Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility

Small bowel accounts for only 0.5% of cancer cases in the US but incidence rates have been rising at 2.4% per year over the past decade. One-third of these are adenocarcinomas but little is known about their molecular pathology and no molecular markers are available for clinical use. Using a retrospective 28 patient matched normal-tumor cohort, next-generation sequencing, gene expression arrays and CpG methylation arrays were used for molecular profiling. Next-generation sequencing identified novel mutations in IDH1, CDH1, KIT, FGFR2, FLT3, NPM1, PTEN, MET, AKT1, RET, NOTCH1 and ERBB4. Array data revealed 17% of CpGs and 5% of RNA transcripts assayed to be differentially methylated and expressed respectively (p < 0.01). Merging gene expression and DNA methylation data revealed CHN2 as consistently hypermethylated and downregulated in this disease (Spearman -0.71, p < 0.001). Mutations in TP53 which were found in more than half of the cohort (15/28) and Kazald1 hypomethylation were both were indicative of poor survival (p = 0.03, HR = 3.2 and p = 0.01, HR = 4.9 respectively). By integrating high-throughput mutational, gene expression and DNA methylation data, this study reveals for the first time the distinct molecular profile of small bowel adenocarcinoma and highlights potential clinically exploitable markers.

Twitter Sentiment Analysis for Security-Related Information Gathering

Analysing public sentiment about future events, such as demonstration or parades, may provide valuable information while estimating the level of disruption and disorder during these events. Social media, such as Twitter or Facebook, provides views and opinions of users related to any public topics. Consequently, sentiment analysis of social media content may be of interest to different public sector organisations, especially in the security and law enforcement sector. In this paper we present a lexicon-based approach to sentiment analysis of Twitter content. The algorithm performs normalisation of the sentiment in an effort to provide intensity of the sentiment rather than positive/negative label. Following this, we evaluate an evidence-based combining function that supports the classification process in cases when positive and negative words co-occur in a tweet. Finally, we illustrate a case study examining the relation between sentiment of twitter posts related to English Defence League and the level of disorder during the EDL related events.

Effect of poly ethylene glycol on the mechanical and thermal properties of bioactive Poly (ε–caprolactone) melt extrudates for pharmaceutical applications

This paper investigates the effects of polyethylene glycol (PEG), on the mechanical and thermal properties of nalidixic acid/ploy ε-caprolactone (NA)/PCL blends prepared by hot melt extrusion. The blends were characterized by tensile and flexural analysis, dynamic mechanical analysis, differential scanning calorimetry, thermogravimetric analysis and X-ray diffraction. Experimental data indicated that the addition of NA caused loss of the tensile strength and toughness of PCL. Thermal analysis of the PCL showed that on addition of the thermally unstable NA, thermal degradation occurred early and was autocatalytic. However, the NA did benefit from the heat shielding provided by the PCL matrix resulting in more thermally stable NA particles. Results show that loading PEG in the PCL had a detrimental effect on the tensile strength and toughness of the blends, reducing them by 20-40%. The partial miscibility of the PCL-PEG system, causes an increase in Tg. While increases in the crystallinity is attributed to the plasticisation effect of PEG and the nucleation effect of NA. The average crystal size increased by 8% upon PEG addition.

Pharmacy students' use and views on over-the-counter (OTC) medicines; a questionnaire study

Introduction
The role of the pharmacist centers on ensuring the safe and effective use of medicines, including over-the-counter (OTC) medicines. It is important to ascertain pharmacy students’ use and opinions on OTC medicines, given that they are the pharmacists of the future and that this market continues to expand. This study aimed to investigate Queen’s University Belfast (QUB) final year pharmacy students’ use and views on OTC medicines. Scarce work has been conducted in this area to date.

Methods
Following ethical approval and a pilot study, all students (n=155) were invited to participate in a self-completed questionnaire (n=20 questions), distributed at a mandatory class. Descriptive statistics and non-parametric tests (Chi-squared and Mann Whitney U-test) were used for data analyses.

Results
The response rate was 99.4% (154/155). The majority (153/155) reported using OTC medicines; the key consideration during personal product selection was effectiveness. Most [96.1% (147/153)] were in agreement that safety was the over-riding concern during OTC consultations. While 96.1% (149/155) considered that using an evidence-based approach improved the quality of patient care, 68.0% (104/153) would be prepared to sell a product that lacks evidence of effectiveness, provided it would not cause harm.

