Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer.

BACKGROUND: Patients with highly mutated tumors, such as melanoma or smoking-related lung cancer, have higher rates of response to immune checkpoint blockade therapy, perhaps due to increased neoantigen expression. Many chemotherapies including platinum compounds are known to be mutagenic, but the impact of standard treatment protocols on mutational burden and resulting neoantigen expression in most human cancers is unknown. METHODS: We sought to quantify the effect of chemotherapy treatment on computationally predicted neoantigen expression for high grade serous ovarian carcinoma patients enrolled in the Australian Ovarian Cancer Study. In this series, 35 of 114 samples were collected after exposure to chemotherapy; 14 are matched with an untreated sample from the same patient. Our approach integrates whole genome and RNA sequencing of bulk tumor samples with class I MHC binding prediction and mutational signatures extracted from studies of chemotherapy-exposed Caenorhabditis elegans and Gallus gallus cells. We additionally investigated the relationship between neoantigens, tumor infiltrating immune cells estimated from RNA-seq with CIBERSORT, and patient survival. RESULTS: Greater neoantigen burden and CD8+ T cell infiltration in primary, pre-treatment samples were independently associated with improved survival. Relapse samples collected after chemotherapy harbored a median of 78% more expressed neoantigens than untreated primary samples, a figure that combines the effects of chemotherapy and other processes operative during relapse. The contribution from chemotherapy-associated signatures was small, accounting for a mean of 5% (range 0-16) of the expressed neoantigen burden in relapse samples. In both treated and untreated samples, most neoantigens were attributed to COSMIC Signature (3), associated with BRCA disruption, Signature (1), associated with a slow mutagenic process active in healthy tissue, and Signature (8), of unknown etiology. CONCLUSION: Relapsed ovarian cancers harbor more predicted neoantigens than primary tumors, but the increase is due to pre-existing mutational processes, not mutagenesis from chemotherapy.

Multiple loci influencing hippocampal degeneration identified by genome scan.

OBJECTIVE: Large genome-wide association studies (GWASs) have identified many novel genes influencing Alzheimer disease (AD) risk, but most of the genetic variance remains unexplained. We conducted a 2-stage GWAS for AD-related quantitative measures of hippocampal volume (HV), total cerebral volume (TCV), and white matter hyperintensities (WMH). METHODS: Brain magnetic resonance imaging measures of HV, TCV, and WMH were obtained from 981 Caucasian and 419 African American AD cases and their cognitively normal siblings in the MIRAGE (Multi Institutional Research in Alzheimer's Genetic Epidemiology) Study, and from 168 AD cases, 336 individuals with mild cognitive impairment, and 188 controls in the Alzheimer's Disease Neuroimaging Initiative Study. A GWAS for each trait was conducted in the 2 Caucasian data sets in stage 1. Results from the 2 data sets were combined by meta-analysis. In stage 2, 1 single nucleotide polymorphism (SNP) from each region that was nominally significant in each data set (p < 0.05) and strongly associated in both data sets (p < 1.0 × 10(-5)) was evaluated in the African American data set. RESULTS: Twenty-two markers (14 for HV, 3 for TCV, and 5 for WMH) from distinct regions met criteria for evaluation in stage 2. Novel genome-wide significant associations (p < 5.0 × 10(-8)) were attained for HV with SNPs in the APOE, F5/SELP, LHFP, and GCFC2 gene regions. All of these associations were supported by evidence in each data set. Associations with different SNPs in the same gene (p < 1 × 10(-5) in Caucasians and p < 2.2 × 10(-4) in African Americans) were also observed for PICALM with HV, SYNPR with TCV, and TTC27 with WMH. INTERPRETATION: Our study demonstrates the efficacy of endophenotypes for broadening our understanding of the genetic basis of AD.

Coronary flow reserve varies depending upon the location within the artery it is assessed and the TIMI myocardial perfusion grade: a PROTECT TIMI-30 analysis.

