Name: a 5-mc dot blot assay quantifying the dna methylation level of chondrocyte dedifferentiation in vitro
Uploaded: 2017-05-17T13:00:00
Description: Watch this Scientific Journal Video about A 5-mC Dot Blot Assay Quantifying the DNA Methylation Level of Chondrocyte Dedifferentiation In Vitro at JoVE.com

This work was supported by the following grants: Natural Science Foundation of China (No. 81572198; No. 81260161; No. 81000460); Natural Science Foundation of Guangdong Province, China (No. 2015A030313772); China Postdoctoral Science Foundation Funded Project (No. 2013M530385); The Medical Research Foundation of Guangdong Province, China (No. A2016314); Shenzhen Science and Technology Projects (No. JCYJ20160301111338144; No. JSGG20151030140325149; No. JSGG20140519105550503; No.GJHZ20130412153906739; No. JCYJ20140414170821160; No.JCYJ20140414170821200).

This study was approved by the Human Ethics Committee of Shenzhen Second People&#39;s Hospital.
1. Human Articular Cartilage Tissue Collection and Chondrocyte Culture
<ol>
	<li>Preparation of materials
	<ol>
		<li>Prepare Dulbecco&#39;s modified eagle medium (DMEM) medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. Prepare 1 mg/mL collagenase II, 0.25% trypsin-EDTA, phosphate-buffered saline (PBS), and a cell strainer (40 &#181;m nylon).</li>
	</...

<ol>
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W., 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=Exploring+Genome-wide+DNA+Methylation+Profiles+Altered+in+Kashin-Beck+Disease+Using+Infinium+Human+Methylation+450+Bead+Chips.">Exploring Genome-wide DNA Methylation Profiles Altered in Kashin-Beck Disease Using Infinium Human Methylation 450 Bead Chips.</a> Biomed Environ Sci. 29 (7), 539-543 (2016).</li><li>Li, X. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimization+of+an+HPLC+Method+for+Determining+the+Genomic+Methylation+Levels+of+Taxus+Cells.">Optimization of an HPLC Method for Determining the Genomic Methylation Levels of Taxus Cells.</a> J Chromatogr Sci. 54 (2), 200-205 (2016).</li><li>Maghbooli, Z., 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=Global+DNA+methylation+as+a+possible+biomarker+fordiabetic+retinopathy.">Global DNA methylation as a possible biomarker fordiabetic retinopathy.</a> Diabetes Metab Res Rev. 31 (2), 183-189 (2015).</li><li>Barlic, A., Drobnic, M., Malicev, E., Kregar-Velikonja, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+analysis+of+gene+expression+in+human+articular+chondrocytes+assigned+for+autologous+implantation.">Quantitative analysis of gene expression in human articular chondrocytes assigned for autologous implantation.</a> J Orthop Res. 26 (6), 847-853 (2008).</li><li>Legendre, F., 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=Enhanced+hyaline+cartilage+matrix+synthesis+in+collagen+sponge+scaffolds+by+using+siRNA+to+stabilizechondrocytes+phenotype+cultured+with+bone+morphogenetic+protein-2+under+hypoxia.">Enhanced hyaline cartilage matrix synthesis in collagen sponge scaffolds by using siRNA to stabilizechondrocytes phenotype cultured with bone morphogenetic protein-2 under hypoxia.</a> Tissue Eng Part C Methods. 19 (7), 550-567 (2013).</li><li>Niethammer, T. 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=Analysis+of+the+autologous+chondrocyte+quality+of+matrix-based+autologous+chondrocyte+implantation+in+the+knee+joint.">Analysis of the autologous chondrocyte quality of matrix-based autologous chondrocyte implantation in the knee joint.</a> Int Orthop. 40 (1), 205-212 (2016).</li><li>Hayatsu, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+bisulfite+genomic+sequencing+used+in+the+analysis+of+epigenetic+states,+a+technique+in+the+emerging+environmental+genotoxicology+research.">The bisulfite genomic sequencing used in the analysis of epigenetic states, a technique in the emerging environmental genotoxicology research.</a> Mutat Res. 659 (1-2), 77-82 (2008).</li><li>Haque, N., Nishiguchi, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bisulfite+sequencing+for+cytosine-methylation+analysis+in+plants.">Bisulfite sequencing for cytosine-methylation analysis in plants.</a> Methods Mol Biol. 744, 187-197 (2011).</li><li>Ananiev, G. 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Chondrocyte dedifferentiation in vitro severely compromises the outcome of ACI in the treatment of cartilage defect repair11,12. To optimize ACI outcome, it is crucial to avoid the use of dedifferentiated chondrocytes13. Studies have suggested that general DNA methylation level is associated with the extent of the chondrocyte dedifferentiation4,6. Thus, it is imperative to...

