bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Throughput Targeted Drug Screening for NF1-associated High-Grade Gliomas with ATRX Deficiency
Authors: Dubey Swati , Rai Simran , Guillen Fabiola , Iyer Ajeeth , Aung Su , Yuan Ming , Eberhart Charles G. , Rodriguez Fausto J 
Published: December 2024

AbstractNeurofibromatosis type 1 (NF1)-associated high-grade gliomas (HGGs) harboring ATRX mutations exhibit an aggressive clinical phenotype, driven by heightened genomic instability and metabolic reprogramming. Existing therapies, including chemotherapy and radiotherapy, are limited by resistance mechanisms and formation of secondary malignancy, underscoring the need for novel therapeutic strategies. Here, we report the results of a high-throughput screening of 10,000 small molecules aimed at identifying compounds selectively targeting vulnerabilities associated with concurrent ATRX and NF1 loss. Among the screened compounds, K784-6195 (ChemDiv ID) emerged as a promising candidate, exhibiting marked selective cytotoxicity in NF1-associated glioma cell lines with ATRX deficiency (IC50 = 4.84 µM). In comparison, wild-type ATRX sporadic glioma cell lines (U251) exhibited significantly reduced sensitivity to K784-6195 (IC50 = 37.03 µM). However, ATRX knockout U251 glioma cells recapitulating concurrent ATRX and NF1 loss exhibited heightened susceptibility to K784-6195 (IC50 = 20-23 µM) compared to their wild-type counterpart. Metabolomic analysis revealed that K784-6195 treatment impairs metabolic pathways, including the pentose phosphate pathway, glutamine metabolism, and redox homeostasis, leading to oxidative stress and impaired cell survival. These findings highlight K784-6195 as a promising candidate for therapeutic development, offering a targeted approach for the treatment of NF-1 associated HGGs with ATRX deficiency.
Molecular and spatial analysis of ganglion cells on retinal flatmounts: diversity, topography, and perivascularity
Authors: Tsai Nicole Y. , Nimkar Kushal , Zhao Mengya , Lum Matthew R. , Yi Yujuan , Garrett Tavita R. , Wang Yixiao , Toma Kenichi , Caval-Holme Franklin , Reddy Nikhil , Ehrlich Aliza T. , Kriegstein Arnold R. , Do Michael Tri H. , Sivyer Benjamin , Shekhar Karthik , Duan Xin 
Published: December 2024

SUMMARYDiverse retinal ganglion cells (RGCs) transmit distinct visual features from the eye to the brain. Recent studies have categorized RGCs into 45 types in mice based on transcriptomic profiles, showing strong alignment with morphological and electrophysiological properties. However, little is known about how these types are spatially arranged on the two-dimensional retinal surface—an organization that influences visual encoding—and how their local microenvironments impact development and neurodegenerative responses. To address this gap, we optimized a workflow combining imaging-based spatial transcriptomics (MERFISH) and immunohistochemical co-staining on thin flatmount retinal sections. We used computational methods to registeren facesomata distributions of all molecularly defined RGC types. More than 75% (34/45) of types exhibited non-uniform distributions, likely reflecting adaptations of the retina’s anatomy to the animal’s visual environment. By analyzing the local neighborhoods of each cell, we identified perivascular RGCs located near blood vessels. Seven RGC types are enriched in the perivascular niche, including members of intrinsically photosensitive RGC (ipRGC) and direction-selective RGC (DSGC) subclasses. Orthologous human RGC counterparts of perivascular types - Melanopsin-enriched ipRGCs and ON DSGCs - were also proximal to blood vessels, suggesting their perivascularity may be evolutionarily conserved. Following optic nerve crush in mice, the perivascular M1-ipRGCs and ON DSGCs showed preferential survival, suggesting that proximity to blood vessels may render cell-extrinsic neuroprotection to RGCs through an mTOR-independent mechanism. Overall, our work offers a resource characterizing the spatial profiles of RGC types, enabling future studies of retinal development, physiology, and neurodegeneration at individual neuron type resolution across the two-dimensional space.
Implications of diabetes mellitus on pathophysiology of Tuberculosis: Role of AGE-RAGE Axis and Glycated Proteins
Authors: Panda Sudhasini , Singh Alankrita , Seelan Diravya M , Arora Alisha , Dagar Gunjan , Ethayathulla Abdul S , Luthra Kalpana , Mohan Anant , Vikram Naval K , Gupta Neeraj Kumar , Singh Mayank , Singh Archana 
Published: December 2024

