Bloom syndrome patients and mice display accelerated epigenetic aging.

Bloom syndrome (BSyn) is an autosomal recessive disorder caused by variants in the BLM gene, which is involved in genome stability. Patients with BSyn present with poor growth, sun sensitivity, mild immunodeficiency, diabetes, and increased risk of cancer, most commonly leukemias. Interestingly, patients with BSyn do not have other signs of premature aging such as early, progressive hair loss and cataracts. We set out to determine epigenetic age in BSyn, which can be a better predictor of health and disease over chronological age. Our results show for the first time that patients with BSyn have evidence of accelerated epigenetic aging across several measures in blood lymphocytes, as compared to carriers. Additionally, homozygous Blm mice exhibit accelerated methylation age in multiple tissues, including brain, blood, kidney, heart, and skin, according to the brain methylation clock. Overall, we find that Bloom syndrome is associated with accelerated epigenetic aging effects in multiple tissues and more generally a strong effect on CpG methylation levels

A mammalian methylation array for profiling methylation levels at conserved sequences

Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed the mammalian methylation array, a single custom array that measures up to 36k CpGs per species that are well conserved across many mammalian species. We designed a set of probes that can tolerate specific cross-species mutations. We annotate the array in over 200 species and report CpG island status and chromatin states in select species. Calibration experiments demonstrate the high fidelity in humans, rats, and mice. The mammalian methylation array has several strengths: it applies to all mammalian species even those that have not yet been sequenced, it provides deep coverage of conserved cytosines facilitating the development of epigenetic biomarkers, and it increases the probability that biological insights gained in one species will translate to others

DNA methylation predicts age and provides insight into exceptional longevity of bats

This work was supported by a Paul G. Allen Frontiers Group grant to S.H., the University of Maryland, College of Computer, Mathematical and Natural Sciences to G.S.W., an Irish Research Council Consolidator Laureate Award to E.C.T., a UKRI Future Leaders Fellowship (MR/T021985/1) to S.C.V. and a Discovery Grant from the Natural Sciences and Engineering Research Council (NSERC) of Canada to P.A.F. S.C.V. and P.D. were supported by a Max Planck Research Group awarded to S.C.V. by the Max Planck Gesellschaft, and S.C.V. and E.Z.L. were supported by a Human Frontiers Science Program Grant (RGP0058/2016) awarded to S.C.V. L.J.G. was supported by an NSERC PGS-D scholarship.Exceptionally long-lived species, including many bats, rarely show overt signs of aging, making it difficult to determine why species differ in lifespan. Here, we use DNA methylation (DNAm) profiles from 712 known-age bats, representing 26 species, to identify epigenetic changes associated with age and longevity. We demonstrate that DNAm accurately predicts chronological age. Across species, longevity is negatively associated with the rate of DNAm change at age-associated sites. Furthermore, analysis of several bat genomes reveals that hypermethylated age- and longevity-associated sites are disproportionately located in promoter regions of key transcription factors (TF) and enriched for histone and chromatin features associated with transcriptional regulation. Predicted TF binding site motifs and enrichment analyses indicate that age-related methylation change is influenced by developmental processes, while longevity-related DNAm change is associated with innate immunity or tumorigenesis genes, suggesting that bat longevity results from augmented immune response and cancer suppression.Publisher PDFPeer reviewe

DNA methylation networks underlying mammalian traits

INTRODUCTION: Comparative epigenomics is an emerging field that combines epigenetic signatures with phylogenetic relationships to elucidate species characteristics such as maximum life span. For this study, we generated cytosine DNA methylation (DNAm) profiles (n = 15,456) from 348mammalian species using amethylation array platform that targets highly conserved cytosines. RATIONALE: Nature has evolved mammalian species of greatly differing life spans. To resolve the relationship ofDNAmwith maximum life span and phylogeny, we performed a largescale cross-species unsupervised analysis. Comparative studies in many species enables the identification of epigenetic correlates of maximum life span and other traits. RESULTS: We first tested whether DNAm levels in highly conserved cytosines captured phylogenetic relationships among species. We constructed phyloepigenetic trees that paralleled the traditional phylogeny. To avoid potential confounding by different tissue types, we generated tissue-specific phyloepigenetic trees. The high phyloepigenetic-phylogenetic congruence is due to differences in methylation levels and is not confounded by sequence conservation. We then interrogated the extent to which DNA methylation associates with specific biological traits. We used an unsupervised weighted correlation network analysis (WGCNA) to identify clusters of highly correlated CpGs (comethylation modules). WGCNA identified 55 distinct comethylation modules, of which 30 were significantly associated with traits including maximum life span, adult weight, age, sex, human mortality risk, or perturbations that modulate murine life span. Both the epigenome-wide association analysis (EWAS) and eigengene-based analysis identified methylation signatures of maximum life span, and most of these were independent of aging, presumably set at birth, and could be stable predictors of life span at any point in life. Several CpGs that are more highly methylated in long-lived species are located near HOXL subclass homeoboxes and other genes that play a role in morphogenesis and development. Some of these life span–related CpGs are located next to genes that are also implicated in our analysis of upstream regulators (e.g., ASCL1 and SMAD6). CpGs with methylation levels that are inversely related to life span are enriched in transcriptional start site (TSS1) and promoter flanking (PromF4, PromF5) associated chromatin states. Genes located in chromatin state TSS1 are constitutively active and enriched for nucleic acid metabolic processes. This suggests that long-living species evolved mechanisms that maintain low methylation levels in these chromatin states that would favor higher expression levels of genes essential for an organism’s survival. The upstreamregulator analysis of the EWAS of life span identified the pluripotency transcription factors OCT4, SOX2, and NANOG. Other factors, such as POLII, CTCF, RAD21, YY1, and TAF1, showed the strongest enrichment for negatively life span–related CpGs. CONCLUSION: The phyloepigenetic trees indicate that divergence of DNA methylation profiles closely parallels that of genetics through evolution. Our results demonstrate that DNA methylation is subjected to evolutionary pressures and selection. The publicly available data from ourMammalian Methylation Consortium are a rich source of information for different fields such as evolutionary biology, developmental biology, and aging

