Blood cells contain functionally important intracellular structures, such as granules, critical to immunity and thrombosis. Quantitative variation in these structures has not been subjected ...previously to large-scale genetic analysis. We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. We identify 2172 distinct variant-trait associations, including associations near genes coding for proteins in organelles implicated in inflammatory and thrombotic diseases. By integrating with epigenetic data we show that many intracellular structures are likely to be determined in immature precursor cells. By integrating with proteomic data we identify the transcription factor FOG2 as an early regulator of platelet formation and α-granularity. Finally, we show that colocalisation of our associations with disease risk signals can suggest aetiological cell-types-variants in IL2RA and ITGA4 respectively mirror the known effects of daclizumab in multiple sclerosis and vedolizumab in inflammatory bowel disease.
Inflammation drives atherosclerotic plaque rupture. Although inflammation can be measured using fluorine-18-labeled fluorodeoxyglucose positron emission tomography (
FFDG PET),
FFDG lacks cell ...specificity, and coronary imaging is unreliable because of myocardial spillover.
This study tested the efficacy of gallium-68-labeled DOTATATE (
Ga-DOTATATE), a somatostatin receptor subtype-2 (SST
)-binding PET tracer, for imaging atherosclerotic inflammation.
We confirmed
Ga-DOTATATE binding in macrophages and excised carotid plaques.
Ga-DOTATATE PET imaging was compared to
FFDG PET imaging in 42 patients with atherosclerosis.
Target SSTR2 gene expression occurred exclusively in "proinflammatory" M1 macrophages, specific
Ga-DOTATATE ligand binding to SST
receptors occurred in CD68-positive macrophage-rich carotid plaque regions, and carotid SSTR2 mRNA was highly correlated with in vivo
Ga-DOTATATE PET signals (r = 0.89; 95% confidence interval CI: 0.28 to 0.99; p = 0.02).
Ga-DOTATATE mean of maximum tissue-to-blood ratios (mTBR
) correctly identified culprit versus nonculprit arteries in patients with acute coronary syndrome (median difference: 0.69; interquartile range IQR: 0.22 to 1.15; p = 0.008) and transient ischemic attack/stroke (median difference: 0.13; IQR: 0.07 to 0.32; p = 0.003).
Ga-DOTATATE mTBR
predicted high-risk coronary computed tomography features (receiver operating characteristics area under the curve ROC AUC: 0.86; 95% CI: 0.80 to 0.92; p < 0.0001), and correlated with Framingham risk score (r = 0.53; 95% CI: 0.32 to 0.69; p <0.0001) and
FFDG uptake (r = 0.73; 95% CI: 0.64 to 0.81; p < 0.0001).
FFDG mTBR
differentiated culprit from nonculprit carotid lesions (median difference: 0.12; IQR: 0.0 to 0.23; p = 0.008) and high-risk from lower-risk coronary arteries (ROC AUC: 0.76; 95% CI: 0.62 to 0.91; p = 0.002); however, myocardial
FFDG spillover rendered coronary
FFDG scans uninterpretable in 27 patients (64%). Coronary
Ga-DOTATATE PET scans were readable in all patients.
We validated
Ga-DOTATATE PET as a novel marker of atherosclerotic inflammation and confirmed that
Ga-DOTATATE offers superior coronary imaging, excellent macrophage specificity, and better power to discriminate high-risk versus low-risk coronary lesions than
FFDG. (Vascular Inflammation Imaging Using Somatostatin Receptor Positron Emission Tomography VISION; NCT02021188).
Long-range interactions between regulatory elements and gene promoters play key roles in transcriptional regulation. The vast majority of interactions are uncharted, constituting a major missing link ...in understanding genome control. Here, we use promoter capture Hi-C to identify interacting regions of 31,253 promoters in 17 human primary hematopoietic cell types. We show that promoter interactions are highly cell type specific and enriched for links between active promoters and epigenetically marked enhancers. Promoter interactomes reflect lineage relationships of the hematopoietic tree, consistent with dynamic remodeling of nuclear architecture during differentiation. Interacting regions are enriched in genetic variants linked with altered expression of genes they contact, highlighting their functional role. We exploit this rich resource to connect non-coding disease variants to putative target promoters, prioritizing thousands of disease-candidate genes and implicating disease pathways. Our results demonstrate the power of primary cell promoter interactomes to reveal insights into genomic regulatory mechanisms underlying common diseases.
