bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting response to cytotoxic chemotherapy
Authors: Thompson Joe Sneath , Madrid Laura , Hernando Barbara , Sauer Carolin M. , Vias Maria , Escobar-Rey Maria , Leung Wing-Kit , Huckstep Jamie , Sekowska Magdalena , Hosking Karen , Jimenez-Linan Mercedes , Reinius Marika A. V. , Dobson Harry , De Silva Dilrini , Fernández-Sanromán Ángel , Sanders Deborah , Martins Filipe Correia , Quintela-Fandino Miguel , Markowetz Florian , Yip Jason , Brenton James D , Piskorz Anna M , Macintyre Geoff
Published: February 2023

Cytotoxic chemotherapies have been a crucial part of cancer treatment for over 40 years. While their primary target is cancer cells, they can also harm normal cells, resulting in dose-limiting toxicity. Most chemotherapies were approved before the advent of precision biomarkers, as such, many patients experience severe toxic side effects without any benefit. To address this challenge, we have developed three precision biomarkers to predict response to platins, taxanes, and anthracyclines. Based on chromosomal instability (CIN) signatures, these biomarkers can be computed from a single genomic test. For platins and taxanes, we used CIN signatures related to impaired homologous recombination, while for anthracyclines, we discovered a CIN signature representing micronuclei induction which predicts resistance. In a clinical study involving 41 high-grade serous ovarian cancers, patients predicted to be sensitive by these biomarkers showed significantly prolonged progression-free survival. To further validate the effectiveness of the taxane and anthracycline predictors, we conducted a retrospective randomised control study involving 182 ovarian and 219 breast cancer patients. Patients predicted as resistant showed increased risk of time to treatment failure compared to standard of care, hazard ratios of 1.73 (95%CI=0.98-3.07) for taxane in ovarian, 3.67 (95%CI=2.12-6.34) for taxane in breast, and 1.93 (95%CI=1.22-3.04) for doxorubicin in ovarian. We also found that liquid biopsies can be used to make these predictions in up to 30% of ovarian cancer patients. Our findings highlight the clinical value of CIN signatures in predicting treatment response to various chemotherapies across multiple different types of cancer. The ability to quantify multiple CIN signature biomarkers using a single genomic test offers a unified approach to guide treatment decisions for cytotoxic chemotherapies. Ultimately, this has the potential to transform the current one-size-fits-all chemotherapy approach into a more precise and tailored form of medicine.
High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study
Authors: Ghafari Mahan , Hall Matthew , Golubchik Tanya , Ayoubkhani Daniel , House Thomas , MacIntyre-Cockett George , Fryer Helen , Thomson Laura , Nurtay Anel , Buck David , Green Angie , Trebes Amy , Piazza Paolo , Lonie Lorne J , Studley Ruth , Rourke Emma , Smith Darren , Bashton Matthew , Nelson Andrew , Crown Matthew , McCann Clare , Young Gregory R , dos Santos Rui Andre Nunes , Richards Zack , Tariq Adnan , Cahuantzi Roberto ,   Wellcome Sanger Institute COVID-19 Surveillance Team,   COVID-19 Infection Survey Group,   The COVID-19 Genomics UK (COG-UK) Consortium, Barrett Jeff , Fraser Christophe , Bonsall David , Walker Ann Sarah , Lythgoe Katrina
Published: February 2023

Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may act as viral reservoirs that could seed future outbreaks1–5, give rise to highly divergent lineages6–8, and contribute to cases with post-acute Coronavirus disease 2019 (COVID-19) sequelae (Long Covid)9,10. However, the population prevalence of persistent infections, their viral load kinetics, and evolutionary dynamics over the course of infections remain largely unknown. We identified 381 infections lasting at least 30 days, of which 54 lasted at least 60 days. These persistently infected individuals had more than 50% higher odds of self-reporting Long Covid compared to the infected controls, and we estimate that 0.09-0.5% of SARS-CoV-2 infections can become persistent and last for at least 60 days. In nearly 70% of the persistent infections we identified, there were long periods during which there were no consensus changes in virus sequences, consistent with prolonged presence of non-replicating virus. Our findings also suggest reinfections with the same major lineage are rare and that many persistent infections are characterised by relapsing viral load dynamics. Furthermore, we found a strong signal for positive selection during persistent infections, with multiple amino acid substitutions in the Spike and ORF1ab genes emerging independently in different individuals, including mutations that are lineage-defining for SARS-CoV-2 variants, at target sites for several monoclonal antibodies, and commonly found in immunocompromised patients11–14. This work has significant implications for understanding and characterising SARS-CoV-2 infection, epidemiology, and evolution.
Cardiac sympathetic denervation prevents sudden cardiac arrest and improves cardiac function by enhancing mitochondrial-antioxidant capacity
Authors: Dey Swati , Joshi Pooja , O’Rourke Brian , Estes Shanea , DeMazumder Deeptankar
Published: February 2023

RATIONALE

Sudden cardiac arrest (SCA) and heart failure (HF) are leading causes of death. The underlying mechanisms are incompletely understood, limiting the design of new therapies. Whereas most autonomic modulation therapies have not shown clear benefit in HF patients, growing evidence indicates cardiac sympathetic denervation (CSD) exerts cardioprotective effects. The underlying molecular and cellular mechanisms remain unexplored.

