bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants
Authors: Desautels Thomas A. , Arrildt Kathryn T. , Zemla Adam T. , Lau Edmond Y. , Zhu Fangqiang , Ricci Dante , Cronin Stephanie , Zost Seth J. , Binshtein Elad , Scheaffer Suzanne M. , Dadonaite Bernadeta , Petersen Brenden K. , Engdahl Taylor B. , Chen Elaine , Handal Laura S. , Hall Lynn , Goforth John W. , Vashchenko Denis , Nguyen Sam , Weilhammer Dina R. , Lo Jacky Kai-Yin , Rubinfeld Bonnee , Saada Edwin A. , Weisenberger Tracy , Lee Tek-Hyung , Whitener Bradley , Case James B. , Ladd Alexander , Silva Mary S. , Haluska Rebecca M. , Grzesiak Emilia A. , Earnhart Christopher G. , Hopkins Svetlana , Bates Thomas W. , Thackray Larissa B. , Segelke Brent W. , Lillo Antonietta Maria , Sundaram Shivshankar , Bloom Jesse , Diamond Michael S. , Crowe James E. , Carnahan Robert H. , Faissol Daniel M. 
Published: October 2022

ABSTRACTThe COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1–3, but also revealed how quickly viral escape can curtail effective options4, 5. With the emergence of the SARS-CoV-2 Omicron variant in late 2021, many clinically used antibody drug products lost potency, including EvusheldTMand its constituent, cilgavimab4, 6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies with a known clinical profile to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign COV2-2130 to rescue in vivo efficacy against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the contemporaneously dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and many variants of concern that subsequently emerged, and provides protectionin vivoagainst the strains tested, WA1/2020, BA.1.1, and BA.5. Deep mutational scanning of tens of thousands pseudovirus variants reveals 2130-1-0114-112 improves broad potency without incurring additional escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Because our approach is computationally driven, not requiring experimental iterations or pre-existing binding data, it could enable rapid response strategies to address escape variants or pre-emptively mitigate escape vulnerabilities.
The NQR complex regulates the immunomodulatory function ofBacteroides thetaiotaomicron
Authors: Engelhart Morgan J. , Glowacki Robert W. P. , Till Jessica M. , Harding Clifford V. , Martens Eric C. , Ahern Philip P. 
Published: October 2022

AbstractThe gut microbiome and intestinal immune system are engaged in a dynamic interplay that provides myriad benefits to host health. However, the microbiome can also elicit damaging inflammatory responses, and thus establishing harmonious immune-microbiome interactions is essential to maintain homeostasis. Gut microbes actively coordinate the induction of anti-inflammatory responses that establish these mutualistic interactions. Despite this, the microbial pathways that govern this dialogue remain poorly understood. We investigated the mechanisms through which the gut symbiontBacteroides thetaiotaomicronexerts its immunomodulatory functions. Our data reveal thatB. thetaiotaomicronstimulates production of the cytokine IL-10 via secreted factors that are packaged into outer membrane vesicles, in a TLR2 and MyD88 dependent manner. Using a transposon mutagenesis based screen, we identified a key role for theB. thetaiotaomicronencoded NQR complex, which regenerates NAD+ during respiration, in this process. Finally, we found that disruption of NQR reduces the capacity ofB. thetaiotaomicronto induce IL-10 by impairing biogenesis of outer membrane vesicles. These data identify a microbial pathway with a previously unappreciated role in gut microbe mediated immunomodulation that may be targeted to manipulate the capacity of the microbiome to shape host immunity.Key pointsTheB. thetaNQR complex coordinates OMV-driven TLR2-dependent IL-10 expression.
Transcriptomic responses to within- and transgenerational environmental warming in a cold-adapted salmonid
Authors: Penney Chantelle M. , Burness Gary , Zapata Gerardo , Lefebvre François , Wilson Chris C. 
Published: October 2022

