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1.
J Am Coll Cardiol ; 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38599256

ABSTRACT

BACKGROUND: In nonobstructive hypertrophic cardiomyopathy (nHCM), there are no approved medical therapies. Impaired myocardial energetics is a potential cause of symptoms and exercise limitation. Ninerafaxstat, a novel cardiac mitotrope, enhances cardiac energetics. OBJECTIVES: To evaluate the safety and efficacy of ninerafaxstat in nHCM. METHODS: Patients with HCM and left ventricular (LV) outflow gradient <30 mmHg, ejection fraction ≥50% and peak VO2 <80% predicted, were randomized to ninerafaxstat 200 mg BID or placebo (1:1) for 12 weeks. Primary endpoint was safety and tolerability with efficacy outcomes also assessed as secondary endpoints. RESULTS: A total of 67 patients with nHCM were enrolled at 12 centers (57 yrs ± 11.8; 55% women). Serious adverse events occurred in 11.8% (4/34) in the ninerafaxstat group and 6.1% of patients (2/33) in placebo. From baseline to 12 weeks, ninerafaxstat was associated with significantly better ventilatory efficiency (VE/VCO2 slope) compared to placebo with a least square (LS) mean difference between the groups of -2.1 (95% CI, -3.4, -0.6; p=0.006), with no significant difference in pVO2 (p=0.9). KCCQ-CCS was directionally though not significantly improved with ninerafaxstat vs. placebo (LS mean, 3.2 [95% CI, -2.9, 9.2; p=0.2]), though was statistically significant when analyzed post-hoc in the 35 patients with baseline KCCQ-CSS ≤80 (LS mean, 9.4 [95% CI, 0.2, 18.5; p=0.04]). CONCLUSIONS: In symptomatic nHCM, novel drug therapy targeting myocardial energetics was safe and well tolerated and associated with better exercise performance and health status among those most symptomatically limited. The findings support assessing ninerafaxstat in a Phase 3 study.

2.
Ultrasound Med Biol ; 49(9): 1996-2005, 2023 09.
Article in English | MEDLINE | ID: mdl-37328385

ABSTRACT

OBJECTIVE: Automated detection of foreshortening, a common challenge in routine 2-D echocardiography, has the potential to improve quality of acquisitions and reduce the variability of left ventricular measurements. Acquiring and labelling the required training data is challenging due to the time-intensive and highly subjective nature of foreshortened apical views. We aimed to develop an automatic pipeline for the detection of foreshortening. To this end, we propose a method to generate synthetic apical-four-chamber (A4C) views with matching ground truth foreshortening labels. METHODS: A statistical shape model of the four chambers of the heart was used to synthesise idealised A4C views with varying degrees of foreshortening. Contours of the left ventricular endocardium were segmented in the images, and a partial least squares (PLS) model was trained to learn the morphological traits of foreshortening. The predictive capability of the learned synthetic features was evaluated on an independent set of manually labelled and automatically curated real echocardiographic A4C images. RESULTS: Acceptable classification accuracy for identification of foreshortened views in the testing set was achieved using logistic regression based on 11 PLS shape modes, with a sensitivity, specificity and area under the receiver operating characteristic curve of 0.84, 0.82 and 0.84, respectively. Both synthetic and real cohorts showed interpretable traits of foreshortening within the first two PLS shape modes, reflected as a shortening in the long-axis length and apical rounding. CONCLUSION: A contour shape model trained only on synthesized A4C views allowed accurate prediction of foreshortening in real echocardiographic images.


