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Primary open-angle glaucoma (POAG), the leading cause of irreversible blindness worldwide, disproportionately affects individuals of African ancestry. We conducted a genome-wide association study (GWAS) for POAG in 11,275 individuals of African ancestry (6,003 cases; 5,272 controls). We detected 46 risk loci associated with POAG at genome-wide significance. Replication and post-GWAS analyses, including functionally informed fine-mapping, multiple trait co-localization, and in silico validation, implicated two previously undescribed variants (rs1666698 mapping to DBF4P2; rs34957764 mapping to ROCK1P1) and one previously associated variant (rs11824032 mapping to ARHGEF12) as likely causal. For individuals of African ancestry, a polygenic risk score (PRS) for POAG from our mega-analysis (African ancestry individuals) outperformed a PRS from summary statistics of a much larger GWAS derived from European ancestry individuals. This study quantifies the genetic architecture similarities and differences between African and non-African ancestry populations for this blinding disease., Competing Interests: Declaration of interests J.M.O. is a member of the scientific advisory board of Life Biosciences and a paid consultant of Atheneum Partners, Cerner Enviza (includes Kantar Health), and Calico. A.G.R. holds intellectual property for the use of gene therapy to treat glaucoma. E.M.-E. is a scientific advisor for Avisi and a paid consultant of Aerie Pharmaceuticals, Allergan, Eyenovia, and Thea Pharma. J.L. receives instrument support from Carl Zeiss Meditech, Inc., and Heidelberg Engineering, GmBH; receives research support from Novartis, Inc.; and is a paid consultant at Thea, Inc., Alcon Laboratories, Inc., Johnson & Johnson, Inc., Abbvie, Inc., Carl Zeiss Meditech, Inc., Genetech, Inc., and ONL Therapeutics, Inc., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Although glaucoma is a disease modulated by eye pressure, the mechanisms of pressure sensing in the eye are not well understood. Here, we investigated associations between mechanosensitive ion channel gene variants and primary open-angle glaucoma (POAG). Common (minor allele frequency > 5%) single nucleotide polymorphisms located within the genomic regions of 20 mechanosensitive ion channel genes in the K2P, TMEM63, PIEZO and TRP channel families were assessed using genotype data from the NEIGHBORHOOD consortium of 3853 cases and 33,480 controls. Rare (minor allele frequency < 1%) coding variants were assessed using exome array genotyping data for 2606 cases and 2606 controls. Association with POAG was analyzed using logistic regression adjusting for age and sex. Two rare PIEZO1 coding variants with protective effects were identified in the NEIGHBOR dataset: R1527H, (OR 0.17, P = 0.0018) and a variant that alters a canonical splice donor site, g.16-88737727-C-G Hg38 (OR 0.38, P = 0.02). Both variants showed similar effects in the UK Biobank and the R1527H also in the FinnGen database. Several common variants also reached study-specific thresholds for association in the NEIGHBORHOOD dataset. These results identify novel variants in several mechanosensitive channel genes that show associations with POAG, suggesting that these channels may be potential therapeutic targets., (© 2023. Springer Nature Limited.)

Diphthamide (DPH), a conserved amino acid modification on eukaryotic translation elongation factor eEF2, is synthesized via a complex, multi-enzyme pathway. While DPH is non-essential for cell viability and its function has not been resolved, diphtheria and other bacterial toxins ADP-ribosylate DPH to inhibit translation. Characterizing Saccharomyces cerevisiae mutants that lack DPH or show synthetic growth defects in the absence of DPH, we show that loss of DPH increases resistance to the fungal translation inhibitor sordarin and increases -1 ribosomal frameshifting at non-programmed sites during normal translation elongation and at viral programmed frameshifting sites. Ribosome profiling of yeast and mammalian cells lacking DPH reveals increased ribosomal drop-off during elongation, and removal of out-of-frame stop codons restores ribosomal processivity on the ultralong yeast MDN1 mRNA. Finally, we show that ADP-ribosylation of DPH impairs the productive binding of eEF2 to elongating ribosomes. Our results reveal that loss of DPH impairs the fidelity of translocation during translation elongation resulting in increased rates of ribosomal frameshifting throughout elongation and leading to premature termination at out-of-frame stop codons. We propose that the costly, yet non-essential, DPH modification has been conserved through evolution to maintain translational fidelity despite being a target for inactivation by bacterial toxins., (Published by Oxford University Press on behalf of Nucleic Acids Research 2023.)

Purpose: Genetic variants in regions that include the mitochondrial genes thioredoxin reductase 2 (TXNRD2) and malic enzyme 3 (ME3) are associated with primary open-angle glaucoma (POAG) in genome-wide association studies (GWASs). To assess their clinical impact, we investigated whether TXNRD2 and ME3 genetic risk scores (GRSs) are associated with specific glaucoma phenotypes., Design: Cross-sectional study., Participants: A total of 2617 patients with POAG and 2634 control participants from the National Eye Institute Glaucoma Human Genetics Collaboration Hereditable Overall Operational Database (NEIGHBORHOOD) consortium., Methods: All POAG-associated single nucleotide polymorphisms (SNPs) in the TXNRD2 and ME3 loci were identified using GWAS data (P < 0.05). Of these, 20 TXNRD2 and 24 ME3 SNPs were selected after adjusting for linkage disequilibrium. The correlation between SNP effect size and gene expression levels was investigated using the Gene-Tissue Expression database. Genetic risk scores were constructed for each individual using the unweighted sum of TXNRD2, ME3, and TXNRD2 + ME3 combined risk alleles. Age- and sex-adjusted odds ratios (ORs) for POAG diagnosis were calculated per decile for each GRS. Additionally, the clinical features of patients with POAG in the top 1%, 5%, and 10% of each GRS were compared with those in the bottom 1%, 5%, and 10%, respectively., Main Outcome Measures: Primary open-angle glaucoma OR per GRS decile, maximum treated intraocular pressure (IOP), and prevalence of paracentral visual field loss among patients with POAG with high versus low GRSs., Results: A larger SNP effect size strongly correlated with higher TXNRD2 and lower ME3 expression levels (r = 0.95 and r = -0.97, respectively; P < 0.05 for both). Individuals in decile 10 of the TXNRD2 + ME3 GRS had the highest odds of POAG diagnosis (OR, 1.79 compared with decile 1; 95% confidence interval, 1.39-2.30; P < 0.001). Patients with POAG in the top 1% of the TXNRD2 GRS showed higher mean maximum treated IOP compared with the bottom 1% (19.9 mmHg vs. 15.6 mmHg; adjusted P = 0.03). Patients with POAG in the top 1% of the ME3 and TXNRD2 + ME3 GRS showed a higher prevalence of paracentral field loss than the bottom 1% (72.7% vs. 14.3% for ME3 GRS and 88.9% vs. 33.3% for TXNRD2+ME3 GRS; adjusted P = 0.03 for both)., Conclusions: Patients with POAG with higher TXNRD2 and ME3 GRSs showed higher treated IOP and a greater prevalence of paracentral field loss. Functional studies exploring how these variants impact mitochondrial function in patients with glaucoma are warranted., Financial Disclosure(s): Proprietary or commercial disclosure may be found after the references., (Copyright © 2023 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.)

A major goal of precision medicine is to stratify patients based on their genetic risk for a disease to inform future screening and intervention strategies. For conditions like primary open-angle glaucoma (POAG), the genetic risk architecture is complicated with multiple variants contributing small effects on risk. Following the tepid success of genome-wide association studies for high-effect disease risk variant discovery, genetic risk scores (GRS), which collate effects from multiple genetic variants into a single measure, have shown promise for disease risk stratification. We assessed the application of GRS for POAG risk stratification in Hispanic-descent (HIS) and European-descent (EUR) Veterans in the Million Veteran Program. Unweighted and cross-ancestry meta-weighted GRS were calculated based on 127 genomic variants identified in the most recent report of cross-ancestry POAG meta-analyses. We found that both GRS types were associated with POAG case-control status and performed similarly in HIS and EUR Veterans. This trend was also seen in our subset analysis of HIS Veterans with less than 50% EUR global genetic ancestry. Our findings highlight the importance of evaluating GRS based on known POAG risk variants in different ancestry groups and emphasize the need for more multi-ancestry POAG genetic studies.