ABSTRACTChronic hyperglycemia in diabetes mellitus promotes the formation of advanced glycation end products (AGEs) via non-enzymatic glycation of plasma proteins. AGEs and their receptor RAGE are central to diabetic complications, as they activate inflammatory pathways and oxidative stress. We studied the AGE-RAGE axis in uncontrolled diabetic individuals having pulmonary TB (PTB+DM), uncontrolled diabetic individuals with no infection (DM), and pulmonary TB patients (PTB). Levels of AGEs and RAGE were measured across these groups and compared to controls. The results showed significantly higher AGEs and RAGE levels in the diabetic milieu, reflecting chronic hyperglycemia. These AGEs were shown to be associated with impaired macrophage function, evidenced by reduced phagocytic capacity. Increased AGEs correlated with disease severity in tuberculosis patients co-affected by diabetes, indicating compromised immune responses. RAGE expression also showed a higher trend in TB patients, although not statistically significant, potentially influencing infection outcomes. Glycated calmodulin was also elevated in diabetic and TB-diabetes comorbid patients and negatively correlated with nitric oxide (NO) levels, suggesting that calmodulin glycation hinders NO production in diabetic conditions. Molecular dynamic studies revealed that glycosylation disrupts calmodulin’s interaction with inducible nitric oxide synthase (iNOS), potentially explaining the decreased NO levels in TB-diabetes comorbid patients. These findings underscore the detrimental impact of AGEs and RAGE in diabetic immune dysregulation, highlighting the need for therapeutic strategies to mitigate their effects on macrophage function and restore immune responses.HighlightsWe conducted this study to examine how hyperglycemia-driven AGEs and RAGE contribute to immune dysfunction and disease severity in diabetic and TB-diabetes patients.High AGEs and RAGE impairs macrophage function, decreasing phagocytic capacity and worsening disease severity in TB-diabetes comorbidity.Glycosylation disrupts calmodulin’s interaction with iNOS, contributing to lower NO levels and weakened immune responses in TB-diabetes comorbidity.The AGE-RAGE axis should be studied further for these comorbid conditions to assess and improve macrophage function and restore immune responses.
Eq-DIAGNOBATCH, a Shiny application for topical product equivalence with batch effect and multivariate outlier analysis
Authors: Monleón-Getino Toni , Ocaña Jordi 
Published: December 2024

AbstractThe Eq-DIAGNOBATCH application presented here complements a previous theoretical article about establishing the equivalence of topical products in a parallel linear model, accounting for a batch effect or not. This application provides a very simple way of carrying out the equivalence test for this type of situation, efficiently obtaining the estimates of the parameters of interest (equivalence intervals, geometric mean ratio, and variance components), and allowing calculations to be performed assuming a batch effect or not. It also examines the statistical implications of the presence of outliers in the sample, from both a univariate and multivariate point of view. The operation and mode of use of Eq-DIAGNOBATCH are presented, including examples related with the quality and equivalence of topical products and bioequivalence analysis. Some of these examples come from the literature and others from real-life industry case studies.
The effects of reactive balance training on cardiorespiratory fitness and muscle strength: a pilot randomized controlled trial
Authors: Devasahayam Augustine J. , Barzideh Azadeh , Jagroop David , Danells Cynthia , Inness Elizabeth L. , Marzolini Susan , Mathur Sunitha , Oh Paul , Mansfield Avril 
Published: December 2024

ABSTRACTBackgroundReactive balance training (RBT) may improve multiple components of physical fitness, including aerobic capacity and muscle strength. However, there have been no studies examining its effects on these factors in people with stroke.ObjectivesThe objectives of this pilot study were to determine the feasibility of a non-inferiority randomized controlled trial, comparing aerobic and strength training (AST) and RBT, considering sample size (primary objective), rates of accrual and withdrawal, intervention adherence, missing data, preliminary effects, and harms (secondary objectives).MethodsPeople who were at least six months’ post-stroke and could stand independently for >30 seconds were recruited. Peak oxygen consumptionwas measured by cardiopulmonary exercise test. Peak isokinetic torques for knee extension and flexion were measured by dynamometer.ResultsTwenty-three participants (6 women) were randomized into AST and RBT groups. Four-hundred participants per group were estimated to be required for the main trial consideringand peak isokinetic torque as primary outcomes. Rates of accrual and withdrawal were 2 participants for every quarter and 30%, respectively. On average, AST participants attended 29.6/36 sessions (range: 18-36) and RBT participants attended 23.5/36 sessions (range: 1-35). Data were missing for(n=2) and ABC scale (n=1) as participants declined testing.and peak knee extension torque of more-affected legs improved post-intervention in both groups. Ten adverse events related to study interventions resolved without medical attention.ConclusionProgressing to a definitive single-site trial is not feasible given the large required sample size, low accrual, and high withdrawal rates.Trial registrationNCT04042961
2-D organoids demonstrate specificity in the interactions of parasitic nematodes and their secreted products at the basal or apical intestinal epithelium
Authors: White Ruby , Bermúdez-Barrientos Jose Roberto , Robertson Elaine , Duque Correa María A. , Buck Amy H. 
Published: December 2024