Subject(s)
Echocardiography , Heart , Echocardiography/methods , Heart Ventricles/diagnostic imaging , Endocardium , Models, Statistical
3.
Am Heart J ; 263: 123-132, 2023 09.
Article in English | MEDLINE | ID: mdl-37192698

ABSTRACT

BACKGROUND: Stress echocardiography (SE) is one of the most commonly used diagnostic imaging tests for coronary artery disease (CAD) but requires clinicians to visually assess scans to identify patients who may benefit from invasive investigation and treatment. EchoGo Pro provides an automated interpretation of SE based on artificial intelligence (AI) image analysis. In reader studies, use of EchoGo Pro when making clinical decisions improves diagnostic accuracy and confidence. Prospective evaluation in real world practice is now important to understand the impact of EchoGo Pro on the patient pathway and outcome. METHODS: PROTEUS is a randomized, multicenter, 2-armed, noninferiority study aiming to recruit 2,500 participants from National Health Service (NHS) hospitals in the UK referred to SE clinics for investigation of suspected CAD. All participants will undergo a stress echocardiogram protocol as per local hospital policy. Participants will be randomized 1:1 to a control group, representing current practice, or an intervention group, in which clinicians will receive an AI image analysis report (EchoGo Pro, Ultromics Ltd, Oxford, UK) to use during image interpretation, indicating the likelihood of severe CAD. The primary outcome will be appropriateness of clinician decision to refer for coronary angiography. Secondary outcomes will assess other health impacts including appropriate use of other clinical management approaches, impact on variability in decision making, patient and clinician qualitative experience and a health economic analysis. DISCUSSION: This will be the first study to assess the impact of introducing an AI medical diagnostic aid into the standard care pathway of patients with suspected CAD being investigated with SE. TRIAL REGISTRATION: Clinicaltrials.gov registration number NCT05028179, registered on 31 August 2021; ISRCTN: ISRCTN15113915; IRAS ref: 293515; REC ref: 21/NW/0199.


Subject(s)
Coronary Artery Disease , Echocardiography, Stress , Humans , Artificial Intelligence , State Medicine , Coronary Artery Disease/diagnostic imaging , Coronary Angiography/methods
4.
Eur Heart J Open ; 2(5): oeac059, 2022 Sep.
Article in English | MEDLINE | ID: mdl-36284642

ABSTRACT

Aims: To evaluate whether left ventricular ejection fraction (LVEF) and global longitudinal strain (GLS), automatically calculated by artificial intelligence (AI), increases the diagnostic performance of stress echocardiography (SE) for coronary artery disease (CAD) detection. Methods and results: SEs from 512 participants who underwent a clinically indicated SE (with or without contrast) for the evaluation of CAD from seven hospitals in the UK and US were studied. Visual wall motion scoring (WMS) was performed to identify inducible ischaemia. In addition, SE images at rest and stress underwent AI contouring for automated calculation of AI-LVEF and AI-GLS (apical two and four chamber images only) with Ultromics EchoGo Core 1.0. Receiver operator characteristic curves and multivariable risk models were used to assess accuracy for identification of participants subsequently found to have CAD on angiography. Participants with significant CAD were more likely to have abnormal WMS, AI-LVEF, and AI-GLS values at rest and stress (all P < 0.001). The areas under the receiver operating characteristics for WMS index, AI-LVEF, and AI-GLS at peak stress were 0.92, 0.86, and 0.82, respectively, with cut-offs of 1.12, 64%, and -17.2%, respectively. Multivariable analysis demonstrated that addition of peak AI-LVEF or peak AI-GLS to WMS significantly improved model discrimination of CAD [C-statistic (bootstrapping 2.5th, 97.5th percentile)] from 0.78 (0.69-0.87) to 0.83 (0.74-0.91) or 0.84 (0.75-0.92), respectively. Conclusion: AI calculation of LVEF and GLS by contouring of contrast-enhanced and unenhanced SEs at rest and stress is feasible and independently improves the identification of obstructive CAD beyond conventional WMSI.

