The use of two kinase inhibitors (2i) enables derivation of mouse embryonic stem cells (ESCs) in the pluripotent ground state. Using whole-genome bisulfite sequencing (WGBS), we show that male 2i ...ESCs are globally hypomethylated compared to conventional ESCs maintained in serum. In serum, female ESCs are hypomethyated similarly to male ESCs in 2i, and DNA methylation is further reduced in 2i. Regions with elevated DNA methylation in 2i strongly correlate with the presence of H3K9me3 on endogenous retroviruses (ERVs) and imprinted loci. The methylome of male ESCs in serum parallels postimplantation blastocyst cells, while 2i stalls ESCs in a hypomethylated, ICM-like state. WGBS analysis during adaptation of 2i ESCs to serum suggests that deposition of DNA methylation is largely random, while loss of DNA methylation during reversion to 2i occurs passively, initiating at TET1 binding sites. Together, our analysis provides insight into DNA methylation dynamics in cultured ESCs paralleling early developmental processes.
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•WGBS reveals dynamics of conversion between hypo- and hypermethylated mESC states•Maintained DNA methylation in 2i ESCs correlates with the presence of H3K9me3•The methylome of ground state 2i ESCs resembles preimplantation blastocyst cells•Hypomethylation in 2i is dependent on both inhibitors and LIF
Genome-wide DNA methylation analysis highlights changes that occur during pluripotent state transitions and identifies regions of methylation stability.
Global demethylation is part of a conserved program of epigenetic reprogramming to naive pluripotency. The transition from primed hypermethylated embryonic stem cells (ESCs) to naive hypomethylated ...ones (serum-to-2i) is a valuable model system for epigenetic reprogramming. We present a mathematical model, which accurately predicts global DNA demethylation kinetics. Experimentally, we show that the main drivers of global demethylation are neither active mechanisms (Aicda, Tdg, and Tet1-3) nor the reduction of de novo methylation. UHRF1 protein, the essential targeting factor for DNMT1, is reduced upon transition to 2i, and so is recruitment of the maintenance methylation machinery to replication foci. Concurrently, there is global loss of H3K9me2, which is needed for chromatin binding of UHRF1. These mechanisms synergistically enforce global DNA hypomethylation in a replication-coupled fashion. Our observations establish the molecular mechanism for global demethylation in naive ESCs, which has key parallels with those operating in primordial germ cells and early embryos.
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•Impaired DNA methylation maintenance is the cause of global demethylation in naive ESCs•Loss of H3K9me2 and UHRF1 lead to impaired maintenance targeting to replication foci•TET enzymes are not required for global demethylation•Mathematical model accurately predicts global 5mC and 5hmC during epigenetic resetting
Global demethylation during epigenetic reprogramming in preimplantation embryos, primordial germ cells, and naive embryonic stem cells is a consequence of impaired DNA methylation maintenance and synergistically regulated by a decrease in UHRF1 and H3K9me2 levels, while locus specific methylation maintenance is guided by specific recruitment of UHRF1 to H3K9me2/3. TET enzymes are dispensable for global DNA methylation reprogramming.
The pluripotent ground state is defined as a basal state free of epigenetic restrictions, which influence lineage specification. While naive embryonic stem cells (ESCs) can be maintained in a ...hypomethylated state with open chromatin when grown using two small-molecule inhibitors (2i)/leukemia inhibitory factor (LIF), in contrast to serum/LIF-grown ESCs that resemble early post-implantation embryos, broader features of the ground-state pluripotent epigenome are not well understood. We identified epigenetic features of mouse ESCs cultured using 2i/LIF or serum/LIF by proteomic profiling of chromatin-associated complexes and histone modifications. Polycomb-repressive complex 2 (PRC2) and its product H3K27me3 are highly abundant in 2i/LIF ESCs, and H3K27me3 is distributed genome-wide in a CpG-dependent fashion. Consistently, PRC2-deficient ESCs showed increased DNA methylation at sites normally occupied by H3K27me3 and increased H4 acetylation. Inhibiting DNA methylation in PRC2-deficient ESCs did not affect their viability or transcriptome. Our findings suggest a unique H3K27me3 configuration protects naive ESCs from lineage priming, and they reveal widespread epigenetic crosstalk in ground-state pluripotency.