ABSTRACTThe intestinal epithelium is a selectively permeable barrier that absorbs water and nutrients, senses the luminal environment, and orchestrates submucosal immune responses. Some gastrointestinal nematodes occupy both submucosal and luminal niches and can cause profound changes in epithelial cells. Yet, there is little understanding of the specificity of parasite-host interactions with epithelial cells and the differential responses at the apical or basal sides. Organoids enable uncoupling of parasite-driven responses from immune-driven effects on the epithelium, and two-dimensional (2-D) organoids allow for controlled access to both sides. Here we used 2-D enteroids to modelin vivolocalisation ofHeligmosomoides bakeri(H. bakeri) fourth-larval (L4) and adult stages and identify localisation-specific effects on gene expression. Using bulk RNA sequencing, we found an enhanced upregulation of IFN-stimulated genes (ISGs) during basal co-culture and an overall stronger response to L4 parasites than adults. Further,H. bakerilive worms induced much stronger effects on gene expression than their isolated excretory-secretory (ES), but cells that internalisedH. bakeriextracellular vesicles (EVs) displayed up-regulation of ISGs, repair genes, and YAP/TAZ signalling. Our results demonstrate that nematodes and their products, including EVs, modify the host epithelium in a localisation-dependent and cell-specific manner.
Early endosome disturbance and endolysosomal pathway dysfunction in Duchenne muscular dystrophy
Authors: Chassagne Julie , Silva Nathalie Da , Akrouf Ines , Cadot Bruno , Julien Laura , Barthélémy Ines , Blot Stéphane , Le Guiner Caroline , Bui Mai Thao , Romero Norma B. , Lainé Jeanne , Pietri-Rouxel France , Meunier Pierre , Mamchaoui Kamel , Lorain Stéphanie , Bitoun Marc , Benkhelifa-Ziyyat Sofia 
Published: December 2024

AbstractDuchenne muscular dystrophy (DMD) is a lethal dystrophy characterized by the progressive loss of muscle fibers caused by mutations inDMDgene and absence of the dystrophin protein. While autophagy and lysosome biogenesis defects have been described in DMD muscles, the endosomal pathway has never been studied. Here, we showed that impaired lysosome formation is associated with altered acidification and reduced degradative function of the endolysosomal pathway in muscle cells derived from DMD patients. Our data demonstrated that early endosomes are increased in these cells as well as in muscle biopsies from DMD patients and two animal models of DMD,mdxmice and GRMD dogs. We determined that these abnormalities are due to the lack of dystrophinper se and could be correlated with disease progression and severity. We further identified an abnormal upregulation of the Rab5 GTPase protein, one key actor of early endosomal biogenesis and fusion, in the three DMD models which may underlie the endosomal defects. Finally, we demonstrated that Rab5 knock-down in human DMD muscle cells as well as dystrophin restoration in GRMD dogs, normalize Rab5 expression levels and rescue endosomal abnormalities. This study unveils a defect in a pathway essential for muscle homeostasis and for efficacy of adeno associated virus vectors and antisense oligonucleotides-mediated therapies.
PinkyCaMP a mScarlet-based calcium sensor with exceptional brightness, photostability, and multiplexing capabilities
Authors: Fink Ryan , Imai Shosei , Gockel Nala , Lauer German , Renken Kim , Wietek Jonas , Lamothe-Molina Paul J. , Fuhrmann Falko , Mittag Manuel , Ziebarth Tim , Canziani Annika , Kubitschke Martin , Kistmacher Vivien , Kretschmer Anny , Sebastian Eva , Schmitz Dietmar , Terai Takuya , Gründemann Jan , Hassan Sami , Patriarchi Tommaso , Reiner Andreas , Fuhrmann Martin , Campbell Robert E. , Masseck Olivia Andrea 
Published: December 2024

