The extracellular matrix differentially directs myoblast motility and differentiation in distinct forms of muscular dystrophy: Dystrophic matrices alter myoblast motility

Extracellular matrix (ECM) pathologic remodeling underlies many disorders, including muscular dystrophy. Tissue decellularization removes cellular components while leaving behind ECM components. We generated "on-slide" decellularized tissue slices from genetically distinct dystrophic mouse models. The ECM of dystrophin- and sarcoglycan-deficient muscles had marked thrombospondin 4 deposition, while dysferlin-deficient muscle had excess decorin. Annexins A2 and A6 were present on all dystrophic decellularized ECMs, but annexin matrix deposition was excessive in dysferlin-deficient muscular dystrophy. Muscle-directed viral expression of annexin A6 resulted in annexin A6 in the ECM. C2C12 myoblasts seeded onto decellularized matrices displayed differential myoblast mobility and fusion. Dystrophin-deficient decellularized matrices inhibited myoblast mobility, while dysferlin-deficient decellularized matrices enhanced myoblast movement and differentiation. Myoblasts treated with recombinant annexin A6 increased mobility and fusion like that seen on dysferlin-deficient decellularized matrix and demonstrated upregulation of ECM and muscle cell differentiation genes. These findings demonstrate specific fibrotic signatures elicit effects on myoblast activity.

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of base editor genome-wide activity

Base editors ( BE ) enable programmable conversion of nucleotides in genomic DNA without double-stranded breaks and have substantial promise to become new transformative genome editing medicines. Sensitive and unbiased detection of base editor off-target effects is important for identifying safety risks unique to base editors and translation to human therapeutics, as well as accurate use in life sciences research. However, current methods for understanding the global activities of base editors have limitations in terms of sensitivity or bias. Here we present CHANGE-seq-BE, a novel method to directly assess the off-target profile of base editors that is simultaneously sensitive and unbiased. CHANGE-seq-BE is based on the principle of selective sequencing of adenine base editor modified genomic DNA in vitro , and provides an accessible, rapid, and comprehensive method for identifying genome-wide off-target mutations of base editors.

The super-healing MRL strain promotes muscle growth in muscular dystrophy through a regenerative extracellular matrix

The Murphy Roths Large (MRL) mouse strain has "super-healing" properties that enhance recovery from injury. In mice, the DBA/2J strain intensifies many aspects of muscular dystrophy, so we evaluated the ability of the MRL strain to suppress muscular dystrophy in the Sgcg-null mouse model of limb girdle muscular dystrophy. A comparative analysis of Sgcg-null mice in the DBA/2J versus MRL strains showed greater myofiber regeneration, with reduced structural degradation of muscle in the MRL strain. Transcriptomic profiling of dystrophic muscle indicated strain-dependent expression of extracellular matrix (ECM) and TGF-β signaling genes. To investigate the MRL ECM, cellular components were removed from dystrophic muscle sections to generate decellularized myoscaffolds. Decellularized myoscaffolds from dystrophic mice in the protective MRL strain had significantly less deposition of collagen and matrix-bound TGF-β1 and TGF-β3 throughout the matrix. Dystrophic myoscaffolds from the MRL background, but not the DBA/2J background, were enriched in myokines like IGF-1 and IL-6. C2C12 myoblasts seeded onto decellularized matrices from Sgcg-/- MRL and Sgcg-/- DBA/2J muscles showed the MRL background induced greater myoblast differentiation compared with dystrophic DBA/2J myoscaffolds. Thus, the MRL background imparts its effect through a highly regenerative ECM, which is active even in muscular dystrophy.

Extracellular matrix contribution to disease progression and dysfunction in myopathy

Myopathic processes affect skeletal muscle and heart. In the muscular dystrophies, which are a subset of myopathies, muscle cells are gradually replaced by fibrosis and fat, impairing muscle function as well as regeneration and repair. In addition to skeletal muscle, these genetic disorders often also affect the heart, where fibrofatty infiltration progressively accumulates in the myocardium, impairing heart function. Although considerable effort has focused on gene-corrective and gene-replacement approaches to stabilize myofibers and cardiomyocytes, the continual and ongoing deposition of extracellular matrix itself contributes to tissue and organ dysfunction. Transcriptomic and proteomic profiling, along with high-resolution imaging and biophysical measurements, have been applied to define extracellular matrix components and their role in contributing to cardiac and skeletal muscle weakness. More recently, decellularization methods have been adapted to an on-slide format to preserve the spatial geography of the extracellular matrix, allowing new insight into matrix remodeling and its direct role in suppressing regeneration in muscle. This review highlights recent literature with focus on the extracellular matrix and molecular mechanisms that contribute to muscle and heart fibrotic disorders. We will also compare how the myopathic matrix differs from healthy matrix, emphasizing how the pathological matrix contributes to disease.

