Increased DNA Methylation Levels Research Articles

Transcriptome and methylome analyses unveil the effects of low and high temperatures on the postharvest senescence of plum fruit

Temperature strongly affects plum fruit senescence, but the epigenetic mechanism is unclear. Analysis of data on firmness, weigh loss rate, and decay rate showed that high temperature (HT) accelerates postharvest senescence, while low temperature (LT) delays it. Transcriptome analysis suggests that genes related to cell wall metabolism are associated with fruit softening. DNA methylation analysis shows that HT promotes fruit senescence accompanied by an increase in DNA methylation level, while LT delays senescence accompanied by a decrease in DNA methylation level. Further analysis suggests that PsDRM2 and PsDML1 may be responsible for regulating changes in methylation level. Association analysis showed that HT accelerates senescence through DNA methylation-mediated regulation of flavonoid metabolism, whereas LT delays senescence through DNA methylation-mediated regulation of lipid metabolism. These findings highlight the importance of temperature and DNA methylation in controlling postharvest senescence and provide valuable insights for developing effective strategies to control fruit senescence.

ZBTB16 inhibits DNA replication and induces cell cycle arrest by targeting WDHD1 transcription in lung adenocarcinoma.

Lung adenocarcinoma is a malignant tumor with high morbidity and mortality. ZBTB16 plays a double role in various tumors; however, the potential mechanism of ZBTB16 in the pathophysiology of lung adenocarcinoma has yet to be elucidated. We herein observed a decreased expression of ZBTB16 mRNA and protein in lung adenocarcinoma and a significantly increased DNA methylation level of ZBTB16 in patients with lung adenocarcinoma. Analysis of public databases and patients' clinical data indicated a close association between ZBTB16 and patient survival. Ectopic expression of ZBTB16 in lung adenocarcinoma cells significantly inhibited cell proliferation, invasion, and migration. It also induced cell cycle arrest in the S phase. Meanwhile, mitotic catastrophe was induced, and DNA damage and apoptosis occurred. In line with these findings, the overexpression of ZBTB16 in xenograft mice resulted in the inhibition of tumor growth. Comprehensive analysis showed that WDHD1 was a potential target for ZBTB16. The overexpression of both isoforms of WDHD1 significantly reversed the ZBTB16-mediated inhibition of lung adenocarcinoma proliferation and cell cycle. These studies suggest that ZBTB16 impedes the progression of lung adenocarcinoma by interfering with WDHD1 transcription, making it a potential novel therapeutic target in the management of lung adenocarcinoma.

Antagonistic interactions safeguard mitotic propagation of genetic and epigenetic information in zebrafish

The stability of cellular phenotypes in developing organisms depends on error-free transmission of epigenetic and genetic information during mitosis. Methylation of cytosine residues in genomic DNA is a key epigenetic mark that modulates gene expression and prevents genome instability. Here, we report on a genetic test of the relationship between DNA replication and methylation in the context of the developing vertebrate organism instead of cell lines. Our analysis is based on the identification of hypomorphic alleles of dnmt1, encoding the DNA maintenance methylase Dnmt1, and pole1, encoding the catalytic subunit of leading-strand DNA polymerase epsilon holoenzyme (Pole). Homozygous dnmt1 mutants exhibit genome-wide DNA hypomethylation, whereas the pole1 mutation is associated with increased DNA methylation levels. In dnmt1/pole1 double-mutant zebrafish larvae, DNA methylation levels are restored to near normal values, associated with partial rescue of mutant-associated transcriptional changes and phenotypes. Hence, a balancing antagonism between DNA replication and maintenance methylation buffers against replicative errors contributing to the robustness of vertebrate development.

Dissecting postharvest chilling injuries in pome and stone fruit through integrated omics.

