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Guan L, Voora D, Myers R, Del Carpio-Cano F, Rao AK. RUNX1 isoforms regulate RUNX1 and target genes differentially in platelets-megakaryocytes: association with clinical cardiovascular events. J Thromb Haemost 2024:S1538-7836(24)00480-X. [PMID: 39181539 DOI: 10.1016/j.jtha.2024.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/18/2024] [Accepted: 07/01/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND Hematopoietic transcription factor RUNX1 is expressed from proximal P2 and distal P1 promoters to yield isoforms RUNX1 B and C, respectively. The roles of these isoforms in RUNX1 autoregulation and downstream gene regulation in megakaryocytes and platelets are unknown. OBJECTIVES To understand the regulation of RUNX1 and its target genes by RUNX1 isoforms. METHODS We performed studies on RUNX1 isoforms in megakaryocytic human erythroleukemia (HEL) cells and HeLa cells (lack endogenous RUNX1), in platelets from 85 healthy volunteers administered aspirin or ticagrelor, and on the association of RUNX1 target genes with acute events in 587 patients with cardiovascular disease (CVD). RESULTS In chromatin immunoprecipitation and luciferase promoter assays, RUNX1 isoforms B and C bound and regulated P1 and P2 promoters. In HeLa cells, RUNX1B decreased and RUNX1C increased P1 and P2 activities, respectively. In HEL cells, RUNX1B overexpression decreased RUNX1C and RUNX1A expression; RUNX1C increased RUNX1B and RUNX1A. RUNX1B and RUNX1C regulated target genes (MYL9, F13A1, PCTP, PDE5A, and others) differentially in HEL cells. In platelets, RUNX1B transcripts (by RNA sequencing) correlated negatively with RUNX1C and RUNX1A; RUNX1C correlated positively with RUNX1A. RUNX1B correlated positively with F13A1, PCTP, PDE5A, RAB1B, and others, and negatively with MYL9. In our previous studies, RUNX1C transcripts in whole blood were protective against acute events in CVD patients. We found that higher expression of RUNX1 targets F13A1 and RAB31 associated with acute events. CONCLUSION RUNX1 isoforms B and C autoregulate RUNX1 and regulate downstream genes in a differential manner, and this is associated with acute events in CVD.
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Affiliation(s)
- Liying Guan
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - Deepak Voora
- Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Rachel Myers
- Duke Clinical Research Unit, Duke University School of Medicine, Durham, North Carolina, USA
| | - Fabiola Del Carpio-Cano
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA
| | - A Koneti Rao
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA; Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania, USA.
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Berger JS, Cornwell MG, Xia Y, Muller MA, Smilowitz NR, Newman JD, Schlamp F, Rockman CB, Ruggles KV, Voora D, Hochman JS, Barrett TJ. A Platelet Reactivity ExpreSsion Score derived from patients with peripheral artery disease predicts cardiovascular risk. Nat Commun 2024; 15:6902. [PMID: 39164233 PMCID: PMC11336089 DOI: 10.1038/s41467-024-50994-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 07/22/2024] [Indexed: 08/22/2024] Open
Abstract
Platelets are key mediators of atherothrombosis, yet, limited tools exist to identify individuals with a hyperreactive platelet phenotype. In this study, we investigate the association of platelet hyperreactivity and cardiovascular events, and introduce a tool, the Platelet Reactivity ExpreSsion Score (PRESS), which integrates platelet aggregation responses and RNA sequencing. Among patients with peripheral artery disease (PAD), those with a hyperreactive platelet response (>60% aggregation) to 0.4 µM epinephrine had a higher incidence of the 30 day primary cardiovascular endpoint (37.2% vs. 15.3% in those without hyperreactivity, adjusted HR 2.76, 95% CI 1.5-5.1, p = 0.002). PRESS performs well in identifying a hyperreactive phenotype in patients with PAD (AUC [cross-validation] 0.81, 95% CI 0.68 -0.94, n = 84) and in an independent cohort of healthy participants (AUC [validation] 0.77, 95% CI 0.75 -0.79, n = 35). Following multivariable adjustment, PAD individuals with a PRESS score above the median are at higher risk for a future cardiovascular event (adjusted HR 1.90, CI 1.07-3.36; p = 0.027, n = 129, NCT02106429). This study derives and validates the ability of PRESS to discriminate platelet hyperreactivity and identify those at increased cardiovascular risk. Future studies in a larger independent cohort are warranted for further validation. The development of a platelet reactivity expression score opens the possibility for a personalized approach to antithrombotic therapy for cardiovascular risk reduction.