Assay interference as a cause of false positive troponin T elevation in emergency department patients

BACKGROUND

Troponin assays are used in the diagnosis of myocardial injury and may show elevated results for a variety of reasons. However it is increasingly recognised that cardiac troponin elevation may in some cases be due to assay interference. This is of significant importance as a misdiagnosis of myocardial injury may lead to unnecessary and potentially harmful investigation and treatment for patients. We sought to confirm the accuracy of cardiac high sensitivity troponin T (chsTnT) elevation in an unselected group of patients presenting to the emergency department, by using a second confirmatory cardiac high sensitivity troponin I (chsTnI) assay.

METHODS

We identified patients presenting to two local emergency departments over a five-day period who had chsTnT levels measured as part of routine clinical care. All samples with elevated chsTnT levels (above the 99% centile URL) were retested for chsTnI in order to confirm true myocardial injury.

RESULTS

A total of 74 samples from 54 patients were analysed for chsTnT and chsTnI. 7 samples (9.5%) had chsTnI levels < 5 ng/L suggesting assay interference as the cause of chsTnT elevation.

CONCLUSIONS

Assay interference leading to false positive troponin elevation may be more common than many physicians appreciate and can potentially lead to harmful investigation and treatment for patients. In cases where the diagnosis of myocardial injury is uncertain, a second alternative troponin assay should be performed to confirm true myocardial injury.

Adjuvant Radiotherapy in Atypical Meningioma: Are the Risks Worth the Benefit?

PURPOSE/OBJECTIVE(S)

Adjuvant radiotherapy (RT) improves progression-free survival (PFS) in atypical meningiomas. Herein, we assess whether the treatment-related acute and long-term toxicity of upfront RT in atypical meningioma patients versus surveillance merits the PFS benefit.

MATERIALS/METHODS

In our prior single institution retrospective study of 230 patients with resected intracranial atypical meningiomas between 2000-2015, adjuvant RT was associated with a significantly lower risk of progression/recurrence compared to surveillance (HR = 0.21 [95% CI 0.11-0.41]; p<0.01), with 36% of surveillance patients eventually requiring salvage RT. In the current study, the acute (≤6 months) and long term (>6 months) RT-related toxicities from the same patient cohort for those who received adjuvant RT (n = 51) were evaluated and compared to those who received salvage RT (n = 64) in the surveillance group. Additionally, overall treatment-related toxicity at time of last follow up was obtained for comparison between the adjuvant RT (n = 51) vs surveillance (n = 179) group. All toxicities were graded per CTCAE v5.0. Kaplan-Meier analysis was used to calculate the cumulative incidence of toxicities; Pearson's chi-squared and log-rank test were used for comparison.

RESULTS

Adjuvant RT as compared to salvage RT was generally associated with greater RT-related toxicities both in the acute (90% vs 69%, p = 0.006) and long term (57% vs 33%, p = 0.010). While there was no significant difference in grade 3-4 acute toxicities, long term grade 3-4 toxicities (including headache, seizure, vision loss, neuromotor deficit, and neurocognitive deficit) were present in 14% of adjuvant vs 3% of salvage RT group (p = 0.035). Radionecrosis occurred in 18% of adjuvant RT vs 8% of salvage RT group (p = 0.11). Between adjuvant RT vs surveillance groups, any-treatment related toxicity at last follow up was greater with adjuvant RT (31% vs 15%; p = 0.006), with trend towards greater grade 3-4 toxicities (including headache, vision loss, neuromotor deficit, neurocognitive deficit, and cerebral edema) as well (8% vs 3%; p = 0.101). Cumulative incidence of treatment-related neuromotor deficit (any grade) was significantly greater in the adjuvant RT vs surveillance group with 14% vs 2% at 10 years (p = 0.004). There was no difference in rate of cerebrovascular accident between adjuvant RT (6%) vs surveillance (4%) groups (p = 0.83).