Conclusions
The importance of evidence of effectiveness was acknowledged, yet many students in this study were prepared to recommend unproven products. Further strategies are required at QUB to ensure this routine consideration alongside safety in practice.

Vitamin D3 suppresses morphological evolution of the cribriform cancerous phenotype

Development of cribriform morphology (CM) heralds malignant change in human colon but lack of mechanistic understanding hampers preventive therapy. This study investigated CM pathobiology in three-dimensional (3D) Caco-2 culture models of colorectal glandular architecture, assessed translational relevance and tested effects of 1,25(OH)2D3, the active form of vitamin D. CM evolution was driven by oncogenic perturbation of the apical polarity (AP) complex comprising PTEN, CDC42 and PRKCZ (phosphatase and tensin homolog, cell division cycle 42 and protein kinase C zeta). Suppression of AP genes initiated a spatiotemporal cascade of mitotic spindle misorientation, apical membrane misalignment and aberrant epithelial configuration. Collectively, these events promoted “Swiss cheese-like” cribriform morphology (CM) comprising multiple abnormal “back to back” lumens surrounded by atypical stratified epithelium, in 3D colorectal gland models. Intestinal cancer driven purely by PTEN-deficiency in transgenic mice developed CM and in human CRC, CM associated with PTEN and PRKCZ readouts. Treatment of PTEN-deficient 3D cultures with 1,25(OH)2D3 upregulated PTEN, rapidly activated CDC42 and PRKCZ, corrected mitotic spindle alignment and suppressed CM development. Conversely, mutationally-activated KRAS blocked 1,25(OH)2D3 rescue of glandular architecture. We conclude that 1,25(OH)2D3 upregulates AP signalling to reverse CM in a KRAS wild type (wt), clinically predictive CRC model system. Vitamin D could be developed as therapy to suppress inception or progression of a subset of colorectal tumors.

Intentionality, morality, and the incest taboo in Madagascar

In a recent article (Astuti & Bloch, 2015), cognitive anthropologists Rita Astuti and Maurice Bloch claim that the Malagasy are ambivalent as to whether considerations of intentionality are relevant to moral judgments concerning incest and its presumed catastrophic consequences: when making moral judgments about those who commit incest, the Malagasy take into account whether the incest is intentional or not, but, when making moral judgments relating to incest’s catastrophic consequences, they do not take intentionality into account. Astuti & Bloch explain the irrelevance of intentionality in terms of incest entailing such a fundamental attack on the transcendental social order that the Malagasy become dumbfounded and leave aside considerations of intentionality. Finally, they claim that a similar dumbfound reaction is what is involved in the moral dumbfounding concerning incest that social psychologist Jonathan Haidt has found in the US. In this article, we argue that (i) Astuti & Bloch are unclear about many aspects of their claims (in particular, about the moral judgments at stake), (ii) they do not provide sufficient evidence that considerations of intentionality are deemed irrelevant to moral judgments relating to incest’s presumed catastrophic consequences (and hence for the claim that the Malagasy are ambivalent), (iii) their hypothesis that conceiving of incest as an attack on the transcendental social renders considerations of intentionality irrelevant lacks coherence, and (iv) the extension of their explanatory account to the moral dumfounding of American students in Haidt’s well-known scenario of intentional incest is unwarranted.

A comparison of endoscopy versus pathology sizing of colorectal adenomas and potential implications for surveillance colonoscopy