AbstractCold-adapted species are particularly threatened by climate change as rates of environmental warming outpace the ability of many populations adapt. Recent evidence suggests that transgenerational thermal plasticity may play a role in the response of cold-adapted organisms to long-term changes in temperature. Using RNA sequencing, we explored differential gene expression of lake trout (Salvelinus namaycush), a cold-adapted species, to examine the molecular processes that respond to elevated temperatures under conditions of within-generation (offspring) and transgenerational (parental) warm acclimation. We hypothesized that genes associated with metabolism, growth and thermal stress/tolerance would be differentially expressed in juvenile lake trout offspring depending on their own acclimation temperature and that of their parents. While parental warm acclimation did have a transgenerational effect on gene expression in their offspring, within-generation (offspring) warm acclimation had a larger effect on the number of differentially expressed genes. Differentially expressed genes enriched pathways for thermal stress, signaling processes, immune function, and transcription regulation and depended on the acclimation temperature of the offspring in isolation or in combination with parental warm acclimation. We provide evidence of the transgenerational response to warming at the transcriptional level in lake trout, which should be useful for future studies of transcriptomics and plasticity in this and other cold-adapted species.
Successful Liver transduction by Re-administration of Different Adeno-Associated Virus Vector Serotypes in Mice
Authors: Baatartsogt Nemekhbayar , Kashiwakura Yuji , Hiramoto Takafumi , Hayakawa Morisada , Kamoshita Nobuhiko , Ohmori Tsukasa 
Published: October 2022

AbstractIntravenous administration of adeno-associated virus (AAV) vector is a promising gene therapy approach for monogenic diseases. However, re-administration of the same AAV serotype is impossible due to the induction of anti-AAV neutralizing antibodies (NAbs). Here we examined the feasibility of re-administration of AAV vectors to change the serotypes. We administered AAV3B, AAV5, or AAV8 vectors targeting the liver of C57BL/6 mice intravenously, and then assessed the emergence of NAbs and the transduction efficacy with a second administration. For all serotypes, we confirmed that re-administration with the same serotype was not possible. Although the highest neutralizing activity of NAb was induced by AAV5; however, the NAbs elicited by AAV5 did not react with any other serotypes, resulting in success in re-administration with the other serotypes. The re-administration of AAV5 was also successful in all mice treated with AAV3B and AAV8. The effective secondary administration of AAV3B and AAV8 was observed in most mice treated with AAV8 and AAV3B, respectively. However, few mice developed NAbs cross-reactive with the other serotypes, especially the serotypes with close sequence homology. In summary, AAV vector administration induced NAbs relatively specific to the serotype administrated. Secondary administration of AAVs targeting liver transduction could be successfully achieved by switching AAV serotypes in mice.
The autism spectrum disorder risk geneNEXMIFalters hippocampal CA1 cellular and network dynamics
Authors: Mount Rebecca A. , Athif Mohamed , O’Connor Margaret , Saligrama Amith , Tseng Hua-an , Sridhar Sudiksha , Zhou Chengqian , Man Heng-Ye , Han Xue 
Published: October 2022

AbstractPerturbations in autism spectrum disorder (ASD) risk genes disrupt neural circuit dynamics and ultimately lead to behavioral abnormalities. To understand how ASD-implicated genes influence network computation during behavior, we performedin vivocalcium imaging from hundreds of individual hippocampal CA1 neurons simultaneously in freely locomoting mice with total knockout ofNEXMIF. NEXMIFis an ASD risk gene most highly expressed in the hippocampus, andNEXMIFknockout in mice creates a range of behavioral deficits, including impaired hippocampal-dependent memory. We found thatNEXMIFknockout does not alter the overall excitability of individual neurons but exaggerates movement-mediated neuronal responses. At the network level,NEXMIFknockout creates over-synchronization of the CA1 circuit, quantified by pairwise correlation and network closeness centrality. These neuronal effects observed uponNEXMIFknockout highlight the network consequences of perturbations in ASD-implicated genes, which have broad implications for cognitive performance and other ASD-related behavioral disruptions.
Genetic polymorphisms lead to major, locus-specific, variation in piRNA production in mouse
Authors: Casas Eduard , Sierra Pío , Moreta-Moraleda Cristina , Cebria Judith , Panzeri Ilaria , Pospisilik J. Andrew , Jimenez-Chillaron Josep C. , Forcales Sonia V. , Vavouri Tanya 
Published: October 2022