Coronary flow reserve (CFR) is a measure of the capacity of the epicardial coronary artery and the microvasculature to achieve maximal blood flow in response to hyperemic stimulation. It is not known whether the CFR varies along the length of the artery. Likewise, the interaction between CFR and the thrombolysis in myocardial infarction (TIMI) myocardial perfusion grade (TMPG) is unknown. CFR was measured using the number of cineframes required for the contrast to traverse the same length of the coronary artery before and following the administration of intracoronary adenosine. Following percutaneous coronary intervention (PCI), CFR was assessed both proximal and distal to the lesion in 192 consecutive patients with non-ST-segment elevation acute coronary syndrome (NSTEACS) from the PROTECT TIMI-30 trial. TMPG was also assessed. The difference between the distal and proximal CFR for patients with TMPG 0/1 (n = 76) was 0.11 (95% CI 0.01-0.20, P = 0.026), while among those with TMPG 2/3 (n = 114) it was -0.02 (95% CI -0.09-0.06, P = 0.65). The difference in the CFR between the distal and proximal segments among patients with TMPG 0/1 and TMPG 2/3 was significant (P interaction = 0.044). Following PCI among patients with impaired TMPG (0/1) in the setting of NSTEACS, CFR varies significantly between the proximal and distal segment of coronary arteries and is associated with higher (greater) distal CFR.

Factors Associated With Trial Completion and Adherence in App-Based N-of-1 Trials: Protocol for a Randomized Trial Evaluating Study Duration, Notification Level, and Meaningful Engagement in the Brain Boost Study.

BACKGROUND: N-of-1 trials promise to help individuals make more informed decisions about treatment selection through structured experiments that compare treatment effectiveness by alternating treatments and measuring their impacts in a single individual. We created a digital platform that automates the design, administration, and analysis of N-of-1 trials. Our first N-of-1 trial, the app-based Brain Boost Study, invited individuals to compare the impacts of two commonly consumed substances (caffeine and L-theanine) on their cognitive performance. OBJECTIVE: The purpose of this study is to evaluate critical factors that may impact the completion of N-of-1 trials to inform the design of future app-based N-of-1 trials. We will measure study completion rates for participants that begin the Brain Boost Study and assess their associations with study duration (5, 15, or 27 days) and notification level (light or moderate). METHODS: Participants will be randomized into three study durations and two notification levels. To sufficiently power the study, a minimum of 640 individuals must begin the study, and 97 individuals must complete the study. We will use a multiple logistic regression model to discern whether the study length and notification level are associated with the rate of study completion. For each group, we will also compare participant adherence and the proportion of trials that yield statistically meaningful results. RESULTS: We completed the beta testing of the N1 app on a convenience sample of users. The Brain Boost Study on the N1 app opened enrollment to the public in October 2019. More than 30 participants enrolled in the first month. CONCLUSIONS: To our knowledge, this will be the first study to rigorously evaluate critical factors associated with study completion in the context of app-based N-of-1 trials. TRIAL REGISTRATION: ClinicalTrials.gov NCT04056650; https://clinicaltrials.gov/ct2/show/NCT04056650. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/16362.

Effect of prasugrel versus clopidogrel on outcomes among patients with acute coronary syndrome undergoing percutaneous coronary intervention without stent implantation: a TRial to assess Improvement in Therapeutic Outcomes by optimizing platelet inhibitioN with prasugrel (TRITON)-Thrombolysis in Myocardial Infarction (TIMI) 38 substudy.

BACKGROUND: Prasugrel led to a significant reduction in ischemic cardiovascular events among patients with acute coronary syndrome (ACS) undergoing percutaneous coronary intervention (PCI) with stent implantation compared to clopidogrel. Whether this benefit extends to patients undergoing PCI without stent implantation is unknown. METHODS: In TRial to assess Improvement in Therapeutic Outcomes by optimizing platelet inhibitioN with prasugrel (TRITON)-Thrombolysis in Myocardial Infarction (TIMI) 38, patients (n = 13 608) undergoing PCI for ACS were randomized to aspirin plus clopidogrel or prasugrel. This postrandomization analysis of a prespecified subgroup was restricted to patients who underwent PCI without stent implantation (n = 569). RESULTS: Patients who underwent PCI without stent implantation were older and had a higher incidence of hypertension, diabetes, prior myocardial infarction (MI), prior coronary artery bypass (CABG) surgery, and renal dysfunction than patients who underwent stent implantation. In the group that did not undergo stent implantation, baseline characteristics were similar between patients receiving clopidogrel and prasugrel. The composite of cardiovascular death, nonfatal MI, and nonfatal stroke occurred in 14.2% of patients receiving prasugrel and 17.1% of patients receiving clopidogrel (HR 0.82, P = .27). There were significant reductions favoring prasugrel in the rates of urgent target vessel revascularization (TVR; HR 0.46, P = .040) and any TVR (HR 0.40, P = .009) and a trend toward a reduction in the incidence of nonfatal MI (HR 0.65, P = .11). CABG-related TIMI major bleeding was more frequent among patients receiving prasugrel. There were no significant interactions between treatment and PCI type. CONCLUSION: Among ACS patients who underwent PCI without stent implantation, prasugrel therapy tended to reduce clinical ischemic events and to increase bleeding events to a similar magnitude as among patients who received stents.