CONCLUSION

Adjuvant RT for patients with atypical meningioma was associated with greater acute and long-term treatment toxicities. Potential RT-related toxicity and impact on quality-of-life should thus be carefully weighed against the tumor control benefit of RT in deciding the optimal use and timing of RT.

High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors

Single-cell nanopore sequencing of full-length mRNAs transforms single-cell multi-omics studies. However, challenges include high sequencing errors and dependence on short-reads and/or barcode whitelists. To address these, we develop scNanoGPS to calculate same-cell genotypes (mutations) and phenotypes (gene/isoform expressions) without short-read nor whitelist guidance. We apply scNanoGPS onto 23,587 long-read transcriptomes from 4 tumors and 2 cell-lines. Standalone, scNanoGPS deconvolutes error-prone long-reads into single-cells and single-molecules, and simultaneously accesses both phenotypes and genotypes of individual cells. Our analyses reveal that tumor and stroma/immune cells express distinct combination of isoforms (DCIs). In a kidney tumor, we identify 924 DCI genes involved in cell-type-specific functions such as PDE10A in tumor cells and CCL3 in lymphocytes. Transcriptome-wide mutation analyses identify many cell-type-specific mutations including VEGFA mutations in tumor cells and HLA-A mutations in immune cells, highlighting the critical roles of different mutant populations in tumors. Together, scNanoGPS facilitates applications of single-cell long-read sequencing technologies.

The super-healing MRL strain promotes muscle growth in muscular dystrophy through a regenerative extracellular matrix

Genetic background shifts the severity of muscular dystrophy. In mice, the DBA/2J strain confers a more severe muscular dystrophy phenotype, whereas the Murphy's Roth Large (MRL) strain has "super-healing" properties that reduce fibrosis. A comparative analysis of the Sgcg null model of Limb Girdle Muscular Dystrophy in the DBA/2J versus MRL strain showed the MRL background was associated with greater myofiber regeneration and reduced structural degradation of muscle. Transcriptomic profiling of dystrophic muscle in the DBA/2J and MRL strains indicated strain-dependent expression of the extracellular matrix (ECM) and TGF-β signaling genes. To investigate the MRL ECM, cellular components were removed from dystrophic muscle sections to generate decellularized "myoscaffolds". Decellularized myoscaffolds from dystrophic mice in the protective MRL strain had significantly less deposition of collagen and matrix-bound TGF-β1 and TGF-β3 throughout the matrix, and dystrophic myoscaffolds from the MRL background were enriched in myokines. C2C12 myoblasts were seeded onto decellularized matrices from Sgcg-/- MRL and Sgcg-/- DBA/2J matrices. Acellular myoscaffolds from the dystrophic MRL background induced myoblast differentiation and growth compared to dystrophic myoscaffolds from the DBA/2J matrices. These studies establish that the MRL background also generates its effect through a highly regenerative ECM, which is active even in muscular dystrophy.

Delineating genotypes and phenotypes of individual cells from long-read single cell transcriptomes

Single-cell nanopore sequencing of full-length mRNAs (scNanoRNAseq) is transforming singlecell multi-omics studies. However, challenges include computational complexity and dependence on short-read curation. To address this, we developed a comprehensive toolkit, scNanoGPS to calculate same-cell genotypes-phenotypes without short-read guidance. We applied scNanoGPS onto 23,587 long-read transcriptomes from 4 tumors and 2 cell lines. Standalone, scNanoGPS accurately deconvoluted error-prone long-reads into single-cells and single-molecules. Further, scNanoGPS simultaneously accessed both phenotypes (expressions/isoforms) and genotypes (mutations) of individual cells. Our analyses revealed that tumor and stroma/immune cells often expressed significantly distinct combinations of isoforms (DCIs). In a kidney tumor, we identified 924 genes with DCIs involved in cell-type-specific functions such as PDE10A in tumor cells and CCL3 in lymphocytes. Moreover, transcriptome-wide mutation analyses identified many cell-type-specific mutations including VEGFA mutations in tumor cells and HLA-A mutations in immune cells, highlighting critical roles of different populations in tumors. Together, scNanoGPS facilitates applications of single-cell long-read sequencing.

