Whole genome methylation array analysis reveals new aspects in Balkan endemic nephropathy etiology

Background Balkan endemic nephropathy (BEN) represents a chronic progressive interstitial nephritis in striking correlation with uroepithelial tumours of the upper urinary tract. The disease has endemic distribution in the Danube river regions in several Balkan countries. DNA methylation is a primary epigenetic modification that is involved in major processes such as cancer, genomic imprinting, gene silencing, etc. The significance of CpG island methylation status in normal development, cell differentiation and gene expression is widely recognized, although still stays poorly understood. Methods We performed whole genome DNA methylation array analysis on DNA pool samples from peripheral blood from 159 affected individuals and 170 healthy individuals. This technique allowed us to determine the methylation status of 27 627 CpG islands throughout the whole genome in healthy controls and BEN patients. Thus we obtained the methylation profile of BEN patients from Bulgarian and Serbian endemic regions. Results Using specifically developed software we compared the methylation profiles of BEN patients and corresponding controls and revealed the differently methylated regions. We then compared the DMRs between all patient-control pairs to determine common changes in the epigenetic profiles. SEC61G, IL17RA, HDAC11 proved to be differently methylated throughout all patient-control pairs. The CpG islands of all 3 genes were hypomethylated compared to controls. This suggests that dysregulation of these genes involved in immunological response could be a common mechanism in BEN pathogenesis in both endemic regions and in both genders. Conclusion Our data propose a new hypothesis that immunologic dysregulation has a place in BEN etiopathogenesis. Keywords: Epigenetics; Whole genome array analysis; Balkan endemic nephropath

Association between endometrial microbiome and implantation success in women with frozen embryo transfer: results of a prospective cohort study

AbstractThe aim of this prospective study was to compare the endometrial microbiome between pregnant and non-pregnant women after frozen embryo transfer (FET) with euploid embryos. Endometrial biopsies were collected from 30 women during the mid-luteal phase in a natural cycle. FET was performed with euploid embryos up to 3 months after the biopsy. Endometrial microbiota composition was analysed using 16S rRNA (v4-v5 region) next generation sequencing (NGS). The analysis of different clinical outcomes after the biopsy (no pregnancy (n = 14), and ultrasound confirmed pregnancy (n = 16)) revealed differences in the endometrial microbiome composition. In total, 271 distinct bacterial species and 668 bacterial genera were identified. The number of unique species found in non-pregnant women was 62 (22.88%), while in the patients who became pregnant after FET it was 39 (14.39%). Among them, bacteria with high frequency of occurrence such as Bacteroides spp., Cutibacterium granulosum, Isoptericola spp., Acetomicrobium spp., Marivivens spp. and Syntrophomonas spp. were found only in non-pregnant patients, while Bosea spp. was present only in pregnant women. The analysis of bacteria relative abundance revealed that Lactobacillus genus was not significantly different between the studied groups. In contrast, Serratia marcescens, Staphylococcus spp., Glutamicibacter spp. and Delftia spp. were significantly enriched in the non-pregnant group. In conclusion, specific bacteria taxa had higher relative abundance in the endometrium of patients with implantation failure after FET with euploid embryos. We hypothesize that an appropriate treatment for optimization of endometrial microbiome content in women with diagnosed microbiome dysbiosis could be beneficial for improvement of pregnancy rates

Detection of pathogenic variants in Alzheimer’s disease related genes in Bulgarian patients by pooled whole-exome sequencing

AbstractIn an effort to better understand the complex genetic background of Alzheimer’s disease (AD) we performed high-coverage whole-exome sequencing of a DNA pool assembled of 66 Bulgarian AD patients. We focused our analysis on genes demonstrated to have association with AD in previous studies, i.e. PSEN1, PSEN2, APP, APOE, TREM2, HFE, CLU and CR1. In these genes, we established six pathogenic/likely pathogenic variants in the sequenced pool, three common and three rare. Two of these variants showed statically non-significant difference between Bulgarian AD patients and Bulgarian control exomes, the hemochromatosis variant rs104894002 (HFE) and rs7412 (APOE), which, notwithstanding its pathogenicity score, has putative protective role against AD. Three of the remaining four pathogenic/likely pathogenic variants were estimated to significantly differ in frequency between the analyzed AD patient pool and controls. These are the rs429358 (APOE) polymorphism, a well-established risk factor for Alzheimer’s disease, the rs28936380 (PSEN2) and rs104894002 (TREM2), also ascertained to be associated with AD. The performed study validates the role of three pathogenic/likely pathogenic variants in AD related genes in the multifaceted genetic etiology of Alzheimer’s disease