Distinctive topology of age-associated epigenetic drift in the human interactome

Recently, it has been demonstrated that DNA methylation, a covalent modification of DNA that can regulate gene expression, is modified as a function of age. However, the biological and clinical significance of this age-associated epigenetic drift is unclear. To shed light on the potential biological significance, we here adopt a systems approach and study the genes undergoing age-associated changes in DNA methylation in the context of a protein interaction network, focusing on their topological properties. In contrast to what has been observed for other age-related gene classes, including longevity- and disease-associated genes, as well as genes undergoing age-associated changes in gene expression, we here demonstrate that age-associated epigenetic drift occurs preferentially in genes that occupy peripheral network positions of exceptionally low connectivity. In addition, we show that these genes synergize topologically with disease and longevity genes, forming unexpectedly large network communities. Thus, these results point toward a potentially distinct mechanistic and biological role of DNA methylation in dictating the complex aging and disease phenotypes

Age-associated epigenetic drift: implications, and a case of epigenetic thrift?

It is now well established that the genomic landscape of DNA methylation gets altered as a function of age, a process we here call "epigenetic drift". The biological, functional, clinical and evolutionary significance of this epigenetic drift however remains unclear. We here provide a brief review of epigenetic drift, focusing on the potential implications for ageing, stem-cell biology and disease risk prediction. It has been demonstrated that epigenetic drift affects most of the genome, suggesting a global deregulation of DNA methylation patterns with age. A component of this drift is tissue specific, allowing remarkably accurate age-predictive models to be constructed. Another component is tissue-independent, targeting stem-cell differentiation pathways and affecting stem cells, which may explain the observed decline of stem cell function with age. Age-associated increases in DNA methylation target developmental genes, overlapping those associated with environmental disease risk factors and with disease itself, notably cancer. In particular, cancers and precursor cancer lesions exhibit aggravated age DNA methylation signatures. Epigenetic drift is also influenced by genetic factors. Thus, drift emerges as a promising biomarker for premature or biological ageing, and could potentially be used in geriatrics for disease risk prediction. Finally, we propose, in the context of human evolution, that epigenetic drift may represent a case of epigenetic thrift, or bet-hedging. In summary, this review demonstrates the growing importance of the "ageing epigenome", with potentially far reaching implications for understanding the effect of age on stem cell function and differentiation, as well as for disease prevention

Interventional multispectral photoacoustic imaging with a clinical ultrasound probe for discriminating nerves and tendons: an ex vivo pilot study

Abstract. Accurate and efficient identification of nerves is an essential component of peripheral nerve blocks. While ultrasound (US) imaging is increasingly used as a guidance modality, it often provides insufficient contrast for identifying nerves from surrounding tissues such as tendons. Electrical nerve stimulators can be used in conjunction with US imaging for discriminating nerves from surrounding tissues, but they are insufficient to reliably prevent neural punctures, so that alternative methods are highly desirable. In this study, an interventional multispectral photoacoustic (PA) imaging system was used to directly compare the signal amplitudes and spectra acquired from nerves and tendons ex vivo, for the first time. The results indicate that the system can provide significantly higher image contrast for discriminating nerves and tendons than that provided by US imaging. As such, photoacoustic imaging could be valuable as an adjunct to US for guiding peripheral nerve blocks

Corruption of the Intra-Gene DNA Methylation Architecture Is a Hallmark of Cancer

Epigenetic processes - including DNA methylation - are increasingly seen as having a fundamental role in chronic diseases like cancer. It is well known that methylation levels at particular genes or loci differ between normal and diseased tissue. Here we investigate whether the intra-gene methylation architecture is corrupted in cancer and whether the variability of levels of methylation of individual CpGs within a defined gene is able to discriminate cancerous from normal tissue, and is associated with heterogeneous tumour phenotype, as defined by gene expression. We analysed 270985 CpGs annotated to 18272 genes, in 3284 cancerous and 681 normal samples, corresponding to 14 different cancer types. In doing so, we found novel differences in intra-gene methylation pattern across phenotypes, particularly in those genes which are crucial for stem cell biology; our measures of intra-gene methylation architecture are a better determinant of phenotype than measures based on mean methylation level alone (K-S test [Formula: see text] in all 14 diseases tested). These per-gene methylation measures also represent a considerable reduction in complexity, compared to conventional per-CpG beta-values. Our findings strongly support the view that intra-gene methylation architecture has great clinical potential for the development of DNA-based cancer biomarkers

Three-dimensional printed ultrasound and photoacoustic training phantoms for vasculature access

