Name: measurement of differentially methylated ins dna species in human serum samples as a biomarker of islet β cell death
Uploaded: 2016-12-21T14:00:00.000+00:00
Duration: 10 min 34 s
Description: Watch this Scientific Journal Video about Measurement of Differentially Methylated INS DNA Species in Human Serum Samples as a Biomarker of Islet Î² Cell Death at JoVE.com

This work was supported by National Institutes of Health grant UC4 DK104166 (to RGM). We wish to acknowledge the assistance of the Indiana Diabetes Research Center Translation Core supported by National Institutes of Health grant P30 DK097512.

Ethics Statement: Protocols were approved by the Indiana University Institutional Review Board. Parents of subjects provided written informed consent, and children older than 7 years provided assent for their participation.
1. Serum Processing
NOTE: The assay as described has been rigorously tested using human serum isolated as follows.
<ol>
	<li>Collect blood in one red top (no-additive; uncoated) blood collection tube.</li>
	<li>Let sit at room temperature for 30 min to allow the clot to form.</li>
	<li>Centrifuge tube at 2,000 x g for 10 min at room temperature. Transfer the supernatant (serum) to a new tube designated for serum storage (polypropylene screw top tubes, size dependent on samples).</li>
	<li>Store samples at -80 &#186;C until ready for DNA isolation.</li>
</ol>
2. Serum DNA Extraction
NOTE: DNA is extracted with a DNA extraction kit using 50 &#181;l of serum (recommended), following manufacturer&#39;s protocol with some modifications.
<ol>
	<li>Prepare 200 &#181;l lysis buffer + 1 &#181;l poly(A) (5 &#181;g) per sample in an microcentrifuge tube. Vortex for 15 sec. Set aside until Step 2.3.</li>
	<li>Take serum samples from -80 &#186;C freezer and thaw at room temperature. Bring serum sample volume up to 200 &#181;l total using phosphate-buffered saline (PBS, with calcium chloride and magnesium chloride).</li>
	<li>Lyse the sample by adding 20 &#181;l protease (1.4 Anson units/ml) to sample, followed by 200 &#181;l lysis buffer/polyA mix (from Step 2.2) and vortex for 8 sec. Incubate sample at 56 &#176;C for 10 min, then briefly centrifuge for 7 sec at top speed in a microcentrifuge (&#62;10,000 x g).</li>
	<li>Precipitate DNA by adding 230 &#181;l 100% ethanol to sample and vortex for 8 sec. Briefly centrifuge for 7 sec at top speed (&#62;10,000 x g).</li>
	<li>Apply the DNA to the spin column by adding 600 &#181;l sample mixture to mini spin column. Centrifuge at 6,000 x g for 1 min. Discard the flow-through and place column in a clean tube.</li>
	<li>Wash the DNA by adding 500 &#181;l wash buffer 1 to the column. Centrifuge at 6,000 x g for 1 min. Discard the flow-through and place column in a clean tube. Add 500 &#181;l wash buffer 2 to column and centrifuge at top speed (&#62;10,000 x g) for 3 min. Place column in a new 1.5 ml microcentrifuge tube and centrifuge at top speed again for 1 min.</li>
	<li>Elute the DNA by placing column in a new 1.5 ml microcentrifuge tube and adding 60 &#181;l elution buffer directly on the filter. It is important to switch tips between samples to prevent cross contamination. Incubate at room temperature for 5 min, then centrifuge at 6,000 x&#160;g for 1 min. Add another 60&#160;&#956;l of elution buffer and centrifuge at 6,000 x g for 1 min.&#160;</li>
	<li>Store DNA at -20 &#186;C for later use, or proceed immediately to bisulfite conversion.</li>
</ol>
3. Bisulfite Conversion
NOTE: Bisulfite conversion is performed using a bisulfite conversion kit, following the manufacturer&#39;s protocol with some modifications.
<ol>
	<li>To convert unmethylated cytosines to uracils, add 130 &#181;l of bisulfite conversion reagent to 20 &#181;l of DNA from step 2.7 in a PCR tube (single 0.2 ml PCR tube or 8-strip PCR tubes). Save the remaining 40 &#181;l of DNA for future use, or use in replicate reactions. Mix 20 times by pipetting up and down and centrifuge briefly to make sure no drops are on sides or lid. Incubate in a water bath or thermal cycler as follows: 98 &#176;C for 8 min, 54 &#176;C for 60 min, 4 &#176;C for 5 min.
	<ol>
		<li>Proceed to step 3.2 or store at 4 &#176;C for up to 20 hr.</li>
	</ol>
	</li>
	<li>Add 600 &#181;l of binding buffer to spin column and place the column in the provided collection tube. Apply the bisulfited DNA to column and mix by pipetting up and down 10 times. Centrifuge at top speed (&#62;10,000 x g) for 30 sec. Discard flow-through.</li>
	<li>Wash DNA by adding 100 &#181;l of wash buffer to column and centrifuge at top speed (&#62;10,000 x g) for 30 sec.</li>
	<li>Perform desulphonation to remove sulphonate group to finalize the conversion of unmethylated cytosines to uracil by adding 200 &#181;l of desulphonation buffer to the column. Let stand at room temperature for 20 min, then centrifuge at top speed (&#62;10,000 x g) for 30 sec.</li>
	<li>Wash DNA by adding 200 &#181;l of wash buffer to the column and centrifuge at full speed for 30 sec. Discard the flow-through and repeat this wash step.</li>
	<li>Place the column into a 1.5 ml microcentrifuge tube. Elute DNA by adding 10 &#181;l elution buffer directly to column filter. Incubate for 1 min. Centrifuge for 30 s at full speed to elute DNA. Quantify recovered DNA by spectrophotometry at A260. 
	NOTE: The DNA detected by spectrophotometry represents primarily the carrier polyA DNA that was added at step 2.3 above. Typically, recovery of polyA is &#8805;85% of the input (&#62;4.25 &#181;g).</li>
	<li>Store DNA at -20 &#176;C until ready to proceed with digital PCR.</li>
</ol>
4. Multiplex Digital PCR
<ol>
	<li>Make a master mix with enough solution for each sample and control. Include at least one sample containing water (negative control), one sample of a plasmid containing unmethylated INS (1 pg, positive control), one sample of plasmid containing methylated INS (1 pg, positive control), and one sample containing a 1:1 mixture of plasmids.
	<ol>
		<li>To prepare the PCR master mix, add 12.5 &#181;l per reaction of PCR buffer (e.g., 125 &#181;l per 10 samples), 1.25 &#181;l per reaction primer/probe mix (e.g., 12.5 &#181;l per 10 samples), 8.25 &#181;l per reaction water (e.g., 82.5 &#181;l per 10 samples), 0.5 &#181;l per reaction EcoR1 enzyme (e.g., 5 &#181;l per 10 samples). 
		NOTE: Primers and probes used here are as follows: Forward Primer: 5&#39;-GGAAATTGTAGTTTTAGTTTTTAGTTATTTGT-3&#39;; Reverse Primer: 5&#39;-AAAACCCATCTCCCCTACCTATCA-3&#39;; FAM probe: FAM-5&#39;-ACCCCTACCACCTAAC-3&#39;-MGB; VIC probe: VIC-5&#39;-ACCCCTACCGCCTAAC-3&#39;-MGB.</li>
	</ol>
	</li>
	<li>Set up multiplex PCR reaction in a 96-well plate. Add 19.5 &#181;l of master mix to each well. Add 2.5 &#181;l of bisulfite converted DNA sample into each appropriate well (save the remaining 7.5 &#181;l of bisulfite converted DNA or use in replicate reactions). Mix by pipetting up and down several times. 
	NOTE: All 8 wells in a row must contain sample or buffer control.</li>
	<li>Seal with a foil seal using a plate sealer and centrifuge in a plate spinner until there is no liquid on the sides of the wells.</li>
	<li>Set up the automated droplet generator on the touchscreen. 
	NOTE: All 8 wells in the cartridge must contain sample or buffer control.
	<ol>
		<li>Set the number of rows being used by touching the row(s) in which samples are loaded into on the 96-well plate from step 4.2 and highlight the row in blue to indicate an active row.</li>
		<li>Load consumables from back to front to avoid contamination. To start, add cartridges along the back row of the instrument. Load tips into center row of the instrument. 
		NOTE: The cartridges can only fit into the holders in the correct orientation.</li>
		<li>Place 96-well plate into the instrument. Remove a cold block from -20 &#176;C freezer and place a new skirted 96-well plate into it. Place it inside the instrument next to the sample loaded 96-well plate.</li>
		<li>Add oil to dispenser in the front of the instrument. Select type of oil on touchscreen.</li>
		<li>Touch the blue start button to start the run. Confirm plate setup and touch start run button to begin.</li>
	</ol>
	</li>
	<li>Once finished, remove the 96-well plate that contains the newly formed droplets and seal with a foil seal using a plate sealer.</li>
	<li>Perform PCR10 on a thermal cycler using the following program: 95 &#176;C for 10:00 min; 40 cycles at: 94 &#176;C for 00:30 min, 57.5 &#176;C for 01:00 min; 98 &#176;C for 10:00 min; 12 &#176;C for 10 min or up to 24 hr.</li>
	<li>Place the plate on the droplet reader and set up the reader.
	<ol>
		<li>Click on the setup tab. Open a new template by clicking template &#62; new. Enter a file name.</li>
		<li>Use the well editor to set the parameters for each sample. Give each sample a unique name, set experiment to Rare Event Detection (R-RED), and set master mix to the mix used in step 4.1.</li>
		<li>Give Target 1 a name (i.e., unmethylated) and set Target 1 as unknown (U). Give Target 2 a name (i.e., methylated) and set Target 2 as reference (R).</li>
		<li>Click Run tab to start the run. In the run options window, select the detection chemistry (FAM/VIC).</li>
	</ol>
	</li>
</ol>
5. Data Analysis
<ol>
	<li>Open results in analyze tab and analyze using 2-D plot based on positive controls (see Figure 1).</li>
	<li>Export CSV file generated by droplet reader to a spreadsheet program for data analysis.</li>
	<li>To generate &#34;copies per &#181;l&#34; of serum, use the formula: (concentration*250)/(volume of serum used for DNA isolation in &#181;l).6 
	NOTE: The data is typically converted to log10 when acquired from human serum to ensure normal distribution. Alternatively, data can be plotted on a log10 scale and analyzed by non-parametric statistics.</li>
</ol>
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The authors have nothing to disclose.

