Name: Isolation of High-density Lipoproteins for Non-coding Small RNA Quantification (Video) | JoVE Journal
Uploaded: 2016-11-28T12:30:00.000+00:00
Duration: 10 min 39 s
Description: Learn to isolate high-density lipoproteins for small non-coding RNA quantification using density-gradient ultracentrifugation. This method enables analysis of lipoprotein RNA signatures as potential disease biomarkers.

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5 minutes

This work was supported by awards from the National Institutes of Health, National Heart, Lung and Blood Institute to K.C.V. HL128996, HL113039, and HL116263. This work was also supported by awards from the American Heart Association to K.C.V. CSA2066001, D.L.M POST26630003, and R.M.A. POST25710170.

1. HDL Purification (~ 5.5 days)
<ol>
	<li>Density-Gradient Ultracentrifugation (DGUC, ~ 5 days)
	<ol>
		<li>Add 90 &#956;L&#160;of 100x anti-oxidants to 9 mL&#160;of plasma isolated from fresh venous blood.</li>
		<li>Adjust plasma density with KBr from 1.006 g/mL to 1.025 g/mL by adding 0.251 g KBr to 9 mL of plasma from Step 1.1.1 (0.0278 g/mL KBr plasma). Rock the plasma until all the salt is dissolved at room temperature and transfer to ultracentrifuge tubes and ensure all bubbles rise to the top.</li>
		<li>Bend the tip of an 18-G needle to 90&#176; 1 cm from the tip, bevel side facing up. Using a syringe and the 18-gauge needle, carefully place 3 mL of overlay solution #1 over the plasma (Table 1). 
		NOTE: The bent needle ensures all the VLDL/IDL, LDL, and HDL are removed without mixing with the overlay.</li>
		<li>Remove the majority of the bubbles at the top, leaving 2 - 3 mm space from meniscus to the top of the tube and carefully place the tubes in SW-40Ti buckets.</li>
		<li>Weigh each bucket (with the caps) on the balance, and exactly balance with the opposite bucket (bucket + cap): #1 to #4, #2 to #5, and #3 to #6. 
		NOTE: These buckets must be balanced and matched at all times.</li>
		<li>Place rotor in ultracentrifuge (List of Materials). Centrifuge at 274,400 x g for 24 h at 4 &#176;C with a #4 intermediate brake.</li>
		<li>Carefully remove buckets from rotor and the tubes from buckets.</li>
		<li>Carefully remove 2 mL from the top layer of the overlay using a syringe and bent needle. This will be the VLDL/IDL fraction which can be stored at 4 &#176;C or -80 &#176;C.</li>
		<li>After removing the VLDL/IDL fraction, collect the remaining 7 mL of sample (plasma) and place it into a 15 mL conical tube. Bring the volume of the sample up to 9 mL with overlay solution #2 (Table 1).</li>
		<li>Adjust the sample density from 1.025 g/mL to 1.080 g/mL with KBr using approximately 0.746 g KBr in the 9 mL sample or 0.0828 g/mL KBr of sample. Gently rock the sample until all the KBr is dissolved (approximately 20 min) and transfer to ultracentrifuge tube while ensuring bubbles rise to the top.</li>
		<li>With syringe and needle, carefully place 3 mL of overlay solution #3 over the sample (Table 1). Leave 2 - 3 mm space from meniscus to the top of the tube.</li>
		<li>Remove the majority of any remaining bubbles at the top of the tube and carefully place the filled ultracentrifuge tubes in SW-40Ti buckets.</li>
		<li>Weigh each bucket (with the caps) on the balance, and exactly balance with the opposite bucket + cap, as in 1.1.5.</li>
		<li>Place rotor in ultracentrifuge (see List of Materials). Centrifuge at 274,400 x g for 24 h at 4 &#176;C with a #4 intermediate brake.</li>
		<li>Carefully remove buckets from rotor and the tubes from buckets.</li>
		<li>Carefully remove 2 mL from the top layer of the overlay using a syringe and bent needle. This will be the LDL fraction which can be stored at 4 &#176;C or -80 &#176;C.</li>
		<li>After removing the LDL fraction, collect the remaining approximate 7 mL of sample (plasma) and place it into a new 15 mL conical tube. Bring the volume of the sample (plasma) up to 9 mL with 1.080 g/mL solution #4 (Table 1).</li>
		<li>Adjust the sample density from 1.080 g/mL to 1.30 g/mL with KBr using 3.33 g KBr in the 9 mL sample (plasma) or 0.37 g KBr for each mL of sample. Rock or slightly agitate the sample until all the KBr (salt) is dissolved and transfer to ultracentrifuge tube.</li>
		<li>With syringe and needle, carefully place 3 mL of overlay solution #5 over the sample (Table 1).</li>
		<li>Remove the majority of any remaining bubbles at the top of the tube, leaving 2- 3 mm space from meniscus to the top of the tube and carefully place the filled ultracentrifuge tubes in SW-40Ti buckets.</li>
