C-terminal Domain of T4 gene 32 Protein Enables Rapid Filament Reorganization and Dissociation

Bacteriophage T4 gene 32 protein (gp32) is a single-stranded DNA (ssDNA) binding protein essential for DNA replication. gp32 forms stable protein filaments on ssDNA through cooperative interactions between its core and N-terminal domain. gp32's C-terminal domain (CTD) is believed to primarily help coordinate DNA replication via direct interactions with constituents of the replisome. However, the exact mechanisms of these interactions are not known, and it is unclear how tightly-bound gp32 filaments are readily displaced from ssDNA as required for genomic processing. Here, we utilized truncated gp32 variants to demonstrate a key role of the CTD in regulating gp32 dissociation. Using optical tweezers, we probed the binding and dissociation dynamics of CTD-truncated gp32, *I, to an 8.1 knt ssDNA molecule and compared these measurements with those for full-length gp32. The *I-ssDNA helical filament becomes progressively unwound with increased protein concentration but remains significantly more stable than that of full-length, wild-type gp32. Protein oversaturation, concomitant with filament unwinding, facilitates rapid dissociation of full-length gp32 from across the entire ssDNA segment. In contrast, *I primarily unbinds slowly from only the ends of the cooperative clusters, regardless of the protein density and degree of DNA unwinding. Our results suggest that the CTD may constrain the relative twist angle of proteins within the ssDNA filament such that upon critical unwinding the cooperative interprotein interactions largely vanish, facilitating prompt removal of gp32. We propose a model of CTD-mediated gp32 displacement via internal restructuring of its filament, providing a mechanism for rapid ssDNA clearing during genomic processing.

HIV-1 uncoating requires long double-stranded reverse transcription products

HIV-1 cores, which contain the viral genome and replication machinery, must disassemble (uncoat) during viral replication. However, the viral and host factors that trigger uncoating remain unidentified. Recent studies show that infectious cores enter the nucleus and uncoat near the site of integration. Here, we show that efficient uncoating of nuclear cores requires synthesis of a double-stranded DNA (dsDNA) genome >3.5 kb and that the efficiency of uncoating correlates with genome size. Core disruption by capsid inhibitors releases viral DNA, some of which integrates. However, most of the viral DNA is degraded, indicating that the intact core safeguards viral DNA. Atomic force microscopy and core content estimation reveal that synthesis of full-length genomic dsDNA induces substantial internal strain on the core to promote uncoating. We conclude that HIV-1 cores protect viral DNA from degradation by host factors and that synthesis of long double-stranded reverse transcription products is required to trigger efficient HIV-1 uncoating.

Mechanism of DNA Intercalation by Chloroquine Provides Insights into Toxicity

Chloroquine has been used as a potent antimalarial, anticancer drug, and prophylactic. While chloroquine is known to interact with DNA, the details of DNA-ligand interactions have remained unclear. Here we characterize chloroquine-double-stranded DNA binding with four complementary approaches, including optical tweezers, atomic force microscopy, duplex DNA melting measurements, and isothermal titration calorimetry. We show that chloroquine intercalates into double stranded DNA (dsDNA) with a KD ~ 200 µM, and this binding is entropically driven. We propose that chloroquine-induced dsDNA intercalation, which happens in the same concentration range as its observed toxic effects on cells, is responsible for the drug's cytotoxicity.

Quantifying ATP-Independent Nucleosome Chaperone Activity with Single-Molecule Methods

The dynamics of histone-DNA interactions govern chromosome organization and regulates the processes of transcription, replication, and repair. Accurate measurements of the energies and the kinetics of DNA binding to component histones of the nucleosome under a variety of conditions are essential to understand these processes at the molecular level. To accomplish this, we employ three specific single-molecule techniques: force disruption (FD) with optical tweezers, confocal imaging (CI) in a combined fluorescence plus optical trap, and survival probability (SP) measurements of disrupted and reformed nucleosomes. Short arrays of positioned nucleosomes serve as a template for study, facilitating rapid quantification of kinetic parameters. These arrays are then exposed to FACT (FAcilitates Chromatin Transcription), a non-ATP-driven heterodimeric nuclear chaperone known to both disrupt and tether histones during transcription. FACT binding drives off the outer wrap of DNA and destabilizes the histone-DNA interactions of the inner wrap as well. This reorganization is driven by two key domains with distinct function. FD experiments show the SPT16 MD domain stabilizes DNA-histone contacts, while the HMGB box of SSRP1 binds DNA, destabilizing the nucleosome. Surprisingly, CI experiments do not show tethering of disrupted histones, but increased rates of histone release from the DNA. SI experiments resolve this, showing that the two active domains of FACT combine to chaperone nucleosome reassembly after the timely release of force. These combinations of single-molecule approaches show FACT is a true nucleosome catalyst, lowering the barrier to both disruption and reformation.

DNA damage alters binding conformations of E. coli single-stranded DNA-binding protein

Single-stranded DNA-binding proteins (SSBs) are essential cellular components, binding to transiently exposed regions of single-stranded DNA (ssDNA) with high affinity and sequence non-specificity to coordinate DNA repair and replication. Escherichia coli SSB (EcSSB) is a homotetramer that wraps variable lengths of ssDNA in multiple conformations (typically occupying either 65 or 35 nt), which is well studied across experimental conditions of substrate length, salt, pH, temperature, etc. In this work, we use atomic force microscopy to investigate the binding of SSB to individual ssDNA molecules. We introduce non-canonical DNA bases that mimic naturally occurring DNA damage, synthetic abasic sites, as well as a non-DNA linker into our experimental constructs at sites predicted to interact with EcSSB. By measuring the fraction of DNA molecules with EcSSB bound as well as the volume of protein bound per DNA molecule, we determine the protein binding affinity, cooperativity, and conformation. We find that, with only one damaged nucleotide, the binding of EcSSB is unchanged relative to its binding to undamaged DNA. In the presence of either two tandem abasic sites or a non-DNA spacer, however, the binding affinity associated with a single EcSSB tetramer occupying the full substrate in the 65-nt mode is greatly reduced. In contrast, the binding of two EcSSB tetramers, each in the 35-nt mode, is preserved. Changes in the binding and cooperative behaviors of EcSSB across these constructs can inform how genomic repair and replication processes may change as environmental damage accumulates in DNA.

Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes

The histone chaperone FACT (facilitates chromatin transcription) enhances transcription in eukaryotic cells, targeting DNA-protein interactions. FACT, a heterodimer in humans, comprises SPT16 and SSRP1 subunits. We measure nucleosome stability and dynamics in the presence of FACT and critical component domains. Optical tweezers quantify FACT/subdomain binding to nucleosomes, displacing the outer wrap of DNA, disrupting direct DNA-histone (core site) interactions, altering the energy landscape of unwrapping, and increasing the kinetics of DNA-histone disruption. Atomic force microscopy reveals nucleosome remodeling, while single-molecule fluorescence quantifies kinetics of histone loss for disrupted nucleosomes, a process accelerated by FACT. Furthermore, two isolated domains exhibit contradictory functions; while the SSRP1 HMGB domain displaces DNA, SPT16 MD/CTD stabilizes DNA-H2A/H2B dimer interactions. However, only intact FACT tethers disrupted DNA to the histones and supports rapid nucleosome reformation over several cycles of force disruption/release. These results demonstrate that key FACT domains combine to catalyze both nucleosome disassembly and reassembly.

Left versus right: Exploring the effects of chiral threading intercalators using optical tweezers

Small-molecule DNA-binding drugs have shown promising results in clinical use against many types of cancer. Understanding the molecular mechanisms of DNA binding for such small molecules can be critical in advancing future drug designs. We have been exploring the interactions of ruthenium-based small molecules and their DNA-binding properties that are highly relevant in the development of novel metal-based drugs. Previously we have studied the effects of the right-handed binuclear ruthenium threading intercalator ΔΔ-[μ-bidppz(phen)4Ru2]4+, or ΔΔ-P for short, which showed extremely slow kinetics and high-affinity binding to DNA. Here we investigate the left-handed enantiomer ΛΛ-[μ-bidppz(phen)4Ru2]4+, or ΛΛ-P for short, to study the effects of chirality on DNA threading intercalation. We employ single-molecule optical trapping experiments to understand the molecular mechanisms and nanoscale structural changes that occur during DNA binding and unbinding as well as the association and dissociation rates. Despite the similar threading intercalation binding mode of the two enantiomers, our data show that the left-handed ΛΛ-P complex requires increased lengthening of the DNA to thread, and it extends the DNA more than double the length at equilibrium compared with the right-handed ΔΔ-P. We also observed that the left-handed ΛΛ-P complex unthreads three times faster than ΔΔ-P. These results, along with a weaker binding affinity estimated for ΛΛ-P, suggest a preference in DNA binding to the chiral enantiomer having the same right-handed chirality as the DNA molecule, regardless of their common intercalating moiety. This comparison provides a better understanding of how chirality affects binding to DNA and may contribute to the development of enhanced potential cancer treatment drug designs.

18F-sodium fluoride positron emission tomography and coronary plaque radiomics derived from computed tomography angiography for prediction of myocardial infarction

Background

Assessments of coronary disease activity with 18F-sodium fluoride positron emission tomography (18F-NaF PET) and radiomics-based precision coronary plaque phenotyping derived from contrast-enhanced computed tomography (CT) have both been shown to enhance risk stratification in patients with coronary artery disease (CAD). To date, no study has investigated whether these two promising methods (which can be obtained during a single imaging session on a hybrid PET/CT scanner) are interchangeable or can provide superior predictive performance when used in combination.

Purpose

We sought to investigate whether the prognostic information provided by latent morphological radiomic coronary plaque features and assessments of disease activity by 18F-NaF PET are complementary in prediction of myocardial infarction.

Methods

Patients with known CAD underwent coronary 18F-NaF PET and CT angiography on a hybrid PET/CT scanner. Coronary 18F-NaF uptake was determined by the coronary microcalcification activity (CMA). We performed quantitative plaque analysis of coronary CT angiography datasets. Additionally, coronary plaque segmentations on CT angiography were used to extract 1103 radiomic features. Using weighted correlation network analysis we derived latent morphological features of coronary plaques which were aggregated to patient-level radiomic normograms to predict myocardial infarction using univariate and multivariate Cox proportional hazard models.

Results

The study cohort comprised of 260 patients with established CAD (age: 65±9 years; 84% men); 179 (69%) participants showed increased coronary 18F-NaF activity (CMA >0). Over 53 [40–59] months of follow-up 18 patients had a myocardial infarction. Using weighted correlation network analysis, from the 1103 radiomic features we derived 15 distinct eigen radiomic features representing latent morphological coronary plaque patterns. On univariate cox modelling 7 of these emerged as predictors of myocardial infarction (Figure). Following adjustments for calcified, noncalcified and low-density noncalcified plaque volumes and 18F-NaF CMA 4 radiomic features (related to texture and geometry) remained independent predictors of myocardial infarction (Figure).

Conclusion(s)

In patients with established CAD latent morphological features of coronary plaques are predictors of myocardial infarction above and beyond plaque volumes and 18F-NaF uptake. Comprehensive plaque analysis with radiomics may enhance risk stratification of CAD patients.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): NIH, Wellcome Trust

Unsupervised machine learning improves risk stratification of patients with visual normal SPECT myocardial perfusion imaging assessments

Background

Unsupervised machine learning has the potential to identify new cardiovascular phenotypes and more accurately assess individual risk in an unbiased fashion.

Purpose

We aimed to use unsupervised learning to identify, analyze, and risk-stratify subgroups of patients with normal perfusion by visual interpretation on single-photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI).

Methods

We included consecutive patients with visual normal clinical assessment (summed stress score of 0) from the multicenter (9 sites), REFINE SPECT registry. We considered 23 clinical, 17 image-acquisition, and 26 imaging variables. Optimal dimensionality reduction (Uniform Manifold Approximation and Projection), clustering (Gaussian Mixture Model), and number of clusters were selected to maximize the silhouette coefficient (how similar a patient is to those in their own cluster compared to other clusters). Risk stratification for all-cause mortality (ACM) and major adverse cardiac events (MACE) was assessed within these clusters and compared to risk stratification by quantitative ischemia (<5%, 5–10%, >10%) using Kaplan-Meier curves and Cox Proportional-Hazards analysis.

