bluuebunny/crossref_metadata_2025 huggingface dataset:
Septins function in exocytosis via physical interactions with the exocyst complex in fission yeast cytokinesis
Authors: Singh Davinder , Liu Yajun , Zhu Yi-Hua , Zhang Sha , Naegele Shelby , Wu Jian-Qiu
Published: July 2024

Septins can function as scaffolds for protein recruitment, membrane-bound diffusion barriers, or membrane curvature sensors. Septins are important for cytokinesis, but their exact roles are still obscure. In fission yeast, four septins (Spn1 to Spn4) accumulate at the rim of the division plane as rings. The octameric exocyst complex, which tethers exocytic vesicles to the plasma membrane, exhibits a similar localization and is essential for plasma membrane deposition during cytokinesis. Without septins, the exocyst spreads across the division plane but absent from the rim during septum formation. These results suggest that septins and the exocyst physically interact for proper localization. Indeed, we predicted six pairs of direct interactions between septin and exocyst subunits by AlphaFold2 ColabFold, most of them are confirmed by co-immunoprecipitation and yeast two-hybrid assays. Exocyst mislocalization results in mistargeting of secretory vesicles and their cargos, which leads to cell-separation delay in septin mutants. Our results indicate that septins guide the targeting of exocyst complex on the plasma membrane for vesicle tethering during cytokinesis through direct physical interactions.
TIM-3 blockade enhances ex vivo stimulated allogeneic NK cell therapy for relapsed murine neuroblastoma after hematopoietic cell transplant
Authors: Quamine Aicha , Mohrdieck Nicholas R , King Chloe A , Griggs Anastasia A , Kline Jillian M , Cho Monica Moonkyung , Rinella Sean P , Tippins Katharine E , Bates Paul D , Shi Lei , Song Longzhen , Hess Nicholas J , Kearl Tyce J , Johnson Bryon D , Capitini Christian M
Published: July 2024

Background: High-risk neuroblastoma (HR-NBL) is an aggressive tumor of the sympathetic nervous system with high risk of relapse and poor overall survival. Allogeneic hematopoietic cell transplant (allo-HCT) has been used previously in HR-NBL patients; however, graft-versus-host-disease (GVHD) and disease progression have limited clinical application. Ex-vivo stimulated allogeneic natural killer (NK) cells represent a potential approach to enhance the graft-versus-tumor (GVT) effect without exacerbation of GVHD but have not shown efficacy in NBL. Methods: Ex-vivo stimulated NK cells from C57BL/6NCr (B6) mice were expanded with soluble IL-15/IL-15Rα alone or with irradiated CD137L/CD54+ AgN2a-4P (15-4P) at a 1:1 ratio for 10-12 days. Allogeneic NK cells were then analyzed for activation, proliferation, cytokine production, and cytotoxicity against two murine NBL cell lines, Neuro2a and NXS2, in the absence or presence of anti-TIM-3. Lethally irradiated B6AJF1 Mice received allo-HCT from B6 donors followed by NBL challenge after 7 days to mimic tumor relapse. Select groups received anti-TIM-3 starting on day 9 for every 4 days with/without infusions of 15-4P B6 NK cells on days 14, 21, and 28. In select experiments, T cell and NK cells were selectively depleted to establish their contribution to the GVT effect. All groups were analyzed for tumor growth, GVHD and overall survival. Results: Co-culturing NK cells with 15-4P results in 78-fold expansion with increased expression of Ki-67 and NKG2D, NKp46, TRAIL and TIM-3. 15-4P stimulated allogeneic NK cells showed enhanced cytotoxicity against NBL compared to IL-15 NK cells alone but was limited in part due to high expression of TIM-3 ligands on Neuro-2a compared to NXS2. The addition of TIM-3 blockade further enhanced NK cytotoxicity versus Neuro-2a, with enhanced 15-4P NK cell degranulation, Eomes, TRAIL and FasL expression observed. Analysis of RNA from 15-4P NK cells exposed to TIM-3 blockade showed gene expression of chemokines, NKG2D/DAP12 signaling, non-canonical NF-κb pathway and TRAIL signaling. Blockade of NKG2D, TRAIL or FasL on 15-4P NK cells abrogated cytotoxicity. In vivo, the combination of 15-4P stimulated allogeneic NK cells and TIM-3 blockade after allo-HCT resulted in prolonged survival against NBL with decreased tumor burden compared to NK cells or anti-TIM-3 alone, without inducing GVHD. Depletion of NK cells, but not T cells, abrogated the GVT effect. Conclusion: Allo-HCT can be a platform for treating NBL using combination ex-vivo stimulated allogeneic NK cell therapy with TIM-3 blockade to enhance the GVT effect without inducing GVHD.
Metabolic PCTA-Based Shift Reagents for the Selective Detection of Extracellular Lactate Using CEST MRI
Authors: Chiaffarelli Remy , Cruz Pedro , Zimmermann Max , Geraldes Carlos F. G. C. , Jurek Paul , F. Martins Andre
Published: July 2024