		<li>Weigh each bucket (with the caps) on the balance, and exactly balance with the opposite bucket + cap, as in 1.1.5.</li>
		<li>Place rotor in ultracentrifuge (see List of Materials). Centrifuge at 274,400 x g for 48 h at 4 &#176;C with a #4 brake.</li>
		<li>Carefully remove buckets from rotor and the tubes from buckets.</li>
		<li>Carefully remove approximately 2 mL from the top layer of the overlay using a syringe and bent needle. This is the HDL fraction, which can be stored at 4 &#176;C or -80 &#176;C. 
		NOTE: Following DGUC HDL may be dialyzed to remove the high-salt solutions.</li>
		<li>To dialyze, place the collected HDL fraction in a sealed dialysis sleeve (10,000 m.w. cut-off) and dialyze overnight in 1 L 1x PBS. Change dialysis buffer (1x PBS) 3 times over 24 h. Gentle perturbation of the PBS with a magnetic stir-bar will improve dialysis.</li>
		<li>Determine the protein concentration of the DGUC-HDL using a BCA method8.</li>
	</ol>
	</li>
	<li>Fast-Protein Liquid Chromatography (FPLC) or Size-Exclusion Chromatography (~ 6 h)
	<ol>
		<li>Filter 1.2 mg of DGUC-HDL (total protein) in 500 &#181;L through a 0.22 &#181;m micro-centrifugal filter (see List of Materials), immediately prior to injection. 
		NOTE: An additional filtering of the DGUC-HDL sample through a 0.45 &#181;m micro-centrifugal filter prior to the 0.22 &#181;m filter may be required for some samples.</li>
		<li>Collect the filtered DGUC-HDL sample, load the FPLC (fill) injection syringe, and ensure there are no bubbles in the syringe before injecting into the FPLC.</li>
		<li>Set the FPLC flow rate to 0.3 mL/min with a pressure limit at 2.6 MPa. Equilibrate columns with 0.2 column volumes (approximately 15 mL) of buffer, prior to sample injection. Inject the sample with 3 mL of buffer into the FPLC (injection loop) instrument and start the run. Collect 1.5 mL fractions for a total of 72 fractions.</li>
	</ol>
	</li>
</ol>
2. High-throughput Small RNA Sequencing (sRNAseq, ~ 9 days)
<ol>
	<li>RNA Isolation (~ 1 day)
	<ol>
		<li>Identify the FPLC fractions corresponding to DGUC-HDL by determining total cholesterol levels using a colorimetric kit according to the manufacturer&#39;s instructions. Using this FPLC set-up, expect to find 6 - 7 FPLC fractions containing DGUC-HDL.</li>
		<li>Collect all the volume (approximately 8 -1 0 mL pool of 1.45 mL fraction volumes) from DGUC-HDL FPLC fractions and concentrate using 10 kDa m.w. cut-off centrifugal filter units at 4,000 x g for 1 h at 4 &#176;C or until HDL concentrate is approximately 100 &#181;L.</li>
		<li>Collect the HDL concentrate and quantify HDL total protein concentration using the BCA method8.</li>
		<li>Determine the highest concentration of HDL total protein, up to 1 mg, that can be aliquoted from each sample in the set. For example, isolate RNA from the same amount of HDL total protein for each sample.</li>
		<li>Perform RNA Isolation using a modified protocol (see List of Materials).
		<ol>
			<li>Add 10x volume of phenol lysis reagent (see List of Materials) sample and vortex for 1 min.</li>
			<li>Incubate at room temperature for 5 min.</li>
			<li>Add chloroform (20% of phenol lysis reagent volume used in step 2.1.5.1) and shake vigorously for 15 s.</li>
			<li>Incubate at room temperature for 2 - 3 min.</li>
			<li>Centrifuge for 15 min at 12,000 x g at 4 &#176;C in a refrigerated centrifuge.</li>
			<li>Transfer the upper aqueous phase to a new tube, avoiding the interphase.</li>
			<li>Add 1.5x volume of 100% ethanol to the aqueous phase and vortex for 1 min.</li>
			<li>Store samples for at least 1 h or overnight at -80 &#176;C.</li>
			<li>Continue with the RNA isolation protocol using the provided mini columns.</li>
			<li>Elute with 30 &#181;L of RNase-free H2O. First add 15 &#181;L of H2O directly to the frit, spin at low speed (2,000 x g) for 2 min, and then spin at high speed (max) for 1 min. Repeat this step with an additional 15 &#181;L of H2O.</li>
		</ol>
		</li>
		<li>Immediately proceed to sRNA library generation or store at -80 &#176;C.</li>
	</ol>
	</li>
	<li>Library Generation (~ 6 h)
	<ol>
		<li>Prepare sRNA cDNA libraries using the sRNA library generation kit protocol, as per manufacturer&#39;s instructions with one modification to the PCR amplification as detailed below.
		<ol>
			<li>Prepare the PCR mastermix on ice containing 0.5 &#181;L DNase/RNase-free H2O, 15 &#181;L PCR Mix (PML) and 1 &#181;L RNA PCR Primer (RP1) per sample (include an additional 10% for pipetting error).</li>
