HiCognition: a visual exploration and hypothesis testing tool for 3D genomics.

Genome browsers facilitate integrated analysis of multiple genomics datasets yet visualize only a few regions at a time and lack statistical functions for extracting meaningful information. We present HiCognition, a visual exploration and machine-learning tool based on a new genomic region set concept, enabling detection of patterns and associations between 3D chromosome conformation and collections of 1D genomics profiles of any type. By revealing how transcription and cohesion subunit isoforms contribute to chromosome conformation, we showcase how the flexible user interface and machine learning tools of HiCognition help to understand the relationship between the structure and function of the genome.

Cohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase.

Genetic information is stored in linear DNA molecules, which are highly folded inside cells. DNA replication along the folded template path yields two sister chromatids that initially occupy the same nuclear region in an intertwined arrangement. Dividing cells must disentangle and condense the sister chromatids into separate bodies such that a microtubule-based spindle can move them to opposite poles. While the spindle-mediated transport of sister chromatids has been studied in detail, the chromosome-intrinsic mechanics presegregating sister chromatids have remained elusive. Here, we show that human sister chromatids resolve extensively already during interphase, in a process dependent on the loop-extruding activity of cohesin, but not that of condensins. Increasing cohesin's looping capability increases sister DNA resolution in interphase nuclei to an extent normally seen only during mitosis, despite the presence of abundant arm cohesion. That cohesin can resolve sister chromatids so extensively in the absence of mitosis-specific activities indicates that DNA loop extrusion is a generic mechanism for segregating replicated genomes, shared across different Structural Maintenance of Chromosomes (SMC) protein complexes in all kingdoms of life.

Effects of percutaneous coronary intervention on dyspnea in stable coronary artery disease.

BACKGROUND: Dyspnea is a frequent symptom in patients with stable coronary artery disease (CAD) and is recognized as a possible angina equivalent. OBJECTIVES: This study was to assess the impact of percutaneous coronary intervention (PCI) on dyspnea, quality of life, and angina pectoris in patients with stable CAD. METHODS: The prospective, multi-center PLA-pCi-EBO-pilot trial included 144 patients with symptomatic stable CAD and successful PCI. The prespecified endpoints angina pectoris (Seattle Angina Questionnaire-SAQ) and dyspnea (NYHA scale) were assessed 6 months after PCI. Predictors for symptomatic improvement were assessed with uni- and multivariable logistic regression analyses. RESULTS: Patients with concomitant dyspnea had worse SAQ physical limitation scores at baseline (49.5 ± 21.0 vs 58.9 ± 22.0, p = 0.013) but showed no difference for angina frequency or quality of life. Overall, symptomatic burden of angina pectoris and dyspnea was alleviated by PCI. However, patients with concomitant dyspnea had markedly worse scores for physical limitation (78.9 ± 25.0 vs 94.3 ± 10.6, p < 0.001), angina frequency (77.9 ± 22.8 vs 91.1 ± 12.4, p < 0.001), and quality of life (69.4 ± 24.1 vs 82.5 ± 14.4, p < 0.001) after PCI. The prevalence of dyspnea (NYHA class ≥ 2) declined from 73% before PCI to 54%. Of 95 initially dyspneic patients, 57 (60%) improved at least one NYHA class 6 months after PCI. In a multivariable logistic regression analysis, "atypical angina pectoris" was associated with improved NYHA class, whereas "diabetes mellitus" had a negative association. CONCLUSION: PCI effectively reduced dyspnea, which is a frequent and demanding symptom in patients with CAD. The German Clinical Trials Register registration number is DRKS0001752 ( www.drks.de ).

A mitotic chromatin phase transition prevents perforation by microtubules.

Dividing eukaryotic cells package extremely long chromosomal DNA molecules into discrete bodies to enable microtubule-mediated transport of one genome copy to each of the newly forming daughter cells1-3. Assembly of mitotic chromosomes involves DNA looping by condensin4-8 and chromatin compaction by global histone deacetylation9-13. Although condensin confers mechanical resistance to spindle pulling forces14-16, it is not known how histone deacetylation affects material properties and, as a consequence, segregation mechanics of mitotic chromosomes. Here we show how global histone deacetylation at the onset of mitosis induces a chromatin-intrinsic phase transition that endows chromosomes with the physical characteristics necessary for their precise movement during cell division. Deacetylation-mediated compaction of chromatin forms a structure dense in negative charge and allows mitotic chromosomes to resist perforation by microtubules as they are pushed to the metaphase plate. By contrast, hyperacetylated mitotic chromosomes lack a defined surface boundary, are frequently perforated by microtubules and are prone to missegregation. Our study highlights the different contributions of DNA loop formation and chromatin phase separation to genome segregation in dividing cells.

