An antiplatelet response gene expression signature is associated with bleeding
Deepak Voora, William Kraus, Svati Shah and colleagues developed a gene expression based score, the Antiplatelet Response Signature (ARS), measured in whole blood samples that is increased by aspirin and ticagrelor. ARS and other similar gene expression scores may inform future strategies to personalize antithrombotic therapy to balance bleeding and ischemic risk.
Single Cell RNA-Seq Analysis of Human Red Cells
Ashley Chi, Simon Gregory and team performed single red cell RNA-seq of circulating red blood cells from three healthy donors that had been storied for one or 15 days and found that the expression pattern of single red blood cells separates into distinct cellular clusters. Their results show new insights into gene expression regulation and heterogeneity among red blood cells.
Myoblast deactivation within engineered human skeletal muscle creates a transcriptionally heterogeneous population of quiescent satellite-like cells
Nenad Bursac, Yarui Diao and colleagues investigated the specific roles that muscle fibers, a critical niche constituent, have in human satellite cell maintenance and injury-induced activation by utilizing human myobundles made from purified myogenic cells.
Serum metabolomic analysis of men on a low-carbohydrate diet for biochemically recurrent prostate cancer reveals the potential role of ketogenesis to slow tumor growth: A secondary analysis of the CAPS2 diet trial
Ashley Chi and colleagues investigated the effect a low-carbohydrate diet had on prostate cancer growth using both animal models and participants in the Carbohydrate and Prostate Study 2 (CAPS2) clinical study.
Modulation of microbial community dynamics by spatial partitioning
Lingchong You, Lawrence David and team investigated spatial partitioning of microbial communities and its effects on biodiversity. Their results reveal a general mechanism underlying the maintenance of microbial diversity and have implications for natural and engineered communities.
The preference for sugar over sweetener depends on a gut sensor cell
Diego Bohorquez and colleagues discovered that cholecystokinin (CCK)-labeled duodenal neuropod cells can tell the difference between sugars and artificial sweeteners. They showed that preference for sugar over sweetener in mice depends on neuropod cell glutamatergic signaling. By swiftly discerning the precise identity of nutrient stimuli, gut neuropod cells serve as the entry point to guide nutritive choices.
Steroid-sensitive nephrotic syndrome candidate gene CLVS1 regulates podocyte oxidative stress and endocytosis
Rasheed Gbadegesin, Gentzon Hall, Alejandro Ochoa and colleagues performed next generation sequencing in patients with familiar steroid sensitive nephrotic syndrome, a common pediatric kidney disease that is responsive to steroids. They identified a homozygous segregating variant in the gene encoding clavesin-1 in a family with three affected individuals.
Role of DNA methylation on the association between physical activity and cardiovascular diseases: Results from the longitudinal multi-ethnic study of atherosclerosis (MESA) cohort
Yongmei Liu and colleagues used the Multi-Ethnic Study of Atherosclerosis (MESA) cohort to examine the role of DNA methylation on the association between physical activity and cardiovascular disease.
Repurposing cancer drugs identifies kenpaullone which ameliorates pathologic pain in preclinical models via normalization of inhibitory neurotransmission
Ru-Rong Ji and colleagues surveyed the "junkyard of cancer drugs" that might have the potential to be repurposed to aid in chronic pain and discovered that kenpaullone and similarly-acting kinase-inhibitory compounds, as well as delta-CAT gene therapy, have the potential to become new tools in our toolbox against chronic refractory pain, including nerve injury pain and cancer bone pain, and likely against other forms of chronic pain.
Bevacizumab-induced hypertension and proteinuria: a genome-wide study of 1000+ patients
Kouros Owzar was part of a team that conducted a GWAS meta-analysis on 1039 patients of European ancestry who have been treated with bevacizumab, a medication used to treat a number of types of cancers. This is the largest study of bevacizumab toxicity and it provides new markers of drug safety for further evaluation.
Predictions of primate–parasite coextinction
Charlie Nunn worked with Duke professors James Herrera and James Moody to analyze potential effects on parasite existence and biodiversity if primates threatened with extinction go extinct.
Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy
Matthew Kelly, Sweta Patel, John Rawls and colleagues studied the nasopharyngeal microbiomes of 179 mother-infant dyads in Botswana. They examined changes in microbiome diversity and composition during infancy, evaluated associations between the nasopharyngeal microbiome and pneumococcal colonization risk, and identified environmental factors that influence nasopharyngeal microbiome composition during infancy.
Circadian clock, carcinogenesis, chronochemotherapy connections
David Hsu collaborated with UNC Chapel Hill to investigate sites of DNA damage and repair following anti-cancer drug treatments. They mapped these sites genome wide at single nucleotide resolution and as a function of circadian time. This data might help provide valuable information for creating rational chronochemotherapy regimens.
