Cationic Residues of the HIV-1 Nucleocapsid Protein Enable DNA Condensation to Maintain Viral Core Particle Stability during Reverse Transcription

The HIV-1 nucleocapsid protein (NC) is a multifunctional viral protein necessary for HIV-1 replication. Recent studies have demonstrated that reverse transcription (RT) completes in the intact viral capsid, and the timing of RT and uncoating are correlated. How the small viral core stably contains the ~10 kbp double stranded (ds) DNA product of RT, and the role of NC in this process, are not well understood. We showed previously that NC binds and saturates dsDNA in a non-specific electrostatic binding mode that triggers uniform DNA self-attraction, condensing dsDNA into a tight globule against extending forces up to 10 pN. In this study, we use optical tweezers and atomic force microscopy to characterize the role of NC's basic residues in dsDNA condensation. Basic residue mutations of NC lead to defective interaction with the dsDNA substrate, with the constant force plateau condensation observed with wild-type (WT) NC missing or diminished. These results suggest that NC's high positive charge is essential to its dsDNA condensing activity, and electrostatic interactions involving NC's basic residues are responsible in large part for the conformation, size, and stability of the dsDNA-protein complex inside the viral core. We observe DNA re-solubilization and charge reversal in the presence of excess NC, consistent with the electrostatic nature of NC-induced DNA condensation. Previous studies of HIV-1 replication in the presence of the same cationic residue mutations in NC showed significant defects in both single- and multiple-round viral infectivity. Although NC participates in many stages of viral replication, our results are consistent with the hypothesis that cationic residue mutations inhibit genomic DNA condensation, resulting in increased premature capsid uncoating and contributing to viral replication defects.

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.