			<li>Add 16.5 &#181;L of the PCR mix to each (cDNA) sample.</li>
			<li>Assign an index/barcode number to each sample for multiplexing and add 1 &#181;L PCR Primer Index (to the corresponding number) to the sample.</li>
			<li>Perform a quick spin using the microfuge. 
			NOTE: Total volume should now be 30 &#181;L per sample.</li>
			<li>Perform the cycling conditions for PCR amplification as detailed in Tables 2 and 3.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Size Select sRNA Library to Remove Adapter:Adapters (~ 1.5 h)
	<ol>
		<li>Perform library size-selection using automatic DNA size selector as per manufacturer&#39;s instructions with the following size parameters: Target: 156 bp, Start: 135 bp, End: 177 bp, Range Flag: Broad.</li>
	</ol>
	</li>
	<li>DNA Clean Up (~0.5 h)
	<ol>
		<li>Clean up size-selected sRNA cDNA according to the manufacturer&#39;s instructions.</li>
		<li>Elute clean and concentrated sRNA cDNA with 2 x 7 &#181;L DNase/RNase-free H2O.</li>
	</ol>
	</li>
	<li>Quantify and Assess sRNA cDNA Library Yield and Quality (~ 1 h)
	<ol>
		<li>Assess sRNA cDNA library quality and size using a high-sensitivity DNA chip on a bioanalyzer (List of Materials) as per manufacturer&#39;s instructions.</li>
		<li>Quantify the individual sRNA cDNA library concentrations using a high-sensitivity DNA assay (List of Materials), as per manufacturer&#39;s instructions. 
		NOTE: It is recommended to have all samples with different indices be run on the same lane of the flow cell if possible. If more than one lane is required, mix case and control samples appropriately.</li>
	</ol>
	</li>
	<li>High-throughput sRNA Sequencing (~ 7 days)
	<ol>
		<li>Pool individual indexed sRNA libraries based on equimolar concentrations.</li>
		<li>Screen pooled sRNA libraries for quality using high-sensitivity DNA chip on the bioanalyzer and determine library DNA concentration as in 2.5.1 - 2.5.2.</li>
		<li>Perform quantitative PCR (qPCR) of adapter content to ensure appropriate sequencing depth using the sequencing library qPCR quantification kit as per manufacturer&#39;s instructions (List of Materials).</li>
		<li>Perform sequencing using a single read, 50 bp protocol to reach a depth of approximately 20 - 25 M reads/sample, as per manufacturer&#39;s instructions.</li>
	</ol>
	</li>
</ol>
3. Data Analysis (~ 1 day)
<ol>
	<li>Use bcl2fastq2, as per user guide instructions, to preprocess raw fastq files of demultiplexed samples (List of Materials).</li>
	<li>Use Cutadapt to trim adapters9 and remove reads &#60; 16 nucleotides (nts) in length, as per user guide instructions (List of Materials).</li>
	<li>Remove contamination sequences present in the sRNA libraries, including stop solution sequence (STP: CCACGTTCCCGTGG) and adapter carry-over (CTACAGTCCGACGATC) using removeSequenceInFastq function in NGSPERL framework, as per user guide instructions (List of Materials).</li>
	<li>Perform quality control metrics by FastQC using Center for Quantitative Sciences (CQS) tools, as per user guide instructions (List of Materials).</li>
	<li>Generate non-redundant list of &#34;identical&#34; reads (collapse redundant reads) and record copy numbers using CQSTools, as per user guide instructions (List of Materials).</li>
	<li>Align reads to human genome using Bowtie1.1.2 allowing 1 mismatch (options: -a -m 100 --best --strata -v 1), as per user guide instructions (List of Materials).</li>
	<li>Perform read alignment, counting, and result summarization tasks using NGSPERL, as per user guide instructions.</li>
	<li>Convert exported count table to a spreadsheet file.</li>
	<li>Normalize reads of a specific class (e.g., miRNAs) to total number of reads for that class (e.g., total number of miRNAs reads) and report signals as Reads Per Mapped miRNA (RPMM). (e.g., RPMM =(miR-X/Total # of miRNA reads)*1,000,000).</li>
	<li>Input normalized count table as generic single color technology into software for low-level and high-level differential analyses as per user guide instructions (List of Materials). 
	NOTE: Currently, there are no well-characterized housekeeping genes/sRNAs for HDL-sRNA. A spike-in control may be used, but can be problematic. Normalizing to HDL total protein input or volume is advised. Most importantly, it is recommended to validate sequencing results by one of the various strategies to quantify miRNAs and sRNAs using real-time PCR or quantitative PCR.</li>
</ol>

