The role of DNA methylation in human pancreatic neuroendocrine tumours

Pancreatic neuroendocrine tumours (PNETs) are the second most common pancreatic tumour. However, relatively little is known about their tumourigenic drivers, other than mutations involving the multiple endocrine neoplasia 1 (MEN1), ATRX chromatin remodeler, and death domain-associated protein genes, which are found in ~40% of sporadic PNETs. PNETs have a low mutational burden, thereby suggesting that other factors likely contribute to their development, including epigenetic regulators. One such epigenetic process, DNA methylation, silences gene transcription via 5’methylcytosine (5mC), and this is usually facilitated by DNA methyltransferase enzymes at CpG-rich areas around gene promoters. However, 5’hydroxymethylcytosine, which is the first epigenetic mark during cytosine demethylation, and opposes the function of 5mC, is associated with gene transcription, although the significance of this remains unknown, as it is indistinguishable from 5mC when conventional bisulfite conversion techniques are solely used. Advances in array-based technologies have facilitated the investigation of PNET methylomes and enabled PNETs to be clustered by methylome signatures, which has assisted in prognosis and discovery of new aberrantly regulated genes contributing to tumourigenesis. This review will discuss the biology of DNA methylation, its role in PNET development, and impact on prognostication and discovery of epigenome-targeted therapies

Towards a practical framework for managing the risks of selecting technology to support independent living

Information and communication technology applications can help increase the independence and quality of life of older people, or people with disabilities who live in their own homes. A risk management framework is proposed to assist in selecting applications that match the needs and wishes of particular individuals. Risk comprises two components: the likelihood of the occurrence of harm and the consequences of that harm. In the home, the social and psychological harms are as important as the physical ones. The importance of the harm (e.g., injury) is conditioned by its consequences (e.g., distress, costly medical treatment). We identify six generic types of harm (including dependency, loneliness, fear and debt) and four generic consequences (including distress and loss of confidence in ability to live independently). The resultant client-centred framework offers a systematic basis for selecting and evaluating technology for independent living

Engaging and empowering first-year students through curriculum design: perspectives from the literature

There is an increasing value being placed on engaging and empowering first-year students and first-year curriculum design is a key driver and opportunity to ensure early enculturation into successful learning at university. This paper summarises the literature on first-year curriculum design linked to student engagement and empowerment. We present conceptualisations of ‘curriculum’ and examples from first-year curriculum design. We also note the limited literature where students have been involved in designing first-year curricula. The results of the literature review suggest that key characteristics of engaging first-year curricula include active learning, timely feedback, relevance and challenge. The literature also points to the importance of identifying students' abilities on entry to university as well as being clear about desired graduate attributes and developmental goals. Acknowledging realities and constraints, we present a framework for the first-year curriculum design process based on the literature

Genetic background influences tumour development in heterozygous Men1 knockout mice

Multiple endocrine neoplasia type 1 (MEN1), an autosomal dominant disorder caused by MEN1 germline mutations, is characterised by parathyroid, pancreatic and pituitary tumours. MEN1 mutations also cause familial isolated primary hyperparathyroidism (FIHP), a milder condition causing hyperparathyroidism only. Identical mutations can cause either MEN1 or FIHP in different families, thereby implicating a role for genetic modifiers in altering phenotypic expression of tumours. We therefore investigated the effects of genetic background and potential for genetic modifiers on tumour development in adult Men1+/- mice, which develop tumours of the parathyroids, pancreatic islets, anterior pituitary, adrenal cortex and gonads, that had been backcrossed to generate C57BL/6 and 129S6/SvEv congenic strains. A total of 275 Men1+/- mice, aged 5–26 months were macroscopically studied, and this revealed that genetic background significantly influenced the development of pituitary, adrenal and ovarian tumours, which occurred in mice over 12 months of age and more frequently in C57BL/6 females, 129S6/SvEv males and 129S6/SvEv females, respectively. Moreover, pituitary and adrenal tumours developed earlier, in C57BL/6 males and 129S6/SvEv females, respectively, and pancreatic and testicular tumours developed earlier in 129S6/SvEv males. Furthermore, glucagon-positive staining pancreatic tumours occurred more frequently in 129S6/SvEv Men1+/- mice. Whole genome sequence analysis of 129S6/SvEv and C57BL/6 Men1+/- mice revealed >54,000 different variants in >300 genes. These included, Coq7, Dmpk, Ccne2, Kras, Wnt2b, Il3ra and Tnfrsf10a, and qRT-PCR analysis revealed that Kras was significantly higher in pituitaries of male 129S6/SvEv mice. Thus, our results demonstrate that Kras and other genes could represent possible genetic modifiers of Men1

MiR-15a/miR-16-1 expression inversely correlates with cyclin D1 levels in Men1 pituitary NETs

