Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets

BACKGROUND: Genome-wide microarrays have been useful for predicting chemical-genetic interactions at the gene level. However, interpreting genome-wide microarray results can be overwhelming due to the vast output of gene expression data combined with off-target transcriptional responses many times induced by a drug treatment. This study demonstrates how experimental and computational methods can interact with each other, to arrive at more accurate predictions of drug-induced perturbations. We present a two-stage strategy that links microarray experimental testing and network training conditions to predict gene perturbations for a drug with a known mechanism of action in a well-studied organism. RESULTS: S. cerevisiae cells were treated with the antifungal, fluconazole, and expression profiling was conducted under different biological conditions using Affymetrix genome-wide microarrays. Transcripts were filtered with a formal network-based method, sparse simultaneous equation models and Lasso regression (SSEM-Lasso), under different network training conditions. Gene expression results were evaluated using both gene set and single gene target analyses, and the drug’s transcriptional effects were narrowed first by pathway and then by individual genes. Variables included: (i) Testing conditions – exposure time and concentration and (ii) Network training conditions – training compendium modifications. Two analyses of SSEM-Lasso output – gene set and single gene – were conducted to gain a better understanding of how SSEM-Lasso predicts perturbation targets. CONCLUSIONS: This study demonstrates that genome-wide microarrays can be optimized using a two-stage strategy for a more in-depth understanding of how a cell manifests biological reactions to a drug treatment at the transcription level. Additionally, a more detailed understanding of how the statistical model, SSEM-Lasso, propagates perturbations through a network of gene regulatory interactions is achieved.Published versio

Perturbation Detection Through Modeling of Gene Expression on a Latent Biological Pathway Network: A Bayesian hierarchical approach

Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are essential in determining the cell's fate. Here our goal is the identification of perturbed pathways from high-throughput gene expression data. We develop a three-level hierarchical model, where (i) the first level captures the relationship between gene expression and biological pathways using confirmatory factor analysis, (ii) the second level models the behavior within an underlying network of pathways induced by an unknown perturbation using a conditional autoregressive model, and (iii) the third level is a spike-and-slab prior on the perturbations. We then identify perturbations through posterior-based variable selection. We illustrate our approach using gene transcription drug perturbation profiles from the DREAM7 drug sensitivity predication challenge data set. Our proposed method identified regulatory pathways that are known to play a causative role and that were not readily resolved using gene set enrichment analysis or exploratory factor models. Simulation results are presented assessing the performance of this model relative to a network-free variant and its robustness to inaccuracies in biological databases

Lung cancer screening: what do long-term smokers know and believe?

Objective To explore knowledge and beliefs of long-term smokers about lung cancer, associated risk factors and lung cancer screening. Design Qualitative study theoretically framed by the expanded Health Belief Model based on four focus group discussions. Content analysis was performed to identify themes of knowledge and beliefs about lung cancer, associated risk factors and lung cancer screening among long-term smokers' who had and had not been screened for lung cancer. Methods Twenty-six long-term smokers were recruited; two groups (n = 9; n = 3) had recently been screened and two groups (n = 7; n = 7) had never been screened. Results While most agreed lung cancer is deadly, confusion or inaccurate information exists regarding the causes and associated risk factors. Knowledge related to lung cancer screening and how it is performed was low; awareness of long-term smoking's association with lung cancer risk remains suboptimal. Perceived benefits of screening identified include: (i) finding lung cancer early; (ii) giving peace of mind; and (iii) motivation to quit smoking. Perceived barriers to screening identified include: (i) inconvenience; (ii) distrust; and (iii) stigma. Conclusions Perceived barriers to lung cancer screening, such as distrust and stigma, must be addressed as lung cancer screening becomes more widely implemented. Heightened levels of health-care system distrust may impact successful implementation of screening programmes. Perceived smoking-related stigma may lead to low levels of patient engagement with medical care and decreased cancer screening participation. It is also important to determine modifiable targets for intervention to enhance the shared decision-making process between health-care providers and their high-risk patients

