bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of frailty instruments in acute coronary syndrome patients
Authors: Langsted Anne , Benatar Jocelyn , Kerr Andrew , Bloomfield Katherine , Devlin Gerry , Sasse Alex , Smythe David , To Andrew , Wilkins Gerry , White Harvey , Stewart Ralph
Published: November 2023

Background

Recognising frailty is important to guide clinical decisions in older patients with cardiac disease. The relative strengths of different frailty instruments to predict mortality and hospitalization risk are uncertain.

Methods

The Edmonton Frail Scale (EFS), Fried Criteria (Fried), Clinical Frailty Scale (CFS), Katz score (Katz), GP Cognition test (GPCog), and Euroscore II a disease based risk score, were completed in 1174 clinically stable inpatients >70 years of age admitted with an acute coronary syndrome to 5 New Zealand hospitals. Associations with all cause mortality (n=353, 29%) during a median follow-up of 5.1 (IQR: 4.6-5.5) years and hospitalization for > 10 days in the next year (n=267, 22%) were evaluated.

Results

There were graded associations between increasing frailty assessed by each tool and all cause mortality. For the EFS, which scores up to 17 points on different dimensions of frailty, hazard ratios for high (score 9-17, n=197) compared to low frailty (score 0-2, n=331) were 5.0 (95%CI: 3.4-7.4) for mortality, and 5.3 (3.4-8.3) for hospitalization. Discrimination for all-cause mortality according to Harrell’s C-index for each instrument were EFS 0.663, Euroscore II 0.654, Fried 0.648, CFS 0.640, GPCog 0.608, and Katz 0.593, P<0.001 for all. C-statistics for hospitalization >10 days were EFS 0.649, Fried 0.628, Katz 0.602, Euroscore II 0.589, CFS 0.584, and GPCog 0.552, P<0.001 for all. When combining tools integrated discrimination improvement for both mortality and hospitalization were greater for EFS than for other frailty instruments.

Conclusion

In acute coronary syndrome patients aged >70 years greater ‘frailty’ assessed using all tools was associated with higher mortality and hospitalization. The Edmonton Frail Scale, which provides a graded measure of severity of frailty based on information relevant to clinical care, discriminated the risk of mortality and hospitalization as well or better than other frailty instruments.
Dissecting the Vascular-Cognitive Nexus: Energetic vs. Conventional Hemodynamic Parameters
Authors: Cheng Hao-Min , Wang Jiun-Jr , Chuang Shao-Yuan , Lin Chen-Hua , Mitchell Gary F. , Huang Chi-Jung , Wang Pei-Ning , Chung Chih-Ping , Chen Liang-Kung , Pan Wen-Harn , Peng Li-Ning , Chen Chen-Huan
Published: November 2023

Background

Blood flow measurements are being studied in relation to vascular health and cognitive function, but their role is unclear.

Objective

We investigated whether energetic hemodynamic parameters, such as aortic and carotid mean and pulsatile energy, and energy pulsatility index (PI), provide a more nuanced understanding of the vascular-cognitive link, as assessed by the Montreal Cognitive Assessment (MoCA), than conventional flow and flow PI.

Methods

Cognitive evaluation and hemodynamic measurements, including aortic and carotid pressure and flow waves, were performed on 1858 MoCA participants. Energy was calculated by integrating pressure time flow. An asymmetric bifurcation model was used to calculate aortic and carotid mean, pulsatile energy, and hemodynamic parameters across the interface.

Results

After adjusting for age, sex, education, depression score, heart rate, BMI, HDL-cholesterol, and glucose levels, energetic hemodynamic parameters were more associated with MoCA score than aortic and carotid flow and flow PI. In particular, carotid mean energy was most significantly positively associated with MoCA (standardized beta = 0.053, P = 0.0253) and energy PI was most significantly negatively associated (standardized beta = -0.093, P = 0.0002), surpassing conventional metrics like carotid PI. Aortic pressure reflection coefficient at the aorta-carotid bifurcation was positively correlated with mean carotid energy and weakly negatively correlated with PI. Aortic characteristic impedance positively correlated with carotid energy PI but not mean energy.

Conclusion

Our study shows that energetic hemodynamic parameters, particularly carotid mean energy and energy PI, better explain the vascular-cognitive nexus than conventional measures.
“In Vivo Imaging of Bone Collagen Dynamics in zebrafish”
Authors: Hino Hiromu , Kuroda Junpei , Kondo Shigeru
Published: November 2023

Type I collagen plays a pivotal role in shaping bone morphology and determining its physical properties by serving as a template for ossification. Nevertheless, the mechanisms underlying bone collagen formation, particularly the principles governing its orientation, remain unknown due to the lack of a method enabling continuous in vivo observation. To address this challenge, we constructed a method to visualize bone collagen by tagging with GFP in zebrafish and observed the interactions between the osteoblasts and collagen fiber during bone formation in vivo. When Col1a2-GFP was expressed under the control of the osteoblast-specific promotersosxoroscin zebrafish, bone collagen could be observed clearly enough to identify their localization, but collagen from other organs did not. Therefore, we determined that this method was of sufficient quality for detailed in vivo observation of bone collagen. Next, bone collagen in the scales, fin ray, and opercular bones was observed in detail in zebrafish, when bone formation is more active.

