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Many congratulations to Dr Simona Valletta, a postdoctoral research in MRC MHU, who was awarded an Intermediate Research Fellowship from the Kay Kendall Leukaemia Fund.
Treatment and Care of Patients with ST-Segment Elevation Myocardial Infarction—What Challenges Remain after Three Decades of Primary Percutaneous Coronary Intervention?
Primary percutaneous coronary intervention (pPCI) has revolutionized the prognosis of ST-segment elevation myocardial infarction (STEMI) and is the gold standard treatment. As a result of its success, the number of pPCI centres has expanded worldwide. Despite decades of advancements, clinical outcomes in STEMI patients have plateaued. Out-of-hospital cardiac arrest and cardiogenic shock remain a major cause of high in-hospital mortality, whilst the growing burden of heart failure in long-term STEMI survivors presents a growing problem. Many elements aiming to optimize STEMI treatment are still subject to debate or lack sufficient evidence. This review provides an overview of the most contentious current issues in pPCI in STEMI patients, with an emphasis on unresolved questions and persistent challenges.
An Explainable Coarse-to-Fine Survival Analysis Method on Multi-Center Whole Slide Images
Survival models based on whole slide images (WSIs) arewidely used in precision medicine to treat cancer patients better. Most previous studies attempted to address the challenge ofWSIs' gigapixel resolutions to survival models, but they failed in terms of computational efficiency and interpretability ofmodels. This study proposes a coarse-to-fine survival model called WSISur based on graph neural networks, which not only solves the above two problems but also achieves the best survival prediction performance. To solve the issue of computational efficiency, coarse WSI graphs are first constructed on low-resolution images in WSIs, and then fine WSI graphs are built with high-resolution images on the basis of coarse WSI graphs. Subsequent survival analysis is performed on the constructed WSI graphs. To solve the issue of interpretability of the model,WSIs' regions most relevant to patients' lifetimes are identified by gradient-weighted class activation mapping. Nevertheless, due to the imbalance of data labels, there is a problem of probability failure in end-to-end mini-batch training. To this end, a survival event sampling strategy is proposed to balance data labels. In addition, a series of experiments are carried out on multicenter datasets to evaluate the proposed model.Experimental results show that WSISur achieves the state-of-the-art result compared with other existing related methods, and has stronger domain invariance. Results also demonstrate the interpretability of WSISur. Impact Statement-Survival models based on WSI play an important role in precision medicine. Existing WSI based survival models have lowcomputational efficiency and lack of interpretability. A novel survival model we propose in this study overcomes these limitations. The proposed survival model is not only computationally efficient but also interpretable. Moreover, the proposed survival model also shows a performance improvement of nearly 23%~29% over existing methods on multi-center datasets.
Gastroschisis: A National Cohort Study to Describe Contemporary Surgical Strategies and Outcomes
This was a survey of all the cases of gastroschisis (n = 393) managed within the 28 neonatal surgical units in the UK and Ireland (18 months in 2006-2008) from a predicted birth cohort of 1.1 million. Results: Infants were divided into simple gastroschisis (n = 336, 85.5%) and complex gastroschisis (n = 45, 11.5%) - unknown category (n =12, 3%). Virtually all were detected antenatally (n = 385, 98%). Operative primary closure (n = 170, 51%) and staged closure after a preformed silo (n = 120, 36%) were the most commonly used techniques by intension for simple gastroschisis. There were 6 (2%) neonatal deaths (all in the simple group). Outcomes for infants in the complex group were significantly worse. They were more likely to be ventilated postoperatively (risk ratio [RR], 1.21; 95% CI, 1.09-1.33), more likely to require reoperation (RR, 6.53; 95% CI, 4.70-9.09), more likely to develop intestinal failure associated liver disease (RR, 8.21; 95% CI,3.70-18.2) and more likely to receive total parenteral nutrition for >28 days (RR, 2.07; 95% CI, 1.71-2.51). Conclusions: This study provided a comprehensive picture of current UK and Ireland practice for gastroschisis and a national benchmark.
A Novel Macrophage Subpopulation Conveys Increased Genetic Risk of Coronary Artery Disease.