Glaucoma is the leading cause of irreversible blindness worldwide. Primary open-angle glaucoma (POAG), the most common glaucoma subtype, is more prevalent and severe in individuals of African ancestry. Unfortunately, this ancestral group has been historically under-represented among genetic studies of POAG. Moreover, both genetic and polygenic risk scores (GRS, PRS) that are typically based on genetic data from European-descent populations are not transferable to individuals without a majority of European ancestry. Given the aspirations of leveraging genetic information for precision medicine, GRS and PRS demonstrate clinical potential but fall short, in part due to the lack of diversity in these studies. Prioritizing diversity in the discovery of risk variants will improve the performance and utility of GRS and PRS-derived risk estimation for disease stratification, which could bring about earlier POAG intervention and treatment for a disease that often goes undetected until significant damage has occurred.

The availability of electronic health record (EHR)-linked biobank data for research presents opportunities to better understand complex ocular diseases. Developing accurate computable phenotypes for ocular diseases for which gold standard diagnosis includes imaging remains inaccessible in most biobank-linked EHRs. The objective of this study was to develop and validate a computable phenotype to identify primary open-angle glaucoma (POAG) through accessing the Department of Veterans Affairs (VA) Computerized Patient Record System (CPRS) and Million Veteran Program (MVP) biobank. Accessing CPRS clinical ophthalmology data from VA Medical Center Eye Clinic (VAMCEC) patients, we developed and iteratively refined POAG case and control algorithms based on clinical, prescription, and structured diagnosis data (ICD-CM codes). Refinement was performed via detailed chart review, initially at a single VAMCEC (n = 200) and validated at two additional VAMCECs (n = 100 each). Positive and negative predictive values (PPV, NPV) were computed as the proportion of CPRS patients correctly classified with POAG or without POAG, respectively, by the algorithms, validated by ophthalmologists and optometrists with access to gold-standard clinical diagnosis data. The final algorithms performed better than previously reported approaches in assuring the accuracy and reproducibility of POAG classification (PPV >83% and NPV >97%) with consistent performance in Black or African American and in White Veterans. Applied to the MVP to identify cases and controls, genetic analysis of a known POAG-associated locus further validated the algorithms. We conclude that ours is a viable approach to use combined EHR-genetic data to study patients with complex diseases that require imaging confirmation.

Purpose: Primary open-angle glaucoma (POAG) is a degenerative eye disease for which early treatment is critical to mitigate visual impairment and irreversible blindness. POAG-associated loci individually confer incremental risk. Genetic risk score(s) (GRS) could enable POAG risk stratification. Despite significantly higher POAG burden among individuals of African ancestry (AFR), GRS are limited in this population. A recent large-scale, multi-ancestry meta-analysis identified 127 POAG-associated loci and calculated cross-ancestry and ancestry-specific effect estimates, including in European ancestry (EUR) and AFR individuals. We assessed the utility of the 127-variant GRS for POAG risk stratification in EUR and AFR Veterans in the Million Veteran Program (MVP). We also explored the association between GRS and documented invasive glaucoma surgery (IGS)., Design: Cross-sectional study., Participants: MVP Veterans with imputed genetic data, including 5830 POAG cases (445 with IGS documented in the electronic health record) and 64 476 controls., Methods: We tested unweighted and weighted GRS of 127 published risk variants in EUR (3382 cases and 58 811 controls) and AFR (2448 cases and 5665 controls) Veterans in the MVP. Weighted GRS were calculated using effect estimates from the most recently published report of cross-ancestry and ancestry-specific meta-analyses. We also evaluated GRS in POAG cases with documented IGS., Main Outcome Measures: Performance of 127-variant GRS in EUR and AFR Veterans for POAG risk stratification and association with documented IGS., Results: GRS were significantly associated with POAG (P < 5 × 10 -5 ) in both groups; a higher proportion of EUR compared with AFR were consistently categorized in the top GRS decile (21.9%-23.6% and 12.9%-14.5%, respectively). Only GRS weighted by ancestry-specific effect estimates were associated with IGS documentation in AFR cases; all GRS types were associated with IGS in EUR cases., Conclusions: Varied performance of the GRS for POAG risk stratification and documented IGS association in EUR and AFR Veterans highlights (1) the complex risk architecture of POAG, (2) the importance of diverse representation in genomics studies that inform GRS construction and evaluation, and (3) the necessity of expanding diverse POAG-related genomic data so that GRS can equitably aid in screening individuals at high risk of POAG and who may require more aggressive treatment., (Published by Elsevier Inc.)

Importance: Tobacco 21 (T21) policies raise the minimum legal age to purchase tobacco from 18 to 21 years to curb youth access to tobacco products. While some studies have found that T21 is associated with reducing prevalence of youth tobacco use, little is known about the impact it may have on youth of different racial and ethnic identities., Objective: To evaluate the association of T21 policy with the prevalence of high school youth tobacco use across sex, race, and ethnicity., Design, Setting, and Participants: This survey study used representative survey data collected from the local biennial Youth Risk Behavior Survey from 2013 to 2017 comparing Cleveland, Ohio (which has a T21 policy), to proximal jurisdictions in the first-ring suburbs in Cuyahoga County (which do not have T21 policies). Within-Cleveland demographic information was also collected for 2013 to 2019. Overall high school youth tobacco use rates were compared between Cleveland and the first-ring suburbs and then examined within Cleveland among Hispanic, non-Hispanic Black, and non-Hispanic White high school students. Percentage data were adjusted to more closely align with local population demographics. Data were analyzed from January to June 2022., Exposures: T21 was implemented in Cleveland in 2016 and not adopted in proximal jurisdictions or at the state and federal level until at least 1 year later., Main Outcomes and Measures: The main outcomes were prevalence of past 30-day cigarette, cigar product, or e-cigarette use, measured using geographically representative high school youth survey data from 2013 to 2015 (prelegislation) and 2017 to 2019 (postlegislation) and compared using a difference-in-differences analysis., Results: The unweighted sample included 12 616 high school students (27.0% [95% CI, 26.9%-28.0%] in 10th grade; 50.9% [95% CI, 50.3%-51.6%] females) participating in 1 or more Youth Risk Behavior Surveys from 2013 to 2019, including 7064 students in Cleveland and 5552 students in the first-ring suburbs. Compared with the first-ring suburbs, Cleveland had a greater proportion of younger students (1623 [28.5%] ninth grade students vs 2179 [34.0%] ninth grade students) and Hispanic students (436 students [1.1%] vs 1433 students [12.6%]) and non-Hispanic Black students (2000 students [53.1%] vs 3971 students [75.1%]). Cigars were the most commonly used tobacco product in Cleveland, with use reported by 6201 students (19.8%) in 2013, 5877 students (21.3%) in 2015, and 5784 students (16.8%) in 2019. Compared with the first-ring suburbs, there was a greater decline in prevalence of use of cigars in Cleveland (β = 0.18 [SE, 0.05]; P < .001). The disparity across race, ethnicity, and sex decreased for all current tobacco product use. For example, the maximum difference between demographic subpopulations in current cigarette use was 11.6 (95% CI, 9.5-13.7) percentage points in 2013 between White females (16.1% [95% CI, 11.3%-20.8%]) and Black males (4.5% [95% CI, 3.5%-5.4%]). This maximum difference in current cigarette use decreased significantly to 5.1 (95% CI, 3.5-6.7) percentage points in 2019 between White females (6.9% [95% CI, 3.4%-10.3%]) and Black females (1.8% [95% CI, 0.7%-2.8%])., Conclusions and Relevance: This survey study found that there was a decline in youth-reported tobacco use across every tobacco product category from 2013 to 2019. This decline changed the trajectory of use among several demographic groups and brought the youth populations with the highest tobacco product use to similar rates of others.