Methylation of cytosines by DNA methyltransferases allows for the epigenetic control of transcription at many genes. The INS gene in humans is almost exclusively expressed in islet &#946; cells, and there appears to be a correlation between the frequency of methylation of cytosines in the INS gene to silencing of its transcription11. As such, most cell types show substantially higher frequencies of methylation of the INS gene at various cytosines compared to &#946; cells11-13. It has been proposed that the prevalence of &#946; cell death could be monitored by analysis of the serum levels of cell-free unmethylated INS DNA, which would arise largely from dying &#946; cells that liberate their DNA12.
The bisulfite reaction converts unmethylated cytosines into uracils, leaving methylated cytosines unchanged14. Sequencing or PCR analysis of bisulfite-converted DNA therefore allows determination of whether the original cytosine was methylated or not. Methylation-specific PCR using dye-based technology exploits differences in PCR efficiency owing to 3&#39; base-pair mismatches between primers and template, and thereby allows distinction of unmethylated vs. methylated cytosines following bisulfite conversion of DNA15. Accordingly, dye-based PCR was used to quantitate the relative ratio of unmethylated to methylated INS in early studies of T1D subjects12,16. However, dye-based PCR technology has several drawbacks, including limited specificity, lack of absolute quantitation of DNA fragment concentrations, and the inability to multiplex (i.e., detect both methylated and unmethylated DNA species in the same reaction). Other groups have performed direct sequencing of cell-free DNA fragments, a technique that allows monitoring of several differentially methylated CpG sites with much greater specificity9. However, the sequencing technique requires large sample volumes, is not easily amenable to use of banked samples, and is expensive.
As a result of these limitations, our group and others have employed digital PCR, a technique that provides absolute quantitation of DNA fragments, requires only microliter quantities of serum from fresh or banked samples, is amenable to multiplexing, shows greater sensitivity than traditional quantitative PCR, and is less expensive than direct sequencing. Digital PCR technology involves the use of conventional primer/probe assays and a microfluidics-based partitioning of a water-in-oil PCR reaction into ~ 20,000 droplets. Following thermal cycling of the partitioned reaction, the droplets are subsequently analyzed by a flow cytometer to identify droplets with positive and negative signals. Poisson statistics is used to calculate absolute quantities (copy numbers) of each DNA species. The conceptual details of digital PCR have been described elsewhere17.
This protocol describes the measurement of &#946; cell death in humans by measuring differentially methylated INS DNA by digital PCR. Our data presented here and elsewhere6 show that primer/probe combinations that detect differential methylation of cytosine at position -69 (relative to the transcriptional start site of INS) exhibit sufficient specificity for either the unmethylated cytosine (FAM probe) or the methylated cytosine (VIC probe) (see Figure 1A and B). Mixtures of plasmids containing both methylated and unmethylated INS fragments at position -69 bp (i.e., bisulfite-converted DNA having either uracil or cytosine at position -69 bp) exhibit droplets containing one or the other plasmid, or both plasmids (double-positive signals in Figure 1C). The Poisson statistical calculation utilizes the droplet numbers that are positive for a given probe (whether single-positive or double-positive) to derive the copy numbers of each methylated or unmethylated DNA fragment.
When utilizing human serum for the measurement of differentially methylated cytosines at position -69 bp in cell-free DNA (Figure 3), our data demonstrate two key features: (1) levels of methylated INS are 5-10-fold higher in these subjects than unmethylated INS (regardless of diagnosis), and (2) absolute levels of both unmethylated and methylated INS are higher in subjects with new-onset T1D compared to controls. Whereas the higher levels of methylated INS compared to unmethylated INS likely reflect the greater burden of cell-free DNA emanating from non-&#946; cells, the higher levels of both species of INS in new-onset T1D subjects likely reflects both an increase in prevalent &#946; cell death (unmethylated INS), and possibly death/turnover of other cell types that are associated with the disease state (e.g., innate and adaptive immune cells). Further speculation on the elevations of both species of INS in new-onset T1D subjects was discussed previously6. Regardless of the sources of both species of INS in serum from these individuals, it is notable that measurement of ratios of unmethylated to methylated INS (as reported by other investigators using dye-based PCR) would not have picked up the significant differences in absolute levels described here and in our recent publication6, thus emphasizing the power of digital PCR for this type of biomarker analysis.
Some precautions and limitations should be noted. We feel it is important that blood is processed within 4 hr of collection and either used immediately for DNA isolation or stored at -80 &#186;C for future use. In unpublished studies, we have observed some loss of DNA recovery after 4 hr of collection, perhaps owing to DNA degradation, as seen in studies of long-term storage of samples18. Because of the increased sensitivity of digital PCR, special care should be taken to avoid contamination of samples that would otherwise not be noticeable in traditional qPCR. Finally, a key limitation of the technique is the analysis of samples in which droplet generation does not exceed ~10,000 droplets. Such samples do not provide reliable Poisson statistics, and as such may be considered uninterpretable. Multiple causes of such low droplet generation might include technical errors in sample handling, technical issues with the droplet generator, or issues related to quality of reagents used.
In summary, this report describes the detailed protocol for measurement of differentially methylated, cell-free INS DNA at position -69 bp by digital PCR. The protocol described here can be adapted to any DNA species for which detection of differentially methylated cytosines is desired, whether from circulation or from isolated cells and tissues, and can provide absolute quantitation of DNA fragments.

