Methylation-specific ligation detection reaction (msLDR): a new approach for multiplex evaluation of methylation patterns

Bormann, Felix; Sers, Christine; Seliger, Barbara; Handke, Diana; Bergmann, Thomas; Seibt, Stephanie; Lehrach, Hans; Dahl, Andreas

doi:10.1007/s00438-011-0645-9

Cited by 6 publications

(5 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The HLA-A locus also has a miR-148a binding site in its 3′UTR, but unlike HLA-C, the seed region in the HLA-A locus is fixed for the form that is inhibited by miR-148a (7,18), so differential miR-148a binding cannot account for variation in HLA-A expression levels. Several studies have identified DNA methylation as an epigenetic mechanism responsible for varied expression levels of genes located within the MHC region (11)(12)(13)(19)(20)(21)(22). Variation in HLA-A methylation levels may play a role in certain cancers (10)(11)(12)(13), but these studies have not addressed whether differential, allelic lineage-specific DNA methylation patterns occur at the locus and whether they affect HLA-A expression levels in a lineage-specific manner.…”

Section: Introductionmentioning

confidence: 99%

Epigenetic regulation of differentialHLA-Aallelic expression levels

et al. 2015

View full text Add to dashboard Cite

MHC class I expression levels influence the strength of immune responses and represent another variable in determining outcome to disease beyond peptide binding alone. Identification of the HLA loci that vary in allelic expression levels and delineating the mechanism responsible for expression variation may provide the opportunity to modify their expression therapeutically. We have examined the expression levels of allelic lineages at the HLA-A locus in a sample of 216 European Americans using a real-time polymerase chain reaction assay, which amplifies all HLA-A lineages specifically with equal efficiency, and observed a gradient of expression that associates with HLA-A allelic lineage (R = 0.6, P = 5 × 10(-25)). DNA methylation of the HLA-A gene appears to contribute to the variation in HLA-A mRNA expression levels, as a significant inverse correlation was observed between HLA-A mRNA expression levels in untreated cells and the degree to which expression is increased after treatment of the cells with a DNA methyltransferase inhibitor (R = 0.6, P = 2.8 × 10(-6)). Further, deep-sequencing and immunoprecipitation assays revealed allelic lineage-specific methylation patterns within the HLA-A promoter region where increased DNA methylation levels correlated significantly with reduced HLA-A expression levels (R = 0.89, P = 3.7 × 10(-9)). These data demonstrate HLA-A allelic lineage-specific variation in expression levels, and DNA methylation as a likely factor in contributing to this variation.

show abstract

Section: Introductionmentioning

confidence: 99%

Epigenetic regulation of differentialHLA-Aallelic expression levels

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Ligases have been used to amplify single-DNA base changes with the ligase chain reaction (LCR) and ligase detection reaction (LDR) assays (25,26 ). Both LCR and LDR have been used to detect methylation at single CpGs and have been coupled to various readout platforms (14, 15, 26 -29 ), but the most common ap- Methylated sites (M, shaded circles) and unmethylated (U, open circles).…”

mentioning

confidence: 99%

DNA Ligase-Based Strategy for Quantifying Heterogeneous DNA Methylation without Sequencing

Wee¹,

Rauf²,

Shiddiky³

et al. 2015

Clinical Chemistry

View full text Add to dashboard Cite

BACKGROUND: DNA methylation is a potential source of disease biomarkers. Typically, methylation levels are measured at individual cytosine/guanine (CpG) sites or over a short region of interest. However, regions of interest often show heterogeneous methylation comprising multiple patterns of methylation (epialleles) on individual DNA strands. Heterogeneous methylation is largely ignored because digital methods are required to deconvolute these usually complex patterns of epialleles. Currently, only singlemolecule approaches, such as next generation sequencing (NGS), can provide detailed epiallele information. Because NGS is not yet feasible for routine practice, we developed a single-molecule-like approach, named for epiallele quantification (EpiQ).

show abstract

“…48 Methylation of ULBP2 and ULBP3 has previously been reported in colon cancer cell lines. 35,49 However, we found that all the ligands analyzed (MICA, MICB, ULBP1, ULBP2 and ULBP3) were unmethylated and highly expressed in colon cancer cell lines. Moreover, analysis of the NKG2DL methylation status in colon cancer patients showed that both normal and tumor tissues from colon cancer patients were hypomethylated independently of the tumor stage.…”

Section: Discussionmentioning

confidence: 86%

Methylation of NKG2D ligands contributes to immune system evasion in acute myeloid leukemia

et al. 2014

View full text Add to dashboard Cite

Engagement of the activating receptor NKG2D (natural killer group 2 member D) with its ligands (NKG2DL) major histocompatibility complex class I related-A and -B (MICA/B), UL-16 binding protein families (ULBPs 1-6) is important to ensure the innate immunity to tumor cells. However, these cells have developed strategies to downregulate NKG2DL expression and avoid immune recognition. We demonstrate that DNA methylation can contribute to the absence of NKG2DL expression during tumor progression. We analyzed the DNA methylation profiles for each NKG2DL by pyrosequencing in acute myeloid leukemia (AML), acute lymphocytic leukemia (ALL), hepatocellular carcinoma (HC), breast cancer and colon cancer cell lines. High levels of DNA methylation for NKG2DL were found in some tumor cell lines, mainly in AML cells. This hypermethylation was correlated with the absence of transcription for NKG2DL. Higher DNA methylation levels for MICA, ULBP1 and ULBP2 were observed in AML patients (n=60) compared with healthy donors (n=25). However, no DNA methylation for NKG2DL was found in colon cancer patients (n=44). Treatment with demethylating agents (5-azacytidine and 5-aza-2'-deoxycytidine) restored the expression of NKG2DL on the cell surface of AML cells, leading to an enhanced recognition by NKG2D-expressing cells. Our data suggest that NKG2DL may be aberrantly silenced by DNA methylation as a consequence of tumor development in AML patients.

show abstract

Methylation-specific ligation detection reaction (msLDR): a new approach for multiplex evaluation of methylation patterns

Cited by 6 publications

References 30 publications

Epigenetic regulation of differentialHLA-Aallelic expression levels

Epigenetic regulation of differentialHLA-Aallelic expression levels

DNA Ligase-Based Strategy for Quantifying Heterogeneous DNA Methylation without Sequencing

Methylation of NKG2D ligands contributes to immune system evasion in acute myeloid leukemia

Contact Info

Product

Resources

About