A multi-cohort genome-wide association study in African ancestry individuals reveals risk loci for primary open-angle glaucoma

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.

Mechanosensitive ion channel gene survey suggests potential roles in primary open angle glaucoma

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.

Mitochondrial TXNRD2 and ME3 genetic risk scores are associated with specific primary open-angle glaucoma phenotypes

PURPOSE

Genetic variants in regions that include the mitochondrial genes TXNRD2 and ME3 are associated with primary open-angle glaucoma (POAG) in genome-wide association studies (GWAS). 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: 2617 POAG cases and 2634 controls from the 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 (GTEx) database. GRSs were constructed for each individual using the unweighted sum of TXNRD2, ME3, and TXNRD2+ME3 combined risk alleles. Age and gender-adjusted odds ratios (ORs) for POAG diagnosis were calculated per decile for each GRS. Additionally, the clinical features of POAG cases in the top 1, 5, and 10% of each GRS were compared to the bottom 1, 5, and 10%, respectively.

MAIN OUTCOME MEASURES

POAG OR per GRS decile; maximal treated intraocular pressure (IOP) and prevalence of paracentral visual field loss among POAG cases with high vs. low GRSs.

RESULTS

Increased SNP effect size strongly correlated with higher TXNRD2 and lower ME3 expression levels (r=0.95 and -0.97, respectively, p<0.05 for both). Individuals in decile 10 of TXNRD2+ME3 GRS had the highest odds of POAG diagnosis (OR=1.79 compared to decile 1, p<0.001). POAG cases in the top 1% of TXNRD2 GRS had higher mean maximal treated IOP compared to the bottom 1% (19.9 mmHg vs 15.6 mmHg, adjusted p=0.03). POAG cases in the top 1% of ME3 and TXNRD2+ME3 GRS had a higher prevalence of paracentral field loss compared to the bottom 1% (72.7-88.9% vs 14.3-33.3%; adjusted p=0.03 for both).

CONCLUSIONS

POAG patients with higher TXNRD2 and ME3 GRSs had higher treated IOP and a greater prevalence of paracentral field loss. Functional studies exploring how these variants impact mitochondrial function in glaucoma patients are warranted.

Diversity is key for cross-ancestry transferability of glaucoma genetic risk scores in Hispanic Veterans in the Million Veteran Program

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.

Diversity in Polygenic Risk of Primary Open-Angle Glaucoma

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.

Development and Evaluation of a Rules-based Algorithm for Primary Open-Angle Glaucoma in the VA Million Veteran Program

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.

Glaucoma Genetic Risk Scores in the Million Veteran Program

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.

Evaluation of Restrictions on Tobacco Sales to Youth Younger Than 21 Years in Cleveland, Ohio, Area

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.

The role of genetic polymorphisms in executive functioning performance in temporal lobe epilepsy

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.

Polygenic Risk Scores

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.

Statistical driver genes as a means to uncover missing heritability for age-related macular degeneration

Background

Age-related macular degeneration (AMD) is a progressive retinal disease contributing to blindness worldwide. Multiple estimates for AMD heritability (h²) exist; however, a substantial proportion of h² 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 h². 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 h², as well as the differential ADV subtype h².

Methods

We performed genomic-relatedness-based restricted maximum-likelihood (GREML) analyses on ADV, geographic atrophy (GA), and choroidal neovascularization (CNV) subtypes to investigate the h² 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 h² was 44.05% for ADV, 46.37% for GA, and 62.03% for CNV. The lead 52 variants’ h² (ADV: 14.52%, GA: 8.02%, CNV: 13.62%) and 34 loci h² (ADV: 13.73%, GA: 8.81%, CNV: 12.89%) indicate that known variants contribute ~ 14% to ADV h². 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.

Genetic Risk Scores

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.

Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration

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.

Meta-analytic framework for modeling genetic coexpression dynamics

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.

Sensitivity and specificity of patient-entered red flags for lower back pain

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.

Accuracy of Linking VR-12 and PROMIS Global Health Scores in Clinical Practice

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.

Burnout and Exposure to Critical Incidents in a Cohort of Emergency Medical Services Workers from Minnesota

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.

Deconstructing progression of amyotrophic lateral sclerosis in stages: a Markov modeling approach

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.

