Epigenetic dimension of oxygen radical injury in spermatogonial epithelial cells

The present work reports a direct role of mitochondrial oxidative stress induced aberrant chromatin regulation, as a central phenomenon, to perturbed genomic integrity in the testicular milieu. Oxygen-radical injury following N-succinimidyl N-methylcarbamate treatment in mouse spermatogonial epithelial (GC-1 spg) cells induced functional derailment of mitochondrial machinery. Mitophagy resulted in marked inhibition of mitochondrial respiration and reduced mtDNA copy number. Impaired cell cycle progression along with altered H3K9me1, H4K20me3, H3, AcH3 and uH2A histone modifications were observed in the treated cells. Dense heterochromatin foci and aberrant expression of HP1α in nuclei of treated cells implied onset of senescence associated secretory phenotype mediated through nuclear accumulation of NF-κB. Neoplastic nature of daughter clones, emerged from senescent mother phenotypes was confirmed by cytogenetic instability, aberrant let-7a and let-7b miRNA expression and anchorage independent growth. Together, our results provide the first insights of redox-dependent epigenomic imbalance in spermatogonia, a previously unknown molecular paradigm.     

Pro-inflammatory and (Epi-)genetic markers in saliva for disease risk in childhood obesity

Background and aimChildhood obesity is an emerging problem often leading to earlier onset of non-communicable diseases in later life. Biomarkers to identify individual risk scores are insufficient in routine clinical practice, which is related to the need for easily sampled, non-invasive survey methods in children. We aimed to investigate and strengthen possible pro-inflammatory markers and epigenetic risk factors in saliva of obese children compared to lean controls.Methods and results19 overweight/obese (OC, 10.1 ± 1.9 years, BMI 27.7 ± 3.2 kg/m²) and 19 lean control children (CC, 9.7 ± 2.5 years, BMI 16.4 ± 1.8 kg/m²) participated in this explorative pilot study. Anthropometric measures, saliva and cheek swab samples were taken. Saliva profiles were examined for acute phase proteins (CRP and neopterin) and pro-inflammatory cytokines (IL-17a/IL-1β/IL-6). Cheek swabs were analyzed to investigate DNA methylation differences with subsequent hierarchical cluster and principal component analyses (PCA). Saliva analysis showed significant increased CRP concentrations in OC compared to CC (p < 0.001). There were no significant differences, but high intra-individual values in neopterin, IL-17a, IL-1β and IL-6. An unsupervised PCA of CpG loci with high variance (σ/σ_max > 0.2) clearly separated OC and CC according to their methylation pattern. Furthermore, a supervised approach revealed 7125 significantly differentially methylated loci, whose corresponding genes were significantly enriched for genes playing roles in e.g., cellular signalling, cytoskeleton organization and cell motility.ConclusionsCRP and methylation status determinations in saliva are suitable as non-invasive methods for early detection of risks for non-communicable diseases in children/adolescents and might be a useful supplementary approach in the routine clinical practice/monitoring.     

肺腺癌患者差异甲基化区域分析

目的探讨DNA甲基化在肺腺癌发生中的作用机制。方法收集2019年1月至12月新疆肿瘤医院确诊的肺腺癌和正常对照者外周血各4例,850K芯片甲基化检测平台检测肺腺癌组与正常对照组甲基化区域,Bump hunter寻找两组差异区域。Gene Ontology数据库和KOBAS软件对差异区域对应目的基因进行GO分析和KEEG分析。结果1.共筛选出DMR-1、DMR-2、DMR-3、DMR-4、DMR-6(以上位于chr6),DMR-5(位于chr11)和DMR-7(位于chr20)(P<0.05)七组差异甲基化区域。DMR-1目的基因为HLA-DPB1、HLA-DPA1,DMR-2的为POU5F1,DMR-3的为RP5-1186N24.3、SCAND3,DMR-4的为ZFP57,DMR-5的为LDHC,DMR-6的为LTA,DMR-7的为OXT。其中HLA-DPB1、HLA-DPA1等为高甲基化,SCANDS3和LTA为低甲基化。2.GO分析表明目的基因主要在干扰素-γ、MHC-Ⅱ类复合物等功能中发挥重要作用。KEGG分析显示目的基因甲基化主要在Ⅰ型糖尿病、NF-κB信号通路中高度富集。结论1.肺腺癌患者DNA甲基化的状态可能是引起肺腺癌发生的关键因素,尤其是HLA-DP,POU5F1及LDHC的甲基化状态,在肺腺癌的发生中起着重要的作用。2.在GO功能和KEGG通路中,阐明了DNA甲基化异常导致疾病发展的作用机制。     