OBJECTIVE

Based on the hypothesis that mitochondrial reactive oxygen species (mROS) drive the pathogenesis of HF and SCA, we investigated whether CSD prevents SCA and HF by improving mitochondrial antioxidant capacity and redox balance, to correct impaired Ca2+handling and repolarization reserve.

METHODS AND RESULTS

We interrogated CSD-specific responses in pressure-overload HF models with spontaneous SCA usingin vivoechocardiographic and electrocardiographic studies andin vitrobiochemical and functional studies including ratiometric measures of mROS, Ca2+and sarcomere dynamics in left ventricular myocytes. Pressure-overloaded HF reduced mitochondrial antioxidant capacity and increased mROS, which impaired β-adrenergic signaling and caused SR Ca2+leak, reducing SR Ca2+and increasing diastolic Ca2+, impaired myofilament contraction and further increased the sympathetic stress response. CSD improved contractile function and mitigated mROS-mediated diastolic Ca2+overload, dispersion of repolarization, triggered activity and SCA by upregulating mitochondrial antioxidant and NADPH-producing enzymes.

CONCLUSIONS

Our findings support a fundamental role of sympathetic stress-induced downregulation of mROS scavenging enzymes and RyR-leak mediated diastolic Ca2+overload in HF and SCA pathogenesis that are mitigated by CSD. This first report on the molecular and cellular mechanisms of CSD supports its evaluation in additional high-risk patient groups.

BRIEF SUMMARY

Cardiac sympathetic denervation (CSD) confers cardioprotective effects via unclear mechanisms. In a guinea pig model that uniquely mimics human pressure-overload heart failure (HF) with spontaneous sudden cardiac arrest (SCA), we interrogated CSD-specific responses using echocardiographic, electrocardiographic and biochemical measures, and ratiometric measures of mitochondrial reactive oxygen species (mROS), Ca2+and sarcomere dynamics. Consistent with our hypothesis, CSD rescued cardioprotection by upregulating mitochondrial antioxidant and NADPH-producing enzymes, which mitigate mROS-mediated Ca2+derangements, repolarization lability, triggered activity, HF and SCA. Our findings provide the first molecular and cellular mechanistic basis for evaluating CSD therapy in a broader group of high-risk patients.
PlasmodiumARK2-EB1 axis drives the unconventional spindle dynamics, scaffold formation and chromosome segregation of sexual transmission stages
Authors: Zeeshan Mohammad , Rea Edward , Abel Steven , Vukušić Kruno , Markus Robert , Brady Declan , Eze Antonius , Raspa Ravish , Balestra Aurelia , Bottrill Andrew R. , Brochet Mathieu , Guttery David S. , Tolić Iva M. , Holder Anthony A. , Roch Karine G. Le , Tromer Eelco C. , Tewari Rita
Published: February 2023

Mechanisms of cell division are remarkably diverse, suggesting the underlying molecular networks among eukaryotes differ extensively. The Aurora family of kinases orchestrates the process of chromosome segregation and cytokinesis during cell division through precise spatiotemporal regulation of their catalytic activities by distinct scaffolds.Plasmodiumspp., the causative agents of malaria, are unicellular eukaryotes that have three divergent aurora-related kinases (ARKs) and lack most canonical scaffolds/activators. The parasite uses unconventional modes of chromosome segregation during endomitosis and meiosis in sexual transmission stages within mosquito host. This includes a rapid threefold genome replication from 1N to 8N with successive cycles of closed mitosis, spindle formation and chromosome segregation within eight minutes (termed male gametogony). Kinome studies had previously suggested likely essential functions for all threePlasmodiumARKs during asexual mitotic cycles; however, little is known about their location, function, or their scaffolding molecules during unconventional sexual proliferative stages. Using a combination of super-resolution microscopy, mass spectrometry, and live-cell fluorescence imaging, we set out to investigate the role of the atypical Aurora paralog ARK2 to proliferative sexual stages using rodent malaria modelPlasmodium berghei. We find that ARK2 primarily localises to the spindle apparatus in the vicinity of kinetochores during both mitosis and meiosis. Interactomics and co-localisation studies reveal a unique ARK2 scaffold at the spindle including the microtubule plus end-binding protein EB1, lacking conserved Aurora scaffold proteins. Gene function studies indicate complementary functions of ARK2 and EB1 in driving endomitotic divisions and thereby parasite transmission. Our discovery of a novel Aurora kinase spindle scaffold underlines the emerging flexibility of molecular networks to rewire and drive unconventional mechanisms of chromosome segregation in the malaria parasitePlasmodium.
Expanding the coverage of spatial proteomics
Authors: Sun Huangqingbo , Li Jiayi , Murphy Robert F
Published: February 2023

Multiplexed protein imaging methods provide valuable information about complex tissue structure and cellular heterogeneity. However, the number of markers that can be measured in the same tissue sample is currently limited. In this paper, we present an efficient method to choose a minimal predictive subset of markers that for the first time allows the prediction of full images for a much larger set of markers. We demonstrate that our approach also outperforms previous methods for predicting cell-level marker composition. Most importantly, we demonstrate that our approach can be used to select a marker set that enables prediction of a much larger set that could not be measured concurrently.
Protracted morphine withdrawal corresponds with sex-specific alterations to motivated behavior and mesoaccumbal subcircuit dopamine cell plasticity
Authors: Gomez Devan M. , Kahl Taytum , Berrington Emily , Hearing Matthew C.
Published: February 2023

Background

Opioid use disorder is associated with enduring psychological withdrawal symptoms believed to contribute to drug abuse. Amongst these are shifts in motivational states, wherein pursuit of drug consumption exceeds that of non-drug rewards, reinforcing escalated opioid use and relapse vulnerability. A critical regulator of behavioral reinforcement, the mesoaccumbal dopamine (DA) system is thought to be both necessary and sufficient for opioid motivation. However, previous research into its involvement in opioid withdrawal has been limited to acute vs protracted timepoints, global neuroadaptations vs those in subcircuits, and overwhelmingly focused on males vs females.