Improved Outcomes With Integrated Intensivist Consultation for Cardiac Surgery Patients

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.

Discontinuation of disease-modifying therapy in patients with multiple sclerosis over age 60

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.

Postoperative respiratory failure necessitating transfer to the intensive care unit in orthopedic surgery patients: risk factors, costs, and outcomes

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.

Prehospital Lactate Measurement by Emergency Medical Services in Patients Meeting Sepsis Criteria

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.

Randomized Trial of a Web-Based Intervention to Address Barriers to Clinical Trials

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.

Financial Concerns About Participation in Clinical Trials Among Patients With Cancer

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.

Application of best practice approaches for designing decision support tools: the preparatory education about clinical trials (PRE-ACT) study

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.

Attitudinal barriers to participation in oncology clinical trials: factor analysis and correlates of barriers

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.

Knowledge, attitudes, and self-efficacy as predictors of preparedness for oncology clinical trials: a mediational model

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.

Health care worker attitudes about clinical trials at a comprehensive cancer center

e20633

Background: Cancer patient (pt) participation in clinical trials (CT) is low. Little is known about the beliefs and attitudes of health care workers (HCW) and how they impact intention to discuss CT with pts. The overall goal of this project was to develop a conceptual model to guide future interventions to enhance communication about CT between HCW and cancer pts. Methods: Two email surveys of non-physician HCW at an NCI-designated comprehensive cancer center were conducted. The first was sent to a random sample of 150 HCW. The second was sent to 80 who completed the first survey. Based on our prior work (Eads et al. ASCO 2011) and Ajzen’s Theory of Planned Behavior, domains of the first included CT knowledge (19 items, agree/disagree) and attitudes (27 items, 5-point Likert); the second included normative beliefs about institutional attitudes toward CT (6 items, 5-point Likert), self-efficacy about engaging in discussion about CT (14 items, 5-point Likert), and intention to discuss CT with pts (4 items, 7-point Likert). Results: 41 HCW completed both anonymous surveys; 27 could be matched by demographics. Median age of matched respondents was 44.3 yrs (range 24-63), 26 female, 22 caucasian, 9 nurses. Overall, CT knowledge was high (median 17/19 items correct). There were strong associations between attitudes and self-efficacy (Spearman r=-0.425, p=0.03), as well as perceived normative beliefs and self-efficacy (r=0.651, p=0.0002). These associations were strong amongst nurses (r=-0.818, p=0.007 and r=0.656, p=0.05, respectively), with a particularly strong correlation between self-efficacy and intention to discuss clinical trials with pts (r=0.891, p=0.001). Conclusions: In spite of a small sample size, these pilot data strongly support a behavioral framework to understand and address the impact of HCW attitudes and beliefs about CT on discussions of CT with pts. Insofar as HCW (especially nurses) have substantial pt contact, and serve as a resource for pts regarding treatment decisions, educational interventions to address HCW barriers to discussing CT with pts (i.e. attitudes, beliefs, and self-efficacy) could positively impact pt attitudes and improve decision making.

Randomized trial of a web-based intervention to address barriers to clinical trials

6500

Background: Cancer patients (pts) have knowledge and attitudinal barriers to participation in clinical trials (CT). We developed PRE-ACT (Preparatory Education About Clinical Trials), a tailored, interactive, web-based intervention to address these barriers and improve preparation for consideration of CT as a treatment option. Methods: We conducted a prospective, randomized, multicenter, phase III clinical trial of PRE-ACT vs. control (general text about CT excerpted from NCI materials). All assessments and interventions were conducted online. Cancer pts >18 years old were enrolled before initial oncologist consultation. Pts completed a baseline assessment including CT knowledge (19-item); CT attitudes (28-item); preparation for decision making (10-item); and validated measures of preferences for shared decision making and quality/length of life. PRE-ACT pts received a summary of their preferences and a list of their top CT barriers. Based on ranking of individual barriers, pts were presented with a video library of 30-90 second clips addressing their top barriers (10 maximum). After the educational intervention a follow up survey reassessed CT barriers and preparation. Results: 1255 pts were randomized; median age 59 (range 20-88); 58% female; 12% non-white / 2% Hispanic; 76.4% some college education. 1081 pts completed baseline and post-intervention assessments. The control and PRE-ACT groups both had improved knowledge, reduced attitudinal barriers, and improved preparation (p<.0001 for all comparisons). PRE-ACT was more effective than control in improving knowledge (p=.0006) and attitudes (p<.0001). Furthermore, pts in the PRE-ACT arm were more satisfied with the amount (p=.002) and format (<.0001) of information, and felt more prepared to consider CT (p=.0003). Conclusions: This large-scale randomized trial of a tailored, web-based, video intervention demonstrates that educational information delivered online before the oncologist visit can significantly reduce knowledge barriers and attitudinal barriers and improve preparation for consideration of clinical trials. Both text and PRE-ACT are effective, with greater improvements and satisfaction in the PRE-ACT group. Clinical trial information: NCT00750009.

