ABSTRACT
Brugada syndrome (BS) is an autosomal dominant inheritance cardiac arrhythmia disorder associated with sudden death in young adults. Thailand has the highest prevalence of BS worldwide, and over 60% of patients with BS still have unclear disease etiology. Here, we performeda new viral metagenome analysis pipeline called VIRIN and validated it with whole genome sequencing (WGS) data of HeLa cell lines and hepatocellular carcinoma. Then the VIRIN pipelinewas applied to identify viral integration positions from unmapped WGS data of Thai males, including 100 BS patients (case) and 100 controls. Even though the sample preparation had noviral enrichment step, we can identify several virus genes from our analysis pipeline. The predominance of human endogenous retrovirus K (HERV-K) viruses was found in both cases andcontrols by blastn and blastx analysis. This study is the first report on the full-length HERV-Kassembled genomes in the Thai population. Furthermore, the HERV-K integration breakpointpositions were validated and compared between the case and control datasets. Interestingly,Brugada cases contained HERV-K integration breakpoints at promoters five times more oftenthan controls. Overall, the highlight of this study is the BS-specific HERV-K breakpoint positionsthat were found at the gene coding region "NBPF11" (n = 9), "NBPF12" (n = 8) and longnon-coding RNA (lncRNA) "PCAT14" (n = 4) region. The genes and the lncRNA have been reported to be associated with congenital heart and arterial diseases. These findings provide another aspect of the BS etiology associated with viral genome integrations within the humangenome.
ABSTRACT
Background: Down-regulation of Piwil2 (P-element induced wimpy testis like 2) expression induced hypomethylation, the loss of methylation levels, of long interspersed nuclear element-1 (LINE-1 or L1) sequences in the testes of mutant mice. Moreover, the expression of Piwil2 can be found in various cancers. The levels of LINE-1 hypomethylation in cancers are not only generally varied, but also possess a locus-specific pattern. Objective: This study focused on the association between Piwil2 and LINE-1 methylation. Methods: Eleven WSU-HN cancer cell lines were examined for the expression of Piwil2 using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR). Genome-wide and specific loci LINE-1 methylation levels were measured using Combined Bisulfite Restriction Analysis (COBRA) and COBRA for unique LINE-1 (CU-L1), respectively. Results: The levels of Piwil2 expression and LINE-1 methylation were varied. Significant association between Piwil2 RNA and LINE-1 methylation of two loci, L1-EPHA3IVS5 and L1-SPOCK3, was observed (Pearson’s r = 0.7332; p ≤ 0.01 and r = 0.6124; p \< 0.05, respectively). There was no association with both genome wide LINE- 1 methylation and the other 15 loci. Conclusion: Piwil2 expression may be associated with LINE-1 methylation of selective loci in cancer cells.