Methylation Status of Alu and LINE-1 Interspersed Repetitive Sequences in Behcet’s Disease Patients

Yüksel, Şahru; Kucukazman, Selma Ozbek; Karataş, Gülten Sungur; Öztürk, Mehmet Akif; Prombhul, Sasiprapa; Hirankarn, Nattiya

doi:10.1155/2016/1393089

Cited by 15 publications

(8 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Regarding cIMT, the results of this study revealed a statistically highly significant difference (P< 0.001), being higher in group Іa (0.82±0.03) than group Іb (0.50±0.04) and healthy controls (0.47±0.04). In agreement with our results, the studies by Ozturk et al [21] and Yuksel et al [22] revealed that cIMT was greater in patients with BD than in control participants (0.55±0.07 vs. 0.48±0.05, P<0.001, and 0.523±0.090 vs. 0.417±0.035 mm, P<0.001, respectively).…”

Section: Resultssupporting

confidence: 93%

Neutrophil-to-lymphocyte ratio: relation to disease activity and carotid intima-media thickness in Behçet’s disease

Elden

Hmmad

Farouk

et al. 2018

Egypt Rheumatol Rehabil

View full text Add to dashboard Cite

Background Behçet's disease (BD) is an autoinflammatory disorder. Disease activity could be detected by changes in peripheral blood cell components. The aim of this study was to assess the relationship between neutrophil-to-lymphocyte ratio (NLR) with disease activity and carotid intima-media thickness (cIMT) in patients with BD. Patients and methods This study was conducted on 20 adult patients with BD (group І). This group was subdivided according to cIMT into group Іa, which included patients with increased cIMT, and group Іb, which included patients with cIMT within normal ranges. Moreover, 20 age-matched and sex-matched apparently healthy volunteers were included as a control group (group ІІ). Patients with BD were subjected to full history taking, thorough clinical examination, and assessment of disease activity according to Behçet's Disease Current Activity Form score. The white blood cell count, neutrophil count, and lymphocytes count were recorded, and NLR was calculated. cIMT assessment was done for all participants. Results There were statistically significant differences (P< 0.05) regarding lymphocytes count and NLR and highly statistically significant difference (P< 0.001) regarding neutrophil count, being higher in patients with BD. There was a statistically highly significant difference (P< 0.001) regarding cIMT, being higher in group Іa patients (0.82±0.03) than group Іb patients (0.50±0.04) and healthy control group (0.47 ±0.04). There was a statistically significance positive correlation (R=639, P=0.005) between NLR and Behçet's Disease Current Activity Form score. In conclusion, higher NLR values were recorded in patients with BD. Furthermore, patients with active BD had higher NLR values than inactive, and NLR is higher in patients with increased cIMT; thus, NLR may be an important bio-index for detecting BD activity and the presence of vascular affection.

show abstract

Section: Resultssupporting

confidence: 93%

Neutrophil-to-lymphocyte ratio: relation to disease activity and carotid intima-media thickness in Behçet’s disease

Elden

Hmmad

Farouk

et al. 2018

Egypt Rheumatol Rehabil

View full text Add to dashboard Cite

show abstract

“…In order to try to confirm the methylation status characteristics in the VSMCs affected by Hcy, we detected global methylation levels were measured. In general, Alu and LINE-1 elements are methylated in somatic tissues, however are hypomethylated in human cancer (36). In the present study, Hcy was observed to reduce the methylation levels of Alu and LINE-1.…”

Section: Discussionsupporting

confidence: 44%

Aberrant promoter methylation of multiple genes in VSMC proliferation induced by Hcy

Cao

Zhang

et al. 2017

Molecular Medicine Reports

View full text Add to dashboard Cite

Vascular smooth muscle cell (VSMC) proliferation is a primary pathological event in atherosclerosis (AS), and homocysteine (Hcy) is an independent risk factor for AS. However, the underlying mechanisms are still lagging. Studies have used the combination of methylation of promoters of multiple genes to diagnose tumors, thus the aim of the current study was to investigate the role of methylation status of several genes in VSMCs treated with Hcy. CpG islands were identified in the promoters of platelet‑derived growth factor (PDGF), p53, phosphatase and tensin homologue on chromosome 10 (PTEN) and mitofusin 2 (MFN2). Hypomethylation was observed to occur in the promoter region of PDGF, hypermethylation in p53, PTEN and MFN2, and hypomethylation in two global methylation indicators, aluminium (Alu) and long interspersed nucleotide element‑1 (Line‑1). This was accompanied by an increase in the expression of PDGF, and reductions of p53, PTEN and MFN2, both in mRNA and protein levels. An elevation of S‑adenosylmethionine (SAM) and a reduction of S‑adenosylhomocysteine (SAH) and the SAM/SAH ratio were also identified. In conclusion, Hcy impacted methylation the of AS‑associated genes and global methylation status that mediate the cell proliferation, which may be a character of VSMCs treated with Hcy. The data provided evidence for mechanisms of VSMCs proliferation in AS induced by Hcy and may provide a new perspective for AS induced by Hcy.