Methods

Evaluations of effort-based motivated behavior for both sucrose and morphine reward were combined with patch clamp electrophysiological assessments of synaptic plasticity within lateral vs medial DA neurons projecting to the lateral vs medial nucleus accumbens shell during protracted morphine withdrawal in male and female mice. Further effects of mesoaccumbal subcircuit inhibition on motivated behavior for sucrose were also measured.

Results

Protracted morphine withdrawal was found to be associated with elevations in morphine seeking, intake, and motivation compared to saline controls in both sexes. Escalation of intake was paralleled by a male-exclusive reduction in motivation for the non-drug reward, sucrose. Male-exclusive neuroadaptations during protracted withdrawal were also found, with reductions in neuronal excitability and increased inhibitory (GABAAR-dependent) synaptic transmission found in lateral ventral tegmental area (VTA) DA neurons projecting to the lateral nucleus accumbens shell, though not in medial DA projections to the medial shell. Finally, chemogenetic inhibition of the lateral but not medial subcircuit was found to significantly reduce motivated responding for sucrose in male morphine-naïve mice.

Conclusions

These data suggest that protracted opioid withdrawal is associated with a sex-independent increase in opioid consumption and motivation. They also suggest that male-specific reductions in motivation for non-drug reward during protracted withdrawal may be driven by a hypoactive state in a lateral mesoaccumbal DA subcircuit driven in part by increased inhibition of DA cells. These insights may be useful in development of therapies that temper withdrawal-associated psychological states predisposed towards prolonged and escalated opioid intake, a major treatment goal for OUD patients.
Quantitative Annotations of T-Cell Repertoire Specificity
Authors: Luo Jiaqi , Wang Xueying , Zou Yiping , Chen Lingxi , Liu Wei , Zhang Wei , Li Shuai Cheng
Published: February 2023

The specificity of a T-cell receptor (TCR) repertoire determines personalized immune capacity. Existing methods have modelled the qualitative aspects of TCR specificity, while the quantitative aspects remained unaddressed. We developed a package, TCRanno, to quantify the specificity of TCR repertoires. Applying TCRanno to 4,195 TCR repertoires revealed quantitative changes in repertoire specificity upon infections, autoimmunity and cancers. Specifically, TCRanno found cytomegalovirus-specific TCRs in seronegative healthy individuals, supporting the possibility of abortive infections. TCRanno discovered age-accumulated fraction of SARS-CoV2-specific TCRs in pre-pandemic samples, which may explain the aggressive symptoms and age-related severity of COVID-19. TCRanno also identified the encounter of Hepatitis B antigens as a potential trigger of systemic lupus erythematosus. TCRanno annotations showed capability in distinguishing TCR repertoires of healthy and cancers including melanoma, lung and breast cancers. TCRanno may also facilitate single-cell TCRseq+gene expression data analyses by isolating T-cells with the specificity of interest.
The Diagnostic and Triage Accuracy of the GPT-3 Artificial Intelligence Model
Authors: Levine David M , Tuwani Rudraksh , Kompa Benjamin , Varma Amita , Finlayson Samuel G. , Mehrotra Ateev , Beam Andrew
Published: February 2023

Importance

Artificial intelligence (AI) applications in health care have been effective in many areas of medicine, but they are often trained for a single task using labeled data, making deployment and generalizability challenging. Whether a general-purpose AI language model can perform diagnosis and triage is unknown.

Objective

Compare the general-purpose Generative Pre-trained Transformer 3 (GPT-3) AI model’s diagnostic and triage performance to attending physicians and lay adults who use the Internet.

Design

We compared the accuracy of GPT-3’s diagnostic and triage ability for 48 validated case vignettes of both common (e.g., viral illness) and severe (e.g., heart attack) conditions to lay people and practicing physicians. Finally, we examined how well calibrated GPT-3’s confidence was for diagnosis and triage.

Setting and Participants

The GPT-3 model, a nationally representative sample of lay people, and practicing physicians.

Exposure

Validated case vignettes (<60 words; <6thgrade reading level).

Main Outcomes and Measures

Correct diagnosis, correct triage.

Results

Among all cases, GPT-3 replied with the correct diagnosis in its top 3 for 88% (95% CI, 75% to 94%) of cases, compared to 54% (95% CI, 53% to 55%) for lay individuals (p<0.001) and 96% (95% CI, 94% to 97%) for physicians (p=0.0354). GPT-3 triaged (71% correct; 95% CI, 57% to 82%) similarly to lay individuals (74%; 95% CI, 73% to 75%; p=0.73); both were significantly worse than physicians (91%; 95% CI, 89% to 93%; p<0.001). As measured by the Brier score, GPT-3 confidence in its top prediction was reasonably well-calibrated for diagnosis (Brier score = 0.18) and triage (Brier score = 0.22).