Lactate is a key metabolic driver in oncology and immunology. Even in the presence of physiological oxygen levels, most cancer cells upregulate anaerobic glycolysis, resulting in abnormal lactate production and accumulation in the tumor micro-environment. The development of more effective, sensitive, and safe probes for detecting extracellular lactate holds the potential to impact cancer metabolic profiling and staging significantly. Macrocyclic-based PARACEST agents have been report-ed to act as shift reagents (SRs) and detect extracellular lactate via CEST MRI. Here, we introduce a new family of SRs based on the PCTA ligand, an inherently stable and kinetically inert group of molecules with the potential for (pre)clinical translation. We observed that Yb-PCTA and Eu-PCTA can significantly shift lactate -OH signals in CEST spectra. In vitro, CEST MRI experiments proved that imaging extracellular lactate with these complexes is feasible and maintains high specificity even in the presence of competing small metabolites in blood and the tumor microenvironment. In vivo, preclinical imaging demonstrated that Yb-PCTA can be safely administered intravenously in mice to detect extracellular lactate non-invasively. This work represents a significant step towards precision and molecular imaging, demonstrating that the PCTA-ligand is a promising scaffold for developing molecular imaging sensors. These chemical sensors have broad medical applications, particularly in oncology and physiology.
Physical interaction with Ephrin B1 promotes CXCR4 intracellular localization and oncogenic potential
Authors: Rabbito Alessandro , Otun Omolade , Fumagalli Amos , Séveno Martial , Galant Sonya , Counson Manuel , Durroux Thierry , Bechara Cherine , Smit Martine J , Granier Sébastien , Szpakowska Martyna , Chevigné Andy , Chaumont-Dubel Séverine , Marin Philippe
Published: July 2024

Chemokine receptor 4 (CXCR4) is a member of the chemokine receptor exclusively activated by the chemokine CXCL12. While CXCR4 regulates numerous physiological processes associated with cell migration and embryogenesis, its overexpression has been involved in various cancer types. Studies suggest that intracellular CXCR4 expression rather than CXCR4-operated signaling underlies its pro-tumorigenic functions. Given the role of GPCR interacting proteins in their trafficking and subcellular localization, we characterized the CXCR4 interactome using an affinity purification coupled to mass spectrometry (AP-MS) strategy. The most abundant protein identified in the CXCR4 interactome is Ephrin B1, a member of the Ephrin protein family that shares several functions with CXCR4, such as the regulation of cell migration and proliferation. Further studies showed that interaction between CXCR4 and Ephrin B1 is direct and enhanced by treating cell with CXCL12. They also indicated that Ephrin B1 prevents CXCR4 N-glycosylation, decreases CXCR4 cell surface expression and consistently inhibits CXCL12-induced CXCR4 coupling to Gαi1-3and the recruitment of β-arrestins 1 and 2. Conversely, Ephrin B1 signals to Erk1,2 through CXCR4 activation and mediates the decrease in Death Receptor 5 expression elicited by intracellular CXCR4. Collectively, these findings identify Ephrin B1 as a key mediator of CXCR4 tumorigenic signaling.
Improved characterization of single-cell RNA-seq libraries with paired-end avidity sequencing
Authors: Chamberlin John T , Gillen Austin E , Quinlan Aaron R
Published: July 2024

Prevailing poly(dT)-primed 3' single-cell RNA-seq protocols generate barcoded cDNA fragments containing the reverse transcriptase priming site, which is expected to be the poly(A) tail or a genomic adenine homopolymer. Direct sequencing across this priming site was historically difficult because of DNA sequencing errors induced by the homopolymeric primer at the "barcode" end. Here, we evaluate the capability of "avidity base chemistry" DNA sequencing from Element Biosciences to sequence through this homopolymer accurately, and the impact of the additional cDNA sequence on read alignment and precise quantification of polyadenylation site usage. We find that the Element Aviti instrument sequences through the thymine homopolymer into the subsequent cDNA sequence without detectable loss of accuracy. The resulting paired-end alignments enable direct and independent assignment of reads to polyadenylation sites, which bypasses complexities and limitations of conventional approaches but does not consistently improve read mapping rates compared to single-end alignment. We also characterize low-level artifacts and arrive at an adjusted adapter trimming and alignment workflow that significantly improves the alignment of sequence data from Element and Illumina, particularly in the context of extended read lengths. Our analyses confirm that Element avidity sequencing is an effective alternative to Illumina sequencing for standard single-cell RNA-seq, particularly for polyadenylation site analyses but do not rule out the potential for similar performance from other emerging platforms.
Dual inhibition of ATR and DNA-PKcs radiosensitizes ATM-mutant prostate cancer
Authors: Hofstad Mia , Woods Andrea , Parra Karla , Sychev Zoi E. , Mazzagatti Alice , Yu Lan , Gilbreath Collin , Ly Peter , Drake Justin M. , Kittler Ralf
Published: July 2024

In advanced castration resistant prostate cancer (CRPC), mutations in the DNA damage response (DDR) geneataxia telangiectasia mutated(ATM) are common. While poly(ADP-ribose) polymerase inhibitors are approved in this context, their clinical efficacy remains limited. Thus, there is a compelling need to identify alternative therapeutic avenues forATMmutant prostate cancer patients. Here, we generated matched ATM-proficient and ATM-deficient CRPC lines to elucidate the impact of ATM loss on DDR in response to DNA damage via irradiation. Through unbiased phosphoproteomic screening, we unveiled that ATM-deficient CRPC lines maintain dependence on downstream ATM targets through activation of ATR and DNA-PKcs kinases. Dual inhibition of ATR and DNA-PKcs effectively inhibited downstream γH2AX foci formation in response to irradiation and radiosensitized ATM-deficient lines to a greater extent than either ATM-proficient controls or single drug treatment. Further, dual inhibition abrogated residual downstream ATM pathway signaling and impaired replication fork dynamics. To circumvent potential toxicity, we leveraged the RUVBL1/2 ATPase inhibitor Compound B, which leads to the degradation of both ATR and DNA-PKcs kinases. Compound B effectively radiosensitized ATM-deficient CRPCin vitroandin vivo, and impacted replication fork dynamics. Overall, dual targeting of both ATR and DNA-PKcs is necessary to block DDR in ATM-deficient CRPC, and Compound B could be utilized as a novel therapy in combination with irradiation in these patients.