Results

In total, 17,527 (of 30,351) patients in the registry had visually normal perfusion, 49.7% female, median age of 64 [55, 72] years. There were 1,138 ACM events and 2,091 MACE events with a median follow-up of 4.1 [2.9, 5.7] years. Unsupervised learning provided better risk stratification for both ACM and MACE compared to quantitative ischemia (Figure). Notably, the high-risk cluster by unsupervised learning had a hazard ratio (HR) of 9.5 (95% confidence interval [CI]: 7.7–11.7) compared to 1.4 (95% CI: 1.1–1.9) for quantitative ischemia >10%. The high-risk cluster had proportionally more women (45% [low-risk], 51% [medium-risk], 57% [high-risk], all p<0.001), higher body mass indices (26.9, 27.4, 29.6, all p<0.001), prevalence of diabetes (17%, 22%, 33%, all p<0.001), and abnormal rest ECGs (30%, 43%, 64%, p<0.001); with lower rates of family history of coronary artery disease (40%, 33%, 24%, p<0.001). Patients in the low-risk cluster were more likely to undergo exercise stress (100%, 38%, 0%, all p<0.001), had lower rest peak systolic blood pressure (130, 131, 140 mmHg, all p<0.001), and higher stress peak systolic blood pressure (164, 150, 131 mmHg, all p<0.001). Patients in the high-risk cluster had higher left ventricular mass (129, 135.45, 143.9 g, all p<0.001) and stress volume (57, 59, 66 ml, all p<0.001).

Conclusion

Unsupervised learning identified new phenotypic clusters for SPECT MPI patients with visual normal assessments which provided improved risk stratification for ACM and MACE compared to SPECT ischemia. Such individualized risk assessment may allow better targeted management of patients with visually normal perfusion.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): Research reported in this publication was supported by the National Heart, Lung, And Blood Institute of the National Institutes of Health under Award Number R01HL089765. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

HIV-1 Nucleocapsid Protein Binds Double-Stranded DNA in Multiple Modes to Regulate Compaction and Capsid Uncoating

The HIV-1 nucleocapsid protein (NC) is a multi-functional protein necessary for viral replication. Recent studies have demonstrated reverse transcription occurs inside the fully intact viral capsid and that the timing of reverse transcription and uncoating are correlated. How a nearly 10 kbp viral DNA genome is stably contained within a narrow capsid with diameter similar to the persistence length of double-stranded (ds) DNA, and the role of NC in this process, are not well understood. In this study, we use optical tweezers, fluorescence imaging, and atomic force microscopy to observe NC binding a single long DNA substrate in multiple modes. We find that NC binds and saturates the DNA substrate in a non-specific binding mode that triggers uniform DNA self-attraction, condensing the DNA into a tight globule at a constant force up to 10 pN. When NC is removed from solution, the globule dissipates over time, but specifically-bound NC maintains long-range DNA looping that is less compact but highly stable. Both binding modes are additionally observed using AFM imaging. These results suggest multiple binding modes of NC compact DNA into a conformation compatible with reverse transcription, regulating the genomic pressure on the capsid and preventing premature uncoating.

In vivo coronary artery thrombus imaging with 18F-GP1 PET-CT

Background

Coronary artery thrombus is typically present in type 1 myocardial infarction, but small volumes in the setting of an uncertain culprit lesion may be beyond the detection limit of current imaging modalities.

Purpose

Using a novel glycoprotein IIb/IIIa-receptor radiotracer, 18F-GP1, we investigated whether positron emission tomography-computed tomography (PET-CT) could detect thrombus formation in coronary arteries.

Methods

In a single centre cross-sectional study, patients over 40 years of age with myocardial infarction were recruited after myocardial infarction and underwent underwent CT angiography and 18F-GP1 PET-CT. Stable patients with and without coronary artery disease formed a control cohort. Coronary artery 18F-GP1 uptake was visually assessed and quantified using maximum target-to-background ratios (TBRmax).

Results

Ninety-four (44 post-myocardial infarction and 50 control patients) were included in the cross-sectional analysis. The mean age of the post-myocardial infarction group was 61±9 years, three-quarters were male and two thirds had presented with ST elevation on electrocardiography. 34 (80%) patients post-myocardial infarction, but none of the control patients, demonstrated focal 18F-GP1 uptake in the coronary arteries.

Of 42 vessels with an angiographic culprit lesion, 35 (83%) had 18F-GP1 uptake which was significantly higher than non-culprit vessels (p<0.0001) as well as control vessels (p<0.0001), while non-culprit vessel uptake was similar to control vessel uptake (p=0.567): culprit vessel median TBRmax 1.2 [interquartile range 0.96–1.44], non-culprit vessel TBRmax 0.96 [0.84–1.03] and control vessel TBRmax 0.9 [0.76 to 0.94]. Linear regression models demonstrated univariable associations between coronary 18F-GP1 TBRmax and time from myocardial infarction, male sex and presence of culprit vessel. On multivariable analysis, only culprit vessel status was associated with TBRmax (adjusted R2= 0.22, P<0.001). Based on the Youden's index of the ROC curves, the optimal cut-off of predicting the presence of a culprit vessel was 1.20 with a specificity of 97%, accuracy of 83%, sensitivity (60%) and c-statictic of 0.74.

A patient with ectatic vessel and visual thrombus demonstrated the most intense 18F-GP1 uptake (TBRmax 2.0, highest in the cohort) in the region of heaviest thrombus burden (Figure 2). Extra-coronary uptake was seen in regions of left ventricular thrombus, left atrial appendage thrombus, pulmonary thromboembolism and intramyocardial microvascular obstruction.

Conclusions

18F-GP1 PET-CT is able to detect coronary artery thrombus in culprit lesions following myocardial infarction, as well as extra-coronary thrombotic pathologies that may be important in guiding patient management. 18F-GP1 is highly specific in recognising a culprit lesion from a non-culprit lesion both visually as well as quantitatively.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): British Heart Foundation Figure 1Figure 2

Troponin to risk stratify patients with suspected acute coronary syndrome for computed tomography coronary angiography

Background

Patients with suspected acute coronary syndrome in whom myocardial infarction has been ruled-out are at risk of future adverse cardiac events. However, the optimal approach to risk stratify and investigate these patients is uncertain.