Autologous chondrocyte implantation (ACI) is a relatively new, state-of-the-art procedure to treat articular cartilage defects1,2. One of the crucial steps in ACI is amplification of chondrocytes via monolayer culture in vitro. During amplification, the hyaline chondrocytes easily lose their phenotype and become dedifferentiated, which is undesirable for ACI treatment3,4. To optimize the outcome of ACI treatment, the extent of chondrocyte dedifferentiation should be determined before replantation. It is imperative to establish an economic and rapid way to determine the chondrocytes&#39; status. Recently, the association between DNA methylation and chondrocyte dedifferentiation has attracted much attention4,5,6. DNA methylation is a process by which methyl groups are added to DNA, resulting in the conversion of cytosine residues to 5-methylcytosine (5-mC).
To elucidate the biology of DNA methylation in chondrocyte dedifferentiation, the first step is to evaluate the DNA methylation level of chondrocytes, which so far has proven challenging. Bisulfite genomic sequencing is the most widely used technique to analyze DNA methylation7,8. In this assay, bisulfite conversion causes DNA degradation, and thus a substantial amount of sample must be provided for the assay. Also, high-performance liquid chromatography (HPLC) has been used to quantify global DNA methylation levels9,10. However, HPLC analysis requires genomic DNA digestion. Furthermore, advanced and expensive experimental instruments are required. Therefore, in addition to the high cost, these experimental procedures are time consuming. Anti-5-mC antibodies have now become commercially available, which has created the possibility for immune blotting of 5-mC-containing genomic DNA from complex genomes.
In this report, we extracted genomic DNA from chondrocytes grown in a series of monolayer cultures. We used a dot blot assay to evaluate the 5-mC content in human chondrocytes with different numbers of passages. We found that 5-mC content was increased in highly dedifferentiated chondrocytes compared to chondrocytes with low-grade dedifferentiation. Additionally, we identified a relationship between dedifferentiation status and 5-mC levels. Finally, we reported that the changes in 5-mC content were associated with the chondrocyte phenotype. Therefore, the 5-mC dot blot assay is a reliable, simple, and rapid method to detect the DNA methylation level in chondrocytes.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM&#160;&#160;</td>
			<td>Gibco Inc.</td>
			<td>11965&#8211;092</td>
			<td>Warm in 37 &#176;C water bath before use</td>
		</tr>
		<tr>
			<td rowspan="2">Phosphate-Buffered Saline(PBS)</td>
			<td rowspan="2">HyClone Inc.</td>
			<td rowspan="2">SH30256.01B</td>
			<td>D-PBS, free of&#160;</td>
		</tr>
		<tr>
			<td>Ca2+/Mg2+</td>
		</tr>
		<tr>
			<td>FBS</td>
			<td>Gibco Inc.</td>
			<td>10099-141</td>
			<td></td>
		</tr>
		<tr>
			<td>0.25%Trypsin/EDTA</td>
			<td>Gibco Inc.</td>
			<td>25200-056</td>
			<td></td>
		</tr>
		<tr>
			<td>1%Penicillin-Streptomycin</td>
			<td>Gibco Inc.</td>
			<td>15140-122</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Mallinckrodt</td>
			<td>4440</td>
			<td></td>
		</tr>
		<tr>
			<td>Isoamyl Alcohol</td>
			<td>Sigma</td>
			<td>I-3643</td>
			<td></td>
		</tr>
		<tr>
			<td>Phenol</td>
			<td>Gibco BRL</td>
			<td>15513-039</td>
			<td></td>
		</tr>
		<tr>
			<td>Proteinase K</td>
			<td>Gibco BRL</td>
			<td>24568-2</td>
			<td></td>
		</tr>
		<tr>
			<td>TAE buffer&#160;</td>
			<td>Bio Whittaker</td>
			<td>16-011V</td>
			<td></td>
		</tr>
		<tr>
			<td>Distilled Water</td>
			<td>Gibco BRL</td>
			<td>15230-170</td>
			<td></td>
		</tr>
		<tr>
			<td>1 M Tris-HCl</td>
			<td>Biosharp Inc.</td>
			<td>BL514A</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween20</td>
			<td>Biotopped Inc.</td>
			<td>C58H114O26</td>
			<td></td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Proliant Inc.</td>
			<td>68700</td>
			<td></td>
		</tr>
		<tr>
			<td>Collagenase, Type II</td>
			<td>Sigma-Aldrich</td>
			<td>C6885</td>
			<td></td>
		</tr>
		<tr>
			<td>Names&#160;&#160;&#160;&#160;&#160;</td>
			<td>Company&#160;&#160;&#160;&#160;&#160;&#160;&#160;</td>
			<td>Catalog number&#160;&#160;&#160;&#160;&#160;&#160;&#160;</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Strainer(40&#956;m nylon&#65289;</td>
			<td>FALCON Inc.</td>
			<td>352340</td>
			<td></td>
		</tr>
		<tr>
			<td>Hemocytometer</td>
			<td>ISOLAB Inc.</td>
			<td>075.03.001</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon 100 mm&#160; dish</td>
			<td>Corning</td>
			<td>353003</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge Tubes</td>
			<td>TPP AG</td>
			<td>91050</td>
			<td>Gamma-sterilized</td>
		</tr>
		<tr>
			<td>High-speed centrifuge</td>
			<td>Eppendorf</td>
			<td>5804R</td>
			<td></td>
		</tr>
		<tr>
			<td>ThermoMixer</td>
			<td>MIULAB</td>
			<td>MTH-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Carbon dioxide cell incubator</td>
			<td>Thermo scientific</td>
			<td>3111</td>
			<td></td>
		</tr>
		<tr>
			<td>Chemi-imaging Analyse System</td>
			<td>UVITEC Cambridge</td>
			<td>ALLIANCE</td>
			<td></td>
		</tr>
	</tbody>
</table>