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<li>Laurent, L. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Meeting+report%3A+discussions+and+preliminary+findings+on+extracellular+RNA+measurement+methods+from+laboratories+in+the+NIH+Extracellular+RNA+Communication+Consortium%5BTitle%5D)+AND+%22J+Extracell+Vesicles%22%5BJournal%5D)">Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium.</a> J Extracell Vesicles. 4, 26533(2015).</li>
</ol>

The authors have nothing to disclose.

This protocol is designed to quantify miRNAs and other sRNAs by high-throughput sequencing or real-time PCR on highly pure HDL. As with any approach, special considerations should be given to each step in the process of purifying HDL and RNA and then quantifying sRNAs. This protocol is designed for projects starting with &#8805; 2 mL of plasma. Nevertheless, high quality RNA analyses can successfully be completed with HDL purified from as little as 80 &#181;L of human or mouse plasma using affinity chromatography; howeve...

Extracellular non-coding small RNAs (sRNAs) represent a new class of disease biomarkers and potential therapeutic targets and likely facilitate cell-to-cell communication1. The most widely studied type of sRNA are microRNAs (miRNA) which are approximately 22 nts in length and are processed from longer precursor forms and primary transcripts2. miRNAs have been demonstrated to post-transcriptionally regulate gene expression through suppression of protein translation and induction of mRNA degradation2. Nevertheless, miRNAs are just one of many types of sRNAs; as sRNAs can be cleaved from parent tRNAs (tRNA-derived sRNAs, tDR), small nuclear RNAs (sRNA-derived sRNAs, sndRNA), small nucleolar RNAs (snoRNA-derived sRNAs, snRNA), ribosomal RNAs (rRNA-derived sRNAs, rDR), Y RNAs (yDR), and other miscellaneous RNAs1. A few examples of these novel sRNAs have been reported to function similar to miRNAs; however, the biological functions of many of these sRNAs remains to be determined, although roles in gene regulation are likely3-6. Most interestingly, miRNAs and other sRNAs are stably present in extracellular fluids, including saliva, plasma, urine, and bile. Extracellular sRNAs are likely protected from RNases through their association with extracellular vesicles (EV), lipoproteins, and/or extracellular ribonucleoprotein complexes.
Previously, we reported that lipoproteins, namely high-density lipoproteins (HDL), transport miRNAs in plasma7. In this study, HDL were isolated using a sequential method of density-gradient ultracentrifugation (DGUC), fast-protein liquid chromatography (size-exclusion chromatography gel filtration, FPLC), and affinity chromatography (anti-apolipoprotein A-I (apoA-I) immunoprecipitation)7. Using both real-time PCR-based low-density arrays and individual miRNA assays, miRNA levels were quantified on HDL isolated from healthy and hypercholesterolemic subjects7. Using this approach, we were able to profile miRNAs and quantify specific miRNAs in highly pure HDL preparations. Since 2011, we have determined that although affinity chromatography enhances HDL purity, antibody saturation greatly limits yield, and can be cost-prohibitive. Currently, our protocol recommends a two-step sequential tandem method of DGUC followed by FPLC, which also produces high quality HDL samples for down-stream RNA isolation and sRNA quantification. Due to recent advances in high-throughput sequencing of sRNAs (sRNAseq), e.g., miRNAs, and the increased awareness of other non-miRNA sRNA classes, sRNAseq is the current state-of-the-art in miRNA and sRNA profiling. As such, our protocol recommends quantifying miRNAs and other sRNAs on HDL samples using sRNAseq. Nonetheless, total RNA isolated from HDL can also be used to quantify individual miRNAs and other sRNAs or validate sRNAseq results using real-time PCR approaches. Here we describe in detail a protocol for the collection, purification, quantification, data analysis, and validation of highly pure HDL-sRNAs.
The overall goal of this paper is to demonstrate the feasibility and process of sRNA quantification in highly pure HDL isolated from human plasma.

