bluuebunny/crossref_metadata_2025 huggingface dataset:
Lower estimated glomerular filtration rate relates to cognitive impairment and brain alterations
Authors: Rahayel Shady , Goupil Rémi , Genest Dominique Suzanne , Lamarche Florence , Agharazii Mohsen , Ayral Violette , Tremblay Christina , Madore François
Published: September 2024

Introduction

Chronic kidney disease is associated with cognitive decline and changes in brain structure. However, their associations remain unclear, particularly the selective vulnerability characteristics that make some brain regions more vulnerable.

Methods

We investigated the association between eGFR and cognitive function in 15,897 individuals from the CARTaGENE cohort. We performed vertex-based MRI analyses between eGFR and cortical thickness in the 1,397 participants who underwent brain MRI after six years. Imaging transcriptomics was used to characterize the gene expression and neurodegenerative features associated with this association.

Results

Lower eGFR correlated with reduced cognitive performance and brain structure. Brain regions associated with eGFR were enriched for mitochondrial and inflammatory-related genes. These associations occurred independently from age, sex, education, body mass index, Framingham risk score, and white matter lesion volume.

Discussion

This study highlights the link between reduced eGFR, cognitive impairment, and brain structure, revealing some of the kidney-brain axis mechanisms.
Decoding the Deadly Dance: NETosis Genes Predict Neonatal Sepsis Fate
Authors: Shaw Deepshikha , Santhanam Sridhar , Som Tapas Kumar , Bhattacharjee Samsiddhi , Mohapatra Saroj Kant
Published: September 2024

Background

Neonatal sepsis, a systemic inflammatory response to infection, is a major cause of morbidity and mortality in newborns. Neutrophil extracellular trap formation (NETosis), while crucial for pathogen clearance, can contribute to organ dysfunction in sepsis. This study aimed to identify key NETosis-related genes for prognostication in neonatal sepsis.

Methods

We analysed whole blood transcriptome datasets (GSE26440, GSE26378, GSE25504) from neonates with sepsis and controls. Differentially expressed NETosis genes (DE-NET genes) were identified, and a machine learning approach was used to select the most influential genes. A NET score model was constructed and validated using single-sample gene set enrichment analysis (ssGSEA). The model’s performance was evaluated using ROC analysis. The interplay between key-NET genes and the complement-coagulation (CC) system was investigated. Clinical samples were also collected for validation.

Results

Sixteen DE-NET genes were identified, and LASSO further refined these to 8 key-NET genes. The key-NET gene signature and NET score model showed excellent predictive performance (AUCs > 89%) in distinguishing survivors from non-survivors. Mediation analysis revealed that key-NET gene expression precedes and potentially drives complement-coagulation activation.

Conclusions

We present an 8-gene prognostic model for risk stratification in neonatal sepsis, based on early blood transcript signatures in neonates. Our findings underscore the central role of NETosis in sepsis- induced coagulopathy, revealing potential therapeutic targets for intervention.

Abstract Figure
ROBIN: A unified nanopore-based sequencing assay integrating real-time, intraoperative methylome classification and next-day comprehensive molecular brain tumour profiling for ultra-rapid tumour diagnostics
Authors: Deacon S , Cahyani I , Holmes N , Fox G , Munro R , Wibowo S , Murray T , Mason H , Housley M , Martin D , Sharif A , Patel A , Goldspring R , Brandner S , Sahm F , Smith S , Paine SML , Loose M
Published: September 2024

Background

Advances in our technological capacity to interrogate brain tumour biology has led to the ever-increasing use of genomic sequencing in routine diagnostic decision making. Presently, brain tumours are routinely classified based on their epigenetic signatures, leading to a paradigm shift in diagnostic pathways. Such testing can be performed so rapidly using nanopore sequencing that results can be provided intraoperatively. This information greatly improves upon the fidelity of smear diagnosis and can help surgeons tailor their approach, balancing the risks of surgery with the likely benefit. Nevertheless, full integrated diagnosis may require subsequent additional assays to detect pathognomonic somatic mutations and structural variants, thereby delaying the time to final diagnosis.

Methods

Here, we present ROBIN, a tool based upon PromethION nanopore sequencing technology that can provide both real-time, intraoperative methylome classification and next-day comprehensive molecular profiling within a single assay. ROBIN uniquely integrates three methylation classifiers1–3to improve diagnostic performance in the intraoperative setting.

Findings

We demonstrate classifier performance on 50 prospective intraoperative cases, achieving a diagnostic turnaround time under 2 hours and generating robust tumour classifications within minutes of sequencing. Furthermore, ROBIN can detect single nucleotide variants (SNVs), copy number variants (CNVs) and structural variants (SVs) in real-time, and is able to inform a complete integrated diagnosis within 24 hours. Classifier performance demonstrated concordance with final integrated diagnosis in 90% of prospective cases.

Interpretation

Nanopore sequencing can greatly improve upon the turnaround times for standard of care diagnostic testing, including sequencing, and is furthermore able to reliably provide clinically actionable intraoperative tumour classification.

Funding

The Jean-Shanks Foundation, the Pathological Society of Great Britain and Ireland, the British Neuropathological Society, and the Wellcome Trust.
Cardiovascular Risk Factors in Nurses at a Teaching Hospital
Authors: Kleebank Fernandes Lucas , Brasil Nobre Chaves Rangel Gisele , Luís Martins Renan , Fernando Martin Danilo , Fernandes de Godoy Moacir
Published: September 2024

Objective

To identify the prevalence of modifiable and non-modifiable risk factors related to cardiovascular diseases [CVDs] in the nursing team of a tertiary hospital in the interior of the state of São Paulo and suggest preventive practices.