By simultaneously observing bone collagen and osteoblasts, we successfully observed dynamic changes in the morphology and position of osteoblasts from the early stages of bone formation. It was also found that the localization pattern and orientation of bone collagen significantly differed depending on the choice of expression promoter. Both promoters (osxandosc) used in this study are osteoblast-specific, but their Col1a2-GFP localizing regions within bone are exclusive, withosxregion localizing mainly the outer edge of bone andoscregion localizing the central area of bone. This suggests the existence of distinct subpopulations of osteoblasts with various gene expression profiles, each of which may play a unique role in the osteogenic process.

These findings would contribute to a better understanding of the mechanisms governing bone collagen formation by osteoblasts.
Neural representation of association strength and prediction error during novel symbol-speech sounds learning
Authors: Fraga-González Gorka , Haller Patrick , Willinger David , Gehrig Vanessa , Frei Nada , Brem Silvia
Published: November 2023

Efficient learning of letters-speech sound associations leads to specialization of visual and audiovisual brain regions and is necessary to develop adequate reading skills. We still do not understand the brain dynamics of this learning process, and the involvement of learning and performance monitoring networks is still underexplored. Here we examined a feedback learning task with two mutually dependent parts in which novel symbol-speech sound associations were learned by 39 healthy adults. We used functional magnetic resonance (fMRI) and a reinforcement learning drift diffusion model that described learning across trials. The model-based analysis showed that posterior-occipital activations during stimulus processing were positively modulated by the trial-by-trial learning, described by the increase in association strength of each audiovisual pair. Prediction errors, describing the update mechanism to learn with feedback across trials, modulated activations in several mid-frontal, striatal and cingulate regions. The two task parts yielded a similar pattern of results although they varied in their relative difficulty. This study demonstrates which processes during audiovisual learning contribute to the rapid visual specialization within an experimental session and delineates a set of coactivated regions engaged in learning from feedback. Our paradigm provides a framework to advance our understanding of the neurobiology of learning and reading development.
coRIC map: a framework for the exploration of multifaceted subcellular RNA-binding proteins
Authors: Lv Yuan , Guo Xiangpeng , Hu Jieyi , Kanwal Shahzina , Yuan Jianwen , Tariq Muqddas , Zheng Jingxia , Sun Mingwei , Lu Yuanyuan , Wang Jingjing , Jiang Mengling , Wang Aiping , Castells-Garcia Alvaro , Zheng Xiyuan , Peng Bin , Wang Dongye , Volpe Giacomo , Wu Liang , Mazid Md. Abdul , Li Wenjuan , Lai Yiwei , Aguilo Francesca , Zhou Yu , Cosma Maria Pia , Xu Xingzhi , Lundberg Emma , Mulder Jan , Hutchins Andrew P. , Maxwell Patrick H. , Croce Luciano Di , Zhang Xiaofei , Esteban Miguel A.
Published: November 2023

The ability of RNA-binding proteins (RBPs) to form complexes with other biomolecules underpins a broad range of functions and remarkable structural properties. Understanding the precise spatiotemporal dynamics of RBPs and their interacting partners in the steady state and upon perturbation is key to deciphering these aspects. Here, we present the coRIC (compartmentalizedRNA InteractomeCapture) map, an experimental resource and analytical pipeline to study the subcellular dynamics of RBPs through multimodal dataset integration and machine learning. Using this approach, we have generated an atlas comprising 1,768 RBPs distributed in a broad panel of subcellular compartments and delineated their intermolecular and intercompartmental relationships. We have also defined the hierarchy of RBP-containing complexes at multiple scales across the cell, uncovering previously unknown functions of multiple RBPs. Furthermore, we have investigated the changes in RBP complex composition and subcellular distribution in response toC9ORF72amyotrophic lateral sclerosis/frontotemporal dementia dipeptide repeats and DNA damage stress. The coRIC map provides a valuable new approach for defining the roles of RBPs in homeostasis and disease.
Linking place and view: Organizing space through saccades and fixations between primate posterior parietal cortex and hippocampus
Authors: Vericel Marie , Baraduc Pierre , Duhamel Jean René , Wirth Sylvia
Published: November 2023

Humans primarily rely on vision to explore and guide actions in spatial environments. The parietal cortex is thought to withhold a unified representation of the visual space allowing to direct saccades to salient cues, while the hippocampus provides a memory-based cognitive place map of the environment. Understanding how these two representations interact during navigation is a key question. To probe the link between view and place, we compared neural activity in the posterior parietal cortex and hippocampus of macaques navigating in a virtual maze. When analyzed as a function of the animal’s position in the virtual environment, more neurons in the parietal cortex displayed spatial selectivity compared to the hippocampus. We hypothesized that such modulation by self-position in the parietal cortex might stem from processing visual cues of the environment through exploratory saccades and fixations. However, we established that position-selectivity was not solely correlated with simple oculomotor dynamics. Rather, spatial selectivities in the PPC and the HPC originated from cells driven by direct fixations of maze paths or landmarks. However, while a substantial proportion of PPC and HPC cells displayed selectivity towards landmarks’ features, such as their side of appearance or their identity, we also revealed different task-related maze segmentation between regions. Indeed, when animal gazed at paths, activity in parietal cortex revealed anticipation of reward while that of the hippocampus suggested reward outcome processing. On the other hand, when animals gazed at a landmark already present in the field of view, parietal activity tended to occur close to intersections, while that of hippocampus was more spatially distributed. Finally, at the population level, neurons in both regions anticipated landmarks before they appeared in the field of view, suggesting a shared knowledge of the spatial layout and a collective active role in memory-guided visual exploration across regions. Taken together, these findings shed light on the neural processes that link place and view, through action- and memory-driven exploration of objects in space.
Cytokinin Dehydrogenase in Xylem Sap Reveals A Direct Link Between Cytokinin Metabolism and Long-Distance Transport
Authors: Nedvěd Daniel , Motyka Václav , Raimanová Ivana , Dobrev Petre I. , Kopečný David , Briozzo Pierre , Brunoni Federica , Müller Karel , Hoyerová Klára
Published: November 2023