AbstractPIWI-interacting RNAs (piRNAs) are small noncoding RNAs that silence transposons in the animal germline. PiRNAs are produced from long single-stranded non-coding transcripts, from protein-coding transcripts, as well as from transposons. While some sites that produce piRNAs are in deeply conserved syntenic regions, in general, piRNAs and piRNA-producing loci turnover faster than other functional parts of the genome. To learn about the sequence changes that contribute to the fast evolution of piRNAs, we set out to analyse piRNA expression between genetically different mice. Here we report the sequencing and analysis of small RNAs from the mouse male germline of four classical inbred strains, one inbred wild-derived strain and one outbred strain. We find that genetic differences between individuals underlie variation in piRNA expression. We report significant differences in piRNA production at loci with endogenous retrovirus insertions. Strain-specific piRNA-producing loci include protein-coding genes. Our findings provide evidence that transposable elements contribute to inter-individual differences in expression, and potentially to the fast evolution of piRNA-producing loci in mammals.
Light Activated BioID (LAB): an optically activated proximity labeling system to study protein-protein interactions
Authors: Shafraz Omer , Orduno Davis Carolyn Marie , Sivasankar Sanjeevi 
Published: October 2022

AbstractProximity labeling with genetically encoded enzymes is widely used to study protein-protein interactions in cells. However, the resolution and accuracy of proximity labeling methods are limited by a lack of control over the enzymatic labeling process. Here, we present a high spatial and temporal resolution technology that can be activated on demand using light, for high accuracy proximity labeling. Our system, called Light Activated BioID (LAB), is generated by fusing the two halves of the split-TurboID proximity labeling enzyme to the photodimeric proteins CRY2 and CIB1. Using live cell imaging, immunofluorescence, western blotting, and mass spectrometry, we show that upon exposure to blue light, CRY2 and CIB1 dimerize, reconstitute the split-TurboID enzyme, and biotinylate proximate proteins. Turning off the light halts the biotinylation reaction. We validate LAB in different cell types and demonstrate that it can identify known binding partners of proteins while reducing background labeling and false positives.
Real-time Detection of Acute Lymphoblastic Leukemia Cells Using Deep Learning
Authors: Chen Emma , Shalaginov Mikhail Y. , Liao Rory , Zeng Tingying Helen 
Published: October 2022

AbstractAcute lymphoblastic leukemia (ALL) is one of the most common types of cancer among children. It can rapidly become fatal within weeks, hence early diagnosis is critical. Problematically, the ALL diagnosis mainly involves manual blood smear analysis relying on the expertise of medical professionals, which is error-prone and time-consuming. Thus, it is important to develop artificial intelligence tools that will identify leukemic cells from a microscopic image faster, more accurately, and cheaper. Here, we investigate the capabilities of a traditional convolutional neural network (CNN) and You Only Look Once (YOLO) models for real-time detection of leukemic cells. The YOLOv5s model shows 97.2% accuracy for the task of object detection of ALL cells, with the inference speed allowing 80 image frames to be processed per second. These new findings can provide valuable insight in applying real-time object detection algorithms for improving the efficiency of blood cancer diagnosis.
Occurrence and classification of T-shaped interactions between nucleobases in RNA structures
Authors: Ali Zakir , Kukhta Teagan , Jhunjhunwala Ayush , Trant John F. , Sharma Purshotam 
Published: October 2022

ABSTRACTUnderstanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid–protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3262 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date dataset of high-resolution crystal structures deposited in the Protein Databank. These analyses add to the understanding of the physicochemical forces that are responsible for structure and dynamics of RNA.
Fibre-specific mitochondrial protein abundance is linked to resting and post-training mitochondrial content in human muscle
Authors: Reisman E. , Botella J. , Huang C. , Schittenhelm R. B. , Stroud D. A. , Granata C. , Chandrasiri S. , Ramm G. , Oorschot V. , Caruana N. J. , Bishop D. J. 
Published: October 2022

AbstractAnalyses of mitochondrial adaptations in human skeletal muscle have mostly used whole-muscle samples, where results may be confounded by the presence of a mixture of type I and II muscle fibres. Using our adapted mass spectrometry-based proteomics workflow, we provide new insights into fibre-specific mitochondrial differences in human skeletal muscle before and after training. Our findings challenge previous conclusions regarding the extent of fibre-type-specific remodelling of the mitochondrial proteome and highlight that most baseline differences in mitochondrial protein abundances between fibre types reported by us, and others, might be due to differences in total mitochondrial content or a consequence of adaptations to habitual physical activity (or inactivity). Most training-induced changes in different mitochondrial functional groups, in both fibre types, were stoichiometrically linked to changes in markers of mitochondrial content.
A genome wide association study identifies a new variant associated with word reading fluency in Chinese children
Authors: Wang Zhengjun , Zhao Shunan , Zhang Liming , Yang Qing , Cheng Chen , Ding Ning , Zhu Zijian , Shu Hua , Liu Chunyu , Zhao Jingjing 
Published: October 2022

AbstractReading disability exhibited defects in different cognitive domains, including word reading fluency, word reading accuracy, phonological awareness, rapid automatized naming, and morphological awareness. To identify the genetic basis of Chinese reading disability, we conducted a genome wide association study (GWAS) of the cognitive traits related to Chinese reading disability in 2284 unrelated Chinese children. Among the traits analyzed in the present GWAS, we detected one genome wide significant association (p<5×10-8) on reading fluency for one SNP on 4p16.2, within EVC genes (rs6446395,p=7.55×10−10). Rs6446395 also showed significant association with word reading accuracy (p=3.39×10−4), phonological awareness (p=7.12×10−3), and rapid automatized naming (p=4.71×10−3), implying multiple effects of this variant. Gene-based analyses identified a gene to be associated with reading fluency at the genome-wide level. The eQTL data showed that rs6446395 affected EVC expression in the cerebellum. Our study discovered a new candidate susceptibility variant for reading ability and provide new insights into the genetics of development dyslexia in Chinese Children.
Machine learning approaches based on fibroblast morphometry confidently identify stress but have limited ability to predict ALS
Authors: Konrad Csaba , Woo Evan , Bredvik Kirsten , Liu Bangyan , Fuchs Thomas J. , Manfredi Giovanni 
Published: October 2022

AbstractObjectiveAmyotrophic lateral sclerosis (ALS) is a devastating neuromuscular disease with limited therapeutic options. Diagnostic and surrogate endpoint biomarkers are needed for early disease detection, clinical trial design, and personalized medicine.MethodsWe tested the predictive power of a large set of primary skin fibroblast (n=443) from sporadic and familial ALS patients and healthy controls. We measured morphometric features of endoplasmic reticulum, mitochondria, and lysosomes by imaging with vital dyes. We also analysed immunofluorescence images of ALS-linked proteins, including TDP-43 and stress granule components. We studied fibroblasts under basal conditions and under metabolic (galactose medium), oxidative (arsenite), and heat stress conditions. We then employed machine learning (ML) techniques on the dataset to develop biomarkers.ResultsStress perturbations caused robust changes in the measured features, such as organellar morphology, stress granule formation, and TDP-43 mislocalization. ML approaches were able to predict the perturbation with near perfect performance (ROC-AUC > 0.99). However, when trying to predict disease state or disease groups (e.g., sporadic, or familial ALS), the performance of the ML algorithm was more modest (ROC-AUC Control vs ALS = 0.63). We also detected modest but significant scores when predicting clinical features, such as age of onset (ROC-AUC late vs early = 0.60).ConclusionsOur findings indicate that the ML morphometry we developed can accurately predict if human fibroblasts are under stress, but the differences between ALS and controls, while statistically significant, are small and pose a challenge for the development of biomarkers for clinical use by these approaches.
SUsPECT: A pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation
Authors: Salz Renee , Saraiva-Agostinho Nuno , Vorsteveld Emil , van der Made Caspar I. , Kersten Simone , Stemerdink Merel , Allen Jamie , Volders Pieter-Jan , Hunt Sarah E. , Hoischen Alexander , ’t Hoen Peter A.C. 
Published: October 2022