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Affiliation(s)
- Jeffrey S Berger
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA.
- Department of Surgery, New York University Langone Health, New York, NY, USA.
| | - Macintosh G Cornwell
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA
| | - Yuhe Xia
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Matthew A Muller
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA
| | - Nathaniel R Smilowitz
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- Cardiology Section, Department of Medicine, Veterans Affairs New York Harbor Health Care System, New York, NY, USA
| | - Jonathan D Newman
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Florencia Schlamp
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Caron B Rockman
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Kelly V Ruggles
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA
| | - Deepak Voora
- Department of Medicine, Duke Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Judith S Hochman
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Tessa J Barrett
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA.
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Guan L, Voora D, Myers R, Del Carpio-Cano F, Rao AK. RUNX1 Isoforms Regulate RUNX1 and Target-Genes Differentially in Platelets-Megakaryocytes: Association with Clinical Cardiovascular Events. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599563. [PMID: 38948740 PMCID: PMC11212995 DOI: 10.1101/2024.06.18.599563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background Hematopoietic transcription factor RUNX1 is expressed from proximal P2 and distal P1 promoter to yield isoforms RUNX1 B and C, respectively. The roles of these isoforms in RUNX1 autoregulation and downstream-gene regulation in megakaryocytes and platelets are unknown. Objectives To understand the regulation of RUNX1 and its target genes by RUNX1 isoforms. Methods We performed studies on RUNX1 isoforms in megakaryocytic HEL cells and HeLa cells (lack endogenous RUNX1), in platelets from 85 healthy volunteers administered aspirin or ticagrelor, and on the association of RUNX1 target genes with acute events in 587 patients with cardiovascular disease (CVD). Results In chromatin immunoprecipitation and luciferase promoter assays, RUNX1 isoforms B and C bound and regulated P1 and P2 promoters. In HeLa cells RUNX1B decreased and RUNX1C increased P1 and P2 activities, respectively. In HEL cells, RUNX1B overexpression decreased RUNX1C and RUNX1A expression; RUNX1C increased RUNX1B and RUNX1A. RUNX1B and RUNX1C regulated target genes (MYL9, F13A1, PCTP, PDE5A and others) differentially in HEL cells. In platelets RUNX1B transcripts (by RNAseq) correlated negatively with RUNX1C and RUNX1A; RUNX1C correlated positively with RUNX1A. RUNX1B correlated positively with F13A1, PCTP, PDE5A, RAB1B, and others, and negatively with MYL9. In our previous studies, RUNX1C transcripts in whole blood were protective against acute events in CVD patients. We found that higher expression of RUNX1 targets F13A1 and RAB31 associated with acute events. Conclusions RUNX1 isoforms B and C autoregulate RUNX1 and regulate downstream genes in a differential manner and this associates with acute events in CVD.