Graphical Abstract
A multiomic atlas of human early skeletal development
Authors: To Ken , Fei Lijiang , Patrick Pett J. , Roberts Kenny , Polański Krzysztof , Li Tong , Yayon Nadav , He Peng , Xu Chuan , Cranley James , Li Ruoyan , Kanemaru Kazumasa , Huang Ni , Megas Stathis , Richardson Laura , Kapuge Rakesh , Perera Shani , Tuck Elizabeth , Wilbrey-Clark Anna , Mulas Ilaria , Memi Fani , Cakir Batuhan , Predeus Alexander V. , Horsfall David , Murray Simon , Prete Martin , Mazin Pavel , He Xiaoling , Meyer Kerstin B. , Haniffa Muzlifah , Barker Roger A. , Bayraktar Omer , Buckley Christopher D. , Teichmann Sarah A.
Published: July 2024

Bone and joint formation in the developing skeleton rely on co-ordinated differentiation of progenitors in the nascent developing limbs and joints. The cell states, epigenetic processes and key regulatory factors underlying their lineage commitment to osteogenic and other mesenchymal populations during ossification and joint formation remain poorly understood and are largely unexplored in human studies. Here, we apply paired single-nuclei transcriptional and epigenetic profiling of 336,000 droplets, in addition to spatial transcriptomics, to construct a comprehensive atlas of human bone, cartilage and joint development in the shoulder, hip, knee and cranium from 5 to 11 post-conception weeks. Spatial mapping of cell clusters to our highly multiplexed in situ sequencing (ISS) data using our newly developed tool ISS-Patcher revealed new cellular mechanisms of zonation during bone and joint formation. Combined modelling of chromatin accessibility and RNA expression allowed the identification of the transcriptional and epigenetic regulatory landscapes that drive differentiation of mesenchymal lineages including osteogenic and chondrogenic lineages, and novel chondrocyte cell states. In particular, we define regionally distinct limb and cranial osteoprogenitor populations and trajectories across the fetal skeleton and characterise differential regulatory networks that govern intramembranous and endochondral ossification. We also introduce SNP2Cell, a tool to link cell-type specific regulatory networks to numerous polygenic traits such as osteoarthritis. We also conductin silicoperturbations of genes that cause monogenic craniosynostosis and implicate potential pathogenic cell states and disease mechanisms involved. This work forms a detailed and dynamic regulatory atlas of human fetal skeletal maturation and advances our fundamental understanding of cell fate determination in human skeletal development.
Proteome-Wide Bioinformatic Annotation and Functional Validation of the Monotopic Phosphoglycosyl Transferase Superfamily
Authors: Durand Theo , Dodge Greg J. , Siuda Roxanne P. , Higinbotham Hugh R. , Arbour Christine A. , Ghosh Soumi , Allen Karen N. , Imperiali Barbara
Published: July 2024

Phosphoglycosyl transferases (PGTs) are membrane proteins that initiate glycoconjugate biosynthesis by transferring a phospho-sugar moiety from a soluble nucleoside diphosphate sugar to a membrane-embedded polyprenol phosphate acceptor. The centrality of PGTs in complex glycan assembly and the current lack of functional information make these enzymes high-value targets for biochemical investigation. In particular, the small monotopic PGT family is exclusively bacterial and represents the minimal functional unit of the monotopic PGT superfamily. Here, we combine a sequence similarity network (SSN) analysis with a generalizable, luminescence-based activity assay to probe the substrate specificity of this family of monoPGTs in a bacterial cell-membrane fraction. This strategy allows us to identify specificity on a far more significant scale than previously achievable and correlate preferred substrate specificities with predicted structural differences within the conserved monoPGT fold. Finally, we present the proof-of-concept for a small-scale inhibitor screen (eight nucleoside analogs) with four monoPGTs of diverse substrate specificity, thus building a foundation for future inhibitor discovery initiatives.

Significance

Uncovering the function and specificity of enzymes responsible for glycoconjugate biosynthesis traditionally requires a multi-faceted and individually curated approach. This is especially true for bacterial glycoconjugates due to greater monosaccharide diversity and a paucity of established structural information. Here we leverage bioinformatic and in-vitro tools to predict and validate substrate specificity for a unique, exclusively bacterial family of enzymes responsible for the first step in many of these glycan assembly pathways. We further show that this platform is suitable for enhanced functional annotation and inhibitor testing, paving the way for the development of urgently needed antibiotics.
Opening the digital doorway to sexual healthcare: Recommendations from a Behaviour Change Wheel analysis of barriers and facilitators to seeking online sexual health information and support among underserved populations
Authors: McLeod Julie , Estcourt Claudia S. , MacDonald Jennifer , Gibbs Jo , Woode Owusu Melvina , Mapp Fiona , Gallego Marquez Nuria , McInnes-Dean Amelia , Saunders John , Blandford Ann , Flowers Paul
Published: July 2024

Background

The ability to access and navigate online sexual health information and support is increasingly needed in order to engage with wider sexual healthcare. However, people from underserved populations may struggle to pass though this “digital doorway”. Therefore, using a behavioural science approach, we first aimed to identify barriers and facilitators to: i) seeking online sexual health information and ii) seeking online sexual health support. Subsequently, we aimed to generate theory-informed recommendations to improve these access points.