AbstractOur incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular in transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are predicted to be benign using the reference transcript annotation. In further support of SUsPECT’s utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.
RANKL inhibition with denosumab improves fibrous dysplasia by decreasing lesional cell proliferation and increasing osteogenesis
Authors: de Castro Luis F , Whitlock Jarred M , Michel Zachary , Pan Kristen , Taylor Jocelyn , Szymczuk Vivian , Paravastu Sriram S , Saboury Babak , Papadakis Georgios Z , Chernomordik Leonid V , Li Xiaobai , Milligan Kelly , Boyce Brendan , Paul Scott , Martin Daniel , Collins Michael T , Boyce Alison M 
Published: October 2022

ABSTRACTBACKGROUNDFibrous dysplasia (FD) is a rare, disabling disease with no established treatments. Growing evidence supports inhibiting the pro-osteoclastic factor receptor activator of nuclear Kappa-B ligand (RANKL) as a potential treatment strategy. We conducted a phase 2 trial evaluating the anti-RANKL drug denosumab in adults with FD, with an emphasis on investigating post-discontinuation bone turnover rebound, and cellular mechanisms underlying anti-RANKL effects on FD osteoprogenitors.METHODSEight subjects received denosumab for 6-months and were observed for 8-months post-discontinuation. Efficacy and safety were evaluated using bone turnover markers,18F-NaF PET/CT, and lesion biopsies. RANKL neutralization effects were assessed by histology, RNASeq, and an FD mouse model. Interplay between osteoclasts and FD osteoprogenitors was assessed in anex vivolesion model.RESULTSDenosumab markedly reduced bone turnover and radiographic lesional activity in all subjects. Denosumab was well-tolerated during the treatment period, however post-discontinuation turnover reached or exceeded pre-treatment in six subjects, associated with severe hypercalcemia in one. Histology and whole-exome RNA sequencing showed reduced FD cell proliferation and increased osteogenic maturation, with increased lesional bone formation. Theex vivomodel supported the dependence of FD cell proliferation on osteoclast activation.CONCLUSIONSOsteoclast inhibition by anti-RANKL decreased FD cell proliferation and lesional activity, enabling osteogenic maturation and bone formation. These findings provide new understanding of FD pathogenesis as driven by crosstalk between osteoclasts and pre-osteoblast/osteoblasts, and support denosumab as a mechanistically-driven treatment strategy. Marked bone turnover rebound with post-discontinuation hypercalcemia occurs in a subset of patients, particularly younger individuals with high disease burden.TRIAL REGISTRATIONClinicalTrials.govNCT03571191FUNDINGThis work was supported by the Intramural Research Program of the NIDCR, NICHD, and Clinical Center, National Institutes of Health. Clinical trialNCT03571191was conducted as an investigator-sponsored study supported by Amgen, Inc. This research was supported in part by the NIDCR Genomics and Computational Biology Core: ZIC DC000086 and Veterinary Resources Core: ZIC DE000740-05. Work in MTC lab and LVC labs were supported by the of Research on Women’s Health (ORWH) through the Bench to Bedside Program award #884515.