Methods

This is a prospective-analytical epidemiological study, of a quantitative nature, carried out on 226 employees, in two stages: collection of self-declared data and measurement of anthropometric data.

Results

Risk factors such as family history of CVD (82.7%), alcoholism (57.1%), sedentary lifestyle (49.1%), insufficient sleep time (27.9%), high consumption of processed meals (98.2%) and sugary beverages (81.7%) were observed, among others. From anthropometric data, it was identified that 69.4% of participants are overweight (38.7%) or obese (30.6%) - evidenced by high waist circumference (48.6%) and a high waist-to-hip ratio (64.0%) - in addition to 17.1% who had blood pressure levels indicative of arterial hypertension. The majority reported not having a diagnosis of CVDs (76.1%), however, among those who do, more than half (53.7%) do not treat them properly.

Conclusion

It is observed that the prevalence of CVDs is not irrelevant in the group evaluated and that there is the presence of risk factors indicating a tendency for participants to develop new CVDs or worsen existing ones, due to the presence of harmful habits associated with an unhealthy lifestyle and lack of adherence to treatments. This study suggests the implementation of multidisciplinary action programs with employees, so that the main areas identified as deficient are addressed.
High-intensity focused ultrasound in treatment of primary breast cancer: a systematic review and meta-analysis
Authors: Alikarami Sogol , Harandi Hamid , Jahanshahi Ali , Zakavi Seyed Sina , Frounchi Negin , Mahalleh Mehrdad , Momtazmanesh Sara
Published: September 2024

Abstracts

Background

In recent years, the tumor management strategies have focused on less invasive methods, aiming to yield optimal efficacy while minimizing further complications and enhancing the overall outcome of patients. High-intensity focused ultrasound (HIFU), a known thermal ablative technique, has shown promising results in breast cancer treatment. Therefore, we performed this systematic review and meta-analysis to assess the clinical, histopathologic, immunologic, and radiologic outcomes of HIFU ablative therapy and its complications in patients with primary breast cancer.

Methods

We searched PubMed and Scopus databases to identify the eligible articles. Data extraction was conducted by two independent authors. A random effect model was employed to pool the proportion of remaining tumor after HIFU therapy in breast cancer. Pooled CD4/CD8 ratio mean difference between HIFU and radical mastectomy was, measured using a fixed-effect model.

Results

We included 26 studies and 677 participants in the systematic review. Tumor necrosis rates varied, with 4 studies reporting less than 50% complete necrosis and 5 more than 50%. Two studies observed HIFU-induced disturbances in microvasculature of the targeted tissue. Six noted no contrast enhancement in successfully treated areas, two observed a thin rim indicating necrosis or fibrosis, and four reported a persistent enhancement in MRI images associated with a residual viable tumor. The weighted proportion of patients with residual tumor was 58.45 (95% C: 45.48 – 71.42). The CD4/CD8 ratio was higher in the HIFU group, with a weighted mean difference of 0.6 (95% CI: 0.41 – 0.78). The most prevalent side effects were pain (47.14%) and skin burn (2.59%).

Conclusions

HIFU is a relatively safe procedure for treatment of breast cancer as an independent or conjugated therapy and its effectiveness is promising regarding histopathological response, immunological reactivity, and vascular damage in the targeted area.
ATP-dependent remodeling of chromatin condensates uncovers distinct mesoscale effects of two remodelers
Authors: Moore Camille , Wong Emily , Kaur Upneet , Chio Un Seng , Zhou Ziling , Ostrowski Megan , Wu Ke , Irkliyenko Iryna , Wang Sean , Ramani Vijay , Narlikar Geeta J
Published: September 2024

ATP-dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. Here, we investigate effects of two major remodelers, ACF and RSC using chromatin condensates and single-molecule footprinting. We find that both remodelers inhibit the formation of condensed chromatin. However, the remodelers have distinct effects on pre-formed chromatin condensates. ACF spaces nucleosomes without de-condensing the chromatin, explaining how ACF maintains nucleosome organization in transcriptionally repressed genomic regions. In contrast, RSC catalyzes ATP-dependent de-condensation of chromatin. Surprisingly, RSC also drives micron-scale movements of entire condensates. These newly uncovered activities of RSC explain its central role in transcriptional activation. The biological importance of remodelers may thus reflect both their effects on nucleosome mobilization and the corresponding consequences on chromatin dynamics at the mesoscale.
The holobiont's extracellular microbiome modulates the adaptation of an intracellular endosymbiont
Authors: Imchen Madangchanok , Kaur Rupinder , McGarry Angelina , Bordenstein Seth R
Published: September 2024

Animal holobionts contain two broad classes of microorganisms, intra- and extracellular microbes, that are largely studied in symbiotic siloes. Here we demonstrate the impact of the extracellular gut microbiome on an intracellular reproductive endosymbiont using the Drosophila melanogaster holobiont and its endosymbiont Wolbachia that adaptively cause a paternal-effect lethality of embryos termed cytoplasmic incompatibility (CI). We report the endosymbiont's adaptation is not only self-sufficient but stronger in a host without an extracellular microbiome. Indeed, host transcripts associated with the CI adaptation are enhanced, while cell biological hallmarks exhibit complex quantitative and qualitative differences in microbiome-free hosts. Decreases in the gut bacteria Lactobacillus specifically link with high penetrance of the CI adaptation. Notably, both the extracellular microbiome and endosymbiont harbor markedly higher cellular densities in a complete holobiont setting than when either constituent is reared alone. Altogether, this study uncovers a novel interaction whereby the extracellular microbiome modulates the phenotype of an intracellular endosymbiont, revealing intricate symbiotic networks within the holobiont.
Curriculum Learning: sequential acquisition of task complexity enhances neuronal discriminability
Authors: Shujah Maria , Joshi Suyash , Nakamura Mari , Barkat Tania Rinaldi
Published: September 2024

