SummaryTransmissible cancers are clonal lineages that spread through populations via contagious cancer cells. Although rare in nature, two facial tumor clones affect Tasmanian devils. Here we perform comparative genetic and functional characterization of these lineages. The two cancers have similar patterns of mutation and show no evidence of exposure to exogenous mutagens or viruses. Genes encoding PDGF receptors have copy number gains and are present on extrachromosomal double minutes. Drug screening indicates causative roles for receptor tyrosine kinases and sensitivity to inhibitors of DNA repair. Y chromosome loss from a male clone infecting a female host suggests immunoediting. These results imply that Tasmanian devils may have inherent susceptibility to transmissible cancers and present a suite of therapeutic compounds for use in conservation.

The expression of the pluripotency factors OCT4, SOX2, KLF4, and MYC (OSKM) can convert somatic differentiated cells into pluripotent stem cells in a process known as reprogramming. Notably, partial and reversible reprogramming does not change cell identity but can reverse markers of aging in cells, improve the capacity of aged mice to repair tissue injuries, and extend longevity in progeroid mice. However, little is known about the mechanisms involved. Here, we have studied changes in the DNA methylome, transcriptome, and metabolome in naturally aged mice subject to a single period of transient OSKM expression. We found that this is sufficient to reverse DNA methylation changes that occur upon aging in the pancreas, liver, spleen, and blood. Similarly, we observed reversion of transcriptional changes, especially regarding biological processes known to change during aging. Finally, some serum metabolites and biomarkers altered with aging were also restored to young levels upon transient reprogramming. These observations indicate that a single period of OSKM expression can drive epigenetic, transcriptomic, and metabolomic changes toward a younger configuration in multiple tissues and in the serum.

While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.

Background Epigenetic clocks are mathematical models that predict the biological age of an individual using DNA methylation data and have emerged in the last few years as the most accurate biomarkers of the aging process. However, little is known about the molecular mechanisms that control the rate of such clocks. Here, we have examined the human epigenetic clock in patients with a variety of developmental disorders, harboring mutations in proteins of the epigenetic machinery. Results Using the Horvath epigenetic clock, we perform an unbiased screen for epigenetic age acceleration in the blood of these patients. We demonstrate that loss-of-function mutations in the H3K36 histone methyltransferase NSD1, which cause Sotos syndrome, substantially accelerate epigenetic aging. Furthermore, we show that the normal aging process and Sotos syndrome share methylation changes and the genomic context in which they occur. Finally, we found that the Horvath clock CpG sites are characterized by a higher Shannon methylation entropy when compared with the rest of the genome, which is dramatically decreased in Sotos syndrome patients. Conclusions These results suggest that the H3K36 methylation machinery is a key component of the epigenetic maintenance system in humans, which controls the rate of epigenetic aging, and this role seems to be conserved in model organisms. Our observations provide novel insights into the mechanisms behind the epigenetic aging clock and we expect will shed light on the different processes that erode the human epigenetic landscape during aging. Electronic supplementary material The online version of this article (10.1186/s13059-019-1753-9) contains supplementary material, which is available to authorized users.