Lowering the storage temperature is an effective method to extend the postharvest and shelf life of fruits. Nevertheless, this technique often leads to physiological disorders, commonly known as chilling injuries. Apples and pears are susceptible to chilling injuries, among which superficial scald is the most economically relevant. Superficial scald is due to necrotic lesions of the first layers of hypodermis manifested through skin browning. In peaches and nectarines, chilling injuries are characterized by internal symptoms, such as mealiness. Fruits with these aesthetic or compositional/structural defects are not suitable for fresh consumption. Genetic variation is a key factor in determining fruit susceptibility to chilling injuries; however, physiological, or technical aspects such as harvest maturity and storage conditions also play a role. Multi-omics approaches have been used to provide an integrated explanation of chilling injury development. Metabolomics in pome fruits specifically targets the identification of ethylene, phenols, lipids, and oxidation products. Genomics and transcriptomics have revealed interesting connections with metabolomic datasets, pinpointing specific genes linked to cold stress, wax synthesis, farnesene metabolism, and the metabolic pathways of ascorbate and glutathione. When applied to Prunus species, these cutting-edge approaches have uncovered that the development of mealiness symptoms is linked to ethylene signaling, cell wall synthesis, lipid metabolism, cold stress genes, and increased DNA methylation levels. Emphasizing the findings from multi-omics studies, this review reports how the integration of omics datasets can provide new insights into understanding of chilling injury development. This new information is essential for successfully creating more resilient fruit varieties and developing novel postharvest strategies.

Cadmium exposure-induced rat testicular dysfunction and its mechanism of chronic stress

Cadmium is a common environmental pollutant in daily life, the toxic mechanisms of chronic cadmium exposure on the testes have not been fully elucidated. This study aimed to explore the effects of cadmium exposure on male reproductive health and its mechanism. The results showed that cadmium exposure led widened interstitial spaces, abnormal seminiferous tubule morphology, and decreased Leydig cell numbers. Moreover, sperm quality was significantly reduced, along with a decrease in fertility rate. And cadmium exposure could activate the hypothalamic-pituitary-adrenal (HPA) axis, elevate blood glucocorticoid levels, subsequently increase glucocorticoid receptor (GR) expression and activation in testicular Leydig cells.Then GR act on the glucocorticoid receptor element (GRE) in the DNA methyltransferase 3 A (DNMT3A) promoter region and upregulate DNMT3A expression. Consequently, this led to an increase in DNA methylation levels in the angiotensin II receptor 2 (AT2R) promoter region, resulting in reduced AT2R expression and inhibiting testicular steroidogenesis. This study systematically elucidated that cadmium exposure could lead to testicular steroidogenesis suppression and decreased fertility through the GR/DNMT3A/AT2R signaling pathway. This research further provides theoretical and experimental evidence for confirming the threat of cadmium exposure to human reproduction, and contributes to the guidance and protection of male reproductive health.

DNA methylation regulates biosynthesis of tanshinones and phenolic acids during growth of Salvia miltiorrhiza.

DNA methylation plays a crucial role in the regulation of plant growth and the biosynthesis of secondary metabolites. Danshen (Salvia miltiorrhiza) is a valuable Chinese herbal medicine commonly used to treat cardiovascular diseases; its active ingredients are tanshinones and phenolic acids, which primarily accumulate in roots. Here, we conducted a targeted metabolic analysis of S. miltiorrhiza roots at 3 distinct growth stages: 40 d old (r40), 60 d old (r60), and 90 d old (r90). The contents of tanshinones (cryptotanshinone, tanshinone I, tanshinone IIA, and rosmariquinone) and phenolic acids (rosmarinic acid and salvianolic acid B) gradually increased during plant development. Whole-genome bisulfite sequencing and transcriptome sequencing of roots at the 3 growth stages revealed an increased level of DNA methylation in the CHH context (H represents A, T, or C) context at r90 compared with r40 and r60. Increased DNA methylation levels were associated with elevated expression of various genes linked to epigenetic regulations, including CHROMOMETHYLASE2 (SmCMT2), Decrease in DNA Methylation 1 (SmDDM1), Argonaute 4 (SmAGO4), and DOMAINS REARRANGED METHYLTRANSFERASE 1 (SmDRM1). Moreover, expression levels of many genes involved in tanshinone and salvianolic acid biosynthesis, such as copalyldiphosphate synthase 5 (SmCPS5), cytochrome P450-related enzyme (SmCYP71D464), geranylgeranyl diphosphate synthase (SmGGPPS1), geranyl diphosphate synthase (SmGPPS), hydroxyphenylpyruvate reductase (SmHPPR), and hydroxyphenylpyruvate dioxygenase (SmHPPD), were altered owing to hyper-methylation, indicating that DNA methylation plays an important role in regulating tanshinone and phenolic acid accumulation. Our data shed light on the epigenetic regulation of root growth and the biosynthesis of active ingredients in S. miltiorrhiza, providing crucial clues for further improvement of active compound production via molecular breeding in S. miltiorrhiza.