Type 1 diabetes (T1D) is an autoimmune disease that is characterized by the destruction of insulin-producing islet &#946; cells by autoreactive T cells1. The diagnosis of T1D is typically made upon measurement of hyperglycemia (blood glucose &#62; 200 mg/dl) in a lean, young individual, who might present with ketoacidosis as evidence of insulin deficiency. At the time of diagnosis of T1D, there is evidence for substantial loss of &#946; cell function and mass (from 50 - 90%)2. In clinical studies, several immune modulatory drugs that were instituted at the time of diagnosis resulted in the stabilization of &#946; cell function (and presumably mass), but none have resulted in clinical remission of disease, a finding that has raised the call for the development of biomarkers for earlier detection of the disease and for the longitudinal tracking of effectiveness of combination therapies3,4. Efforts by international consortia, such as the Human Islet Research Network Consortium at the National Institutes of Heath5, have emphasized the need to develop biomarkers that focus on &#946; cell stress and death in T1D.
In line with these efforts, our group and others have recently developed biomarker assays that measure circulating, epigenetically modified DNA fragments that arise primarily from dying &#946; cells6-9. In all of the published assays to date, the focus has been on the quantitation of the human gene encoding preproinsulin (INS), which demonstrates greater degrees of unmethylated CpG sites in the coding and promoter regions compared to other cell types. The liberation of unmethylated INS DNA fragments was hypothesized as arising primarily from dying (necrotic, apoptotic) &#946; cells. Our recent studies showed that in youth, elevations in both unmethylated and methylated INS DNA at position -69 bp (relative to the transcriptional start site) were observed in new-onset T1D, and together served as specific biomarkers for this population6. These biomarker assays involve the isolation of cell-free DNA from serum or plasma using commercial spin kits, followed by a bisulfite conversion of the isolated DNA (to convert non-methylated cytosines to uracils, leaving methylated cytosines intact).
In this report, we describe the technical aspects of serum sample collection, isolation of cell-free DNA from serum, bisulfite conversion, and performance of droplet digital PCR (henceforth, digital PCR) for differentially methylated INS DNA.

