The relationship between the prognosis of children with acute arterial stroke and polymorphisms of CDKN2B, HDAC9, NINJ2, NAA25 genes

Association of DNA Methylation in Blood Pressure-Related Genes With Ischemic Stroke Risk and Prognosis

Background

A genome-wide association study identified 12 genetic loci influencing blood pressure and implicated a role of DNA methylation. However, the relationship between methylation and ischemic stroke has not yet been clarified. We conducted a large-sample sequencing study to identify blood leukocyte DNA methylations as novel biomarkers for ischemic stroke risk and prognosis based on previously identified genetic loci.

Methods

Methylation levels of 17 genes were measured by sequencing in 271 ischemic stroke cases and 323 controls, and the significant associations were validated in another independent sample of 852 cases and 925 controls. The associations between methylation levels and ischemic stroke risk and prognosis were evaluated.

Results

Methylation of AMH, C17orf82, HDAC9, IGFBP3, LRRC10B, PDE3A, PRDM6, SYT7 and TBX2 was significantly associated with ischemic stroke. Compared to participants without any hypomethylated targets, the odds ratio (OR) (95% confidence interval, CI) for those with 9 hypomethylated genes was 1.41 (1.33–1.51) for ischemic stroke. Adding methylation levels of the 9 genes to the basic model of traditional risk factors significantly improved the risk stratification for ischemic stroke. Associations between AMH, HDAC9, IGFBP3, PDE3A and PRDM6 gene methylation and modified Rankin Scale scores were significant after adjustment for covariates. Lower methylation levels of AMH, C17orf82, PRDM6 and TBX2 were significantly associated with increased 3-month mortality. Compared to patients without any hypomethylated targets, the OR (95% CI) for those with 4 hypomethylated targets was 1.12 (1.08–1.15) for 3-month mortality (P = 2.28 × 10−10).

Conclusion

The present study identified blood leukocyte DNA methylations as potential factors affecting ischemic stroke risk and prognosis among Han Chinese individuals.

Knockdown of NAA25 Suppresses Breast Cancer Progression by Regulating Apoptosis and Cell Cycle

NAA25 gene variants were reported as risk factors for type 1 diabetes, rheumatoid arthritis and acute arterial stroke. But it’s unknown whether it could contribute to breast cancer. We identified rs11066150 in lncHSAT164, which contributes to breast cancer, in our earlier genome-wide long non-coding RNA association study on Han Chinese women. However, rs11066150 A/G variant is also located in NAA25 intron. Based on the public database, such as TCGA and Curtis dataset, NAA25 gene is highly expressed in breast cancer tissues and this result has also been proved in our samples and cell lines through RT-qPCR and western blot analysis. To better understand the function of NAA25 in breast cancer, we knocked down the expression of NAA25 in breast cancer cell lines, FACS was used to detect cell apoptosis and cell cycle and colony formation assay was used to detect cell proliferation. We found that NAA25-deficient cells could increase cell apoptosis, delay G2/M phase cell and decrease cell clone formation. RNA sequencing was then applied to analyze the molecular profiles of NAA25−deficient cells, and compared to the control group, NAA25 knockdown could activate apoptosis-related pathways, reduce the activation of tumor-associated signaling pathways and decrease immune response-associated pathways. Additionally, RT-qPCR was employed to validate these results. Taken together, our results revealed that NAA25 was highly expressed in breast cancer, and NAA25 knockdown might serve as a therapeutic target in breast cancer.

ZNF718, HOXA4, and ZFP57 are differentially methylated in periodontitis in comparison with periodontal health: Epigenome-wide DNA methylation pilot study

OBJECTIVE

To investigate the differences in the epigenomic patterns of DNA methylation in peripheral leukocytes between patients with periodontitis and gingivally healthy controls evaluating its functional meaning by functional enrichment analysis.

BACKGROUND

The DNA methylation profiling of peripheral leukocytes as immune-related tissue potentially relevant as a source of biomarkers between periodontitis patients and gingivally healthy subjects has not been investigated.

