Time-resolved FRET method for typing polymorphic alleles of the human leukocyte antigen system by using a single DNA probe

Genome-wide DNA methylation profile analysis identifies differentially methylated loci associated with ankylosis spondylitis

Background

Ankylosing spondylitis (AS) is a chronic rheumatic and autoimmune disease. Little is known about the potential role of DNA methylation in the pathogenesis of AS. This study was undertaken to explore the potential role of DNA methylation in the genetic mechanism of AS.

Methods

In this study, we compared the genome-wide DNA methylation profiles of peripheral blood mononuclear cells (PBMCs) between five AS patients and five healthy subjects, using the Illumina Infinium HumanMethylation450 BeadChip. Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) was performed to validate the relevance of the identified differentially methylated genes for AS, using another independent sample of five AS patients and five healthy subjects.

Results

Compared with healthy controls, we detected 1915 differentially methylated CpG sites mapped to 1214 genes. The HLA-DQB1 gene achieved the most significant signal (cg14323910, adjusted P = 1.84 × 10^–6, β difference = 0.5634) for AS. Additionally, the CpG site cg04777551 of HLA-DQB1 presented a suggestive association with AS (adjusted P = 1.46 × 10^–3, β difference = 0.3594). qRT-PCR observed that the mRNA expression level of HLA-DQB1 in AS PBMCs was significantly lower than that in healthy control PBMCs (ratio = 0.48 ± 0.10, P < 0.001). Gene Ontology (GO) and KEGG pathway enrichment analysis of differentially methylated genes identified four GO terms and 10 pathways for AS, functionally related to antigen dynamics and function.

Conclusions

Our results demonstrated the altered DNA methylation profile of AS and implicated HLA-DQB1 in the development of AS.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-017-1382-1) contains supplementary material, which is available to authorized users.

Effects of non-CpG site methylation on DNA thermal stability: a fluorescence study

Cytosine methylation is a widespread epigenetic regulation mechanism. In healthy mature cells, methylation occurs at CpG dinucleotides within promoters, where it primarily silences gene expression by modifying the binding affinity of transcription factors to the promoters. Conversely, a recent study showed that in stem cells and cancer cell precursors, methylation also occurs at non-CpG pairs and involves introns and even gene bodies. The epigenetic role of such methylations and the molecular mechanisms by which they induce gene regulation remain elusive. The topology of both physiological and aberrant non-CpG methylation patterns still has to be detailed and could be revealed by using the differential stability of the duplexes formed between site-specific oligonucleotide probes and the corresponding methylated regions of genomic DNA. Here, we present a systematic study of the thermal stability of a DNA oligonucleotide sequence as a function of the number and position of non-CpG methylation sites. The melting temperatures were determined by monitoring the fluorescence of donor-acceptor dual-labelled oligonucleotides at various temperatures. An empirical model that estimates the methylation-induced variations in the standard values of hybridization entropy and enthalpy was developed.

Human Leukocyte Antigen DQB1 (HLA-DQB1) Polymorphisms and the Risk for Guillain-Barré Syndrome: A Systematic Review and Meta-Analysis

Guillain-Barré syndrome (GBS) is an autoimmune disorder of the peripheral nervous system. There is no consensus regarding reported associations between human leukocyte antigen DQB1 (HLA-DQB1) polymorphisms and the risk for developing GBS. Here, we evaluated possible associations between HLA-DQB1 polymorphisms and the risk for GBS using a meta-analysis. We searched PubMed for case-control genetic association studies for HLA-DQB1 polymorphisms (*020x, *030x, *040x, *050x, and *060x) and the risk for GBS. Fixed-effect meta-analytical methods were used for the outcome measure and subgroup analyses. Estimated odds ratios (ORs) and 95% confidence intervals (CIs) were used to investigate the associations between HLA-DQB1 polymorphisms and the risk for GBS. Nine case-control studies involving 780 cases of GBS and 1353 controls were identified in the current study. The meta-analysis demonstrated no significant associations between HLA-DQB1 polymorphisms and the risk for GBS in Asian and Caucasian populations. There were two associations that approached significance: HLA-DQB1*030x in Asian patients (P = 0.07; OR: 0.76, 95% CI: 0.57–1.03) and HLA-DQB1*060x in all patients (P = 0.08; OR: 1.48, 95% CI: 0.96–2.29). Additional studies with larger sample sizes are required to establish a definitive assessment of the contribution of HLA-DQB1 polymorphisms to GBS risk.