Methods

The PROGRESS framework guided purposive recruitment (October 2021–April 2022) of 35 UK participants from diverse backgrounds, including 51% from the most deprived areas and 26% from minoritised ethnic groups. Semi-structured interviews and thematic analysis identified barriers and facilitators to seeking online sexual health information and support. A Behaviour Change Wheel (BCW) analysis then identified recommendations to better meet the needs of underserved populations.

Results

We found diverse barriers and facilitators. Barriers included low awareness of and familiarity with online information and support; perceptions that online information and support were unlikely to meet the needs of underserved populations; overwhelming volume of information sources; lack of personal relevancy; chatbots/automated responses; and response wait times. Facilitators included clarity about credibility and quality; inclusive content; and in-person assistance. Recommendations included: Education and Persuasion e.g., online and offline promotion and endorsement by healthcare professionals and peers; Training and Modelling e.g., accessible training to enhance searching skills and credibility appraisal; and Environmental Restructuring and Enablement e.g., modifications to ensure online information and support are simple and easy to use, including video/audio options for content.

Conclusions

Given that access to many sexual health services is now digital, our analyses produced recommendations pivotal to increasing access to wider sexual healthcare among underserved populations. Implementing these recommendations could reduce inequalities associated with accessing and using online sexual health service.
ADHD symptom reduction after following an FFD is associated with gut microbiome composition
Authors: Hontelez S , Guthrie M , Stobernack T , van Baarlen P , Rousseau C , Boks MP , Rodrigues Pereira R , Boekhorst J , Kleerebezem M
Published: July 2024

Attention-deficit hyperactivity disorder (ADHD) is one of the most common childhood neuropsychiatric conditions. Both (epi)genetic and environmental factors are suggested to contribute to the aetiology of ADHD. In the last decade, nutrition has received considerable attention as potential environmental factor triggering ADHD behaviour. Studies applying a few-foods diet (FFD) can lead to behavioural improvements of at least 40% in 50-64% of children with ADHD. It is conceivable that the Microbiota-Gut-Brain (MGB) axis is involved in the mechanism of action underlying the behavioural improvements observed in children with ADHD after following the FFD. This study investigated potential associations between changes in ADHD symptoms in children that followed an FFD. We identified a significant association between microbiota composition and change in ADHD symptoms in food-associated ADHD.
The higher benefit of lecanemab in males compared to females in CLARITY AD is probably due to a real sex effect
Authors: Andrews Daniel , Ducharme Simon , Chertkow Howard , Sormani Maria Pia , Collins D. Louis ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: July 2024

INTRODUCTION

The Phase 3 trial CLARITY AD found that lecanemab slowed cognitive decline by a statistically significant 27% vs. placebo. However, the subgroup analysis indicated a significant sex difference in the effect, and recent work has implied that lecanemab has either no or limited effectiveness in females. To resolve this ambiguity, we used simulations constrained by the trial design to determine whether the difference could be explained by known sex differences in Alzheimer’s progression, or as an isolated random event.

METHODS

Simulations were generated using linear mixed models of cognitive decline fit to data from ADNI participants who satisfied CLARITY AD inclusion criteria.

RESULTS

The statistically nonsignificant 7.9% sex difference in cognitive decline rate observed in our selected ADNI participants does not explain the trial’s 31% sex difference in lecanemab’s effect. A ≥31% difference occurred randomly in only 12 of our 10,000 simulations, signifying a probability of 0.0012.

DISCUSSION

Our results are consistent with those from CLARITY AD. Lecanemab likely affects females and males differently, but we cannot conclude that the drug is ineffective in females.
Fundamental limits to the effectiveness of traveler screening with molecular tests
Authors: Bubar Kate M. , Middleton Casey E. , Larremore Daniel B. , Gostic Katelyn M.
Published: July 2024

Despite the appeal of screening travelers during emerging infectious disease outbreaks, evidence shows that syndromic and questionnaire-based programs are largely ineffective in preventing or delaying the geographic spread of infection. Molecular tests offer high sensitivity and specificity, and can detect infections earlier than symptom screening, suggesting potential for improved outcomes, yet molecular tests were used to screen travelers for COVID-19 with mixed success. To investigate why screening for COVID-19 was not more successful, and to quantify the limits of screening for other pathogens of concern, we developed a probabilistic model that incorporates within-host viral kinetics. We then evaluated the potential effectiveness of screening travelers with molecular tests for influenza A, SARS-CoV-1, SARS-CoV-2, and Ebola virus. Even under highly optimistic assumptions about behavior and test characteristics, we find screening effectiveness is always limited because the infections with the highest transmission potential are undetectable at the time of travel, an idea we term the fundamental limit of traveler screening. We also demonstrate how estimates of ascertainment are a misleading substitute for screening effectiveness because they overestimate reductions in transmission at the destination. Understanding these limitations can guide the deployment of future traveler screening programs and inform strategies to improve outbreak prevention and control.
His-MMDM: Multi-domain and Multi-omics Translation of Histopathological Images with Diffusion Models
Authors: Li Zhongxiao , Su Tianqi , Zhang Bin , Han Wenkai , Zhang Sibin , Sun Guiyin , Cong Yuwei , Chen Xin , Qi Jiping , Wang Yujie , Zhao Shiguang , Meng Hongxue , Liang Peng , Gao Xin
Published: July 2024