Altered Transcript Levels of MMP13 and VIT Genes in the Muscle and Connective Tissue of Pigs with Umbilical Hernia.

Umbilical hernia (UH) and inguinal hernia (IH) are among the most common defects in pigs, affecting their welfare and resulting in economic losses. In this study, we aimed to verify the association of previously reported differences in transcript levels of the ACAN, COL6A5, MMP13, and VIT genes with the occurrence of UH and IH. We examined mRNA levels in muscle and connective tissue from 68 animals-34 affected by UH and 34 controls. In a second cohort, we examined inguinal channel samples from 46 pigs (in four groups). We determined DNA methylation levels in muscle tissue for the UH and control animals. The transcript level of MMP13 changed in the UH cases, being upregulated and downregulated in muscle and connective tissue, respectively, and the VIT gene also showed an increased muscular mRNA level. The transcript of the ACAN gene significantly decreased in old pigs with IH. We further observed an increased DNA methylation level for one CpG site within the MMP13 gene in UH individuals. We conclude that these alterations in gene mRNA levels in the UH animals depend on the tissue and can sometimes be a consequence of, not a cause of, the affected phenotype.

Methylome and transcriptome analysis of flowering branches building of Citrus plants induced by drought stress

Citrus plants exhibit positive floral response under water stress conditions, however, the mechanistic understanding of floral induction remains largely unexplored in water deficit. In this study, DNA methylomic and transcriptomic analyses were integrated to explore the flowering bud formation as well as branches building after light drought stress. While comparing with the conventional watering group (CK), the light drought group treated with five months (LD) showed a significant increase in the flowering branches, whereas an apparent decrease in vegetative branches. Global DNA methylation analysis showed that the LD Group acquired DNA methylation in more than 70,090 genomic regions and lost DNA methylation in about 18,421 genomic regions compared with normal watering group, this indicates that water deficiency leads to a global increase in the expression of DNA methylation in citrus. In the same time, we verified that the increase of DNA methylation level in LD group was correlated with the decrease of DNA demethylase related gene expression.Interestingly, in transcription analysis, it was found that the promoting flower genes of the LD group did not increase but decreased similarly with repressing genes, which is contrary to the intended result. Thus, we thought the lower expression of suppressors FLC and BFT were the key influencing factor to stimulate the flowering branches formation after LD treatment. Moreover, there was a strong negative correlation between the genes expression level and methylation level of the flowering induction/flower development genes. In general, we thought high global DNA methylation level induced by water deficit regulate the flowering branches building by reducing FLC and BFT genes expression.

The Effect of Metformin and Carbohydrate-Controlled Diet on DNA Methylation and Gene Expression in the Endometrium of Women with Polycystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) is an endocrine disease associated with infertility and metabolic disorders in reproductive-aged women. In this study, we evaluated the expression of eight genes related to endometrial function and their DNA methylation levels in the endometrium of PCOS patients and women without the disease (control group). In addition, eight of the PCOS patients underwent intervention with metformin (1500 mg/day) and a carbohydrate-controlled diet (type and quantity) for three months. Clinical and metabolic parameters were determined, and RT-qPCR and MeDIP-qPCR were used to evaluate gene expression and DNA methylation levels, respectively. Decreased expression levels of HOXA10, GAB1, and SLC2A4 genes and increased DNA methylation levels of the HOXA10 promoter were found in the endometrium of PCOS patients compared to controls. After metformin and nutritional intervention, some metabolic and clinical variables improved in PCOS patients. This intervention was associated with increased expression of HOXA10, ESR1, GAB1, and SLC2A4 genes and reduced DNA methylation levels of the HOXA10 promoter in the endometrium of PCOS women. Our preliminary findings suggest that metformin and a carbohydrate-controlled diet improve endometrial function in PCOS patients, partly by modulating DNA methylation of the HOXA10 gene promoter and the expression of genes implicated in endometrial receptivity and insulin signaling.