Yeast as a sensor of factors affecting the accuracy of protein synthesis

The cell monitors and maintains the fidelity of translation during the three stages of protein synthesis: initiation, elongation and termination. Errors can arise by multiple mechanisms, such as altered start site selection, reading frame shifts, misincorporation or nonsense codon suppression. All of these events produce incorrect protein products. Translational accuracy is affected by both cis- and trans-acting elements that insure the proper peptide is synthesized by the protein synthetic machinery. Many cellular components are involved in the accuracy of translation, including RNAs (transfer RNAs, messenger RNAs and ribosomal RNAs) and proteins (ribosomal proteins and translation factors). The yeast Saccharomyces cerevisiae has proven an ideal system to study translational fidelity by integrating genetic approaches with biochemical analysis. This review focuses on the ways studies in yeast have contributed to our understanding of the roles translation factors and the ribosome play in assuring the accuracy of protein synthesis.

Mutation of a conserved CDK site converts a metazoan Elongation Factor 1Bbeta subunit into a replacement for yeast eEF1Balpha

Elongation factor subunit eEF1Bbeta (formerly EF-1beta in plants and EF-1delta in animals) was identified and cloned in a screen for proteins from pea that interact with a cyclin-dependent kinase (CDK). CDKs are enzymes that regulate progression through meiotic and mitotic cell cycles in eukaryotes. eEF1Bbeta and the related protein eEF1Balpha (formerly EF-1beta' in plants and EF-1beta in animals and fungi) can catalyze GTP/GDP exchange on the G-protein eEF1A (formerly EF-1alpha in plants, animals and fungi) during the elongation phase of protein synthesis in eukaryotes. Recombinant Cdc2 and its native homologues from pea extracts associated both in vitro and in vivo with eEF1Bbeta. A Cdc2-cyclin B complex phosphorylated recombinant plant eEF1Bbetas, but not eEF1Balpha. These interactions between CDK and eEF1Bbeta prompted investigations into the in vivo consequences of this relationship. Expression of cDNAs encoding rice or pea eEF1Bbeta subunits failed to complement a Saccharomyces cerevisiae mutant deleted for the eEF1Balpha gene, as was previously observed for the human eEF1Bbeta. However, replacement of Thr91, the sole consensus CDK phosphorylation site in pea eEF1Bbeta, with alanine allowed the pea protein to substitute for eEF1Balpha function in vivo. In addition, this rescued strain was severely cold sensitive, and more sensitive to translational inhibitors than wild-type yeast. Taken together, these results suggest a physiological connection between the cyclin-dependent class of kinases and a translational elongation factor in mitotic cells, and provide the first in vivo evidence that an altered form of eEF1Bbeta can serve as the guanine nucleotide exchange factor for eEF1A.

Identification of a role for actin in translational fidelity in yeast

Numerous studies have suggested a role for actin in translation, but the molecular details of this role are unknown. To elucidate the function(s) of actin in translation, we have studied 25 isogenic, conditional yeast actin mutants. Strikingly, analysis of these mutants indicates that none of those tested have conditional growth defects caused by reduced rates of protein synthesis; and analysis of latrunculin A-treated wild-type cells indicates that even complete disruption of the actin cytoskeleton has no significant effect on the rate of translation. However, analysis of the effect of the 25 actin mutations on fidelity and sensitivity to translation inhibitors identified two mutations ( act1-2 and act1-122) that cause a significant reduction in the fidelity of translation, as assayed by nonsense suppression, and several mutants that are sensitive to paromomycin, which affects translational fidelity. Translation elongation factor 1A (eEF1A) also has a role in fidelity, and in the presence of excess eEF1A four of the mutants ( act1-2, act1-20, act1-120, and act1-125) are even more sensitive to paromomycin, while one mutant ( act1-122) becomes less sensitive. Together, these findings suggest that actin may not be important for the rate of translation, but may have a critical role in ensuring translational fidelity.