Generative AI (GenAI) has advanced computational pathology through various image translation models. These models synthesize histopathological images from existing ones, facilitating tasks such as color normalization and virtual staining. Current models, while effective, are mostly dedicated to specific source-target domain pairs and lack scalability for multi-domain translations. Here we introduce His-MMDM, a diffusion model-based framework enabling multi-domain and multi-omics histopathological image translation. His-MMDM is not only effective in performing existing tasks such as transforming cryosectioned images to FFPE ones and virtual immunohistochemical (IHC) staining but can also facilitate knowledge transfer between different tumor types and between primary and metastatic tumors. Additionally, it performs genomics-and/or transcriptomics-guided editing of histopathological images, illustrating the impact of driver mutations and oncogenic pathway alterations on tissue histopathology and educating pathologists to recognize them. These versatile capabilities position His-MMDM as a versatile tool in the GenAI toolkit for future pathologists.
Phosphoproteomics uncovers exercise intensity-specific signaling networks underlying high-intensity interval training in human skeletal muscle
Authors: Hoffman Nolan J. , Whitfield Jamie , Xiao Di , Radford Bridget E. , Suni Veronika , Blazev Ronnie , Yang Pengyi , Parker Benjamin L. , Hawley John A.
Published: July 2024

In response to exercise, protein kinases and signaling networks are rapidly engaged in skeletal muscle to maintain energy homeostasis. High-intensity interval training (HIIT) induces superior or similar health-promoting skeletal muscle and whole-body adaptations compared to prolonged, moderate-intensity continuous training (MICT). However, the exercise intensity-specific signaling pathways underlying HIIT versus MICT are unknown. Ten healthy male participants completed bouts of work- and duration-matched HIIT and MICT cycling in randomized crossover trials. Mass spectrometry-based phosphoproteomic analysis of human muscle biopsies mapped acute signaling responses to HIIT and MICT, identifying 14,931 phosphopeptides and 8,509 phosphosites. Bioinformatics uncovered >1,000 phosphosites significantly regulated by HIIT and/or MICT, including 92 and 348 respective HIIT-specific phosphosites after 5 and 10 min and >3,000 total phosphosites significantly correlated with plasma lactate. This first human muscle HIIT signaling network map has revealed rapid exercise intensity-specific regulation of kinases, substrates and pathways that may contribute to HIIT’s unique health-promoting effects.
Is aging acceleration mediating the association between hemoglobin glycation index and cardiovascular disease?
Authors: Liu Na , Li Yun , Li Mengying , Wang Yi , Li Bo , Lian Yongqiang , Fu Jianfang , Li Xiaomiao , Zhou Jie
Published: July 2024

Background

The potential factors beyond HbA1c that increase the risk of cardiovascular disease and age more quickly in people with diabetes are not yet clear. This study sought to determine the prospective associations between discrepancies in observed and predicted HbA1c levels, also known as the hemoglobin glycation index (HGI), and cardiovascular disease risk. Additionally, the interactions of HGI with accelerated aging in relation to cardiovascular disease risk were evaluated.

Method

This cross-sectional study included 9167 adults from the National Health and Nutrition Examination Survey 1999–2010. The HGI is used to assess individual blood glucose variability, and phenotypic age acceleration is employed to evaluate accelerated aging. Regression analysis, restricted cubic spline and mediation analysis explore the potential roles of phenotypic age acceleration in the relationship between HGI and CVD mortality.

Results

Among the 9167 eligible participants (aged 20 years or older), 4390 (47.9%) were males, and the median (IQR) age was 48.0 (15.0) years; 4403 (48.0%) had prediabetes and diabetes, and 985 (10.7%) had cardiovascular disease. Restricted cubic splines showed that the association between HGI and CVD risk was nonlinear (p < 0.001). The greater the negative value of the HGI was, the greater the risk of CVD, and the association was independent of age, sex and HbA1c. Mediation analyses confirmed that phenotypic age acceleration acted as a mediator in the association between HGI and CVD risk (mediated effect: OR, 68.7%, 95% CI: 36.4%-153%,P=0.002).

Conclusion and Relevance

The HGI serves as a robust biomarker for assessing the acceleration of aging, regardless of HbA1c levels, and is associated with increased susceptibility to cardiovascular disease, particularly among individuals characterized by negative HGI.
Application of Principal Component Analysis to Heterogenous Fontan Registry Data Identifies Independent Contributing Factors to Decline
Authors: Ferrari Margaret R. , Schäfer Michal , Hunter Kendall S. , Di Maria Michael V.
Published: July 2024

Single ventricle heart disease is a severe and life-threatening illness, and improvements in clinical outcomes of those with Fontan circulation have not yet yielded acceptable survival over the past two decades. Patients are at risk of developing a diverse variety of Fontan-associated comorbidities that ultimately requires heart transplant. Our observational cohort study goal was to determine if principal component analysis (PCA) applied to data collected from a substantial Fontan cohort can predict functional decline (N=140). Heterogeneous data broadly consisting of measures of cardiac and vascular function, exercise (VO2max), lymphatic biomarkers, and blood biomarkers were collected over 11 years at a single site; in that time, 16 events occurred that are considered here in a composite outcome measure. After standardization and PCA, principal components (PCs) representing >5% of total variance were thematically labeled based on their constituents and tested for association with the composite outcome. Our main findings suggest that the 6thPC (PC6), representing 7.1% percent of the total variance in the set, is greatly influenced by blood serum biomarkers and superior vena cava flow, is a superior measure of proportional hazard compared to EF, and displayed the greatest accuracy for classifying Fontan patients as determined by AUC. In bivariate hazard analysis, we found that models combining systolic function (EF or PC5) and lymphatic dysfunction (PC6) were most predictive, with the former having the greatest AIC, and the latter having the highest c-statistic. Our findings support our hypothesis that a multifactorial model must be considered to improve prognosis in the Fontan population.
The skin microbiome as a new potential biomarker in the domestication and welfare of Octopus vulgaris
Authors: Costas-Imbernon Daniel , Costas-Prado Carolina , Sequeiro Teresa , Tourinan Pablo , Garcia-Fernandez Pablo , Tur Ricardo , Chavarrias David , Saura Maria , Rotllant Josep
Published: July 2024