Use of the TIMI frame count in the assessment of coronary artery blood flow and microvascular function over the past 15 years.

Since its introduction, the TIMI frame count method has contributed to the understanding of the pathophysiology of coronary artery disease. In this article, the evolution of the TFC method and its applicability in the assessment of various therapeutic modalities are described.

Significance of papillary muscle abnormalities identified by cardiovascular magnetic resonance in hypertrophic cardiomyopathy.

Increased thickness of the left ventricular (LV) wall is the predominant feature of the hypertrophic cardiomyopathy (HC) phenotype. The structural characteristics of the LV papillary muscles (PMs) have received little attention. In this study, cardiovascular magnetic resonance (CMR) was used to characterize PM morphology in a large HC population. Cine and delayed enhancement (DE) CMR images were obtained in 201 patients with HC and 43 control subjects. PM number and mass index were greater in patients with HC compared with controls (2.5 vs 2.1, p <0.001, and 6 +/- 2 vs 3 +/- 2 g/m(2), p <0.001, respectively), including 109 (54%) with PM mass > or =7 g/m(2) (> or =2 SDs above the mean for controls). Greater LV wall mass index was associated with more substantial PM mass (r = 0.09, p <0.001). Furthermore, 12 patients with HC (19%) had normal LV mass with localized wall thickness but increased PM mass. In patients with HC with LV outflow obstruction at rest, PMs were positioned closer to the ventricular septum (displaced anteriorly: 58% vs 42% for subjects without obstruction, p = 0.02), with more marked hypertrophy (9 +/- 5 vs 6 +/- 4 g/m(2), p <0.001). Preoperative CMR identified 3 patients with accessory, anteriorly displaced PMs judged to contribute to outflow obstruction, which were resected during septal myectomy. DE of the PMs was identified in 13 patients with HC (6%), including 3 with DE confined to PMs. In conclusion, CMR demonstrates LV PMs to be part of the cardiomyopathic process in HC, with increases in number and mass, and not uncommonly associated with remodeling with DE. The identification of accessory PMs may be useful in planning preoperative strategy.

Relation of hyperemic epicardial flow to outcomes among patients with ST-segment elevation myocardial infarction receiving fibrinolytic therapy.

In patients with ST-segment elevation myocardial infarction (STEMI), the restoration of normal epicardial flow following fibrinolytic administration is associated with improved clinical outcomes. The goal of this analysis was to examine the relation between hyperemic flow and outcomes following fibrinolytic administration for STEMI. In Clopidogrel as Adjunctive Reperfusion Therapy-Thrombolysis In Myocardial Infarction 28 (CLARITY-TIMI 28), patients with STEMI (n=3,491) treated with fibrinolytic therapy were scheduled to undergo angiography 48 to 192 hours after randomization. Corrected TIMI frame count (CTFC) and TIMI myocardial perfusion grade (TMPG) were assessed, and their associations with outcomes at 30 days were evaluated. When evaluating initial angiography of the infarct-related artery, there was a nearly linear relation between CTFC and 30-day mortality, with faster flow (lower CTFC) associated with improved outcomes. Conversely, in patients who underwent percutaneous coronary intervention (PCI), very fast flow (CTFC<14) after intervention was associated with worse outcomes. Post-PCI hyperemic flow (CTFC<14) was associated with a higher incidence of mortality (p=0.056), recurrent myocardial infarction (p=0.011), and a composite of death or myocardial infarction (p<0.001) compared with normal flow (CTFC 14 to 28). When post-PCI CTFC was further stratified by TMPG, there was a U-shaped relation between mortality and CTFC in patients with poor myocardial perfusion (TMPG 0 or 1). This relation appeared to be linear in patients with TMPG 2 or 3. In conclusion, in patients who undergo PCI after fibrinolytic therapy for STEMI, hyperemic flow on coronary angiography is associated with an increased incidence of adverse outcomes. Hyperemic flow with associated impaired myocardial perfusion may be a marker of more extensive downstream microembolization.