<table><tbody><tr><td>Ultracentrifuge&amp;nbsp;</td><td>Beckman Coulter</td><td>A99839</td><td>Optima XPN-80</td></tr><tr><td>Ultracentrifuge Rotor</td><td>Beckman Coulter</td><td>331362</td><td>SW-41Ti</td></tr><tr><td>AKTA Pure FPLC System</td><td>GE Healthcare</td><td>29018224</td><td></td></tr><tr><td>3x FPLC Superdex 200 Increase Columns In-line</td><td>GE Healthcare</td><td>28990944</td><td>10/300 gl</td></tr><tr><td>SynergyMx</td><td>BioTek Instruments</td><td>7191000</td><td></td></tr><tr><td>Tabletop centrifuge</td><td>Thermo Scientific</td><td>75004525</td><td>Sorvall ST40R</td></tr><tr><td>Refrigerated centrifuge</td><td>Eppendorf</td><td>22629867</td><td>5417R (purchased through USA Scientific)</td></tr><tr><td>Microfuge&amp;nbsp;</td><td>USA Scientific</td><td>2631-0006</td><td></td></tr><tr><td>PippenPrep</td><td>Sage Science</td><td>PIP0001</td><td></td></tr><tr><td>2100 Bioanalyzer&amp;nbsp;</td><td>Agilent</td><td>G2938B</td><td></td></tr><tr><td>High Sensitivity DNA Assay</td><td>Agilent</td><td>5067-4626</td><td></td></tr><tr><td>Sequencing Library qPCR Quantification Kit</td><td>Illumina</td><td>SY-930-1010</td><td></td></tr><tr><td>ProFlex Thermal Cycler</td><td>Applied Biosystems</td><td>4484073</td><td></td></tr><tr><td>QuantStudio 12k Flex</td><td>Applied Biosystems</td><td>4471134</td><td></td></tr><tr><td>EpMotion Robot</td><td>Eppendorf</td><td>960000111</td><td>5070</td></tr><tr><td>Ultra-clear centrifuge tubes</td><td>Beckman Coulter</td><td>344059</td><td></td></tr><tr><td>Potassium Bromide</td><td>Fisher Chemicals</td><td>P205-500</td><td></td></tr><tr><td>15 mL conical tube</td><td>Thermo Scientific</td><td>339650</td><td></td></tr><tr><td>Micro-centrifugal filters 0.45 &amp;micro;m</td><td>Millipore</td><td>UFC30HV00</td><td></td></tr><tr><td>Micro-centrifugal filters 0.22 &amp;micro;m</td><td>Millipore</td><td>UFC30GV00</td><td></td></tr><tr><td>miRNAEasy Total RNA Isolation Kits</td><td>Qiagen</td><td>217004</td><td></td></tr><tr><td>Total Cholesterol colormetric kit</td><td>Cliniqa (Raichem)</td><td>R80035</td><td></td></tr><tr><td>10,000 m.w. cut-off centrifugation filter</td><td>Amicon</td><td>UFC801024</td><td>purchased through Millipore</td></tr><tr><td>PCR strip tubes</td><td>Axygen</td><td>PCR-0208-C</td><td>purchased through Fisher</td></tr><tr><td>microRNA RT kit</td><td>Life Technologies</td><td>4366597</td><td>For 1000 reactions</td></tr><tr><td>PCR master mix</td><td>Life Technologies</td><td>4440041</td><td>50 mL bottle</td></tr><tr><td>Pierce BCA kit</td><td>Thermo Scientific</td><td>23225</td><td></td></tr><tr><td>Clean and Concentrator Kit</td><td>Zymo</td><td>D4014</td><td></td></tr><tr><td>Dialysis tubing</td><td>Spectrum Labs</td><td>132118</td><td>purchased through Fisher</td></tr><tr><td>bcl2fastq2</td><td>Illumina</td><td>n/a</td><td>Software</td></tr><tr><td>Cutadapt</td><td>https://github.com/marcelm/cutadapt</td><td>n/a</td><td>Software</td></tr><tr><td>NGSPERL</td><td>github.com/shengqh/ngsperl</td><td>n/a</td><td>Software</td></tr><tr><td>CQSTools</td><td>github.com/shengqh/CQS.Tools</td><td>n/a</td><td>Software</td></tr><tr><td>Bowtie 1.1.2&amp;nbsp;</td><td>http://bowtie-bio.sourceforge.net</td><td>n/a</td><td>Software</td></tr><tr><td>GeneSpringGX13.1.1</td><td>Agilent</td><td>n/a</td><td>Software</td></tr></tbody></table>