BACKGROUND: Coronary artery disease (CAD), the leading cause of death worldwide, is influenced by both environmental and genetic factors. Although over 250 genetic risk loci have been identified through genome-wide association studies, the specific causal variants and their regulatory mechanisms are still largely unknown, particularly in disease-relevant cell types like macrophages. METHODS: We utilized single-cell RNA-seq and single-cell multiomics approaches in primary human monocyte-derived macrophages to explore the transcriptional regulatory network involved in a critical pathogenic event of coronary atherosclerosis-the formation of lipid-laden foam cells. The relative genetic contribution to CAD was assessed by partitioning disease heritability across different macrophage subpopulations. Meta-analysis of single-cell RNA-seq data sets from 38 human atherosclerotic samples was conducted to provide high-resolution cross-referencing to macrophage subpopulations in vivo. RESULTS: We identified 18 782 cis-regulatory elements by jointly profiling the gene expression and chromatin accessibility of >5000 macrophages. Integration with CAD genome-wide association study data prioritized 121 CAD-related genetic variants and 56 candidate causal genes. We showed that CAD heritability was not uniformly distributed and was particularly enriched in the gene programs of a novel CD52-hi lipid-handling macrophage subpopulation. These CD52-hi macrophages displayed significantly less lipoprotein accumulation and were also found in human atherosclerotic plaques. We investigated the cis-regulatory effect of a risk variant rs10488763 on FDX1, implicating the recruitment of AP-1 and C/EBP-β in the causal mechanisms at this locus. CONCLUSIONS: Our results provide genetic evidence of the divergent roles of macrophage subsets in atherogenesis and highlight lipid-handling macrophages as a key subpopulation through which genetic variants operate to influence disease. These findings provide an unbiased framework for functional fine-mapping of genome-wide association study results using single-cell multiomics and offer new insights into the genotype-environment interactions underlying atherosclerotic disease.
Single nucleus and spatial transcriptomic profiling of healthy human hamstring tendon.
The molecular and cellular basis of health in human tendons remains poorly understood. Among human tendons, hamstring tendon has markedly low pathology and can provide a prototypic healthy tendon reference. The aim of this study was to determine the transcriptomes and location of all cell types in healthy hamstring tendon. Using single nucleus RNA sequencing, we profiled the transcriptomes of 10 533 nuclei from four healthy donors and identified 12 distinct cell types. We confirmed the presence of two fibroblast cell types, endothelial cells, mural cells, and immune cells, and identified cell types previously unreported in tendons, including different skeletal muscle cell types, satellite cells, adipocytes, and undefined nervous system cells. The location of these cell types within tendon was defined using spatial transcriptomics and imaging, and potential transcriptional networks and cell-cell interactions were analyzed. We demonstrate that fibroblasts have the highest number of potential cell-cell interactions in our dataset, are present throughout the tendon, and play an important role in the production and organization of extracellular matrix, thus confirming their role as key regulators of hamstring tendon homeostasis. Overall, our findings underscore the complexity of the cellular networks that underpin healthy human tendon function and the central role of fibroblasts as key regulators of hamstring tendon tissue homeostasis.
The circadian clock component BMAL1 regulates SARS-CoV-2 entry and replication in lung epithelial cells.
The COVID-19 pandemic, caused by SARS-CoV-2 coronavirus, is a global health issue with unprecedented challenges for public health. SARS-CoV-2 primarily infects cells of the respiratory tract, via Spike glycoprotein binding angiotensin-converting enzyme (ACE2). Circadian rhythms coordinate an organism’s response to its environment and can regulate host susceptibility to virus infection. We demonstrate a circadian regulation of ACE2 in lung epithelial cells and show that silencing BMAL1 or treatment with a synthetic REV-ERB agonist SR9009 reduces ACE2 expression and inhibits SARS-CoV-2 entry. Treating infected cells with SR9009 limits viral replication and secretion of infectious particles, showing that post-entry steps in the viral life cycle are influenced by the circadian system. Transcriptome analysis revealed that Bmal1 silencing induced a wide spectrum of interferon stimulated genes in Calu-3 lung epithelial cells, providing a mechanism for the circadian pathway to dampen SARS-CoV-2 infection. Our study suggests new approaches to understand and improve therapeutic targeting of SARS-CoV-2.
Broadly neutralizing aptamers to SARS-CoV-2: A diverse panel of modified DNA antiviral agents.
Since its discovery, COVID-19 has rapidly spread across the globe and has had a massive toll on human health, with infection mortality rates as high as 10%, and a crippling impact on the world economy. Despite numerous advances, there remains an urgent need for accurate and rapid point-of-care diagnostic tests and better therapeutic treatment options. To contribute chemically distinct, non-protein-based affinity reagents, we report here the identification of modified DNA-based aptamers that selectively bind to the S1, S2, or receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Several aptamers inhibit the binding of the spike protein to its cell-surface receptor angiotensin-converting enzyme 2 (ACE2) and neutralize authentic SARS-CoV-2 virus in vitro, including all variants of concern. With a high degree of nuclease resistance imparted by the base modifications, these reagents represent a new class of molecules with potential for further development as diagnostics or therapeutics.
Recombinant single-cycle influenza virus with exchangeable pseudotypes allows repeated immunization to augment anti-tumour immunity with immune checkpoint inhibitors.