5.
J Am Soc Echocardiogr ; 35(12): 1226-1237.e7, 2022 12.
Article in English | MEDLINE | ID: mdl-35863542

ABSTRACT

BACKGROUND: Transthoracic echocardiography is the leading cardiac imaging modality for patients admitted with COVID-19, a condition of high short-term mortality. The aim of this study was to test the hypothesis that artificial intelligence (AI)-based analysis of echocardiographic images could predict mortality more accurately than conventional analysis by a human expert. METHODS: Patients admitted to 13 hospitals for acute COVID-19 who underwent transthoracic echocardiography were included. Left ventricular ejection fraction (LVEF) and left ventricular longitudinal strain (LVLS) were obtained manually by multiple expert readers and by automated AI software. The ability of the manual and AI analyses to predict all-cause mortality was compared. RESULTS: In total, 870 patients were enrolled. The mortality rate was 27.4% after a mean follow-up period of 230 ± 115 days. AI analysis had lower variability than manual analysis for both LVEF (P = .003) and LVLS (P = .005). AI-derived LVEF and LVLS were predictors of mortality in univariable and multivariable regression analysis (odds ratio, 0.974 [95% CI, 0.956-0.991; P = .003] for LVEF; odds ratio, 1.060 [95% CI, 1.019-1.105; P = .004] for LVLS), but LVEF and LVLS obtained by manual analysis were not. Direct comparison of the predictive value of AI versus manual measurements of LVEF and LVLS showed that AI was significantly better (P = .005 and P = .003, respectively). In addition, AI-derived LVEF and LVLS had more significant and stronger correlations to other objective biomarkers of acute disease than manual reads. CONCLUSIONS: AI-based analysis of LVEF and LVLS had similar feasibility as manual analysis, minimized variability, and consequently increased the statistical power to predict mortality. AI-based, but not manual, analyses were a significant predictor of in-hospital and follow-up mortality.


Subject(s)
COVID-19 , Ventricular Function, Left , Humans , Stroke Volume , Artificial Intelligence , COVID-19/diagnosis , Echocardiography/methods
6.
Mol Biol Evol ; 39(3)2022 03 02.
Article in English | MEDLINE | ID: mdl-35192718

ABSTRACT

The indigenous population of the United Arab Emirates (UAE) has a unique demographic and cultural history. Its tradition of endogamy and consanguinity is expected to produce genetic homogeneity and partitioning of gene pools while population movements and intercontinental trade are likely to have contributed to genetic diversity. Emiratis and neighboring populations of the Middle East have been underrepresented in the population genetics literature with few studies covering the broader genetic history of the Arabian Peninsula. Here, we genotyped 1,198 individuals from the seven Emirates using 1.7 million markers and by employing haplotype-based algorithms and admixture analyses, we reveal the fine-scale genetic structure of the Emirati population. Shared ancestry and gene flow with neighboring populations display their unique geographic position while increased intra- versus inter-Emirati kinship and sharing of uniparental haplogroups, reflect the endogamous and consanguineous cultural traditions of the Emirates and their tribes.


Subject(s)
Genetic Structures , Genetics, Population , Consanguinity , Geography , Humans , United Arab Emirates
7.
Eur Heart J Cardiovasc Imaging ; 23(5): 689-698, 2022 04 18.
Article in English | MEDLINE | ID: mdl-34148078