Here we provide the first genome-wide in vivo analysis of the Na + /Ca 2+ exchanger family in the model system Caenorhabditis elegans. We source all members of this family within the Caenorhabditis genus and reconstruct their phylogeny across humans and Drosophila melanogaster. Next, we provide a description of the expression pattern for each exchanger gene in C. elegans, revealing a wide expression in a number of tissues and cell types including sensory neurons, interneurons, motor neurons, muscle cells, and intestinal tissue. Finally, we conduct a series of behavioral and functional analyses through mutant characterization in C. elegans.From these data we demonstrate that, similar to mammalian systems, the expression of Na + /Ca 2+ exchangers in C. elegans is skewed toward excitable cells, and we propose that C. elegans may be an ideal model system for the study of Na + /Ca 2+ exchangers.C ALCIUM functions as a diverse signaling molecule in a variety of cell types through activation and conformational changes of proteins, as well as via modulation of cellular capacitance (Berridge et al. 2000(Berridge et al. , 2003Bootman et al. 2001). Neurotransmitter release, muscular contraction, apoptosis, and lymphocyte activation are some of the many cellular processes mediated by calcium signaling, and accordingly, strict balance of calcium levels must be maintained to prevent cellular dysfunction. Cells accomplish this primarily by extruding calcium through plasma membraneembedded plasma membrane Ca 2+ ATPase (PMCA) pumps and utilizing exchanger ion transporters. PMCA proteins are high-affinity/low-capacity pumps that maintain calcium homeostasis over sustained periods of time by removing one Ca 2+ ion for every ATP hydrolyzed (Tidow et al. 2012). Exchangers such as Na + /Ca 2+ exchangers (NCX), Na + /Ca 2+ /K + exchangers (NCKX), and calcium/cation exchangers (CCX) are low-affinity/high-capacity ion transporters that rapidly expel calcium ions (Philipson and Nicoll 2000;Philipson et al. 2002;Lytton 2007;Nicoll et al. 2013). The NCX, NCKX, and CCX families of exchangers comprise the three branches of the family of Na + /Ca 2+ exchangers in animals (Cai and Lytton 2004a,b;Lytton 2007). Under normal physiological conditions, NCX ion transporters utilize the energy stored in the transmembrane gradient to allow influx of three Na + ions and extrusion of one Ca 2+ ion (Hilge 2012;Ottolia and Philipson 2013). In the case of the NCKX transporter, there is one Ca 2+ and one K + ion exchanged in return for Na + ion influx, and in the case of the CCX exchangers, both Na + /Ca 2+ and Li + /Ca 2+ exchanges have been observed (Lytton. 2007;Visser and Lytton 2007). As of yet, the nematode Caenorhabditis elegans has not been used as an in vivo model organism to study the NCX, NCKX, CCX exchanger family. Here we provide a detailed description of the phylogeny of this family of transporters in C. elegans, examine the expression patterns of each member, and uncover roles for one NCX member and one CCX member in muscle contracti...

The expression of the pluripotency factors OCT4, SOX2, KLF4 and MYC (OSKM) can convert somatic differentiated cells into pluripotent stem cells in a process known as reprogramming. Notably, cycles of brief OSKM expression do not change cell identity but can reverse markers of aging in cells and extend longevity in progeroid mice. However, little is known about the mechanisms involved. Here, we have studied changes in the DNA methylome, transcriptome and metabolome in naturally aged mice subject to a single period of transient OSKM expression. We found that this is sufficient to reverse DNA methylation changes that occur upon aging in the pancreas, liver, spleen and blood. Similarly, we observed reversion of transcriptional changes, especially regarding biological processes known to change during aging. Finally, some serum metabolites altered with aging were also restored to young levels upon transient reprogramming. These observations indicate that a single period of OSKM expression can drive epigenetic, transcriptomic and metabolomic changes towards a younger configuration in multiple tissues and in the serum.

Clean freshwater lies at the heart of human society and monitoring its quality is paramount. In addition to chemical controls, traditional microbiological water tests focus on the detection of specific bacterial pathogens. The direct tracing of all aquatic DNA poses a more profound alternative. Yet, this has hitherto been underused due to challenges in cost and logistics. Here we present a simple, fast, inexpensive and comprehensive freshwater diagnostics workflow centred around portable nanopore DNA sequencing. Using defined bacterial compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), our study shows how nanopore sequencing can be readily integrated for the assessment of aquatic bacterial diversity and pollution. We provide a computational benchmark that features more than ten taxonomic classification tools to derive guidelines for bacterial DNA analyses with nanopore data. Through complementary physicochemical measurements, we find that nanopore metagenomics can depict fine temporal gradients along the main hydrological axis of an urban-rural interface and yield high-resolution pathogen maps that address concerns of public health.

DNA methylation is an important epigenetic modification in many species that is critical for development, and implicated in ageing and many complex diseases, such as cancer. Many cost-effective genome-wide analyses of DNA modifications rely on restriction enzymes capable of digesting genomic DNA at defined sequence motifs. There are hundreds of restriction enzyme families but few are used to date, because no tool is available for the systematic evaluation of restriction enzyme combinations that can enrich for certain sites of interest in a genome. Herein, we present customised Reduced Representation Bisulfite Sequencing (cuRRBS), a novel and easy-to-use computational method that solves this problem. By computing the optimal enzymatic digestions and size selection steps required, cuRRBS generalises the traditional MspI-based Reduced Representation Bisulfite Sequencing (RRBS) protocol to all restriction enzyme combinations. In addition, cuRRBS estimates the fold-reduction in sequencing costs and provides a robustness value for the personalised RRBS protocol, allowing users to tailor the protocol to their experimental needs. Moreover, we show in silico that cuRRBS-defined restriction enzymes consistently out-perform MspI digestion in many biological systems, considering both CpG and CHG contexts. Finally, we have validated the accuracy of cuRRBS predictions for single and double enzyme digestions using two independent experimental datasets.