Detection of EpCAM-Negative and Cytokeratin-Negative Circulating Tumor Cells in Peripheral Blood

Enrichment of rare circulating tumor cells (CTCs) in blood is typically achieved using antibodies to epithelial cell adhesion molecule (EpCAM), with detection using cytokeratin (CK) antibodies. However, EpCAM and CK are not expressed in some tumors and can be downregulated during epithelial-to-mesenchymal transition. A micro-fluidic system, not limited to EpCAM or CK, was developed to use multiple antibodies for capture followed by detection using CEE-Enhanced (CE), a novel in situ staining method that fluorescently labels the capture antibodies bound to CTCs. Higher recovery of CTCs was demonstrated using antibody mixtures compared to anti-EpCAM. In addition, CK-positive breast cancer cells were found in 15 of 24 samples (63%; range 1–60 CTCs), while all samples contained additional CE-positive cells (range 1–41; median = 11; P = .02). Thus, antibody mixtures against a range of cell surface antigens enables capture of more CTCs than anti-EpCAM alone and CE staining enables the detection of CK-negative CTCs

Benchmark Acetylene Binding Affinity and Separation through Induced Fit in a Flexible Hybrid Ultramicroporous Material

Structural changes at the active site of an enzyme induced by binding to a substrate molecule can result in enhanced activity in biological systems. Herein, we report that the new hybrid ultramicroporous material sql-SIFSIX-bpe-Zn exhibits an induced fit binding mechanism when exposed to acetylene, C₂H₂. The resulting phase change affords exceptionally strong C₂H₂ binding that in turn enables highly selective C₂H₂/C₂H₄ and C₂H₂/CO₂ separation demonstrated by dynamic breakthrough experiments. sql-SIFSIX-bpe-Zn was observed to exhibit at least four phases: as-synthesised (α); activated (β); and C₂H₂ induced phases (β' and γ). sql-SIFSIX-bpe-Zn-β exhibited strong affinity for C₂H₂ at ambient conditions as demonstrated by benchmark isosteric heat of adsorption (Qst ) of 67.5 kJ mol⁻¹ validated through in situ pressure gradient differential scanning calorimetry (PG-DSC). Further, in situ characterisation and DFT calculations provide insight into the mechanism of the C₂H₂ induced fit transformation, binding positions and the nature of host-guest and guest-guest interactions

A Risk Assessment Tool for Predicting Fragility Fractures and Mortality in the Elderly

Existing fracture risk assessment tools are not designed to predict fracture-associated consequences, possibly contributing to the current undermanagement of fragility fractures worldwide. We aimed to develop a risk assessment tool for predicting the conceptual risk of fragility fractures and its consequences. The study involved 8965 people aged >= 60 years from the Dubbo Osteoporosis Epidemiology Study and the Canadian Multicentre Osteoporosis Study. Incident fracture was identified from X-ray reports and questionnaires, and death was ascertained though contact with a family member or obituary review. We used a multistate model to quantify the effects of the predictors on the transition risks to an initial and subsequent incident fracture and mortality, accounting for their complex interrelationships, confounding effects, and death as a competing risk. There were 2364 initial fractures, 755 subsequent fractures, and 3300 deaths during a median follow-up of 13 years (interquartile range [IQR] 7-15). The prediction model included sex, age, bone mineral density, history of falls within 12 previous months, prior fracture after the age of 50 years, cardiovascular diseases, diabetes mellitus, chronic pulmonary diseases, hypertension, and cancer. The model accurately predicted fragility fractures up to 11 years of follow-up and post-fracture mortality up to 9 years, ranging from 7 years after hip fractures to 15 years after non-hip fractures. For example, a 70-year-old woman with aT-score of -1.5 and without other risk factors would have 10% chance of sustaining a fracture and an 8% risk of dying in 5 years. However, after an initial fracture, her risk of sustaining another fracture or dying doubles to 33%, ranging from 26% after a distal to 42% post hip fracture. A robust statistical technique was used to develop a prediction model for individualization of progression to fracture and its consequences, facilitating informed decision making about risk and thus treatment for individuals with different risk profiles. (c) 2020 American Society for Bone and Mineral Research