ABSTRACT

AIMS: Stress echocardiography is widely used to identify obstructive coronary artery disease (CAD). High accuracy is reported in expert hands but is dependent on operator training and image quality. The EVAREST study provides UK-wide data to evaluate real-world performance and accuracy of stress echocardiography. METHODS AND RESULTS: Participants undergoing stress echocardiography for CAD were recruited from 31 hospitals. Participants were followed up through health records which underwent expert adjudication. Cardiac outcome was defined as anatomically or functionally significant stenosis on angiography, revascularization, medical management of ischaemia, acute coronary syndrome, or cardiac-related death within 6 months. A total of 5131 patients (55% male) participated with a median age of 65 years (interquartile range 57-74). 72.9% of studies used dobutamine and 68.5% were contrast studies. Inducible ischaemia was present in 19.3% of scans. Sensitivity and specificity for prediction of a cardiac outcome were 95.4% and 96.0%, respectively, with an accuracy of 95.9%. Sub-group analysis revealed high levels of predictive accuracy across a wide range of patient and protocol sub-groups, with the presence of a resting regional wall motion abnormalitiy significantly reducing the performance of both dobutamine (P < 0.01) and exercise (P < 0.05) stress echocardiography. Overall accuracy remained consistently high across all participating hospitals. CONCLUSION: Stress echocardiography has high accuracy across UK-based hospitals and thus indicates stress echocardiography is being delivered effectively in real-world practice, reinforcing its role as a first-line investigation in the assessment of patients with stable chest pain.


Subject(s)
Coronary Artery Disease , Echocardiography, Stress , Aged , Chest Pain , Coronary Artery Disease/diagnostic imaging , Dobutamine , Exercise Test , Female , Humans , Male
8.
JACC Cardiovasc Imaging ; 15(5): 715-727, 2022 05.
Article in English | MEDLINE | ID: mdl-34922865

ABSTRACT

OBJECTIVES: The purpose of this study was to establish whether an artificially intelligent (AI) system can be developed to automate stress echocardiography analysis and support clinician interpretation. BACKGROUND: Coronary artery disease is the leading global cause of mortality and morbidity and stress echocardiography remains one of the most commonly used diagnostic imaging tests. METHODS: An automated image processing pipeline was developed to extract novel geometric and kinematic features from stress echocardiograms collected as part of a large, United Kingdom-based prospective, multicenter, multivendor study. An ensemble machine learning classifier was trained, using the extracted features, to identify patients with severe coronary artery disease on invasive coronary angiography. The model was tested in an independent U.S. STUDY: How availability of an AI classification might impact clinical interpretation of stress echocardiograms was evaluated in a randomized crossover reader study. RESULTS: Acceptable classification accuracy for identification of patients with severe coronary artery disease in the training data set was achieved on cross-fold validation based on 31 unique geometric and kinematic features, with a specificity of 92.7% and a sensitivity of 84.4%. This accuracy was maintained in the independent validation data set. The use of the AI classification tool by clinicians increased inter-reader agreement and confidence as well as sensitivity for detection of disease by 10% to achieve an area under the receiver-operating characteristic curve of 0.93. CONCLUSIONS: Automated analysis of stress echocardiograms is possible using AI and provision of automated classifications to clinicians when reading stress echocardiograms could improve accuracy, inter-reader agreement, and reader confidence.


Subject(s)
Coronary Artery Disease , Artificial Intelligence , Coronary Artery Disease/diagnostic imaging , Echocardiography/methods , Humans , Predictive Value of Tests , Prospective Studies
9.
J Am Soc Echocardiogr ; 35(3): 295-304, 2022 03.
Article in English | MEDLINE | ID: mdl-34752928