Docosahexaenoic acid (DHA) intake estimated from a 7-question survey identifies pregnancies most likely to benefit from high-dose DHA supplementation

BACKGROUND

Two randomized trials found women with low blood docosahexaenoic acid (DHA; an omega 3 fatty acid) had fewer early preterm births (<34 weeks gestation) if they were assigned to high dose DHA supplementation, however, there is currently no capacity for clinicians who care for pregnancies to obtain a blood assessment of DHA. Determining a way to identify women with low DHA intake whose risk could be lowered by high dose DHA supplementation is desired.

OBJECTIVE

To determine if assessing DHA intake can identify pregnancies that benefit from high dose DHA supplementation.

STUDY DESIGN

This secondary analysis used birth data from 1310 pregnant women who completed a 7-question food frequency questionnaire (DHA-FFQ) at 16.8 ± 2.5 weeks gestation that is validated to assess DHA status. They were then randomly assigned to a standard (200 mg/day) or high dose (800 or 1000 mg/day) DHA supplement for the remainder of pregnancy. Bayesian logistic regressions were fitted for early preterm birth and preterm birth as a function of DHA intake and assigned DHA dose.

RESULTS

Participants who consumed less than 150 mg/day DHA prior to 20 weeks' gestation (n = 810/1310, 58.1%) had a lower Bayesian posterior probability (pp) of early preterm birth if they were assigned to high dose DHA supplementation (1.4% vs 3.9%, pp = 0.99). The effect on preterm birth (<37 weeks) was also significant (11.3% vs 14.8%, pp = 0.97).

CONCLUSION

The DHA-FFQ can identify pregnancies that will benefit most from high dose DHA supplementation and reduce the risk of preterm birth. The DHA-FFQ is low burden to providers and patients and could be easily implemented in obstetrical practice.

Development and validation of the HARMS2-AF lifestyle risk score to predict incident AF

Background

Lifestyle risk factors (RFs) are a modifiable target in atrial fibrillation (AF) management. However, the relative contribution of individual lifestyle RFs to AF incidence has not been described.

Purpose

Development and validation of a novel AF-lifestyle risk score to determine AF risk in the general population.

Methods

The UK Biobank (UKB) is a large prospective cohort with outcomes measured &gt;10 years. In the UKB, we performed regression analysis of AF lifestyle RFs which were then evaluated in a multivariable model and a weighted score was developed. Next, the risk score was externally validated in the Framingham Heart Study (FHS) population. Kaplan-Meier estimates ascertained the 10-year risk of AF development.

Results

In the UKB, AF incidence was 5.3% among 302,926 participants, with a median time to AF 7.3 years (IQR 4.3–9.8). Hypertension, sleep apnoea, male sex, age, obesity (BMI&gt;30 kg/m2), alcohol and smoking were predictive variables (all p&lt;0.001); physical inactivity (OR 1.02,95% CI 0.97–1.10, p=0.3), diabetes (OR 0.98,95% CI 0.91–1.06, p=0.2) and BMI 27–30 kg/m2 (OR 1.02, 95% CI 0.97–1.07, p=0.424) were not significant. The HARMS2-AF score (Figure 1) had similar predictive performance (AUC=0.782, LogLoss 0.178, Brier Score 0.046) to the unweighted regression model (AUC 0.808) in the UKB. Validation in the FHS (AF incidence 6.7% of 7206 participants) maintained excellent predictive performance with an AUC of 0.747 (95% CI 0.724–0.769, Figure 2). A higher HARMS2-AF score (&gt;5 points) was associated with a heightened 10-year AF risk (score 5–9: OR 9.35, score 10–14: OR 33.34).

Conclusions

The HARMS2-AF score is a novel lifestyle risk score which may help identify individuals at risk of AF and assists in general population screening.

Funding Acknowledgement

Type of funding sources: None.

