Search

Amber L Beitelshees,1,* Deepak Voora,2,* Joshua P Lewis,1,* 1Program for Personalized and Genomic Medicine and Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA; 2Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke School of Medicine, Durham, NC, USA*All authors contributed equally to this work Abstract: In recent years, substantial effort has been made to better understand the influence of genetic factors on the efficacy and safety of numerous medications. These investigations suggest that the use of pharmacogenetic data to inform physician decision-making has great potential to enhance patient care by reducing on-treatment clinical events, adverse drug reactions, and health care-related costs. In fact, integration of such information into the clinical setting may be particularly applicable for antiplatelet and anticoagulation therapeutics, given the increasing body of evidence implicating genetic variation in variable drug response. In this review, we summarize currently available pharmacogenetic information for the most commonly used antiplatelet (ie, clopidogrel and aspirin) and anticoagulation (ie, warfarin) medications. Furthermore, we highlight the currently known role of genetic variability in response to next-generation antiplatelet (prasugrel and ticagrelor) and anticoagulant (dabigatran) agents. While compelling evidence suggests that genetic variants are important determinants of antiplatelet and anticoagulation therapy response, significant barriers to clinical implementation of pharmacogenetic testing exist and are described herein. In addition, we briefly discuss development of new diagnostic targets and therapeutic strategies as well as implications for enhanced patient care. In conclusion, pharmacogenetic testing can provide important information to assist clinicians with prescribing the most personalized and effective antiplatelet and anticoagulation therapy. However, several factors may limit its usefulness and should be considered. Keywords: pharmacogenetics, clopidogrel, warfarin, anticoagulant, aspirin, precision medicine

Although aspirin is a well-established antiplatelet agent, the mechanisms of aspirin resistance remain poorly understood. Metabolomics allows for measurement of hundreds of small molecules in biological samples, enabling detailed mapping of pathways involved in drug response. We defined the metabolic signature of aspirin exposure in subjects from the Heredity and Phenotype Intervention Heart Study. Many metabolites, including known aspirin catabolites, changed on exposure to aspirin, and pathway enrichment analysis identified purine metabolism as significantly affected by drug exposure. Furthermore, purines were associated with aspirin response, and poor responders had higher postaspirin adenosine and inosine levels than did good responders (n = 76; both P < 4 × 10(-3)). Using our established "pharmacometabolomics-informed pharmacogenomics" approach, we identified genetic variants in adenosine kinase associated with aspirin response. Combining metabolomics and genomics allowed for more comprehensive interrogation of mechanisms of variation in aspirin response--an important step toward personalized treatment approaches for cardiovascular disease.

The DEIMOS spectrograph is a multi-object spectrograph being built for Keck II. DEIMOS was delivered in February 2002, became operational in May, and is now about three-quarters of the way through its commissioning period. This paper describes the major problems encountered in completing the spectrograph, with particular emphasis on optical quality and image motion. The strategies developed to deal with these problems are described. Overall, commissioning is going well, and it appears that DEIMOS will meet all of its major performance goals.

Understanding the ecological interactions that underlie marine ecosystem functioning requires sufficient data describing habitat use by mobile species. Hawksbill turtles Eretmochelys imbricata are considered a key species in coral reef-associated communities, owing to their specific foraging preferences, yet new information is still revealing details of the spatial and temporal aspects of habitat use. We used passive acoustic telemetry to monitor the movements of 18 juvenile hawksbills (minimum curved carapace length: 32.0-59.7 cm, mean ± SD = 43.9 ± 6.7 cm) at a developmental foraging site in a Mesoamerican barrier reef, Lighthouse Reef Atoll in Belize (tracking duration 10-1414 d, mean ± SD = 570 ± 484 d). Although specific home ranges were difficult to quantify, several turtles showed high site fidelity over timescales of months to years, with occasional wide-ranging use of the atoll. Diel variation in the number of detections received strongly suggest nocturnal resting. Long-term tracking data reveal 3 degrees of site fidelity across the atoll, based on the number of detection days near individual stations: high residency (n = 4 turtles), sequential residency (n = 5), and transient behavior (n = 4). These variations in movement raise questions about the differentiation of foraging habitats and degree of individual specialization within this population, as well as the influences of microhabitats and human disturbance.

While many unconventional treatments are benign or helpful, potentially dangerous quackeries are still being peddled. Can you winnow the wheat from the chaff? [ABSTRACT FROM AUTHOR]

Geographical remoteness, limited resources, and socioeconomic disparities contribute to the migration of rural Alaska Native Elders to urban areas to access medical services and resources, improve economic situations, or reunite with family. We compared the discourse of 12 Elders in Anchorage who previously lived in four remote traditional villages in the Norton Sound region (ages 60-84) and 13 Elders in those villages (ages 48-80). Using Gee's discourse analysis framework, two patterns emerged detailing cultural effects on identity and Eldership, illuminating differences in the self-evaluation of successful aging based on cultural influences and the role of contextual factors.