show abstract

“…This connection between TE indels and SNP-density XOs confirms our previous finding that the dimorphic Alu and SVA are located close to or within putative recombination hotspots throughout the MHC classes I, II, and III genomic regions (Kulski et al, 2011(Kulski et al, , 2021, suggesting that they might be involved in DNA repair in response to genomic stress and damage (Kulski et al, 2000a). Although the expression of most Alu elements in the human genome is silenced by methylation, they are transcriptionally active in germ cells during early development and in response to cellular and genomic stress and damage as a result of heat shock (Schmid, 1996), viral infections (Chu et al, 1998;Tucker and Glaunsinger, 2017), autoimmune diseases (Yüksel et al, 2016;Wu et al, 2019), and cancer pathogenesis (Moolhuijzen et al, 2010;Kaczkowski et al, 2016). Many Alu elements of the AluJ, AluS, and AluY subfamilies are transcriptionally active with highly expressed selfcleaving ribozyme activity during T-cell activation and thermal and endoplasmic reticulum stress (Hernandez et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region

2021

View full text Add to dashboard Cite

The major histocompatibility complex (MHC) on chromosome 6p21 is one of the most single-nucleotide polymorphism (SNP)-dense regions of the human genome and a prime model for the study and understanding of conserved sequence polymorphisms and structural diversity of ancestral haplotypes/conserved extended haplotypes. This study aimed to follow up on a previous analysis of the MHC class I region by using the same set of 95 MHC haplotype sequences downloaded from a publicly available BioProject database at the National Center for Biotechnology Information to identify and characterize the polymorphic human leukocyte antigen (HLA)-class II genes, the MTCO3P1 pseudogene alleles, the indels of transposable elements as haplotypic lineage markers, and SNP-density crossover (XO) loci at haplotype junctions in DNA sequence alignments of different haplotypes across the extended class II region (∼1 Mb) from the telomeric PRRT1 gene in class III to the COL11A2 gene at the centromeric end of class II. We identified 42 haplotypic indels (20 Alu, 7 SVA, 13 LTR or MERs, and 2 indels composed of a mosaic of different transposable elements) linked to particular HLA-class II alleles. Comparative sequence analyses of 136 haplotype pairs revealed 98 unique XO sites between SNP-poor and SNP-rich genomic segments with considerable haplotype shuffling located in the proximity of putative recombination hotspots. The majority of XO sites occurred across various regions including in the vicinity of MTCO3P1 between HLA-DQB1 and HLA-DQB3, between HLA-DQB2 and HLA-DOB, between DOB and TAP2, and between HLA-DOA and HLA-DPA1, where most XOs were within a HERVK22 sequence. We also determined the genomic positions of the PRDM9-recombination suppression sequence motif ATCCATG/CATGGAT and the PRDM9 recombination activation partial binding motif CCTCCCCT/AGGGGAG in the class II region of the human reference genome (NC_ 000006) relative to published meiotic recombination positions. Both the recombination and anti-recombination PRDM9 binding motifs were widely distributed throughout the class II genomic regions with 50% or more found within repeat elements; the anti-recombination motifs were found mostly in L1 fragmented repeats. This study shows substantial haplotype shuffling between different polymorphic blocks and confirms the presence of numerous putative ancestral recombination sites across the class II region between various HLA class II genes.

show abstract

Methylation Status of Alu and LINE-1 Interspersed Repetitive Sequences in Behcet’s Disease Patients

Cited by 15 publications

References 40 publications

Neutrophil-to-lymphocyte ratio: relation to disease activity and carotid intima-media thickness in Behçet’s disease

Neutrophil-to-lymphocyte ratio: relation to disease activity and carotid intima-media thickness in Behçet’s disease

Aberrant promoter methylation of multiple genes in VSMC proliferation induced by Hcy

Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region

Contact Info

Product

Resources

About