<table><tbody><tr><td>Red Top Vacutainer&amp;nbsp;</td><td>Beckon Dickinson</td><td>366441</td><td>no additive, uncoated interior, 10 ml</td></tr><tr><td>Cryovial Tube</td><td>Simport</td><td>T310-3A</td><td>polypropylene, screw cap tube, any size</td></tr><tr><td>QIAamp DNA Blood Mini Kit</td><td>Qiagen</td><td>51106</td><td></td></tr><tr><td>Poly(A)</td><td>Sigma</td><td>P9403</td><td>disloved in TE buffer (10 mM Tris-Cl pH 8.0 + 1 mM EDTA) to 5 &amp;micro;g/&amp;micro;l&amp;nbsp;</td></tr><tr><td>Absolute Ethanol (200 Proof)</td><td>Fisher Scientific</td><td>BP2818-500</td><td></td></tr><tr><td>DPBS (with CaCl&lt;sub&gt;2&lt;/sub&gt; and MgCl&lt;sub&gt;2&lt;/sub&gt;)</td><td>Sigma</td><td>D8662</td><td></td></tr><tr><td>0.2 ml PCR 8-strip Tubes</td><td>MidSci</td><td>AVST</td><td></td></tr><tr><td>8-strip Caps, Dome</td><td>MidSci</td><td>AVSTC-N</td><td></td></tr><tr><td>EZ DNA Methylation-Lightning Kit</td><td>Zymo</td><td>D5031</td><td></td></tr><tr><td>ddPCR Supermix for Probes (No dUTP)</td><td>Biorad</td><td>1863024</td><td></td></tr><tr><td>Buffer Control for Probes</td><td>Biorad</td><td>1863052</td><td></td></tr><tr><td>Human Unmethylated/Methylated Primer/Probe mix</td><td>Life Technologies</td><td>AH21BH1</td><td></td></tr><tr><td>EcoR1</td><td>New England Biolabs</td><td>R0101L</td><td></td></tr><tr><td>twin.tec PCR Plate 96, semi-skirted</td><td>Eppendorf</td><td>951020346</td><td></td></tr><tr><td>Pierceable Foil Heat Seal</td><td>Biorad</td><td>1814040</td><td></td></tr><tr><td>PX1 PCR Plate Sealer</td><td>Biorad</td><td>1814000</td><td></td></tr><tr><td>QX200 AutoDG Droplet Digital PCR System</td><td>Biorad</td><td>1864101</td><td></td></tr><tr><td>Automated Droplet Generation Oil for Probes</td><td>Biorad</td><td>186-4110</td><td></td></tr><tr><td>DG32 Cartridge for Automated Droplet Generator</td><td>Biorad</td><td>186-4108</td><td></td></tr><tr><td>Pipet Tips for Automated Droplet Generator</td><td>Biorad</td><td>186-4120</td><td></td></tr><tr><td>Pipet Tip Bins for Automated Droplet Generator</td><td>Biorad</td><td>186-4125</td><td></td></tr><tr><td>C1000 Touch Thermal Cycler</td><td>Biorad</td><td>1851197</td><td></td></tr><tr><td>QX200 Droplet Reader</td><td>Biorad</td><td>186-4003</td><td></td></tr><tr><td>ddPCR Droplet Reader Oil</td><td>Biorad</td><td>186-3004</td><td></td></tr></tbody></table>

measurement of differentially methylated ins dna species in human serum samples as a biomarker of islet &#946; cell death

The death of islet &#946; cells is thought to underlie the pathogenesis of virtually all forms of diabetes and to precede the development of frank hyperglycemia, especially in type 1 diabetes. The development of sensitive and reliable biomarkers of &#946; cell death may allow for early therapeutic intervention to prevent or delay the development of diabetes. Recently, several groups including our own have reported that cell-free, differentially methylated DNA encoding preproinsulin (INS) in the circulation is correlated to &#946; cell death in pre-type 1 diabetes and new-onset type 1 diabetes. Here, we present a step-by-step protocol using digital PCR for the measurement of cell-free INS DNA that is differentially methylated at cytosine at position -69 bp (relative to the transcriptional start site). We demonstrate that the assay can distinguish between methylated and unmethylated cytosine at position -69 bp, is linear across several orders of magnitude, provides absolute quantitation of DNA copy numbers, and can be applied to samples of human serum from individuals with new-onset type 1 diabetes and disease-free controls. The protocol described here can be adapted to any DNA species for which detection of differentially methylated cytosines is desired, whether from circulation or from isolated cells and tissues, and can provide absolute quantitation of DNA fragments.