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•High-resolution maps of promoter interactions in 17 human primary blood cell types•Interaction patterns are cell type specific and segregate with the hematopoietic tree•Promoter-interacting regions enriched for regulatory chromatin features and eQTLs•Promoter interactions link non-coding GWAS variants with putative target genes
This study deploys a promoter capture Hi-C approach in 17 primary blood cell types to match collaborating regulatory regions and identify genes regulated by noncoding disease-associated variants. Explore this and other papers at the Cell Press IHEC webportal at http://www.cell.com/consortium/IHEC.
This work is aimed at improving the understanding of cardiometabolic syndrome pathophysiology and its relationship with thrombosis by generating a multi-omic disease signature.
We combined classic ...plasma biochemistry and plasma biomarkers with the transcriptional and epigenetic characterisation of cell types involved in thrombosis, obtained from two extreme phenotype groups (morbidly obese and lipodystrophy) and lean individuals to identify the molecular mechanisms at play, highlighting patterns of abnormal activation in innate immune phagocytic cells. Our analyses showed that extreme phenotype groups could be distinguished from lean individuals, and from each other, across all data layers. The characterisation of the same obese group, 6 months after bariatric surgery, revealed the loss of the abnormal activation of innate immune cells previously observed. However, rather than reverting to the gene expression landscape of lean individuals, this occurred via the establishment of novel gene expression landscapes. NETosis and its control mechanisms emerge amongst the pathways that show an improvement after surgical intervention.
We showed that the morbidly obese and lipodystrophy groups, despite some differences, shared a common cardiometabolic syndrome signature. We also showed that this could be used to discriminate, amongst the normal population, those individuals with a higher likelihood of presenting with the disease, even when not displaying the classic features.
The interindividual variation in the functional response of platelets to activation by agonists is heritable. Genome-wide association studies (GWASs) of quantitative measures of platelet function ...have identified fewer than 20 distinctly associated variants, some with unknown mechanisms. Here, we report GWASs of pathway-specific functional responses to agonism by adenosine 5′-diphosphate, a glycoprotein VI–specific collagen mimetic, and thrombin receptor-agonist peptides, each specific to 1 of the G protein–coupled receptors PAR-1 and PAR-4, in subsets of 1562 individuals. We identified an association (P = 2.75 × 10−40) between a common intronic variant, rs10886430, in the G protein–coupled receptor kinase 5 gene (GRK5) and the sensitivity of platelets to activate through PAR-1. The variant resides in a megakaryocyte-specific enhancer that is bound by the transcription factors GATA1 and MEIS1. The minor allele (G) is associated with fewer GRK5 transcripts in platelets and the greater sensitivity of platelets to activate through PAR-1. We show that thrombin-mediated activation of human platelets causes binding of GRK5 to PAR-1 and that deletion of the mouse homolog Grk5 enhances thrombin-induced platelet activation sensitivity and increases platelet accumulation at the site of vascular injury. This corroborates evidence that the human G allele of rs10886430 is associated with a greater risk for cardiovascular disease. In summary, by combining the results of pathway-specific GWASs and expression quantitative trait locus studies in humans with the results from platelet function studies in Grk5−/− mice, we obtain evidence that GRK5 regulates the human platelet response to thrombin via the PAR-1 pathway.
•Platelet reactivity via the PAR-1 thrombin receptor is mediated by GRK5.•Platelet GRK5 is associated with thrombus formation in humans and mice.