Full genotyping of a highly polymorphic human gene trait by time-resolved fluorescence resonance energy transfer

The ability of detecting the subtle variations occurring, among different individuals, within specific DNA sequences encompassed in highly polymorphic genes discloses new applications in genomics and diagnostics. DQB1 is a gene of the HLA-II DQ locus of the Human Leukocyte Antigens (HLA) system. The polymorphisms of the trait of the DQB1 gene including codons 52-57 modulate the susceptibility to a number of severe pathologies. Moreover, the donor-receiver tissue compatibility in bone marrow transplantations is routinely assessed through crossed genotyping of DQB and DQA. For the above reasons, the development of rapid, reliable and cost-effective typing technologies of DQB1 in general, and more specifically of the codons 52-57, is a relevant although challenging task. Quantitative assessment of the fluorescence resonance energy transfer (FRET) efficiency between chromophores labelling the opposite ends of gene-specific oligonucleotide probes has proven to be a powerful tool to type DNA polymorphisms with single-nucleotide resolution. The FRET efficiency can be most conveniently quantified by applying a time-resolved fluorescence analysis methodology, i.e. time-correlated single-photon counting, which allows working on very diluted template specimens and in the presence of fluorescent contaminants. Here we present a full in-vitro characterization of the fluorescence responses of two probes when hybridized to oligonucleotide mixtures mimicking all the possible genotypes of the codons 52-57 trait of DQB1 (8 homozygous and 28 heterozygous). We show that each genotype can be effectively tagged by the combination of the fluorescence decay constants extrapolated from the data obtained with such probes.

Nucleic acid fluorescent probes for biological sensing

Nucleic acid fluorescent probes are playing increasingly important roles in biological sensing in recent years. In addition to the conventional functions of single-stranded DNA/RNA to hybridize with their complementary strands, affinity nucleic acids (aptamers) with specific target binding properties have also been developed, which has greatly broadened the application of nucleic acid fluorescent probes to the detection of a large variety of analytes, including small molecules, proteins, ions, and even whole cells. Another chemical property of nucleic acids is to act as substrates for various nucleic acid enzymes. This property can be utilized not only to detect those enzymes and screen their inhibitors, but also employed to develop effective signal amplification systems, which implies extensive applications. This review mainly covers the biosensing methods based on the above three types of nucleic acid fluorescent probes. The most widely used intensity-based biosensing assays are covered first, including nucleic acid probe-based signal amplification methods. Then fluorescence lifetime, fluorescence anisotropy, and fluorescence correlation spectroscopy assays are introduced, respectively. As a rapidly developing field, fluorescence imaging approaches are also briefly summarized.

Typing of a polymorphic human gene conferring susceptibility to insulin-dependent diabetes mellitus by picosecond-resolved FRET on non-purified/non-amplified genomic DNA

This work concerns the identification of the alleles of the polymorphic DQB1 gene of the human leukocyte antigen system, conferring susceptibility to the development of insulin-dependent diabetes mellitus (IDDM) in non-PCR amplified DNA samples and, more importantly, in crude cell extracts. Our method is based on the time-resolved analysis of a Förster energy-transfer mechanism that occurs in a dual-labelled fluorescent probe specific for the IDDM-associated DQB1-0201 allele. Such an oligonucleotide probe is labelled, at the two ends, by a pair of chromophores that operate as donor and acceptor in a Förster resonant energy transfer. The donor fluorescence is quenched with an efficiency that is strongly dependent on the donor-to-acceptor distance, hence on the configuration of the probe after hybridization with the various DQB1 alleles. By time-correlated single-photon counting, performed with an excitation/detection system endowed with 30-ps resolution, we measure the time-resolved fluorescence decay of the donor and discriminate, by means of the decay–time value, the DNA bearing the ‘susceptible’ allele from the DNAs bearing any other sequence in the same region of the DQB1 gene. We could also distinguish the presence of the DQB1-0201 allele in a homozygous versus a heterozygous condition.