To interpret data appropriately, we use plasmid controls for both the unmethylated and methylated target INS DNA in each digital PCR run. These controls ensure that signals corresponding to methylated and unmethylated DNA are clearly distinguishable. Figure 1 shows the 2-D scatter plots corresponding to droplets for plasmid controls containing bisulfite-converted unmethylated INS DNA (Figure 1A), methylated INS DNA (Figure 1B), and a 1:1 mixture of the two plasmids (Figure 1C). Plasmid containing unmethylated INS is indicated by the droplets positive for the 6-Carboxyfluorescein (FAM) signal, whereas plasmid containing methylated INS is indicated by the droplets positive for the VIC signal. In the 1:1 plasmid mixture, a population of double-positive droplets is seen, corresponding to droplets containing both species of DNA. To distinguish positive droplets from negative droplets, data are gated using these 2-D plots. Note that in Figure 1A, there is a slight shift of the FAM-positive droplets into the VIC channel, indicating that the probe for the methylated INS DNA exhibits some cross-reactivity for the unmethylated INS DNA. Similarly, in Figure 1B, there is a very slight shift of the VIC-positive droplets into the FAM channel, indicating cross-reactivity of the probe for the unmethylated DNA with methylated DNA. A major advantage of digital PCR is it can still discriminate specific signals even when probes are not 100% specific. For appropriate Poisson statistical calculations by the software, each PCR reaction should partition into at least 10,000 total droplets, display a cluster of negative droplets, and show a clear amplitude difference between negative and positive droplets (for reliable gating). To demonstrate linearity of our primers, we performed mixtures of the two plasmids across several orders of magnitude. As shown in Figure 2, varying concentrations of one plasmid can be linearly detected in the presence of a constant amount of the second plasmid. For new labs performing this procedure, we recommend constructing a similar mixture experiment to ensure that the assay is operating in a linear detection fashion.
Next, we obtained serum of three subjects with new-onset T1D (within 2 days of diagnosis) and three control individuals without T1D (see Table 1 for clinical characteristics). Protocols were approved by the Indiana University Institutional Review Board. Parents of subjects provided written informed consent. Figure 3 shows the quantitation of unmethylated and methylated INS DNA copy numbers/&#181;l serum, converted to log10 from these controls and T1D subjects. The data show that individuals with T1D exhibit elevated levels of both methylated and unmethylated INS DNA compared to controls, similar to data reported previously6.
<img alt="Figure 1" src="/files/ftp_upload/54838/54838fig1.jpg" /> 
Figure 1: Representative 2-D Plots of Plasmid Controls. Plasmid standards were generated by cloning fragments of bisulfite-converted INS DNA harboring unmethylated or methylated cytosine at position -69 bp relative to the INS transcriptional start site. Shown are 2-D plots using plasmid containing unmethylated (A) and methylated (B) INS DNA and for a 1:1 mixture of the two plasmids (C). Arrows identify the unmethylated, methylated, and unmethylated + methylated (double- positive) INS DNA-containing droplets. FAM = Target 1; VIC = Target 2. <a href="http://cloudflare.jove.com/files/ftp_upload/54838/54838fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" src="/files/ftp_upload/54838/54838fig2.jpg" /> 
Figure 2: Quantitation of DNA Targets using Control Plasmid Mixtures. Plasmid standards containing cloned fragments of bisulfite-converted INS DNA harboring unmethylated or methylated cytosine at position -69 bp relative to the INS transcriptional start site were mixed at the various combinations shown, then subjected to multiplex digital PCR. The figure shows the quantitation of target DNA fragments, presented as copies/&#181;l; r2 = 0.989 for unmethylated INS DNA and r2 = 0.998 for methylated INS DNA. <a href="http://cloudflare.jove.com/files/ftp_upload/54838/54838fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" src="/files/ftp_upload/54838/54838fig3.jpg" /> 
Figure 3: Circulating Unmethylated and Methylated INS DNA Levels in Controls and Subjects with T1D. Serum samples were collected from 4 youth with new-onset T1D and from 4 disease-free, unrelated controls, then processed for measurement of differentially methylated INS DNA by digital PCR. Shown are results of digital PCR assays for unmethylated (A) and methylated (B) INS DNA. Data is displayed as individual points and mean &#177; SEM. Statistics were analyzed by a two-tailed parametric Students t test. <a href="http://cloudflare.jove.com/files/ftp_upload/54838/54838fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>&#160;
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td></td>
			<td>Controls</td>
			<td>T1D at onset</td>
		</tr>
		<tr>
			<td>Age (years)</td>
			<td>10.3 &#177; 1.3</td>
			<td>9.2 &#177; 1.0</td>
		</tr>
		<tr>
			<td>Female/Male</td>
			<td>1:3</td>
			<td>1:3</td>
		</tr>
		<tr>
			<td>BMI Z-Score</td>
			<td>0.30 &#177; 0.9</td>
			<td>0.74 &#177; 0.9</td>
		</tr>
		<tr>
			<td>HbA1C (%)</td>
			<td></td>
			<td>11.1 &#177; 0.6</td>
		</tr>
		<tr>
			<td>C-Peptide (pmol/L)</td>
			<td></td>
			<td>285.5 &#177; 37.0</td>
		</tr>
	</tbody>
</table>
Table 1: Demographics of Controls and Subjects with T1D.

Watch this Scientific Journal Video about Measurement of Differentially Methylated INS DNA Species in Human Serum Samples as a Biomarker of Islet Î² Cell Death at JoVE.com

Measurement of Differentially Methylated INS DNA Species in Human Serum Samples as a Biomarker of Islet &#946; Cell Death

Islet &#946; cell death precedes development of type 1 diabetes, and detecting this process may allow for early therapeutic intervention. Here, we provide a detailed description of how to measure differentially methylated INS DNA species in human serum as a biomarker of &#946; cell death.

The death of islet &#946; cells is thought to underlie the pathogenesis of virtually all forms of diabetes and to precede the development of frank ...

measurement-differentially-methylated-ins-dna-species-human-serum

Nanyang Technological University

Research

JoVE Journal

Genetics

6.4K Views.  Indiana University School of Medicine. Islet β cell death precedes development of type 1 diabetes, and detecting this process may allow for early therapeutic intervention. Here, we provide a detailed description of how to measure differentially methylated INS DNA species in human serum as a biomarker of β cell death. 

Video: Measurement of Differentially Methylated INS DNA Species in Human Serum Samples as a Biomarker of Islet β Cell Death

Methods to Assess Beta Cell Death Mediated by Cytotoxic T Lymphocytes

Type 1 diabetes (T1D) is a T cell mediated autoimmune disease. During the pathogenesis, patients become progressively more insulinopenic as 
insulin production is lost, presumably this results from the destruction of pancreatic beta cells by T cells. Understanding the mechanisms of beta cell death during 
the development of T1D will provide insights to generate an effective cure for this disease. Cell-mediated lymphocytotoxicity (CML) assays have historically used the 
radionuclide Chromium 51 (51Cr) to label target cells. These targets are then exposed to effector cells and the release of 51Cr from target 
cells is read as an indication of lymphocyte-mediated cell death. Inhibitors of cell death result in decreased release of 51Cr.
 As effector cells, we used an activated autoreactive clonal population of CD8+ Cytotoxic T lymphocytes (CTL) isolated from a mouse stock transgenic for both the alpha and beta chains of the AI4 T cell receptor (TCR). Activated AI4 T cells were co-cultured with 51Cr labeled target NIT cells for 16 hours, release of 51Cr was recorded to calculate specific lysis 
Mitochondria participate in many important physiological events, such as energy production, regulation of signaling transduction, and apoptosis. The study of beta cell mitochondrial functional changes during the development of T1D is a novel area of research. Using the mitochondrial membrane potential dye Tetramethyl Rhodamine Methyl Ester (TMRM) and confocal microscopic live cell imaging, we monitored mitochondrial membrane potential over time in the beta cell line NIT-1. For imaging studies, effector AI4 T cells were labeled with the fluorescent nuclear staining dye Picogreen. NIT-1 cells and T cells were co-cultured in chambered coverglass and mounted on the microscope stage equipped with a live cell chamber, controlled at 37&deg;C, with 5% CO2, and humidified. During these experiments images were taken of each cluster every 3 minutes for 400 minutes.
Over a course of 400 minutes, we observed the dissipation of mitochondrial membrane potential in NIT-1 cell clusters where AI4 T cells were attached. In the simultaneous control experiment where NIT-1 cells were co-cultured with MHC mis-matched human lymphocyte Jurkat cells, mitochondrial membrane potential remained intact. This technique can be used to observe real-time changes in mitochondrial membrane potential in cells under attack of cytotoxic lymphocytes, cytokines, or other cytotoxic reagents.