Previous studies have suggested that phosphorylation of translation elongation factor 1A (eEF1A) can alter its function, and large-scale phospho-proteomic analyses in Saccharomyces cerevisiae have identified 14 eEF1A residues phosphorylated under various conditions. Here, a series of eEF1A mutations at these proposed sites were created and the effects on eEF1A activity were analyzed. The eEF1A-S53D and eEF1A-T430D phosphomimetic mutant strains were inviable, while corresponding alanine mutants survived but displayed defects in growth and protein synthesis. The activity of an eEF1A-S289D mutant was significantly reduced in the absence of the guanine nucleotide exchange factor eEF1Bα and could be restored by an exchange-deficient form of the protein, suggesting that eEF1Bα promotes eEF1A activity by a mechanism other than nucleotide exchange. Our data show that several of the phosphorylation sites identified by high-throughput analysis are critical for eEF1A function., (© 2021 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)

Objective: To explore the role of several genetic polymorphisms (APOE ε4, BDNF Met, and COMT Val) in executive functioning performance in patients with pharmacoresistant temporal lobe epilepsy (TLE)., Methods: Ninety-three adults (51 female, mean age = 39 years) with TLE completed executive functioning measures as part of a comprehensive preoperative neuropsychological evaluation, including Trail Making Test (Part B), Wisconsin Card Sorting Test (Conceptual Level Responses and Perseverative Errors), Color Word Interference from the Delis Kaplan Executive Function System, and measures of phonemic and semantic verbal fluency. Genotyping of the APOE, BDNF, and COMT genes was conducted using DNA extracted from peripheral blood or brain tissue (from epilepsy surgery)., Results: After adjustment for general cognitive ability, COMT Val carriers showed poorer performance on semantic verbal fluency and color word interference than non-carriers, and BDNF Met carriers showed poorer performance on phonemic verbal fluency than those without a Met allele., Significance: Results suggest that COMT and BDNF polymorphisms are associated with performance on several EF measures in patients with TLE, including tasks assessing verbal fluency and response inhibition and account for up to 16% of the variance in test performance. The APOE polymorphism was not significantly associated with any of the executive function measures analyzed., (Copyright © 2021 Elsevier Inc. All rights reserved.)

As genome-wide association studies have continued to identify loci associated with complex traits, the implications of and necessity for proper use of these findings, including prediction of disease risk, have become apparent. Many complex diseases have numerous associated loci with detectable effects implicating risk for or protection from disease. A common contemporary approach to using this information for disease prediction is through the application of genetic risk scores. These scores estimate an individual's liability for a specific outcome by aggregating the effects of associated loci into a single measure as described in the previous version of this article. Although genetic risk scores have traditionally included variants that meet criteria for genome-wide significance, an extension known as the polygenic risk score has been developed to include the effects of more variants across the entire genome. Here, we describe common methods and software packages for calculating and interpreting polygenic risk scores. In this revised version of the article, we detail information that is needed to perform a polygenic risk score analysis, considerations for planning the analysis and interpreting results, as well as discussion of the limitations based on the choices made. We also provide simulated sample data and a walkthrough for four different polygenic risk score software. © 2021 Wiley Periodicals LLC., (© 2021 Wiley Periodicals LLC.)

Glaucoma leads to millions of cases of visual impairment and blindness around the world. Its susceptibility is shaped by both environmental and genetic risk factors. Although over 120 risk loci have been identified for glaucoma, a large portion of its heritability is still unexplained. Here we describe the foundation of the Genetics of GLaucoma Evaluation in the AMish (GGLEAM) study to investigate the genetic architecture of glaucoma in the Ohio Amish, which exhibits lower genetic and environmental heterogeneity compared to the general population. To date, we have enrolled 81 Amish individuals in our study from Holmes County, Ohio. As a part of our enrollment process, 62 GGLEAM study participants (42 glaucoma-affected and 20 unaffected individuals) received comprehensive eye examinations and glaucoma evaluations. Using the data from the Anabaptist Genealogy Database, we found that 80 of the GGLEAM study participants were related to one another through a large, multigenerational pedigree containing 1586 people. We plan to integrate the health and kinship data obtained for the GGLEAM study to interrogate glaucoma genetics and pathophysiology in this unique population.

Background: Age-related macular degeneration (AMD) is a progressive retinal disease contributing to blindness worldwide. Multiple estimates for AMD heritability (h 2 ) exist; however, a substantial proportion of h 2 is not attributable to known genomic loci. The International AMD Genomics Consortium (IAMDGC) gathered the largest dataset of advanced AMD (ADV) cases and controls available and identified 34 loci containing 52 independent risk variants defining known AMD h 2 . To better define AMD heterogeneity, we used Pathway Analysis by Randomization Incorporating Structure (PARIS) on the IAMDGC data and identified 8 statistical driver genes (SDGs), including 2 novel SDGs not discovered by the IAMDGC. We chose to further investigate these pathway-based risk genes and determine their contribution to ADV h 2 , as well as the differential ADV subtype h 2 ., Methods: We performed genomic-relatedness-based restricted maximum-likelihood (GREML) analyses on ADV, geographic atrophy (GA), and choroidal neovascularization (CNV) subtypes to investigate the h 2 of genotyped variants on the full DNA array chip, 34 risk loci (n = 2758 common variants), 52 variants from the IAMDGC 2016 GWAS, and the 8 SDGs, specifically the novel 2 SDGs, PPARA and PLCG2., Results: Via GREML, full chip h 2 was 44.05% for ADV, 46.37% for GA, and 62.03% for CNV. The lead 52 variants' h 2 (ADV: 14.52%, GA: 8.02%, CNV: 13.62%) and 34 loci h 2 (ADV: 13.73%, GA: 8.81%, CNV: 12.89%) indicate that known variants contribute ~ 14% to ADV h 2 . SDG variants account for a small percentage of ADV, GA, and CNV heritability, but estimates based on the combination of SDGs and the 34 known loci are similar to those calculated for known loci alone. We identified modest epistatic interactions among variants in the 2 SDGs and the 52 IAMDGC variants, including modest interactions between variants in PPARA and PLCG2., Conclusions: Pathway analyses, which leverage biological relationships among genes in a pathway, may be useful in identifying additional loci that contribute to the heritability of complex disorders in a non-additive manner. Heritability analyses of these loci, especially amongst disease subtypes, may provide clues to the importance of specific genes to the genetic architecture of AMD.

Glaucoma, a disease characterized by progressive optic nerve degeneration, can be prevented through timely diagnosis and treatment. We characterize optic nerve photographs of 67,040 UK Biobank participants and use a multitrait genetic model to identify risk loci for glaucoma. A glaucoma polygenic risk score (PRS) enables effective risk stratification in unselected glaucoma cases and modifies penetrance of the MYOC variant encoding p.Gln368Ter, the most common glaucoma-associated myocilin variant. In the unselected glaucoma population, individuals in the top PRS decile reach an absolute risk for glaucoma 10 years earlier than the bottom decile and are at 15-fold increased risk of developing advanced glaucoma (top 10% versus remaining 90%, odds ratio = 4.20). The PRS predicts glaucoma progression in prospectively monitored, early manifest glaucoma cases (P = 0.004) and surgical intervention in advanced disease (P = 3.6 × 10 - 6 ). This glaucoma PRS will facilitate the development of a personalized approach for earlier treatment of high-risk individuals, with less intensive monitoring and treatment being possible for lower-risk groups.