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Affiliation(s)
- Liying Guan
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Deepak Voora
- Department of Medicine, Duke University, Durham, NC
| | - Rachel Myers
- Duke Clinical Research Unit, Duke University School of Medicine, Durham, NC
| | - Fabiola Del Carpio-Cano
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - A. Koneti Rao
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
- Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
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Myers RA, Ortel TL, Waldrop A, Cornwell M, Newman JD, Levy NK, Barrett TJ, Ruggles K, Sowa MA, Dave S, Ginsburg GS, Berger JS, Voora D. Platelet RNA Biomarker of Ticagrelor-Responsive Genes Is Associated With Platelet Function and Cardiovascular Events. Arterioscler Thromb Vasc Biol 2024; 44:423-434. [PMID: 38059352 PMCID: PMC10843550 DOI: 10.1161/atvbaha.123.319759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Identifying patients with the optimal risk:benefit for ticagrelor is challenging. The aim was to identify ticagrelor-responsive platelet transcripts as biomarkers of platelet function and cardiovascular risk. METHODS Healthy volunteers (n=58, discovery; n=49, validation) were exposed to 4 weeks of ticagrelor with platelet RNA data, platelet function, and self-reported bleeding measured pre-/post-ticagrelor. RNA sequencing was used to discover platelet genes affected by ticagrelor, and a subset of the most informative was summarized into a composite score and tested for validation. This score was further analyzed (1) in CD34+ megakaryocytes exposed to an P2Y12 inhibitor in vitro, (2) with baseline platelet function in healthy controls, (3) in peripheral artery disease patients (n=139) versus patient controls (n=30) without atherosclerosis, and (4) in patients with peripheral artery disease for correlation with atherosclerosis severity and risk of incident major adverse cardiovascular and limb events. RESULTS Ticagrelor exposure differentially expressed 3409 platelet transcripts. Of these, 111 were prioritized to calculate a Ticagrelor Exposure Signature score, which ticagrelor reproducibly increased in discovery and validation cohorts. Ticagrelor's effects on platelets transcripts positively correlated with effects of P2Y12 inhibition in primary megakaryocytes. In healthy controls, higher baseline scores correlated with lower baseline platelet function and with minor bleeding while receiving ticagrelor. In patients, lower scores independently associated with both the presence and extent of atherosclerosis and incident ischemic events. CONCLUSIONS Ticagrelor-responsive platelet transcripts are a biomarker for platelet function and cardiovascular risk and may have clinical utility for selecting patients with optimal risk:benefit for ticagrelor use.
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Affiliation(s)
- Rachel A Myers
- Duke Clinical Research Unit, Duke University School of Medicine, Durham NC
| | - Thomas L Ortel
- Departments of Medicine, Duke University Medical Center, Durham NC
| | - Alexander Waldrop
- Departments of Medicine, Duke University Medical Center, Durham NC
- Center for Genomics and Computational Biology, Duke University, Durham, NC
| | - MacIntosh Cornwell
- NYU Grossman School of Medicine, Leon H. Charney Division of Cardiology, New York, NY
| | - Jonathan D. Newman
- NYU Grossman School of Medicine, Leon H. Charney Division of Cardiology, New York, NY
| | - Natalie K Levy
- NYU Grossman School of Medicine, Leon H. Charney Division of Cardiology, New York, NY
| | - Tessa J. Barrett
- NYU Grossman School of Medicine, Leon H. Charney Division of Cardiology, New York, NY
| | - Kelly Ruggles