Characterization of a general stabilizer element that blocks deadenylation-dependent mRNA decay

mRNA degradation is a regulated process that can play an important role in determining the level of expression of specific genes. The rate at which a specific mRNA is degraded depends largely on specific cis-acting sequences located throughout the transcript. cis-Acting destabilizer sequences that promote increased rates of decay have been identified in several short-lived mRNAs. However, little is known about elements that promote stability, known as stabilizer elements (STEs), and how they function. The work presented here describes the characterization of a STE in the PGK1 transcript. The PGK1 stabilizer element (P-STE) has been delineated to a 64-nucleotide sequence from the coding region that can stabilize a chimeric transcript containing the instability elements from the 3'-untranslated region of the MFA2 transcript. The P-STE is located within the PGK1 coding region and functions when located in the translated portion of the transcript and at a minimum distance from the 3'-untranslated region. These results further support the link between translation and mRNA degradation. A conserved sequence in the TEF1/2 transcript has been identified that also functions as a STE, suggesting that this sequence element maybe a general stability determinant found in other yeast mRNAs.

Crystal structures of nucleotide exchange intermediates in the eEF1A-eEF1Balpha complex

In the elongation cycle of protein biosynthesis, the nucleotide exchange factor eEF1Balpha catalyzes the exchange of GDP bound to the G-protein, eEF1A, for GTP. To obtain more information about the recently solved eEF1A-eEF1Balpha structure, we determined the structures of the eEF1A-eEF1Balpha-GDP-Mg2+, eEF1A-eEF1Balpha-GDP and eEF1A-eEF1Balpha-GDPNP complexes at 3.0, 2.4 and 2.05 A resolution, respectively. Minor changes, specifically around the nucleotide binding site, in eEF1A and eEF1Balpha are consistent with in vivo data. The base, sugar and alpha-phosphate bind as in other known nucleotide G-protein complexes, whereas the beta- and gamma-phosphates are disordered. A mutation of Lys 205 in eEF1Balpha that inserts into the Mg2+ binding site of eEF1A is lethal. This together with the structures emphasizes the essential role of Mg2+ in nucleotide exchange in the eEF1A-eEF1Balpha complex.

Overexpression of translation elongation factor 1A affects the organization and function of the actin cytoskeleton in yeast

The translation elongation factor 1 complex (eEF1) plays a central role in protein synthesis, delivering aminoacyl-tRNAs to the elongating ribosome. The eEF1A subunit, a classic G-protein, also performs roles aside from protein synthesis. The overexpression of either eEF1A or eEF1B alpha, the catalytic subunit of the guanine nucleotide exchange factor, in Saccharomyces cerevisiae results in effects on cell growth. Here we demonstrate that overexpression of either factor does not affect the levels of the other subunit or the rate or accuracy of protein synthesis. Instead, the major effects in vivo appear to be at the level of cell morphology and budding. eEF1A overexpression results in dosage-dependent reduced budding and altered actin distribution and cellular morphology. In addition, the effects of excess eEF1A in actin mutant strains show synthetic growth defects, establishing a genetic connection between the two proteins. As the ability of eEF1A to bind and bundle actin is conserved in yeast, these results link the established ability of eEF1A to bind and bundle actin in vitro with nontranslational roles for the protein in vivo.

Crystallization of the yeast elongation factor complex eEF1A-eEF1B alpha

Crystals of the Saccharomyces cerevisiae elongation factor eEF1A (formerly EF-1 alpha) in complex with a catalytic C-terminal fragment of the nucleotide-exchange factor eEF1B alpha (formerly EF-1 beta) were grown by the sitting-drop vapour-diffusion technique, using polyethylene glycol 2000 monomethyl ether as precipitant. Crystals diffract to better than 1.7 A and belong to the space group P2(1)2(1)2(1). The unit-cell parameters of the crystals are sensitive to the choice of cryoprotectant. The structure of the 61 kDa complex was determined with the multiple anomalous dispersion technique using three selenomethionine residues in a 11 kDa eEF1B alpha fragment generated by limited proteolysis of full-length eEF1B alpha expressed in Escherichia coli.

Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eEF1A:eEF1Balpha

The crystal structure of a complex between the protein biosynthesis elongation factor eEF1A (formerly EF-1alpha) and the catalytic C terminus of its exchange factor, eEF1Balpha (formerly EF-1beta), was determined to 1.67 A resolution. One end of the nucleotide exchange factor is buried between the switch 1 and 2 regions of eEF1A and destroys the binding site for the Mg(2+) ion associated with the nucleotide. The second end of eEF1Balpha interacts with domain 2 of eEF1A in the region hypothesized to be involved in the binding of the CCA-aminoacyl end of the tRNA. The competition between eEF1Balpha and aminoacylated tRNA may be a central element in channeling the reactants in eukaryotic protein synthesis. The recognition of eEF1A by eEF1Balpha is very different from that observed in the prokaryotic EF-Tu:EF-Ts complex. Recognition of the switch 2 region in nucleotide exchange is, however, common to the elongation factor complexes and those of Ras:Sos and Arf1:Sec7.

Hsl7p, the yeast homologue of human JBP1, is a protein methyltransferase

The yeast protein Hsl7p is a homologue of Janus kinase binding protein 1, JBP1, a newly characterized protein methyltransferase. In this report, Hsl7p also is shown to be a methyltransferase. It can be crosslinked to [(3)H]S-adenosylmethionine and exhibits in vitro protein methylation activity. Calf histones H2A and H4 and bovine myelin basic protein were methylated by Hsl7p, whereas histones H1, H2B, and H3 and bovine cytochrome c were not. We demonstrated that JBP1 can complement Saccharomyces cerevisiae with a disrupted HSL7 gene as judged by a reduction of the elongated bud phenotype, and a point mutation in the JBP1 S-adenosylmethionine consensus binding sequence eliminated all complementation by JBP1. Therefore, we conclude the yeast protein Hsl7p is a sequence and functional homologue of JBP1. These data provide evidence for an intricate link between protein methylation and macroscopic changes in yeast morphology.

Mutations in a GTP-binding motif of eukaryotic elongation factor 1A reduce both translational fidelity and the requirement for nucleotide exchange

A series of mutations in the highly conserved N(153)KMD(156)GTP-binding motif of the Saccharomyces cerevisiae translation elongation factor 1A (eEF1A) affect the GTP-dependent functions of the protein and increase misincorporation of amino acids in vitro. Two critical regulatory processes of translation elongation, guanine nucleotide exchange and translational fidelity, were analyzed in strains with the N153T, D156N, and N153T/D156E mutations. These strains are omnipotent suppressors of nonsense mutations, indicating reduced A site fidelity, which correlates with changes either in total translation rates in vivo or in GTPase activity in vitro. All three mutant proteins also show an increase in the K(m) for GTP. An in vivo system lacking the guanine nucleotide exchange factor eukaryotic elongation factor 1Balpha (eEF1Balpha) and supported for growth by excess eEF1A was used to show the two mutations with the highest K(m) for GTP restore most but not all growth defects found in these eEF1Balpha deficient-strains to near wild type. An increase in K(m) alone, however, is not sufficient for suppression and may indicate eEF1Balpha performs additional functions. Additionally, eEF1A mutations that suppress the requirement for guanine nucleotide exchange may not effectively perform all the functions of eEF1A in vivo.

Mutations in elongation factor 1beta, a guanine nucleotide exchange factor, enhance translational fidelity

Translation elongation factor 1beta (EF-1beta) is a member of the family of guanine nucleotide exchange factors, proteins whose activities are important for the regulation of G proteins critical to many cellular processes. EF-1beta is a highly conserved protein that catalyzes the exchange of bound GDP for GTP on EF-1alpha, a required step to ensure continued protein synthesis. In this work, we demonstrate that the highly conserved C-terminal region of Saccharomyces cerevisiae EF-1beta is sufficient for normal cell growth. This region of yeast and metazoan EF-1beta and the metazoan EF-1beta-like protein EF-1delta is highly conserved. Human EF-1beta, but not human EF-1delta, is functional in place of yeast EF-1beta, even though both EF-1beta and EF-1delta have previously been shown to have guanine nucleotide exchange activity in vitro. Based on the sequence and functional homology, mutagenesis of two C-terminal residues identical in all EF-1beta protein sequences was performed, resulting in mutants with growth defects and sensitivity to translation inhibitors. These mutants also enhance translational fidelity at nonsense codons, which correlates with a reduction in total protein synthesis. These results indicate the critical function of EF-1beta in regulating EF-1alpha activity, cell growth, translation rates, and translational fidelity.