Methods

We performed a prospective cohort study of 250 patients presenting to the Emergency Department with suspected acute coronary syndrome and troponin concentrations below the sex-specific 99th centile (16 ng/L for women and 34 ng/L for men). Patients were recruited in a 2:1 fashion stratified by peak high-sensitivity cardiac troponin I concentration above and below the early rule-out threshold of 5 ng/L (167 patients with intermediate troponin concentrations between 5 ng/L and the sex-specific 99th centile threshold and 83 patients with troponin concentrations <5 ng/L). All patients underwent computed tomography coronary angiography after they were discharged from hospital.

Results

Overall, 37.6% (94/250) of patients had normal coronary arteries whilst 36.0% (90/250) and 26.4% (66/250) had non-obstructive and obstructive coronary artery disease, respectively. Patients with intermediate troponin concentrations were more likely to have coronary artery disease than those with troponin concentrations <5 ng/L (71.9% [120/167] versus 43.4% [36/83]; odds ratio 3.33 [95% confidence interval 1.92–5.78]). This association persisted irrespective of whether patients had anginal symptoms. Conversely, there was no difference in the prevalence of coronary artery disease between those with and without anginal symptoms (63.2% [67/106] and versus 61.8% [89/144]; odds ratio 0.92 [0.48–1.76]). The majority of patients found to have coronary artery disease did not have a prior diagnosis and were not on optimal preventative medical therapy prior to undergoing computed tomography coronary angiography (50.8% [61/120] and 61.0% [22/36], versus 61.7% [74/120] and 69.4% [25/36] in patients with intermediate versus low troponin concentrations, respectively).

Conclusions

In patients with suspected acute coronary syndrome who have myocardial infarction ruled out, those with intermediate cardiac troponin concentrations are three-times more likely to have coronary artery disease than those with low troponin concentrations. Conversely anginal symptoms did not discriminate between those with and without coronary artery disease. Further studies are required to determine if targeting computed tomography coronary angiography to those with intermediate cardiac troponin concentrations can improve the use of preventative medical therapies and clinical outcomes.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): The British Heart Foundation Odds ratio of coronary artery diseaseCumulative proportion with CAD

Pericoronary adipose tissue attenuation, low-attenuation plaque burden and 5-year risk of myocardial infarction

Introduction

Pericoronary adipose tissue (PCAT) attenuation has emerged as a surrogate marker of pericoronary inflammation. To date, no studies have compared the impact of pericoronary adipose tissue (PCAT) attenuation and quantitative plaque burden on cardiac outcomes.

Purpose

We aimed to establish the relative merits of these approaches to risk prediction and hypothesised that the combination of PCAT attenuation and quantitative plaque burden measures could provide additive and improved prediction of myocardial infarction in patients with stable chest pain.

Methods

In a post-hoc analysis of a randomized controlled trial, we investigated the association between the future risk of fatal or non-fatal myocardial infarction and PCAT attenuation measured from CT coronary angiography using multivariable Cox regression models including plaque burden, obstructive coronary disease and cardiac risk score (incorporating age, sex, diabetes, smoking, hypertension, hyperlipidaemia and family history of cardiovascular disease).

Results

In 1697 evaluable participants (mean age 58±10 years), there were 37 myocardial infarctions after a median follow-up of 4.7 [interquartile interval, 4.0–5.7] years. Median low-attenuation plaque burden was 4.20 [0–6.86] % and mean PCAT −76±8 Hounsfield units (HU).

PCAT attenuation of the right coronary artery (RCA) was predictive of myocardial infarction (hazard ratio [HR] 1.55, 95% CI 1.08–2.22; p=0.017, per 1 standard deviation increment) with an optimum threshold of −70.5 HU [Hazards ratio (HR) 2.45, 95% CI 1.2–4.9; p=0.01]. Univariable analysis also identified the burden of non-calcified, low-attenuation and calcified plaque as well as Agatston coronary calcium score, presence of obstructive coronary artery disease and cardiovascular risk score were predictors of myocardial infarction (Figure 1). In multivariable analysis, only the low-attenuation plaque burden (HR 1.80, 95% CI 1.16 to 2.81, p=0.011, per doubling) and PCAT-RCA (HR 1.47 95%1.02 to 2.13, p=0.040, per standard deviation increment) remained predictors of myocardial infarction (Figure 1).

In multivariable analysis, adding PCAT-RCA ≥-70.5 HU to low-attenuation plaque burden >4% (optimum threshold for future myocardial infarction; HR = 4.87, 95% CI 2.03–11.78; p<0.0001) led to improved prediction of future myocardial infarction (HR 11.7, 95% CI 3.3–40.9; p<0.0001); Figure 2. In ROC analysis, integration of PCAT-RCA attenuation and LAP burden, increased the prediction for myocardial infarction compared to LAP alone (ΔAUC=0.04; p=0.01).

Conclusion

CT coronary angiography defined PCAT attenuation and low-attenuation plaque have marked and additive predictive value for the risk of fatal or non-fatal myocardial infarction.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): The Chief Scientist Office of the Scottish Government Health and Social Care Directorates, British Heart Foundation, National Institute of Health/National Heart, Lung, and Blood Institute grant

Deep learning-based plaque quantification from coronary computed tomography angiography: external validation and comparison with intravascular ultrasound

Background

Atherosclerotic plaque quantification from coronary computed tomography angiography (CTA) enables accurate assessment of coronary artery disease burden, progression, and prognosis. However, quantitative plaque analysis is time-consuming and requires high expertise. We sought to develop and externally validate an artificial intelligence (AI)-based deep learning (DL) approach for CTA-derived measures of plaque volume and stenosis severity. We compared the performance of DL to expert readers and the gold standard of intravascular ultrasound (IVUS).

Methods

This was a multicenter study of patients undergoing coronary CTA at 11 sites, with software-based quantitative plaque measurements performed at a per-lesion level by expert readers. AI-based plaque analysis was performed by a DL novel convolutional neural network which automatically segmented the coronary artery wall, lumen, and plaque for the computation of plaque volume and stenosis severity. Using expert measurements as ground truth, the DL algorithm was trained on 887 patients (4,686 lesions). Thereafter, the algorithm was applied to an independent test set of 221 patients (1,234 lesions), which included an external validation cohort of 171 patients from the SCOT-HEART (Scottish Computed Tomography of the Heart) trial as well as 50 patients who underwent IVUS within one month of CTA. We report the performance of AI-based plaque analysis in the independent test set.