Genome-wide variation data with millions of genetic markers have become commonplace. However, the potential for interpretation and application of these data for clinical assessment of outcomes of interest, and prediction of disease risk, is currently not fully realized. Many common complex diseases now have numerous, well-established risk loci and likely harbor many genetic determinants with effects too small to be detected at genome-wide levels of statistical significance. A simple and intuitive approach for converting genetic data to a predictive measure of disease susceptibility is to aggregate the effects of these loci into a single measure, the genetic risk score. Here, we describe some common methods and software packages for calculating genetic risk scores and polygenic risk scores, with focus on studies of common complex diseases. We review the basic information needed, as well as important considerations for constructing genetic risk scores, including specific requirements for phenotypic and genetic data, and limitations in their application. © 2019 by John Wiley & Sons, Inc., (© 2019 John Wiley & Sons, Inc.)

Purpose: Age-related macular degeneration (AMD) is the worldwide leading cause of blindness among the elderly. Although genome-wide association studies (GWAS) have identified AMD risk variants, their roles in disease etiology are not well-characterized, and they only explain a portion of AMD heritability., Methods: We performed pathway analyses using summary statistics from the International AMD Genomics Consortium's 2016 GWAS and multiple pathway databases to identify biological pathways wherein genetic association signals for AMD may be aggregating. We determined which genes contributed most to significant pathway signals across the databases. We characterized these genes by constructing protein-protein interaction networks and performing motif analysis., Results: We determined that eight genes (C2, C3, LIPC, MICA, NOTCH4, PLCG2, PPARA, and RAD51B) "drive" the statistical signals observed across pathways curated in the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and Gene Ontology (GO) databases. We further refined our definition of statistical driver gene to identify PLCG2 as a candidate gene for AMD due to its significant gene-level signals (P < 0.0001) across KEGG, Reactome, GO, and NetPath pathways., Conclusions: We performed pathway analyses on the largest available collection of advanced AMD cases and controls in the world. Eight genes strongly contributed to significant pathways from the three larger databases, and one gene (PLCG2) was central to significant pathways from all four databases. This is, to our knowledge, the first study to identify PLCG2 as a candidate gene for AMD based solely on genetic burden. Our findings reinforce the utility of integrating in silico genetic and biological pathway data to investigate the genetic architecture of AMD.

Background: The risk-benefit ratio of continuing immunomodulating disease-modifying therapy (DMT) in older multiple sclerosis (MS) patients is unknown., Objective: To evaluate clinical and patient-reported outcomes after stopping DMT in older MS patients., Methods: Retrospective, observational study identifying patients from our MS clinics who were aged over 60 and on DMT > 2 years. Cause-specific Cox proportional hazards regression modeled time to discontinuation and time to reinitiation of therapy. Pre- and post-discontinuation comparisons of Performance Scales (PS), Timed 25-Foot Walk, and Patient Health Questionnaire-9 (PHQ9) were analyzed using linear mixed models., Results: A total of 600 patients were included, with 178 (29.7%) discontinuing. Discontinuers were 2.2 years older, had 3.2 years longer disease duration, and 1.6 years lesser treatment exposure. Providers initiated discontinuation more than patients (68.0%). Only one clinical relapse occurred in discontinuers. A proportion (10.7%) reinitiated DMT. Provider-initiated discontinuers restarted less often (hazard ratio (HR): 0.34; 95% confidence interval (CI): 0.12-0.9). In discontinuers, relapsing-remitting patients had lower PS on average than primary progressive. Provider-initiated discontinuation was associated with lower PS than patient- initiated discontinuation. PHQ9 scores appeared higher in those stopping intravenous (IV) therapies than interferons. Lower PS and PHQ9 indicate better outcomes., Conclusion: Most patients over age 60, who discontinued DMT, remained off DMT. This study provides real-world data that may guide clinicians considering discontinuing DMT.

Methods for exploring genetic interactions have been developed in an attempt to move beyond single gene analyses. Because biological molecules frequently participate in different processes under various cellular conditions, investigating the changes in gene coexpression patterns under various biological conditions could reveal important regulatory mechanisms. One of the methods for capturing gene coexpression dynamics, named liquid association (LA), quantifies the relationship where the coexpression between two genes is modulated by a third "coordinator" gene. This LA measure offers a natural framework for studying gene coexpression changes and has been applied increasingly to study regulatory networks among genes. With a wealth of publicly available gene expression data, there is a need to develop a meta-analytic framework for LA analysis. In this paper, we incorporated mixed effects when modeling correlation to account for between-studies heterogeneity. For statistical inference about LA, we developed a Markov chain Monte Carlo (MCMC) estimation procedure through a Bayesian hierarchical framework. We evaluated the proposed methods in a set of simulations and illustrated their use in two collections of experimental data sets. The first data set combined 10 pancreatic ductal adenocarcinoma gene expression studies to determine the role of possible coordinator gene USP9X in the Hippo pathway. The second experimental data set consisted of 907 gene expression microarray Escherichia coli experiments from multiple studies publicly available through the Many Microbe Microarray Database website (http://m3d.bu.edu/) and examined genes that coexpress with serA in the presence of coordinator gene Lrp.

Background Context: Red flags are questions typically ascertained by providers to screen for serious underlying spinal pathologies. The utility of patient-reported red flags in guiding clinical decision-making for spine care, however, has not been studied., Purpose: The aim of this study was to quantify the sensitivity and specificity of patient-reported red flags in predicting the presence of serious spinal pathologies., Study Design: This was a retrospective nested case-control study., Patient Sample: This study consisted of 120 patients with International Classification of Diseases, Ninth Revision, Clinical Modification codes for spinal pathologies and 380 randomly selected patients, from a population of 4,313 patients seen at a large tertiary care spine clinic between October 9, 2013 and June 30, 2014., Outcome Measures: The presence of patient-reported red flags and red flags obtained from medical records was verified for chart review. The spinal pathology (ie, malignancy, fractures, infections, or cauda equina syndrome) was noted for each patient., Methods: The sensitivity and specificity of patient-reported red flags for detecting serious spinal pathologies were calculated from data obtained from the 500 patients. Youden's J was used to rank performance. Agreement between patient-reported red flags and those obtained from medical record review was assessed via Cohen's kappa statistic., Results: "History of cancer" was the best performing patient-reported red flag to identify malignancy (sensitivity=0.75 [95% confidence intervals, CI 0.53-0.90], specificity=0.79 [95% CI 0.75-0.82]). The best performing patient-reported red flag for fractures was the presence of at least one of the following: "Osteoporosis," "Steroid use," and "Trauma" (sensitivity=0.59 [95% CI 0.44-0.72], specificity=0.65 [95% CI 0.60-0.69]). The prevalence of infection and cauda equina diagnoses was insufficient to gauge sensitivity and specificity. Red flags from medical records had better performance than patient-reported red flags. There was poor agreement between patient red flags and those obtained from medical record review., Conclusions: Patient-reported red flags had low sensitivity and specificity for identification of serious pathologies. They should not be used in insolation to make treatment decisions, although they may be useful to prompt further probing to determine if additional investigation is warranted., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Introduction: Very little quantitative data on occupational burnout and exposure to critical incidents are available from contemporary United States emergency medical services (EMS) cohorts. Given that burnout has been associated positively with turnover intentions and absenteeism in EMS workers, studies that uncover correlates of burnout may be integral to combating growing concerns around retention in the profession., Methods: We administered a 167-item electronic survey that included the Maslach Burnout Inventory (MBI) and a modified version of the Critical Incident History Questionnaire (n=29 incident types) to paramedics, emergency medical technicians (EMTs), and dispatchers of a single ambulance service. We defined the presence of burnout as a high score on either the emotional exhaustion or depersonalization subscales of the MBI., Results: Survey respondents who provided regular 911 response at the time of the survey and completed the MBI portion of the survey were included in our analysis (190 paramedics/EMTs, 19 dispatchers; 54% response). The overall prevalence of burnout was 18%, with prevalence reaching 32% among dispatchers. The seven pediatric critical incident types presented in the survey accounted for seven of the top eight rated most difficult to cope with, and severity ratings for pediatric critical incidents did not differ by parental status (all p>0.30). A significant number of respondents reported that they had been threatened with a gun/weapon (43%) or assaulted by a patient (68%) at least once while on duty. Being over the age of 50, a parent, or in a committed relationship was associated with reduced odds of burnout in unadjusted models; however, these associations did not remain statistically significant in multivariate analysis. Increasing tertile of career exposure to critical incidents was not associated with burnout., Conclusion: Medical dispatchers may be an EMS subgroup particularly susceptible to burnout. These data also demonstrate quantitatively that in this EMS agency, responders find pediatric critical incidents especially distressing and that violence against responders is commonplace. In this study, a simple measure of career exposure to potentially critical incidents was not associated with burnout; however, individual reactions to incidents are heterogeneous, and assessment tools that more accurately enumerate encounters that result in distress are needed., Competing Interests: Conflicts of Interest: By the WestJEM article submission agreement, all authors are required to disclose all affiliations, funding sources and financial or management relationships that could be perceived as potential sources of bias. No author has professional or financial relationships with any companies that are relevant to this study. There are no conflicts of interest or sources of funding to declare.