Measuring noncalcified coronary atherosclerotic plaque using voxel analysis with MDCT angiography: phantom validation.

OBJECTIVE: This purpose of this study was to evaluate the accuracy and reproducibility of a voxel analysis technique for measuring noncalcified plaque in the coronary arteries. MATERIALS AND METHODS: Polyethylene phantoms representing noncalcified plaque were scanned in both MDCT and micro-CT scanners and inter- and intrareader variability of volume calculation was performed. RESULTS: Volume measurements by both MDCT and micro-CT were comparable to the true volume as measured by micrometry (< 3%, p = 0.05). CONCLUSION: There appears to be no significant difference (< 3%) between MDCT and micro-CT measurements.

Prognostic utility of heart-type fatty acid binding protein in patients with acute coronary syndromes.

BACKGROUND: Heart-type fatty acid binding protein (H-FABP) is a cytosolic protein that is released rapidly from the cardiomyocyte in response to myocardial injury. Although it has been investigated as an early marker of acute myocardial infarction, its prognostic utility in acute coronary syndromes has not been established. METHODS AND RESULTS: We measured H-FABP in 2287 patients with acute coronary syndromes from the OPUS-TIMI 16 trial. H-FABP was elevated (> 8 ng/mL) in 332 patients (14.5%). Patients with an elevated H-FABP were more likely to suffer death (hazard ratio [HR], 4.1; 95% CI, 2.6 to 6.5), recurrent myocardial infarction (HR, 1.6; 95% CI, 1.0 to 2.5), congestive heart failure (HR, 4.5; 95% CI, 2.6 to 7.8), or the composite of these end points (HR, 2.6; 95% CI, 1.9 to 3.5) through the 10-month follow-up period. H-FABP predicted the risk of the composite end point both in patients who were troponin I negative (HR, 2.1; 95% CI, 1.3 to 3.4) and in those who were troponin I positive (HR, 3.3; 95% CI, 2.0 to 5.3). In a Cox proportional-hazards model that adjusted for baseline variables, including demographics, clinical characteristics, creatinine clearance, ST deviation, index diagnosis, and troponin I, elevated H-FABP remained a significant predictor of the composite end point (HR, 1.9; 95% CI, 1.3 to 2.7), as well as the individual end points of death (HR, 2.7; 95% CI, 1.5 to 4.9) and CHF (HR, 2.4; 95% CI, 1.2 to 5.0). In a multimarker approach, H-FABP, troponin I, and B-type natriuretic peptide provided complementary information. CONCLUSIONS: Elevation of H-FABP is associated with an increased risk of death and major cardiac events in patients presenting across the spectrum of acute coronary syndromes and is independent of other established clinical risk predictors and biomarkers.

Global outcomes of ST-elevation myocardial infarction: comparisons of the Enoxaparin and Thrombolysis Reperfusion for Acute Myocardial Infarction Treatment-Thrombolysis In Myocardial Infarction study 25 (ExTRACT-TIMI 25) registry and trial.