Metabolic degradation of plant hormones cytokinins (CKs) co-regulates their homeostasis and signalling. In this work, we employed a large-scale bioinformatical analysis to address a diversity of cytokinin oxidase/dehydrogenase (CKX) substrate specificities previously described in several case studies. We present a three-way correlation of the entire CKX amino acid sequences, a variable motif involved in substrate binding, and subcellular localizations predicted by a deep learning model. This correlation is conserved in monocotyledonous plants, suggesting that the CKX diversity in a single species allows a precise tuning of the CK homeostasis. Following these findings, we detected CKX activity in xylem sap for the first time, using the oat (Avena sativa) as a model plant. Further investigation of the substrate specificity and glycosylation of this xylem-located CKX suggested that it originates in roots. We have identified 27 putative CKXs in oats and attributed the xylem-located activity to the extracellular isoforms AsCKX1a,c,d. Finally, we show that the xylem-located CKX activity responds to the nitrate supply, highlighting its physiological relevance. Taken together, we show that CKX directly modulates root-to-shoot CK translocation through metabolic degradation of the transported CKs.
Entorhinal cortex vulnerability to human APP expression promotes hyperexcitability and tau pathology
Authors: Goettemoeller Annie M , Banks Emmie , Kumar Prateek , Olah Viktor J , McCann Katharine E , South Kelly , Ramelow Christina C , Eaton Anna , Duong Duc M , Seyfried Nicholas T , Weinshenker David , Rangaraju Srikant , Rowan Matthew JM
Published: November 2023

Preventative treatment for Alzheimer’s Disease is of dire importance, and yet, cellular mechanisms underlying early regional vulnerability in Alzheimer’s Disease remain unknown. In human patients with Alzheimer’s Disease, one of the earliest observed pathophysiological correlates to cognitive decline is hyperexcitability. In mouse models, early hyperexcitability has been shown in the entorhinal cortex, the first cortical region impacted by Alzheimer’s Disease. The origin of hyperexcitability in early-stage disease and why it preferentially emerges in specific regions is unclear. Using cortical-region and cell-type-specific proteomics coupled withex vivoandin vivoelectrophysiology, we uncovered differential susceptibility to human-specific amyloid precursor protein (hAPP) in a model of sporadic Alzheimer’s. Unexpectedly, our findings reveal that early entorhinal hyperexcitability may result from intrinsic vulnerability of parvalbumin (PV) interneurons, rather than the suspected layer II excitatory neurons. This vulnerability of entorhinal PV interneurons is specific to hAPP, as it could not be recapitulated with increased murine APP expression. However, partial replication of the findings could be seen after introduction of a murine APP chimera containing a humanized amyloid-beta sequence. Surprisingly, neurons in the Somatosensory Cortex showed no such vulnerability to adult-onset hAPP expression. hAPP-induced hyperexcitability in entorhinal cortex could be ameliorated by enhancing PV interneuron excitabilityin vivo.Co-expression of human Tau with hAPP decreased circuit hyperexcitability, but at the expense of increased pathological tau species. This study suggests early disease interventions targeting non-excitatory cell types may protect regions with early vulnerability to pathological symptoms of Alzheimer’s Disease and downstream cognitive decline.
Shared representations of human actions across vision and language
Authors: Dima Diana C. , Janarthanan Sugitha , Culham Jody C. , Mohsenzadeh Yalda
Published: November 2023

Humans can recognize and communicate about many actions performed by others. How are actions organized in the mind, and is this organization shared across vision and language? We collected similarity judgments of human actions depicted through naturalistic videos and sentences, and tested four models of action categorization, defining actions at different levels of abstraction ranging from specific (action verb) to broad (action target: whether an action is directed towards an object, another person, or the self). The similarity judgments reflected a shared organization of action representations across videos and sentences, determined mainly by the target of actions, even after accounting for other semantic features. Language model embeddings predicted the behavioral similarity of action videos and sentences, and captured information about the target of actions alongside unique semantic information. Together, our results show how action concepts are organized in the human mind and in large language model representations.
Pauperization of Emerin from nuclear envelope during chromatin bridge resolution drives prostate cancer cell migration and invasiveness
Authors: Popęda Marta , Kowalski Kamil , Wenta Tomasz , Beznoussenko Galina V. , Rychłowski Michał , Mironov Alexander , Lavagnino Zeno , Barozzi Sara , Richert Julia , Bertolio Rebecca , Szade Jolanta , Miszewski Kevin , Matuszewski Marcin , Żaczek Anna J. , Braga Luca , Sal Giannino Del , Bednarz-Knoll Natalia , Maiuri Paolo , Nastały Paulina
Published: November 2023