Cell-mediated lymphocytotoxicity (CML) assays can be used to test autoreactive responses and study mechanisms of cell death in vitro. However, using live-cell confocal microscopic imaging techniques with fluorescent dyes, the type and kinetics of cell death as well as the pathways utilized can be studied in greater detail.

Type 1 diabetes (T1D) is a T cell mediated autoimmune disease.  During the pathogenesis, patients become progressively more insulinopenic as 
insulin ...

Immunology and Infection

Isolation of Human Islets from Partially Pancreatectomized Patients

Investigations into the pathogenesis of type 2 diabetes and islets of Langerhans malfunction 1 have been hampered by the limited availability of type 2 diabetic islets from organ donors2. Here we share our protocol for isolating islets from human pancreatic tissue obtained from type 2 diabetic and non-diabetic patients who have undergone partial pancreatectomy due to different pancreatic diseases (benign or malignant pancreatic tumors, chronic pancreatitis, and common bile duct or duodenal tumors). All patients involved gave their consent to this study, which had also been approved by the local ethics committee. The surgical specimens were immediately delivered to the pathologist who selected soft and healthy appearing pancreatic tissue for islet isolation, retaining the damaged tissue for diagnostic purposes. We found that to isolate more than 1,000 islets, we had to begin with at least 2 g of pancreatic tissue. Also essential to our protocol was to visibly distend the tissue when injecting the enzyme-containing media and subsequently mince it to aid digestion by increasing the surface area.
To extend the applicability of our protocol to include the occasional case in which a large amount (&gt;15g) of human pancreatic tissue is available , we used a Ricordi chamber (50 ml) to digest the tissue. During digestion, we manually shook the Ricordi chamber3 at an intensity that varied by specimen according to its level of tissue fibrosis. A discontinous Ficoll gradient was then used to separate the islets from acinar tissue. We noted that the tissue pellet should be small enough to be homogenously resuspended in Ficoll medium with a density of 1.125 g/ml. After isolation, we cultured the islets under stress free conditions (no shaking or rotation) with 5% CO2 at 37 &deg;C for at least 48 h in order to facilitate their functional recovery. Widespread application of our protocol and its future improvement could enable the timely harvesting of large quantities of human islets from diabetic and clinically matched non-diabetic subjects, greatly advancing type 2 diabetes research.

The supply of type 2 diabetic islets for research is insufficient. Here we share our protocol for isolating islets from patients undergoing partial pancreatectomy. This approach represents a unique venue for obtaining islets from type 2 diabetic and clinically matched non-diabetic subjects in adequate numbers for basic and clinical studies.

Investigations into the pathogenesis of type 2 diabetes and islets of Langerhans malfunction 1 have been hampered by the limited availability of type 2 ...

Medicine

Methylated DNA Immunoprecipitation

The identification of DNA methylation patterns is a common procedure in the study of epigenetics, as methylation is known to have significant effects on gene expression, and is involved with normal development as well as disease 1-4. Thus, the ability to discriminate between methylated DNA and non-methylated DNA is essential for generating methylation profiles for such studies. Methylated DNA immunoprecipitation (MeDIP) is an efficient technique for the extraction of methylated DNA from a sample of interest 5-7. A sample of as little as 200 ng of DNA is sufficient for the antibody, or immunoprecipitation (IP), reaction. DNA is sonicated into fragments ranging in size from 300-1000 bp, and is divided into immunoprecipitated (IP) and input (IN) portions. IP DNA is subsequently heat denatured and then incubated with anti-5'mC, allowing the monoclonal antibody to bind methylated DNA. After this, magnetic beads containing a secondary antibody with affinity for the primary antibody are added, and incubated. These bead-linked antibodies will bind the monoclonal antibody used in the first step. DNA bound to the antibody complex (methylated DNA) is separated from the rest of the DNA by using a magnet to pull the complexes out of solution. Several washes using IP buffer are then performed to remove the unbound, non-methylated DNA. The methylated DNA/antibody complexes are then digested with Proteinase K to digest the antibodies leaving only the methylated DNA intact. The enriched DNA is purified by phenol:chloroform extraction to remove the protein matter and then precipitated and resuspended in water for later use. PCR techniques can be used to validate the efficiency of the MeDIP procedure by analyzing the amplification products of IP and IN DNA for regions known to lack and known to contain methylated sequences. The purified methylated DNA can then be used for locus-specific (PCR) or genome-wide (microarray and sequencing) methylation studies, and is particularly useful when applied in conjunction with other research tools such as gene expression profiling and array comparative genome hybridization (CGH) 8. Further investigation into DNA methylation will lead to the discovery of new epigenetic targets, which in turn, may be useful in developing new therapeutic or prognostic research tools for diseases such as cancer that are characterized by aberrantly methylated DNA 2, 4, 9-11.

This video demonstrates the protocol for methylated DNA immunoprecipitation (MeDIP). MeDIP is a two day procedure that selectively extracts methylated DNA fragments from a genomic DNA sample using antibodies with specificity for 5 -methylcytosine (anti-5 mC).

The identification of DNA methylation patterns is a common procedure in the study of epigenetics, as methylation is known to have significant effects on ...

Biology

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

Pancreatic islets comprise of endocrine cells with distinctive hormone expression patterns. The endocrine cells show functional differences in response to normal and pathological conditions. The goal of this protocol is to generate high-quality, large-scale transcriptome data of each endocrine cell type with the use of a droplet-based microfluidic single-cell RNA sequencing technology. Such data can be utilized to build the gene expression profile of each endocrine cell type in normal or specific conditions. The process requires careful handling, accurate measurement, and rigorous quality control. In this protocol, we describe detailed steps for human pancreatic islets dissociation, sequencing, and data analysis. The representative results of about 20,000 human single islet cells demonstrate the successful application of the protocol.

Here, we present a protocol to generate high-quality, large-scale transcriptome data of single cells from isolated human pancreatic islets using a droplet-based microfluidic single-cell RNA sequencing technology.