BACKGROUND: Outcomes in patients with ST-elevation myocardial infarction (STEMI) differ between those in clinical trials and those in routine practice, as well as across different regions. We hypothesized that adjustment for baseline risk would minimize such variations. METHODS: The Enoxaparin and Thrombolysis Reperfusion for Acute Myocardial Infarction Treatment-Thrombolysis In Myocardial Infarction (ExTRACT-TIMI) 25 registry was an observational study of patients with STEMI presenting to hospitals participating in the ExTRACT-TIMI 25 randomized clinical trial. Consecutive patients with STEMI who were not enrolled in the trial were entered into the registry. Demographics, in-hospital therapies, and in-hospital events were collected. Baseline risk was assessed using the TIMI Risk Index for STEMI. To adjust for differences among the countries from which the patients presented, the gross national income per annum per capita (GNI) was used. RESULTS: A total of 3726 patients were registered from 109 sites in 25 countries. Patients in the registry had a higher baseline risk than those in the trial; they had more extensive prior cardiac histories and more comorbidities. Unadjusted in-hospital mortality was higher in the registry (8.3%) than in the trial (6.6%) (hazard ratio, 1.30; P < .001); however, after adjusting for TIMI Risk Index, mortality was similar (hazard ratio(adj), 1.00; P = .97). The GNI was not significantly predictive of in-hospital mortality in the multivariable model of the registry. CONCLUSION: Patients in the registry had higher mortality than those in the trial. This difference could be explained by the higher baseline risk of patients in the registry. After adjusting for baseline risk, the GNI of the country in which the patient presented did not contribute to predicting in-hospital mortality.

Impact of iodinated contrast injections on percent diameter coronary arterial stenosis and implications for trials of intracoronary pharmacotherapies in patients with ST-elevation myocardial infarction.

Administration of fibrinolytic, antiplatelet, and antithrombotic agents by the intracoronary route may disaggregate clot, but the potential role of the mechanical force of the injection itself in decreasing clot burden has not been studied. Patients with ST-segment elevation myocardial infarction who were pretreated in the emergency room (ER) with unfractionated heparin and aspirin in the TITAN-TIMI 34 study were randomized to treatment with eptifibatide in the ER (n = 131) versus after diagnostic catheterization (n = 150). Quantitative coronary angiography was used to assess change in diameter stenosis from time of first contrast injection to injection before percutaneous coronary intervention (PCI) immediately preceding wire placement down the culprit artery in a matching view. Successful perfusion of the myocardium was assessed after PCI by the presence of Thrombolysis In Myocardial Infarction myocardial perfusion grade of 2 or 3. In patients treated with eptifibatide in the ER, there was a 1.3% absolute improvement in diameter stenosis from the first injection to the injection before PCI (p = 0.02), whereas there was no change in diameter stenosis in patients not treated with eptifibatide in the ER (0.0%, p = NS). Each 1% improvement in percent diameter stenosis during diagnostic injections before PCI was strongly correlated with an open muscle after PCI (adjusted odds ratio 1.09, 95% confidence interval 1.02 to 1.16, p = 0.012). In conclusion, the mechanical force of a contrast injection decreases thrombotic burden in patients with ST-segment elevation myocardial infarction pretreated with eptifibatide but not with placebo. Future trials of intracoronary pharmacotherapies should include a control arm in which saline is injected to account for the potential clot disaggregation that occurs as a result of iodinated contrast injections, particularly if the patient has been pretreated with aggressive pharmacotherapy.

Hemodynamic significance of periprocedural myocardial injury assessed with N-terminal pro-B-type natriuretic peptide after percutaneous coronary intervention in patients with stable and unstable coronary artery disease (from the JUMBO-TIMI 26 trial).

The clinical relevance of periprocedural myocardial injury related to percutaneous coronary intervention (PCI) remains controversial. N-terminal pro-B-type natriuretic peptide (NT-pro-BNP) is a sensitive indicator of hemodynamic stress and when increased is associated with higher mortality in patients with acute and chronic ischemic heart disease. We measured the serum level of NT-pro-BNP using the Elecsys 2010 proBNP assay at baseline, 4 to 6 hours, and 12 to 24 hours in 747 patients undergoing elective or urgent PCI and enrolled in the JUMBO-TIMI 26 trial. Periprocedural myocardial infarction (MI) was independently adjudicated and required a new increase in creatine kinase-MB >3 times the upper limit of normal distinct from MI as the indication for PCI. Patients with procedural MI had significantly higher levels of NT-pro-BNP at 12 to 24 hours (405 vs 146 pg/ml, p <0.001). Moreover, the greater increase in NT-pro-BNP in patients with periprocedural MI was independent of each clinical and other procedural correlates of NT-pro-BNP after PCI (p <0.001). In addition, the magnitude of increase in NT-pro-BNP correlated strongly with extent of myocardial injury, including in patients with evidence of injury (creatine kinase-MB 1 to 3 times upper limit of normal) not meeting criteria for MI (p = 0.001) or low-level increase in troponin T (p = 0.001). In conclusion, periprocedural myocardial injury, even at low levels, during PCI is associated with increased hemodynamic stress as measured by increasing NT-pro-BNP. This finding supports the physiologic relevance of procedural MI and the continued effort to define therapies that decrease the risk of this complication.