Catheter ablation in atrial fibrillation and heart failure with preserved ejection fraction improves peak pulmonary capillary wedge pressure, exercise capacity and quality of life: RCT STALL HFpEF

Introduction

Atrial fibrillation (AF) frequently accompanies heart failure with preserved ejection fraction (HFpEF). AF exacerbates HFpEF through adverse haemodynamic effects. In turn, HFpEF promotes AF through adverse left atrial remodelling. Observational data suggest sinus rhythm restoration improves outcomes in patients with AF and HFpEF. However, there are no randomised data examining the effects of rhythm control with catheter-based AF ablation on HFpEF outcomes.

Purpose

To compare the effects of AF ablation versus usual medical therapy on markers of HFpEF severity, including exercise haemodynamics, natriuretic peptide levels and patient symptoms.

Methods

Patients with symptomatic AF and HFpEF underwent exercise right heart catheterization (RHC) and cardiopulmonary exercise testing (CPET). HFpEF diagnosis was based on left ventricular ejection fraction (LVEF) ≥50%, elevated natriuretic peptide and echocardiographic diastolic impairment. HFpEF was confirmed on exercise RHC based on peak exercise pulmonary capillary wedge pressure (PCWP) of ≥25mmHg. Patients were randomised to AF ablation versus medical therapy, with investigations repeated at 6 months. The primary outcome was change in PCWP on follow-up.

Results

31 patients aged 66.1±7.5 years were randomized to AF ablation (16) versus medical therapy (15), with 51.6% female and 80.6% persistent AF. Baseline characteristics were comparable across groups. Paired analyses of ablation cohort showed significant reductions in peak PCWP (29.6±3.7 vs 25.9±4.6 mmHg, p&lt;0.01), PCWP indexed for workload (39.0±57.9 vs 33.0±50.5 mmHg/W/kg, p&lt;0.01), and BNP (146.2±80.5 vs 82.2±75.4 pg/mL, p=0.01); and increased resting cardiac output (4.6±0.9 vs 5.6±1.2 L/min, p=0.01), peak cardiac output (9.6±4.2 vs 10.4±3.7 L/min, p=0.02), peak (30s averaged) VO2 (1875.1±759.2 vs 2193.7±878.1 mL/min, p&lt;0.01), peak absolute VO2 (1937.3±739.3 vs 2216.3±861.9 mL/min, p&lt;0.01), peak (30s averaged) relative VO2 (19.4±5.9 vs 22.9±7.4 ml/kg/min) and peak workload (162.0±81.1 vs 184.4±83.4 W, p&lt;0.01). Quality of life scores improved: AFEQT (45.3±20.9 vs 75±20.7, p&lt;0.01) and MLHF (53±23.3 vs 17.5±22.8, p&lt;0.01). Reversal of HFpEF by PCWP criteria occurred in 31.2% following AF ablation, and 50% among those free from arrhythmia recurrence. In the medical arm, there were no significant differences in RHC, CPET, and natriuretic peptide outcomes on follow-up versus baseline. Repeated measures mixed ANOVA testing showed significant time-randomisation interaction on peak VO2, absolute peak VO2, peak relative VO2, AFEQT/ MLHF scores, suggesting that significant improvements in these parameters were related to AF ablation.

Conclusion

In patients with concomitant AF and HFpEF, AF ablation improves invasive exercise haemodynamic parameters, increases exercise capacity, and enhances quality of life. Successful AF ablation may reverse the clinical syndrome of HFpEF in a subset of cases.

Funding Acknowledgement

Type of funding sources: None.

Clinical risk prediction for left atrial appendage thrombus among patients with atrial fibrillation

Background

Exclusion of left atrial appendage thrombus (LAAT) by transoesophageal echocardiography (TOE) is recommended in patients with inadequate anticoagulation prior to direct cardioversion (DCR) or catheter ablation for atrial fibrillation/flutter (AF/AFL). LAAT risk factors in this population remain poorly defined.

Purpose

Determine LAAT predictors in AF/AFL patients undergoing pre-procedural TOE.

Methods

We evaluated available clinical and transthoracic echocardiographic (TTE) parameters in AF/AFL patients undergoing TOE between 1999–2022 in our institution in Melbourne, Australia. Regression analysis identified predictors of LAAT, which were applied to a weighted score developed in the derivation cohort (70%) and validated in the remaining 30%.