Pancreatic islets comprise of endocrine cells with distinctive hormone expression patterns. The endocrine cells show functional differences in response to ...

Improved Protocol For Laser Microdissection Of Human Pancreatic Islets From Surgical Specimens

Laser microdissection (LMD) is a technique that allows the recovery of selected cells and tissues from minute amounts of parenchyma 1,2. The dissected cells can be used for a variety of investigations, such as transcriptomic or proteomic studies, DNA assessment or chromosomal analysis 2,3. An especially challenging application of LMD is transcriptome analysis, which, due to the lability of RNA 4, can be particularly prominent when cells are dissected from tissues that are rich of RNases, such as the pancreas. A microdissection protocol that enables fast identification and collection of target cells is essential in this setting in order to shorten the tissue handling time and, consequently, to ensure RNA preservation. 
Here we describe a protocol for acquiring human pancreatic beta cells from surgical specimens to be used for transcriptomic studies 5. Small pieces of pancreas of about 0.5-1 cm3 were cut from the healthy appearing margins of resected pancreas specimens, embedded in Tissue-Tek O.C.T. Compound, immediately frozen in chilled 2-Methylbutane, and stored at -80 &deg;C until sectioning. Forty serial sections of 10 &mu;m thickness were cut on a cryostat under a -20 &deg;C setting, transferred individually to glass slides, dried inside the cryostat for 1-2 min, and stored at -80 &deg;C. 
Immediately before the laser microdissection procedure, sections were fixed in ice cold, freshly prepared 70% ethanol for 30 sec, washed by 5-6 dips in ice cold DEPC-treated water, and dehydrated by two one-minute incubations in ice cold 100% ethanol followed by xylene (which is used for tissue dehydration) for 4 min; tissue sections were then air-dried afterwards for 3-5 min. Importantly, all steps, except the incubation in xylene, were performed using ice-cold reagents - a modification over a previously described protocol 6. utilization of ice cold reagents resulted in a pronounced increase of the intrinsic autofluorescence of beta cells, and facilitated their recognition. For microdissection, four sections were dehydrated each time: two were placed into a foil-wrapped 50 ml tube, to protect the tissue from moisture and bleaching; the remaining two were immediately microdissected. This procedure was performed using a PALM MicroBeam instrument (Zeiss) employing the Auto Laser Pressure Catapulting (AutoLPC) mode. The completion of beta cell/islet dissection from four cryosections required no longer than 40-60 min. Cells were collected into one AdhesiveCap and lysed with 10 &mu;l lysis buffer. Each single RNA specimen for transcriptomic analysis was obtained by combining 10 cell microdissected samples, followed by RNA extraction using the Pico Pure RNA Isolation Kit (Arcturus). This protocol improves the intrinsic autofluorescence of human beta cells, thus facilitating their rapid and accurate recognition and collection. Further improvement of this procedure could enable the dissection of phenotypically different beta cells, with possible implications for better understanding the changes associated with type 2 diabetes.

Laser microdissection is a technique that allows the recovery of selected cells from minute amounts of parenchyma. Here we describe a protocol for acquiring human pancreatic islets from surgical specimens to be used for transcriptomic studies. Our protocol improves the intrinsic autofluorescence of human beta cells, thus facilitating their collection.

Laser microdissection (LMD) is a technique that allows the recovery of selected cells and tissues from minute amounts of parenchyma 1,2. The dissected ...

In situ Quantification of Pancreatic Beta-cell Mass in Mice

Tracing changes of specific cell populations in health and disease is an important goal of biomedical research. The process of monitoring pancreatic beta-cell proliferation and islet growth is particularly challenging. We have developed a method to capture the distribution of beta-cells in the intact pancreas of transgenic mice with fluorescence-tagged beta-cells with a macro written for ImageJ (rsb.info.nih.gov/ij/). Following pancreatic dissection and tissue clearing, the entire pancreas is captured as a virtual slice, after which the GFP-tagged beta-cells are examined. The analysis includes the quantification of total beta-cell area, islet number and size distribution with reference to specific parameters and locations for each islet and for small clusters of beta-cells. The entire distribution of islets can be plotted in three dimensions, and the information from the distribution on the size and shape of each islet allows a quantitative and qualitative comparison of changes in overall beta-cell area at a glance.

In situ Quantification of Pancreatic Beta-cell Mass in Mice

The following protocol outlines the process of pancreatic dissection for virtual slice imaging, and the subsequent quantification of all GFP-tagged beta-cells in the entire pancreas.

Tracing changes of specific cell populations in health and disease is an important goal of biomedical research. The process of monitoring pancreatic ...

Leprdb Mouse Model of Type 2 Diabetes: Pancreatic Islet Isolation and Live-cell 2-Photon Imaging Of Intact Islets

Type 2 diabetes is a chronic disease affecting 382 million people in 2013, and is expected to rise to 592 million by 2035 1. During the past 2 decades, the role of beta-cell dysfunction in type 2 diabetes has been clearly established 2. Research progress has required methods for the isolation of pancreatic islets. The protocol of the islet isolation presented here shares many common steps with protocols from other groups, with some modifications to improve the yield and quality of isolated islets from both the wild type and diabetic Leprdb (db/db) mice. A live-cell 2-photon imaging method is then presented that can be used to investigate the control of insulin secretion within islets.

Leprdb Mouse Model of Type 2 Diabetes: Pancreatic Islet Isolation and Live-cell 2-Photon Imaging Of Intact Islets

We present here a protocol for the isolation of islets from the mouse model of type 2 diabetes, Leprdb and details of a live-cell assay for measurement of insulin secretion from intact islets that utilizes 2 photon microscopy.

Type 2 diabetes is a chronic disease affecting 382 million people in 2013, and is expected to rise to 592 million by 2035 1. During the past 2 decades, ...