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Background Inflammation drives atherosclerotic plaque rupture. Although inflammation can be measured using fluorine-18-labeled fluorodeoxyglucose positron emission tomography (18FFDG PET), 18FFDG ...lacks cell specificity, and coronary imaging is unreliable because of myocardial spillover. Objectives This study tested the efficacy of gallium-68-labeled DOTATATE (68Ga-DOTATATE), a somatostatin receptor subtype-2 (SST2)-binding PET tracer, for imaging atherosclerotic inflammation. Methods We confirmed68Ga-DOTATATE binding in macrophages and excised carotid plaques.68Ga-DOTATATE PET imaging was compared to 18FFDG PET imaging in 42 patients with atherosclerosis. Results TargetSSTR2gene expression occurred exclusively in “proinflammatory” M1 macrophages, specific68Ga-DOTATATE ligand binding to SST2receptors occurred in CD68-positive macrophage-rich carotid plaque regions, and carotidSSTR2mRNA was highly correlated with in vivo68Ga-DOTATATE PET signals (r = 0.89; 95% confidence interval CI: 0.28 to 0.99; p = 0.02).68Ga-DOTATATE mean of maximum tissue-to-blood ratios (mTBRmax) correctly identified culprit versus nonculprit arteries in patients with acute coronary syndrome (median difference: 0.69; interquartile range IQR: 0.22 to 1.15; p = 0.008) and transient ischemic attack/stroke (median difference: 0.13; IQR: 0.07 to 0.32; p = 0.003).68Ga-DOTATATE mTBRmaxpredicted high-risk coronary computed tomography features (receiver operating characteristics area under the curve ROC AUC: 0.86; 95% CI: 0.80 to 0.92; p < 0.0001), and correlated with Framingham risk score (r = 0.53; 95% CI: 0.32 to 0.69; p <0.0001) and 18FFDG uptake (r = 0.73; 95% CI: 0.64 to 0.81; p < 0.0001). 18FFDG mTBRmaxdifferentiated culprit from nonculprit carotid lesions (median difference: 0.12; IQR: 0.0 to 0.23; p = 0.008) and high-risk from lower-risk coronary arteries (ROC AUC: 0.76; 95% CI: 0.62 to 0.91; p = 0.002); however, myocardial 18FFDG spillover rendered coronary 18FFDG scans uninterpretable in 27 patients (64%). Coronary68Ga-DOTATATE PET scans were readable in all patients. Conclusions We validated68Ga-DOTATATE PET as a novel marker of atherosclerotic inflammation and confirmed that68Ga-DOTATATE offers superior coronary imaging, excellent macrophage specificity, and better power to discriminate high-risk versus low-risk coronary lesions than 18FFDG. (Vascular Inflammation Imaging Using Somatostatin Receptor Positron Emission Tomography VISION;NCT02021188)
Inflammation drives atherosclerotic plaque rupture. Although inflammation can be measured using fluorine-18-labeled fluorodeoxyglucose positron emission tomography (18FFDG PET), 18FFDG lacks cell ...specificity, and coronary imaging is unreliable because of myocardial spillover.
This study tested the efficacy of gallium-68-labeled DOTATATE (68Ga-DOTATATE), a somatostatin receptor subtype-2 (SST2)-binding PET tracer, for imaging atherosclerotic inflammation.
We confirmed 68Ga-DOTATATE binding in macrophages and excised carotid plaques. 68Ga-DOTATATE PET imaging was compared to 18FFDG PET imaging in 42 patients with atherosclerosis.
Target SSTR2 gene expression occurred exclusively in “proinflammatory” M1 macrophages, specific 68Ga-DOTATATE ligand binding to SST2 receptors occurred in CD68-positive macrophage-rich carotid plaque regions, and carotid SSTR2 mRNA was highly correlated with in vivo 68Ga-DOTATATE PET signals (r = 0.89; 95% confidence interval CI: 0.28 to 0.99; p = 0.02). 68Ga-DOTATATE mean of maximum tissue-to-blood ratios (mTBRmax) correctly identified culprit versus nonculprit arteries in patients with acute coronary syndrome (median difference: 0.69; interquartile range IQR: 0.22 to 1.15; p = 0.008) and transient ischemic attack/stroke (median difference: 0.13; IQR: 0.07 to 0.32; p = 0.003). 68Ga-DOTATATE mTBRmax predicted high-risk coronary computed tomography features (receiver operating characteristics area under the curve ROC AUC: 0.86; 95% CI: 0.80 to 0.92; p < 0.0001), and correlated with Framingham risk score (r = 0.53; 95% CI: 0.32 to 0.69; p <0.0001) and 18FFDG uptake (r = 0.73; 95% CI: 0.64 to 0.81; p < 0.0001). 18FFDG mTBRmax differentiated culprit from nonculprit carotid lesions (median difference: 0.12; IQR: 0.0 to 0.23; p = 0.008) and high-risk from lower-risk coronary arteries (ROC AUC: 0.76; 95% CI: 0.62 to 0.91; p = 0.002); however, myocardial 18FFDG spillover rendered coronary 18FFDG scans uninterpretable in 27 patients (64%). Coronary 68Ga-DOTATATE PET scans were readable in all patients.