isolation of high-density lipoproteins for non-coding small rna quantification

Isolation of High-density Lipoproteins for Non-coding Small RNA Quantification

The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most interestingly, sRNAs are also found outside of cells and are stably present in all biological fluids. As such, extracellular sRNAs represent a novel class of disease biomarkers and are likely involved in cell signaling and intercellular communication networks. To assess their potential as biomarkers, sRNAs can be quantified in plasma, urine, and other fluids. Nevertheless, to fully understand the impact of extracellular sRNAs as endocrine signals, it is important to determine which carriers are transporting and protecting them in biological fluids (e.g., plasma), which cells and tissues contribute to extracellular sRNA pools, and cells and tissues capable of accepting and utilizing extracellular sRNA. To accomplish these goals, it is critical to isolate highly pure populations of extracellular carriers for sRNA profiling and quantification. We have previously demonstrated that lipoproteins, particularly high-density lipoproteins (HDL), transport functional microRNAs (miRNA) between cells and HDL-miRNAs are significantly altered in disease. Here, we detail a new protocol that utilizes tandem HDL isolation with density-gradient ultracentrifugation (DGUC) and fast-protein-liquid chromatography (FPLC) to obtain highly pure HDL for downstream profiling and quantification of all sRNAs, including miRNAs, using both high-throughput sequencing and real-time PCR approaches. This protocol will be a valuable resource for the investigation of sRNAs on HDL.

This protocol is a series of established methods linked together to allow for the quantification of sRNAs on highly pure HDL by high-throughput sequencing or real-time PCR (Figure 1). To demonstrate the feasibility and impact of this protocol, HDL was purified from human plasma by the tandem DGUC and FPLC method. Collected FPLC fractions corresponding to HDL (by cholesterol distribution) were concentrated and total RNA was isolated from 1 mg of HDL (total protein). sRNA l...

This protocol describes the isolation and quantification of high-density lipoprotein small RNAs.

The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most ...

