Citations

Abstract Motivation Testing SNP–SNP interactions is considered as a key for overcoming bottlenecks of genetic association studies. However, related statistical methods for testing SNP–SNP interactions are underdeveloped. Results We propose the SNP Interaction Pattern Identifier (SIPI), which tests 45 biologically meaningful interaction patterns for a binary outcome. SIPI takes non-hierarchical models, inheritance modes and mode coding direction into consideration. The simulation results show that SIPI has higher power than MDR (Multifactor Dimensionality Reduction), AA_Full, Geno_Full (full interaction model with additive or genotypic mode) and SNPassoc in detecting interactions. Applying SIPI to the prostate cancer PRACTICAL consortium data with approximately 21 000 patients, the four SNP pairs in EGFR-EGFR, EGFR-MMP16 and EGFR-CSF1 were found to be associated with prostate cancer aggressiveness with the exact or similar pattern in the discovery and validation sets. A similar match for external validation of SNP–SNP interaction studies is suggested. We demonstrated that SIPI not only searches for more meaningful interaction patterns but can also overcome the unstable nature of interaction patterns. Availability and Implementation The SIPI software is freely available at http://publichealth.lsuhsc.edu/LinSoftware/. Supplementary information Supplementary data are available at Bioinformatics online.

AbstractAs part of the 2016 Academic Emergency Medicine Consensus Conference, “Shared Decision Making in the Emergency Department: Development of a Policy‐relevant Patient‐centered Research Agenda,” a panel of representatives from the Office of Emergency Care Research, the Patient‐Centered Outcomes Research Institute, the American Heart Association, the John A. Hartford Foundation, and the Emergency Care Coordination Center were assembled to discuss funding opportunities for future research in this field. This article summarizes their discussion of funding priorities and examples of successfully funded projects related to shared decision making in emergency medicine.

Abstract Treatment paradigms have changed rapidly for multiple myeloma, and immune therapies have taken center stage. Advances in therapies for myeloma have led to a dramatic improvement in the survival of patients with this incurable malignancy. The immune system is significantly impaired in patients with myeloma as a result of the disease leading to suppression of normal plasma cells as well the negative effects on cellular immunity. Given this scenario, immune approaches have not been successful until recently. Monoclonal antibodies directed against CD38 (daratumumab) and SLAMF7 (elotuzumab) are already in the clinic, and several other antibodies directed against different plasma cell antigens are under evaluation. Although immune checkpoint inhibition with PD-1 inhibitors had no clinical efficacy when the inhibitors were used as single agents, it has led to some dramatic results when the inhibitors are combined with immunomodulatory drugs such as lenalidomide and pomalidomide. Vaccination strategies have shown in vivo immune responses but no clear clinical efficacy. Newer approaches to vaccination with multiple antigens, used in combinations with immunomodulatory drugs and in the setting of minimal residual disease, have all increased possibility of this approach succeeding. Ex vivo effector cell expansion also appears to be promising and is in clinical trials. Finally, a chimeric antigen receptor T-cell approach appears to have some promise based on isolated reports of success and remains an area of intense investigation. Immune-based approaches can potentially augment or even supplant some of the current approaches and, given the low toxicity profile, may hold great potential in the early treatment of precursor-stage diseases. Clin Cancer Res; 22(22); 5453–60. ©2016 AACR. See all articles in this CCR Focus section, “Multiple Myeloma: Multiplying Therapies.”

AbstractBackgroundLangerhans cell histiocytosis (LCH) is a clonal neoplasm characterized by widely varied clinical presentations, including multisystem involvement and systemic inflammatory symptoms. The AKT pathway is relevant to survival and proliferation of dendritic cells, and is also often upregulated in hematopoietic malignancies. A clinical response in an adult patient with LCH participating in the first‐in‐human trial of afuresertib prompted this prospective trial.ProcedureThe population in the current study included treatment‐naïve (n = 7) and recurrent/refractory patients with LCH (n = 10), who received oral afuresertib (125 mg). The majority of patients were treated for > 24 weeks, with four patients receiving treatment for > 48 weeks.ResultsPharmacokinetic analysis showed similar exposures in previously reported patients with other hematologic malignancies. Primary drug‐related toxicities included Grade 1/2 nausea, diarrhea, dyspepsia, and vomiting. Grade 3 toxicities included fatigue, diarrhea, and pain (one of each). Another severe adverse event involved soft tissue necrosis. The overall response rate in evaluable subjects was 33% in treatment‐naïve patients and 28% in patients with recurrent/refractory disease, which did not meet the predefined Bayesian criteria for efficacy.ConclusionAfuresertib has clinical activity in some patients with newly diagnosed and advanced LCH.