Sister chromatid-sensitive Hi-C to map the conformation of replicated genomes.

Chromosome conformation capture (Hi-C) techniques map the 3D organization of entire genomes. How sister chromatids fold in replicated chromosomes, however, cannot be determined with conventional Hi-C because of the identical DNA sequences of sister chromatids. Here, we present a protocol for sister chromatid-sensitive Hi-C (scsHi-C) that enables the distinction of DNA contacts within individual sister chromatids (cis sister contacts) from those between sister chromatids (trans sister contacts), thereby allowing investigation of the organization of replicated genomes. scsHi-C is based on live-cell labeling of nascent DNA by the synthetic nucleoside 4-thio-thymidine (4sT), which incorporates into a distinct DNA strand on each sister chromatid because of semi-conservative DNA replication. After purification of genomic DNA and in situ Hi-C library preparation, 4sT is chemically converted into 5-methyl-cytosine in the presence of OsO4/NH4Cl to introduce T-to-C signature point mutations on 4sT-labeled DNA. The Hi-C library is then sequenced, and ligated fragments are assigned to sister chromatids on the basis of strand orientation and the presence of signature mutations. The ensemble of scsHi-C contacts thereby represents genome-wide contact probabilities within and across sister chromatids. scsHi-C can be completed in 2 weeks, has been successfully applied in HeLa cells and can potentially be established for any cell type that allows proper cell cycle synchronization and incorporation of sufficient amounts of 4sT. The genome-wide maps of replicated chromosomes detected by scsHi-C enable investigation of the molecular mechanisms shaping sister chromatid topologies and the relevance of sister chromatid conformation in crucial processes like DNA repair, mitotic chromosome formation and potentially other biological processes.

Conformation of sister chromatids in the replicated human genome.

The three-dimensional organization of the genome supports regulated gene expression, recombination, DNA repair, and chromosome segregation during mitosis. Chromosome conformation capture (Hi-C)1,2 analysis has revealed a complex genomic landscape of internal chromosomal structures in vertebrate cells3-7, but the identical sequence of sister chromatids has made it difficult to determine how they topologically interact in replicated chromosomes. Here we describe sister-chromatid-sensitive Hi-C (scsHi-C), which is based on labelling of nascent DNA with 4-thio-thymidine and nucleoside conversion chemistry. Genome-wide conformation maps of human chromosomes reveal that sister-chromatid pairs interact most frequently at the boundaries of topologically associating domains (TADs). Continuous loading of a dynamic cohesin pool separates sister-chromatid pairs inside TADs and is required to focus sister-chromatid contacts at TAD boundaries. We identified a subset of TADs that are overall highly paired and are characterized by facultative heterochromatin and insulated topological domains that form separately within individual sister chromatids. The rich pattern of sister-chromatid topologies and our scsHi-C technology will make it possible to investigate how physical interactions between identical DNA molecules contribute to DNA repair, gene expression, chromosome segregation, and potentially other biological processes.

Diagnosis of obstructive coronary artery disease using computed tomography angiography in patients with stable chest pain depending on clinical probability and in clinically important subgroups: meta-analysis of individual patient data.