Electrochemiluminescence Assays for Human Islet Autoantibodies

Pinpointing islet autoantibodies associated with type 1 diabetes (T1D) leads the way to project and deter this disease in the general population. A novel ECL assay is a nonradioactive fluid phase assay for islet autoantibodies with higher sensitivity and specificity than the current 'gold' standard radio-binding assay (RBA). ECL assays can more precisely define the onset of presymptomatic T1D by distinguishing the high-risk, high-affinity autoantibodies from the low-risk, low-affinity autoantibodies generated in RBAs, and conventional enzyme-linked immunosorbent assays (ELISA). The antigen protein used in this ECL assay is labeled with Sulfo-tag and Biotin, respectively. Each ECL autoantibody assay that uses a particular antigen protein needs an optimization step before it can be used for laboratory application. This step is especially vital in determining the requirements for serum acid treatments, concentrations, and ratios of the two different antigens labeled with Sulfo-tag and Biotin. To perform the assay, serum samples are mixed with Sulfo-tag-conjugated and biotinylated capture antigen protein in phosphate buffered solution (PBS), containing 5% Bovine Serum Albumin (BSA). Afterwards, the samples are incubated overnight at 4 &#176;C. The same day, a streptavidin-coated plate is prepared with blocker buffer and incubated overnight at 4 &#176;C. On the second day, wash the streptavidin plate and transfer the serum-antigen mixture onto the plate. Place the plate on the plate shaker, set it at low speed, and incubate at room temperature for 1 h. Subsequently, the plate is washed again, and reader buffer is added. The plate is then counted on the plate reader machine. The results are conveyed through an index, which is generated from internal standard positive and negative control serum samples.

Here, we presented the methods to detect human islet autoantibodies using electrochemiluminescence (ECL) assays. The protocol, used to predict type 1 diabetes, can be expanded upon to detect autoantibodies for other autoimmune diseases.

Pinpointing islet autoantibodies associated with type 1 diabetes (T1D) leads the way to project and deter this disease in the general population. A novel ...

Detergent-Free Decellularization of the Human Pancreas for Soluble Extracellular Matrix (ECM) Production

Islet transplantation (ITx) has the potential to become the standard of care in beta cell replacement medicine but its results remain inferior to those obtained with whole pancreas transplantation. The protocols currently used for human islet isolation are under scrutiny because they are based on the enzymatic digestion of the organ, whereby the pancreas is demolished, its connections to the body are lost and islets are irreversibly damaged. Islet damage is characterized by critical factors such as the destruction of the extracellular matrix (ECM), which represents the 3D framework of the islet niche and whose loss is incompatible with islet euphysiology. Researchers are proposing the use of ECM-based scaffolds derived from the mammalian pancreas to address this problem and ultimately improve islet viability, function, and lifespan. Currently available methods to obtain such scaffolds are harsh because they are largely detergent based. Thus, we propose a new, detergent-free method that creates less ECM damage and can preserve critical components of pancreatic ECM. The results show that the newly developed decellularization protocol allowed the achievement of complete DNA clearance while the ECM components were retained. The ECM obtained was tested for cytotoxicity and encapsulated with human pancreatic islets which showed a positive cellular behavior with insulin secretion when stimulated with glucose challenge. Collectively, we propose a new method for the decellularization of the human pancreas without the use of conventional ionic and non-ionic chemical detergents. This protocol and the ECM obtained with it could be of use for both in vitro and in vivo applications.

Detergent-Free Decellularization of the Human Pancreas for Soluble Extracellular Matrix ECM Production

The protocol described in this manuscript explains the steps for the fabrication of a soluble extracellular matrix (ECM) from the human pancreas. The solubilized ECM powder obtained through this protocol may be used for the recapitulation of pancreatic islets&#8217; microenvironment in vitro and, potentially, in vivo settings.

Islet transplantation (ITx) has the potential to become the standard of care in beta cell replacement medicine but its results remain inferior to those ...

Bioengineering

Isolated Pancreatic Islet Treatment and Apoptosis Measurement

This study investigates the effect of pro-inflammatory cytokines on pancreatic islets, particularly insulin-producing &#946;-cells, using a combination of fluorescence staining techniques and confocal microscopy to assess cell viability, apoptosis, and &#946;-cell-specific death. Isolated mouse islets were treated with varying concentrations of a cytokine cocktail, including TNF-&#945;, IL-1&#946;, and IFN-&#947;, to mimic immune-mediated apoptosis during the development of type 1 diabetes. The viability of islet cells was evaluated with FDA/PI dual staining, where FDA conversion to fluorescein indicated viable cells, and PI marked membrane-compromised cells. YOPRO-1 and nuclear staining provided additional data on apoptosis, with Annexin-V confirming early apoptotic cells. Quantitative analysis revealed significant increases in apoptosis and cell death rates in cytokine-treated islets. To specifically assess effects on &#946;-cells, Zn2+ selective indicator staining was used to label insulin-producing cells through the zinc association in insulin granules, revealing substantial &#946;-cell loss following treatment of islets with pro-inflammatory cytokines for 24 h. These multi-staining protocols effectively capture and quantify the extent of cytokine-induced damage in islets and can be used to evaluate therapeutics designed to prevent &#946;-cell apoptosis in early type 1 diabetes.

This study utilizes multi-staining fluorescence-based markers of cell death and apoptosis combined with confocal microscopy to assess cytokine-induced apoptosis and &#946;-cell-specific death in pancreatic islets. It reveals spatial and temporal changes in cell death and apoptosis in response to extracellular stimuli.

This study investigates the effect of pro-inflammatory cytokines on pancreatic islets, particularly insulin-producing &#946;-cells, using a combination of ...

Measurement of Differentially Methylated INS DNA Species in Human Serum Samples as a Biomarker of Islet β Cell Death

Summary

Explore More Videos

Chapters in this video

Methods to Assess Beta Cell Death Mediated by Cytotoxic T Lymphocytes

Isolation of Human Islets from Partially Pancreatectomized Patients

Methylated DNA Immunoprecipitation

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

Improved Protocol For Laser Microdissection Of Human Pancreatic Islets From Surgical Specimens

In situ Quantification of Pancreatic Beta-cell Mass in Mice

Lepr^db Mouse Model of Type 2 Diabetes: Pancreatic Islet Isolation and Live-cell 2-Photon Imaging Of Intact Islets

Electrochemiluminescence Assays for Human Islet Autoantibodies

Detergent-Free Decellularization of the Human Pancreas for Soluble Extracellular Matrix (ECM) Production

Isolated Pancreatic Islet Treatment and Apoptosis Measurement