Chicken embryo thermal manipulation alleviates postnatal heat stress-induced jejunal inflammation by inhibiting Transient Receptor Potential V4

Intestinal inflammation induced by heat stress is an important factor restricting the healthy growth of broilers. The aim of this study was to evaluate the effect of chicken embryo thermal manipulation (39.5 ℃ and 65 % RH for 3 h daily during 16–18 th embryonic age) on intestinal inflammation in broilers under postnatal heat stress and to investigate whether transient receptor potential V4 (TRPV4) plays a role in this process. Our results suggest that broilers with embryo thermal manipulation experience could delay the rising of rectal temperature during postnatal heat stress (P < 0.05), and had better production performance (P < 0.05), intestinal morphological parameters (P < 0.05) and higher expression of tight junction related genes (P < 0.05). The increased serum lipopolysaccharide (LPS) content, activation of nuclear factor-kappa B (NF-κB) signaling pathway and the increased expression of pro-inflammatory cytokines interleukin (IL)-1β, IL-6 and tumor necrosis factor alpha (TNF-α) in jejunum during postnatal heat stress were alleviated by embryo thermal manipulation (P < 0.05). Postnatal heat stress induced an increase in mRNA and protein expression of TRPV4 in jejunum (P < 0.05), but had no effect on broilers which experienced embryo thermal manipulation (P > 0.05). Inhibition of TRPV4 reduced LPS-induced Ca2+ influx and restrained the activation of NF-κB signaling pathway and the expression of downstream pro-inflammatory cytokines (P < 0.05). The expression of DNA methyltransferase (DNMT) in the jejunum of broilers exposed to postnatal heat stress was increased by embryo thermal manipulation (P < 0.05). The DNA methylation level of TRPV4 promoter region was detected, and the results showed that embryo thermal manipulation increased the DNA methylation level of TRPV4 promoter region (P < 0.05). In conclusion, Chicken embryo thermal manipulation can alleviate jejunal inflammation in broilers under postnatal heat stress. This may be due to the decreased circulating LPS or the increased DNA methylation level in the promoter region of TRPV4, which inhibits TRPV4 expression, thereby reducing Ca2+ influx, and finally alleviating inflammation by affecting NF-κB signaling pathway. The work is an attempt to understand the mechanism involved in alleviation of adverse effects of heat stress during postnatal life through prenatal thermal manipulation and to reveal the important role of epigenetics.

New Insights into the Genetics and Epigenetics of Aging Plasticity.

Biological aging is characterized by irreversible cell cycle blockade, a decreased capacity for tissue regeneration, and an increased risk of age-related diseases and mortality. A variety of genetic and epigenetic factors regulate aging, including the abnormal expression of aging-related genes, increased DNA methylation levels, altered histone modifications, and unbalanced protein translation homeostasis. The epitranscriptome is also closely associated with aging. Aging is regulated by both genetic and epigenetic factors, with significant variability, heterogeneity, and plasticity. Understanding the complex genetic and epigenetic mechanisms of aging will aid the identification of aging-related markers, which may in turn aid the development of effective interventions against this process. This review summarizes the latest research in the field of aging from a genetic and epigenetic perspective. We analyze the relationships between aging-related genes, examine the possibility of reversing the aging process by altering epigenetic age.