Micronuclei (MN) can arise from many causes, including the breakage of aberrant cytokinetic chromatin bridge. The frequent observation of MN in tumors raises the specter that they might not merely be passive elements but could instead play active roles in tumor progression. Here, we test the hypothesis that the presence of micronuclei could induce specific phenotypic and functional changes to the cell and lead to increased cancer invasive potential. With a variety of imaging and molecular methodsin vitroand in clinical samples from prostate cancer (PCa) patients, we show that chromosome bridge resolution can lead to EMD accumulation and formation of EMD-rich MN. Such structure is negative for Lamin A/C and positive for LBR and Sec6β. It can cause EMD pauperization from NE affecting migratory and invasive properties of a cell and can be translated to PCa patient’s poor prognosis.
Genome assembly of the dyeing poison frog provides insights into the dynamics of transposable element and genome-size evolution
Authors: Dittrich Carolin , Hölzl Franz , Smith Steve , Fouilloux Chloe A. , Parker Darren J. , O’Connell Lauren A. , Knowles Lucy S. , Hughes Margaret , Fewings Ade , Morgan Rhys , Rojas Bibiana , Comeault Aaron A.
Published: November 2023

Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display the greatest variation in genome size, making them ideal models to explore the causes and consequences of genome size variation. However, high-quality genome assemblies for amphibians have, until recently, been rare. Here, we generate a high-quality genome assembly for the dyeing poison frog,Dendrobates tinctorius. We compare this assembly to publicly-available frog genomes and find evidence for both large-scale conserved synteny and widespread rearrangements between frog lineages. Comparing conserved orthologs annotated in these genomes revealed a strong correlation between genome size and gene size. To explore the cause of gene-size variation, we quantified the location of transposable elements relative to gene features and find that the accumulation of transposable elements in introns has played an important role in the evolution of gene size inD. tinctorius, while estimates of insertion times suggest that many insertion events are recent and species-specific. Finally, we show that the diversity and abundance of transposable elements in poison frog genomes can complicate genotyping efforts that rely on repetitive elements as sequence anchors. Our results show that transposable elements have clearly played an important role in the evolution of large genome size inD. tinctorius. Future studies are needed to fully understand the dynamics of transposable element evolution and to optimise primer or bait design for cost-effective population-level genotyping in species with large, repetitive genomes.

Significance

Amphibians display more variation in genome size than any other vertebrate lineage. Complexities associated with large genomes frequently hamper genome assembly and population genetic studies. Here we use long-read HiFi sequences to generate a high-quality 6.3 Gbp genome assembly of the poison frogDendrobates tinctorius. We use this genome and leverage comparative genomics andde novoannotations to quantify aspects of genome evolution driven by repetitive transposable genetic elements. Our results provide support for the dynamic role that transposable elements play in driving the evolution of “genomic gigantism” in amphibians. We also show how transposable elements can be leveraged for cost-efficient population genetic studies using limited input material.
Capturing the blue-light activated state of the Phot-LOV1 domain fromChlamydomonas reinhardtiiusing time-resolved serial synchrotron crystallography
Authors: Gotthard Guillaume , Mous Sandra , Weinert Tobias , Antonelli Maia Raiza Nara , James Daniel , Dworkowski Florian , Gashi Dardan , Furrer Antonia , Ozerov Dmitry , Panepucci Ezequiel , Wang Meitian , Schertler Gebhard F. X. , Heberle Joachim , Standfuss Joerg , Nogly Przemyslaw
Published: November 2023

Light-Oxygen-Voltage (LOV) domains are small photosensory flavoprotein modules that allow converting external stimuli (sunlight) into intracellular signals responsible for various cell behavior (e.g.,phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that results in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the observation of the activation cascade of the LOV domain in real-time, which has been elusive.

In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 fromChlamydomonas reinhardtii(CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to the actual data collection process, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the obtained crystals preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations ofCrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process.
Oleoylethanolamide effects on stress-induced alcohol consumption: a lipid at crossroads between stress, reward and neuroinflammation
Authors: González-Portilla Macarena , Montagud-Romero Sandra , Mellado Susana , Rodríguez de Fonseca Fernando , Pascual María , Rodríguez-Arias Marta
Published: November 2023

The endocannabinoid system is involved in multiple drug-related behavior as well as in the stress response. The transient increase in endogenous cannabinoids as well as endocannabinoid-like molecules contributes to healthy adaptation to stress exposure. In this study, we tested the effect of systemic OEA treatment (10mg/kg) before or after social defeat (SD) on alcohol self-administration (SA). Mice were divided into non-stressed (EXP) and stressed mice (SD) and randomly assigned to a treatment condition (CTRL, OEA or 10OEA). Mice in the EXP/SD-OEA group received four doses before each SD encounter while mice in the EXP/SD-10OEA mice received 10 daily doses after stress exposure. Three weeks after SD, mice were trained to alcohol 20% (vol/vol) SA. Upon extinction, a cue-induced reinstatement test was performed. Our results showed that only multiple-dose chronic OEA treatment (SD-10OEA group) was effective in preventing the stress-induced increase in alcohol consumption observed in defeated mice. We did not observe any effects of OEA on relapse-like behavior. Altogether, these data suggest that exogenously increasing OEA levels counteracts the adverse effects of stress on alcohol drinking.
Circadian coupling of mitochondria in a deep-diving mammal
Authors: Ciccone Chiara , Kante Fayiri , Folkow Lars P. , Hazlerigg David G. , West Alexander C. , Wood Shona H.
Published: November 2023