Curriculum Learning (CL) is a strategy where concepts with increasing complexity are acquired sequentially. Despite its widespread application, its putative neural mechanisms are poorly understood. In this study, using a multi-staged Go/No-Go auditory discrimination paradigm for mice, we show that CL improves and accelerates learning in a unidirectional way. By combining behavioral data within vivoelectrophysiological recordings of the auditory cortex, we demonstrate that neuronal discriminability is enhanced with sequential training. This improvement suggests that CL involves a convergence of common discriminable features in the auditory stimuli shared across tasks of different complexity. Our findings uncover specific properties of CL at the level of neuronal discriminability, distinguishing it from other forms of learning strategies.
Human CCR4-NOT globally regulates gene expression and is a novel silencer of retrotransposon activation
Authors: Kulkarni Shardul , Morrissey Alexis , Sebastian Aswathy , Giardine Belinda , Smith Courtney , Akinniyi Oluwasegun T. , Keller Cheryl A. , Arnaoutov Alexei , Albert Istvan , Mahony Shaun , Reese Joseph C.
Published: September 2024

CCR4-NOT regulates multiple steps in gene regulation and has been well studied in budding yeast, but much less is known about the human complex. Auxin-induced degradation was used to rapidly deplete the scaffold subunit CNOT1, and CNOT4, to characterize the functions of human CCR4-NOT in gene regulation. Depleting CNOT1 increased RNA levels and caused a widespread decrease in RNA decay. In contrast, CNOT4 depletion only modestly changed steady-state RNA levels and, surprisingly, led to a global acceleration in mRNA decay. Further, depleting either subunit resulted in a global increase in RNA synthesis. In contrast to most of the genome, the transcription of KRAB-Zinc-Finger-protein (KZNFs) genes, especially those on chromosome 19, was repressed. KZNFs are transcriptional repressors of retrotransposable elements (rTEs), and consistent with the decreased KZNFs expression, rTEs, mainly Long Interspersed Nuclear Elements (LINEs), were activated. These data establish CCR4-NOT as a global regulator of gene expression and a novel silencer of rTEs.
Shox2 is necessary for normal thalamic spindle function
Authors: Febbo Isabella , Maroteaux Matthieu , Yu Diankun , Warkins Valerie , Martinez LA , Anderson AE , Galazo MJ , Schrader LA
Published: September 2024

The cellular identity of thalamocortical neurons (TCNs), namely their firing properties, dictates brain-wide activity patterns, such as sleep spindles. Transcription factors are critical to the determination of cellular identity. Previously, we discovered that a subset of TCNs express the transcription factor, Shox2, and, in a globalShox2KO, established that TCNs within the anterior nucleus of the thalamus rely on the expression ofShox2to regulate key ion channels that are necessary to maintain their firing properties. From this, we hypothesized thatShox2expression, through the regulation of firing properties of TCNs, is critical for the thalamocortical circuit to generate spindle oscillations. We exploited the somatosensory thalamocortical circuit to investigate this by creating a primary somatosensory thalamus (VB)Shox2knockdown mouse model. We delivered Cre into the VB of P21 Shox2fl/flmice using viral infection and comparedin vitro, patch-clamp recordings fromShox2+andShox2knockdown TCNs, finding thatShox2expression is indeed critical to maintain burst and tonic firing properties of VB TCNs. Since Shox2 is important developmentally and firing from TCNs to cortex during development structures the circuit, we performed ultrasound-guided P3 injections at P3 to generate an early-stage, Shox2 VB knockdown, but found no changes in the layer four, barrel map (VB cortical target). Despite this, Shox2 knockdown mice exhibit reduced sleep-spindle EEG density. Further, key behaviors associated with spindles and proper VB thalamic function—memory consolidation and somatosensory perception—are significantly impaired. These results indicate that the impact on spindle function is likely due to cell autonomous changes to TCNs rather than circuit changes, confirming our hypothesis thatShox2is necessary for normal thalamic spindle function and implicating a potential role forShox2in autism and schizophrenia pathologies.
Small mammals in biodiversity hotspot harbor viruses of epidemic potential
Authors: Feng Yun , Kuang Guopeng , Pan Yuanfei , Wang Jing , Yang Weihong , Wu Wei-chen , Pan Hong , Wang Juan , Han Xi , Yang Lifen , Xin Gen-yang , Shan Yong-tao , Gou Qin-yu , Liu Xue , Guo Deyin , Liang Guodong , Holmes Edward C. , Gao Zihou , Shi Mang
Published: September 2024