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•Integrative proteomic analysis of the mouse ground-state pluripotent epigenome•Ground-state pluripotency is characterized by highly abundant PRC2 and H3K27me3•PRC2 protects 2i ESCs from primed-like features such as DNA methylation•The pluripotent ground state is independent of both H3K27me3 and DNA methylation
Marks and colleagues use integrative mass spectrometry to profile post-translational histone modifications and the chromatin-associated proteome in ground-state pluripotency. This reveals H3K27me3 and PRC2 as widespread hallmarks on euchromatin and heterochromatin. They show that ubiquitous chromatin-associated PRC2 protects the epigenome from priming, in particular from gaining DNA methylation.
Within the myelodysplastic syndrome (MDS) work package of the European LeukemiaNet, an Expert Panel was selected according to the framework elements of the National Institutes of Health Consensus ...Development Program. A systematic review of the literature was performed that included indexed original papers, indexed reviews and educational papers, and abstracts of conference proceedings. Guidelines were developed on the basis of a list of patient- and therapy-oriented questions, and recommendations were formulated and ranked according to the supporting level of evidence. MDSs should be classified according to the 2008 World Health Organization criteria. An accurate risk assessment requires the evaluation of not only disease-related factors but also of those related to extrahematologic comorbidity. The assessment of individual risk enables the identification of fit patients with a poor prognosis who are candidates for up-front intensive treatments, primarily allogeneic stem cell transplantation. A high proportion of MDS patients are not eligible for potentially curative treatment because of advanced age and/or clinically relevant comorbidities and poor performance status. In these patients, the therapeutic intervention is aimed at preventing cytopenia-related morbidity and preserving quality of life. A number of new agents are being developed for which the available evidence is not sufficient to recommend routine use. The inclusion of patients into prospective clinical trials is strongly recommended.
Anemia is a major and currently poorly understood clinical manifestation of hematopoietic aging. Upon aging, hematopoietic clones harboring acquired leukemia-associated mutations expand and become ...detectable, now referred to as clonal hematopoiesis (CH). To investigate the relationship between CH and anemia of the elderly, we explored the landscape and dynamics of CH in older individuals with anemia. From the prospective, population-based Lifelines cohort (n = 167 729), we selected all individuals at least 60 years old who have anemia according to World Health Organization criteria (n = 676) and 1:1 matched control participants. Peripheral blood of 1298 individuals was analyzed for acquired mutations at a variant allele frequency (VAF) of 1% or higher in 27 driver genes. To track clonal evolution over time, we included all available follow-up samples (n = 943). CH was more frequently detected in individuals with anemia (46.6%) compared with control individuals (39.1%; P = .007). Although no differences were observed regarding commonly detected DTA mutations (DNMT3A, TET2, ASXL1) in individuals with anemia compared with control individuals, other mutations were enriched in the anemia cohort, including TP53 and SF3B1. Unlike individuals with nutrient deficiency (P = .84), individuals with anemia of chronic inflammation and unexplained anemia revealed a higher prevalence of CH (P = .035 and P = .017, respectively) compared with their matched control individuals. Follow-up analyses revealed that clones may expand and decline, generally showing only a subtle increase in VAF (mean, 0.56%) over the course of 44 months, irrespective of the presence of anemia. Specific mutations were associated with different growth rates and propensities to acquire an additional hit. In contrast to smaller clones (<5% VAF), which did not affect overall survival, larger clones were associated with increased risk for death.
•Specific mutations, including TP53 and SF3B1, but not DNMT3A, TET2, and ASXL1, were enriched in older individuals with anemia.•In general, clones only confer a limited selective advantage over time, which is differentially affected by specific driver genes.
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Following implantation, the naive pluripotent epiblast of the mouse blastocyst generates a rosette, undergoes lumenogenesis and forms the primed pluripotent egg cylinder, which is able to generate ...the embryonic tissues. How pluripotency progression and morphogenesis are linked and whether intermediate pluripotent states exist remain controversial. We identify here a rosette pluripotent state defined by the co-expression of naive factors with the transcription factor OTX2. Downregulation of blastocyst WNT signals drives the transition into rosette pluripotency by inducing OTX2. The rosette then activates MEK signals that induce lumenogenesis and drive progression to primed pluripotency. Consequently, combined WNT and MEK inhibition supports rosette-like stem cells, a self-renewing naive-primed intermediate. Rosette-like stem cells erase constitutive heterochromatin marks and display a primed chromatin landscape, with bivalently marked primed pluripotency genes. Nonetheless, WNT induces reversion to naive pluripotency. The rosette is therefore a reversible pluripotent intermediate whereby control over both pluripotency progression and morphogenesis pivots from WNT to MEK signals.