Conclusions and Relevance

A general-purpose AI language model without any content-specific training could perform diagnosis at levels close to, but below physicians and better than lay individuals. The model was performed less well on triage, where its performance was closer to that of lay individuals.
A versatile synaptotagmin-1 nanobody provides perturbation-free live synaptic imaging and low linkage-error in super-resolution microscopy
Authors: Villa Real Karine Queiroz Zetune , Mougios Nikolaos , Rehm Ronja , Sograte-Idrissi Shama , Albert László , Rahimi Amir Mohammad , Maidorn Manuel , Hentze Jannik , Martínez-Carranza Markel , Hosseini Hassan , Saal Kim-Ann , Oleksiievets Nazar , Prigge Matthias , Tsukanov Roman , Stenmark Pål , Fornasiero Eugenio F. , Opazo Felipe
Published: February 2023

Imaging of living synapses has relied for over two decades on the overexpression of synaptic proteins fused to fluorescent reporters. This strategy changes the stoichiometry of synaptic components and ultimately affects synapse physiology. To overcome these limitations, here we introduce a nanobody that binds the calcium sensor synaptotagmin-1 (NbSyt1). This nanobody functions in living neurons as an intrabody (iNbSyt1) and is minimally invasive, leaving synaptic transmission almost unaffected, as demonstrated by the crystal structure of the NbSyt1 bound to synaptotagmin-1 and by our physiological data. Its single-domain nature enables the generation of protein-based fluorescent reporters, as we showcase here by measuring spatially-localized presynaptic Ca2+with an NbSyt1-jGCaMP8 chimera. Moreover, its small size makes the NbSyt1 ideal for various super-resolution imaging methods. Overall, NbSyt1 is a versatile binder that will enable imaging in cellular and molecular neuroscience at a higher precision than possible in the past, over multiple spatiotemporal scales.
ARHGAP29 is required for keratinocyte proliferation and migration
Authors: Reeb Tanner , Rhea Lindsey , Adelizzi Emily , Garnica Bailey , Dunnwald Elliot , Dunnwald Martine
Published: February 2023

BACKGROUND

RhoA GTPase plays critical roles in actin cytoskeletal remodeling required for controlling a diverse range of cellular functions including cell proliferation, cell adhesions, migration and changes in cell shape. RhoA cycles between an active GTP-bound and an inactive GDP-bound form, a process that is regulated by guanine nucleotide exchange factors (GEFs), and GTPase-activating proteins (GAPs). ARHGAP29 is a GAP expressed in keratinocytes of the skin and is decreased in the absence of Interferon Regulator Factor 6, a critical regulator of cell proliferation and migration. However, the role for ARHGAP29 in keratinocyte biology is unknown.

RESULTS

Novel ARHGAP29 knockdown keratinocyte cell lines were generated using both CRISPR/Cas9 and shRNA technologies. Knockdown cells exhibited significant reduction of ARHGAP29 protein (50-80%) and displayed increased filamentous actin (stress fibers), phospho-myosin light chain (contractility), cell area and population doubling time. Furthermore, we found that ARHGAP29 knockdown keratinocytes displayed significant delays in scratch wound closure in both single cell and collective cell migration conditions. Particularly, our results show a reduction in path lengths, speed, directionality and persistence in keratinocytes with reduced ARHGAP29. The delay in scratch closure was rescued by both adding back ARHGAP29 or adding a ROCK inhibitor to ARHGAP29 knockdown cells.

CONCLUSIONS

These data demonstrate that ARHGAP29 is required for keratinocyte morphology, proliferation and migration mediated through the RhoA pathway.
Reduced dimension stimulus decoding and column-based modeling reveal architectural differences of primary somatosensory finger maps between younger and older adults
Authors: Kalyani Avinash , Contier Oliver , Klemm Lisa , Azañon Elena , Schreiber Stefanie , Speck Oliver , Reichert Christoph , Kuehn Esther
Published: February 2023

The primary somatosensory cortex (SI) contains fine-grained tactile representations of the body, arranged in an orderly fashion. Using ultra-high resolution fMRI data to describe such detailed individual topographic maps or to detect group differences is challenging, because group alignment often does not preserve the high spatial detail of the data. Here, we use shared response modeling (SRM), a technique that allows group analyses by mapping individual stimulus-driven responses to a lower dimensional shared feature space, to detect age-related differences in sensory representations between younger and older adults using 7T-fMRI data. Using this method, we show that finger representations are more precise in Brodmann-Area (BA) 3b and BA1 compared to BA2 and motor areas, and that this hierarchical processing is preserved across age groups. By combining SRM with column-based decoding (C-SRM), we further show that the number of columns that optimally describes finger maps in SI is higher in younger compared to older adults in BA1, indicating a greater columnar size in older adults’ SI. Taken together, we conclude that SRM is suitable for finding fine-grained group differences in SI fMRI data at ultra-high-resolution, and we provide first evidence that the columnar architecture of a functional area changes with increasing age.
Homocysteine accelerates hepatocyte autophagy by upregulation of TFEB via DNMT3b-mediated DNA hypomethylation
Authors: Yang Anning , Zeng Wen , Hao Yinju , Zhang Hongwen , Wang Qingqing , Sun Yue , Quan Shangkun , Ding Ning , Yang Xiaoling , Sun Jianmin , Zhang Huiping , Liu Bin , Jiao Yun , Wu Kai , Jiang Yideng
Published: February 2023