Multiple Endocrine Neoplasia type 1 (MEN1) is an autosomal dominant disorder characterised by the combined occurrence of parathyroid, pituitary and pancreatic islet tumours, and is due to mutations of the MEN1 gene, which encodes the tumour suppressor protein menin. Menin has multiple roles in genome stability, transcription, cell division and proliferation, but its mechanistic roles in tumourigenesis remain to be fully elucidated. MicroRNAs (miRNA) are non-coding single stranded RNAs that post-transcriptionally regulate gene expression and have been associated with tumour development, although the contribution of miRNAs to MEN1-associated tumourigenesis and their relationship with menin expression are not fully understood. Alterations in miRNA expression, including downregulation of three putative ‘tumour suppressor’ miRNAs, miR-15a, miR-16-1 and let 7a, have been reported in several tumour types including non-MEN1 pituitary adenomas. We have therefore investigated the expression of miR-15a, miR-16-1 and let-7a in pituitary tumours that developed after 12 months of age in female mice with heterozygous knock out of the Men1 gene (Men1+/- 41 mice). The miRNAs miR-15a, miR-16-1 and let-7a were significantly downregulated in pituitary tumours (by 2.3-fold, p<0.05; 2.1-fold p<0.01 and 1.6-fold p<0.05, respectively) of Men1+/- 43 mice, compared to normal wild type pituitaries. MiR-15a and miR-16-1 expression inversely correlated with expression of cyclin D1, a known pro-tumourigenic target of these miRNAs, and knock down of menin in a human cancer cell line (HeLa), and AtT20 mouse pituitary cell line resulted in significantly decreased expression of miR-15a (p<0.05), indicating that the decrease in miR-15a may be a direct result of lost menin expression

On Time Series Classification with Dictionary-Based Classifiers

A family of algorithms for time series classification (TSC) involve running a sliding window across each series, discretising the window to form a word, forming a histogram of word counts over the dictionary, then constructing a classifier on the histograms. A recent evaluation of two of this type of algorithm, Bag of Patterns (BOP) and Bag of Symbolic Fourier Approximation Symbols (BOSS) found a significant difference in accuracy between these seemingly similar algorithms. We investigate this phenomenon by deconstructing the classifiers and measuring the relative importance of the four key components between BOP and BOSS. We find that whilst ensembling is a key component for both algorithms, the effect of the other components is mixed and more complex. We conclude that BOSS represents the state of the art for dictionary-based TSC. Both BOP and BOSS can be classed as bag of words approaches. These are particularly popular in Computer Vision for tasks such as image classification. We adapt three techniques used in Computer Vision for TSC: Scale Invariant Feature Transform; Spatial Pyramids; and Histogram Intersection. We find that using Spatial Pyramids in conjunction with BOSS (SP) produces a significantly more accurate classifier. SP is significantly more accurate than standard benchmarks and the original BOSS algorithm. It is not significantly worse than the best shapelet-based or deep learning approaches, and is only outperformed by an ensemble that includes BOSS as a constituent module

Individual Differences in the Patient Experience of Relapsing Multiple Sclerosis (RMS): A Multi-Country Qualitative Exploration of Drivers of Treatment Preferences Among People Living with RMS

Aims: The aim of this study was to explore the experiences, values and preferences of people living with relapsing multiple sclerosis (PLwRMS) focusing on their treatments and what drives their treatment preferences. Methods: In-depth, semi-structured, qualitative telephone interviews were conducted using a purposive sampling approach with 72 PLwRMS and 12 health care professionals (HCPs, MS specialist neurologists and nurses) from the United Kingdom, United States, Australia and Canada. Concept elicitation questioning was used to elicit PLwRMS’ attitudes, beliefs and preferences towards features of disease-modifying treatments. Interviews with HCPs were conducted to inform on HCPs’ experiences of treating PLwRMS. Responses were audio recorded and transcribed verbatim and then subjected to thematic analysis. Results: Participants discussed numerous concepts that were important to them when making treatment decisions. Levels of importance participants placed on each concept, as well as reasons underpinning importance, varied substantially. The concepts with the greatest variability in terms of how much PLwRMS found them to be important in their decision-making process were mode of administration, speed of treatment effect, impact on reproduction and parenthood, impact on work and social life, patient engagement in decision making, and cost of treatment to the participant. Findings also demonstrated high variability in what participants described as their ideal treatment and the most important features a treatment should have. HCP findings provided clinical context for the treatment decision-making process and supported patient findings. Conclusions: Building upon previous stated preference research, this study highlighted the importance of qualitative research in understanding what drives patient preferences. Characterized by the heterogeneity of the RMS patient experience, findings indicate the nature of treatment decisions in RMS to be highly individualized, and the subjective relative importance placed on different treatment factors by PLwRMS to vary. Such qualitative patient preference evidence could offer valuable and supplementary insights, alongside quantitative data, to inform decision making related to RMS treatment