Antiviral activity and mechanism of action of edible bird’s nest against influenza A virus strain A/Puerto Rico/8/1934 (H1N1)

Influenza infection is still a high-risk disease affecting human and different animal species by causative agent influenza A virus (IAV). Currently there is neither effective vaccine nor efficient drug to control this infection. Edible Bird’s Nest (EBN) as a popular traditional Chinese medicine (TCM) is believed to have health enhancing effects like anti-tumor and immunomodulatory activities. These natural extracts also have shown antiviral properties against influenza viruses; however, the molecular mechanism of action of these compounds still is not well characterized. Hence, the first aim of this study was to highlight the inhibitory effects of EBNs against influenza A virus (IAV) infection. Accordingly, house EBNs were collected from Teluk Intan and cave nests from Gua Madai in Malaysia and the extractions were prepared based on the established methods with two different enzymatic treatments. The median cytotoxic concentration (CC50) of the EBN extracts were determined on Madin-Darby canine kidney (MDCK) cell line using microculture tetrazolium (MTT) assay and later on the best exposure way and median inhibitory concentration (IC50) of the EBNs were shown against IAV strain A/Puerto Rico/8/1934 (H1N1). The results showed that post inoculation of the EBNs had the highest antiviral effect against IAV. The CC50 of these compounds ranged from 27.5-32 mg/ml with IC50 of 2.5-4.9 mg/ml against IAV and EBNs from Gua Madai had higher selectivity index compared to Teluk Intan. The second aim of this study was to understand the mechanism of action of these natural compounds against different molecular processes of IAV life cycle. These processes included effect of EBN on four viral proteins, virus host immune interactions through cytokines, early endosomes formation and their trafficking, and lastly autophagy process during IAV infection. Consequently, four viral genes and six cytokines were selected to be analyzed by RT-qPCR and ELISA to elucidate the effect of EBNs on the virus and immune system. Later, Western blotting on three GTPases proteins, and immunofluorescent labeling of actin cytoskleton and lysosomes were done to investigate the effects of EBNs on endocytosis, actin cytoskeleton and macroautophagy processes during influenza virus life cycle. Regarding the effect of EBNs on viral genes and cytokines, the results showed that depends on the EBN composition, EBNs could significantly decrease the extracellular NA and NS1 copy number (p<0.05) of the virus along with high immunomodulatory effects against IAV. EBNs showed antiinflammatory effects through decrease of CCL2 and IL-6, and increase of IL-27. In addition, these compounds might affect the virus by increase of TNF-α and activation of NF-κB. Immunofluorescent staining and Western blot results revealed the effects of EBNs on endocytosis, actin filament polymerization and macroautophagy pathways against IAV. EBNs could affect the trafficking of early endosomes by significant (p<0.05) decrease in GTPase proteins like RAB5 and RhoA, also ameliorating the actin filaments distress. These natural mixtures could efficiently inhibit the autophagy process involved in IAV life cycle by decrease (p<0.05) in LC3-II protein and augmentation of lysosome activity. In conclusion, EBNs can inhibit influenza infection by affecting critical steps of the virus life cycle. EBNs from different locations would show different mechanisms against IAV. Hence, after screening for the composition, these natural remedies have the potential to be used as an alternative antiviral agent against future influenza disasters. Further in vitro and in vivo studies are required to detect the bioactive agents and investigate the clinical applications of this natural medicine against influenza