Autophagy plays a critical role in the physiology and pathophysiology of hepatocytes. High levels of homocysteine (Hcy) promote autophagy in hepatocytes, but the underlying mechanism is still unknown. Here, we investigated the relation between Hcy increased autophagy levels and the expression of nuclear transcription factor EB (TFEB). We demonstrate that Hcy increased autophagy levels is mediated by upregulation of TFEB. Silencing TFEB decreases the autophagy-related protein LC3BII/I and increases p62 expression levels in hepatocytes after exposure to Hcy. Moreover, the effect of Hcy on the expression of TFEB is regulated by hypomethylation of TFEB promoter catalyzed by DNA methyltransferase 3b (DNMT3b). In summary, this study shows that Hcy can activate autophagy by inhibiting DNMT3b-mediated DNA methylation and upregulating TFEB expression. These findings provide another new mechanism for Hcy-induced autophagy in hepatocytes.
Single cell ATAC sequencing identifies sleepy macrophages during reciprocity of cytokines inL.majorinfection
Authors: Khandibharad Shweta , Kharat Komal , Singh Shailza
Published: February 2023

Hallmark for macrophages is their ability to possess plasticity which enables them to respond to changing microenvironment.Leishmaniatakes use of the phenotypic plasticity of macrophages to create favorable position for intracellular survival and persistent infection through regulatory cytokine like IL10. However, these effector cells can eliminate infection through modulation of critical cytokines such as IL12 and key players involved in its production. Using sophisticated tool of single cell ATAC sequencing we analyzed the regulatory axis of IL10 and IL12 in time dependent manner forL.majorinfection in macrophages. We recognized the cellular heterogeneity post infection with the regulators of IL10 and IL12 and observed a reciprocal relationship between them. Our prominent findings also exposed sleepy macrophages and its role in IL10 and IL12 reciprocity. To summarize, role of NFAT5 was vital in identification of sleepy macrophages which is a transient state where transcription factors controlled the epigenetic remodeling and expression of genes involved in pro-inflammatory cytokine production and recruitment of immune cells.

Abstract Figure

Graphical abstract summary of single cell ATAC sequencing forL.majorinfected RAW264.7 mouse macrophage cell line. (A) Reciprocal relationship identified in cell populations which is governed through chromatin remodeling. (B) Single cell ATAC pipeline for analysis of dataset (C) Identification of sleepy macrophages which may play potential role in reciprocity.
TXNIP in liver sinusoidal endothelial cells ameliorates alcohol-associated liver disease
Authors: Jung Eunhye , Baek Eun Bok , Hong Eun-Ju , Kang Jee Hyun , Park Suyoung , Hong Eui-Ju , Cho Young-Eun , Ko Je-Won , Won Young-Suk , Kwon Hyo-Jung
Published: February 2023

The authors have withdrawn their manuscript because it was posted without the consent of all authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Glucose deprivation promotes pseudo-hypoxia and de-differentiation in lung adenocarcinoma
Authors: Saggese Pasquale , Pandey Aparamita , Fung Eileen , Hall Abbie , Yanagawa Jane , Rodriguez Erika F. , Grogan Tristan R. , Giurato Giorgio , Nassa Giovanni , Salvati Annamaria , Weisz Alessandro , Dubinett Steven M. , Scafoglio Claudio
Published: February 2023

Increased utilization of glucose is a hallmark of cancer. Several studies are investigating the efficacy of glucose restriction by glucose transporter blockade or glycolysis inhibition. However, the adaptations of cancer cells to glucose restriction are unknown. Here, we report the discovery that glucose restriction in lung adenocarcinoma (LUAD) induces cancer cell de-differentiation, leading to a more aggressive phenotype. Glucose deprivation causes a reduction in alpha-ketoglutarate (αKG), leading to attenuated activity of αKG-dependent histone demethylases and histone hypermethylation. We further show that this de-differentiated phenotype depends on unbalanced EZH2 activity, causing inhibition of prolyl-hydroxylase PHD3 and increased expression of hypoxia inducible factor 1α (HIF1α), triggering epithelial to mesenchymal transition. Finally, we identified an HIF1α-dependent transcriptional signature with prognostic significance in human LUAD. Our studies further current knowledge of the relationship between glucose metabolism and cell differentiation in cancer, characterizing the epigenetic adaptation of cancer cells to glucose deprivation and identifying novel targets to prevent the development of resistance to therapies targeting glucose metabolism.
Intra-ripple frequency accommodation in an inhibitory network model for hippocampal ripple oscillations
Authors: Schieferstein Natalie , Schwalger Tilo , Lindner Benjamin , Kempter Richard
Published: February 2023