ABSTRACT

BACKGROUND: COVID-19 infection is known to cause a wide array of clinical chronic sequelae, but little is known regarding the long-term cardiac complications. We aim to report echocardiographic follow-up findings and describe the changes in left (LV) and right ventricular (RV) function that occur following acute infection. METHODS: Patients enrolled in the World Alliance Societies of Echocardiography-COVID study with acute COVID-19 infection were asked to return for a follow-up transthoracic echocardiogram. Overall, 198 returned at a mean of 129 days of follow-up, of which 153 had paired baseline and follow-up images that were analyzable, including LV volumes, ejection fraction (LVEF), and longitudinal strain (LVLS). Right-sided echocardiographic parameters included RV global longitudinal strain, RV free wall strain, and RV basal diameter. Paired echocardiographic parameters at baseline and follow-up were compared for the entire cohort and for subgroups based on the baseline LV and RV function. RESULTS: For the entire cohort, echocardiographic markers of LV and RV function at follow-up were not significantly different from baseline (all P > .05). Patients with hyperdynamic LVEF at baseline (>70%), had a significant reduction of LVEF at follow-up (74.3% ± 3.1% vs 64.4% ± 8.1%, P < .001), while patients with reduced LVEF at baseline (<50%) had a significant increase (42.5% ± 5.9% vs 49.3% ± 13.4%, P = .02), and those with normal LVEF had no change. Patients with normal LVLS (<-18%) at baseline had a significant reduction of LVLS at follow-up (-21.6% ± 2.6% vs -20.3% ± 4.0%, P = .006), while patients with impaired LVLS at baseline had a significant improvement at follow-up (-14.5% ± 2.9% vs -16.7% ± 5.2%, P < .001). Patients with abnormal RV global longitudinal strain (>-20%) at baseline had significant improvement at follow-up (-15.2% ± 3.4% vs -17.4% ± 4.9%, P = .004). Patients with abnormal RV basal diameter (>4.5 cm) at baseline had significant improvement at follow-up (4.9 ± 0.7 cm vs 4.6 ± 0.6 cm, P = .019). CONCLUSIONS: Overall, there were no significant changes over time in the LV and RV function of patients recovering from COVID-19 infection. However, differences were observed according to baseline LV and RV function, which may reflect recovery from the acute myocardial injury occurring in the acutely ill. Left ventricular and RV function tends to improve in those with impaired baseline function, while it tends to decrease in those with hyperdynamic LV or normal RV function.


Subject(s)
COVID-19 , COVID-19/complications , Echocardiography/methods , Follow-Up Studies , Heart Ventricles/diagnostic imaging , Humans , SARS-CoV-2 , Stroke Volume , Ventricular Function, Left , Ventricular Function, Right
10.
Circulation ; 144(7): 559-574, 2021 08 17.
Article in English | MEDLINE | ID: mdl-34162223

ABSTRACT

BACKGROUND: Aging myocardium undergoes progressive cardiac hypertrophy and interstitial fibrosis with diastolic and systolic dysfunction. Recent metabolomics studies shed light on amino acids in aging. The present study aimed to dissect how aging leads to elevated plasma levels of the essential amino acid phenylalanine and how it may promote age-related cardiac dysfunction. METHODS: We studied cardiac structure and function, together with phenylalanine catabolism in wild-type (WT) and p21-/- mice (male; 2-24 months), with the latter known to be protected from cellular senescence. To explore phenylalanine's effects on cellular senescence and ectopic phenylalanine catabolism, we treated cardiomyocytes (primary adult rat or human AC-16) with phenylalanine. To establish a role for phenylalanine in driving cardiac aging, WT male mice were treated twice a day with phenylalanine (200 mg/kg) for a month. We also treated aged WT mice with tetrahydrobiopterin (10 mg/kg), the essential cofactor for the phenylalanine-degrading enzyme PAH (phenylalanine hydroxylase), or restricted dietary phenylalanine intake. The impact of senescence on hepatic phenylalanine catabolism was explored in vitro in AML12 hepatocytes treated with Nutlin3a (a p53 activator), with or without p21-targeting small interfering RNA or tetrahydrobiopterin, with quantification of PAH and tyrosine levels. RESULTS: Natural aging is associated with a progressive increase in plasma phenylalanine levels concomitant with cardiac dysfunction, whereas p21 deletion delayed these changes. Phenylalanine treatment induced premature cardiac deterioration in young WT mice, strikingly akin to that occurring with aging, while triggering cellular senescence, redox, and epigenetic changes. Pharmacological restoration of phenylalanine catabolism with tetrahydrobiopterin administration or dietary phenylalanine restriction abrogated the rise in plasma phenylalanine and reversed cardiac senescent alterations in aged WT mice. Observations from aged mice and human samples implicated age-related decline in hepatic phenylalanine catabolism as a key driver of elevated plasma phenylalanine levels and showed increased myocardial PAH-mediated phenylalanine catabolism, a novel signature of cardiac aging. CONCLUSIONS: Our findings establish a pathogenic role for increased phenylalanine levels in cardiac aging, linking plasma phenylalanine levels to cardiac senescence via dysregulated phenylalanine catabolism along a hepatic-cardiac axis. They highlight phenylalanine/PAH modulation as a potential therapeutic strategy for age-associated cardiac impairment.