Crop Updates - 2003 Oilseeds

This session covers fifteen papers from different authors ACKNOWLEDGMENTS VARIETIES Large scale canola varietal evaluation in WA, Peter Nelson, Oilseeds WA Performance of IT and TT canola varieties in the medium and high rainfall agzones of WA 2001-02, Graham Walton, Hasan Zaheer and Paul Carmody, Department of Agriculture QUALITY Reproductive biology, cotyledon development and oil accumulation in canola, J.A. Fortescue and D.W. Turner, School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia Plant and environmental factors affecting oil concentration in canola – a mini-review, D.W. Turner, School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia Potential benefits from interspecific crosses between canola and ‘near canola’ quality Indian mustard, Janet Wroth, School of Plant Biology, The University of Western Australia (UWA), Wallace Cowling, School of Plant Biology, UWA and CBWA Pty Ltd, Anh-Van Pham, School of Mathematics and Statistics, UWA NUTRITION, AGRONOMY AND MACHINERY Timing of nitrogen application for producing canola grain and oil, R. F. Brennan, Department of Agriculture Managing canola for soil type and moisture stress, Paul Carmody and Hasan Zaheer Department of Agriculture Machinery lessons from 2002 – canola establishment, Glen Riethmuller, Greg Hamilton and Jo Hawksley, Department of Agriculture Machinery lessons from 2002 – harvesting short crops, Glen Riethmuller, Department of Agriculture Does increasing canola seeding rate reduce the competitiveness of grass weeds? Zaicou-Kunesch, C.M., Zaheer, S.H. and Eksteen, D, Department of Agriculture PESTS AND DISEASES Aphid damage to canola – not all cultivars are equal, Françoise A. Berlandier and Christiaan Valentine, Department of Agriculture Should we be worried about developing insecticide resistance in aphids? Owain Edwards, CSIRO Entomology Benefits provided by treating canola seed with imidacloprid seed dressing, Roger Jones, Brenda Coutts, Lisa Smith and Jenny Hawkes, Department of Agriculture, and Centre for Legumes in Mediterranean Agriculture Blackleg levels in canola in 2002, Ravjit Khangura1, Moin Salam1, Art J Diggle1 and Martin J Barbetti1,2 1Department of Agriculture, 2University of Western Australia DBM in canola, Kevin Walden, Department of Agricultur

Genetic Burden of TNNI3K in Diagnostic Testing of Patients With Dilated Cardiomyopathy and Supraventricular Arrhythmias

BACKGROUND: Genetic variants in TNNI3K (troponin-I interacting kinase) have previously been associated with dilated cardiomyopathy (DCM), cardiac conduction disease, and supraventricular tachycardias. However, the link between TNNI3K variants and these cardiac phenotypes shows a lack of consensus concerning phenotype and protein function. METHODS: We describe a systematic retrospective study of a cohort of patients undergoing genetic testing for cardiac arrhythmias and cardiomyopathy including TNNI3K. We further performed burden testing of TNNI3K in the UK Biobank. For 2 novel TNNI3K variants, we tested cosegregation. TNNI3K kinase function was estimated by TNNI3K autophosphorylation assays.RESULTS: We demonstrate enrichment of rare coding TNNI3K variants in DCM patients in the Amsterdam cohort. In the UK Biobank, we observed an association between TNNI3K missense (but not loss-of-function) variants and DCM and atrial fibrillation. Furthermore, we demonstrate genetic segregation for 2 rare variants, TNNI3K-p.Ile512Thr and TNNI3K-p.His592Tyr, with phenotypes consisting of DCM, cardiac conduction disease, and supraventricular tachycardia, together with increased autophosphorylation. In contrast, TNNI3K-p.Arg556_Asn590del, a likely benign variant, demonstrated depleted autophosphorylation. CONCLUSIONS: Our findings demonstrate an increased burden of rare coding TNNI3K variants in cardiac patients with DCM. Furthermore, we present 2 novel likely pathogenic TNNI3K variants with increased autophosphorylation, suggesting that enhanced autophosphorylation is likely to drive pathogenicity.</p