Hippocampal ripple oscillations have been implicated in important cognitive functions such as memory consolidation and planning. Multiple computational models have been proposed to explain the emergence of ripple oscillations, relying either on excitation or inhibition as the main pacemaker. Nevertheless, the generating mechanism of ripples remains unclear. An interesting dynamical feature of experimentally measured ripples, which may advance model selection, is intra-ripple frequency accommodation (IFA): a decay of the instantaneous ripple frequency over the course of a ripple event. So far, only the “bifurcation-based” inhibition-first model, which is based on delayed inhibitory synaptic coupling, has been shown to reproduce IFA. Here we use an analytical mean-field approach and numerical simulations of a leaky integrate-and-fire spiking network to explain the mechanism of IFA. We develop a drift-based approximation for the oscillation dynamics of the population rate and the mean membrane potential of interneurons under strong drive and strong inhibitory coupling. We demonstrate that IFA arises due to a speed-dependent hysteresis effect in the dynamics of the mean membrane potential, when the interneurons receive transient, sharp wave-associated excitation. We thus predict that the IFA asymmetry vanishes in the limit of slowly changing drive, but is otherwise a robust feature of the bifurcation-based inhibition-first ripple model.
Engineering sensory ganglion multicellular system to model tissue nerve ingrowth
Authors: Ma Junxuan , Tognato Riccardo , Eglauf Janick , Grad Sibylle , Alini Mauro , Serra Tiziano
Published: February 2023

Discogenic pain is associated with deep nerve ingrowth in annulus fibrosus tissue (AF) of intervertebral disc (IVD). To model AF nerve ingrowth, primary bovine dorsal root ganglion (DRG) micro-scale tissue units are spatially organized around an AF explant by mild hydrodynamic forces within a collagen matrix. This results in a densely packed multicellular system mimicking the native DRG tissue morphology and a controlled AF-neuron distance. Such a multicellular organization is essential to evolve populational-level cellular functions andin vivo-like morphologies. Pro-inflammatory cytokine-primed AF demonstrates its neurotrophic and neurotropic effects on nociceptor axons. Both effects depend on the AF-neuron distance underpinning the role of recapitulating inter-tissue/organ anatomical proximity when investigating their crosstalk. This is the firstin vitromodel studying AF nerve ingrowth by engineering mature and large animal tissues in a morphologically and physiologically relevant environment. Our new approach can be used to biofabricate multi-tissue/organ models for untangling pathophysiological conditions and develop novel therapies.
Architecture of the cortical actomyosin network driving apical constriction inC. elegans
Authors: Zhang Pu , Medwig-Kinney Taylor N. , Goldstein Bob
Published: February 2023

Apical constriction is a cell shape change that drives key morphogenetic events during development, including gastrulation and neural tube formation. The forces driving apical constriction are primarily generated through the contraction of apicolateral and/or medioapical actomyosin networks. In theDrosophilaventral furrow, the medioapical actomyosin network has a sarcomere-like architecture, with radially polarized actin filaments and centrally enriched non-muscle myosin II and myosin activating kinase. To determine if this is a broadly conserved actin architecture driving apical constriction, we examined actomyosin architecture duringC. elegansgastrulation, in which two endodermal precursor cells internalize from the surface of the embryo. Quantification of protein localization showed that neither the non-muscle myosin II NMY-2 nor the myosin-activating kinase MRCK-1 is enriched at the center of the apex. Further, visualization of barbed- and pointed-end capping proteins revealed that actin filaments do not exhibit radial polarization at the apex. Taken together with observations made in other organisms, our results demonstrate that diverse actomyosin architectures are used in animal cells to accomplish apical constriction.

Through live-cell imaging of endogenously-tagged proteins, Zhang, Medwig-Kinney, and Goldstein show that the medioapical actomyosin network driving apical constriction duringC. elegansgastrulation is organized diffusely, in contrast to the sarcomere-like architecture previously observed in theDrosophilaventral furrow.
Assessing the biogeography of marine giant viruses in four oceanic transects
Authors: Ha Anh D. , Moniruzzaman Mohammad , Aylward Frank O.
Published: February 2023

Viruses of the phylumNucleocytoviricotaare ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the orderImiterviralesand 54 in the orderAlgavirales. We found that most viruses appeared to be prevalent in shallow waters (<150 meters), and that viruses of theMesomimiviridae(Imitervirales) andPrasinoviridae(Algavirales) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinctNucleocytoviricotacommunities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.
Left-hemisphere cortical language regions respond equally to observed dialogue and monologue
Authors: Olson Halie , Chen Emily , Lydic Kirsten , Saxe Rebecca
Published: February 2023

Much of the language we encounter in our everyday lives comes in the form of conversation, yet the majority of research on the neural basis of language comprehension has used input from only one speaker at a time. 20 adults were scanned while passively observing audiovisual conversations using functional magnetic resonance imaging. In a block-design task, participants watched 20-second videos of puppets speaking either to another puppet (the “dialogue” condition) or directly to the viewer (“monologue”), while the audio was either comprehensible (played forward) or incomprehensible (played backward). Individually functionally-localized left-hemisphere language regions responded more to comprehensible than incomprehensible speech but did not respond differently to dialogue than monologue. In a second task, participants watched videos (1-3 minutes each) of two puppets conversing with each other, in which one puppet was comprehensible while the other’s speech was reversed. All participants saw the same visual input but were randomly assigned which character’s speech was comprehensible. In left-hemisphere cortical language regions, the timecourse of activity was correlated only among participants who heard the same character speaking comprehensibly, despite identical visual input across all participants. For comparison, some individually-localized theory of mind regions and right hemisphere homologues of language regions responded more to dialogue than monologue in the first task, and in the second task, activity in some regions was correlated across all participants regardless of which character was speaking comprehensibly. Together, these results suggest that canonical left-hemisphere cortical language regions are not sensitive to differences between observed dialogue and monologue.
Borrelia burgdorferiPlzA is a cyclic-di-GMP dependent DNA and RNA binding protein
Authors: Jusufovic Nerina , Krusenstjerna Andrew C. , Savage Christina R. , Saylor Timothy C. , Brissette Catherine A. , Zückert Wolfram R. , Schlax Paula J. , Motaleb Md A. , Stevenson Brian
Published: February 2023