Regulation of mitochondrial oxidative phosphorylation is essential to match energy supply to changing cellular energy demands, and to cope with periods of hypoxia. Recent work implicates the circadian molecular clock in control of mitochondrial function and hypoxia sensing. Since diving mammals experience intermittent episodes of severe hypoxia, with diel patterning in dive depth and duration, it is interesting to consider circadian - mitochondrial interaction in this group. Here we demonstrate that the hooded seal (Cystophora cristata), a deep diving Arctic pinniped, shows strong daily patterning of diving behaviour in the wild. Cultures of hooded seal skin fibroblasts exhibit robust circadian oscillation of the core clock genesper2andarntl. In liver tissue collected from captive hooded seals, expression ofarntlwas some 4-fold higher in the middle of night than in the middle of the day. To explore the clock-mitochondria relationship, we measured the mitochondrial oxygen consumption in synchronized hooded seal skin fibroblasts and found a circadian variation in mitochondrial activity, with higher coupling efficiency of complex I coinciding with the trough ofarntlexpression. These results open the way for further studies of circadian - hypoxia interactions in pinnipeds during diving.

SUMMARY STATEMENT

A functional clockwork and circadian variation in mitochondrial complex I efficiency is demonstrated in skin fibroblasts from the deep diving hooded seal.
Myospreader improves gene editing in skeletal muscle by myonuclear propagation
Authors: Poukalov Kiril K. , Valero M. Carmen , Muscato Derek R. , Adams Leanne M. , Chun Heejae , Lee Young il , Andrade Nadja S. , Zeier Zane , Sweeney H. Lee , Wang Eric T.
Published: November 2023

Successful CRISPR/Cas9-based gene editing in skeletal muscle is dependent on efficient propagation of Cas9 to all myonuclei in the myofiber. However, nuclear-targeted gene therapy cargos are strongly restricted to their myonuclear domain of origin. By screening nuclear localization signals and nuclear export signals, we identify “Myospreader”, a combination of short peptide sequences that promotes myonuclear propagation. Appending Myospreader to Cas9 enhances protein stability and myonuclear propagation in myoblasts and myofibers. AAV-delivered Myospreader dCas9 better inhibits transcription of toxic RNA in a myotonic dystrophy mouse model. Furthermore, Myospreader Cas9 achieves higher rates of gene editing in CRISPR reporter and Duchenne muscular dystrophy mouse models. Myospreader reveals design principles relevant to all nuclear-targeted gene therapies and highlights the importance of the spatial dimension in therapeutic development.
Antiproliferative Activity of Cephalotaxus Esters: Overcoming Chemoresistance in Cancer Therapy
Authors: Yong-Gonzalez Vladimir , Radu Constantine , Calder Paul A. , Shum David , Gin David Y. , Frattini Mark G. , Djaballah Hakim
Published: November 2023

Omacetaxine, a semisynthetic form of Homoharringtonine (HHT), was approved for the treatment of chronic myeloid leukemia (CML). Previously, we published the synthesis of this natural alkaloid and three of its derivatives: deoxyharringtonine (DHT), deoxyhomoharringtonine (DHHT), and bis(demethyl)-deoxyharringtonine (BDHT); and reported on its refractory activity against the HL-60/RV+ cells over-expressing P-glycoprotein 1 (MDR1). In this study, we explored the extent of this resistance by first expanding the panel of established cell lines and second, using a panel of 21 leukemia patient derived primary cells. Here, we report a consistent resistance to HTT in K562 derived cells and in MES-SA/MX2 derived cells resistant to mitoxanthrone; all of them over-express MDR1, while we found U87MG-ABCG2 and H69AR cells to be very sensitive to HTT. In contrast, DHT, DHHT, and BDHT seemingly overcome this resistance due to the changes made to the acyl chain of HTT rendering the derivatives less susceptible to efflux. Surprisingly, the leukemia primary cells were very sensitive to HHT and its derivatives with low nanomolar potencies, followed by a new class of CDC7 kinase inhibitors, the anthracycline class of topoisomerase inhibitors, the DNA intercalator actinomycin-D, and the vinca alkaloid class of microtubule inhibitors. The mechanism of cell death induced by HTT and DHHT was found to be mediated via Caspase 3 cleavage leading to apoptosis. Taken together, our results confirm that HHT is a substrate for MDR1. It opens the door to a new opportunity to clinically evaluate HHT and its derivatives for the treatment of AML and other cancers.
Advance Glycation End-products accelerate amyloid deposits in adipocyte’s lipid droplets
Authors: Izgilov Roza , Kislev Nadav , Omari Eman , Benayahu Dafna
Published: November 2023

Adipose tissue dysfunction is central to insulin resistance, and the emergence of type 2 diabetes (T2D) is associated with elevated levels of carbonyl metabolites from glucose metabolism. In this study, using methylglyoxal (MGO) and glycolaldehyde (GAD) carbonyl metabolites, induced protein glycation leading to misfolding and β-sheet formation and generation of advanced glycation end products (AGEs). The formed AGEs compromise adipocytes activity.