Metagenomic sequencing has transformed our understanding of viral diversity in wildlife and its threat to human health. Despite this progress, many studies have lacked systematic and ecologically informed sampling, which has left numerous potentially emergent viruses undiscovered, and the drivers of their ecology and evolution poorly understood. We conducted an extensive analysis of viruses in the lung, spleen, and gut of 1,688 animals from 38 mammalian species across 428 sites in Yunnan, China—a hotspot for zoonotic diseases. We identified 162 mammalian viral species, including 102 novel species and 24 posing potential risks to humans due to their relationships with known pathogens associated with serious diseases and their ability to cross major host species barriers. Our findings offer an in-depth view of virus organotropism, cross-species transmission, host sharing patterns, and the ecological factors influencing viral evolution, all of which are critical for anticipating and mitigating future zoonotic outbreaks.
Effects Of Extrinsic Reward Based Skill Learning On Motor Plasticity
Authors: Yadav Goldy , Vassiliadis Pierre , Dubuc Cecile , Hummel Friedhelm C. , Derosiere Gerard , Duque Julie
Published: September 2024

Human motor skill acquisition is improved by performance feedback and coupling such feedback with extrinsic reward (such as money) can enhance skill learning. However, the neurophysiology underlying such behavioral effect is unclear. To bridge this gap, we assessed the effects of reward on multiple forms of motor plasticity during skill learning. Sixty-five healthy participants divided in three groups performed a pinch-grip skill task with sensory feedback only, sensory and reinforcement feedback or both feedback coupled with an extrinsic monetary reward during skill training. To probe motor plasticity, we applied transcranial magnetic stimulation on the left primary motor cortex at rest before, during and after training in the three groups. We evaluated the amplitude and variability of corticospinal output, GABA-ergic short-intracortical inhibition and use-dependent plasticity before training and at two time points during and after training. At the behavioral level, monetary reward accelerated skill learning. In parallel, corticospinal output became less variable early on during training in the presence of extrinsic reward. Interestingly, this effect was particularly pronounced for participants who were more sensitive to reward, as evaluated in an independent questionnaire. Other measures of motor excitability remained comparable across groups. These findings highlight that a mechanism underlying the benefit of reward on motor skill learning is the fine tuning of early-training resting-state corticospinal variability.

SIGNIFICANCE STATEMENT

Skill acquisition is enhanced in the presence of reward. Despite its potential clinical relevance for motor rehabilitation, the underlying neurophysiological mechanisms remain largely unexplored. Specifically, whether reward affects the plasticity of motor cortex in the context of skill learning is unclear. We show that reward reduces the variability of corticospinal output at an early stage during training and that this effect correlates with individual sensitivity to reward. Our results suggest that a key mechanism underlying the beneficial effect of reward on motor skill learning may be an increase in the stability of motor output in response to training during early stages of skill learning.
Astrocyte ezrin defines resilience to stress-induced depressive behaviours in mice
Authors: Lin Si-Si , Zhou Bin , Liu Si-Le , Ren Xing-Ying , Guo Jing , Tong Jing-Lin , Chen Bin-Jie , Jiang Ruo-Tian , Semyanov Alexey , Yi Chenju , Niu Jianqin , Illes Peter , Li Baoman , Tang Yong , Verkhratsky Alexei
Published: September 2024

Astrocyte atrophy is the main histopathological hallmark of major depressive disorder (MDD) in humans and in animal models of depression. Here we demonstrated that manipulating with ezrin expression specifically in astrocytes significantly increases the resilience of mice to chronic unpredictable mild stress (CUMS). Overexpression of ezrin in astrocytes from prefrontal cortex (PFC) rescued depressive-like behaviours induced by CUMS, whereas down-regulation of ezrin in astrocytes from PFC increased mice susceptibility to CUMS and promoted depressive-like behaviours. These behavioural changes correlated with astrocytic morphology. Astrocytes from PFC of mice sensitive to CUMS demonstrated significant atrophy; similar atrophy was found in astrocytes from animals with down-regulated ezrin expression. To the contrary morphology remains unchanged astrocytes in animals resistant to CUMS and in animals with astrocytic overexpression of ezrin. Morphological changes also correlated with ezrin immunoreactivity which was low in mice with depressive-like behaviours and high in mice resistant to stress. We conclude that Ezrin-dependent morphological remodelling of astrocytes defines the sensitivity of mice to stress: high ezrin expression renders them stress resilient, whereas low ezrin expression promotes depressive-like behaviour in response to chronic stress.
A High Frequency of Detection of Recombinant Koala Retrovirus (recKoRV) in Victorian Koalas Suggests Historic Integration of KoRV
Authors: Zheng Louize , Legione Alistair R
Published: September 2024

Recombinant koala retrovirus (recKoRV) is a recently discovered variant of koala retrovirus (KoRV), which likely emerged due to the insertion of another retrovirus (likely Phascolarctos endogenous retrovirus) into the backbone of KoRV. KoRV endogenisation was thought to be ongoing in Victoria based on the low prevalence of the virus based on molecular detection of thepolgene, however recKoRV was not incorporated into the previous KoRV diagnostic test results. In this study, a new 5’-region-based PCR assay was developed, capable of detecting both intact KoRV and recKoRV. Using this assay, 319 archived DNA samples from 287 Victorian koalas were retested to investigate KoRV endogenisation. We found a 98.3% (282/287) of these samples were positive for the KoRV-5’ fragment, the majority of which were KoRV-polnegative (222/287) on prior testing. Our findings demonstrate extensive KoRV integration into the Victorian koala populations, suggestive of a historic presence of KoRV in Victorian koalas. This finding makes biological sense relative to the translocation history of Victorian koalas, compared to the prior paradigm of ongoing endogenisation, and provides new epidemiological and practical management implications.
The two-component system ArlRS is essential for wall teichoic acid glycoswitching inStaphylococcus aureus
Authors: Kuijk Marieke M. , Tusveld Emma , Lehmann Esther , van Dalen Rob , Lasa Iñigo , Ingmer Hanne , Pannekoek Yvonne , van Sorge Nina M.
Published: September 2024