Background and AimsTo compare endoscopy and pathology sizing in a large population-based series of colorectal adenomas and to evaluate the implications for patient stratification into surveillance colonoscopy.MethodsEndoscopy and pathology sizes available from intact adenomas removed at colonoscopies performed as part of the Northern Ireland Bowel Cancer Screening Programme, from 2010 to 2015, were included in this study. Chi-squared tests were applied to compare size categories in relation to clinicopathological parameters and colonoscopy surveillance strata according to current American Gastroenterology Association and British Society of Gastroenterology guidelines.ResultsA total of 2521 adenomas from 1467 individuals were included. There was a trend toward larger endoscopy than pathology sizing in 4 of the 5 study centers, but overall sizing concordance was good. Significantly greater clustering with sizing to the nearest 5 mm was evident in endoscopy versus pathology sizing (30% vs 19%, p<0.001), which may result in lower accuracy. Applying a 10-mm cut-off relevant to guidelines on risk stratification, 7.3% of all adenomas and 28.3% of those 8 to 12 mm in size had discordant endoscopy and pathology size categorization. Depending upon which guidelines are applied, 4.8% to 9.1% of individuals had differing risk stratification for surveillance recommendations, with the use of pathology sizing resulting in marginally fewer recommended surveillance colonoscopies.ConclusionsChoice of pathology or endoscopy approaches to determine adenoma size will potentially influence surveillance colonoscopy follow-up in 4.8% to 9.1% of individuals. Pathology sizing appears more accurate than endoscopy sizing, and preferential use of pathology size would result in a small, but clinically important, decreased burden on surveillance colonoscopy demand. Careful endoscopy sizing is required for adenomas removed piecemeal.

Challenging the cancer molecular stratification dogma: Intratumoral heterogeneity undermines consensus molecular subtypes and potential diagnostic value in colorectal cancer

Purpose:
A number of independent gene expression profiling studies have identified transcriptional subtypes in colorectal cancer (CRC) with potential diagnostic utility, culminating in publication of a CRC Consensus Molecular Subtype classification. The worst prognostic subtype has been defined by genes associated with stem-like biology. Recently, it has been shown that the majority of genes associated with this poor prognostic group are stromal-derived. We investigated the potential for tumor misclassification into multiple diagnostic subgroups based on tumoral region sampled.

Experimental Design:
We performed multi-region tissue RNA extraction/transcriptomic analysis using Colorectal Specific Arrays on invasive front, central tumor and lymph node regions selected from tissue samples from 25 CRC patients.

Results:
We identified a consensus 30 gene list which represents the intratumoral heterogeneity within a cohort of primary CRC tumors. Using a series of online datasets, we showed that this gene list displays prognostic potential (HR=2.914 (CI 0.9286-9.162) in stage II/III CRC patients, but in addition we demonstrated that these genes are stromal derived, challenging the assumption that poor prognosis tumors with stem-like biology have undergone a widespread Epithelial Mesenchymal Transition (EMT). Most importantly, we showed that patients can be simultaneously classified into multiple diagnostically relevant subgroups based purely on the tumoral region analysed.

Conclusions:
Gene expression profiles derived from the non-malignant stromal region can influence assignment of CRC transcriptional subtypes, questioning the current molecular classification dogma and highlighting the need to consider pathology sampling region and degree of stromal infiltration when employing transcription-based classifiers to underpin clinical decision-making in CRC.

Immune-derived PD-L1 gene expression defines a subgroup of stage II/III colorectal cancer patients with favorable prognosis that may be harmed by adjuvant chemotherapy

A recent phase 2 study of metastatic colorectal carcinoma (CRC) patients showed that mismatch repair gene status was predictive of clinical response to PD-1-targeting immune checkpoint blockade. Further examination revealed strong correlation between PD-L1 protein expression and microsatellite instability (MSI) in stage IV CRC, suggesting that the amount of PD-L1 protein expression could identify late stage patients who may benefit from immunotherapy. To assess whether the clinical associations between PD-L1 gene expression and MSI identified in metastatic CRC are also present in stage II/III CRC, we used in silico analysis to elucidate the cell types expressing the PD-L1 gene. We found a significant association of PD-L1 gene expression with MSI in early stage CRC (P < 0.001) and show that unlike in non-CRC tumors, PD-L1 is derived predominantly from the immune infiltrate. We demonstrate that PD-L1 gene expression has positive prognostic value in the adjuvant disease setting (PD-L1low v PD-L1high HR = 9.09; CI, 2.11-39.10). PD-L1 gene expression had predictive value, as patients with high PD-L1 expression appear to be harmed by standard-of-care treatment (HR = 4.95; CI,1.10-22.35). Building on the promising results from the metastatic CRC PD-1-targeting trial, we provide compelling evidence that PD-L1high/MSI/immunehigh stage II/III CRC patients should not receive standard chemotherapy. This conclusion supports the rationale to clinically evaluate this patient subgroup for PD-1 blockade treatment.