The overall goal of this protocol is to quantify small non-coding RNAs on purified lipoproteins. This protocol can help answer key questions in the lipoprotein field, such as defining lipoprotein small RNA signatures in health and disease, as well as advancing lipoprotein small RNAs as disease biomarkers, or cell to cell messages. The main advantage of this technique is one can analyze highly pure lipoproteins for small RNA changes in disease or experimental conditions.The implications of this technique extends for the therapy of cardiometabolic diseases, because extracellular RNAs are a new class of disease biomarkers and lipoprotein small RNA hold exciting potential as drug targets in future studies. Though this method is designed for HDL small RNAs, it can also be adapted for very low density and low density lipoprotein small RNAs. Generally, individuals new to this method may struggle, because of lack of proper equipment and expertise in preparing samples for density-gradient ultracentrifugation.This protocol is composed of established methods linked together for the quantification of small RNAs on highly pure HDL, using high throughput sequencing, or real time PCR. This video deals with the purification of the HDL. This protocol's gonna be demonstrated by my assistant, Evan Shadari.To begin, add 90 microliters of 100x antioxidants to nine milliliters of plasma. Then, adjust the plasma's density to 1.025 grams per milliliter, by adding 0.251 grams of potassium bromide to every nine milliliters of plasma. Rock the plasma at room temperature, until all the salt has dissolved.Then, transfer the plasma to ultra-centrifuge tubes, and make sure to have a layer of bubbles at the top. There should be no air trapped under the plasma. Next, prepare an 18 gauge needle by adding a 90 degree bend one centimeter from the tip, with the beveled side facing up.Then, using a syringe and the bent needle, carefully place three milliliters of overlay solution number one onto the plasma. Remove the majority of the bubbles on the surface, and leave two to three millimeters between the meniscus and the tube's edge. Then, carefully place the tubes into SW 40 Ti buckets.Weigh each bucket with the caps, and exactly balance the buckets that will occupy opposite positions in the centrifuge. Next, place the rotor into the ultra-centrifuge, and run it at 274, 400 times G for 24 hours at four degrees Celsius, with the break set intermediately at a value of four. The next day, carefully remove the buckets from the rotor, and lift the tubes from the buckets.Then, slowly remove two milliliters from the top layer of the overlay, using a syringe and bent needle. This is the VLDL IDL fraction. Then, collect the remaining seven milliliters of plasma, and transfer it to a 15 milliliter conical tube.Bring the volume of the plasma up to nine milliliters by adding overlay solution number two. Then, adjust the density to 1.080 grams per milliliter by adding 0.746 grams of potassium bromide. Next, gently rock the sample to dissolve the salt, which will take about 20 minutes.Then, transfer the sample to an ultra-centrifuge tube without trapping any air. Ensure that a layer of bubbles is made at the top. Using the bent needle, carefully overlay three milliliters of overlay solution number three.Then, remove the majority of the bubbles and carefully load the tubes into SW 40 Ti bucket. Balance them and spin them, as previously described, for 24 hours. The next day, carefully remove two milliliters from the top layer of the overlay using the bent needle.This is the LDL fraction. Then, transfer the remaining sample to a new 15 milliliter conical tube, and bring the volume up to nine milliliters with solution number four. Now adjust the density to 1.30 grams per milliliter by adding about 3.33 grams of potassium bromide and rocking the sample until the salt dissolves.Then, transfer the sample to an ultra-centrifuge tube and carefully overly three milliliters of solution number five. Now, ultra-centrifuge the sample as before, but for 48 hours. Two days later, collect the top two milliliters of the overlay using a syringe and bent needle.This constitutes the HDL fraction. To remove the high salt solutions, transfer the HDL fraction to a wet dialysis sleeve with a 10, 000 molecular weight cutoff. Then, dialyze it for 24 hours in a liter of one XPBS with gentle stirring at four degrees Celsius.Replace the PBS solution three times over the 24 hour period. Later, determine the protein concentration of the HDL fraction using a BCA method. Extracellular vesicles, or exosomes, have a similar density to small HDL, and thus could be present in the same density fraction as the HDL.Thus, the HDL fraction requires further purification by FPLC. Immediately prior to using the FPLC, run 1.2 milligrams of the DGUC HDL fraction in 500 microliters of solution through a 0.22 micron centrifugal filter. Collect the filtered sample into an FDLC injection syringe, ensuring that no air bubbles get trapped.Next, set the FPLC flow rate to 0.3 milliliters per minute with a pressure limit at 2.6 megapascals. Then, equilibrate the columns with 0.2 column volumes of buffer. Now inject the sample with three milliliters of buffer into the FPLC instrument, and start the run.Collect 1.5 milliliter fractions for a total of 72 fractions. Identify the FPLC fractions corresponding to DGUC HDL by determining total cholesterol levels using a colorimetric kit according to the manufacturer's instructions. Expect to find six to seven FPLC fractions containing DGUC HDL.Pool all the HDL containing fractions and concentrate them using a 10 kilodalton cutoff centrifugal filter at 4, 000 times G for an hour at four degrees Celsius, or until HDL concentrate is approximately 100 microliters. Then, collect the HDL concentrate and quantify the protein using the BCA method. Later, use the same amount of HDL total protein to isolate RNA.Human plasma was fractionated by FPLC without the use of density-gradient separation. Six fractions corresponded to HDL and six to very low density lipoprotein. Lipids in black, cholesterol in red, and protein in blue were all measured by colorimetric kits.By comparison, use of density-gradient ultra-centrifugation before FPLC resulted in finding lipid protein and cholesterol almost exclusively in HDL fractions. From HDL taken from four healthy plasma donors, total RNA was isolated and sequenced using a single read 50 base pair protocol. The distribution of normalized reads illustrates and enrichment of small RNAs around 21 and 34 nucleotides.Analysis of the library showed 38 percent of the reads were micro RNAs, and 37 percent were derived from TRNAs. Miscellaneous RNAs, ribosomal RNAs, small RNAs, small nucleolar RNAs, and long non-coding RNAs were also present. Once mastered, this technique can be performed within ten days, when done properly.While attempting this procedure, it is important to remember to validate HDL small RNA changes observed with high throughput sequencing with another method, such as PCR or northern blotting. Following this procedure, other methods, like HDL cholesterol e-flux acceptance capacity and HDL anti-inflammatory SAs, can be performed during the RNA isolation steps and sequencing prep steps to answer additional questions, like determining the correlation between HDL small RNA changes and HDL function. After its development, this technique paved a way for researchers in the fields of lipids and lipoproteins, to study non-cholesterol cargo, particularly nucleic acids and metabolic diseases, for example hypercholesterolemia or diabetes.And don't forget, working with human plasma can be extremely hazardous, and one should have proper training in bloodborne pathogens, and appropriate personal protective equipment should be worn when performing this technique.