The PilZ domain-containing protein, PlzA, is the only known cyclic di-GMP binding protein encoded by all Lyme disease spirochetes. PlzA has been implicated in the regulation of many borrelial processes, but the effector mechanism of PlzA was not previously known. Here we report that PlzA can bind DNA and RNA and that nucleic acid binding requires c-di-GMP, with the affinity of PlzA for nucleic acids increasing as concentrations of c-di-GMP were increased. A mutant PlzA that is incapable of binding c-di-GMP did not bind to any tested nucleic acids. We also determined that PlzA interacts predominantly with the major groove of DNA and that sequence length plays a role in DNA binding affinity. PlzA is a dual-domain protein with a PilZ-like N-terminal domain linked to a canonical C-terminal PilZ domain. Dissection of the domains demonstrated that the separated N-terminal domain bound nucleic acids independently of c-di-GMP. The C-terminal domain, which includes the c-di-GMP binding motifs, did not bind nucleic acids under any tested conditions. Our data are supported by computational docking, which predicts that c-di-GMP binding at the C-terminal domain stabilizes the overall protein structure and facilitates PlzA-DNA interactions via residues in the N-terminal domain. Based on our data, we propose that levels of c-di-GMP during the various stages of the enzootic life cycle direct PlzA binding to regulatory targets.
CRISPR-based editing of the ω- and γ-gliadin gene clusters reduces wheat immunoreactivity without affecting grain protein quality
Authors: Yu Zitong , Yunusbaev Ural , Fritz Allan , Tilley Michael , Akhunova Alina , Trick Harold , Akhunov Eduard
Published: February 2023

Wheat immunotoxicity is associated with abnormal reaction to gluten-derived peptides. Attempts to reduce immunotoxicity using breeding and biotechnology often affect dough quality. Here, the multiplexed CRISPR-Cas9 editing of cultivar Fielder was used to modify the ω -and γ-gliadin gene clusters abundant in immunoreactive peptides identified in the genomes assembled using the long-read sequencing technologies. The whole genome sequencing of an edited line showed editing or deletion of nearly all ω-gliadin and half of the γ-gliadin gene copies and lack of editing in the α/β-gliadin genes. The detected 62% and 52% reduction in ω- and γ-gliadin content, respectively, had no negative impact on grain protein quality. A 47-fold immunoreactivity reduction compared to wild-type was detected using antibodies against immunotoxic peptides. Our results indicate that genome profiling to identify gliadin gene copies abundant in immunoreactive peptides and their targeted editing could be an effective mean for reducing immunotoxicity of wheat cultivars while minimizing the impact of editing on protein quality.
The role of pneumococcal extracellular vesicles on the pathophysiology of the kidney disease Hemolytic Uremic Syndrome
Authors: Battista Miriana , Hoffmann Bianca , Bachelot Yann , Zimmermann Lioba , Teuber Laura , Jost Aurélie , Linde Susanne , Westermann Martin , Müller Mario M. , Slevogt Hortense , Hammerschmidt Sven , Figge Marc Thilo , Vilhena Cláudia , Zipfel Peter F.
Published: February 2023

Streptococcus pneumoniae-induced hemolytic uremic syndrome (Sp-HUS) is a kidney disease characterized by microangiopathic hemolytic anemia, thrombocytopenia, and acute kidney injury. This disease is frequently underdiagnosed and its pathophysiology is poorly understood. In this work, we compared clinical strains, isolated from infant Sp-HUS patients, to a reference pathogenic strain D39, for host cytotoxicity and further explored the role of Sp-derived extracellular vesicles (EVs) in the pathogenesis of a HUS infection. In comparison with the WT strain, pneumococcal HUS strains caused significant lysis of human erythrocytes and increased the release of hydrogen peroxide. Isolated Sp-HUS EVs were characterized by performing dynamic light-scattering microscopy and proteomic analysis. Sp-HUS strain released EVs at a constant concentration during growth, yet the size of the EVs varied and several subpopulations emerged at later time points. The cargo of the Sp-HUS EVs included several virulence factors at high abundance, i.e., the ribosomal subunit assembly factor BipA, the Pneumococcal Surface Protein A (PspA), the lytic enzyme LytC, several sugar utilization and fatty acid synthesis proteins. Sp-HUS EVs strongly downregulated the expression of the endothelial surface marker PECAM-1 and were internalized by human endothelial cells. Sp-HUS EVs elicited the release of pro-inflammatory cytokines (IL-1ß, IL-6) and chemokines (CCL2, CCL3, CXCL1) by human monocytes. These findings shed new light on the overall function of Sp-EVs, in the scope of infection-mediated HUS, and suggest new avenues of research for exploring the usefulness of Sp-EVs as therapeutic and diagnostic targets.