Circulating long chain acylcarnitines and outcomes in diabetic heart failure
James Bain, Chris Newgard, William Kraus, Robert McGarrah, Svati and team used metabolomic profiling to identify biomarkers that report on exercise capacity, clinical outcomes and differential response to exercise in heart failure patients with and without diabetes mellitus.
Altered skeletal muscle metabolic pathways, age, systemic inflammation, and low cardiorespiratory fitness associate with improvements in disease activity following HIIT in persons with RA
William Kraus, David Bartlett, Kim Huffman and team identified connections between skeletal muscle molecular pathways, rheumatoid arthritis (RA) disease activity, and RA disease activity improvements following high intensity interval training.
Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity
William Kraus and Svati Shah were part of a large collaboration that sequenced over 640,000 exomes from people in the US, UK and Mexico to estimate associations of rare coding variants with body mass index (BMI). They found that inhibiting GPR75 may be a therapeutic strategy for obesity.
Genome-Wide Variants Associated With Longitudinal Survival Outcomes Among Individuals With Coronary Artery Disease
William Kraus, Elizabeth Hauser, Carol Haynes and team used a genome-wide screening approach to identify gene variants associated with all-cause mortality among individuals with clinically phenotyped coronary artery disease.
Metabolomic profiling identifies complex lipid species and amino acid analogues associated with response to weight loss interventions
Laura Svetkey, Chris Newgard, William Kraus and Svati Shah worked to identify metabolic biomarkers associated with beneficial metabolic changes to weight loss that identify individuals with obesity who would most benefit from a given type of intervention.
An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility
A team at Duke featuring Ricardo Henao, Micah McClain, Ephraim Tsalik, Geoff Ginsburg, Xiling Shen, Chris Woods, Beth Hauser and Dennis Ko created an interactive web database that helps explore and quickly analyze user-uploaded GWAS summary statistics. The database generated novel hypotheses to explain the pathophysiology of common diseases.
Three-dimensional tissue-engineered human skeletal muscle model of Pompe disease
Nenad Bursac, Dwight Koeberl, Priya Kishnani and team developed a 3-D model of infantile-onset Pompe disease that demonstrates the signature pathological features of the disease.
Mucosal Associated Invariant T Cell Responses Differ by Sex in COVID-1
A collaboration including Ephraim Tsalik, Micah McClain, Chris Woods, Xilng Shen and other Duke faculty carried out sex-balanced sampling of peripheral blood mononuclear cells from confirmed 30 COVID-19 inpatients and outpatients, uninfected close contacts, and healthy controls for 36- 31 color flow cytometry and single cell RNA-sequencing.
A Rare Autosomal Dominant Variant in Regulator of Calcineurin Type 1 (RCAN1) Gene Confers Enhanced Calcineurin Activity and May Cause FSGS
Nephrotic syndrome (NS) is a kidney disorder that causes the body to pass too much protein in its urine. Rasheed Gbadegesin and team conducted whole-genome sequencing on 320 individuals of unclear genetic etiology and analyzed data from several patient cohorts to gain insight into the genetic architecture of the condition.
CHG Bathing Reduces Number of Bloodstream Infections in Adults Undergoing Inpatient Hematopoietic Cell Transplantation
Anthony Sung, Julia Messina, Sin-Ho Jung, Li Ma and team conducted a prospective cohort study with historical controls to assess the impact of chlorhexidine gluconate bathing on the rate of bloodstream infections and gut microbiota composition among adults undergoing inpatient HCT at the Duke University Medical Center.
Clinical implementation of an oncology‐specific family health history risk assessment tool
Ryanne Wu, Geoff Ginsburg, Lori Orlando and colleagues used MeTree, a patient-facing family health history risk assessment platform, in a pilot study to test its impact in an oncology setting.
In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration
Ken Poss and team used a transgenic BioID2 strategy to capture cell-specific proteome changes in cardiomyocytes during heart regeneration in adult zebrafish.
Benchmarking DNA isolation kits used in analyses of the urinary microbiome
Cindy Amundsen and Nazema Siddiqui collaborated with Oregon Health and Science University and the University of Alabama in Huntsville to compare the performance of several DNA isolation kits used in microbiome studies to see if recovered microbes identified by 16S rRNA sequencing differ based on the DNA isolation protocol.
Alterations in acylcarnitines, amines, and lipids inform about the mechanism of action of citalopram/escitalopram in major depression
The Proteomics & Metabolomics Core Facility and Jessica Tennenbaum were part of a large collaboration that used a targeted metabolomics approach utilizing a panel of 180 metabolites to gain insights into mechanisms of action and response to certain SSRIs used to treat major depressive disorder.