Downregulation of DNA methyltransferase-3a ameliorates the osteogenic differentiation ability of adipose-derived stem cells in diabetic osteoporosis via Wnt/β-catenin signaling pathway

BackgroundDiabetes-related osteoporosis (DOP) is a chronic disease caused by the high glucose environment that induces a metabolic disorder of osteocytes and osteoblast-associated mesenchymal stem cells. The processes of bone defect repair and regeneration become extremely difficult with DOP. Adipose-derived stem cells (ASCs), as seed cells in bone tissue engineering technology, provide a promising therapeutic approach for bone regeneration in DOP patients. The osteogenic ability of ASCs is lower in a DOP model than that of control ASCs. DNA methylation, as a mechanism of epigenetic regulation, may be involved in DNA methylation of various genes, thereby participating in biological behaviors of various cells. Emerging evidence suggests that increased DNA methylation levels are associated with activation of Wnt/β-catenin signaling pathway. The purpose of this study was to investigate the influence of the diabetic environment on the osteogenic potential of ASCs, to explore the role of DNA methylation on osteogenic differentiation of DOP-ASCs via Wnt/β-catenin signaling pathway, and to improve the osteogenic differentiation ability of ASCs with DOP.MethodsDOP-ASCs and control ASCs were isolated from DOP C57BL/6 and control mice, respectively. The multipotency of DOP-ASCs was confirmed by Alizarin Red-S, Oil Red-O, and Alcian blue staining. Real-time polymerase chain reaction (RT-PCR), immunofluorescence, and western blotting were used to analyze changes in markers of osteogenic differentiation, DNA methylation, and Wnt/β-catenin signaling. Alizarin Red-S staining was also used to confirm changes in the osteogenic ability. DNMT small interfering RNA (siRNA), shRNA-Dnmt3a, and LVRNA-Dnmt3a were used to assess the role of Dnmt3a in osteogenic differentiation of control ASCs and DOP-ASCs. Micro-computed tomography, hematoxylin and eosin staining, and Masson staining were used to analyze changes in the osteogenic capability while downregulating Dnmt3a with lentivirus in DOP mice in vivo.ResultsThe proliferative ability of DOP-ASCs was lower than that of control ASCs. DOP-ASCs showed a decrease in osteogenic differentiation capacity, lower Wnt/β-catenin signaling pathway activity, and a higher level of Dnmt3a than control ASCs. When Dnmt3a was downregulated by siRNA and shRNA, osteogenic-related factors Runt-related transcription factor 2 and osteopontin, and activity of Wnt/β-catenin signaling pathway were increased, which rescued the poor osteogenic potential of DOP-ASCs. When Dnmt3a was upregulated by LVRNA-Dnmt3a, the osteogenic ability was inhibited. The same results were obtained in vivo.ConclusionsDnmt3a silencing rescues the negative effects of DOP on ASCs and provides a possible approach for bone tissue regeneration in patients with diabetic osteoporosis.

Transgenerational effects of parental bisphenol S exposure on zebrafish (Danio rerio) reproduction

Bisphenol S (BPS) is extensively used for production of polycarbonates and other commodities, and is often detected in environment and biota. Parental BPS exposure has been reported to interfere with reproductive development of offspring, but limited information is available on its multigenerational reproductive toxicity. In our present study, zebrafish (Danio rerio) were exposed to BPS (1 and 100 μg/L) from 3 hpf to 120 dpf, and the effects on reproduction, sex steroid hormones, DNA methylation levels and gene transcription involved in steroidogenesis and DNA methylation were investigated in unexposed F1-2 offspring. The results showed that 100 μg/L BPS exposure increased DNA methylation in F1 testes, and 1 μg/L BPS led to DNA methylation in F2 ovaries. The increased DNA methylation levels led to decreased expression of steroidogenic enzymes, including cyp11a, cyp17 and 3βhsd, which might be a main reason for the elevated plasma 17β-estradiol and decreased testosterone levels. In addition, sex ratio indicated a female dominance trend, and reproductive capacity of male fish was severely impaired. Overall, these findings suggest that parental BPS exposure impairs reproductive development of unexposed offspring via DNA methylation and BPS-induced epigenetic modification inheritance has a long-term effect on the fitness and sustainability of fish populations.