Abstract The emergence of tumor cells with certain stem-like characteristics, such as high aldehyde dehydrogenase (ALDH) activity due to ALDH1A1 expression, contributes to chemotherapy resistance and tumor relapse. However, clinically applicable inhibitors of ALDH activity have not been reported. There is evidence to suggest that epigenetic regulation of stem-related genes contributes to chemotherapy efficacy. Here, we show that bromodomain and extraterminal (BET) inhibitors suppress ALDH activity by abrogating BRD4-mediated ALDH1A1 expression through a super-enhancer element and its associated enhancer RNA. The clinically applicable small-molecule BET inhibitor JQ1 suppressed the outgrowth of cisplatin-treated ovarian cancer cells both in vitro and in vivo. Combination of JQ1 and cisplatin improved the survival of ovarian cancer–bearing mice in an orthotopic model. These phenotypes correlate with inhibition of ALDH1A1 expression through a super-enhancer element and other stem-related genes in promoter regions bound by BRD4. Thus, targeting the BET protein BRD4 using clinically applicable small-molecule inhibitors, such as JQ1, is a promising strategy for targeting ALDH activity in epithelial ovarian cancer. Cancer Res; 76(21); 6320–30. ©2016 AACR.

Advances in the field of defibrillation have brought to practice different types of devices that include the transvenous implantable cardioverter-defibrillator (ICD) with or without cardiac resynchronization therapy, the subcutaneous ICD (S-ICD), and the wearable cardioverter-defibrillator. To ensure optimal use of these devices and to achieve best patient outcomes, clinicians need to understand how these devices work, learn the characteristics of patients who qualify them for one type of device versus another, and recognize the remaining gaps in knowledge surrounding these devices. The transvenous ICD has been shown in several randomized clinical trials to improve the survival of patients resuscitated from near-fatal ventricular fibrillation and those with sustained ventricular tachycardia with syncope or systolic heart failure as a result of ischemic or nonischemic cardiomyopathy despite receiving guideline-directed medical therapy. Important gaps in knowledge regarding the transvenous ICD involve the role of the ICD in patient subgroups not included, or not well represented, in clinical trials and the need to refine the selection criteria for the ICD in patients who are indicated for it. S-ICDs were recently introduced into the clinical arena as another option for many patients who have an approved indication for a transvenous ICD. The main advantage of the S-ICD is a lower risk of infection and lead-related complications; however, the S-ICD does not offer bradycardia or antitachycardia pacing. The S-ICD may be ideal for patients with limited vascular access, high infection risk, or some congenital heart diseases. However, more data are needed regarding the efficacy and effectiveness of the S-ICD in comparison to transvenous ICDs, the extent of defibrillation testing required, and the use of the S-ICD with other novel technologies, including leadless pacemakers. Cardiac resynchronization therapy-defibrillators are indicated in patients with a left ventricular ejection fraction ≤35%, QRS width ≥130 ms, and New York Heart Association class II, III, or ambulatory IV symptoms despite treatment with guideline-directed medical therapy. Multiple randomized controlled trials have shown that the cardiac resynchronization therapy-defibrillator improves survival, quality of life, and several echocardiographic measures. One main challenge related to cardiac resynchronization therapy-defibrillators is the 30% nonresponse rate. Many initiatives are underway to address this challenge including improved cardiac resynchronization therapy and imaging technologies and enhanced selection of patients and device programming.

Coffee consumption has been shown in some studies to be associated with lower risk of prostate cancer. However, it is unclear if this association is causal or due to confounding or reverse causality. We conducted a Mendelian randomisation analysis to investigate the causal effects of coffee consumption on prostate cancer risk and progression. We used two genetic variants robustly associated with caffeine intake (rs4410790 and rs2472297) as proxies for coffee consumption in a sample of 46,687 men of European ancestry from 25 studies in the PRACTICAL consortium. Associations between genetic variants and prostate cancer case status, stage and grade were assessed by logistic regression and with all‐cause and prostate cancer‐specific mortality using Cox proportional hazards regression. There was no clear evidence that a genetic risk score combining rs4410790 and rs2472297 was associated with prostate cancer risk (OR per additional coffee increasing allele: 1.01, 95% CI: 0.98,1.03) or having high‐grade compared to low‐grade disease (OR: 1.01, 95% CI: 0.97,1.04). There was some evidence that the genetic risk score was associated with higher odds of having nonlocalised compared to localised stage disease (OR: 1.03, 95% CI: 1.01, 1.06). Amongst men with prostate cancer, there was no clear association between the genetic risk score and all‐cause mortality (HR: 1.00, 95% CI: 0.97,1.04) or prostate cancer‐specific mortality (HR: 1.03, 95% CI: 0.98,1.08). These results, which should have less bias from confounding than observational estimates, are not consistent with a substantial effect of coffee consumption on reducing prostate cancer incidence or progression.

Abstract Background: Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers, and cancer-related traits. Methods: The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background. Results: The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis. Conclusions: Results from these analyses will enable researchers to identify new susceptibility loci, perform fine-mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental, and lifestyle-related exposures. Impact: Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126–35. ©2016 AACR.