Microscopic and spectroscopic assays were used to examine the impact of MGO and GAD on lipid droplet - associated proteins. The results provide information about how glycation leads to the appearance of amyloidogenic proteins formation that hinders metabolism and autophagy in adipocytes. We measured the beneficial effects of metformin, an anti-diabetic drug, on misfolded protein as assessed by thioflavin (ThT) spectroscopy and improved autophagy. In vitro findings were complemented by in vivo analysis of white adipose tissue (WAT), where lipid droplet-associated β-amyloid deposits were predominantly linked to adipose triglyceride lipase (ATGL), a lipid droplet protein. Bioinformatics, imaging, and biochemical methods affirm ATGL’s role in β-sheet secondary structure creation. Our results highlighted the pronounced presence of amyloidogenic proteins in adipocytes treated with carbonyl compounds, potentially reshaping our understanding of adipocyte pathology in the context of T2D. This in-depth exploration offers novel perspectives on related pathophysiology and underscores the potential of adipocytes as pivotal therapeutic targets, bridging T2D, amyloidosis, protein glycation, and adipocyte malfunction.

Significance Statement

The generation of advanced glycation end products (AGEs) has a strong connection to diabetes severity . Adipose tissue is known to play a key role in the metabolic impairment and obesity associated with diabetes. We used the carbonyl compounds methylglyoxal (MGO) and glycolaldehyde (GAD) to create AGEs in adipocytes. The results of this study indicate that glycation not only affects cell metabolism and impairs adipocyte lipolysis, but also alters autophagy and increases protein amyloid deposits related to the membrane of lipid droplets. We identify the ATGL as a protein prone to β sheet alteration. consequently, ATGL emerges as a pivotal actor in lipid droplet metabolism and a prospective therapeutic target for T2D complications.
Potential climate change effects on the distribution of urban and sylvatic dengue and yellow fever vectors
Authors: Aliaga-Samanez Alisa , Romero David , Murray Kris , Segura Marina , Real Raimundo , Olivero Jesús
Published: November 2023

Climate change may increase the risk of dengue and yellow fever transmission by urban and sylvatic mosquito vectors. Previous research primarily focused onAedes aegyptiandAedes albopictus. However, these diseases involve a complex transmission cycle in which sylvatic vectors are also involved. Our aim was to analyse which mosquito species could contribute to the increased risk of transmission of these diseases due to climate change, and to identify where the risk increase could most likely occur. Using a biogeographical approach, we mapped areas where mosquito favourability could increase, decrease or remain stable in the near (2041-2060) and distant (2061-2080) future.

Models predict dengue vectors expanding in West and Central Africa and in South-East Asia, reaching Borneo. Yellow fever vectors could spread in West and Central Africa and in the Amazon. In Europe, the models suggest a re-establishment ofAe. aegypti, whileAe. albopictuswill continue to find new favourable areas. The results underline the need to focus more on vectorsAe. vittatus,Ae. luteocephalusandAe. africanusin West and Central sub-Saharan Africa, especially Cameroon, Central Africa Republic, and northern Democratic Republic of Congo; and suggest the need for a protocol to prevent dengue and yellow fever that include surveillance of neglected sylvatic vectors.
Enzalutamide Induces Cytotoxicity in Desmoplastic Small Round Cell Tumor Independent of the Androgen Receptor
Authors: Magrath Justin W. , Goldberg Ilon N. , Truong Danh D. , Hartono Alifiani B. , Sampath Shruthi Sanjitha , Jackson Chandler E. , Ghosh Anushka , Cardin Derrick L. , Zhang Haitao , Ludwig Joseph A. , Lee Sean B.
Published: November 2023

Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, pediatric cancer caused by the EWSR1::WT1 fusion protein. DSRCT predominantly occurs in males, which comprise 80-90% of the patient population. While the reason for this male predominance remains unknown, one hypothesis is that the androgen receptor (AR) plays a critical role in DSRCT and elevated testosterone levels in males help drive tumor growth. Here, we demonstrate that AR is highly expressed in DSRCT relative to other fusion-driven sarcomas and that the AR antagonists enzalutamide and flutamide reduce DSRCT growth. However, despite these findings, which suggest an important role for AR in DSRCT, we show that DSRCT cell lines form xenografts in female mice at the same rate as male mice and AR depletion does not significantly alter DSRCT growthin vitro. Further, we find that AR antagonists reduce DSRCT growth in cells depleted of AR, establishing an AR-independent mechanism of action. These findings suggest that AR dependence is not the reason for male predominance in DSRCT and that AR-targeted therapies may provide therapeutic benefit primarily through an AR-independent mechanism that requires further elucidation.
PROLONG: Penalized Regression for Outcome guided Longitudinal Omics analysis with Network and Group constraints
Authors: Broll Steve , Basu Sumanta , Lee Myung Hee , Wells Martin T.
Published: November 2023

Motivation

There is a growing interest in longitudinal omics data, but there are gaps in existing methodology in the high-dimensional setting. This paper focuses on selecting metabolites that co-vary with Tuberculosis mycobacterial load. The proposed method is applied to general continuous longitudinal outcomes with continuous longitudinal omics predictors. Simple longitudinal models examining a single omic predictor at a time do not leverage the correlation across predictors, thus losing power. We propose a penalized regression approach on the first differences of the data that extends the lasso + Laplacian method (Li and Li 2008) to a longitudinal group lasso + Laplacian approach. Our method, PROLONG, leverages the first differences of the data to address the piecewise linear structure and the observed time dependence. The Laplacian network constraint incorporates the dependence structure of the predictors, and the group lasso constraint induces sparsity while grouping metabolites across their first differenced observations.

