Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.

Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g. metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (i) tools to search this comprehensive resource, (ii) a download site offering integrated bulk sets of pathway data (e.g. tables of interactions and gene sets), (iii) reusable software libraries for working with pathway information in several programming languages (Java, R, Python and Javascript) and (iv) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4794 detailed human biochemical processes (i.e. pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.

Role of t-tubule remodeling on mechanisms of abnormal calcium release during heart failure development in canine ventricle.

The goal of this work was to investigate the role of t-tubule (TT) remodeling in abnormal Ca2+ cycling in ventricular myocytes of failing dog hearts. Heart failure (HF) was induced using rapid right ventricular pacing. Extensive changes in echocardiographic parameters, including left and right ventricular dilation and systolic dysfunction, diastolic dysfunction, elevated left ventricular filling pressures, and abnormal cardiac mechanics, indicated that severe HF developed. TT loss was extensive when measured as the density of total cell volume, derived from three-dimensional confocal image analysis, and significantly increased the distances in the cell interior to closest cell membrane. Changes in Ca2+ transients indicated increases in heterogeneity of Ca2+ release along the cell length. When critical properties of Ca2+ release variability were plotted as a function of TT organization, there was a complex, nonlinear relationship between impaired calcium release and decreasing TT organization below a certain threshold of TT organization leading to increased sensitivity in Ca2+ release below a TT density threshold of 1.5%. The loss of TTs was also associated with a greater incidence of triggered Ca2+ waves during rapid pacing. Finally, virtually all of these observations were replicated by acute detubulation by formamide treatment, indicating an important role of TT remodeling in impaired Ca2+ cycling. We conclude that TT remodeling itself is a major contributor to abnormal Ca2+ cycling in HF, reducing myocardial performance. The loss of TTs is also responsible for a greater incidence of triggered Ca2+ waves that may play a role in ventricular arrhythmias arising in HF.NEW & NOTEWORTHY Three-dimensional analysis of t-tubule density showed t-tubule disruption throughout the whole myocyte in failing dog ventricle. A double-linear relationship between Ca2+ release and t-tubule density displays a steeper slope at t-tubule densities below a threshold value (∼1.5%) above which there is little effect on Ca2+ release (T-tubule reserve). T-tubule loss increases incidence of triggered Ca2+ waves. Chemically induced t-tubule disruption suggests that t-tubule loss alone is a critical component of abnormal Ca2+ cycling in heart failure.

Readability of online sources of information regarding epilepsy surgery and its impact on decision-making processes.

INTRODUCTION: People with epilepsy can have cognitive deficits, including difficulty with reading tasks. This can potentially impact on how written information is understood. Websites increasingly provide information about different medical interventions including epilepsy surgery. Our aim was to assess the readability of a sample of one hundred patient-oriented educational English language websites related to epilepsy surgery. METHODS: A Google search was carried out using the terms epilepsy and surgery, and a sample of forty-nine websites from both the UK and the US were chosen. These websites were uploaded to a freely available online readability scoring tool (readabilityformulas.com) and seven measures of readability generated were examined. Other data including use of figures/diagrams, patient narratives, and mention of the risks/benefits of surgery were noted. RESULTS: The majority of the websites analyzed in this study were found to be 'difficult' to read for the average reading level of the population (n = 1-impossible, 10-very difficult, 23-difficult, 14 fairly difficult). Only 1 website was considered suitable for average reading level. The use of infographics was variable - some webpages used them extensively to reiterate the textual information and other websites did not. DISCUSSION AND CONCLUSION: The available online patient information literature is likely to be too difficult for the average reader to understand. It is important that websites are accessible, reliable, and aid understanding related to epilepsy surgery, taking potential cognitive deficits into consideration.

"The Brain Society": The First Two Years of an Undergraduate Neuroscience Society in Northern Ireland.

The Queen's University Belfast Brain Society was set up in September 2018 to promote interest in the human brain. There were three main goals: firstly to provide opportunities for medical students to learn from neurologists and neurosurgeons outside their formal curriculum; secondly the Brain Society aimed to organise events that included students from other disciplines and to members of the general public who were interested in learning about aspects of neuroscience; thirdly to tackle neurophobia. In the last two years, there have been 14 events, ranging from formal lectures, to practical sessions and to patient-focused information evenings. We have sold over 1,600 tickets. This article covers how the Brain Society was set up, to inform students in other universities about the Belfast experience.

Triggered Ca2+ Waves Induce Depolarization of Maximum Diastolic Potential and Action Potential Prolongation in Dog Atrial Myocytes.