Subject(s)
Aging/metabolism , Myocardium/metabolism , Phenylalanine/metabolism , Aging/pathology , Amino Acids/metabolism , Animals , Biomarkers , Biopterins/analogs & derivatives , Biopterins/pharmacology , Catalysis , Cellular Senescence/drug effects , Disease Models, Animal , Disease Susceptibility , Heart Diseases/etiology , Heart Diseases/metabolism , Heart Diseases/pathology , Heart Diseases/physiopathology , Humans , Liver/drug effects , Liver/metabolism , Male , Mice , Mice, Knockout , Models, Biological , Myocardium/pathology , Myocytes, Cardiac/metabolism , Phenylalanine/blood , Rats
11.
J Ethnobiol Ethnomed ; 17(1): 14, 2021 Mar 20.
Article in English | MEDLINE | ID: mdl-33743778

ABSTRACT

BACKGROUND: This is the first comprehensive report on the traditional and novel uses of medicinal plants practiced by the indigenous communities of the Sudhnoti district of Azad Jammu and Kashmir (AJK), Pakistan. The area is rich in folklore and indigenous medicinal knowledge due to a unique tribal composition and socioeconomic conditions. This study aimed to document traditional knowledge of native plant use by the local communities, particularly those used for therapeutic purposes. METHODS: Field surveys were conducted from September 2015 to March 2017. Interviews with 125 local inhabitants of different tribes, age groups, genders, and occupations were conducted using structured and semi-structured questions along with group discussions. Data gathered on plant uses, local names, and modes of application of each plant species were organized in tables. Ethnobotanical indices such as use value (UV) and cultural significance index (CSI) were used to produce quantitative information on the plant use category, frequency, and cultural preference of species. Reports on therapeutic uses of medicinal plants were compared with previous studies. RESULTS: In all, 88 plant species from 45 families were reported, out of which 67 (77%) were used in ethnomedical applications. Asteraceae, Rosaceae, Fabaceae, and Lamiaceae were the dominant families. Berberis lycium was the most valued plant species, followed by Zanthoxylum armatum and Taraxacum officinale. Mentha arvensis had the highest cultural significance, followed by Mentha longifolia, Punica granatum, and Zanthoxylum armatum. Leaves were the most preferred plant parts in the preparation of medicine exclusively or mixed with other parts. The most frequently used process of crude preparation of medicinal plants was cooking. Oral intake was the predominant route of administration. CONCLUSIONS: Our comparative analysis confirmed that most of the plants documented have uses that match those previously reported for the region and other parts of the world, with the exception of novel medicinal uses for 11 plant species, including Verbascum thapsus for earache, Elaeagnus umbellata for hepatitis, Achillea millefolium for oral care, Dicliptera roxburghiana to prevent sunstroke in cattle, Rumex hastatus for allergy antidote, Pyrus pashia for hepatitis, and Nerium oleander for diabetes.


Subject(s)
Ethnopharmacology , Plants, Medicinal , Adult , Aged , Female , Humans , Knowledge , Male , Medicine, Traditional , Middle Aged , Pakistan , Phytotherapy , Plant Preparations/therapeutic use , Plants, Medicinal/classification
12.
Echo Res Pract ; 5(1): G1-G10, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29551755

ABSTRACT

Sudden cardiac death (SCD) in an athlete is a rare but tragic event. In view of this, pre-participation cardiac screening is mandatory across many sporting disciplines to identify those athletes at risk. Echocardiography is a primary investigation utilized in the pre-participation setting and in 2013 the British Society of Echocardiography and Cardiac Risk in the Young produced a joint policy document providing guidance on the role of echocardiography in this setting. Recent developments in our understanding of the athlete's heart and the application of echocardiography have prompted this 2018 update.