Results

With an automated selection of model hyper-parameters, PROLONG correctly selects target metabolites with high specificity and sensitivity across simulation scenarios and sizes. PROLONG selects a set of metabolites from the real data that includes interesting targets identified during EDA.

Availability

R package ‘prolong’ is in development.

Conclusions

PROLONG is a powerful method for selecting interesting features in high dimensional longitudinal omics data that co-vary with some continuous clinical outcome.

Contact

sb2643@cornell.edu
Methylation of histone H3 lysine 36 is a barrier for therapeutic interventions of head and neck squamous cell carcinoma
Authors: Caeiro Lucas D. , Nakata Yuichiro , Borges Rodrigo L. , Garcia-Martinez Liliana , Bañuelos Carolina P. , Stransky Stephanie , Chan Ho Lam , Brabson John , Domínguez Diana , Zhang Yusheng , Lewis Peter W. , Aznar-Benitah Salvador , Cimmino Luisa , Bilbao Daniel , Sidoli Simone , Verdun Ramiro E. , Morey Lluis
Published: November 2023

Approximately 20% of head and neck squamous cell carcinomas (HNSCC) exhibit reduced methylation on lysine 36 of histone H3 (H3K36me) due to mutations in histone methylase NSD1 or a lysine-to-methionine mutation in histone H3 (H3K36M). Whether such alterations of H3K36me can be exploited for therapeutic interventions is still unknown. Here, we show that HNSCC models expressing H3K36M can be divided into two groups: those that display aberrant accumulation of H3K27me3 and those that maintain steady levels of H3K27me3. The first group shows decreased proliferation, genome instability, and increased sensitivity to genotoxic agents, such as PARP1/2 inhibitors. In contrast, the H3K36M HNSCC models with steady H3K27me3 levels do not exhibit these characteristics unless H3K27me3 levels are elevated, either by DNA hypomethylating agents or by inhibiting the H3K27me3 demethylases KDM6A/B. Mechanistically, we found that H3K36M reduces H3K36me by directly impeding the activities of the histone methyltransferase NSD3 and the histone demethylase LSD2. Notably, we found that aberrant H3K27me3 levels induced by H3K36M expression is not a bona fide epigenetic mark in HNSCC since it requires continuous expression of H3K36M to be inherited. Moreover, increased sensitivity of H3K36M HNSCC models to PARP1/2 inhibitors solely depends on the increased H3K27me3 levels. Indeed, aberrantly high H3K27me3 levels decrease BRCA1 and FANCD2-dependent DNA repair, resulting in higher sensitivity to DNA breaks and replication stress. Finally, in support of our in vitro findings, a PARP1/2 inhibitor alone reduce tumor burden in a H3K36M HNSCC xenograft model with elevated H3K27me3, whereas in a H3K36M HNSCC xenograft model with consistent H3K27me3 levels, a combination of PARP1/2 inhibitors and agents that upregulate H3K27me3 proves to be successful. In conclusion, our findings underscore a delicate balance between H3K36 and H3K27 methylation, essential for maintaining genome stability. This equilibrium presents promising therapeutic opportunities for patients with H3K36me-deficient tumors.
Hidden rAAV Breakpoints Detected Using Single-Molecule, Modified Base Sequencing
Authors: Hanscom Terrence , Soares Luis M M , Zheng Alice , Bourgeois Nathanael , Gall Katherine , St Martin Thia , Wright Jason , Selby Donald E
Published: November 2023

The AAV genome is a single stranded DNA molecule packaged in an icosahedral protein capsid. Vector genomes of plus and minus polarities are packaged and complementary genomic strands hybridize when lysedin vitro. Standard sequencing library methods cause loss of information from individual genomes when mismatches and gaps are repaired. To retain original molecular information, modified bases are used during the repair step which allows pre-existing DNA to be distinguished from DNA added during library preparation. Modified bases introduced during repair are identified using the Sequel II system and used to detect HIDdEN DNA breakpoints (HIDEN-Seq). The most frequent breakpoints in an AAV vector subject to high strand breakage during packaging were linked to adjacent secondary structure, prompting changes in nearby sequences to reduce breakage. This use of modified bases for localizing DNA breaks enables better vector design, resulting in higher quality gene therapy vectors. The same approach can be used in other systems where knowledge of pre-existing sequence and structure is important.
Loss of function ofAtrxleads to activation of alternative lengthening of telomeres in a primary mouse model of sarcoma
Authors: Pierpoint Matthew , Floyd Warren , Wisdom Amy J. , Luo Lixia , Ma Yan , Waitkus Matthew S. , Kirsch David G.
Published: November 2023