Epigenetic age estimation in saliva and in buccal cells

Age estimation based on epigenetic markers is a DNA intelligence tool with the potential to provide relevant information for criminal investigations, as well as to improve the inference of age-dependent physical characteristics such as male pattern baldness or hair color. Age prediction models have been developed based on different tissues, including saliva and buccal cells, which show different methylation patterns as they are composed of different cell populations. On many occasions in a criminal investigation, the origin of a sample or the proportion of tissues is not known with certainty, for example the provenance of cigarette butts, so use of combined models can provide lower prediction errors.In the present study, two tissue-specific and seven age-correlated CpG sites were selected from publicly available data from the Illumina HumanMethylation 450 BeadChip and bibliographic searches, to help build a tissue-dependent, and an age-prediction model, respectively. For the development of both models, a total of 184 samples (N = 91 saliva and N = 93 buccal cells) ranging from 21 to 86 years old were used. Validation of the models was performed using either k-fold cross-validation and an additional set of 184 samples (N = 93 saliva and N = 91 buccal cells, 21–86 years old).The tissue prediction model was developed using two CpG sites (HUNK and RUNX1) based on logistic regression that produced a correct classification rate for saliva and buccal swab samples of 88.59 % for the training set, and 83.69 % for the testing set. Despite these high success rates, a combined age prediction model was developed covering both saliva and buccal cells, using seven CpG sites (cg10501210, LHFPL4, ELOVL2, PDE4C, HOXC4, OTUD7A and EDARADD) based on multivariate quantile regression giving a median absolute error (MAE): ± 3.54 years and a correct classification rate ( %CP±PI) of 76.08 % for the training set, and an MAE of ± 3.66 years and a %CP±PI of 71.19 % for the testing set. The addition of tissue-of origin as a co-variate to the model was assessed, but no improvement was detected in age predictions. Finally, considering the limitations usually faced by forensic DNA analyses, the robustness of the model and the minimum recommended amount of input DNA for bisulfite conversion were evaluated, considering up to 10 ng of genomic DNA for reproducible results. The final multivariate quantile regression age predictor based on the models we developed has been placed in the open-access Snipper forensic classification website.     

DNA甲基化和胃液固有荧光光谱联合检测在胃癌诊断中的意义

目的探索在胃癌患者胃液、外周血清中检测基因甲基化的可行性，并结合胃液稀释固有荧光光谱评价二者在胃癌诊断中的作用。方法采用甲基化特异性PCR方法，检测50例胃癌患者的原发肿瘤组织、外周血清和胃液脱落细胞的死亡相关蛋白（DAP）激酶、p16基因启动子区域甲基化状态，并以胃良性溃疡和慢性浅表性胃炎各20例、慢性萎缩性胃炎30例作为对照，同时检测胃癌患者和对照者的胃液稀释固有荧光光谱。结果50例胃癌患者的肿瘤组织、外周血清和胃液脱落细胞中p16和DAP激酶基因甲基化阳性率分别为74．4％和68．1％、52．0％和58．0％、58．6％和76．0％，20例慢性浅表性胃炎患者中均未检测到基因异常甲基化；20例胃溃疡患者溃疡周边组织、胃液脱落细胞中p16和DAP激酶甲基化阳性率为10．0％和20．0％、5．0％和15．0％，在外周血清中未检测到异常甲基化；30例慢性萎缩性胃炎患者胃黏膜组织、外周血清、胃液脱落细胞p16和DAP激酶基因甲基化阳性率分别为10．0％和23．3％、3．3％和3．3％、3．3％和20．0％。胃癌患者胃液固有荧光光谱强度较对照者明显增强（P〈0．05）；以P1FI≥111．8为分界点分析胃液固有荧光光谱诊断胃癌的敏感性和特异性分别为76．1％和78．6％。p16和DAP激酶基因甲基化和胃液固有荧光光谱结合后诊断胃癌的敏感性提高到95．6％和97．8％。结论胃癌患者外周血清及胃液脱落细胞中可检测到与原发肿瘤组织一致的基因异常甲基化，胃液固有荧光光谱和DNA甲基化联合对检测胃癌有良好的临床应用价值。