Results

Within the external validation cohort, there was excellent agreement between DL and expert reader measurements of total plaque volume (intraclass correlation coefficient [ICC] 0.876), noncalcified plaque volume (ICC 0.869), and percent diameter stenosis (ICC 0.850; all p<0.001). When compared with IVUS, there was excellent agreement for DL total plaque volume (ICC 0.945), total plaque burden (ICC 0.853), minimal luminal area (ICC 0.864), and percent area stenosis (ICC 0.805; all p<0.001); with strong correlation between DL and IVUS for total plaque volume (r=0.915; p<0.001; Figure). The average DL plaque analysis time was 20 seconds per patient, compared with 25–30 minutes taken by experts.

Conclusions

AI-based plaque quantification from coronary CTA using an externally validated DL approach enables rapid measurements of plaque volume and stenosis severity in close agreement with expert readers and IVUS.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Heart, Lung, and Blood Institute, United States

Long-term cardiac risk in individuals with low calcium score on coronary computed tomography angiography can be stratified by the pericoronary fat radiomic profile (FRP)

Funding Acknowledgements

Type of funding sources: Foundation. Main funding source(s): UKRI, British Heart Foundation

Background

Inflammation in the coronaries induces macroscopic changes in perivascular adipose tissue composition, detectable by the pericoronary Fat Radiomic Profile (FRP) on coronary computed tomography angiography (CCTA).

Purpose

To assess the ability of FRP to stratify cardiac risk in patients with Coronary Artery Calcium (CAC) score below 100 following routine CCTA.

Methods

1,575 participants from the CCTA arm of the SCOT-HEART trial (NCT01149590) eligible for image analysis were included. Pericoronary FRP mapping was performed in perivascular adipose tissue segmentations around the proximal sites of the right and left coronary arteries, as previously validated. We first tested the prognostic value of FRP in the sub-cohort of patients with CAC < 100. We further analysed a sub-group based on the absence of high risk plaque (HRP) features and obstructive coronary artery disease (CAD). The association with future incidence of major adverse cardiac events (MACE: cardiac mortality or non-fatal myocardial infarction) or a composite endpoint of MACE ± late revascularization (MACE-ReVasc) was assessed using adjusted Cox regression models [adjusted for age, sex, systolic blood pressure (SBP), diabetes mellitus (DM), body mass index (BMI), smoking, CAD (≥50% stenosis), total cholesterol, high-density lipoprotein (HDL), and HRP features].

Results

In total, 1,032 patients (53.9% female sex) were found with low CAC score (CAC < 100), with a median age of 55 years. Over a mean follow-up of 4.87 ± 1.06 years, 12 MACE and 47 MACE-ReVasc were recorded. High FRP was associated with a 14.4-fold (95% CI: 3.80-54.78, p < 0.001) higher adjusted risk of MACE and a 2.8-fold (95% CI: 1.49-5.36, p = 0.001) higher adjusted risk of MACE-ReVasc (A). Addition of high FRP to a baseline model consisting of traditional risk factors (age, sex, systolic blood pressure, diabetes mellitus, BMI, smoking, CAD (≥50% stenosis), total cholesterol, HDL, HRP) significantly enhanced (deltaAUC at 5 years:0.15, p = 0.03) the model’s performance and reclassified individuals (NRI = 0.59, p = 0.02, B). Interestingly, after more rigorous filtering of the population by absence of HRP features and obstructive CAD, high FRP remained an independent predictor of MACE (n = 756, Adj.HR = 28.1, p = 0.003).

Conclusion

In individuals with low CAC scores the Fat Radiomic Profile biormarker significantly improves risk prediction for adverse clinical events beyond the current state-of-the-art. Non-invasive profiling of pericoronary adipose tissue using CCTA-derived FRP captures irreversible changes in perivascular adipose tissue composition associated with chronic vascular inflammation and atherosclerotic disease, and can supplement the traditional anatomical assessment of the coronary vasculature with a functional marker of disease activity.

Multiprotein E. coli SSB-ssDNA complex shows both stable binding and rapid dissociation due to interprotein interactions

Escherichia coli SSB (EcSSB) is a model single-stranded DNA (ssDNA) binding protein critical in genome maintenance. EcSSB forms homotetramers that wrap ssDNA in multiple conformations to facilitate DNA replication and repair. Here we measure the binding and wrapping of many EcSSB proteins to a single long ssDNA substrate held at fixed tensions. We show EcSSB binds in a biphasic manner, where initial wrapping events are followed by unwrapping events as ssDNA-bound protein density passes critical saturation and high free protein concentration increases the fraction of EcSSBs in less-wrapped conformations. By destabilizing EcSSB wrapping through increased substrate tension, decreased substrate length, and protein mutation, we also directly observe an unstable bound but unwrapped state in which ∼8 nucleotides of ssDNA are bound by a single domain, which could act as a transition state through which rapid reorganization of the EcSSB-ssDNA complex occurs. When ssDNA is over-saturated, stimulated dissociation rapidly removes excess EcSSB, leaving an array of stably-wrapped complexes. These results provide a mechanism through which otherwise stably bound and wrapped EcSSB tetramers are rapidly removed from ssDNA to allow for DNA maintenance and replication functions, while still fully protecting ssDNA over a wide range of protein concentrations.

Influence of Surface Oxygen Vacancies and Ruthenium Valence State on the Catalysis of Pyrochlore Oxides

Proton exchange membrane (PEM) water electrolysis is a promising energy storage solution by electrochemically splitting water into hydrogen fuel and oxygen. However, the sluggish kinetics, high operating potential, and corrosive acidic environment during the oxygen evolution reaction (OER) require the use of scarce and costly Ir-based oxides, tremendously hampering its large-scale commercialization. Hence, developing active and stable anode catalysts with reduced precious-metal usage is desperately essential. For the first time, we report a group of Y_2-xBa_xRu₂O₇ pyrochlore oxides and employ them in acid OER and PEM electrolyzers. We reveal the mechanism for the promoted OER performance of Ba-doped Y₂Ru₂O₇ in which partially replacing Y³⁺ by Ba²⁺ in Y₂Ru₂O₇ greatly facilitates the hole-doping effect, which generates massive oxygen vacancy and multivalence of Ru⁵⁺/Ru⁴⁺, thus boosting the OER performance of Y_2-xBa_xRu₂O₇. This work provides an effective method and paradigm for improving the electrocatalytic property of pyrochlore oxides.