Ultrasound (US) imaging is widely used to guide vascular access procedures such as arterial and venous cannulation. As needle visualisation with US imaging can be very challenging, it is easy to misplace the needle in the patient and it can be life threating. Photoacoustic (PA) imaging is well suited to image medical needles and catheters that are commonly used for vascular access. To improve the success rate, a certain level of proficiency is required that can be gained through extensive practice on phantoms. Unfortunately, commercial training phantoms are expensive and custom-made phantoms usually do not replicate the anatomy very well. Thus, there is a great demand for more realistic and affordable ultrasound and photoacoustic imaging phantoms for vasculature access procedures training. Three-dimensional (3D) printing can help create models that replicate complex anatomical geometries. However, the available 3D printed materials do not possess realistic tissue properties. Alternatively, tissue-mimicking materials can be employed using casting and 3D printed moulds but this approach is limited to the creation of realistic outer shapes with no replication of complex internal structures. In this study, we developed a realistic vasculature access phantom using a combination of mineral oil based materials as background tissue and a non-toxic, water dissolvable filament material to create complex vascular structure using 3D printing. US and PA images of the phantoms comprising the complex vasculature network were acquired. The results show that 3D printing can facilitate the fabrication of anatomically realistic training phantoms, with designs that can be customized and shared electronically. © (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

Fiber optic photoacoustic probe with ultrasonic tracking for guiding minimally invasive procedures

In a wide range of clinical procedures, accurate placement of medical devices such as needles and catheters is critical to optimize patient outcomes. Ultrasound imaging is often used to guide minimally invasive procedures, as it can provide real-time visualization of patient anatomy and medical devices. However, this modality can provide low image contrast for soft tissues, and poor visualization of medical devices that are steeply angled with respect to the incoming ultrasound beams. Photoacoustic sensors can provide information about the spatial distributions of tissue chromophores that could be valuable for guiding minimally invasive procedures. In this study, a system for guiding minimally invasive procedures using photoacoustic sensing was developed. This system included a miniature photoacoustic probe with three optical fibers: one with a bare end for photoacoustic excitation of tissue, a second for photoacoustic excitation of an optically absorbing coating at the distal end to transmit ultrasound, and a third with a Fabry-Perot cavity at the distal end for receiving ultrasound. The position of the photoacoustic probe was determined with ultrasonic tracking, which involved transmitting pulses from a linear-array ultrasound imaging probe at the tissue surface, and receiving them with the fiber-optic ultrasound receiver in the photoacoustic probe. The axial resolution of photoacoustic sensing was better than 70 μm, and the tracking accuracy was better than 1 mm in both axial and lateral dimensions. By translating the photoacoustic probe, depth scans were obtained from different spatial positions, and two-dimensional images were reconstructed using a frequency-domain algorithm

An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways

Epigenetic changes have been associated with ageing and cancer. Identifying and interpreting epigenetic changes associated with such phenotypes may benefit from integration with protein interactome models. We here develop and validate a novel integrative epigenome-interactome approach to identify differential methylation interactome hotspots associated with a phenotype of interest. We apply the algorithm to cancer and ageing, demonstrating the existence of hotspots associated with these phenotypes. Importantly, we discover tissue independent age-associated hotspots targeting stem-cell differentiation pathways, which we validate in independent DNA methylation data sets, encompassing over 1000 samples from different tissue types. We further show that these pathways would not have been discovered had we used a non-network based approach and that the use of the protein interaction network improves the overall robustness of the inference procedure. The proposed algorithm will be useful to any study seeking to identify interactome hotspots associated with common phenotypes

An Introduction to the Chalk Aquifers of Northern Europe

We briefly outline the progressive development of approaches to both the characterization and simulation of the hydrogeology of northern European chalk aquifers, which were some of the first in the world to be studied. The volume's scope includes work on water resources and quality, chalk streams and wetland ecosystems, chalks as heat reservoirs for building temperature regulation, sources of groundwater flood risk and impacts of engineering on the subsurface, and diffuse and point-source pollution affecting these aquifers. It excludes hydrocarbon-related studies and those focused on offshore chalk sequences. We briefly outline the current state of knowledge of hydrogeological processes, characterization, assessment and modelling, and the increasingly recognized importance of karst features. The latter were little discussed 20 years ago and are still often neglected. There follows a brief quantitative analysis of publication topics relating to chalk hydrogeology in the scientific literature over the past three decades, which highlights key trends including both the purposes of studies and the methods employed. We present a summary of the topics and contributions within this volume, and conclude by identifying the key issues that need to be addressed in order to ensure the sustainability of our chalk aquifers for the future