Usefulness of clopidogrel in abolishing the increased risk of reinfarction associated with higher platelet counts in patients with ST-elevation myocardial infarction (results from CLARITY-TIMI 28).

Previous studies have demonstrated an association between increased baseline platelet counts and poorer clinical and angiographic outcomes in patients with ST-elevation myocardial infarction (STEMI). We hypothesized that antiplatelet therapy would mitigate the effect of high baseline platelet counts on clinical outcomes. Data were obtained from 3,491 patients with STEMI in the CLARITY-TIMI 28 trial. Patients were categorized into 3 groups based on their baseline platelet counts: <200 x 10(3)/microl (group 1), 200 to 300 x 10(3)/microl (group 2), and >300 x 10(3)/microl (group 3). Among placebo-treated patients, reinfarction rates increased in a stepwise fashion as platelet counts increased (3.6%, 5.4%, and 9.0%, respectively, p for trend = 0.0025). When confounders of high platelet counts and correlates of reinfarction were adjusted for in a multivariate model, high platelet counts remained independently associated with increased rates of reinfarction at 30 days in placebo-treated patients; using group 1 as a reference group, multivariate odds ratios were 1.45 (95% confidence interval 0.91 to 2.31, p = 0.119) for patients in group 2 and 1.78 (95% confidence interval 1.03 to 3.08, p = 0.038) for patients in group 3. In contrast, among clopidogrel-treated patients, there was no increase in the risk of reinfarction as the platelet count increased (3.2%, 4.1%, and 3.3%, respectively; p for trend = 0.9073, p for interaction=0.064). In conclusion, among patients with STEMI who are treated with aspirin and a fibrinolytic agent, high platelet counts on presentation are independently associated with increased rates of reinfarction. Clopidogrel therapy abolishes this increase in the risk of reinfarction as platelet counts increase. These data are consistent with a putative role of platelets in reinfarction.

Peripheral arterial disease, acute coronary syndromes, and early invasive management: the TACTICS TIMI 18 trial.

BACKGROUND: Patients with peripheral arterial disease (PAD) represent a high-risk patient subset in the setting of non-ST-segment elevation acute coronary syndromes (NSTE ACS). The efficacy and safety of early invasive management for such patients remains unclear. HYPOTHESIS: Early invasive management would be well tolerated and effective among patients with NSTE ACS and PAD. METHODS: Patients from the Treat angina with Aggrastat and determine Cost of Therapy with an Invasive or Conservative Strategy-Thrombolysis In Myocardial Infarction (TACTICS-TIMI) 18 trial were stratified by the presence or absence of PAD and assessed with respect to baseline clinical factors. The outcomes of patients with PAD and NSTE ACS were examined with respect to treatment assignment to either early invasive therapy or conservative treatment of NSTE ACS. Finally, the bleeding and stroke rates of patients with PAD managed invasively were compared with patients with PAD managed conservatively. RESULTS: Of 2219 patients with NSTE ACS overall, 166 (7.5%) had concomitant PAD. Compared with those patients without PAD, those with PAD were older (75 vs. 62 years, p < 0.001) and were more likely to have high-risk clinical features, including prior histories of bypass surgery (39 vs. 20%, p < 0.001) or diabetes mellitus (38 vs. 27%, p = 0.002), and more ST-segment depression on their 12-lead electrocardiogram (43 vs. 29%, p < 0.001). Among such patients, early invasive management was associated with significant reductions in the risk of myocardial infarction (MI) at 30 days (11.4 vs. 2.3%, p = 0.03). At 180 days, compared with early conservative management, early invasive treatment for patients with PAD and NSTE ACS was associated with similar reductions in MI (12.7 vs. 3.5%, p = 0.04), and was also accompanied by significant reductions in risk of death (10.1 vs. 2.3%, p = 0.05). No excess in bleeding or stroke rates was noted among patients with PAD managed invasively. CONCLUSIONS: Among patients with NSTE ACS and a history of PAD, early invasive management is well tolerated and accompanied by significant reductions in morbidity and mortality when compared with a more conservative, ischemia-driven approach.