Specific Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein Deduced from Hairpin Unfolding

RNA and DNA hairpin formation and disruption play key regulatory roles in a variety of cellular processes. The 59-nucleotide transactivation response (TAR) RNA hairpin facilitates the production of full-length transcripts of the HIV-1 genome. Yet the stability of this long, irregular hairpin becomes a liability during reverse transcription as 24 base pairs must be disrupted for strand transfer. Retroviral nucleocapsid (NC) proteins serve as nucleic acid chaperones that have been shown to both destabilize the TAR hairpin and facilitate strand annealing with its complementary DNA sequence. Yet it has remained difficult to elucidate the way NC targets and dramatically destabilizes this hairpin while only weakly affecting the annealed product. In this work, we used optical tweezers to measure the stability of TAR and found that adding NC destabilized the hairpin and simultaneously caused a distinct change in both the height and location of the energy barrier. This data was matched to an energy landscape predicted from a simple theory of definite base pair destabilization. Comparisons revealed the specific binding sites found by NC along the irregular TAR hairpin. Furthermore, specific binding explained both the unusual shift in the transition state and the much weaker effect on the annealed product. These experiments illustrate a general method of energy landscape transformation that exposes important physical insights.

HIV restriction factor APOBEC3G binds in multiple steps and conformations to search and deaminate single-stranded DNA

APOBEC3G (A3G), an enzyme expressed in primates with the potential to inhibit human immunodeficiency virus type 1 (HIV-1) infectivity, is a single-stranded DNA (ssDNA) deoxycytidine deaminase with two domains, a catalytically active, weakly ssDNA binding C-terminal domain (CTD) and a catalytically inactive, strongly ssDNA binding N-terminal domain (NTD). Using optical tweezers, we measure A3G binding a single, long ssDNA substrate under various applied forces to characterize the binding interaction. A3G binds ssDNA in multiple steps and in two distinct conformations, distinguished by degree of ssDNA contraction. A3G stabilizes formation of ssDNA loops, an ability inhibited by A3G oligomerization. Our data suggests A3G securely binds ssDNA through the NTD, while the CTD samples and potentially deaminates the substrate. Oligomerization of A3G stabilizes ssDNA binding but inhibits the CTD's search function. These processes explain A3G's ability to efficiently deaminate numerous sites across a 10,000 base viral genome during the reverse transcription process.

Coronary artery calcification is associated with mortality independent of pulmonary embolism severity: a retrospective cohort study

AIM

To assess coronary artery calcification (CAC) and vascular calcification in patients with pulmonary embolism (PE) and correlate this with mortality.

MATERIALS AND METHODS

PE severity was quantified using computed tomography pulmonary angiography (CTPA) in 400 consecutive cases using the modified Miller score (1-5, mild; 6-11, moderate; 12-16, severe). Right ventricle strain was assessed using the right/left ventricle diameter (RV/LV) ratio. CAC score (CACS) was assessed using a four-point scale (CACS mild 1-3, moderate 4-8, severe 9-12) for each vessel and summed to give the total CACS. Follow-up for mortality was obtained at 3 years.

RESULTS

PE severity was classified as mild in 48%, moderate in 21%, and severe in 32% of cases. The median modified Miller score was 6 (Interquartile range [IQR] 2, 14) and median total CACS was 2 (IQR 0, 7). All-cause mortality occurred in 128 (32%) patients. Patients with CAC were three times more likely to die than patients without CAC (Hazard ratio [HR] 2.96; 95% CI 1.84, 4.77; p<0.001), and patients with severe CAC were at the highest risk (HR 4.62; 95% CI 2.73, 7.83, p<0.001). Gender, modified Miller score and RV/LV ratio were not predictive of mortality. In multivariate analysis both CACS and age were independent predictors of 3-year all-cause mortality. Of the patients with CAC who died, the presence of coronary artery disease was only documented in 34 (32%).

CONCLUSION

CACS is an independent predictor of all-cause mortality in patients with PE, and has important implications for subsequent patient management.

1269Dual antiplatelet therapy to inhibit myocardial injury in patients with high-risk coronary artery plaque: a randomized controlled trial

Background

High-risk coronary atherosclerotic plaque is associated with higher plasma troponin concentrations suggesting ongoing myocardial injury that may be a target for dual antiplatelet therapy.

Purpose

To determine whether ticagrelor reduces high-sensitivity troponin I concentrations in patients with established coronary artery disease and high-risk coronary plaque with 18F-fluoride uptake.

Methods

In a randomized double-blind placebo-controlled trial, patients with multivessel coronary artery disease underwent coronary 18F-fluoride positron emission tomography-computed tomography and measurement of high-sensitivity cardiac troponin I and were randomized (1:1) to ticagrelor 90 mg twice daily or matched placebo. The primary endpoint was troponin I concentration at 30 days in patients with increased coronary 18F-fluoride uptake.

Results

In total, 202 patients were randomized and 191 met the pre-specified criteria for inclusion in the primary analysis. In patients with increased coronary 18F-fluoride uptake (n=120/191) there was no evidence that ticagrelor had an effect on plasma troponin concentrationsat 30 days (ratio of geometric means for ticagrelor versusplacebo, 1.11, [95% confidence interval 0.90 to 1.36], p=0.32) (Table 1). Over 1 year, ticagrelor had no effect on troponin concentrations in patients with increased coronary 18F-fluoride uptake (ratio of geometric means, 0.86, 95% confidence interval 0.63 to 1.17, p=0.33).