IL-7 promoted the development of thymic DN3 cells in aged mice via DNA demethylation of Bcl2 and c-Myc genes

IL-7 promotes the development of thymic double negative (DN) T cells during β-selection, which might contribute to the remission of aging-associated thymic involution. Methylation levels of CpG sites is correlated with aging and modulates the development. To determine the involvement of DNA methylation/demethylation instructed by IL-7 signaling during the expansion of double negative (DN) T cells, the aged mice were treated with recombinant Adeno-Associated Virus 2-mediated IL-7 (rAAV2-IL-7) and the DNA methylation/demethylation modifications in this process were analyzed. The results showed that rAAV2-IL-7 increased the number of thymocytes, especially the DN3 thymocytes during β-selection in aged mice. With aging, the methylation levels of Bcl2 and c-Myc promoter regions were increased in DN3 cells. Following rAAV2-IL-7 treatment, DNA methyltransferase Dnmt3a and Dnmt3b decreased, DNA demethylation factors TET2 and TET3 increased, and the methylation levels of Bcl2 and c-Myc in DN3 cells were reduced during DN3 stage in aged mice, consequently, resulting in the upregulation of Bcl2 and c-Myc and the larger increase of DN3 cells in thymus. In conclusion, these findings showed that Bcl2 and c-Myc genes of DN3 cells had an increased DNA methylation levels in aged mice compared to the young, and the hypermethylation in aged mice could be restored following rAAV2-IL-7 treatment.

DNA demethylation affects imprinted gene expression in maize endosperm

BackgroundDNA demethylation occurs in many species and is involved in diverse biological processes. However, the occurrence and role of DNA demethylation in maize remain unknown.ResultsWe analyze loss-of-function mutants of two major genes encoding DNA demethylases. No significant change in DNA methylation has been detected in these mutants. However, we detect increased DNA methylation levels in the mutants around genes and some transposons. The increase in DNA methylation is accompanied by alteration in gene expression, with a tendency to show downregulation, especially for the genes that are preferentially expressed in endosperm. Imprinted expression of both maternally and paternally expressed genes changes in F1 hybrid with the mutant as female and the wild-type as male parental line, but not in the reciprocal hybrid. This alteration in gene expression is accompanied by allele-specific DNA methylation differences, suggesting that removal of DNA methylation of the maternal allele is required for the proper expression of these imprinted genes. Finally, we demonstrate that hypermethylation in the double mutant is associated with reduced binding of transcription factor to its target, and altered gene expression.ConclusionsOur results suggest that active removal of DNA methylation is important for transcription factor binding and proper gene expression in maize endosperm.

FDDM1 and FDDM2, Two SGS3-like Proteins, Function as a Complex to Affect DNA Methylation in Arabidopsis.

DNA methylation is an important epigenetic modification required for the specific regulation of gene expression and the maintenance of genome stability in plants and animals. However, the mechanism of DNA demethylation remains largely unknown. Here, we show that two SGS3-like proteins, FACTOR OF DNA DEMETHYLATION 1 (FDDM1) and FDDM2, negatively affect the DNA methylation levels at ROS1-dependend DNA loci in Arabidopsis. FDDM1 binds dsRNAs with 5′ overhangs through its XS (rice gene X and SGS3) domain and forms a heterodimer with FDDM2 through its XH (rice gene X Homology) domain. A lack of FDDM1 or FDDM2 increased DNA methylation levels at several ROS1-dependent DNA loci. However, FDDM1 and FDDM2 may not have an additive effect on DNA methylation levels. Moreover, the XS and XH domains are required for the function of FDDM1. Taken together, these results suggest that FDDM1 and FDDM2 act as a heterodimer to positively modulate DNA demethylation. Our finding extends the function of plant-specific SGS3-like proteins.

MiR-30a-5p promotes glomerular podocyte apoptosis via DNMT1-mediated hypermethylation under hyperhomocysteinemia.