δ-Catenin is genetically and biologically associated with cortical cataract and future Alzheimer-related structural and functional brain changes.

Multiple lines of evidence suggest that specific subtypes of age-related cataract (ARC) and Alzheimer disease (AD) are related etiologically. To identify shared genetic factors for ARC and AD, we estimated co-heritability of quantitative measures of cataract subtypes with AD-related brain MRI traits among 1,249 members of the Framingham Eye Study who had a brain MRI scan approximately ten years after the eye exam. Cortical cataract (CC) was found to be co-heritable with future development of AD and with several MRI traits, especially temporal horn volume (THV, ρ = 0.24, P<10(-4)). A genome-wide association study using 187,657 single nucleotide polymorphisms (SNPs) for the bivariate outcome of CC and THV identified genome-wide significant association with CTNND2 SNPs rs17183619, rs13155993 and rs13170756 (P<2.6 × 10(-7)). These SNPs were also significantly associated with bivariate outcomes of CC and scores on several highly heritable neuropsychological tests (5.7 × 10(-9) ≤ P<3.7 × 10(-6)). Statistical interaction was demonstrated between rs17183619 and APP SNP rs2096488 on CC (P = 0.0015) and CC-THV (P = 0.038). A rare CTNND2 missense mutation (G810R) 249 base pairs from rs17183619 altered δ-catenin localization and increased secreted amyloid-ß(1-42) in neuronal cell culture. Immunohistopathological analysis of lens tissue obtained from two autopsy-confirmed AD subjects and two non-AD controls revealed elevated expression of δ-catenin in epithelial and cortical regions of lenses from AD subjects compared to controls. Our findings suggest that genetic variation in delta catenin may underlie both cortical lens opacities in mid-life and subsequent MRI and cognitive changes that presage the development of AD.

Comprehensive search for Alzheimer disease susceptibility loci in the APOE region.

OBJECTIVE: To evaluate the association of risk and age at onset (AAO) of Alzheimer disease (AD) with single-nucleotide polymorphisms (SNPs) in the chromosome 19 region including apolipoprotein E (APOE) and a repeat-length polymorphism in TOMM40 (poly-T, rs10524523). DESIGN: Conditional logistic regression models and survival analysis. SETTING: Fifteen genome-wide association study data sets assembled by the Alzheimer's Disease Genetics Consortium. PARTICIPANTS: Eleven thousand eight hundred forty AD cases and 10 931 cognitively normal elderly controls. MAIN OUTCOME MEASURES: Association of AD risk and AAO with genotyped and imputed SNPs located in an 800-Mb region including APOE in the entire Alzheimer's Disease Genetics Consortium data set and with the TOMM40 poly-T marker genotyped in a subset of 1256 cases and 1605 controls. RESULTS: In models adjusting for APOE ε4, no SNPs in the entire region were significantly associated with AAO at P.001. Rs10524523 was not significantly associated with AD or AAO in models adjusting for APOE genotype or within the subset of ε3/ε3 subjects. CONCLUSIONS: APOE alleles ε2, ε3, and ε4 account for essentially all the inherited risk of AD associated with this region. Other variants including a poly-T track in TOMM40 are not independent risk or AAO loci.

Novel late-onset Alzheimer disease loci variants associate with brain gene expression.