AbstractGenetically encoded calcium (Ca2+) indicators (GECIs) are widely used for imaging neuronal activity, yet current limitations of existing red fluorescent GECIs have constrained their applicability. The inherently dim fluorescence and low signal-to-noise ratio of red-shifted GECIs have posed significant challenges. More critically, several red-fluorescent GECIs exhibit photoswitching when exposed to blue light, thereby limiting their applicability in all-optical experimental approaches. Here, we present the development of PinkyCaMP, the first mScarlet-based Ca2+sensor that outperforms current red fluorescent sensors in brightness, photostability, signal-to-noise ratio, and compatibility with optogenetics and neurotransmitter imaging. PinkyCaMP is well-tolerated by neurons, showing no toxicity or aggregation, bothin vitroandin vivo. All imaging approaches, including single-photon excitation methods such as fiber photometry, widefield imaging, miniscope imaging, as well as two-photon imaging in awake mice, are fully compatible with PinkyCaMP.
Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation
Authors: Billingsley Kimberley J. , Meredith Melissa , Daida Kensuke , Alvarez Jerez Pilar , Negi Shloka , Malik Laksh , Genner Rylee M. , Moller Abraham , Zheng Xinchang , Gibson Sophia B. , Mastoras Mira , Baker Breeana , Kouam Cedric , Paquette Kimberly , Jarreau Paige , Makarious Mary B. , Moore Anni , Hong Samantha , Vitale Dan , Shah Syed , Monlong Jean , Pantazis Caroline B. , Asri Mobin , Shafin Kishwar , Carnevali Paolo , Marenco Stefano , Auluck Pavan , Mandal Ajeet , Miga Karen H. , Rhie Arang , Reed Xylena , Ding Jinhui , Cookson Mark R. , Nalls Mike , Singleton Andrew , Miller Danny E. , Chaisson Mark , Timp Winston , Gibbs J. Raphael , Phillippy Adam M. , Kolmogorov Mikhail , Jain Miten , Sedlazeck Fritz J. , Paten Benedict , Blauwendraat Cornelis 
Published: December 2024

AbstractStructural variants (SVs) drive gene expression in the human brain and are causative of many neurological conditions. However, most existing genetic studies have been based on short-read sequencing methods, which capture fewer than half of the SVs present in any one individual. Long-read sequencing (LRS) enhances our ability to detect disease-associated and functionally relevant structural variants (SVs); however, its application in large-scale genomic studies has been limited by challenges in sample preparation and high costs. Here, we leverage a new scalable wet-lab protocol and computational pipeline for whole-genome Oxford Nanopore Technologies sequencing and apply it to neurologically normal control samples from the North American Brain Expression Consortium (NABEC) (European ancestry) and Human Brain Collection Core (HBCC) (African or African admixed ancestry) cohorts. Through this work, we present a publicly available long-read resource from 351 human brain samples (median N50: 27 Kbp and at an average depth of ∼40x genome coverage). We discover approximately 234,905 SVs and produce locally phased assemblies that cover 95% of all protein-coding genes in GRCh38. Utilizing matched expression datasets for these samples, we apply quantitative trait locus (QTL) analyses and identify SVs that impact gene expression in post-mortem frontal cortex brain tissue. Further, we determine haplotype- specific methylation signatures at millions of CpGs and, with this data, identify cis-acting SVs. In summary, these results highlight that large-scale LRS can identify complex regulatory mechanisms in the brain that were inaccessible using previous approaches. We believe this new resource provides a critical step toward understanding the biological effects of genetic variation in the human brain.
An opioid efficacy switch for reversible optical control of peripheral analgesia
Authors: Posa Luca , Romano Giovanna , Ji Xiang , Khan Saif , Paz Bruno Matos , Han Gye Won , Nazarova Antonina L. , Zaidi Saheem A. , Ranjbar Mohsen , Pleil Kristen , Katritch Vsevolod , Gati Cornelius , Trauner Dirk , Levitz Joshua 
Published: December 2024

AbstractThe mu-opioid receptor (MOR) is a major target for the treatment of pain. However, opioids are prone to side effects which limit their effectiveness as analgesics and can lead to opioid use disorders or, even, lethal overdose. The systemic administration of opioid agonists makes it both very difficult to decipher their underlying circuit mechanisms of action and to limit drug action to specific receptor subpopulations to isolate therapeutic effects from adverse side effects. Here we design, synthesize, and characterize a reversibly photoswitchable morphinan agonist termed “azo-morphine-3” (AM-3) which interconverts from low to high efficacy in response to different wavelengths of light to enable optical control of MOR signaling. Cryo-EM structures of the low efficacy “trans” and high efficacy “cis” states ofAM-3bound to the MOR reveal distinct binding modes of the photoswitchable azobenzene moiety, each inducing unique structural dynamics, providing insight into the molecular basis of agonist efficacy. In mice,AM-3drives reversible and repeatable optical control of anti-nociception with a reduced side effect profile owing to its restriction to the periphery and its ability to be locally activated at the site of pain.
BACH2-driven tissue resident memory programs promote HIV-1 persistence
Authors: Wei Yulong , Ma Haocong Katherine , Wong Michelle E. , Papasavvas Emmanouil , Konnikova Liza , Tebas Pablo , Morgenstern Ricardo , Montaner Luis J. , Ho Ya-Chi 
Published: December 2024