14.
Oxf Med Case Reports ; 2015(1): 167-9, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25988068

ABSTRACT

We describe a case of recurrent multivessel coronary stent thrombosis in the absence of the typical hallmarks of this phenomenon: (i) discontinuation or poor compliance with double antiplatelet therapy; (ii) stent malapposition and (iii) stent underexpansion. In this case, the recurrence of stent thrombosis was indeed manifestation of a more complex underlying disease, and eventually allowed the clinicians to come to the final diagnosis of paroxysmal nocturnal haemoglobinuria.

15.
Br J Hosp Med (Lond) ; 75(7): 402-5, 2014 Jul.
Article in English | MEDLINE | ID: mdl-25040520

ABSTRACT

The British Junior Cardiologists' Association surveyed members to analyse their perception and experience of training. Cardiology trainees perceive significant limitations with the current training structure. This article gives suggestions which could lead to improvements in training and patient care.


Subject(s)
Cardiology/education , Clinical Competence , Internal Medicine/education , Accreditation , Adult , Feedback , Female , Humans , Male , Surveys and Questionnaires , United Kingdom
16.
Echo Res Pract ; 1(1): D9-D14, 2014 Sep 01.
Article in English | MEDLINE | ID: mdl-26693292

ABSTRACT

Training in core echocardiography skills within the UK has been the focus of considerable discussion following recent national surveys. This article reports the proceedings of a joint meeting held by the British Society of Echocardiography and British Junior Cardiologists' Association. It considers the current issues impacting on high-quality training and presents potential solutions for the future.

17.
Nature ; 467(7314): 460-4, 2010 Sep 23.
Article in English | MEDLINE | ID: mdl-20827270

ABSTRACT

Combined analyses of gene networks and DNA sequence variation can provide new insights into the aetiology of common diseases that may not be apparent from genome-wide association studies alone. Recent advances in rat genomics are facilitating systems-genetics approaches. Here we report the use of integrated genome-wide approaches across seven rat tissues to identify gene networks and the loci underlying their regulation. We defined an interferon regulatory factor 7 (IRF7)-driven inflammatory network (IDIN) enriched for viral response genes, which represents a molecular biomarker for macrophages and which was regulated in multiple tissues by a locus on rat chromosome 15q25. We show that Epstein-Barr virus induced gene 2 (Ebi2, also known as Gpr183), which lies at this locus and controls B lymphocyte migration, is expressed in macrophages and regulates the IDIN. The human orthologous locus on chromosome 13q32 controlled the human equivalent of the IDIN, which was conserved in monocytes. IDIN genes were more likely to associate with susceptibility to type 1 diabetes (T1D)-a macrophage-associated autoimmune disease-than randomly selected immune response genes (P = 8.85 × 10(-6)). The human locus controlling the IDIN was associated with the risk of T1D at single nucleotide polymorphism rs9585056 (P = 7.0 × 10(-10); odds ratio, 1.15), which was one of five single nucleotide polymorphisms in this region associated with EBI2 (GPR183) expression. These data implicate IRF7 network genes and their regulatory locus in the pathogenesis of T1D.