OBJECTIVE: To determine whether coronary computed tomography angiography (CTA) should be performed in patients with any clinical probability of coronary artery disease (CAD), and whether the diagnostic performance differs between subgroups of patients. DESIGN: Prospectively designed meta-analysis of individual patient data from prospective diagnostic accuracy studies. DATA SOURCES: Medline, Embase, and Web of Science for published studies. Unpublished studies were identified via direct contact with participating investigators. ELIGIBILITY CRITERIA FOR SELECTING STUDIES: Prospective diagnostic accuracy studies that compared coronary CTA with coronary angiography as the reference standard, using at least a 50% diameter reduction as a cutoff value for obstructive CAD. All patients needed to have a clinical indication for coronary angiography due to suspected CAD, and both tests had to be performed in all patients. Results had to be provided using 2×2 or 3×2 cross tabulations for the comparison of CTA with coronary angiography. Primary outcomes were the positive and negative predictive values of CTA as a function of clinical pretest probability of obstructive CAD, analysed by a generalised linear mixed model; calculations were performed including and excluding non-diagnostic CTA results. The no-treat/treat threshold model was used to determine the range of appropriate pretest probabilities for CTA. The threshold model was based on obtained post-test probabilities of less than 15% in case of negative CTA and above 50% in case of positive CTA. Sex, angina pectoris type, age, and number of computed tomography detector rows were used as clinical variables to analyse the diagnostic performance in relevant subgroups. RESULTS: Individual patient data from 5332 patients from 65 prospective diagnostic accuracy studies were retrieved. For a pretest probability range of 7-67%, the treat threshold of more than 50% and the no-treat threshold of less than 15% post-test probability were obtained using CTA. At a pretest probability of 7%, the positive predictive value of CTA was 50.9% (95% confidence interval 43.3% to 57.7%) and the negative predictive value of CTA was 97.8% (96.4% to 98.7%); corresponding values at a pretest probability of 67% were 82.7% (78.3% to 86.2%) and 85.0% (80.2% to 88.9%), respectively. The overall sensitivity of CTA was 95.2% (92.6% to 96.9%) and the specificity was 79.2% (74.9% to 82.9%). CTA using more than 64 detector rows was associated with a higher empirical sensitivity than CTA using up to 64 rows (93.4% v 86.5%, P=0.002) and specificity (84.4% v 72.6%, P<0.001). The area under the receiver-operating-characteristic curve for CTA was 0.897 (0.889 to 0.906), and the diagnostic performance of CTA was slightly lower in women than in with men (area under the curve 0.874 (0.858 to 0.890) v 0.907 (0.897 to 0.916), P<0.001). The diagnostic performance of CTA was slightly lower in patients older than 75 (0.864 (0.834 to 0.894), P=0.018 v all other age groups) and was not significantly influenced by angina pectoris type (typical angina 0.895 (0.873 to 0.917), atypical angina 0.898 (0.884 to 0.913), non-anginal chest pain 0.884 (0.870 to 0.899), other chest discomfort 0.915 (0.897 to 0.934)). CONCLUSIONS: In a no-treat/treat threshold model, the diagnosis of obstructive CAD using coronary CTA in patients with stable chest pain was most accurate when the clinical pretest probability was between 7% and 67%. Performance of CTA was not influenced by the angina pectoris type and was slightly higher in men and lower in older patients. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42012002780.

Renovascular hypertension: endovascular therapy in complicated aortic Stanford type B dissection.

A 63 years old male with a history of arterial hypertension presented with a current onset of chest pain and discrete headaches accompanied with dizziness. His blood pressure, 210/110 mmHg, had worsened and showed a reversed circadian rhythm with an average of 150/90 mmHg during night time. A CT angiography of the aorta demonstrated a type B dissection involving the right renal artery causing reduced perfusion of the right kidney. Subsequent invasive aortic angiography showed a continuously moving aortic dissection flap resulting in a dynamic stenosis proven by varying pressure gradients of between 5 and 35 mmHg. Stent placement of the renal artery ostium kept the vessel open and fixed the reno-aortic dissection flap in order to prevent it from progressing into the right kidney. Follow-up examinations revealed improved blood pressure control allowing for physiologic drop of blood pressure during night-time.

Correction to: Applicability and accuracy of pretest probability calculations implemented in the NICE clinical guideline for decision making about imaging in patients with chest pain of recent onset.

The original version of this article, published on 19 March 2018, unfortunately contained a mistake. The following correction has therefore been made in the original: The names of the authors Philipp A. Kaufmann, Ronny Ralf Buechel and Bernhard A. Herzog were presented incorrectly.

Applicability and accuracy of pretest probability calculations implemented in the NICE clinical guideline for decision making about imaging in patients with chest pain of recent onset.

OBJECTIVES: To analyse the implementation, applicability and accuracy of the pretest probability calculation provided by NICE clinical guideline 95 for decision making about imaging in patients with chest pain of recent onset. METHODS: The definitions for pretest probability calculation in the original Duke clinical score and the NICE guideline were compared. We also calculated the agreement and disagreement in pretest probability and the resulting imaging and management groups based on individual patient data from the Collaborative Meta-Analysis of Cardiac CT (CoMe-CCT). RESULTS: 4,673 individual patient data from the CoMe-CCT Consortium were analysed. Major differences in definitions in the Duke clinical score and NICE guideline were found for the predictors age and number of risk factors. Pretest probability calculation using guideline criteria was only possible for 30.8 % (1,439/4,673) of patients despite availability of all required data due to ambiguity in guideline definitions for risk factors and age groups. Agreement regarding patient management groups was found in only 70 % (366/523) of patients in whom pretest probability calculation was possible according to both models. CONCLUSIONS: Our results suggest that pretest probability calculation for clinical decision making about cardiac imaging as implemented in the NICE clinical guideline for patients has relevant limitations. KEY POINTS: • Duke clinical score is not implemented correctly in NICE guideline 95. • Pretest probability assessment in NICE guideline 95 is impossible for most patients. • Improved clinical decision making requires accurate pretest probability calculation. • These refinements are essential for appropriate use of cardiac CT.