This study examined the impact of integrated intensivist consultation in the immediate postoperative period on outcomes for cardiac surgery patients. A retrospective cohort study was conducted in 1711 adult cardiac surgery patients from a single quaternary care center in Minnesota. Outcomes were compared across 2 consecutive 2-year time periods reflecting an elective intensivist model (n = 801) and an integrated intensivist model (n = 910). Patients under the 2 models were comparable with respect to demographics, comorbidities, procedure types, and Society for Thoracic Surgery predicted risk of mortality score; however, patients in the earlier cohort were slightly older and more likely to have chronic kidney disease ( P = .003). Integrated intensivist involvement was associated with reduced postoperative ventilator time, length of stay (LOS), stroke, encephalopathy, and reoperations for bleeding (all P < .01) but was not associated with mortality. Intensivist integration into the postoperative care of cardiac surgery patients may reduce ventilator time, LOS, and complications but may not improve survival.

Objectives: Propose an empirical amyotrophic lateral sclerosis (ALS) staging approach called Fine'til 9 (FT9) based on how many of the patient's ALS functional rating scale (ALSFRS-R) subscores are 9 or less (of normal 12). Gain insights into progression of ALS by applying Markov models to ALS stages by multiple systems (King's, Milan-Torino system (MITOS) and FT9)., Methods: Patients from the Pooled Resource Open-Access ALS Clinical Trials (PRO-ACT) dataset were staged using ALSFRS-R responses. Risks of progression through stages and death were estimated, as were effects of prognostic variables on these risks., Results: A total of 29,947 time points in 3199 patients from the PRO-ACT dataset were assigned stages. Although the three systems were moderately correlated, MITOS stages were heavily skewed toward advanced disease, whereas King's and FT9 stages were more balanced. Non-sequential progression was observed with King's system. Markov models adequately described transitions from stage to stage in the first year of observation, but underestimated risks beyond that point. Regardless of staging method, initial rate of ALSFRS-R decline had a powerful effect on rate of progression through sequential stages, whereas age predominantly influenced stage-specific mortality., Conclusion: King's and FT9 are more sensitive to observed progression of disease in clinical trials than MITOS. FT9 can partition the course similar to King's, and may have advantages of sequential progression and easy applicability to retrospective data. Markov transition intensity estimates may be of value for counseling, health economic studies, and research design. In particular, this framework permits estimation of multidimensional effects of variables (including treatment) on outcome.

Objectives: To examine the accuracy of general health cross-walk tables in a clinical sample of patients with spine disorders. Published tables (Schalet BD, Rothrock NE, Hays RD, et al. Linking physical and mental health summary scores from the Veterans RAND 12-Item Health Survey (VR-12) to the PROMIS(®) Global Health Scale. J Gen Intern Med 2015;30:1524-30) link scores from the Veterans RAND 12-Item Health Survey (VR-12) to the 10-Item Patient-Reported Outcome Measurement Information System (PROMIS), a global health scale metric for both mental (GMH) and physical (GPH) summary scores., Methods: We assessed the accuracy of administered PROMIS and VR-12 scores with scores predicted by cross-walks in 4606 adult patients seen in a spine clinic from October 2015 to 2016. Accuracy of linking scores was evaluated using Pearson correlation, intraclass correlation coefficients, and mean and SD of score differences. Bland-Altman plots were used to graphically assess the levels of agreement. The consistency in scores' discrimination across levels of pain severity, depression, and other patient characteristics was assessed. Bootstrap methods estimated linking precision across varying sample sizes., Results: Actual and cross-walked PROMIS scores showed moderate correlation (ICC(3,1): GMH 0.73; GPH 0.81), with Bland-Altman plots suggesting smaller differences between scores in patients with lower and higher general health. Significant discrimination between patient subgroups was demonstrated reliably by both actual and estimated scores. Bootstrapped resamples indicated adequate precision for 200 patients (95% confidence interval for mean difference: GMH -1.38 to 0.60; GPH 0.39 to 1.93)., Conclusions: VR-12 and PROMIS global health scores can be accurately linked within a sample of patients with spine disorders; nevertheless, bias is high and precision is low for linking on the patient level. Linked scores at the group level for more than 200 patients can be used in comparative effectiveness research and for comparing results across studies., (Copyright © 2018 ISPOR--The Professional Society for Health Economics and Outcomes Research. Published by Elsevier Inc. All rights reserved.)

Purpose: Electrographic seizures detected by continuous electroencephalography (CEEG) in critically ill patients with altered mental status is becoming increasingly recognized. Data guiding the appropriate selection of patients to be monitored on CEEG are lacking. The aims of this article were to study the incidence of seizures in the critical care setting and to evaluate for clinical predictors to improve the efficiency of CEEG monitoring., Methods: Retrospective review of the CEEG and clinical data on 1,123 consecutive patients who had continuous video EEG over a 24-month period., Results: Seizures were recorded in 215 patients on CEEG monitoring (19.1%). In total, 89.3% of these seizures occurred without clinical signs. Patients who were in a coma were more likely to have EEG seizures (odds ratio, 3.64; 95% confidence interval, 2.23-5.95) compared with those awake. The incidence of seizures was overrepresented in patients with extra-axial tumors (41.9%), multiple sclerosis (35.7%), and intra-axial tumors (33.0%). Lateralized periodic discharges were predictive (odds ratio, 8.27; 95% confidence interval, 5.52-12.46) of seizure occurrence compared with those with no epileptiform patterns. Only generalized periodic discharges with triphasic morphology had no increased odds of seizure (odds ratio, 1.02; 95% confidence interval, 0.24-3.03). When present, electroencephalography seizures were detected within 24 hours in 92% of monitored patients., Conclusions: Continuous electroencephalography monitoring in the critical care setting demonstrates a linear increase in seizure incidence with declining mental status. Recognizing clinical conditions and electroencephalography markings may help in the appropriate selection of critically ill patients for CEEG monitoring.

In most eukaryotic organisms, translation elongation requires two highly conserved elongation factors eEF1A and eEF2. Fungal systems are unique in requiring a third factor, the eukaryotic Elongation Factor 3 (eEF3). For decades, eEF3, a ribosome-dependent ATPase, was considered "fungal-specific", however, recent bioinformatics analysis indicates it may be more widely distributed among other unicellular eukaryotes. In order to determine whether divergent eEF3-like proteins from other eukaryotic organisms can provide the essential functions of eEF3 in budding yeast, the eEF3-like proteins from Schizosaccharomyes pombe and an oomycete, Phytophthora infestans, were cloned and expressed in Saccharomyces cerevisiae. Plasmid shuffling experiments showed that both S. pombe and P. infestans eEF3 can support the growth of S. cerevisiae in the absence of endogenous budding yeast eEF3. Consistent with its ability to provide the essential functions of eEF3, P. infestans eEF3 possessed ribosome-dependent ATPase activity. Yeast cells expressing P. infestans eEF3 displayed reduced protein synthesis due to defects in translation elongation/termination. Identification of eEF3 in divergent species will advance understanding of its function and the ribosome specific determinants that lead to its requirement as well as contribute to the identification of functional domains of eEF3 for potential drug discovery.