Table 1 Adjusted Geometric Mean (GSE) Ratio of Geometric Means p-value Ticagrelor Placebo (95% CI) Cardiac troponin I, ng/L (18F-fluoride activity) 3.8 (1.1) 3.4 (1.1) 1.11 (0.90 to 1.36) 0.32 Cardiac Troponin I, ng/L (No 18F-fluoride activity) 2.4 (1.1) 2.3 (1.1) 1.02 (0.80 to 1.31) 0.87 Plasma high-sensitivity cardiac troponin I concentration (ng/L) at 30 days for the per-protocol population.Estimates are back transformed estimates from analysis of log transformed values at 30 days adjusting for age, sex and log transformed baseline troponin. Ratio of geometric means is Ticagrelor divided by Placebo. GSE, geometric standard error.

Conclusions

Dual antiplatelet therapy with ticagrelor does not reduce plasma troponin concentrations in patients with coronary 18F-fluoride uptake. This suggests that subclinical plaque thrombosis does not contribute to ongoing myocardial injury in this setting.

Clinical Trials Study ID: NCT02110303Study ID: NCT02110303

Acknowledgement/Funding

Wellcome Trust Senior Investigator Award WT103782AIA

P2237National trends in coronary artery disease imaging

Background

The 2010 National Institute of Clinical Excellence (NICE) Clinical Guideline 95 (CG95) recommended coronary computed tomographic angiography (CTA) for low-intermediate risk patients with stable chest pain. The indications for CTA broadened substantially in the 2016 update, which recommended CTA for all patients with possible angina and diagnostic uncertainty.

Purpose

To examine trends in the use of imaging for the investigation of coronary artery disease (CAD) in England in the years before and after the 2016 CG95 guideline update.

Methods

Numbers of invasive coronary angiography (ICA), single positron emission tomography (SPECT), stress echocardiography (SE), CTA, and positron emission tomography (PET) scans performed from 2012–2018 were extracted from a national database of imaging procedures performed in England. Per capita average annual growth was calculated at a national and healthcare provider level, and comparisons were made before and after the 2016 CG95 update. Healthcare providers with greater than median CTA growth were compared to those with less than median growth to ascertain the impact of CTA on other forms of CAD investigation. Total healthcare provider costs for imaging were calculated using NHS tariff costs.

Results

From 2012–2018, 1,792,655 imaging examinations were performed for the investigation of CAD, with an overall annualized growth rate of 4%. Average annual growth (per 100,000 population per year) from 2012–2018 was 1±31% for ICA, 28±39% for CTA, −11±22% for SPECT, 0±1% for PET, 1±2% for SE and 5±16% for MRI. Following the 2016 CG95 update, there was an increase in the year-to-year average annual growth of CTA scans performed (53±79 versus 2±53 tests/100,000/yr, p<0.001) compared with a fall in the rate of ICA use (−13±48 versus +5±36 tests/100,000/yr, p=0.03). SPECT underwent a consistent fall in utilisation over the study period, with an average annual growth rate of −4%, with no difference before or after the 2016 CG95 update (P>0.1). Rates of change in the utilization of SE, PET, and MRI did not change following the introduction of the 2016 CG95 update. Regions with an above median average annual growth in CTA exhibited a greater decline in SPECT use (−19±28 versus −4±11 tests/100,000/yr, p=0.037) than regions with a below median growth in CTA use, with no difference in the average annual growth of ICA, SE, PET or MRI (p>0.1 for all; Figure 1). Per capita healthcare costs remained stable throughout the study period, with no significant change following CG95 (p>0.1).

Figure 1. CTA, SPECT and ICA growth rate

Conclusion

There is a clear and consistent trend towards increased imaging for the diagnosis and management of CAD. The 2016 NICE CG95 update resulted in a rise in the use of CTA, and a fall in ICA. Importantly, rates of ICA utilization fell despite a rise in CTA usage. Centres with the greatest growth in CTA had the greatest fall in SPECT utilisation and consequently, overall imaging costs were unchanged.

Single and double box HMGB proteins differentially destabilize nucleosomes

Nucleosome disruption plays a key role in many nuclear processes including transcription, DNA repair and recombination. Here we combine atomic force microscopy (AFM) and optical tweezers (OT) experiments to show that high mobility group B (HMGB) proteins strongly disrupt nucleosomes, revealing a new mechanism for regulation of chromatin accessibility. We find that both the double box yeast Hmo1 and the single box yeast Nhp6A display strong binding preferences for nucleosomes over linker DNA, and both HMGB proteins destabilize and unwind DNA from the H2A–H2B dimers. However, unlike Nhp6A, Hmo1 also releases half of the DNA held by the (H3–H4)₂ tetramer. This difference in nucleosome destabilization may explain why Nhp6A and Hmo1 function at different genomic sites. Hmo1 is enriched at highly transcribed ribosomal genes, known to be depleted of histones. In contrast, Nhp6A is found across euchromatin, pointing to a significant difference in cellular function.

Quantifying the stability of oxidatively damaged DNA by single-molecule DNA stretching

One of the most common DNA lesions is created when reactive oxygen alters guanine. 8-oxo-guanine may bind in the anti-conformation with an opposing cytosine or in the syn-conformation with an opposing adenine paired by transversion, and both conformations may alter DNA stability. Here we use optical tweezers to measure the stability of DNA hairpins containing 8-oxoguanine (8oxoG) lesions, comparing the results to predictive models of base-pair energies in the absence of the lesion. Contrasted with either a canonical guanine-cytosine or adenine-thymine pair, an 8oxoG-cytosine base pair shows significant destabilization of several k_BT. The magnitude of destabilization is comparable to guanine-thymine ‘wobble’ and cytosine-thymine mismatches. Furthermore, the measured energy of 8oxoG-adenine corresponds to theoretical predictions for guanine-adenine pairs, indicating that oxidative damage does not further destabilize this mismatch in our experiments, in contrast to some previous observations. These results support the hypothesis that oxidative damage to guanine subtly alters the direction of the guanine dipole, base stacking interactions, the local backbone conformation, and the hydration of the modified base. This localized destabilization under stress provides additional support for proposed mechanisms of enzyme repair.

Breast arterial calcification on mammography and risk of coronary artery disease: a SCOT-HEART sub-study

AIM

To assess the prevalence of breast arterial calcification (BAC) in patients who also underwent routine surveillance mammography, and to determine the association with cardiovascular risk factors, coronary artery calcification, and coronary artery disease on coronary computed tomography angiography (CCTA).