Over the past decade, there has been a growing interest in common octopus aquaculture, prompted by the increasing market demand, the decline in overall fisheries and the search for a more sustainable food resource. Nevertheless, this interest has raised concerns about the potential impact of large-scale production and intensified farming practices in the future. Given the growing interest in octopus aquaculture and society's increasing concern for animal welfare, this study investigates the mucosal skin microbiota of wild and captive-bred common octopuses. The primary aim is to determine if breeding in captivity affects these communities and consequently animal welfare, using 16S ribosomal RNA metabarcoding. The core microbiota of common octopus mucosal skin is composed of the phyla Bacteroidota, Proteobacteria, Campylobacterota and Verrucomicrobiota, according to our findings. Although variations in abundance were observed, wild and aquaculture octopuses had comparable microbiota composition and diversity. Gammaproteobacteria were found to be enriched in wild mucosal skin samples, and some of the species were described as potentially pathogenic. However, these species were absent or in lower abundance in aquaculture mucosal skin samples. Additionally, analysis of KEGGs predictions showed that wild mucosal skin samples had a higher overall enrichment in functional pathways, primarily associated with xenobiotic remediation pathways, compared to the aquaculture mucosal skin samples. This is the first study to characterize the mucosal skin microbiome of the common octopus and compare the microbiome of wild and aquaculture individuals of this species. The results indicate that current aquaculture practices align with animal welfare through the use of controlled hatchery environments and high-quality water conditions. This study offers valuable insights into the microbiome of the common octopus, which can serve as a biomarker for evaluating animal welfare. It also explores the implications of these findings for the development of sustainable and responsible aquaculture practices.
Phages carry orphan antitoxin-like enzymes to neutralize the DarTG1 toxin-antitoxin defense system
Authors: Johannesman Anna , Carlson Nico A , LeRoux Michele
Published: July 2024

The astounding number of anti-phage defenses encoded by bacteria is countered by an elaborate set of phage counter-defenses, though their evolutionary origins are often unknown. Here, we discover an orphan antitoxin counter-defense element in T4-like phages that can overcome the bacterial toxin-antitoxin phage defense system, DarTG1. The DarT1 toxin, an ADP-ribosyltransferase, modifies phage DNA to prevent replication while its cognate antitoxin, DarG1, is an ADP-ribosylglycohydrolase that reverses these modifications in uninfected bacteria. The orphan phage DarG1-like protein, which we term anti-DarT factor NADAR (AdfN), removes ADP-ribose modifications from phage DNA during infection thereby enabling replication in DarTG1-containing bacteria. AdfN, like DarG1, is in the NADAR superfamily of ADP-ribosylglycohydrolases found across domains of life. We find divergent NADAR proteins in unrelated phages that likewise exhibit anti-DarTG1 activity, underscoring the importance of ADP-ribosylation in bacterial-phage interactions, and revealing the function of a substantial subset of the NADAR superfamily.
SSR42 is a Novel Regulator of Cytolytic Activity inStaphylococcus aureus
Authors: Jobson Mary-Elizabeth , Tomlinson Brooke R. , Mustor Emilee M. , Felton Emily A. , Weiss Andy , Caswell Clayton C. , Shaw Lindsey N.
Published: July 2024

SSR42 is the longest noncoding RNA in theS. aureuscell and the second-most abundant transcript in the stationary phase transcriptome, second only to RNAIII. It is highly conserved across strains and exhibits pronounced stability in stationary phase, however the mechanism behind its regulatory role has yet to be fully elucidated. Herein, we used transcriptomic and proteomic approaches to probe the role of SSR42, revealing that it is a powerful, novel activator of the primary leukocidin LukAB. SSR42 is required for cytotoxicity towards, and escape from within, human neutrophils, and also mediates survival within human blood. We show that SSR42 wields this role via derepression by the peroxide repressor PerR in response to the presence of human neutrophils and governslukABinduction in this niche. Importantly, this regulation is driven by direct RNA-RNA interaction, as we show binding of the 5’ UTR of thelukABtranscript with the 3’ end of SSR42, which ultimately modulates transcript stability as well as translational activity. Finally, we demonstrate that this behavior is absolutely required for full virulence ofS. aureusin murine models of both pneumonia and sepsis. Collectively, we present SSR42 as a pleiotropic regulatory RNA that acts as a nexus between environmental sensing and the regulation of pathogenesis, responding to environmental stimuli and host immune factors to bolster cytotoxic behavior and facilitate infection inS. aureus.