Importance

Streptococcus pneumoniaeis a life-threatening human pathogen associated with severe illnesses in the upper respiratory tract. Disseminated infections also occur, as the kidney disease hemolytic uremic syndrome. Even though vaccination is available, this pathogen is responsible for a worldwide high mortality rate, especially among children from least developed countries, where vaccination strategies are poor or inexistent. It is estimated that 30% of invasive pneumococcal diseases are caused by antibiotic resistant bacteria, leading to the classification of “serious threat” by the World Health Organization. In order to prevent cases of severe illness, investigation in the direction of new vaccine candidates is of upmost importance. Pneumococcal extracellular vesicles pose as ideal candidates for a serotype-independent vaccine formulation. To this purpose, the aspects of vesicle formation, cargo allocation and function need to be understood in detail.

Graphical Abstract
Glycoproteomics-compatible MS/MS-based quantification of glycopeptide isomers
Authors: Maliepaard Joshua C.L. , Damen J. Mirjam A. , Boons Geert-Jan P.H. , Reiding Karli R.
Published: February 2023

Glycosylation is an essential protein modification occurring on the majority of extracellular human proteins, mass spectrometry (MS) being an indispensable tool for its analysis. Not only can MS determine glycan compositions, but also position the glycan at specific sites via glycoproteomics. However, glycans are complex branching structures with monosaccharides interconnected in a variety of biologically relevant linkages - isomeric properties which are invisible when the readout is mass alone.

Here, we developed an LC-MS/MS-based workflow for determining glycopeptide isomer ratios. Making use of isomerically-defined glyco(peptide) standards, we observed marked differences in fragmentation behavior between isomer pairs when subjected to collision energy gradients, specifically in terms of galactosylation/sialylation branching and linkage. These behaviors were developed into component variables that allowed relative quantification of isomerism within mixtures. Importantly, at least for small peptides, the isomer quantification appeared largely independent from the peptide portion of the conjugate, allowing broad application of the method.
Activation of Ca2+phosphatase Calcineurin regulates Parkin translocation to mitochondria and mitophagy
Authors: Marchesan Elena , Nardin Alice , Mauri Sofia , Di Paola Simone , Chinellato Monica , von Stockum Sophia , Chakraborty Joy , Herkenne Stephanie , Basso Valentina , Schrepfer Emilie , Marin Oriano , Cendron Laura , Medina Diego L. , Scorrano Luca , Ziviani Elena
Published: February 2023

Selective removal of dysfunctional mitochondria via autophagy is crucial for the maintenance of cellular homeostasis. This event is initiated by the translocation of the E3 ubiquitin ligase Parkin to damaged mitochondria, and it requires the Serine/Threonine-protein kinase PINK1. In a coordinated set of events, PINK1 operates upstream of Parkin in a linear pathway that leads to the phosphorylation of Parkin, Ubiquitin, and Parkin mitochondrial substrates, to promote ubiquitination of outer mitochondrial membrane proteins. Ubiquitin decorated mitochondria are selectively recruiting autophagy receptors,which are required to terminate the organelle via autophagy. In this work we show a previously uncharacterized molecular pathway that correlates the activation of the Ca2+-dependent phosphatase Calcineurin to Parkin-dependent mitophagy. Calcineurin downregulation or genetic inhibition prevents Parkin translocation to CCCP-treated mitochondria, and impairs stress-induced mitophagy, whereas Calcineurin activation promotes Parkin mitochondrial recruitment and basal mitophagy. Calcineurin interacts with Parkin, and promotes Parkin translocation in the absence of PINK1, but requires PINK1 expression to execute mitophagy in MEF cells. Genetic activation of Calcineurinin vivoboosts basal mitophagy in neurons, and corrects locomotor dysfunction and mitochondrial respiratory defects of aDrosophilamodel of impaired mitochondrial functions.

Our study identifies Calcineurin as a novel key player in the regulation of Parkin translocation and mitophagy.
Drug-induced eRF1 degradation promotes readthrough and reveals a new branch of ribosome quality control
Authors: Gurzeler Lukas-Adrian , Link Marion , Ibig Yvonne , Schmidt Isabel , Galuba Olaf , Schoenbett Julian , Gasser-Didierlaurant Christelle , Parker Christian N. , Mao Xiaohong , Bitsch Francis , Schirle Markus , Couttet Philipp , Sigoillot Frederic , Ziegelmüller Jana , Uldry Anne-Christine , Schmiedeberg Niko , Mühlemann Oliver , Reinhardt Jürgen
Published: February 2023

Suppression of premature termination codons (PTC) by translational readthrough is a promising strategy to treat a wide variety of severe genetic diseases caused by nonsense mutations. Here, we present two novel and potent readthrough promoters – NVS1.1 and NVS2.1 – that restore substantial levels of functional full-length CFTR and IDUA proteins in disease models for cystic fibrosis and Hurler syndrome, respectively. In contrast to other readthrough promoters that affect stop codon decoding, the NVS compounds stimulate PTC suppression by triggering rapid proteasomal degradation of the translation termination factor eRF1. Our results show that this occurs by trapping eRF1 in the terminating ribosome, causing ribosome stalls and subsequent ribosome collisions, activating a novel branch of the ribosome-associated quality control (RQC) network that involves the translational stress sensor GCN1 and the catalytic activity of the E3 ubiquitin ligases RNF14 and RNF25.