Efficacy of a one-catheter concept for transradial coronary angiography.

INTRODUCTION: Transradial coronary angiography (TRC) can be performed with a one-catheter approach for the right and left coronary ostium (R/LCO). We investigated the performance of a special diagnostic catheter widely used for the one-catheter-approach, the Tiger (Tiger II, TerumoTM). METHODS: In a dual center registry we analyzed 1412 TRC-procedures exclusively performed by experienced TRC-operators. We compared the performance of the Tiger with Judkins catheters by retrospectively judging ostial catheter stability during contrast injection, and by measuring contrast use, fluoroscopy time (FT) and complication rate. RESULTS: Poor or failed ostial engagement was found in 40.5% in the Tiger group, compared to 46.6% with the use of Judkins catheters (p<0.183). Ostial instability of the Tiger was found more often during engagement of the LCO than the RCO (34.4% vs. 10.8%, p<0.001), whereas it was similar in the LCO and RCO for Judkins catheters (27.4% vs. 26.7%, p = 0.840). TRC-procedures performed with Tiger catheters were associated with less contrast volume (63.48 ± 29.83mL vs. 82.51 ± 56.58mL, p<0.004) and shorter FT than with Judkins catheters. (198.27 ± 194.8sec vs. 326.85 ± 329.70sec). Forearm hematomas occurred less often with the Tiger (1.2% vs. 6.6%, p< 0.02). CONCLUSION: The Tiger employed as a single catheter in TRC is an effective tool to achieve lower contrast volume and fluoroscopy time at a low complication rate. Unstable engagement affects predominantly the left coronary artery, but its overall frequency is similar for both, the Tiger and Judkins catheters.

Transradial Coronary Angiography--Insights to the One-Catheter Concept.

Transradial coronary angiography (TRC) can be performed applying only one catheter fitting into the right and left coronary ostia (R/LCO). In this bicentric study (n = 2953), we analyzed the ostial performance of the Tiger_II_catheter widely used in TRC. Compared to Judkins catheters, the Tiger_II is frequently associated with ostial instability within the LCO but fits better into the RCO-irrespective of tube size. Judkins catheters generally need more peri-procedural contrast and radiation exposure. TRC may be started using a 5F_Tiger_II on the right side in order to be switched to 5F Judkins in case of propable LCO instability.

Myocardial Fibrosis in Hypertrophic Cardiomyopathy: Volumetric Assessment of Late Enhancement Provided by Cardiac Computed Tomography.

INTRODUCTION: With subgroups of patients with hypertrophic cardiomyopathy (HCM) confers a 4% to 5% risk for adverse prognosis. Besides left-ventricular muscle mass (LV-MM) myocardial fibrosis (MF) assessable by late gadolinium enhancement in cardiovascular magnetic resonance (LGE-CMR) has been related to that. Myocardial fibrosis can also be demonstrated by late enhancement (LE) in late-enhanced multislice computed tomography (leMDCT). This analysis investigates leMDCT whether to enable quantification of LE load in terms of LE mass by percent LV-MM in HCM. METHODS: In a prospective validation study, we included 30 consecutive patients with HCM who underwent leMDCT (64 slice) and LGE-CMR (1.5 T). The leMDCT scan was performed 7 minutes after injection of iodine contrast (Iopromid). Endocardial and epicardial planimetry served for the assessment of LV-MM. Visually detectable LE was quantified using the manual quantification method resulting in LE by percent LV-MM (%LE). The LGE-CMR data served for validation. RESULTS: Mean (SD) age was 64.1 (13.9) years. Myocardial fibrosis prevalence was 63.3% (19/30 patients indentified by both leMDCT and LGE-CMR). In leMDCT, tissue density in LE areas compared with normal myocardium was higher (138.2 [23.9] HU vs 98.4 [16.5] HU, P < 0.001) but lower than in the LV cavity (138.2 [23.9] HU vs 169.2 [35.9] HU, P < 0.001). Late enhancement mass in leMDCT seemed to be 7.9 (8.5) g LE versus 8.6 [11] g LGE in CMR (P = 0.497, r = 0.95) resulting in a leMDCT/LGE-CMR relation of 1.2. Referring LE mass to LV-MM gave an LE proportion measured by leMDCT of 4 (3.9) %LE versus 3.9 (4.1) %LGE in LGE-CMR (r = 0.88, P = 0.75). Intraobserver/interobserver reliability of LE mass assessment showed an intraclass correlation coefficient of 0.99 and 0.97. CONCLUSIONS: In patients with HCM, leMDCT provides volumetric assessment of LE mass-absolutely and by percent LV-MM.