Mutations in the MOF2/SUI1 gene affect both translation and nonsense-mediated mRNA decay

Recent studies have demonstrated that cells have evolved elaborate mechanisms to rid themselves of aberrant proteins and transcripts. The nonsense-mediated mRNA decay pathway (NMD) is an example of a pathway that eliminates aberrant mRNAs. In yeast, a transcript is recognized as aberrant and is rapidly degraded if a specific sequence, called the DSE, is present 3' of a premature termination codon. Results presented here show that strains harboring the mof2-1, mof4-1, mof5-1, and mof8-1 alleles, previously demonstrated to increase the efficiency of programmed -1 ribosomal frameshifting, decrease the activity of the NMD pathway. The effect of the mof2-1 allele on NMD was characterized in more detail. Previous results demonstrated that the wild-type MOF2 gene is identical to the SUI1 gene. Studies on the mof2-1 allele of the SUI1 gene indicate that in addition to its role in recognition of the AUG codon during translation initiation and maintenance of the appropriate reading frame during translation elongation, the Mof2 protein plays a role in the NMD pathway. The Mof2p/Sui1 p is conserved throughout nature and the human homolog of the Mof2p/Sui1p functions in yeast cells to activate NMD. These results suggest that factors involved in NMD are general modulators that act in several aspects of translation and mRNA turnover.

The Mof2/Sui1 protein is a general monitor of translational accuracy

Although it is essential for protein synthesis to be highly accurate, a number of cases of directed ribosomal frameshifting have been reported in RNA viruses, as well as in procaryotic and eucaryotic genes. Changes in the efficiency of ribosomal frameshifting can have major effects on the ability of cells to propagate viruses which use this mechanism. Furthermore, studies of this process can illuminate the mechanisms involved in the maintenance of the normal translation reading frame. The yeast Saccharomyces cerevisiae killer virus system uses programmed -1 ribosomal frameshifting to synthesize its gene products. Strains harboring the mof2-1 allele demonstrated a fivefold increase in frameshifting and prevented killer virus propagation. In this report, we present the results of the cloning and characterization of the wild-type MOF2 gene. mof2-1 is a novel allele of SUI1, a gene previously shown to play a role in translation initiation start site selection. Strains harboring the mof2-1 allele demonstrated a mutant start site selection phenotype and increased efficiency of programmed -1 ribosomal frameshifting and conferred paromomycin sensitivity. The increased frameshifting observed in vivo was reproduced in extracts prepared from mof2-1 cells. Addition of purified wild-type Mof2p/Sui1p reduced frameshifting efficiencies to wild-type levels. Expression of the human SUI1 homolog in yeast corrects all of the mof2-1 phenotypes, demonstrating that the function of this protein is conserved throughout evolution. Taken together, these results suggest that Mof2p/Sui1p functions as a general modulator of accuracy at both the initiation and elongation phases of translation.

Translational misreading: mutations in translation elongation factor 1alpha differentially affect programmed ribosomal frameshifting and drug sensitivity

The translation elongation feactor 1alpha (EF-1alpha) catalyzes the critical step of delivering aminoacyl-tRNAs to the elongating ribosome. A series of Saccharomyces cerevisiae strains containing mutant alleles of the TEF2 gene encoding EF-1alpha have phenotypes consistent with effects on cellular processes related to translation. These include (1) conditional growth defects, (2) antibiotic sensitivity or resistance, (3) altered +1 or -1 ribosomal frameshifting efficiencies, and (4) altered maintenance of the killer phenotype. Although all the mutant alleles were isolated as dominant +1 frameshift suppressors, the effects of these mutations on the cell are quite different when present as the only form of EF-1alpha. Allele-specific effects are observed with regard to their ability to alter the efficiency of programmed +1 frameshifting as opposed to programmed -1 ribosomal frameshifting. The significantly altered efficiency of -1 frameshifting in strains containing the TEF2-4 and TEF2-9 mutant alleles further correlates with a reduced ability to maintain the killer phenotype and the M1 satellite virus of L-A, an in vivo assay of translational fidelity. In light of the proposed models regarding the different A- and P-site occupancy states required for +1 or -1 ribosomal frameshifting, these results aid analysis of interactions between EF-1alpha and the translational apparatus.