Staphylococcus aureusis among the leading causes of hospital-acquired infections. Critical toS. aureusbiology and pathogenesis are the cell wall-anchored glycopolymers wall teichoic acids (WTA). Approximately one-third ofS. aureusisolates decorates WTA with a mixture of α1,4- and β1,4-N-acetylglucosamine (GlcNAc), which requires the dedicated glycosyltransferases TarM and TarS, respectively. Environmental conditions, such as high salt concentrations, affect the abundance and ratio of α1,4- and β1,4-GlcNAc WTA decorations, thereby impacting biological properties such as antibody binding and phage infection. To identify regulatory mechanisms underlying WTA glycoswitching, we screened 1,920S. aureusmutants (Nebraska Transposon Mutant Library) by immunoblotting for differential expression of WTA-linked α1,4- or β1,4-GlcNAc using specific monoclonal antibody Fab fragments. Three two-component systems (TCS), GraRS, ArlRS, and AgrCA, were among the 230 potential hits. Using isogenic TCS mutants, we demonstrated that ArlRS is essential for WTA β1,4-GlcNAc decoration through regulation oftarMbut nottarS. ArlRS regulatedtarMexpression through the transcriptional regulator MgrA, which was responsive to Mg2+, but not Na+. Importantly, ArlRS-mediated regulation of WTA glycosylation affectedS. aureusinteraction with the innate receptor langerin and lysis by β1,4-GlcNAc-dependent phages. Since WTA represents a promising target for future immune-based treatments and vaccines, our findings provide important insight to align targeting strategies with theS. aureusWTA glycosylation patterns during infection.

Importance

Staphylococcus aureusis a common colonizer of mucosal surfaces, but is also a frequent cause of severe infections in humans. Development of antibiotic resistance complicates treatment ofS. aureusinfections, increasing the need for antibiotic alternatives such as vaccines and therapies with bacterial viruses also known as phages. Wall teichoic acids (WTA) are abundantly-expressed glycosylated structures of theS. aureuscell wall that have gained attention as a promising target for new treatments. Importantly, WTA glycosylation patterns show variation depending on environmental conditions, thereby impacting phage binding and interaction with host factors, such as antibodies and innate pattern-recognition receptors. Here, we show that the two-component system ArlRS through its effector MgrA is involved in regulation of WTA glycosylation by responding to environmental changes in Mg2+concentration. These findings may support the design of new treatment strategies that target WTA glycosylation patterns ofS. aureusduring infection.
Disrupted development of sensory systems and the cerebellum in a zebrafishebf3amutant
Authors: Dang Nghi D. P. , Conklin Claire L. , Truong Thinh Q. , Vivian Michael D. , Wang Jun , Thomas Holly R. , Parant John M. , Yeo Nan Cher , Thyme Summer B.
Published: September 2024

Mutations in the transcription factorEBF3results in a neurodevelopmental disorder, and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss, however, have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here, we generated and characterized a zebrafishebf3aloss-of-function mutant. We discovered morphological and neural phenotypes, including an overall smaller brain size, particularly in the hypothalamus, cerebellum, and hindbrain. Brain function was also compromised, with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA-sequencing of developing larvae, notable changes included significant downregulation of genes that mark olfactory sensory neurons, the lateral line, and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen.
A cell and transcriptome atlas of the human arterial vasculature
Authors: Zhao Quanyi , Pedroza Albert , Sharma Disha , Gu Wenduo , Dalal Alex , Weldy Chad , Jackson William , Li Daniel Yuhang , Ryan Yana , Nguyen Trieu , Shad Rohan , Palmisano Brian T. , Monteiro João P. , Worssam Matthew , Berezwitz Alexa , Iyer Meghana , Shi Huitong , Kundu Ramendra , Limbu Lasemahang , Kim Juyong Brian , Kundaje Anshul , Fischbein Michael , Wirka Robert , Quertermous Thomas , Cheng Paul
Published: September 2024

Vascular beds show different propensities for different vascular pathologies, yet mechanisms explaining these fundamental differences remain unknown. We sought to build a transcriptomic, cellular, and spatial atlas of human arterial cells across multiple different arterial segments to understand this phenomenon. We found significant cell type-specific segmental heterogeneity. Determinants of arterial identity are predominantly encoded in fibroblasts and smooth muscle cells, and their differentially expressed genes are particularly enriched for vascular disease-associated loci and genes. Adventitial fibroblast-specific heterogeneity in gene expression coincides with numerous vascular disease risk genes, suggesting a previously unrecognized role for this cell type in disease risk. Adult arterial cells from different segments cluster not by anatomical proximity but by embryonic origin, with differentially regulated genes heavily influenced by developmental master regulators. Non-coding transcriptomes across arterial cells contain extensive variation in lnc-RNAs expressed in cell type- and segment-specific patterns, rivaling heterogeneity in protein coding transcriptomes, and show enrichment for non-coding genetic signals for vascular diseases.
Absence of biofilm adhesin proteins changes surface attachment and cell strategy forDesulfovibrio vulgarisHildenborough
Authors: Pete Pickens C. , Wang Dongyu , Pan Chongle , De León Kara B.
Published: September 2024