Late enhanced computed tomography in Hypertrophic Cardiomyopathy enables accurate left-ventricular volumetry.

OBJECTIVES: Late enhancement (LE) multi-slice computed tomography (leMDCT) was introduced for the visualization of (intra-) myocardial fibrosis in Hypertrophic Cardiomyopathy (HCM). LE is associated with adverse cardiac events. This analysis focuses on leMDCT derived LV muscle mass (LV-MM) which may be related to LE resulting in LE proportion for potential risk stratification in HCM. METHODS: N=26 HCM-patients underwent leMDCT (64-slice-CT) and cardiovascular magnetic resonance (CMR). In leMDCT iodine contrast (Iopromid, 350 mg/mL; 150mL) was injected 7 minutes before imaging. Reconstructed short cardiac axis views served for planimetry. The study group was divided into three groups of varying LV-contrast. LeMDCT was correlated with CMR. RESULTS: The mean age was 64.2 ± 14 years. The groups of varying contrast differed in weight and body mass index (p < 0.05). In the group with good LV-contrast assessment of LV-MM resulted in 147.4 ± 64.8 g in leMDCT vs. 147.1 ± 65.9 in CMR (p > 0.05). In the group with sufficient contrast LV-MM appeared with 172 ± 30.8 g in leMDCT vs. 165.9 ± 37.8 in CMR (p > 0.05). Overall intra-/inter-observer variability of semiautomatic assessment of LV-MM showed an accuracy of 0.9 ± 8.6 g and 0.8 ± 9.2 g in leMDCT. All leMDCT-measures correlated well with CMR (r > 0.9). CONCLUSIONS: LeMDCT primarily performed for LE-visualization in HCM allows for accurate LV-volumetry including LV-MM in > 90% of the cases. KEY POINTS: • LeMDCT of relatively low contrast allows for LV planimetry in HCM. • The correlation of leMDCT-based LV volumetry with gold-standard CMR was excellent (r > 0.9). • LeMDCT requires approximately 2.0mL/kgBW of dye to achieve acceptable contrast.

Very large left atrial myxoma: an unusual differential diagnosis of bronchial hyper-reactivity.

Intra- and paracardiac tumors are rare. Clinical symptoms are typically secondary to mechanical effects of the mass. We describe a patient, who was in good general health, presenting with a 6-month history of unspecific symptoms considered consistent with reccurrent lower airway infections by her primary care physician. A chest X-ray suggested left-atrial enlargement and a questionable mass, which eventually was identified as large left-atrial tumor partially obstructing the mitral orifice. The case demonstrates that even a very large left-atrial tumor, causing intermittent partial obstruction of the mitral valve may present with mild unspecific symptoms.

Elite athletes with mitral or aortic regurgitation and their cardiopulmonary capability.

BACKGROUND: Aortic or mitral valvular regurgitation (left cardiac valvular regurgitation, LCVR) of less than second-degree (< degree II) occasionally found in competitive athletes is of questionable relevance. Precisely detectable by echocardiography there is scarce published data that clarifies cardiopulmonary capacity or any limitations LCVR < degree ll may cause. METHODS: In this single-centre study we consecutively recruited highly trained athletes (n= 14) with LCVR < degree ll detected in 2D echo. Not included were athletes with multi- or right-cardiac valvular dysfunction and structural heart disease other than bicuspid aortic valve or mitral valve prolaps. Target parameters were determined by 2D echo and spiroergometry. RESULTS: There were no significant differences with regard to age and body mass index. Echocardiographically determined muscle mass index was increased in both groups (134 14.7 vs 129.6+/-27.5; P=0.69), whereas the left-ventricular end-diastolic diameter index was significant higher in the LCVR < degree II group (27.3 +/- 1.3 vs 25.2 +/- 2.4; P = 0.04). However, there were no significant differences with regard to (oxygen uptake) V02, at baseline (athletes with LCVR < degree II 5.7 +/- 0.9 vs controls 5 +/- 0.96, P= 0.06), at the anaerobic threshold (athletes with LCVR < degree II 47.3 +/-8.4 vs controls 47.4 +/- 5, P= 0.97) and maximally (VO2max; athletes with LCVR < degree II 57.7 6.3 vs controls 57.1 +/- 5.1, P= 0.81). Neither levels of lactate nor of brain natriuretic peptide differed significantly. CONCLUSION: High level athletes presenting with aortic or mitral regurgitation < degree II in are not disadvantaged with regard to their cardiopulmonary capability.