GNAQ/GNA11 Mosaicism Causes Aberrant Calcium Signaling Susceptible to Targeted Therapeutics

Mosaic variants in genes GNAQ or GNA11 lead to a spectrum of vascular and pigmentary diseases including Sturge-Weber syndrome, in which progressive postnatal neurological deterioration led us to seek biologically targeted therapeutics. Using two cellular models, we find that disease-causing GNAQ/11 variants hyperactivate constitutive and G-protein coupled receptor ligand–induced intracellular calcium signaling in endothelial cells. We go on to show that the aberrant ligand-activated intracellular calcium signal is fueled by extracellular calcium influx through calcium-release-activated channels. Treatment with targeted small interfering RNAs designed to silence the variant allele preferentially corrects both the constitutive and ligand-activated calcium signaling, whereas treatment with a calcium-release-activated channel inhibitor rescues the ligand-activated signal. This work identifies hyperactivated calcium signaling as the primary biological abnormality in GNAQ/11 mosaicism and paves the way for clinical trials with genetic or small molecule therapies

The great time series classification bake off: a review and experimental evaluation of recent algorithmic advances

In the last five years there have been a large number of new time series classification algorithms proposed in the literature. These algorithms have been evaluated on subsets of the 47 data sets in the University of California, Riverside time series classification archive. The archive has recently been expanded to 85 data sets, over half of which have been donated by researchers at the University of East Anglia. Aspects of previous evaluations have made comparisons between algorithms difficult. For example, several different programming languages have been used, experiments involved a single train/test split and some used normalised data whilst others did not. The relaunch of the archive provides a timely opportunity to thoroughly evaluate algorithms on a larger number of datasets. We have implemented 18 recently proposed algorithms in a common Java framework and compared them against two standard benchmark classifiers (and each other) by performing 100 resampling experiments on each of the 85 datasets. We use these results to test several hypotheses relating to whether the algorithms are significantly more accurate than the benchmarks and each other. Our results indicate that only 9 of these algorithms are significantly more accurate than both benchmarks and that one classifier, the Collective of Transformation Ensembles, is significantly more accurate than all of the others. All of our experiments and results are reproducible: we release all of our code, results and experimental details and we hope these experiments form the basis for more rigorous testing of new algorithms in the future

A mouse model with a frameshift mutation in the nuclear factor I/X (NFIX) gene has phenotypic features of Marshall-Smith syndrome

The nuclear factor I/X (NFIX) gene encodes a ubiquitously expressed transcription factor whose mutations lead to two allelic disorders characterized by developmental, skeletal, and neural abnormalities, namely, Malan syndrome (MAL) and Marshall–Smith syndrome (MSS). NFIX mutations associated with MAL mainly cluster in exon 2 and are cleared by nonsense-mediated decay (NMD) leading to NFIX haploinsufficiency, whereas NFIX mutations associated with MSS are clustered in exons 6–10 and escape NMD and result in the production of dominant-negative mutant NFIX proteins. Thus, different NFIX mutations have distinct consequences on NFIX expression. To elucidate the in vivo effects of MSS-associated NFIX exon 7 mutations, we used CRISPR-Cas9 to generate mouse models with exon 7 deletions that comprised: a frameshift deletion of two nucleotides (Nfix Del2); in-frame deletion of 24 nucleotides (Nfix Del24); and deletion of 140 nucleotides (Nfix Del140). Nfix+/Del2, Nfix+/Del24, Nfix+/Del140, NfixDel24/Del24, and NfixDel140/Del140 mice were viable, normal, and fertile, with no skeletal abnormalities, but NfixDel2/Del2 mice had significantly reduced viability (p Nfix Del2 was not cleared by NMD, and NfixDel2/Del2 mice, when compared to Nfix+/+ and Nfix+/Del2 mice, had: growth retardation; short stature with kyphosis; reduced skull length; marked porosity of the vertebrae with decreased vertebral and femoral bone mineral content; and reduced caudal vertebrae height and femur length. Plasma biochemistry analysis revealed NfixDel2/Del2 mice to have increased total alkaline phosphatase activity but decreased C-terminal telopeptide and procollagen-type-1-N-terminal propeptide concentrations compared to Nfix+/+ and Nfix+/Del2 mice. NfixDel2/Del2 mice were also found to have enlarged cerebral cortices and ventricular areas but smaller dentate gyrus compared to Nfix+/+ mice. Thus, NfixDel2/Del2 mice provide a model for studying the in vivo effects of NFIX mutants that escape NMD and result in developmental abnormalities of the skeletal and neural tissues that are associated with MSS