METHODS

A DNA methylation epigenome-wide study of peripheral leukocytes was conducted using the Illumina MethylationEPIC platform in sixteen subjects, eight diagnosed with periodontitis patients and eight age-matched and sex-matched periodontally healthy controls. A trained periodontist performed the clinical evaluation. Global DNA methylation was estimated using methylation-sensitive high-resolution melting in LINE1. Routine cell count cytometry and metabolic laboratory tests were also performed. The analysis of differentially methylated positions (DMPs) and differentially methylated regions (DMRs) was made using R/Bioconductor environment considering leukocyte populations assessed in both routine cell counts and using the FlowSorted.Blood.EPIC package. Finally, a DMP and DMR intersection analysis was performed. Functional enrichment analysis was carried out with the differentially methylated genes found in DMP.

RESULTS

DMP analysis identified 81 differentially hypermethylated genes and 21 differentially hypomethylated genes. Importantly, the intersection analysis showed that zinc finger protein 718 (ZNF718) and homeobox A4 (HOXA4) were differentially hypermethylated and zinc finger protein 57 (ZFP57) was differentially hypomethylated in periodontitis. The functional enrichment analysis found clearly immune-related ontologies such as "detection of bacterium" and "antigen processing and presentation."

CONCLUSION

The results of this study propose three new periodontitis-related genes: ZNF718, HOXA4, and ZFP57 but also evidence the suitability and relevance of studying leukocytes' DNA methylome for biological interpretation of systemic immune-related epigenetic patterns in periodontitis.

De novo assembly and functional annotation of the Red-striped golden stink bug (Poecilocoris lewisi) transcriptome

Insect antimicrobial peptides (AMPs) have a wide range of functions and potential applications, and have recently attracted attention as alternative foods and medicines for humans. Our study performed transcriptome analysis to explore the potential of the red-striped golden stink bug (Poecilocoris lewisi), and as a result, we have discovered new features of P. lewisi that have not been identified. Specifically, defensin found in P. lewisi is a well-known AMP and is expressed by various plants, animals and fungi for host defense. Moreover, the discovery of defensin in P. lewisi provides new research and important information. In this study, we identified AMP and related DEG in P. lewisi that are closely related to human disease and immune response. These findings will provide the basis and important information for future research on P. lewisi that has not yet been studied.

NINJ2 Gene Polymorphisms and Susceptibility to Ischemic Stroke: An Updated Meta-Analysis

BACKGROUND

Ischemic stroke (IS) is a significant disease which threatens human health condition. Genome-wide association studies (GWAS) have demonstrated that two intergenic single- nucleotide polymorphisms (SNPs) rs11833579 and rs12425791 G>A on chromosome 12p13 are associated with IS susceptibility. However, later studies came to contradictory outcomes. Thus, we carried out a meta-analysis to identify the association between nerve injury-induced protein 2 (NINJ2) gene polymorphisms (rs11833579 and rs12425791) and the risk of IS.

METHODS

PubMed, Embase, Web of Science, CBM, Wanfang, VIP, and CNKI databases were searched until March 2019. Data was analyzed by RevMan 5.3 and STATA 12.0 software. The pooled odds ratio (OR) and 95% confidence interval (CI) were used to evaluate the strength of the association.

RESULTS

Eighteen qualified articles were selected in total. For rs12425791 and rs11833579, a total of 14055 cases with 13148 controls and 10635 cases with 10462 controls, respectively, were identified for the present study. Our meta-analysis found that rs12425791 was associated with IS for three genetic models (allele model: OR=1.04, 95% CI: 1.00-1.08, P=0.04; dominant model: OR=1.06, 95% CI: 1.01-1.12, P=0.01 and heterozygous model: OR=1.07, 95% CI: 1.01-1.12, P=0.02). Whereas rs11833579 polymorphism was not associated with IS among different genetic models.

CONCLUSION

NINJ2 gene rs12425791 confers a susceptible factor for IS, while there is no association between NINJ2 gene rs11833579 and IS. Larger sample size studies should be performed to find the association between NINJ2 gene and IS.