Ubiquitous in nature, biofilms provide stability in a fluctuating environment and provide protection from stressors. Biofilms formed in industrial processes are exceedingly problematic and costly. While biofilms of sulfate-reducing bacteria in the environment are often beneficial because of their capacity to remove toxic metals from water, in industrial pipelines, these biofilms cause a major economic impact due to their involvement in metal and concrete corrosion. The mechanisms by which biofilms of sulfate-reducing bacteria form, however, is not well understood. Our previous work identified two proteins, named by their gene loci DVU1012 and DVU1545, as adhesins in the model sulfate-reducing bacterium,Desulfovibrio vulgarisHildenborough. Both proteins are localized to the cell surface and the presence of at least one of the proteins, with either being sufficient, is necessary for biofilm formation to occur. In this study, differences in cell attachment and early biofilm formation in single deletion mutants of these adhesins were identified. Cells lacking DVU1012 had a different attachment strategy from wild-type and ΔDVU1545 cells, more often attaching as single cells than aggregates, which indicated that DVU1012 was more important for cell-to-cell attachment. ΔDVU1545 cells had increased cell attachment compared to wild-type cells when grown in static cultures. To date, comparisons of theD. vulgarisHildenborough have been made to the large adhesion protein (Lap) system in environmental pseudomonads. Yet, we and others have shown distinct mechanistic differences in the systems. We propose to name these proteins inD. vulgarisHildenborough biofilm formation system (Bfs) to facilitate comparisons.

Importance

Biofilms of sulfate-reducing bacteria contribute to biocorrosion, costing the U.S. hundreds of millions of dollars annually. In contrast, these biofilms can be used to bioremediate toxic heavy metals and to generate bioelectricity. As one of the most abundant groups of organisms on Earth, it is pertinent to better understand mechanistically how the biofilms of sulfate-reducing bacteria form so we may use this knowledge to help in efforts to mitigate biocorrosion, to promote bioremediation, and to produce clean energy. This study shows that the absence of either one of two biofilm adhesins impacts surface colonization by a sulfate-reducing bacterium, and that these two biofilm adhesins differ in their effect on cell attachment compared to other well-documented bacteria such asPseudomonasspecies.
Epidermal Growth Factor Receptor Signaling Governs the Host Inflammatory Response to Invasive Aspergillosis
Authors: Liu Hong , Lin Jianfeng , Phan Quynh T. , Bruno Vincent M. , Filler Scott G.
Published: September 2024

The epidermal growth factor receptor (EGFR) has been identified as an epithelial cell receptor for Mucorales fungi andCandida albicans. Blocking EGFR with small molecule inhibitors reduces disease severity in mouse models of mucormycosis and oropharyngeal candidiasis. In contrast, cases of invasive aspergillosis have been reported in cancer patients who were treated with EGFR inhibitors, suggesting that EGFR signaling may play a protective role in the host defense against this infection. Here, we analyzed transcriptomic data from the lungs of mice with invasive aspergillosis and found evidence thatAspergillus fumigatusinfection activates multiple genes that are predicted to function in the EGFR signaling pathway. We also found thatA. fumigatusinfection activates EGFR in both a human small airway epithelial (HSAE) cell line and in the lungs of immunosuppressed mice. EGFR signaling in HSAE cells is required for maximal endocytosis ofA. fumigatusand for fungal-induced proinflammatory cytokine and chemokine production. In a corticosteroid immunosuppressed mouse model of invasive pulmonary aspergillosis, inhibition of EGFR with gefitinib decreased whole lung chemokine levels and reduced accumulation of phagocytes in the lung, leading to a decrease in fungal killing, an increase in pulmonary fungal burden, and accelerated mortality. Thus, EGFR signaling is required for pulmonary epithelial cells to orchestrate the host innate immune defense against invasive aspergillosis in immunosuppressed hosts.

Importance

WhenA. fumigatusinfects the lungs, it invades epithelial cells that line the airways. During this process, the fungus interacts with epithelial cell receptors. This interaction stimulates epithelial cells to endocytose the fungus. It also induces these cells to secret proinflammatory cytokines and chemokines that recruit phagocytes to the site of infection where they can kill the fungus. Here, we show that in small airway epithelial cells, the epidermal growth factor receptor (EGFR) acts a sensor forA. fumigatusthat triggers the production of chemokines in response to fungal infection. In corticosteroid-immunosuppressed mice, blocking EGFR with the kinase inhibitor, gefitinib reduces chemokine production in the lungs. This leads to decreased accumulation of neutrophils and dendritic cell in the lungs, reducedA. fumigatuskilling, and increased mortality. These results provide a potential explanation as to why some cancer patients who are treated with EGFR inhibitors develop invasive aspergillosis.
The fission yeast SUMO-targeted Ubiquitin Ligase Slx8 functionally associates with clustered centromeres and the silent mating type region at the nuclear periphery
Authors: Chakraborty Shrena , Strachan Joanna , Schirmeisen Kamila , Besse Laetitia , Mercier Eve , Fréon Karine , Zhang Haidao , Zhao Ning , Bayne Elizabeth H , Lambert Sarah AE
Published: September 2024