a 5-mc dot blot assay quantifying the dna methylation level of chondrocyte dedifferentiation in vitro

The dedifferentiation of hyaline chondrocytes into fibroblastic chondrocytes often accompanies monolayer expansion of chondrocytes in vitro. The global DNA methylation level of chondrocytes is considered to be a suitable biomarker for the loss of the chondrocyte phenotype. However, results based on different experimental methods can be inconsistent. Therefore, it is important to establish a precise, simple, and rapid method to quantify global DNA methylation levels during chondrocyte dedifferentiation.
Current genome-wide methylation analysis techniques largely rely on bisulfite genomic sequencing. Due to DNA degradation during bisulfite conversion, these methods typically require a large sample volume. Other methods used to quantify global DNA methylation levels include high-performance liquid chromatography (HPLC). However, HPLC requires complete digestion of genomic DNA. Additionally, the prohibitively high cost of HPLC instruments limits HPLC&#39;s wider application.
In this study, genomic DNA (gDNA) was extracted from human chondrocytes cultured with varying number of passages. The gDNA methylation level was detected using a methylation-specific dot blot assay. In this dot blot approach, a gDNA mixture containing the methylated DNA to be detected was spotted directly onto an N+ membrane as a dot inside a previously drawn circular template pattern. Compared with other gel electrophoresis-based blotting approaches and other complex blotting procedures, the dot blot method saves significant time. In addition, dot blots can detect overall DNA methylation level using a commercially available 5-mC antibody. We found that the DNA methylation level differed between the monolayer subcultures, and therefore could play a key role in chondrocyte dedifferentiation. The 5-mC dot blot is a reliable, simple, and rapid method to detect the general DNA methylation level to evaluate chondrocyte phenotype.

Chondrocytes were cultured in a monolayer up to passage 6 (P6). Chondrocytes showed progressive phenotypic changes with successive passages of the monolayer culture. The P0 chondrocyte morphology was round, whereas the cells became highly pinched and flattened with successive passages up to P6 (Figure 1). This morphology change is typical of the chondrocyte dedifferentiation process. Meanwhile, results of the heat map indicated that the general methylation level of CpG si...

Watch this Scientific Journal Video about A 5-mC Dot Blot Assay Quantifying the DNA Methylation Level of Chondrocyte Dedifferentiation In Vitro at JoVE.com

A 5-mC Dot Blot Assay Quantifying the DNA Methylation Level of Chondrocyte Dedifferentiation In Vitro

We present a method to quantify DNA methylation based on the 5-methylcytosine (5-mC) dot blot. We determined the 5-mC levels during chondrocyte dedifferentiation. This simple technique could be used to quickly determine the chondrocyte phenotype in ACI treatment.

A 5-mC Dot Blot Assay Quantifying the DNA Methylation Level of Chondrocyte Dedifferentiation In Vitro

The dedifferentiation of hyaline chondrocytes into fibroblastic chondrocytes often accompanies monolayer expansion of chondrocytes in vitro. The global ...

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