BACKGROUND: We have identified a novel form of abnormal Ca2+ wave activity in normal and failing dog atrial myocytes which occurs during the action potential (AP) and is absent during diastole. The goal of this study was to determine if triggered Ca2+ waves affect cellular electrophysiological properties. METHODS: Simultaneous recordings of intracellular Ca2+ and APs allowed measurements of maximum diastolic potential and AP duration during triggered calcium waves (TCWs) in isolated dog atrial myocytes. Computer simulations then explored electrophysiological behavior arising from TCWs at the tissue scale. RESULTS: At 3.3 to 5 Hz, TCWs occurred during the AP and often outlasted several AP cycles. Maximum diastolic potential was reduced, and AP duration was significantly prolonged during TCWs. All electrophysiological responses to TCWs were abolished by SEA0400 and ORM10103, indicating that Na-Ca exchange current caused depolarization. The time constant of recovery from inactivation of Ca2+ current was 40 to 70 ms in atrial myocytes (depending on holding potential) so this current could be responsible for AP activation during depolarization induced by TCWs. Modeling studies demonstrated that the characteristic properties of TCWs are potentially arrhythmogenic by promoting both conduction block and reentry arising from the depolarization induced by TCWs. CONCLUSIONS: Triggered Ca2+ waves activate inward NCX and dramatically reduce atrial maximum diastolic potential and prolong AP duration, establishing the substrate for reentry which could contribute to the initiation and maintenance of atrial arrhythmias.

Combined Targeting of Estrogen Receptor Alpha and XPO1 Prevent Akt Activation, Remodel Metabolic Pathways and Induce Autophagy to Overcome Tamoxifen Resistance.

A majority of breast cancer specific deaths in women with ERα (+) tumors occur due to metastases that are resistant to endocrine therapy. There is a critical need for novel therapeutic approaches to resensitize recurrent ERα (+) tumors to endocrine therapies. The objective of this study was to elucidate mechanisms of improved effectiveness of combined targeting of ERα and the nuclear transport protein XPO1 in overcoming endocrine resistance. Selinexor (SEL), an XPO1 antagonist, has been evaluated in multiple late stage clinical trials in patients with relapsed and /or refractory hematological and solid tumor malignancies. Our transcriptomics analysis showed that 4-Hydroxytamoxifen (4-OHT), SEL alone or their combination induced differential Akt signaling- and metabolism-associated gene expression profiles. Western blot analysis in endocrine resistant cell lines and xenograft models validated differential Akt phosphorylation. Using the Seahorse metabolic profiler, we showed that ERα-XPO1 targeting changed the metabolic phenotype of TAM-resistant breast cancer cells from an energetic to a quiescent profile. This finding demonstrated that combined targeting of XPO1 and ERα rewired the metabolic pathways and shut down both glycolytic and mitochondrial pathways that would eventually lead to autophagy. Remodeling metabolic pathways to regenerate new vulnerabilities in endocrine resistant breast tumors is novel, and given the need for better strategies to improve therapy response in relapsed ERα (+) tumors, our findings show great promise for uncovering the role that ERα-XPO1 crosstalk plays in reducing cancer recurrences.

Effects of losartan on left ventricular hypertrophy and fibrosis in patients with nonobstructive hypertrophic cardiomyopathy.

OBJECTIVES: The aim of this study was to evaluate the effects of losartan on left ventricular (LV) hypertrophy and fibrosis in patients with nonobstructive hypertrophic cardiomyopathy (HCM). BACKGROUND: Despite evidence that myocardial hypertrophy and fibrosis are mediated by angiotensin II and are important determinants of morbidity and mortality in patients with HCM, no prior studies have evaluated the effects of angiotensin receptor blockers on LV hypertrophy and fibrosis with cardiac magnetic resonance imaging. METHODS: In double-blind fashion, 20 patients (3 women, 17 men; age: 51 ± 13 years) with HCM were randomly assigned to receive placebo (n = 9) or losartan 50 mg twice a day (n = 11) for 1 year. Cardiac magnetic resonance imaging was performed at baseline and 1 year to measure LV mass and extent of fibrosis as assessed by late gadolinium enhancement. RESULTS: There was a trend toward a significant difference in the percent change in LV mass (median [interquartile range]: +5% [-4% to +21%] with placebo vs. -5% [-11% to -0.9%] with losartan; p = 0.06). There was a significant difference in the percent change in extent of late gadolinium enhancement, with the placebo group experiencing a larger increase (+31% ± 26% with placebo vs. -23% ± 45% with losartan; p = 0.03). CONCLUSIONS: This pilot study suggests attenuation of progression of myocardial hypertrophy and fibrosis with losartan in patients with nonobstructive HCM. Confirmation of these results in a larger trial is required to confirm a place for angiotensin receptor blockers in the management of patients with HCM. (Effect of Losartan in Patients With Nonobstructive Hypertrophic Cardiomyopathy; NCT01150461).