MATERIALS AND METHODS

Four hundred and five female participants were identified who had undergone CCTA and subsequent mammography in the SCOT-HEART randomised controlled trial of CCTA in patients with suspected stable angina. Mammograms were assessed visually for the presence and severity of BAC.

RESULTS

BAC was identified in 93 (23%) patients. Patients with BAC were slightly older (63±7 versus 59±8 years, p<0.001), with a higher cardiovascular risk score (19±11 versus 16±10, p=0.022) and were more likely to be non-smokers (73% versus 49%, p<0.001). In patients with BAC, coronary artery calcification was present in 58 patients (62%; relative risk [RR] 1.26, 95% confidence intervals [CI]: 1.04, 1.53; p=0.02), non-obstructive coronary artery disease in 58 (62%; RR 1.27, 95% CI: 1.04 to 1.54, p=0.02), and obstructive coronary artery disease in 19 (20%; RR 1.62, 95% CI: 0.98, 2.66; p=0.058). Patients without BAC were very unlikely to have severe coronary artery calcification (negative predictive value 95%) but the diagnostic accuracy of BAC to identify coronary artery disease was poor (AUC 0.547).

CONCLUSION

Although BAC is associated with the presence and severity of coronary artery calcification, the diagnostic accuracy to identify patients with coronary artery disease or obstructive coronary artery disease is poor.

•

Breast arterial calcification occurs in a fifth of patients referred for CCTA who tend to be older non-smokers.

•

It is associated with higher coronary artery calcium but this is predominantly dependent on age and cardiovascular risks.

•

Absence of breast arterial calcification excludes severe coronary artery calcification, negative predictive value of 95%.

DNA Intercalation Facilitates Efficient DNA-Targeted Covalent Binding of Phenanthriplatin

Phenanthriplatin, a monofunctional anticancer agent derived from cisplatin, shows significantly more rapid DNA covalent-binding activity compared to its parent complex. To understand the underlying molecular mechanism, we used single-molecule studies with optical tweezers to probe the kinetics of DNA-phenanthriplatin binding as well as DNA binding to several control complexes. The time-dependent extensions of single λ-DNA molecules were monitored at constant applied forces and compound concentrations, followed by rinsing with a compound-free solution. DNA-phenanthriplatin association consisted of fast and reversible DNA lengthening with time constant τ ≈ 10 s, followed by slow and irreversible DNA elongation that reached equilibrium in ∼30 min. In contrast, only reversible fast DNA elongation occured for its stereoisomer  trans-phenanthriplatin, suggesting that the distinct two-rate kinetics of phenanthriplatin is sensitive to the geometric conformation of the complex. Furthermore, no DNA unwinding was observed for pyriplatin, in which the phenanthridine ligand of phenanthriplatin is replaced by the smaller pyridine molecule, indicating that the size of the aromatic group is responsible for the rapid DNA elongation. These findings suggest that the mechanism of binding of phenanthriplatin to DNA involves rapid, partial intercalation of the phenanthridine ring followed by slower substitution of the adjacent chloride ligand by, most likely, the N7 atom of a purine base. The cis isomer affords the proper stereochemistry at the metal center to facilitate essentially irreversible DNA covalent binding, a geometric advantage not afforded by trans-phenanthriplatin. This study demonstrates that reversible DNA intercalation provides a robust transition state that is efficiently converted to an irreversible DNA-Pt bound state.

The role of the C-domain of bacteriophage T4 gene 32 protein in ssDNA binding and dsDNA helix-destabilization: Kinetic, single-molecule, and cross-linking studies

The model single-stranded DNA binding protein of bacteriophage T4, gene 32 protein (gp32) has well-established roles in DNA replication, recombination, and repair. gp32 is a single-chain polypeptide consisting of three domains. Based on thermodynamics and kinetics measurements, we have proposed that gp32 can undergo a conformational change where the acidic C-terminal domain binds internally to or near the single-stranded (ss) DNA binding surface in the core (central) domain, blocking ssDNA interaction. To test this model, we have employed a variety of experimental approaches and gp32 variants to characterize this conformational change. Utilizing stopped-flow methods, the association kinetics of wild type and truncated forms of gp32 with ssDNA were measured. When the C-domain is present, the log-log plot of k vs. [NaCl] shows a positive slope, whereas when it is absent (*I protein), there is little rate change with salt concentration, as expected for this model.A gp32 variant lacking residues 292-296 within the C-domain, ΔPR201, displays kinetic properties intermediate between gp32 and *I. The single molecule force-induced DNA helix-destabilizing activitiesas well as the single- and double-stranded DNA affinities of ΔPR201 and gp32 truncated at residue 295 also fall between full-length protein and *I. Finally, chemical cross-linking of recombinant C-domain and gp32 lacking both N- and C-terminal domains is inhibited by increasing concentrations of a short single-stranded oligonucleotide, and the salt dependence of cross-linking mirrors that expected for the model. Taken together, these results provide the first evidence in support of this model that have been obtained through structural probes.

Protein-nucleic acid interactions of LINE-1 ORF1p

Long interspersed nuclear element 1 (LINE-1 or L1) is the dominant retrotransposon in mammalian genomes. L1 encodes two proteins ORF1p and ORF2p that are required for retrotransposition. ORF2p functions as the replicase. ORF1p is a coiled coil-mediated trimeric, high affinity RNA binding protein that packages its full- length coding transcript into an ORF2p-containing ribonucleoprotein (RNP) complex, the retrotransposition intermediate. ORF1p also is a nucleic acid chaperone that presumably facilitates the proposed nucleic acid remodeling steps involved in retrotransposition. Although detailed mechanistic understanding of ORF1p function in this process is lacking, recent studies showed that the rate at which ORF1p can form stable nucleic acid-bound oligomers in vitro is positively correlated with formation of an active L1 RNP as assayed in vivo using a cell culture-based retrotransposition assay. This rate was sensitive to minor amino acid changes in the coiled coil domain, which had no effect on nucleic acid chaperone activity. Additional studies linking the complex nucleic acid binding properties to the conformational changes of the protein are needed to understand how ORF1p facilitates retrotransposition.