Results

Of 627 patients (age 62±12 years, 27% female, AF 84%,AFL 16%, left ventricular ejection fraction (LVEF) 44±20%), 24% had LAAT and 13.8% dense spontaneous echo contrast precluding DCR. Anticoagulation was NOAC 56.5%, warfarin 32.1% and none in 11.4%. In the LAAT cohort, thrombus resolution occurred in 39% on serial transoesophageal imaging with a median time to resolution of 131 days (IQR 54–398).

Diabetes (p=0.004), prior stroke (p=0.009), coronary disease (p=0.015), renal impairment (p&lt;0.001) and CHADS2VASc &gt;2 (73% vs. 55%, p&lt;0.001) were higher in the LAAT cohort. Age (p=0.093), gender (p=0.689), BMI (p=0.828), anticoagulant type (p=0.316) and diabetes (p=0.107) were not univariate predictors, whereas anticoagulation duration (&lt;30 days), creatinine and TTE markers of remodeling (LVEF, LAVI, RVSP and TAPSE) were independent predictors on univariate and multivariate regression; CHADS2VASc was not significant after adjustment (p=0.090). The weighted risk model included continuous (age, creatinine, LVEF, LAVI, TAPSE and RVSP) and categorical (anticoagulation duration) variables with excellent predictive performance: AUC 0.872 (95% CI 0.798–0.946), PPV 91%, NPV 70% and accuracy 80%.

Conclusion

A novel LAAT risk model comprising clinical and echocardiographic parameters enhances risk prediction over CHADS2VASc in AF/AFL and may guide the need for pre-procedural TOE imaging.

Funding Acknowledgement

Type of funding sources: None.

Patients and healthcare professionals views on injectables for cardiovascular disease

Introduction

Injectable medicines are increasingly used to manage risk factors for cardiovascular (CV) events, such as PCSK-9 inhibitors in dyslipidaemia and GLP-1 agonists in diabetes. However, there is a paucity of data around the administrative and clinical practicalities when using these injectables, and limited information on patient and healthcare professionals' perceptions.

Purpose

To identify the facilitators and barriers on the use of injectable therapies with CV benefits by undertaking interviews with patients, caregivers and healthcare professionals (HCPs).

Methods

Interviews were conducted via telephone and using MS Teams due to Covid-19 restrictions in the United Kingdom (London and Leeds) and Italy (Rome and Milan) in 2021. Coding was undertaken using NVivo and thematic analysis performed.

Results

A total of 56 patients were interviewed: 30 in the U.K. (mean age 66 yrs, 60% male) and 26 patients in Italy (mean age 63 yrs, 80% male) and 11 caregivers (mean age 59 yrs, 73% female). A total of 38 HCPs were interviewed, 19 in each country and composed of physicians (n=18), pharmacists (n=10), nurses (n=9) and pharmacy technician (n=1). Three distinct themes were identified: (i) Organisational and governance issues - relating to prescribing restrictions and availability of the drugs locally (PCSK9i are initiated and supplied from hospitals) and lack of communication between hospital and primary care setting; (ii) Clinical issues around HCPs' skills and experience - including: lack of experience with these injectables, lack of time to provide education to patients and caregivers, therapeutic inertia (HCPs not adopting a change in practice despite the evidence or due to bureaucratic restrictions) as well as lack of knowledge on long-term effects, and finally (iii) Patient-related issues - relating to behaviours and beliefs such as reluctance about using injectable therapies, and lack of education about these injectables in terms of indications/clinical benefits for use. Despite some differences in the prescribing of these injectables in the two countries, the analysis captured similar facilitators and barriers. Facilitators included prior use of injectables (e.g. insulin), and the ability to reach a clinical target of lower cholesterol by having just a “one shot”. HCPs stated that access to rapid pathology tests would aid uptake of injectables with CV benefit as well as having educational tools on these injectables in practice.

Conclusion

This qualitative study identified barriers to initiation, continuation, and adherence with injectable therapies with CV benefits but also highlighted areas where changes can be made especially around education and support for patients and HCPs.