Conservation and diversity of eukaryotic translation initiation factor eIF3

The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA. We report the cloning and characterization of human cDNAs encoding two of its subunits, p110 and p36. It was found that the second slowest band during polyacrylamide gel electrophresis of eIF3 subunits in sodium dodecyl sulfate contains two proteins: p110 and p116. Analysis of the cloned cDNA encoding p110 indicates that its amino acid sequence is 31% identical to that of the yeast protein, Nip1. The p116 cDNA was cloned and characterized as a human homolog of yeast Prt1, as described elsewhere (Methot, N., Rom, E., Olsen, H., and Sonenberg, N. (1997) J. Biol. Chem. 272, 1110-1116). p36 is a WD40 repeat protein, which is 46% identical to the p39 subunit of yeast eIF3 and is identical to TRIP-1, a phosphorylation substrate of the TGF-beta type II receptor. The p116, p110, and p36 subunits localize on 40 S ribosomes in cells active in translation and co-immunoprecipitate with affinity-purified antibodies against the p170 subunit, showing that these proteins are integral components of eIF3. Although p36 and p116 have homologous protein subunits in yeast eIF3, the p110 homolog, Nip1, is not detected in yeast eIF3 preparations. The results indicate both conservation and diversity in eIF3 between yeast and humans.

Increased expression of Saccharomyces cerevisiae translation elongation factor 1 alpha bypasses the lethality of a TEF5 null allele encoding elongation factor 1 beta

Translation elongation factor 1beta (EF-1beta) catalyzes the exchange of bound GDP for GTP on EF-1alpha. The lethality of a null allele of the TEF5 gene encoding EF-1beta in Saccharomyces cerevisiae was suppressed by extra copies of the TEF2 gene encoding EF-1alpha. The strains with tef5::TRP1 suppressed by extra copies of TEF were slow growing, cold sensitive, hypersensitive to inhibitors of translation elongation and showed increased phenotypic suppression of +1 frameshift and UAG nonsense mutations. Nine dominant mutant alleles of TEF2 that cause increased suppression of frameshift mutations also suppressed the lethality of tef5::TRP1. Most of the strains in which tef5::TRP1 is suppressed by dominant mutant alleles of TEF2 grew more slowly and were more antibiotic sensitive than strains with tef5::TRP1 is suppressed by wild-type TEF2. Two alleles, TEF2-4 and TEF2-10, interact with tef5::TRP1 to produce strains that showed doubling times similar to tef5::TRP1 strains containing extra copies of wild-type TEF2. These strains were less cold sensitive, drug sensitive and correspondingly less efficient suppressor of +1 frameshift mutations. These phenotypes indicate that translation and cell growth are highly sensitive to changes in EF-1alpha and EF-1beta activity.

Multiple genes encode the translation elongation factor EF-1 gamma in Saccharomyces cerevisiae

A gene encoding a yeast homologue of translation elongation factor 1 gamma (EF-1 gamma), TEF3, was isolated as a gene dosage extragenic suppressor of the cold-sensitive phenotype of the Saccharomyces cerevisiae drs2 mutant. The drs2 mutant is deficient in the assembly of 40S ribosomal subunits. We have identified a second gene, TEF4, that encodes a protein highly related to both the Tef3p protein (Tef3p), and EF-1 gamma isolated from other organisms. In contrast to TEF3, the TEF4 gene contains an intron. Gene disruptions showed that neither gene is required for mitotic growth. Haploid spores containing disruptions of both genes are viable and have no defects in ribosomal subunit composition or polyribosomes. Unlike TEF3, extra copies of TEF4 do not suppress the cold-sensitive 40S ribosomal subunit deficiency of a drs2 strain. Low-stringency genomic Southern hybridization analysis indicates there may be additional yeast genes related to TEF3 and TEF4.