The development of a telomere maintenance mechanism is essential for immortalization in human cancer. While most cancers elongate their telomeres by expression of telomerase, 10-15% of human cancers use a pathway known as alternative lengthening of telomeres (ALT). In this work, we developed a genetically engineered primary mouse model of sarcoma in CAST/EiJ mice which displays multiple molecular features of ALT activation after CRISPR/Cas9 introduction of oncogenicKrasG12Dand loss of function mutations ofTrp53andAtrx.In this model, we demonstrate that the loss ofAtrxcontributes to the development of ALT in an autochthonous tumor, and this process occurs independently of telomerase function by variation of mTR alleles. Furthermore, we find that telomere shortening from the loss of telomerase leads to higher chromosomal instability while loss ofAtrxand activation of ALT lead to an increase in telomeric instability, telomere sister chromatid exchange, c-circle production, and formation of ALT-associated promyelocytic leukemia bodies (APBs). The development of this primary mouse model of ALT could enable future investigations into therapeutic vulnerabilities of ALT activation and its mechanism of action.
Neural markers of reduced arousal and consciousness in Mild Cognitive Impairment
Authors: Estarellas Mar , Huntley Jonathan , Bor Daniel
Published: November 2023

Objectives

People with Alzheimer’s Disease (AD) experience changes in their level and content of consciousness, but there is little research on biomarkers of consciousness in pre-clinical AD and MCI. This study investigated whether levels of consciousness are decreased in people with MCI.

Methods

A multi-site MEG dataset, BIOFIND, comprising 83 people with MCI and 83 age matched controls, was analysed. Arousal (and drowsiness) was assessed by computing the theta-alpha ratio (TAR). The Lempel-Ziv algorithm (LZ) was used to quantify the information content of brain activity, with higher LZ values indicating greater complexity and potentially a higher level of consciousness.

Results

LZ was lower in the MCI group vs controls, indicating a reduced level of consciousness in MCI. TAR was higher in the MCI group vs controls, indicating a reduced level of arousal (i.e. increased drowsiness) in MCI. LZ was also found to be correlated with MMSE scores, suggesting a direct link between cognitive impairment and level of consciousness in people with MCI.

Conclusions

A decline in consciousness and arousal can be seen in MCI. As cognitive impairment worsens, measured by MMSE scores, levels of consciousness and arousal decrease. These findings highlight how monitoring consciousness using biomarkers could help understand and manage impairments found at the preclinical stages of AD. Further research is needed to explore markers of consciousness between people who progress from MCI to dementia and those who do not, and in people with moderate and severe AD, to promote person-centred care.
TBXT dose sensitivity and the decoupling of nascent mesoderm specification from EMT progression in 2D human gastruloids
Authors: Bulger Emily A. , Muncie-Vasic Ivana , Libby Ashley R.G. , McDevitt Todd C. , Bruneau Benoit G.
Published: November 2023

In the nascent mesoderm, levels of Brachyury (TBXT) expression must be precisely regulated to ensure cells exit the primitive streak and pattern the anterior-posterior axis, but how this varying dosage informs morphogenesis is not well understood. In this study, we define the transcriptional consequences of TBXT dose reduction during early human gastrulation using human induced pluripotent stem cell (hiPSC)-based models of gastrulation and mesoderm differentiation. Multiomic single-nucleus RNA and single-nucleus ATAC sequencing of 2D gastruloids comprised of WT, TBXT heterozygous (TBXT-Het), or TBXT null (TBXT-KO) hiPSCs reveal that varying TBXT dosage does not compromise a cell’s ability to differentiate into nascent mesoderm, but that the loss of TBXT significantly delays the temporal progression of the epithelial to mesenchymal transition (EMT). This delay is dependent on TBXT dose, as cells heterozygous for TBXT proceed with EMT at an intermediate pace relative to WT or TBXT-KO. By differentiating iPSCs of the allelic series into nascent mesoderm in a monolayer format, we further illustrate that TBXT dose directly impacts the persistence of junctional proteins and cell-cell adhesions. These results demonstrate that EMT progression can be decoupled from the acquisition of mesodermal identity in the early gastrula and shed light on the mechanisms underlying human embryogenesis.
Refugee and asylum seekers’ engagement with health services during pregnancy: A rapid review
Authors: Green Jennifer , Herbert Jane , Pitts Leissa , Garakasha Nyari , Smithers Lisa Gaye
Published: November 2023

The objective of this work was to summarise and describe antenatal care experiences of people from refugee and asylum seeker backgrounds living in high-income countries with universal healthcare. Academic articles from six databases and grey literature from selected government websites were systematically searched for English-language articles published 2012-2022. Articles describing perinatal care of people from refugee and asylum seeker backgrounds from the service user and service providers perspective were eligible for inclusion. A thematic synthesis of included articles was undertaken with study quality assessed using Critical Appraisal Sills Program tools.

Of the 37 included articles, there were seven qualitative, 15 quantitative, two mixed-methods studies and 13 reviews. Articles were conducted in Australia (57%), Canada (11%), and the remainder from Europe. Three recurring themes of communication, sociocultural and health system factors were described as barriers or challenges to antenatal care experiences but also presented opportunities for improving care. Many issues around antenatal care experiences for people from refugee and asylum seeker backgrounds remain the same as those identified over ten years ago. To improve antenatal care for people from refugee and asylum seeker backgrounds, health services could implement a range of strategies that support communication, sociocultural experiences and system-related issues.