In myelodysplastic syndromes (MDS), deletions of chromosome 7 or 7q are common and correlate with a poor prognosis. The relevant genes on chromosome 7 are unknown. We report here that EZH2, located ...at 7q36.1, is frequently targeted in MDS. Analysis of EZH2 deletions, missense and frameshift mutations strongly suggests that EZH2 is a tumor suppressor. As EZH2 functions as a histone methyltransferase, abnormal histone modification may contribute to epigenetic deregulation in MDS.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Question: How many vegetation plot observations (relevés) are available in electronic databases, how are they geographically distributed, what are their properties and how might they be discovered ...and located for research and application? Location: Global. Methods: We compiled the Global Index of Vegetation-Plot Databases (GIVD; http://www.givd.info), an Internet resource aimed at registering metadata on existing vegetation databases. For inclusion, databases need to (i) contain temporally and spatially explicit species co-occurrence data and (ii) be accessible to the scientific public. This paper summarizes structure and data quality of databases registered in GIVD as of 30 December 2010. Results: On the given date, 132 databases containing more than 2.4 million non-overlapping plots had been registered in GIVD. The majority of these data were in European databases (83 databases, 1.6 million plots), whereas other continents were represented by substantially less (North America 15, Asia 13, Africa nine, South America seven, Australasia two, multi-continental three). The oldest plot observation was 1864, but most plots were recorded after 1970. Most plots reported vegetation on areas of 1 to 1000 m2; some also stored time-series and nested-plot data. Apart from geographic reference (required for inclusion), most frequent information was on altitude (71%), slope aspect and inclination (58%) and land use (38%), but rarely soil properties (<7%). Conclusions: The vegetation plot data in GIVD constitute a major resource for biodiversity research, both through the large number of species occurrence records and storage of species co-occurrence information at a small scale, combined with structural and plot-based environmental data. We identify shortcomings in available data that need to be addressed through sampling under-represented geographic regions, providing better incentives for data collection and sharing, developing user-friendly database exchange standards, as well as tools to analyse and remove confounding effects of sampling biases. The increased availability of data sets conferred by registration in GIVD offers significant opportunities for large-scale studies in community ecology, macroecology and global change research.
Tumor protein p53 (TP53) is the most frequently mutated gene in cancer
. In patients with myelodysplastic syndromes (MDS), TP53 mutations are associated with high-risk disease
, rapid transformation ...to acute myeloid leukemia (AML)
, resistance to conventional therapies
and dismal outcomes
. Consistent with the tumor-suppressive role of TP53, patients harbor both mono- and biallelic mutations
. However, the biological and clinical implications of TP53 allelic state have not been fully investigated in MDS or any other cancer type. We analyzed 3,324 patients with MDS for TP53 mutations and allelic imbalances and delineated two subsets of patients with distinct phenotypes and outcomes. One-third of TP53-mutated patients had monoallelic mutations whereas two-thirds had multiple hits (multi-hit) consistent with biallelic targeting. Established associations with complex karyotype, few co-occurring mutations, high-risk presentation and poor outcomes were specific to multi-hit patients only. TP53 multi-hit state predicted risk of death and leukemic transformation independently of the Revised International Prognostic Scoring System (IPSS-R)
. Surprisingly, monoallelic patients did not differ from TP53 wild-type patients in outcomes and response to therapy. This study shows that consideration of TP53 allelic state is critical for diagnostic and prognostic precision in MDS as well as in future correlative studies of treatment response.
Cancer development is a dynamic process during which the successive accumulation of mutations results in cells with increasingly malignant characteristics. Here, we show the clonal evolution pattern ...in myelodysplastic syndrome (MDS) patients receiving supportive care, with or without lenalidomide (follow-up 2.5-11 years). Whole-exome and targeted deep sequencing at multiple time points during the disease course reveals that both linear and branched evolutionary patterns occur with and without disease-modifying treatment. The application of disease-modifying therapy may create an evolutionary bottleneck after which more complex MDS, but also unrelated clones of haematopoietic cells, may emerge. In addition, subclones that acquired an additional mutation associated with treatment resistance (TP53) or disease progression (NRAS, KRAS) may be detected months before clinical changes become apparent. Monitoring the genetic landscape during the disease may help to guide treatment decisions.
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