SUMMARYTranscription repressor BACH2 redirects short-lived terminally differentiated effector into long-lived memory cells. We postulate that BACH2-mediated long-lived memory programs promote HIV-1 persistence in gut CD4+ T cells. We coupled single-cell DOGMA-seq and TREK-seq to capture chromatin accessibility, transcriptome, surface proteins, T cell receptor, HIV-1 DNA and HIV-1 RNA in 100,744 gut T cells from ten aviremic HIV-1+ individuals and five HIV-1– donors. BACH2 was the leading transcription factor that shaped gut tissue resident memory T cells (TRMs) into long-lived memory with restrained interferon-induced effector function. We found that HIV-1-infected cells were enriched in TRMs (80.8%). HIV-1-infected cells had increased BACH2 transcription factor accessibility, TRM (CD49a, CD69, CD103) and survival (IL7R) gene expression, and Th17 polarization (RORC,CCR6). In vitro gut CD4+ T cell infection revealed preferential infection and persistence of HIV-1 in CCR6+ TRMs. Overall, we found BACH2-driven TRM program promotes HIV-1 persistence and BACH2 as a new therapeutic target.
Nanocoding: Lipid Nanoparticle Barcoding for Multiplexed Single-Cell RNA Sequencing
Authors: Feng Yujun , Chen Donglai , Applegate Catherine C. , Gonzalez Medina Natalia Y. , Kuo Chia-wei , Arogundade Opeyemi H. , Wright Chris L. , Xu Fangxiu , Drnevich Jenny , Smith Andrew M. 
Published: December 2024

AbstractSample multiplexing is an emerging method in single-cell RNA sequencing (scRNA-seq) that addresses high costs and batch effects. Current multiplexing schemes use DNA labels to barcode cell samples but are limited in their stability and extent of labeling across heterogeneous cell populations. Here, we introduce Nanocoding using lipid nanoparticles (LNPs) for high barcode labeling density in multiplexed scRNA-seq. LNPs reduce dependencies on cell surface labeling mechanisms due to multiple controllable means of cell uptake, amplifying barcode loading 10-100-fold and allowing both protection and efficient release by dissolution. In cultured cell lines and heterogeneous cells from tissue digests, Nanocoding occurs in 40 minutes with stability after sample mixing and requires only commercially available reagents without novel chemical modifications. In spleen digests, 6-plex barcoded samples show minimal unlabeled cells, with all barcodes giving bimodal count distributions. Challenging samples containing lipid-rich debris and heterogeneous cells from adipose tissue of obese rodents show more than 95% labeling with all known subtypes identified. Using Nanocoding, we investigate gene expression changes related to aging in adipose tissue, profiling cells that could not be readily identified with current direct conjugate methods using lipid or antibody conjugates. This ease of generating and tuning these constructs may afford efficient and robust whole-sample multiplexing with minimal sample crosstalk.
AlphaFold prediction and analysis of Adhesion-family G protein coupled receptor (aGPCR) structures
Authors: Zhou Xiao Wen (Kelly) , Chen Eddie , Ramachandran Rithwik 
Published: December 2024

AbstractAdhesion GPCRs (aGPCRs), a family of 33 receptors, regulate crucial physiological processes through a unique self-activation mechanism. We employed AlphaFold, a state-of-the-art AI system, to predict 3D structures of aGPCRs in active and inactive conformations. Full-length models were obtained from the AlphaFold Protein Structure Database, while tethered-ligand (TL) exposed structures were predicted using AlphaFold. Comparison with available experimentally solved structures were made to validate accuracy of Alphafold aGPCR model. For receptors without experimentally solved structures, we compare structures of inactive (TL masked) and active (TL exposed) aGPCRs. In the active structures, the tethered-ligand was docked in the transmembrane bundle for several receptors but surprisingly not all receptors. This AI driven analysis of aGPCR structures provides a framework for exploring alternative receptor activation mechanisms. These models also offer valuable insights into receptor conformational changes and TL interactions, paving the way for the development of novel pharmacological tools and accelerating drug discovery efforts targeting this important receptor family.