Importance

S. aureusis a master pathogen due to its formidable collection of virulence factors. These are tightly controlled by a diverse group of regulators that titrate their abundance to adapt to unique infectious niches. The role of regulatory RNAs in stress adaptation and pathogenesis is becoming increasingly more relevant inS. aureus. In this study, we provide the most comprehensive global analysis to date of just such a factor, SSR42. Specifically, we uncover that SSR42 is required for mediating cytotoxicity - one of the pillars of infection - in response to phagocytosis by human neutrophils. We find that SSR42 is induced by components of the host immune system and facilitates downstream activation of cytotoxic factors via RNA-RNA interactions. This illustrates that SSR42 forms a pivotal link between sensing the external environment and mediating resistance to oxidative stress while promoting virulence, solidifying it as a major global regulator inS. aureus.
G-Quadruplex Structures in 16S rRNA Regions Correlate with Thermal Adaptation in Prokaryotes
Authors: Lyu Bo , Song Qisheng
Published: July 2024

G-quadruplex (G4) structure is a nucleic acid secondary structure formed by sequences rich in guanine, playing essential roles in various biological processes such as gene regulation, maintenance of genome stability, and adaptation to environmental stresses. Although prokaryotes growing at high temperatures have higher GC contents, the pattern of G4 structure presence associated with GC content variation in thermal adaptation within genomes and ribosomal genes is rarely reported. In this study, we analyzed 681 bacterial genomes to investigate the role of G4 structures in thermal adaptation. Our findings revealed a strong positive correlation between G4 patterns in the region encoding 16S rRNA genes and optimal growth temperatures (Topt), whereas genomic GC content and overall G4 patterns did not show significant correlations with Topt. Evolutionary analysis showed significant differences in G4 stability betweenThermotoga(Topt≥ 80 °C) andPseudothermotoga(60°C ≤ Topt< 80°C) species, withThermotogaspecies exhibiting higher G4 stability, indicating stronger selective pressure for G4 stability under extreme conditions. Circular dichroism analysis showed that specific base mutations at key sites resulted in the absence of G4 thermal stability and structural integrity inThermotogacompared toPseudothermotoga. Collectively, this study suggests that the G4 structures in 16S rRNA encoding regions emerged as key indicators of thermal adaptation and contributes to our understanding of the molecular basis of thermal adaptation.
Cryo-EM Structures of Clostridium perfringens Enterotoxin Bound to its Human Receptor, Claudin-4
Authors: Rathnayake Sewwandi S. , Erramilli Satchal K. , Kossiakoff Anthony A. , Vecchio Alex J.
Published: July 2024

Pathogenic strains of Clostridium perfringens secrete an enterotoxin (CpE) that causes prevalent, severe, and sometimes deadly gastrointestinal disorders in humans and domesticated animals. CpE binds selectively to membrane protein receptors called claudins on the apical surfaces of small intestinal epithelium. Claudins normally construct tight junctions that regulate epithelial paracellular transport but are hijacked from doing so by CpE and are instead led to form claudin/CpE small complexes. Small complexes are building blocks for assembling oligomeric β-barrel pores that penetrate the plasma membrane and induce gut cytotoxicity. Here we present structures of CpE in complexes with its native claudin receptor in humans, claudin-4, at 4.0 and 2.8 Å using cryogenic electron microscopy. The structures reveal the overall architecture of the small complex, that the small complex can be kinetically trapped, and resolve its key features; like the residues used in claudin/CpE complex binding, the orientation of CpE relative to the membrane, and CpE-induced structural changes to claudin-4. Further, the structures allude to the biophysical procession from small complex to cytotoxic β-barrel pore used by CpE during pathogenesis and the role of trypsin in this process. In full, this work elucidates the structure and mechanism of claudin-bound CpE pore assembly and provides strategies to obstruct its formation to treat CpE-induced gastrointestinal diseases.
Expansion and revision of the genus Xanthobacter and proposal of Roseixanthobacter gen. nov.
Authors: Soltysiak Maximillian P. M. , Jalihal Amogh P. , Christophersen Caroline E. , Ory Audrey L. H. , Lee Andrew D. , Boulton Jessica M. , Springer Michael
Published: July 2024

The nitrogen-fixing, chemolithoautotrophic genus Xanthobacter is found worldwide across numerous diverse environments and is an important member of many ecosystems. These species serve as model systems for their metabolic properties in academic settings and have industrial applications in bioremediation and sustainable protein, food, and fertilizer production. Despite their abundance, interest, and importance, the majority of Xanthobacter strains are without a genome sequence, and only 8 validly published species are known to date. To expand our understanding of the diversity and evolutionary history of the genus, we sequenced the genomes of 37 repository strains and 26 novel environmental strains we isolated. After performing comparative phylogenomic analyses, we expand and revise the genus Xanthobacter and propose the novel genus Roseixanthobacter gen. nov. For the Xanthobacter, we describe 10 novel species, bringing the total to 18: Xanthobacter agilis, Xanthobacter albus sp. nov., Xanthobacter aminoxidans, Xanthobacter autotrophicus, Xanthobacter cornucopiae sp. nov., Xanthobacter dioxanivorans, Xanthobacter flavus, Xanthobacter lutulentifluminis sp. nov., Xanthobacter nonsaccharivorans sp. nov., Xanthobacter oligotrophicus, Xanthobacter pseudotagetidis sp. nov., Xanthobacter sediminis sp. nov., Xanthobacter tagetidis, Xanthobacter toluenivorans sp. nov., Xanthobacter variabilis sp. nov., Xanthobacter versatilis sp. nov., Xanthobacter viscosus, and Xanthobacter wiegelii sp. nov. For the Roseixanthobacter gen. nov., we describe 5 novel species formerly classified as Xanthobacter: Roseixanthobacter finlandensis sp. nov., Roseixanthobacter glucoisosaccharinivorans sp. nov., Roseixanthobacter liquoris sp. nov., Roseixanthobacter pseudopolyaromaticivorans sp. nov., and Roseixanthobacter psychrophilus sp. nov. We characterized the phenotypic properties of these type strains, including temperature, salinity and pH ranges, carbon substrate utilization, motility, antibiotic susceptibility, slime production, autotrophic growth, and enzymatic activities. We discovered a more diverse range of phenotypes across the genus Xanthobacter than previously known and elucidated the evolutionary history within the genus. These findings and genome sequences will help further the application of Xanthobacter biology in academic, industrial, and environmental settings and provide additional insight into the unique biological properties that make these species attractive for such applications.
A novel monocyte-based biomarker of cardiovascular risk: comparison with QRISK3
Authors: Almarri Fatemah , Padayachee Soundrie , Kerr Alexander , Patel Ashish , Ferro Albert
Published: July 2024