The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights
Raphael Valdivia, Lawrence David, Holly Dressman, Christopher Newgard, Svati Shah and John Rawls and team analyzed clinical, metabolomic and microbiome samples from adolescents with obesity as they undergo lifestyle modifications.
Efficacy of metformin and fermentable fiber combination therapy in adolescents with severe obesity and insulin resistance
Christopher Newgard and Michael Freemark are part of an international team that is comparing metabolic effects of metformin and fermentable fibers in combination with those of metformin or fiber alone in adolescents with obesity. They will also determine if therapeutic responses correlate with compositional and functional features of the gut microbiome.
Mutational processes in cancer preferentially affect binding of particular transcription factors
Raluca Gordan collaborated with Duke-NUS to develop the "Signature-QBiC" model that integrates signature profiles of mutational processes with the QBiC estimates of changes in binding affinity to investigate the effect of mutational signatures on the binding of 582 human transcription factors.
Genome-wide analysis identifies novel susceptibility loci for myocardial infarction
William Kraus and Beth Hauser were part of a large international team that performed GWAS studies for myocardial infarction to see if genetic factors that establish atherosclerosis may be distinct from those that predispose to vulnerable plaques and thrombus formation.
Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence
Paul Magwene, Joseph Heitman and team describe the genetic architecture of six traits in C. deneoformans and then used GWAS function-valued QTL mapping to identify genetic differences that underlie variation in those six traits. Their work illustrates the complex effects that variants may have with respect to virulence potential.
Validation of a host gene expression test for bacterial/viral discrimination in immunocompromised hosts
Several members from the Duke Center for Applied Genomics and Precision Medicine collaborated on a study that evaluated the performance of a host gene expression test to discriminate bacterial, viral, and noninfectious illness in immunocompromised patients. Although test performance was marginally lower than in immunocompetent patients, this approach may provide useful diagnostic information in this high-risk population.
Investigating the genetic architecture of noncognitive skills using GWAS-by-subtraction
Avshalom Caspi and Terrie Moffitt were part of a large, international team that used genetic correlation and polygenic score analysis to test if noncognitive skills influence educational and economic attainments and longevity and to investigate traits and behaviors that constitute noncognitive skills. They also conducted hypothesis-free bioinformatic annotation analysis with help from the Genomic Analysis & Bioinformatic core facility to explore the tissues, cell types and brain structures that might distinguish the biology of noncognitive skills from the biology mediating cognitive influences on educational attainment.
Digital Health—The Need to Assess Benefits, Risks, and Value
Geoff Ginsburg, along with Eric Perakslis, published a viewpoint in JAMA about the potential for digital health -- wearable and internal devices, sensors in people, homes, communities and more -- to improve health management. However, the current state of technology development and deployment requires a "buyer beware" cautionary note. Ginsburg was also interviewed by JAMA editor-in-chief Dr. Howard Bauchner.
Air Pollution May Hasten Aging
A collaboration with DMPI, the departments of Biostatistics and Bioinformatics and Psychiatry and Behavorial Sciences, the division of Cardiology, UNC Chapel Hill, Georgia Tech, Durham VA, and EPA found that epigenetic age acceleration may be a biomarker of sensitivity to air pollution, especially traffic-related air pollution in urban cohorts. This research shows a new way to understand sensitivity to air pollution and provides a molecular measure of environmental sensitivity.
Modeling statin myopathy in a human skeletal muscle microphysiological system
Deepak Voora led a collaboration between the Center for Applied Genomics and Precision Medicine and the Department of Biomedical Engineering that developed a "muscle on a chip" platform to study the effects of statin associated musculoskeletal symptoms.
CRISPR dCas9 used to program pluripotent stem cells into adult neuronal cells
A team of researchers at Duke University led by Dr. Charlie Gersbach has developed a new method to discover gene regulatory networks for programming stem cells to become any cell type. Their work, published today in Cell Reports, demonstrates the potential of the approach in making mature adult neuronal cells, but is broadly applicable.
RT-PCR-based 36-gene signature performance over time
Researchers in the Center for Applied Genomics and Precision Medicine assessed the ability of transcriptomic biomarkers to identify naturally acquired respiratory viral infection before symptoms appear.
Novel Murine Models of Cerebral Cavernous Malformations
Doug Marchuk and team developed a genetic mouse model of cerebral cavernous malformations.
Identification of Undetected Monogenic Cardiovascular Disorders
A collaboration between DMPI, Division of Cardiology, Center for Applied Genomics and Precision Medicine as well as Regeneron Genetics Center and Vanderbilt Medical Center shows the large burden of undetected monogenetic cardiovascular disorders.