The SUMO-targeted Ubiquitin ligase (STUbL) family is involved in multiple cellular processes via a wide range of mechanisms to maintain genome stability. One of the evolutionarily conserved functions of STUbL is to promote changes in the nuclear positioning of DNA lesions, targeting them to the nuclear periphery. InSchizossacharomyces pombe, the STUbL Slx8 is a regulator of SUMOylated proteins and promotes replication stress tolerance by counteracting the toxicity of SUMO conjugates. In order to study the dynamic dialectic between Ubiquitinylation and SUMOylation in the nuclear space of theS. pombegenome, we analyzed Slx8 localization. Unexpectedly, we did not detect replication stress-induced Slx8 foci. However, we discovered that Slx8 forms a single nuclear focus, enriched at the nuclear periphery, which marks both clustered centromeres at the spindle pole body and the silent mating type region. The formation of this single Slx8 focus requires the E3 SUMO ligase Pli1, poly-SUMOylation and the histone methyl transferase Clr4 that is responsible for the heterochromatin histone mark H3-K9 methylation. Finally, we established that Slx8 promotes centromere clustering and gene silencing at heterochromatin domains. Altogether, our data highlight evolutionarily conserved and functional relationships between STUbL and heterochromatin domains to promote gene silencing and nuclear organization.

Highlights

TheS. pombeSTUbL Slx8 forms a single nuclear focus enriched at the nuclear periphery in a SUMO-chain-dependent manner.

Slx8 foci mark clustered centromeres and the silenced mating type region but not telomeres.

H3-K9 methylation by Crl4 promotes the single nuclear Slx8 focus

Slx8 promotes centromere clustering and gene silencing.
Mutations Leading to Ceftolozane/Tazobactam and Imipenem/Cilastatin/Relebactam Resistance Duringin vivoexposure to Ceftazidime/Avibactam inPseudomonas aeruginosa
Authors: Rapsinski Glenn J. , Rokes Alecia B. , Van Tyne Daria , Cooper Vaughn S.
Published: September 2024

Identifying resistance mechanisms to novel antimicrobials informs treatment and antimicrobial development, but frequently identifies multiple candidate resistance mutations without resolving the driver mutation. Using whole genome sequencing of longitudinalPseudomonas aeruginosathat developed imipenem/cilastatin/relebactam and ceftolozane/tazobactam resistance during ceftazidime/avibactam treatment, we determined mutations resulting in cross-resistance. Penicillin-binding proteinftsI, transcriptional repressorbepR, and virulence regulatorpvdSwere found in resistant isolates. We conclude that peptidoglycan synthesis gene mutations can alter the efficacy of multiple antimicrobials.
Transendothelial migration of the Lyme disease spirochete involves spirochete internalization as an intermediate step through a transcellular pathway that involves Cdc42 and Rac1
Authors: Alvarez-Olmedo Daiana , Kamaliddin Claire , Verhey Theodore B. , Ho May , DeVinney Rebekah , Chaconas George
Published: September 2024

Despite its importance in pathogenesis, the hematogenous dissemination pathway ofB. burgdorferiis still largely uncharacterized. To probe the molecular details of transendothelial migration more easily, we studied this process using cultured primary or telomerase-immortalized human microvascular endothelial cells in a medium that maintains both the human cells and the spirochetes. InB. burgdorferiinfected monolayers we observed ∼55% of wild-type spirochetes crossing the monolayer. Microscopic characterization revealed entrance points across the cellular surface rather than at cellular junctions, supporting a transcellular route. In support of this pathway, locking the endothelial junctions using a VE-PTP inhibitor did not reduce transendothelial migration. We also used inhibitors to block the most common endocytic pathways to elucidate effectors that might be involved inB. burgdorferiuptake and/or transmigration. Directly inhibiting Cdc42 reduced spirochete transmigration by impeding internalization. However, blocking Rac1 alone dramatically reduced transmigration and resulted in a concomitant increase in spirochete accumulation in the cell. Our combined results support thatB. burgdorferiinternalization is an intermediate step in the transendothelial migration process which requires both Cdc42 and Rac1; Cdc42 is needed for spirochete internalization while Rac1 is required for cellular egress. These are the first two host proteins implicated inB. burgdorferitransmigration across endothelial cells.

IMPORTANCE

Lyme borreliosis is caused byBorrelia burgdorferiand related bacteria. It is the most common tick-transmitted illness in the Northern Hemisphere. The ability of this pathogen to spread to a wide variety of locations results in a diverse set of clinical manisfestations, yet little is known regarding vascular escape of the spirochete, an important pathway for dissemination. Our current work has studied the traversal ofB. burgdorferiacross a monolayer of microvascular endothelial cells grown in culture. We show that this occurs by passage of the spirochetes directly through these cells rather than at cellular junctions and that internalization ofB. burgdorferiis an intermediate step in the transmigration process. We also identify the first two host proteins, Cdc42 and Rac1, that are used by the spirochetes to promote traversal of the cellular monolayer. Our new experimental system also provides a new avenue for further studies of this important process.
Mechanism of Actin Filament Severing and Capping by Gelsolin
Authors: Barrie Kyle R. , Rebowski Grzegorz , Dominguez Roberto
Published: September 2024

Gelsolin is the prototypical member of a family of Ca2+-dependent F-actin severing and capping proteins. A structure of Ca2+-bound full-length gelsolin at the barbed end shows domains G1G6 and the inter-domain linkers wrapping around F-actin. Another structure shows domains G1G3, a fragment produced during apoptosis, on both sides of F-actin. Conformational changes that trigger severing occur on one side of F-actin with G1G6 and on both sides with G1G3. Gelsolin remains bound after severing, blocking subunit exchange.
Anti-phase clustering of regulatory factors shapes gene transcription burst
Authors: Li Bitong , Wong Yew Yan , Flores-Rodriguez Neftali , Davidson Tara , Graus Matthew S , Smialkovska Valeriia , Ohishi Hiroaki , Feldmann Angelika , Ochiai Hiroshi , Francois Mathias
Published: September 2024