Aims

Circulating monocyte-platelet aggregates (MPA) and CD14+/CD16+monocytes are elevated in symptomatic patients with atherosclerotic cardiovascular disease. The aim of this study was to investigate their utility in prediction of early atherosclerosis in asymptomatic subjects, in comparison to a traditional cardiovascular risk calculator, QRISK3.

Methods

Asymptomatic patients attending the hypertension clinic at Guy’s & St Thomas’ Hospitals, London, and healthy volunteer subjects recruited by advertisement, were enrolled (n = 39). Blood (30 mL) was processed for flow cytometry to measure CD14 and CD16 expression on monocytes, and CD14+CD42b+MPA. Using these measurements, a novel index termed the Monocyte Atherosclerotic Risk Score (MARS) was developed. All subjects also underwent carotid artery ultrasonic angiography.

Results

Both QRISK3 and MARS correlated significantly with carotid intima-media thickness (cIMT); however, the correlation was much closer for MARS (r2= 0.8705, P < 0.0001) than for QRISK3 (r2= 0.3012, P = 0.0025). ROC analysis revealed MARS to be highly predictive both of cIMT-determined high cardiovascular risk (C-index = 0.9273, P = 0.0001) and presence of carotid plaque (C-index = 0.9385, P = 0.0022), whereas QRISK3 was not.

Conclusions

MARS appears superior to QRISK3 in predicting both cIMT and carotid plaque disease. This may help to better identify asymptomatic individuals who would benefit from targeted imaging investigations and prophylactic therapies.

LAY SUMMARY

In healthy people with no clinical evidence of cardiovascular disease, prediction of risk of atherosclerotic disease (including coronary heart disease and stroke) is notoriously unreliable; although traditional cardiovascular risk calculators work well at a population level, they are much less reliable in individuals.

We have developed a blood based biomarker, which we term MARS, which is highly predictive of silent atherosclerosis: much more so than the traditional risk calculator QRISK3, currently in use in the UK.

This opens the way to develop a blood test which can be applied clinically to more precisely identify healthy individuals who are at high cardiovascular risk, and who would therefore benefit from further imaging investigations and intensive treatment of cardiovascular risk factors.
Distinct immune signatures are a potent tool in the clinical management of cytokine-related syndrome during immune checkpoint therapy
Authors: Daoudlarian Douglas , Segot Amandine , Latifyan Sofiya , Bartolini Robin , Joo Victor , Mederos Nuria , Bouchaab Hasna , Demicheli Rita , Abdelhamid Karim , Ferahta Nabila , Doms Jacqueline , Stalder Grégoire , Noto Alessandra , Mencarelli Lucrezia , Mosimann Valérie , Berthold Dominik , Stravodimou Athina , Sartori Claudio , Shabafrouz Keyvan , Thompson John A , Wang Yinghong , Peters Solange , Pantaleo Giuseppe , Obeid Michel
Published: July 2024

Immune-related cytokine release syndrome (irCRS) frequently occurs during immune checkpoint inhibitor (ICI) therapy. In the present study, we have attempted to identify biomarkers in oncology patients experiencing irCRS-like symptoms (n=35), including 9 patients with hemophagocytic lymphohistiocytosis (irHLH)-like manifestations (8 classified as Grade (G) 4 irCRS and 1 as G3 irCRS) and 8 with sepsis, differentiating between irCRS, irHLH and sepsis. Patients grouped in three clusters based on distinct cytokine profiles and survival outcomes. We identified 24 biomarkers that significantly discriminated between irHLH and irCRS G3 (P < 0.0455 to < 0.0027). Notably, HGF and ferritin demonstrated superior predictive values over the traditional HScore, with a positive predictive value (PPV) and negative predictive value (NPV) of 100%. Furthermore, CXCL9 not only distinguished between irHLH and irCRS G3, but was also a predictor of treatment intensification with tocilizumab (TCZ) with a PPV of 90% and a NPV of 100%. Other parameters, such as leukocyte count, neutrophils, ferritin, IL-6, IL-7, EGF, fibrinogen, and GM-CSF, were effective in discriminating sepsis from high-grade irCRS with a PPV of 75-80% and an NPV of 100%. In comparison to sepsis, the frequencies of CXCR5+ or CCR4+ CD8 memory, CD38+ ITM monocytes, and CD62L+ neutrophils were observed to be higher in high-Grade irCRS. Of note, TCZ treatment led to complete resolution of clinical symptoms in 12 patients with high-grade irCRS refractory to corticosteroids (CS). These findings demonstrate the power of unique immunologic biomarkers in determining the severity of irCRS, in predicting survival, and distinguishing between high-grade irCRS, irHLH and sepsis. Therefore, these distinct unique signatures are instrumental for the optimal development of personalized clinical and therapeutic management in patients experiencing irCRS patient.