OBJECTIVE: Recent genome-wide association studies (GWAS) of late-onset Alzheimer disease (LOAD) identified 9 novel risk loci. Discovery of functional variants within genes at these loci is required to confirm their role in Alzheimer disease (AD). Single nucleotide polymorphisms that influence gene expression (eSNPs) constitute an important class of functional variants. We therefore investigated the influence of the novel LOAD risk loci on human brain gene expression. METHODS: We measured gene expression levels in the cerebellum and temporal cortex of autopsied AD subjects and those with other brain pathologies (∼400 total subjects). To determine whether any of the novel LOAD risk variants are eSNPs, we tested their cis-association with expression of 6 nearby LOAD candidate genes detectable in human brain (ABCA7, BIN1, CLU, MS4A4A, MS4A6A, PICALM) and an additional 13 genes ±100 kb of these SNPs. To identify additional eSNPs that influence brain gene expression levels of the novel candidate LOAD genes, we identified SNPs ±100 kb of their location and tested for cis-associations. RESULTS: CLU rs11136000 (p = 7.81 × 10(-4)) and MS4A4A rs2304933/rs2304935 (p = 1.48 × 10(-4)-1.86 × 10(-4)) significantly influence temporal cortex expression levels of these genes. The LOAD-protective CLU and risky MS4A4A locus alleles associate with higher brain levels of these genes. There are other cis-variants that significantly influence brain expression of CLU and ABCA7 (p = 4.01 × 10(-5)-9.09 × 10(-9)), some of which also associate with AD risk (p = 2.64 × 10(-2)-6.25 × 10(-5)). CONCLUSIONS: CLU and MS4A4A eSNPs may at least partly explain the LOAD risk association at these loci. CLU and ABCA7 may harbor additional strong eSNPs. These results have implications in the search for functional variants at the novel LOAD risk loci.

Influence of ROBO1 and RORA on risk of age-related macular degeneration reveals genetically distinct phenotypes in disease pathophysiology.

ROBO1 is a strong candidate gene for age-related macular degeneration (AMD) based upon its location under a linkage peak on chromosome 3p12, its expression pattern, and its purported function in a pathway that includes RORA, a gene previously associated with risk for neovascular AMD. Previously, we observed that expression of ROBO1 and RORA is down-regulated among wet AMD cases, as compared to their unaffected siblings. Thus, we hypothesized that contribution of association signals in ROBO1, and interaction between these two genes may be important for both wet and dry AMD. We evaluated association of 19 single nucleotide polymorphisms (SNPs) in ROBO1 with wet and dry stages of AMD in a sibling cohort and a Greek case-control cohort containing 491 wet AMD cases, 174 dry AMD cases and 411 controls. Association signals and interaction results were replicated in an independent prospective cohort (1070 controls, 164 wet AMD cases, 293 dry AMD cases). The most significantly associated ROBO1 SNPs were rs1387665 under an additive model (meta P = 0.028) for wet AMD and rs9309833 under a recessive model (meta P = 6 × 10(-4)) for dry AMD. Further analyses revealed interaction between ROBO1 rs9309833 and RORA rs8034864 for both wet and dry AMD (interaction P<0.05). These studies were further supported by whole transcriptome expression profile studies from 66 human donor eyes and chromatin immunoprecipitation assays from mouse retinas. These findings suggest that distinct ROBO1 variants may influence the risk of wet and dry AMD, and the effects of ROBO1 on AMD risk may be modulated by RORA variants.

Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease.

The Alzheimer Disease Genetics Consortium (ADGC) performed a genome-wide association study of late-onset Alzheimer disease using a three-stage design consisting of a discovery stage (stage 1) and two replication stages (stages 2 and 3). Both joint analysis and meta-analysis approaches were used. We obtained genome-wide significant results at MS4A4A (rs4938933; stages 1 and 2, meta-analysis P (P(M)) = 1.7 × 10(-9), joint analysis P (P(J)) = 1.7 × 10(-9); stages 1, 2 and 3, P(M) = 8.2 × 10(-12)), CD2AP (rs9349407; stages 1, 2 and 3, P(M) = 8.6 × 10(-9)), EPHA1 (rs11767557; stages 1, 2 and 3, P(M) = 6.0 × 10(-10)) and CD33 (rs3865444; stages 1, 2 and 3, P(M) = 1.6 × 10(-9)). We also replicated previous associations at CR1 (rs6701713; P(M) = 4.6 × 10(-10), P(J) = 5.2 × 10(-11)), CLU (rs1532278; P(M) = 8.3 × 10(-8), P(J) = 1.9 × 10(-8)), BIN1 (rs7561528; P(M) = 4.0 × 10(-14), P(J) = 5.2 × 10(-14)) and PICALM (rs561655; P(M) = 7.0 × 10(-11), P(J) = 1.0 × 10(-10)), but not at EXOC3L2, to late-onset Alzheimer's disease susceptibility.