Long-term experience and outcomes with transcatheter closure of patent foramen ovale.

OBJECTIVES: This study sought to examine the frequency of indications for and the immediate and long-term clinical outcomes of transcatheter closure of patent foramen ovale (PFO). BACKGROUND: Transcatheter PFO closure is commonly performed for several indications, including cryptogenic stroke, despite conflicting data regarding the efficacy of this intervention. METHODS: We report the outcomes of 800 consecutive patients (52% male, 50 ± 14 years of age) who underwent PFO closure at our institution after multidisciplinary evaluation over a 16-year period. RESULTS: Indications for closure included cryptogenic cerebrovascular event (94%), hypoxemia (2%), peripheral embolism (3%), and migraine headaches (2%). Procedural success was 99% with effective closure obtained in 93% of patients. At a mean follow-up of 42.7 ± 33.4 months, 21 patients suffered a recurrent ischemic neurologic event (12 strokes, and 9 transient ischemic attacks) for an incidence rate of 0.79 events per 100 person-years and freedom from recurrent events of 91.6% at 10 years. There was no device-based difference in the rate of recurrent ischemic neurologic events (p = 0.82). Only Eustachian valve prominence (hazard ratio: 9.04; 95% confidence interval: 2.07 to 39.44; p = 0.0034) was associated with recurrent neurologic events. CONCLUSIONS: Transcatheter PFO closure is safe and feasible in patients with several clinical indications. The long-term efficacy of this intervention in patients with paradoxical embolism appears superb in this observational study. Carefully selected patients with features suggestive of paradoxical embolism are the most likely to benefit from PFO closure and should be the focus of future investigation.

Management strategy in 249 consecutive patients with obstructive hypertrophic cardiomyopathy referred to a dedicated program.

The likelihood of success of conservative management of obstructive hypertrophic cardiomyopathy (HC) and the predictors of failure of conservative therapy are not known. We therefore evaluated the efficacy of an algorithm for the management of symptoms and predictors of failed conservative therapy in 249 consecutive symptomatic patients with obstructive HC referred to a dedicated HC program for management in general or for septal reduction therapy (SRT) in particular. There was considerable practice variation in the extent to which conservative therapy was optimized before referral for SRT. Over 3.7 ± 2.9-year follow-up, symptoms resolved with addition of or increase in dosage of a ß blocker, calcium channel blocker, or disopyramide in 16%, 10%, and 10% of patients, respectively. Pacing with short atrioventricular delay controlled symptoms in 4 of 9 patients. In 63% of patients, conservative measures failed to control symptoms. Multivariate predictors of failure of conservative therapy were presence of New York Heart Association class III or IV symptoms (hazard ratio 2.0, 95% confidence interval 1.4 to 2.9, p = 0.001) and greater septal wall thickness (hazard ratio 1.06, 95% confidence interval 1.02 to 1.10, p = 0.003) at presentation. At time of presentation, 93 patients (37%) were already on optimal therapy and were referred for SRT. Of the remaining 156 patients who did not require immediate SRT, 93 (60%) were free from a recommendation for SRT at the end of the follow-up period. In conclusion, in symptomatic patients with obstructive HC, conservative therapy is successful in >1/3 of referred patients at 3.7-year follow-up, obviating SRT in these patients. Clinicians in programs offering SRT should optimize conservative therapy before recommending SRT.

Risk stratification for sudden cardiac death after septal myectomy.

BACKGROUND: The importance of risk stratification for sudden cardiac death (SCD) after septal myectomy for hypertrophic obstructive cardiomyopathy (HOCM) has not been emphasized previously. METHODS AND RESULTS: We report 2 patients with SCD or ventricular tachycardia (VT) after septal myectomy for HOCM in whom risk factors for SCD were identified following surgical myectomy. One received an implantable cardioverter-defibrillator (ICD), which subsequently provided appropriate discharges for VT. The other delayed ICD implantation and suffered SCD. CONCLUSION: These cases emphasize the importance of risk stratification for SCD after septal myectomy for HOCM.