Protein synthesis requires factors that are proposed to enhance discrete steps. Eukaryotic initiation factor eIF5A was initially thought to affect initiation; however, it was later shown to facilitate translation elongation at polyproline. Recent work by Schuller et al. demonstrates that eIF5A facilitates both general elongation and termination in yeast, challenging these steps as silos., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Introduction: We aimed to pilot test the delivery of sepsis education to emergency medical services (EMS) providers and the feasibility of equipping them with temporal artery thermometers (TATs) and handheld lactate meters to aid in the prehospital recognition of sepsis., Methods: This study used a convenience sample of prehospital patients meeting established criteria for sepsis. Paramedics received education on systemic inflammatory response syndrome (SIRS) criteria, were trained in the use of TATs and hand-held lactate meters, and enrolled patients who had a recent history of infection, met ≥ 2 SIRS criteria, and were being transported to a participating hospital. Blood lactate was measured by paramedics in the prehospital setting and again in the emergency department (ED) via usual care. Paramedics entered data using an online database accessible at the point of care., Results: Prehospital lactate values obtained by paramedics ranged from 0.8 to 9.8 mmol/L, and an elevated lactate (i.e. ≥ 4.0) was documented in 13 of 112 enrolled patients (12%). The unadjusted correlation of prehospital and ED lactate values was 0.57 (p< 0.001). The median interval between paramedic assessment of blood lactate and the electronic posting of the ED-measured lactate value in the hospital record was 111 minutes. Overall, 91 patients (81%) were hospitalized after ED evaluation, 27 (24%) were ultimately diagnosed with sepsis, and 3 (3%) died during hospitalization. Subjects with elevated prehospital lactate were somewhat more likely to have been admitted to the intensive care unit (23% vs 15%) and to have been diagnosed with sepsis (38% vs 22%) than those with normal lactate levels, but these differences were not statistically significant., Conclusion: In this pilot, EMS use of a combination of objective SIRS criteria, subjective assessment of infection, and blood lactate measurements did not achieve a level of diagnostic accuracy for sepsis that would warrant hospital prenotification and committed resources at a receiving hospital based on EMS assessment alone. Nevertheless, this work provides an early model for increasing EMS awareness and the implementation of novel devices that may enhance the prehospital assessment for sepsis. Additional translational research studies with larger numbers of patients and more robust methods are needed.

Background: Postoperative pulmonary complications in orthopedic surgery patients have been associated with worse clinical outcomes. Identifying patients with respiratory risk factors requiring enhanced monitoring and management modifications is an important part of postoperative care. Patients with unanticipated respiratory decompensation requiring transfer to the intensive care unit (ICU) have not been studied in sufficient detail., Methods: A retrospective case-control study of elective orthopedic surgery patients (knee, hip, shoulder, or spine, n = 51) who developed unanticipated respiratory failure (RF) necessitating transfer to the ICU over a 3-year period was conducted. Controls (n = 153) were frequency matched to cases by gender, age, and surgical procedure. Patient and perioperative care factors, clinical outcomes, and cost of care were examined., Results: Transfer to the ICU occurred within 48 h of surgery in 73 % of the cases, 31 % required non-invasive ventilation, and 18 % required mechanical ventilation. Cases had a higher prevalence of chronic obstructive pulmonary disease (COPD), obstructive sleep apnea (OSA), and regular psychotropic medication use than controls. Cases received more intravenous opioids during the first 24 postoperative hours, were hospitalized 4 days longer, had higher in-hospital mortality, and had excess hospitalization costs of US$26,571. COPD, OSA, preoperative psychotropic medications, and anesthesia time were associated with risk of RF in a multivariate analysis., Conclusions: Unanticipated RF after orthopedic surgery is associated with extended hospitalization, increased mortality, and higher cost of care. Hospital protocols that include risk factor assessment, enhanced monitoring, and a cautious approach to opioid use in high-risk patients may reduce the frequency of this complication.

In this review, we provide an overview of protein synthesis in the yeast Saccharomyces cerevisiae The mechanism of protein synthesis is well conserved between yeast and other eukaryotes, and molecular genetic studies in budding yeast have provided critical insights into the fundamental process of translation as well as its regulation. The review focuses on the initiation and elongation phases of protein synthesis with descriptions of the roles of translation initiation and elongation factors that assist the ribosome in binding the messenger RNA (mRNA), selecting the start codon, and synthesizing the polypeptide. We also examine mechanisms of translational control highlighting the mRNA cap-binding proteins and the regulation of GCN4 and CPA1 mRNAs., (Copyright © 2016 by the Genetics Society of America.)

Purpose: Lack of knowledge and negative attitudes have been identified as barriers to participation in clinical trials by patients with cancer. We developed Preparatory Education About Clinical Trials (PRE-ACT), a theory-guided, Web-based, interactive computer program, to deliver tailored video educational content to patients in an effort to overcome barriers to considering clinical trials as a treatment option., Patients and Methods: A prospective, randomized clinical trial compared PRE-ACT with a control condition that provided general clinical trials information produced by the National Cancer Institute (NCI) in text format. One thousand two hundred fifty-five patients with cancer were randomly allocated before their initial visit with an oncologist to PRE-ACT (n = 623) or control (n = 632). PRE-ACT had three main components: assessment of clinical trials knowledge and attitudinal barriers, values assessment with clarification back to patients, and provision of a video library tailored to address each patient's barriers. Outcomes included knowledge and attitudes and preparation for decision making about clinical trials., Results: Both PRE-ACT and control interventions improved knowledge and attitudes (all P < .001) compared with baseline. Patients randomly allocated to PRE-ACT showed a significantly greater increase in knowledge (P < .001) and a significantly greater decrease in attitudinal barriers (P < .001) than did their control (text-only) counterparts. Participants in both arms significantly increased their preparedness to consider clinical trials (P < .001), and there was a trend favoring the PRE-ACT group (P < .09). PRE-ACT was also associated with greater patient satisfaction than was NCI text alone., Conclusion: These data show that patient education before the first oncologist visit improves knowledge, attitudes, and preparation for decision making about clinical trials. Both text and tailored video were effective. The PRE-ACT interactive video program was more effective than NCI text in improving knowledge and reducing attitudinal barriers., Competing Interests: Authors' disclosures of potential conflicts of interest are found in the article online at www.jco.org. Author contributions are found at the end of this article., (© 2015 by American Society of Clinical Oncology.)

Purpose: The decision to enroll in a clinical trial is complex given the uncertain risks and benefits of new approaches. Many patients also have financial concerns. We sought to characterize the association between financial concerns and the quality of decision making about clinical trials., Methods: We conducted a secondary data analysis of a randomized trial of a Web-based educational tool (Preparatory Education About Clinical Trials) designed to improve the preparation of patients with cancer for making decisions about clinical trial enrollment. Patients completed a baseline questionnaire that included three questions related to financial concerns (five-point Likert scales): "How much of a burden on you is the cost of your medical care?," "I'm afraid that my health insurance won't pay for a clinical trial," and "I'm worried that I wouldn't be able to afford the costs of treatment on a clinical trial." Results were summed, with higher scores indicating greater concerns. We used multiple linear regressions to measure the association between concerns and self-reported measures of self-efficacy, preparation for decision making, distress, and decisional conflict in separate models, controlling for sociodemographic characteristics., Results: One thousand two hundred eleven patients completed at least one financial concern question. Of these, 27% were 65 years or older, 58% were female, and 24% had a high school education or less. Greater financial concern was associated with lower self-efficacy and preparation for decision making, as well as with greater decisional conflict and distress, even after adjustment for age, race, sex, education, employment, and hospital location (P < .001 for all models)., Conclusion: Financial concerns are associated with several psychological constructs that may negatively influence decision quality regarding clinical trials. Greater attention to patients' financial needs and concerns may reduce distress and improve patient decision making., Competing Interests: Authors' disclosures of potential conflicts of interest are found in the article online at www.jco.org. Author contributions are found at the end of this article., (© 2015 by American Society of Clinical Oncology.)