We validated 68Ga-DOTATATE PET as a novel marker of atherosclerotic inflammation and confirmed that 68Ga-DOTATATE offers superior coronary imaging, excellent macrophage specificity, and better power to discriminate high-risk versus low-risk coronary lesions than 18FFDG. (Vascular Inflammation Imaging Using Somatostatin Receptor Positron Emission Tomography VISION; NCT02021188)
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Abstract Background Inflammation drives atherosclerotic plaque rupture. Although inflammation can be measured using fluorine-18-labeled fluorodeoxyglucose positron emission tomography (18 FFDG PET), ...18 FFDG lacks cell specificity, and coronary imaging is unreliable because of myocardial spillover. Objectives This study tested the efficacy of gallium-68-labeled DOTATATE (68 Ga-DOTATATE), a somatostatin receptor subtype-2 (SST2 )-binding PET tracer, for imaging atherosclerotic inflammation. Methods We confirmed68 Ga-DOTATATE binding in macrophages and excised carotid plaques.68 Ga-DOTATATE PET imaging was compared to 18 FFDG PET imaging in 42 patients with atherosclerosis. Results Target SSTR2 gene expression occurred exclusively in “proinflammatory” M1 macrophages, specific68 Ga-DOTATATE ligand binding to SST2 receptors occurred in CD68-positive macrophage-rich carotid plaque regions, and carotid SSTR2 mRNA was highly correlated with in vivo68 Ga-DOTATATE PET signals (r = 0.89; 95% confidence interval CI: 0.28 to 0.99; p = 0.02).68 Ga-DOTATATE mean of maximum tissue-to-blood ratios (mTBRmax ) correctly identified culprit versus nonculprit arteries in patients with acute coronary syndrome (median difference: 0.69; interquartile range IQR: 0.22 to 1.15; p = 0.008) and transient ischemic attack/stroke (median difference: 0.13; IQR: 0.07 to 0.32; p = 0.003).68 Ga-DOTATATE mTBRmax predicted high-risk coronary computed tomography features (receiver operating characteristics area under the curve ROC AUC: 0.86; 95% CI: 0.80 to 0.92; p < 0.0001), and correlated with Framingham risk score (r = 0.53; 95% CI: 0.32 to 0.69; p <0.0001) and 18 FFDG uptake (r = 0.73; 95% CI: 0.64 to 0.81; p < 0.0001). 18 FFDG mTBRmax differentiated culprit from nonculprit carotid lesions (median difference: 0.12; IQR: 0.0 to 0.23; p = 0.008) and high-risk from lower-risk coronary arteries (ROC AUC: 0.76; 95% CI: 0.62 to 0.91; p = 0.002); however, myocardial 18 FFDG spillover rendered coronary 18 FFDG scans uninterpretable in 27 patients (64%). Coronary68 Ga-DOTATATE PET scans were readable in all patients. Conclusions We validated68 Ga-DOTATATE PET as a novel marker of atherosclerotic inflammation and confirmed that68 Ga-DOTATATE offers superior coronary imaging, excellent macrophage specificity, and better power to discriminate high-risk versus low-risk coronary lesions than 18 FFDG. (Vascular Inflammation Imaging Using Somatostatin Receptor Positron Emission Tomography VISION; NCT02021188 )
New minimal invasive diagnostic methods for early detection of lung cancer are urgently needed. It is known that the immune system responds to tumors with production of tumor-autoantibodies. Protein ...microarrays are a suitable highly multiplexed platform for identification of autoantibody signatures against tumor-associated antigens (TAA). These microarrays can be probed using 0.1 mg immunoglobulin G (IgG), purified from 10 µL of plasma. We used a microarray comprising recombinant proteins derived from 15,417 cDNA clones for the screening of 100 lung cancer samples, including 25 samples of each main histological entity of lung cancer, and 100 controls. Since this number of samples cannot be processed at once, the resulting data showed non-biological variances due to "batch effects". Our aim was to evaluate quantile normalization, "distance-weighted discrimination" (DWD), and "ComBat" for their effectiveness in data pre-processing for elucidating diagnostic immune‑signatures. "ComBat" data adjustment outperformed the other methods and allowed us to identify classifiers for all lung cancer cases versus controls and small-cell, squamous cell, large-cell, and adenocarcinoma of the lung with an accuracy of 85%, 94%, 96%, 92%, and 83% (sensitivity of 0.85, 0.92, 0.96, 0.88, 0.83; specificity of 0.85, 0.96, 0.96, 0.96, 0.83), respectively. These promising data would be the basis for further validation using targeted autoantibody tests.
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