust the tissue so that it is flush with the cutting blade and let the tissue sit in the cutting arm for 20 minutes to adjust to the new temperature. The most critical step is allowing the tissue to acclimate in the cryostat cutting arm for as long as necessary. If tissue shreds, purkinje cell visualization will be very difficult.I recommend using smaller, thinner pieces of tissue, to allow the tissue to acclimate faster. After this, slowly move the tissue closer to the blade. Once the tissue has reached the blade, begin the trimming process.Trim the tissue two to three times, until the cortex layers are visible. Next, place and align the anti-roll plate just above the cryostat blade. Cut four to six sections that are 14 micrometers thick, noting that properly cut sections will be flat under the anti-roll plate.Align the cut sections horizontally across the cryostat stage. Angle a slide to pick up all of the tissue pieces simultaneously. Immediately after sectioning the tissue, place the slide in the slide holder with 70%ethanol on ice for two minutes.Transfer the slide to a slide holder with 95%ethanol on ice for 45 seconds. Next, place the slide in the slide holder with 100%ethanol at room temperature for two minutes. Dip the slide three times into the slide holder containing xylene number one at room temperature.Then, place the slide in the slide holder with xylene two at room temperature for five minutes. Stand the slides up in a clean fume hood and let them air dry for at least 30 minutes. If storing the slides, place each one into a separate 50 milliliter tube and place the tubes into a freezer at minus 80 degrees Celsius for up to seven days.First, use RNase decontaminator to clean the microscope stage and the cap collection arm. With gloved hands, place the slide on the microscope and a 500 microliter opaque cap in the collection arm. At a low magnification, align the opaque cap over the cerebellar tissue, insuring that the cap covers the entire area that is visualized in the eye piece.Use a five times to 10 times objective to visualize the cerebellar layers. Place the cursor over the section where molecular layer and granual cell layer intersect. Move to a 40 times magnification and visualize the purkinje cells.Then, begin capturing them. To begin RNA collection after the microdissection, add 50 microliters of cell lysis buffer to the opaque cap with the cap facing up. Carefully close the tube over the cap and proceed with the collection as outlined in the text protocol.In this protocol, fresh, frozen, post-mortem, human brain tissue is prepared for UV laser capture microdissection. Following cryostat's sectioning in the allotted drawing time, the cellular layers of the cerebellum are easily visible with five times and 10 times objective lenses. As seen here, proper xylene incubation causes the tissue to become darker and better delineates cellular layers than does ethanol alone.When cutting at the laser capture microscope, the 40 times objective lens is required to ensure capturing only purkinje cells and not the surrounding tissue. As seen here, proper incubation in xylene produces a high quality morphologically intact image when compared to ethanol fixation alone. The cover slip ability of an opaque cap is then tested while other protocols utilize a liquid-filled cap, these caps can reduce tissue visualization and cause the resulting image to be granular and iridescent under the microscope.However, visualization through an opaque cap results in the smoothened tissue appearance that is softer and sharper in form. Representative images of excised purkinje cells at low power and at high power show precise removal of just the purkinje cell body. After this, high quality Rnase is obtained for subsequent RNA sequencing.Six representative samples underwent RNA extraction and were resuspended in 14 microliters of Rnase-free water and all six samples produced high quality RNA with RNA integrity numbers equal to or greater than eight. The most important thing to remember is that tissue quality is everything. Even cutting and slide placement will make or break this protocol.Following this procedure, any method that investigates RNA or DNA could be performed, specifically we probe our RNA for differential gene expression, but other questions regarding gene regulation could also be investigated. This method could be applied to any tissue type that has specific delineated morphology that does not require the use of antigen or dye-specific reagents for identification of cells of interest. We hope that this technique will help us understand the genetics of essential tremor and other diseases that have a tremor phenotype.The most hazardous chemical used in this protocol is xylene. It should be handled properly in a fume hood, disposed of properly, and slides should be allowed to dry adequately until used in an open space. Additionally, when working with human samples, biohazardous waste management, and safety should be utilized.

Research

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