- NYU Grossman School of Medicine, Leon H. Charney Division of Cardiology, New York, NY
| | - Marcin A Sowa
- NYU Grossman School of Medicine, Leon H. Charney Division of Cardiology, New York, NY
| | - Sandeep Dave
- Departments of Medicine, Duke University Medical Center, Durham NC
- Center for Genomics and Computational Biology, Duke University, Durham, NC
| | | | - Jeffrey S. Berger
- NYU Grossman School of Medicine, Leon H. Charney Division of Cardiology, New York, NY
| | - Deepak Voora
- Departments of Medicine, Duke University Medical Center, Durham NC
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Grgic J. No Pain, No Gain? Examining the Influence of Ibuprofen Consumption on Muscle Hypertrophy. Strength Cond J 2022. [DOI: 10.1519/ssc.0000000000000747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ignatz EH, Hori TS, Kumar S, Benfey TJ, Braden LM, Runighan CD, Westcott JD, Rise ML. RNA-Seq Analysis of the Growth Hormone Transgenic Female Triploid Atlantic Salmon (Salmo salar) Hepatic Transcriptome Reveals Broad Temperature-Mediated Effects on Metabolism and Other Biological Processes. Front Genet 2022; 13:852165. [PMID: 35677560 PMCID: PMC9168996 DOI: 10.3389/fgene.2022.852165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/02/2022] [Indexed: 12/13/2022] Open
Abstract
This study examined the impact of rearing temperature (10.5, 13.5 or 16.5°C) on the hepatic transcriptome of AquAdvantage Salmon (growth hormone transgenic female triploid Atlantic salmon) at an average weight of 800 g. Six stranded PE libraries were Illumina-sequenced from each temperature group, resulting in an average of over 100 M raw reads per individual fish. RNA-sequencing (RNA-seq) results showed the greatest difference in the number of differentially expressed transcripts (1750 DETs), as revealed by both DESeq2 and edgeR (q < 0.05; fold-change > |1.5|), was between the 10.5 and 16.5°C temperature groups. In contrast, 172 and 52 DETs were found in the 10.5 vs. 13.5°C and the 13.5 vs. 16.5°C comparisons, respectively. Considering the DETs between the 10.5 and 16.5°C groups, 282 enriched gene ontology (GO) terms were identified (q < 0.05), including “response to stress”, “immune system process”, “lipid metabolic process”, “oxidation-reduction process”, and “cholesterol metabolic process”, suggesting elevated temperature elicited broad effects on multiple biological systems. Pathway analysis using ClueGO showed additional impacts on amino acid and lipid metabolism. There was a significant positive correlation between RNA-seq and real-time quantitative polymerase chain reaction (RT-qPCR) results for 8 of 9 metabolic-related transcripts tested. RT-qPCR results also correlated to changes in fillet tissue composition previously reported in these salmon (e.g., methionine and lysine concentrations positively correlated with hsp90ab1 transcript expression), suggesting that rearing temperature played a significant role in mediating metabolic/biosynthetic pathways of AquAdvantage Salmon. Many transcripts related to lipid/fatty acid metabolism (e.g., elovl2, fabpi, hacd2, mgll, s27a2, thrsp) were downregulated at 16.5°C compared to both other temperature groups. Additionally, enrichment of stress-, apoptosis- and catabolism-relevant GO terms at 16.5°C suggests that this temperature may not be ideal for commercial production when using freshwater recirculating aquaculture systems (RAS). This study relates phenotypic responses to transcript-specific findings and therefore aids in the determination of an optimal rearing temperature for AquAdvantage Salmon. With approval to grow and sell AquAdvantage Salmon in the United States and Canada, the novel insights provided by this research can help industry expansion by promoting optimal physiological performance and health.