Subject(s)
Diabetes Mellitus, Type 1/genetics , Genetic Loci/genetics , Genetic Predisposition to Disease/genetics , Immunity, Innate/genetics , Viruses/immunology , Animals , Base Sequence , Chromosomes, Human, Pair 13/genetics , Chromosomes, Mammalian/genetics , Diabetes Mellitus, Type 1/immunology , Gene Regulatory Networks/genetics , Genome-Wide Association Study , Humans , Inflammation/genetics , Inflammation/immunology , Interferon Regulatory Factor-7/immunology , Macrophages/immunology , Macrophages/metabolism , Organ Specificity , Polymorphism, Single Nucleotide/genetics , Quantitative Trait Loci/genetics , Rats , Receptors, G-Protein-Coupled/genetics , Receptors, G-Protein-Coupled/metabolism
18.
PLoS Comput Biol ; 6(4): e1000737, 2010 Apr 08.
Article in English | MEDLINE | ID: mdl-20386736

ABSTRACT

The majority of expression quantitative trait locus (eQTL) studies have been carried out in single tissues or cell types, using methods that ignore information shared across tissues. Although global analysis of RNA expression in multiple tissues is now feasible, few integrated statistical frameworks for joint analysis of gene expression across tissues combined with simultaneous analysis of multiple genetic variants have been developed to date. Here, we propose Sparse Bayesian Regression models for mapping eQTLs within individual tissues and simultaneously across tissues. Testing these on a set of 2,000 genes in four tissues, we demonstrate that our methods are more powerful than traditional approaches in revealing the true complexity of the eQTL landscape at the systems-level. Highlighting the power of our method, we identified a two-eQTL model (cis/trans) for the Hopx gene that was experimentally validated and was not detected by conventional approaches. We showed common genetic regulation of gene expression across four tissues for approximately 27% of transcripts, providing >5 fold increase in eQTLs detection when compared with single tissue analyses at 5% FDR level. These findings provide a new opportunity to uncover complex genetic regulatory mechanisms controlling global gene expression while the generality of our modelling approach makes it adaptable to other model systems and humans, with broad application to analysis of multiple intermediate and whole-body phenotypes.


Subject(s)
Bayes Theorem , Gene Expression Profiling/methods , Gene Expression Regulation/genetics , Models, Genetic , Quantitative Trait Loci , Adipose Tissue/metabolism , Adrenal Glands/metabolism , Algorithms , Animals , Gene Regulatory Networks , Heart Ventricles/metabolism , Humans , Kidney/metabolism , Regression Analysis , Reproducibility of Results , Sensitivity and Specificity
20.
Nat Genet ; 40(5): 546-52, 2008 May.
Article in English | MEDLINE | ID: mdl-18443592

ABSTRACT

Left ventricular mass (LVM) and cardiac gene expression are complex traits regulated by factors both intrinsic and extrinsic to the heart. To dissect the major determinants of LVM, we combined expression quantitative trait locus1 and quantitative trait transcript (QTT) analyses of the cardiac transcriptome in the rat. Using these methods and in vitro functional assays, we identified osteoglycin (Ogn) as a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM. We also applied genome-wide QTT analysis to the human heart and observed that, out of 22,000 transcripts, OGN transcript abundance had the highest correlation with LVM. We further confirmed a role for Ogn in the in vivo regulation of LVM in Ogn knockout mice. Taken together, these data implicate Ogn as a key regulator of LVM in rats, mice and humans, and suggest that Ogn modifies the hypertrophic response to extrinsic factors such as hypertension and aortic stenosis.


Subject(s)
Gene Expression Profiling , Glycoproteins/physiology , Heart Ventricles/anatomy & histology , Hypertrophy, Left Ventricular/genetics , Intercellular Signaling Peptides and Proteins/physiology , Rats/genetics , Animals , Aortic Valve Stenosis/complications , Aortic Valve Stenosis/genetics , Blood Pressure/genetics , Chromosome Mapping , Gene Expression Regulation , Genomics , Glycoproteins/genetics , Heart Ventricles/metabolism , Humans , Hypertension/complications , Hypertension/genetics , Intercellular Signaling Peptides and Proteins/genetics , Mice , Mice, Knockout , Organ Size/genetics , Quantitative Trait Loci , Rats, Mutant Strains
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