Abnormal elevation of homocysteine (Hcy) level is closely related to the development and progression of chronic kidney disease (CKD), with the molecular mechanisms that are not fully elucidated. Given the demonstration that miR-30a-5p is specifically expressed in glomerular podocytes, in the present study we aimed to investigate the role and potential underlying mechanism of miR-30a-5p in glomerular podocyte apoptosis induced by Hcy. We found that elevated Hcy downregulates miR-30a-5p expression in the mice and Hcy-treated podocytes, and miR-30a-5p directly targets the 3'-untranslated region (3'-UTR) of the forkhead box A1 (FOXA1) and overexpression of miR-30a-5p inhibits FOXA1 expression. By nMS-PCR and MassARRAY quantitative methylation analysis, we showed the increased DNA methylation level of miR-30a-5p promoter both and . Meanwhile, dual-luciferase reporter assay showed that the region between --1400 and --921 bp of miR-30a-5p promoter is a possible regulatory element for its transcription. Mechanistic studies indicated that DNA methyltransferase enzyme 1 (DNMT1) is the key regulator of miR-30a-5p, which in turn enhances miR-30a-5p promoter methylation level and thereby inhibits its expression. Taken together, our results revealed that epigenetic modification of miR-30a-5p is involved in glomerular podocyte injury induced by Hcy, providing a diagnostic marker candidate and novel therapeutic target in CKD induced by Hcy.

Integrative epigenomics in Sj\xf6gren\xb4s syndrome reveals novel pathways and a strong interaction between the HLA, autoantibodies and the interferon signature

Primary Sjögren’s syndrome (SS) is a systemic autoimmune disease characterized by lymphocytic infiltration and damage of exocrine salivary and lacrimal glands. The etiology of SS is complex with environmental triggers and genetic factors involved. By conducting an integrated multi-omics study, we confirmed a vast coordinated hypomethylation and overexpression effects in IFN-related genes, what is known as the IFN signature. Stratified and conditional analyses suggest a strong interaction between SS-associated HLA genetic variation and the presence of Anti-Ro/SSA autoantibodies in driving the IFN epigenetic signature and determining SS. We report a novel epigenetic signature characterized by increased DNA methylation levels in a large number of genes enriched in pathways such as collagen metabolism and extracellular matrix organization. We identified potential new genetic variants associated with SS that might mediate their risk by altering DNA methylation or gene expression patterns, as well as disease-interacting genetic variants that exhibit regulatory function only in the SS population. Our study sheds new light on the interaction between genetics, autoantibody profiles, DNA methylation and gene expression in SS, and contributes to elucidate the genetic architecture of gene regulation in an autoimmune population.

Genome-wide association and multi-omics studies identify MGMT as a novel risk gene for Alzheimer disease among women.

Increasing evidence suggests epidemiological and pathological links between Alzheimer disease (AD) and breast cancer (BC). The 17q21 locus, including MAPT encoding tau, has been identified in genome-wide association studies (GWAS) for BC in women and AD among persons lacking the APOE ε4 allele (ε4-). We hypothesized that other genes involved in tau-related pathology can be identified by GWAS in women stratified by ε4 status. We conducted a GWAS for AD among ε4- women (3,400 AD and 6,940 controls) in Alzheimer's Disease Genetics Consortium (ADGC) datasets and separately analyzed whole genome sequencing data obtained from five AD cases (all women; ε4+=4) and 26 controls (17 women, 9 men; ε4+=9) in a Hutterite kindred from South Dakota. Association tests were performed using logistic regression with covariates for age and principle components of ancestry in the ADGC datasets and for age, sex, and ε4 in the Hutterites. Potential mechanisms of top-ranked findings were investigated by integrating omics data including gene expression, DNA-methylation (DNAm), and AD-related neuropathological traits in subsets stratified by sex and ε4 status in the Religious Orders Study and Memory and Aging Project (ROSMAP; 339 AD and 229 controls). We identified genome-wide significant associations with one novel locus MGMT in each sample (ADGC: rs12775171, odds ratio [OR]=1.4, P=4.9x10-8 ; Hutterites: rs12256016, OR=2.0, P=1.9x10-14 ). Rs12775171 showed no evidence of association with AD risk in ε4+ women or in men in the ADGC datasets (P>0.05). Rs12775171 is not in linkage disequilibrium with rs12256016. At least one of these SNPs was significantly associated with increased DNAm levels near/within MGMT (best association pair: rs11016864 [proxy for rs12256016] with cg01419164; P=4.0x10-4 in women), which were also significantly associated with lower MGMT expression (P=0.03) and worse tau burden in all AD cohorts (neurofibrillary tangle; P=6.0x10-3 ), women (Braak stage; P=4.0x10-3 ), and ε4- women (neurofibrillary tangle; P=0.03), but not among ε4+ women, all men, or ε4+/ε4- men in ROSMAP. We identified a novel association of AD with the interaction of sex and MGMT. Our omics analysis confirmed that epigenetically regulated expression of MGMT (involved in DNA methylation damage repair) is significantly associated with tau in women.