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Affiliation(s)
- Eric H. Ignatz
- Department of Ocean Sciences, Memorial University of Newfoundland and Labrador, St. John’s, NL, Canada
- *Correspondence: Eric H. Ignatz, ; Matthew L. Rise,
| | | | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland and Labrador, St. John’s, NL, Canada
| | - Tillmann J. Benfey
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Laura M. Braden
- AquaBounty Canada, Inc., Souris, PE, Canada
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | | | - Jillian D. Westcott
- Fisheries and Marine Institute, Memorial University of Newfoundland and Labrador, St. John’s, NL, Canada
| | - Matthew L. Rise
- Department of Ocean Sciences, Memorial University of Newfoundland and Labrador, St. John’s, NL, Canada
- *Correspondence: Eric H. Ignatz, ; Matthew L. Rise,
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Friede KA, Myers RA, Gales J, Zhbannikov I, Ortel TL, Shah SH, Kraus WE, Ginsburg GS, Voora D. OUP accepted manuscript. Cardiovasc Res 2022; 119:551-560. [PMID: 35576481 DOI: 10.1093/cvr/cvac079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 04/10/2022] [Accepted: 04/25/2022] [Indexed: 11/14/2022] Open
Abstract
AIMS Gene expression biosignatures may hold promise to individualize antiplatelet therapy in conjunction with current guidelines and risk scores. The Aspirin Response Signature (ARS) score is comprised of a weighted sum of correlated, pro-thrombotic gene transcripts measured in whole blood. In prior work where volunteers were exposed to aspirin 325 mg daily, higher ARS score was associated with lower platelet function; separately, in a clinical cohort of patients, higher ARS scores were associated with increased risk of adverse cardiovascular events. To better understand this apparent paradox, we measured ARS gene expression and score in volunteers to determine aspirin dose-response and ticagrelor relationships with ARS score and separately in patients to assess whether ARS is associated with incident bleeding. METHODS AND RESULTS Blood samples were collected from volunteers (N = 188) who were exposed to 4 weeks of daily aspirin 81 mg, daily aspirin 325 mg, and/or twice-daily ticagrelor 90 mg. ARS scores were calculated from whole blood RNA qPCR, and platelet function and protein expression were assessed in platelet-rich plasma. In mixed linear regression models, aspirin 81 mg exposure was not associated with changes in ARS gene expression or score. Aspirin 325 mg exposure resulted in a 6.0% increase in ARS gene expression (P = 7.5 × 10-9 vs. baseline, P = 2.1 × 10-4 vs. aspirin 81 mg) and an increase in expression of platelet proteins corresponding to ARS genes. Ticagrelor exposure resulted in a 30.7% increase in ARS gene expression (P < 1 × 10-10 vs. baseline and each aspirin dose) and ARS score (P = 7.0 × 10-7 vs. baseline, P = 3.6 × 10-6 and 5.59 × 10-4 vs. aspirin 81 and 325 mg, respectively). Increases in ARS gene expression or score were associated with the magnitude of platelet inhibition across agents. To assess the association between ARS scores and incident bleeding, ARS scores were calculated in patients undergoing cardiac catheterization (N = 1421), of whom 25.4% experienced bleeding events over a median 6.2 years of follow-up. In a Cox model adjusting for demographics and baseline antithrombotic medication use, patients with ARS scores above the median had a higher risk of incident bleeding [hazard ratio 1.26 (95% CI 1.01-1.56), P = 0.038]. CONCLUSIONS The ARS is an Antiplatelet Response Signature that increases in response to greater platelet inhibition due to antiplatelet therapy and may represent a homeostatic mechanism to prevent bleeding. ARS scores could inform future strategies to prevent bleeding while maintaining antiplatelet therapy's benefit of ischaemic cardiovascular event protection.
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Affiliation(s)
- Kevin A Friede
- Center for Applied Genomics & Precision Medicine, Duke University, 101 Science Dr, DUMC 3382, Durham, NC, USA
- Division of Cardiology, Duke University, Durham, NC, USA
| | - Rachel A Myers
- Center for Applied Genomics & Precision Medicine, Duke University, 101 Science Dr, DUMC 3382, Durham, NC, USA
- Division of Cardiology, Duke University, Durham, NC, USA
| | - Jordan Gales
- Department of Cardiology, Texas Heart Institute, Houston, TX, USA
| | - Ilya Zhbannikov
- Center for Applied Genomics & Precision Medicine, Duke University, 101 Science Dr, DUMC 3382, Durham, NC, USA
- Division of Cardiology, Duke University, Durham, NC, USA
| | - Thomas L Ortel
- Division of Hematology, Duke University, Durham, NC, USA
| | - Svati H Shah
- Division of Cardiology, Duke University, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - William E Kraus
- Division of Cardiology, Duke University, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - Geoffrey S Ginsburg
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Deepak Voora
- Center for Applied Genomics & Precision Medicine, Duke University, 101 Science Dr, DUMC 3382, Durham, NC, USA
- Division of Cardiology, Duke University, Durham, NC, USA
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