Patient participation in cancer clinical trials is low. Little is known about attitudinal barriers to participation, particularly among patients who may be offered a trial during an imminent initial oncology consult. The aims of the present study were to confirm the presence of proposed subscales of a recently developed cancer clinical trial attitudinal barriers measure, describe the most common cancer clinical trials attitudinal barriers, and evaluate socio-demographic, medical and financial factors associated with attitudinal barriers. A total of 1256 patients completed a survey assessing demographic factors, perceived financial burden, prior trial participation and attitudinal barriers to clinical trials participation. Results of a factor analysis did not confirm the presence of the proposed four attitudinal barriers subscale/factors. Rather, a single factor represented the best fit to the data. The most highly-rated barriers were fear of side-effects, worry about health insurance and efficacy concerns. Results suggested that less educated patients, patients with non-metastatic disease, patients with no previous oncology clinical trial participation, and patients reporting greater perceived financial burden from cancer care were associated with higher barriers. These patients may need extra attention in terms of decisional support. Overall, patients with fewer personal resources (education, financial issues) report more attitudinal barriers and should be targeted for additional decisional support., (© 2014 John Wiley & Sons Ltd.)

Apart from its canonical function in translation elongation, eukaryotic translation elongation factor 1A (eEF1A) has been shown to interact with the actin cytoskeleton. Amino acid substitutions in eEF1A that reduce its ability to bind and bundle actin in vitro cause improper actin organization in vivo and reduce total translation. Initial in vivo analysis indicated the reduced translation was through initiation. The mutant strains exhibit increased levels of phosphorylated initiation factor 2α (eIF2α) dependent on the presence of the general control non-derepressible 2 (Gcn2p) protein kinase. Gcn2p causes downregulation of total protein synthesis at initiation in response to increases in deacylated tRNA levels in the cell. Increased levels of eIF2α phosphorylation are not due to a general reduction in translation elongation as eEF2 and eEF3 mutants do not exhibit this effect. Deletion of GCN2 from the eEF1A actin bundling mutant strains revealed a second defect in translation. The eEF1A actin-bundling proteins exhibit changes in their elongation activity at the level of aminoacyl-tRNA binding in vitro. These findings implicate eEF1A in a feedback mechanism for regulating translation at initiation.

Objective: This article describes the rigorous development process and initial feedback of the PRE-ACT (Preparatory Education About Clinical Trials) web-based- intervention designed to improve preparation for decision making in cancer clinical trials., Methods: The multi-step process included stakeholder input, formative research, user testing and feedback. Diverse teams (researchers, advocates and developers) participated including content refinement, identification of actors, and development of video scripts. Patient feedback was provided in the final production period and through a vanguard group (N=100) from the randomized trial., Results: Patients/advocates confirmed barriers to cancer clinical trial participation, including lack of awareness and knowledge, fear of side effects, logistical concerns, and mistrust. Patients indicated they liked the tool's user-friendly nature, the organized and comprehensive presentation of the subject matter, and the clarity of the videos., Conclusion: The development process serves as an example of operationalizing best practice approaches and highlights the value of a multi-disciplinary team to develop a theory-based, sophisticated tool that patients found useful in their decision making process. Practice implications Best practice approaches can be addressed and are important to ensure evidence-based tools that are of value to patients and supports the usefulness of a process map in the development of e-health tools., (Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.)

Objective: This study used the Ottawa Decision Support Framework to evaluate a model examining associations between clinical trial knowledge, attitudinal barriers to participating in clinical trials, clinical trial self-efficacy, and clinical trial preparedness among 1256 cancer patients seen for their first outpatient consultation at a cancer center. As an exploratory aim, moderator effects for gender, race/ethnicity, education, and metastatic status on associations in the model were evaluated., Methods: . Patients completed measures of cancer clinical trial knowledge, attitudinal barriers, self-efficacy, and preparedness. Structural equation modeling (SEM) was conducted to evaluate whether self-efficacy mediated the association between knowledge and barriers with preparedness., Results: . The SEM explained 26% of the variance in cancer clinical trial preparedness. Self-efficacy mediated the associations between attitudinal barriers and preparedness, but self-efficacy did not mediate the knowledge-preparedness relationship., Conclusions: . Findings partially support the Ottawa Decision Support Framework and suggest that assessing patients' level of self-efficacy may be just as important as evaluating their knowledge and attitudes about cancer clinical trials.

Translation elongation is mediated by ribosomes and multiple soluble factors, many of which are conserved across bacteria and eukaryotes. During elongation, eukaryotic elongation factor 1A (eEF1A; EF-Tu in bacteria) delivers aminoacylated-tRNA to the A-site of the ribosome, whereas eEF2 (EF-G in bacteria) translocates the ribosome along the mRNA. Fungal translation elongation is striking in its absolute requirement for a third factor, the ATPase eEF3. eEF3 binds close to the E-site of the ribosome and has been proposed to facilitate the removal of deacylated tRNA from the E-site. eEF3 has two ATP binding cassette (ABC) domains, the second of which carries a unique chromodomain-like insertion hypothesized to play a significant role in its binding to the ribosome. This model was tested in the current study using a mutational analysis of the Sac7d region of the chromodomain-like insertion. Specific mutations in this domain result in reduced growth rate as well as slower translation elongation. In vitro analysis demonstrates that these mutations do not affect the ability of eEF3 to interact with the ribosome. Kinetic analysis revealed a larger turnover number for ribosomes in comparison to eEF3, indicating that the partial reactions involving the ribosome are significantly faster than that of eEF3. Mutations in the chromodomain-like insertion severely compromise the ribosome stimulated ATPase of eEF3, strongly suggesting that it exerts an allosteric effect on the hydrolytic activity of eEF3. The chromodomain-like insertion is, therefore, vital to eEF3 function and may be targeted for developing novel antifungal drugs.

Replication of tombusviruses and other plus-strand RNA viruses depends on several host factors that are recruited into viral replicase complexes. Previous studies have shown that eukaryotic translation elongation factor 1A (eEF1A) is one of the resident host proteins in the highly purified tombusvirus replicase complex. In this paper, we show that methylation of eEF1A by the METTL10-like See1p methyltransferase is required for tombusvirus and unrelated nodavirus RNA replication in yeast model host. Similar to the effect of SEE1 deletion, yeast expressing only a mutant form of eEF1A lacking the 4 known lysines subjected to methylation supported reduced TBSV accumulation. We show that the half-life of several viral replication proteins is decreased in see1Δ yeast or when a mutated eEF1A was expressed as a sole source for eEF1A. Silencing of the plant ortholog of See1 methyltransferase also decreased tombusvirus RNA accumulation in Nicotiana benthamiana., (© 2013 Elsevier Inc. All rights reserved.)

The purpose of this assay is to measure the incorporation of radiolabeled [(35)S]-methionine into newly synthesized proteins in exponentially growing yeast cells. This allows for a quantitative in vivo measurement of total protein synthesis., (© 2014 Elsevier Inc. All rights reserved.)