The ability of stem cells to divide and self-renew depends on a complex choreography of molecular events that maintain the transcriptional oscillation of pluripotency genes. Only a handful of transcription factors (TFs) are necessary to preserve pluripotency and reprogram differentiated cells into stem cells. Paradoxically, while the protein players are known, the challenge remains to decipher the series of steps that TFs undertake to modulate “on” and “off” fluctuations of gene transcription. In this study, we employ a trimodal imaging approach that integrates single-molecule tracking of SOX2 mobility,Nanoglocus diffusion, and real-timeNanogmRNA synthesis (STEAMING-tag reporter) to observe the coordinated activity of this molecular machinery. This combined system uncovered the temporal clustering dynamics of endogenous SOX2 occupancy at theNanoglocus and reveal how these dynamics relate to both transcriptional activity and the underlying chromatin behaviour in live embryonic stem cells. We link different types of SOX2 binding modes to roles in both transcriptional activation and termination or nucleosome repackaging. This redefines a dual function for SOX2 at the same gene locus during both gene expression and silencing processes. This work exposes a new layer of TF regulation, indicating a priming role rather than direct transcription initiation directly relevant to mammalian stem cell biology.
Autophagy across tissues of aging mice
Authors: Carosi Julian M. , Martin Alexis , Hein Leanne K. , Hassiotis Sofia , Hattersley Kathryn J. , Turner Bradley J , Fourrier Célia , Bensalem Julien , Sargeant Timothy J.
Published: September 2024

Autophagy is a ‘waste-disposal’ pathway that protects against age-related pathology. It is widely accepted that autophagy declines with age, yet the role that sex and diet-related obesity play during aging remain unknown. Here, we present the most comprehensivein vivostudy of autophagic flux to date. We employed transgenic mice overexpressing tandem-florescent LC3B (RFP-GFP-LC3B) to measure autophagic flux in the blood (PBMCs), heart, and motor cortex neurons of aging mice that were fed regular chow or a high-fat diet for 6-, 12- or 18-months. In male mice, aging decreased autophagic flux in the heart, increased it in the blood, and had no effect in motor cortex neurons. Age-dependent changes autophagic flux were less pronounced in female mice. High-fat diet influenced autophagic flux in the blood and heart of male but not female mice. Overall, we uncovered sexual dimorphisms that underpin how autophagy changes with age across different tissues and in response to a high-fat diet.
A proteome-wide dependency map of protein interaction motifs
Authors: Marie Ambjørn Sara , Meeusen Bob , Kliche Johanna , Wang Juanjuan , Garvanska Dimitriya H. , Kruse Thomas , Lopez Mendez Blanca , Mann Matthias , Mailand Niels , Hertz Emil P.T. , Davey Norman E. , Nilsson Jakob
Published: September 2024

Short linear motifs (SLiMs) are the most ubiquitous protein interaction modules in the unstructured regions of the human proteome. Despite their central role in protein function, our understanding of the contribution of SLiMs to cellular homeostasis remains limited. To address this, we designed base editor libraries to precisely mutate all curated SLiMs and a set of computationally predicted instances defined by SLiM-like evolutionary patterns. By targeting 7,293 SLiM containing regions with 80,473 mutations, we define a SLiM dependency map identifying 450 known and 264 predicted SLiMs required for normal cell proliferation. Notably, the vast majority of essential predicted SLiMs belong to novel classes of SLiMs. We also uncover the binding partners of several predicted SLiMs and provide mechanistic insight into disease causing mutations. Our study provides a proteome-wide resource on SLiM essentiality and highlights the presence of numerous uncharacterised essential SLiMs in the human proteome.
Single molecule Lipid Biosensors Mitigate Inhibition of Endogenous Effector Proteins
Authors: Holmes Victoria , Ricci Morgan M. C. , Weckerly Claire C. , Worcester Michael , Hammond Gerald R. V.
Published: September 2024

Genetically encoded lipid biosensors uniquely provide real time, spatially resolved kinetic data for lipid dynamics in living cells. Despite clear strengths, these tools have significant drawbacks; most notably, lipid molecules bound to biosensors cannot engage with effectors, potentially inhibiting signaling. Here, we show that although PI 3-kinase (PI3K)-mediated activation of Akt is not significantly reduced in a cell population transfected with a PH-Akt1 PIP3/PI(3,4)P2biosensor, single cells expressing PH-Akt at visible levels have reduced activation. Tagging endogenous AKT1 with neonGreen reveals its EGF-mediated translocation to the plasma membrane. Co-transfection with the PH-Akt1 or other PIP3biosensors eliminates this translocation, despite robust recruitment of the biosensors. Inhibition is even observed with PI(3,4)P2-selective biosensor. However, expressing lipid biosensors at low levels, comparable with those of endogenous AKT, produced no such inhibition. Helpfully, these single-molecule biosensors revealed improved dynamic range and kinetic fidelity compared with over-expressed biosensor. This approach represents a non-invasive way to probe spatiotemporal dynamics of PI3K signaling in living cells.

eTOC summary

Holmes and colleagues show that AKT activation is blocked by commonly used PIP3biosensors, but that this can be overcome by expressing biosensors at single molecule levels – which also improves kinetic fidelity and sensitivity.