Virus-based tumour vaccines offer many advantages compared to other antigen-delivering systems. They generate concerted innate and adaptive immune response, and robust CD8+ T cell responses. We engineered a non-replicating pseudotyped influenza virus (S-FLU) to deliver the well-known cancer testis antigen, NY-ESO-1 (NY-ESO-1 S-FLU). Intranasal or intramuscular immunization of NY-ESO-1 S-FLU virus in mice elicited a strong NY-ESO-1-specific CD8+ T cell response in lungs and spleen that resulted in the regression of NY-ESO-1-expressing lung tumour and subcutaneous tumour, respectively. Combined administration with anti-PD-1 antibody, NY-ESO-1 S-FLU virus augmented the tumour protection by reducing the tumour metastasis. We propose that the antigen delivery through S-FLU is highly efficient in inducing antigen-specific CD8+ T cell response and protection against tumour development in combination with PD-1 blockade.
Inclusion of cGAMP within virus-like particle vaccines enhances their immunogenicity.
Cyclic GMP-AMP (cGAMP) is an immunostimulatory molecule produced by cGAS that activates STING. cGAMP is an adjuvant when administered alongside antigens. cGAMP is also incorporated into enveloped virus particles during budding. Here, we investigate whether inclusion of cGAMP within viral vaccine vectors enhances their immunogenicity. We immunise mice with virus-like particles (VLPs) containing HIV-1 Gag and the vesicular stomatitis virus envelope glycoprotein G (VSV-G). cGAMP loading of VLPs augments CD4 and CD8 T-cell responses. It also increases VLP- and VSV-G-specific antibody titres in a STING-dependent manner and enhances virus neutralisation, accompanied by increased numbers of T follicular helper cells. Vaccination with cGAMP-loaded VLPs containing haemagglutinin induces high titres of influenza A virus neutralising antibodies and confers protection upon virus challenge. This requires cGAMP inclusion within VLPs and is achieved at markedly reduced cGAMP doses. Similarly, cGAMP loading of VLPs containing the SARS-CoV-2 Spike protein enhances Spike-specific antibody titres. cGAMP-loaded VLPs are thus an attractive platform for vaccination.
Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient
The COVID-19 pandemic has had unprecedented health and economic impact, but currently there are no approved therapies. We have isolated an antibody, EY6A, from a late-stage COVID-19 patient and show it neutralises SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds tightly (K D of 2 nM) the receptor binding domain (RBD) of the viral Spike glycoprotein and a 2.6Å crystal structure of an RBD/EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues of this epitope are key to stabilising the pre-fusion Spike. Cryo-EM analyses of the pre-fusion Spike incubated with EY6A Fab reveal a complex of the intact trimer with three Fabs bound and two further multimeric forms comprising destabilized Spike attached to Fab. EY6A binds what is probably a major neutralising epitope, making it a candidate therapeutic for COVID-19.
Neutralization of SARS-CoV-2 by destruction of the prefusion Spike
Summary There are as yet no licenced therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 Å of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilising, CR3022 epitope is inaccessible in the prefusion Spike, suggesting that CR3022 binding would facilitate conversion to the fusion-incompetent post-fusion state. Cryo-EM analysis confirms that incubation of Spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope may be useful therapeutically, possibly in synergy with an antibody blocking receptor attachment. Highlights CR3022 neutralises SARS-CoV-2 Neutralisation is by destroying the prefusion SPIKE conformation This antibody may have therapeutic potential alone or with one blocking receptor attachment
Correction: Breadth and function of antibody response to acute SARS-CoV-2 infection in humans.
[This corrects the article DOI: 10.1371/journal.ppat.1009352.].
Comparison of two assays to detect IgG antibodies to the receptor binding domain of SARS‑CoV‑2 as a surrogate marker for assessing neutralizing antibodies in COVID-19 patients.
BACKGROUND: Neutralizing antibodies (NAbs) are important for protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection. In this study, two assays that are correlated with NAbs were compared: the haemagglutination test (HAT) and the surrogate virus neutralization test (sVNT). METHODS: The specificity of the HAT was compared with the sVNT, and the sensitivity and persistence of antibodies in patients with varying severity of illness was assessed in a cohort of 71 patients at 4-6 weeks and 13-16 weeks. The kinetics were assessed in the first, second, and third weeks in patients with varying severity of acute illness. RESULTS: The specificity of the HAT was >99%, and sensitivity was similar to the sVNT. The levels of HAT were significantly and positively correlated with those of the sVNT (Spearman's r = 0.78, P < 0.0001). Patients with moderate and severe illness had higher HAT titres when compared to those with mild illness. Six of seven patients with severe illness had a titre of >1:640 during the second week of illness, whereas only five of 31 patients with a mild illness had a titre of >1:160 in the second week of illness. CONCLUSIONS: Since the HAT is a simple and very cheap assay to perform, it would be ideal to use as an indicator of NAbs in resource-poor settings.