Funding Acknowledgement

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): ACNAP education grant. Sponsored by Amgem and Novo Nordisk

An attention mechanism-based LSTM network for cancer kinase activity prediction

Despite the endeavours and achievements made in treating cancers during the past decades, resistance to available kinase drugs continues to be a major problem in cancer therapies. Thus, it is highly desirable to develop computational models that can predict the bioactivity of a compound against cancer kinases. Here, we present a Long Short-Term Memory (LSTM) framework for predicting the activities of lead molecules against seven different kinases. A total of 14,907 compounds from the ChEMBL database were selected for model building. Two different molecular representations, namely, 2D descriptors and MACCS fingerprints were subjected to the LSTM method for the training process. We also successfully integrated an attention mechanism into our model, which helped us to interpret the contribution of chemical features on kinase activity. The attention mechanism extracted the significant chemical moieties more effectively by taking them into consideration during the activity prediction. The recorded accuracies in the test sets for both 2D descriptors and MACCS fingerprints-based models were 0.81 and 0.78, respectively. The receiver operating characteristic curve (ROC)-area under the curve (AUC) score for both models was in the range of 0.8-0.99. The proposed framework can be a good starting point for the development of new cancer kinase drugs.

Utility of a 7- question online screener for DHA intake

The secondary analyses of two large, recently completed randomized clinical trials of DHA supplementation in pregnancy found that women with a low baseline DHA status benefited from randomization to a higher dose (800 vs 0 and 1000 vs 200 mg/day DHA). To obtain DHA status, it is necessary to obtain a blood sample and conduct an analysis using gas chromatography (GC) or GC-mass spectrometry (GCMS), both barriers to clinics where pregnant women receive advice on nutrition. Participants consuming less than 150 mg/day of DHA at baseline in our recent trial had a lower risk of early preterm birth and preterm birth when assigned to 1000 vs 200 m/day DHA. DHA intake was determined using a 7-question food frequency questionnaire administered by a trained nutritionist. Because the need for trained personnel to administer the questionnaire would be a barrier to implementing this finding in clinical management of pregnancy, the goal of this study was to determine if an online version of the questionnaire could be validly completed without assistance.

Defining genome-wide CRISPR-Cas genome-editing nuclease activity with GUIDE-seq

Genome-wide unbiased identification of double-stranded breaks enabled by sequencing (GUIDE-seq) is a sensitive, unbiased, genome-wide method for defining the activity of genome-editing nucleases in living cells. GUIDE-seq is based on the principle of efficient integration of an end-protected double-stranded oligodeoxynucleotide tag into sites of nuclease-induced DNA double-stranded breaks, followed by amplification of tag-containing genomic DNA molecules and high-throughput sequencing. Here we describe a detailed GUIDE-seq protocol including cell transfection, library preparation, sequencing and bioinformatic analysis. The entire protocol including cell culture can be completed in 9 d. Once tag-integrated genomic DNA is isolated, library preparation, sequencing and analysis can be performed in 3 d. The result is a genome-wide catalog of off-target sites ranked by nuclease activity as measured by GUIDE-seq read counts. GUIDE-seq is one of the most sensitive cell-based methods for defining genome-wide off-target activity and has been broadly adopted for research and therapeutic use.

A Phytocannabinoid Formula Containing Palmitoylethanolamide, Acmella Oleracea Extract, and Bovine Colostrum Filtrate Inhibited Cytokine and Chemokine Production in Human Peripheral Blood Mononuclear Cells Stimulated Ex Vivo

A phytocannabinoid formula containing copaiba essential oil, palmitoylethanolamide, Sichuan pepper extract, Acmella oleracea extract, cruciferous vegetable extracts blend, and bovine colostrum filtrate was tested for its ex vivo effect on inhibiting stimulated cytokine release in human peripheral blood mononuclear cells. Effects of the phytocannabinoid formula on the peripheral blood mononuclear cells viability were measured by alamarBlue™ to confirm no obvious cytotoxicity. The phytocannabinoid formula was compared to reference compounds for its ability to inhibit both the phytohemagglutinin-stimulated release of the cytokines from T-cells and the lipopolysaccharide-stimulated release of the cytokines from macrophages/monocytes in human peripheral blood mononuclear cells. The T cell cytokine responses measured were those of interleukins (interleukin-1β, interleukin-2, interleukin-4, interleukin-5, interleukin-6, interleukin-8, interleukin-10, and interleukin-13) and interferon-gamma, interferon gamma-induced protein 10, macrophage inflammatory protein-1α, and tumor necrosis factor-α. The macrophage and monocyte cytokine responses measured were of interleukin-1β, interleukin-6, interleukin-8, macrophage inflammatory protein-1α, and tumor necrosis factor-α. For the phytohemagglutinin-stimulated T cell production of cytokines, the peripheral blood mononuclear cells treated with the Phytocannabinoid formula at 2 μg/mL and 20 μg/mL showed significant inhibition of interleukin-2, interleukin-6, interleukin-5, interleukin-8, interleukin-10, interleukin-13, and interferon gamma-induced protein 10 production. The phytocannabinoid formula also significantly reduced the macrophage/monocyte production of interleukin-1β and interleukin-6. Results from the present study showed that the phytocannabinoid formula inhibited cytokines and chemokines production in ex vivo stimulated human peripheral blood mononuclear cells, suggesting a potential immunomodulatory effect.