HcpR is a CRP-family transcriptional regulator found in many Gram-negative anaerobic bacteria. In the perio-pathogen Porphyromonas gingivalis, HcpR is crucial for the response to reactive nitrogen species such as nitric oxide (NO). Binding of NO to the heme group of HcpR leads to transcription of the redox enzyme Hcp. However, the molecular mechanisms of heme binding to HcpR remain unknown. In this study we present the 2.3 Å structure of the P. gingivalis HcpR. Interdomain interactions present in the structure help to form a hydrophobic pocket in the N-terminal sensing domain. A comparison analysis with other CRP-family members reveals that the molecular mechanisms of HcpR-mediated regulation may be distinct from other family members. Using docking studies, we identify a putative heme binding site in the sensing domain. In vitro complementation and mutagenesis studies verify Met68 as an important residue in activation of HcpR. Finally, heme binding studies with purified forms of recombinant HcpR support Met68 and His149 residues as important for proper heme coordination in HcpR.

Genetic studies have identified numerous regions associated with plasma fibrinogen levels in Europeans, yet missing heritability and limited inclusion of non-Europeans necessitates further studies with improved power and sensitivity. Compared with array-based genotyping, whole genome sequencing (WGS) data provides better coverage of the genome and better representation of non-European variants. To better understand the genetic landscape regulating plasma fibrinogen levels, we meta-analyzed WGS data from the NHLBI's Trans-Omics for Precision Medicine (TOPMed) program (n=32,572), with array-based genotype data from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium (n=131,340) imputed to the TOPMed or Haplotype Reference Consortium panel. We identified 18 loci that have not been identified in prior genetic studies of fibrinogen. Of these, four are driven by common variants of small effect with reported MAF at least 10 percentage points higher in African populations. Three signals (SERPINA1, ZFP36L2, and TLR10) contain predicted deleterious missense variants. Two loci, SOCS3 and HPN, each harbor two conditionally distinct, non-coding variants. The gene region encoding the fibrinogen protein chain subunits (FGG;FGB;FGA), contains 7 distinct signals, including one novel signal driven by rs28577061, a variant common in African ancestry populations but extremely rare in Europeans (MAFAFR=0.180; MAFEUR=0.008). Through phenome-wide association studies in the VA Million Veteran Program, we found associations between fibrinogen polygenic risk scores and thrombotic and inflammatory disease phenotypes, including an association with gout. Our findings demonstrate the utility of WGS to augment genetic discovery in diverse populations and offer new insights for putative mechanisms of fibrinogen regulation., (Copyright © 2024 American Society of Hematology.)

Inflammation biomarkers can provide valuable insight into the role of inflammatory processes in many diseases and conditions. Sequencing based analyses of such biomarkers can also serve as an exemplar of the genetic architecture of quantitative traits. To evaluate the biological insight, which can be provided by a multi-ancestry, whole-genome based association study, we performed a comprehensive analysis of 21 inflammation biomarkers from up to 38 465 individuals with whole-genome sequencing from the Trans-Omics for Precision Medicine (TOPMed) program (with varying sample size by trait, where the minimum sample size was n = 737 for MMP-1). We identified 22 distinct single-variant associations across 6 traits-E-selectin, intercellular adhesion molecule 1, interleukin-6, lipoprotein-associated phospholipase A2 activity and mass, and P-selectin-that remained significant after conditioning on previously identified associations for these inflammatory biomarkers. We further expanded upon known biomarker associations by pairing the single-variant analysis with a rare variant set-based analysis that further identified 19 significant rare variant set-based associations with 5 traits. These signals were distinct from both significant single variant association signals within TOPMed and genetic signals observed in prior studies, demonstrating the complementary value of performing both single and rare variant analyses when analyzing quantitative traits. We also confirm several previously reported signals from semi-quantitative proteomics platforms. Many of these signals demonstrate the extensive allelic heterogeneity and ancestry-differentiated variant-trait associations common for inflammation biomarkers, a characteristic we hypothesize will be increasingly observed with well-powered, large-scale analyses of complex traits., (© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Competing Interests: Declaration of Conflicting InterestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Synovial Sarcoma (SS) is driven by the SS18::SSX fusion oncoprotein and is ultimately refractory to therapeutic approaches. SS18::SSX alters ATP-dependent chromatin remodeling BAF (mammalian SWI/SNF) complexes, leading to the degradation of canonical (cBAF) complex and amplified presence of an SS18::SSX-containing non-canonical BAF (ncBAF or GBAF) that drives an SS-specific transcription program and tumorigenesis. We demonstrate that SS18::SSX activates the SUMOylation program and SSs are sensitive to the small molecule SAE1/2 inhibitor, TAK-981. Mechanistically, TAK-981 de-SUMOylates the cBAF subunit SMARCE1, stabilizing and restoring cBAF on chromatin, shifting away from SS18::SSX-ncBAF-driven transcription, associated with DNA damage and cell death and resulting in tumor inhibition across both human and mouse SS tumor models. TAK-981 synergized with cytotoxic chemotherapy through increased DNA damage, leading to tumor regression. Targeting the SUMOylation pathway in SS restores cBAF complexes and blocks the SS18::SSX-ncBAF transcriptome, identifying a therapeutic vulnerability in SS, positioning the in-clinic TAK-981 to treat SS., Competing Interests: Additional Declarations: There is NO Competing Interest. DECLARATION OF INTERESTS A.C.F. is a consultant and equity holder in Treeline Biosciences and has previously served as a scientific advisor for AbbVie and has received research funding from IDP Pharma. K.V. receives support from AstraZeneca. R.L. is an inventor of a provisional patent on targeted killing of EBV-positive cancer cells by CRISPR/dCas9-mediated EBV reactivation. S.B. is Consultant for Caris Lifescience and has received honoraria from SpringWorks for an educational lecture. K.V. receives support from AstraZeneca with no relationship to the present study. The authors declare that these listed activities have no relationship to the present study.