Eukaryotic translation elongation factor 2 (eEF2) facilitates the movement of the peptidyl tRNA-mRNA complex from the A site of the ribosome to the P site during protein synthesis. ADP-ribosylation (ADP(R)) of eEF2 by bacterial toxins on a unique diphthamide residue inhibits its translocation activity, but the mechanism is unclear. We have employed a hormone-inducible diphtheria toxin (DT) expression system in Saccharomyces cerevisiae which allows for the rapid induction of ADP(R)-eEF2 to examine the effects of DT in vivo. ADP(R) of eEF2 resulted in a decrease in total protein synthesis consistent with a defect in translation elongation. Association of eEF2 with polyribosomes, however, was unchanged upon expression of DT. Upon prolonged exposure to DT, cells with an abnormal morphology and increased DNA content accumulated. This observation was specific to DT expression and was not observed when translation elongation was inhibited by other methods. Examination of these cells by electron microscopy indicated a defect in cell separation following mitosis. These results suggest that expression of proteins late in the cell cycle is particularly sensitive to inhibition by ADP(R)-eEF2.

The vast majority of proteins are believed to have one specific function. Throughout the course of evolution, however, some proteins have acquired additional functions to meet the demands of a complex cellular milieu. In some cases, changes in RNA or protein processing allow the cell to make the most of what is already encoded in the genome to produce slightly different forms. The eukaryotic elongation factor 1 (eEF1) complex subunits, however, have acquired such moonlighting functions without alternative forms. In this article, we discuss the canonical functions of the components of the eEF1 complex in translation elongation as well as the secondary interactions they have with other cellular factors outside of the translational apparatus. The eEF1 complex itself changes in composition as the complexity of eukaryotic organisms increases. Members of the complex are also subject to phosphorylation, a potential modulator of both canonical and non-canonical functions. Although alternative functions of the eEF1A subunit have been widely reported, recent studies are shedding light on additional functions of the eEF1B subunits. A thorough understanding of these alternate functions of eEF1 is essential for appreciating their biological relevance., (Copyright © 2012 John Wiley & Sons, Ltd.)

Host factors are recruited into viral replicase complexes to aid replication of plus-strand RNA viruses. In this paper, we show that deletion of eukaryotic translation elongation factor 1Bgamma (eEF1Bγ) reduces Tomato bushy stunt virus (TBSV) replication in yeast host. Also, knock down of eEF1Bγ level in plant host decreases TBSV accumulation. eEF1Bγ binds to the viral RNA and is one of the resident host proteins in the tombusvirus replicase complex. Additional in vitro assays with whole cell extracts prepared from yeast strains lacking eEF1Bγ demonstrated its role in minus-strand synthesis by opening of the structured 3' end of the viral RNA and reducing the possibility of re-utilization of (+)-strand templates for repeated (-)-strand synthesis within the replicase. We also show that eEF1Bγ plays a synergistic role with eukaryotic translation elongation factor 1A in tombusvirus replication, possibly via stimulation of the proper positioning of the viral RNA-dependent RNA polymerase over the promoter region in the viral RNA template.These roles for translation factors during TBSV replication are separate from their canonical roles in host and viral protein translation.

The eukaryotic elongation factor 1A (eEF1A) delivers aminoacyl-tRNAs to the ribosomal A-site during protein synthesis. To ensure a continuous supply of amino acids, cells harbor the kinase Gcn2 and its effector protein Gcn1. The ultimate signal for amino acid shortage is uncharged tRNAs. We have proposed a model for sensing starvation, in which Gcn1 and Gcn2 are tethered to the ribosome, and Gcn1 is directly involved in delivering uncharged tRNAs from the A-site to Gcn2 for its subsequent activation. Gcn1 and Gcn2 are large proteins, and these proteins as well as eEF1A access the A-site, leading us to investigate whether there is a functional or physical link between these proteins. Using Saccharomyces cerevisiae cells expressing His(6)-eEF1A and affinity purification, we found that eEF1A co-eluted with Gcn2. Furthermore, Gcn2 co-immunoprecipitated with eEF1A, suggesting that they reside in the same complex. The purified GST-tagged Gcn2 C-terminal domain (CTD) was sufficient for precipitating eEF1A from whole cell extracts generated from gcn2Δ cells, independently of ribosomes. Purified GST-Gcn2-CTD and purified His(6)-eEF1A interacted with each other, and this was largely independent of the Lys residues in Gcn2-CTD known to be required for tRNA binding and ribosome association. Interestingly, Gcn2-eEF1A interaction was diminished in amino acid-starved cells and by uncharged tRNAs in vitro, suggesting that eEF1A functions as a Gcn2 inhibitor. Consistent with this possibility, purified eEF1A reduced the ability of Gcn2 to phosphorylate its substrate, eIF2α, but did not diminish Gcn2 autophosphorylation. These findings implicate eEF1A in the intricate regulation of Gcn2 and amino acid homeostasis.

The turnover of damaged proteins is critical to cell survival during stressful conditions such as heat shock or oxidative stress. The accumulation of misfolded proteins in the endoplasmic reticulum (ER) is toxic to cells. Therefore these proteins must be efficiently exported from the ER and degraded by the proteasome or the vacuole. Previously it was shown that the loss of eukaryotic elongation factor 1Bγ (eEF1Bγ) from the yeast Saccharomyces cerevisiae results in resistance to oxidative stress. Strains lacking eEF1Bγ show severe defects in protein turnover during conditions of oxidative stress. Furthermore, these strains accumulate a greater amount of oxidized proteins, which correlates with changes in heat shock chaperones. These strains show severe defects in vacuole morphology and defects related to the maturation of carboxypeptidase Y that is not dependent on the catalytic subunit of the eEF1B complex as a guanine nucleotide exchange factor. Finally, eEF1Bγ co-immunoprecipitates with an essential component of ER-Golgi transport vesicles. Taken together, these results support a broader protein metabolism role for eEF1Bγ.

Replication of plus-strand RNA viruses depends on host factors that are recruited into viral replicase complexes. Previous studies showed that eukaryotic translation elongation factor (eEF1A) is one of the resident host proteins in the highly purified tombusvirus replicase complex. Using a random library of eEF1A mutants, we identified one mutant that decreased and three mutants that increased Tomato bushy stunt virus (TBSV) replication in a yeast model host. Additional in vitro assays with whole cell extracts prepared from yeast strains expressing the eEF1A mutants demonstrated several functions for eEF1A in TBSV replication: facilitating the recruitment of the viral RNA template into the replicase complex; the assembly of the viral replicase complex; and enhancement of the minus-strand synthesis by promoting the initiation step. These roles for eEF1A are separate from its canonical role in host and viral protein translation, emphasizing critical functions for this abundant cellular protein during TBSV replication.

Melanomas display poor response rates to adjuvant therapies because of their intrinsic resistance to proapoptotic stimuli. This study indicates that such resistance can be overcome, at least partly, through the targeting of eEF1A elongation factor with narciclasine, an Amaryllidaceae isocarbostyril controlling plant growth. Narciclasine displays IC(50) growth inhibitory values between 30-100 nM in melanoma cell lines, irrespective of their levels of resistance to proapoptotic stimuli. Normal noncancerous cell lines are much less affected. At nontoxic doses, narciclasine also significantly improves (P=0.004) the survival of mice bearing metastatic apoptosis-resistant melanoma xenografts in their brain. The eEF1A targeting with narciclasine (50 nM) leads to 1) marked actin cytoskeleton disorganization, resulting in cytokinesis impairment, and 2) protein synthesis impairment (elongation and initiation steps), whereas apoptosis is induced at higher doses only (≥200 nM). In addition to molecular docking validation and identification of potential binding sites, we biochemically confirmed that narciclasine directly binds to human recombinant and yeast-purified eEF1A in a nanomolar range, but not to actin or elongation factor 2, and that 5 nM narciclasine is sufficient to impair eEF1A-related actin bundling activity. eEF1A is thus a potential target to combat melanomas regardless of their apoptosis-sensitivity, and this finding reconciles the pleiotropic cytostatic of narciclasine. -