1552 'The Modified Cappuccini Audit Tool: Patient Safety in the Operating Theatre'

Aim

To assess our trust over a period of two weeks with regard to safe supervision of surgical and anaesthetic trainees within the operating theatre using the Cappuccini audit tool.

Method

Between 7th of December 2020 and 18th December 2020 the anaesthetic and surgical team were approached and if there was a trainee present, they were asked a set of questions as follows:

If the supervisor is present in theatre no further action would be taken. If the supervisor was not present the volunteer would attempt to contact the supervisor by the method given by the trainee, and they were asked several questions:

Results

146 trainees were identified during our period. Of these the supervisor was present in 93% of cases. Of those not present 90% were contactable by phone, the other 10% were contactable by the trainee themselves. All trainees were happy to answer the questions was explained and all consultants were happy to be contacted. The average time to attend when not present was 2 minutes and 36 seconds.

Conclusions

We have shown the Cappuccini audit tool to be effective in determining safe supervision and found it in general to be well received within surgery and anaesthetics. We found our trust to have safe supervision in the operating theatre.

423 Patient Perspective on the Use of the Independent Sector to Maintain Elective NHS Services During the COVID-19 Pandemic

Introduction

COVID-19 resulted in the suspension of planned treatments for patients worldwide leaving millions suffering the physical and mental effects of delay. Reports indicate that when services have been re-established, patients have been afraid to take up appointments. Hospitals put processes in place to counter this, notably separating emergency and elective patient cohorts. Most notably seen by the co-operation between the NHS and independent private healthcare providers in March 2020 at the height of the pandemic. We undertook a study to ascertain the perceptions of NHS patients who underwent elective treatment at independent ‘cold’ sites during the COVID-19 pandemic.

Method

A cross-sectional study with structured telephone interviews of patients who had planned elective treatments at ‘cold’ independent hospitals between March and September 2020. 1150 patients were identified, and a 20% sample formed a 230 patient study group, with 158 (70%) agreeing to participate.

Results

30% of patients delayed their treatment due to COVID related concerns, with 76% of these only accepting treatment because this was at a ‘cold’ site. 46% of patients perceived treatment at a ‘cold’ site as the most important factor contributing to their safety. 153 patients (97%) supported the paid arrangement between the NHS and the independent sector to provide separate ‘cold’ sites for elective treatments.

Discussion

Safely restarting elective services to allow important planned treatments to take place, as was the pandemic continues, is a priority. Our study indicates that physical separation of patient pathways impacted most on patient confidence, and that the use of ‘cold’ sites is a viable option.

Enhanced homology-directed repair for highly efficient gene editing in hematopoietic stem/progenitor cells

Lentivector gene therapy for X-linked chronic granulomatous disease (X-CGD) has proven to be a viable approach, but random vector integration and subnormal protein production from exogenous promoters in transduced cells remain concerning for long-term safety and efficacy. A previous genome editing-based approach using Streptococcus pyogenes Cas9 mRNA and an oligodeoxynucleotide donor to repair genetic mutations showed the capability to restore physiological protein expression but lacked sufficient efficiency in quiescent CD34+ hematopoietic cells for clinical translation. Here, we report that transient inhibition of p53-binding protein 1 (53BP1) significantly increased (2.3-fold) long-term homology-directed repair to achieve highly efficient (80% gp91phox+ cells compared with healthy donor control subjects) long-term correction of X-CGD CD34+ cells.