Predominantly Western-based biomedical models of successful aging have been used to research, understand, and explain successful aging among diverse populations. With an increasingly heterogeneous older adult population nationwide, scholars have been exploring Indigenous understandings of successful aging. To add to the accumulation of knowledge of diverse Alaska Native populations, this study involved semi-structured qualitative interviews with 20 Unangan Elders from the Aleutian and Pribilof Islands. This community-based participatory research study explores the aging experiences and conceptualization of successful aging of these Elders from this remote and culturally distinct region of Alaska. Thematic analysis was employed to identify themes related to successful aging within this specific region, which supported our previous four themes, or characteristics, of Alaska Native successful aging: physical health, social support and emotional well-being, generativity as a traditional way of life, and community engagement and Inidgenous cultural generativity. Each of these themes or characteristics of Eldership is intertwined and together support successful aging within two remote communities in the Bering Sea. The findings of this study illuminate how Alaska Native Elders can live in geographically diverse regions of the State, yet the values and teachings they possess on successful aging possess the same cultural values and teachings. This study highlighted two new emerging constructs that influence Alaska Native Elders' successful aging based on geographical location. Findings contribute to the thematic saturation of the four main successful aging domains while outlining the importance of future research to conduct deeper investigations into the role of environment and history on Elders' perceptions and understanding of aging., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate as PACER scores for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our mCA fitness estimates, derived by aggregating per-individual PACER scores, were correlated (R 2  = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using population-level distributions of clonal fraction. Among individuals with JAK2 V617F clonal hematopoiesis of indeterminate potential or mCAs affecting the JAK2 gene on chromosome 9, PACER score was strongly correlated with erythrocyte count. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified a TCL1A locus variant associated with mCA clonal expansion rate, with suggestive variants in NRIP1 and TERT., (© 2024. The Author(s).)

Abstract: Coagulation factor VIII (FVIII) and its carrier protein von Willebrand factor (VWF) are critical to coagulation and platelet aggregation. We leveraged whole-genome sequence data from the Trans-Omics for Precision Medicine (TOPMed) program along with TOPMed-based imputation of genotypes in additional samples to identify genetic associations with circulating FVIII and VWF levels in a single-variant meta-analysis, including up to 45 289 participants. Gene-based aggregate tests were implemented in TOPMed. We identified 3 candidate causal genes and tested their functional effect on FVIII release from human liver endothelial cells (HLECs) and VWF release from human umbilical vein endothelial cells. Mendelian randomization was also performed to provide evidence for causal associations of FVIII and VWF with thrombotic outcomes. We identified associations (P < 5 × 10-9) at 7 new loci for FVIII (ST3GAL4, CLEC4M, B3GNT2, ASGR1, F12, KNG1, and TREM1/NCR2) and 1 for VWF (B3GNT2). VWF, ABO, and STAB2 were associated with FVIII and VWF in gene-based analyses. Multiphenotype analysis of FVIII and VWF identified another 3 new loci, including PDIA3. Silencing of B3GNT2 and the previously reported CD36 gene decreased release of FVIII by HLECs, whereas silencing of B3GNT2, CD36, and PDIA3 decreased release of VWF by HVECs. Mendelian randomization supports causal association of higher FVIII and VWF with increased risk of thrombotic outcomes. Seven new loci were identified for FVIII and 1 for VWF, with evidence supporting causal associations of FVIII and VWF with thrombotic outcomes. B3GNT2, CD36, and PDIA3 modulate the release of FVIII and/or VWF in vitro.

Rational design of catalysts relies on a deep understanding of the active centers. The structure and activity distribution of active centers on a surface are two of the central issues in catalysis and important targets of theoretical and experimental investigations. Herein, we report a machine learning-driven adequate sampling (MLAS) framework for obtaining a statistical understanding of the chemical environment near catalyst sites. Combined strategies were implemented to achieve highly efficient sampling, including the decomposition of degrees of freedom, stratified sampling, Gaussian process regression, and well-designed constraint optimization. The MLAS framework was applied to the rate-determining step in NH 3 synthesis, namely the N 2 activation process. We calculated the produced population function, P A , which provides a comprehensive and intuitive understanding of active centers. The MLAS framework can be broadly applied to other more complicated catalyst materials and reaction networks.