isolation-high-density-lipoproteins-for-non-coding-small-rna

Research

JoVE Journal

Biochemistry

This paper demonstrates methods for the isolation, purification and detection of exosomes, as well as techniques for analysis of their molecular content. These methods are adaptable for exosome isolation from both cell culture media and biological fluids, and can beyond analysis of molecular content also be useful in functional studies.

Isolation and Characterization of RNA-Containing Exosomes

A step by step protocol to isolating and identifying RNA associated complexes through RIP-Chip.

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

This protocol describes a method for extracting small RNAs from human serum. We have used this method to isolate microRNAs from cancer serum for use in DNA arrays and also singleplex quantitative PCR. The protocol utilizes phenol and guanidinium thiocyanate reagents with modifications to yield high quality RNA.

Isolation of Small Noncoding RNAs from Human Serum

MicroRNAs (miRNAs) are a widely conserved class of regulatory molecules. Here we describe a miRNA cloning method that relies upon two potent ligation steps followed by high-throughput sequencing. Our method permits accurate genome-wide quantitation of miRNAs.

Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing

Gene expression analysis of a subset of cells in a specific tissue represents a major challenge. This article describes how to isolate high-quality total RNA from a specific cell population by combining a rapid immunolabeling method with laser capture microdissection.

RNA Isolation from Cell Specific Subpopulations Using Laser-capture Microdissection Combined with Rapid Immunolabeling

MicroRNAs play an important regulatory role and are emerging as novel therapeutic targets for various human diseases. It has been shown that miRNAs are carried in high density lipoproteins. We have developed a simplified method to rapidly isolate purified HDL suitable for miRNA analysis from human plasma.

Fast and Simplified Method for High Through-put Isolation of miRNA from Highly Purified High Density Lipoprotein

Epigenetic factors can interact with genetic programs to modulate gene expression and regulate B cell function. By combining in vitro B-cell stimulation, qRT-PCR, and high-throughput microRNA-sequence and mRNA-sequence approaches, we can analyze the epigenetic modulation of miRNA and gene expression in B cells.

Genome-wide Analysis of HDAC Inhibitor-mediated Modulation of microRNAs and mRNAs in B Cells Induced to Undergo Class-switch DNA Recombination and Plasma Cell Differentiation

Lipid droplets are important organelles for the replication of several pathogens, including the Hepatitis C Virus (HCV). We describe a method to isolate lipid droplets for quantitative mass spectrometry of associated proteins; it can be used under a variety of conditions, such as virus infection, environmental stress, or drug treatment.

Lipid Droplet Isolation for Quantitative Mass Spectrometry Analysis

Here, a quantitative real-time polymerase chain reaction-based protocol is presented for the determination of the native micro-RNA content (absolute/relative) of lipoprotein particles. In addition, a method for increasing the micro-RNA level, as well as a method for determining the cellular uptake rate of lipoprotein particles, is demonstrated.

Enrichment of Native Lipoprotein Particles with microRNA and Subsequent Determination of Their Absolute/Relative microRNA Content and Their Cellular Transfer Rate

This protocol provides an efficient collagenase digestion method for isolation of viable adipocytes and stromal vascular fraction-SVF cells from human visceral fat in a single process, including methodology to obtain high-quality RNA from adipocytes and phenotypification of SVF-macrophages through staining of multiple membrane-bound markers for analysis by flow cytometry.

Isolation of Viable Adipocytes and Stromal Vascular Fraction from Human Visceral Adipose Tissue Suitable for RNA Analysis and Macrophage Phenotyping

Learn to isolate high-density lipoproteins for small non-coding RNA quantification using density-gradient ultracentrifugation. This method enables analysis of lipoprotein RNA signatures as potential disease biomarkers.

Isolation of High-density Lipoproteins for Non-coding Small RNA Quantification

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