Increased Sensitivity of Detection of RASSF1A and GSTP1 DNA Fragments in Serum of Prostate Cancer Patients: Optimisation of Diagnostics Using OBBPA-ddPCR.

Simple SummaryProstate carcinoma (PCa) incidence rates have continued to increase over the last 3 decades worldwide and PCa is the most common cancer in men in Germany. Classical tumour markers exhibit unsatisfactory sensitivity and specificity, leading to unnecessary prostate biopsies and associated clinical complications. New, minimally invasive biomarkers with high sensitivity and specificity are required for an early diagnosis and a better prognosis. In the present study, we evaluated the performance of a previously developed analytical method to detect trace amounts of aberrant methylated tumour DNA. The optimised method which was developed in this study evaluates DNA methylation changes of RASSF1A and GSTP1 in the blood of PCa patients at different stages compared to benign prostatic hyperplasia patients and healthy individuals. RASSF1A methylation analysis was found to be beneficial as a complementary biomarker for PCa diagnosis in combination with classical PCa markers. Both RASSF1A and GSTP1 exhibited pathological DNA methylation levels in all metastatic PCa patients, which may improve early detection of PCa metastases and therapeutic outcomes.Identification of aberrant DNA methylation is a promising tool in prostate cancer (PCa) diagnosis and treatment. In this study, we evaluated a two-step method named optimised bias-based preamplification followed by digital PCR (OBBPA-dPCR). The method was used to identify promoter hypermethylation of 2 tumour suppressor genes RASSF1A and GSTP1 in the circulating cell-free DNA (cfDNA) from serum samples of PCa patients (n = 75), benign prostatic hyperplasia (BPH, n = 58), and healthy individuals (controls, n = 155). The PCa cohort was further subdivided into subgroups comprising (I) patients with Gleason Scores (GS) ≤ 7 (n = 55), (II) GS ≥ 8 (n = 10), and (III) patients with metastatic PCa diagnosis (n = 10). We found that RASSF1A methylation levels were significantly increased in all 3 PCa subgroups compared to the controls and BPH cohorts (p < 0.01 for all comparisons). Fractional abundances of methylated GSTP1 DNA fragments were significantly increased in subgroup III of metastatic PCa patients (p < 0.001). RASSF1A methylation analysis was found to be beneficial as a complementary biomarker where further diagnostic validation is most crucial. In combination with free PSA, RASSF1A methylation status helps to identify PCa patients with GS ≥ 8 and grey-zone total PSA values between 2–10 ng/mL. In our study, PCR biases between 80–90% were sufficient to detect minute amounts of tumour DNA with high signal-to-noise ratios as well as high analytical sensitivity and specificity. Both RASSF1A and GSTP1 exhibited strongly increased DNA methylation levels in all metastatic PCa patients. Our data indicates a superior sensitivity of epigenetic biomarker analyses in early detection of PCa metastases that should also help to improve PCa therapy.