Undergraduate Medical Education Reform in Viet Nam for a Primary Health Care Workforce

Strong primary health care (PHC) systems require a robust PHC workforce. Traditionally, medical education takes place in academic medical centres that favour subspecialty care rather than PHC settings. This may undervalue primary care as a career and contribute to a shortage of PHC workers. However, designing undergraduate medical education curricula that incorporate early experiences in clinical care delivery at PHC sites remains a challenge, including in many low- and middle-income countries (LMICs). This paper describes how a collaboration between Harvard Medical School and five medical schools in Vietnam, and in-country collaborations among the Vietnamese medical schools, facilitated curricular innovation and co-creation of coursework relevant to PHC through the development of a Practice of Medicine (POM) course. The collaboration implemented a technical assistance strategy consisting of in-person workshops, focused virtual consultations, on-site ‘office hours’, site visits and observations to each of the five medical universities, and immersion trips to support the creation and implementation of the POM course. A pilot program was started at a single site and then scaled nationally using local customisation, experience, and expertise utilising a train-the-trainers approach. As a result, five new POM courses have been developed by five Vietnamese institutions. Fifty Vietnamese faculty received training to lead the POM course development, and 228 community-based preceptors have been trained to teach students at PHC sites. A total of 52 new PHC and community-based clinical training sites have been added, and 3,615 students have completed or are currently going through a POM course. This experience can serve as a model for future academic collaborations to support the development of a robust PHC workforce for the 21st century

Treatment of osteoarthritis of the knee with a topical diclofenac solution: a randomised controlled, 6-week trial [ISRCTN53366886]

BACKGROUND: Topical NSAIDs have been proven to relieve the symptoms of osteoarthritis (OA) in short-term studies (2 weeks). To justify its chronic use, efficacy of a topical NSAID over a longer term of study should be demonstrated. The efficacy and safety of a topical diclofenac solution over a 6-week treatment course in symptomatic primary OA of the knee was investigated. METHODS: 216 men and women, age 40–85 years, with radiologically confirmed primary OA of the knee and a flare of pain at baseline following discontinuation of prior therapy were enrolled into this double-blind study. Participants applied either a topical diclofenac solution (Pennsaid(®)) or vehicle control solution (carrier with no diclofenac); 40 drops 4 times daily directly to the painful knee(s), without massage, for 6 weeks. Pre-planned primary efficacy outcome measures included the core continuous variables pain relief and improved physical function measured by the Western Ontario and McMaster Universities (WOMAC) LK3.1 OA Index, and improved patient global assessment (PGA). Secondary efficacy measure was reduced stiffness. Safety assessments included adverse events and vital signs. RESULTS: The topical diclofenac group had a significantly greater mean change in score (final minus baseline) compared to the vehicle control group for pain (-5.2 vs. -3.3, p = 0.003), physical function (-13.4 vs. -6.9, p = 0.001), PGA (-1.3 vs. -0.7, p = 0.0001) and stiffness (-1.8 vs. -0.9, p = 0.002). The mean difference between treatment arms (95% confidence interval [CI]) was 1.9 (0.7 to 3.2), 6.5 (2.5 to 10.5), 0.6 (0.2 to 0.9), and 0.9 (0.3 to 1.4), respectively. Safety analyses showed that topical diclofenac caused skin irritation, mostly minor local skin dryness, in 42/107 (39%), leading to discontinuation of treatment in 5/107 (5%) participants. CONCLUSION: This topical diclofenac solution demonstrated relief at 6 weeks of the symptoms of primary osteoarthritis of the knee