bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using genetic information to define idiopathic pulmonary fibrosis in UK Biobank
Authors: Leavy Olivia C , Allen Richard J , Kraven Luke M , Morgan Ann , Tobin Martin D , Quint Jennifer K , Jenkins R Gisli , Wain Louise V 
Published: April 2022

AbstractIntroductionIdiopathic pulmonary fibrosis (IPF) is a rare lung disease characterised by progressive scarring in the alveoli. IPF can be defined in population studies using electronic healthcare records (EHR) but recent genetic studies of IPF using EHR have shown an attenuation of effect size for known genetic risk factors when compared to clinically-derived datasets, suggesting misclassification of cases.MethodsWe used EHR (ICD-10, Read (2 & 3)) and questionnaire data to define IPF cases in UK Biobank, and evaluated these definitions using association results for the largest genetic risk variant for IPF (rs35705950-T, MUC5B). We further evaluated the impact of exclusions based on co-occurring codes for non-IPF pulmonary fibrosis and restricting codes according to changes in diagnostic practice.ResultsOdds ratio (OR) estimates for rs35705950-T associations with IPF defined using EHR and questionnaire data in UK Biobank were significant and ranged from 2.06 to 3.09 which was lower than those reported using clinically-derived IPF datasets (95% confidence intervals: 3.74, 6.66). Code-based exclusions of cases gave slightly closer effect estimates to those previously reported, but sample sizes were substantially reduced.DiscussionWe show that none of the UK Biobank IPF codes replicate the effect size for the association of rs35705950-T on IPF risk when using clinically-derived IPF datasets. Further code-based exclusions also did not lead to effect estimates closer to those expected. Whilst the apparent increased sample sizes available for IPF from general population cohorts may be of benefit, future studies should take these limitations of the case definition into account.Key MessagesWhat is already known on this topicUK Biobank is a very large prospective cohort that can be utilised to increase sample sizes for studies of rare diseases such as idiopathic pulmonary fibrosis (IPF). However, effect size estimates for genetic risk factors for IPF in UK Biobank and other general population cohorts, when defining cases using electronic healthcare records (EHR), are smaller than those estimated from clinically-derived IPF datasets.What this study addsUsing Hospital Episode Statistics (HES) data, primary care data, death registry data and self-report data in UK Biobank, we used the association rs35705950-T, the largest genetic risk factor for IPF, to evaluate code-based definitions of IPF. We show that none of the available IPF coding replicates the effect size for rs35705950-T on IPF risk that is observed in clinically-derived IPF datasets.How this study might affect research, practice or policyResearch using large general population cohorts and datasets for observational studies of IPF should take these limitations of EHR definitions of IPF into consideration.
Single-Molecule Analysis of DNA-binding proteins from Nuclear Extracts (SMADNE)
Authors: Schaich Matthew A. , Schnable Brittani L. , Kumar Namrata , Roginskaya Vera , Jakielski Rachel C. , Urban Roman , Zhong Zhou , Kad Neil M. , Van Houten Bennett 
Published: April 2022

AbstractSingle-molecule characterization of protein-DNA dynamics provides unprecedented mechanistic details about numerous nuclear processes. Here, we describe a new method that rapidly generates single-molecule information for fluorescently tagged proteins isolated from nuclear extracts of human cells. This approach determines binding lifetimes (koff), events per second (∼kon), positional dependence (specificity), and characterizes 1D diffusion along DNA. We demonstrated the wide applicability of this approach on three forms of DNA damage using seven native DNA repair proteins and two structural variants, including: poly(ADP-ribose) polymerase (PARP1), heterodimeric ultraviolet-damaged DNA-binding protein (UV-DDB), xeroderma pigmentosum complementation group C protein (XPC), and 8-oxoguanine glycosylase 1 (OGG1). By measuring multiple fluorescent colors simultaneously, we additionally characterized the assembly and disassembly kinetics of multi-protein complexes on DNA. Thus, Single-Molecule Analysis of DNA-binding proteins from Nuclear Extracts (SMADNE) provides new insights about damage recognition and represents a universal technique that can be used to rapidly characterize numerous protein-DNA interactions.
Highly multiplexed targeted plasma proteomics quantifies several hundred blood proteins in serum from colorectal carcinoma patients
Authors: Lesur Antoine , Bernardin François , Koncina Eric , Letellier Elisabeth , Kruppa Gary , Pierre-Olivier Schmit , Dittmar Gunnar 
Published: April 2022

AbstractThe rapid analysis of human serum and plasma can provide deep insights into changes of the blood proteome in response to different patient treatments or diseases. Targeted proteomics techniques, like SRM and PRM, can be utilized to monitor proteins at high sensitivitym but so far were limited to smaller protein panels, which can be monitored in one experiment. The recently, on a Bruker tims-TOF pro mass spectrometer, developed parallel reaction monitoring-parallel accumulation − serial fragmentation (prm-PASEF) method expands the standard PRM method by using ion-mobility. The use of ion mobility as a fourth separation dimension increases the proteome coverage while reducing the length of the necessary chromatogeaphic separation. By combining an isotope-labeled reference standard, which covers 579 plasma proteins, we were able to quantify 565 proteins in plasma using prm-PASEF, with the least abundant protein being quantified at 7 amol. We continued the analysis by combining the isotype-labeled reference standard with dia-PASEF, which allowed the quantification of 549 proteins. Both methods were used to analyze 20 patient plasma samples from a colorectal cancer (CRC) cohort. The analysis identified 16 differentially regulated proteins between the CRC patient and control individual plasma samples. 15 of the 16 proteins showed a high correlation to the mRNA expression in CRC tumor samples, showing the technique’ s potential for the rapid identification of potential biomarkers in larger cohorts, abolishing the need for preselection of potential biomarker proteins.Graphical abstract
Clinically-relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance
Authors: Mañas Adriana , Aaltonen Kristina , Andersson Natalie , Hansson Karin , Adamska Aleksandra , Seger Alexandra , Yasui Hiroaki , van den Bos Hilda , Radke Katarzyna , Esfandyari Javanshir , Bhave Madhura Satish , Karlsson Jenny , Spierings Diana , Foijer Floris , Gisselsson David , Bexell Daniel 
Published: April 2022

ABSTRACTChemotherapy resistance and relapses are common in high-risk neuroblastoma (NB), an aggressive pediatric solid tumor of the sympathetic nervous system. Here, we developed a clinically-relevant in vivo treatment protocol mimicking the first line five-chemotherapy treatment regimen of high-risk NB and applied this protocol to mice with MYCN-amplified NB patient-derived xenografts (PDXs). Genomic and transcriptomic analyses were used to reveal the genetic and non-genetic mechanisms involved in NB chemoresistance. We observed convergent and parallel evolution of key NB genetic aberrations over time. Intrinsic resistance to chemotherapy was associated with high genetic diversity and an embryonic phenotype. Relapsed NB PDX tumors with acquired resistance showed an immature mesenchymal-like phenotype resembling multipotent Schwann cell precursors that are found in the adrenal gland. NBs with a successful treatment response presented a lineage-committed adrenergic phenotype similar to normal neuroblasts, reduced cell cycle gene expression, and negative regulation of the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) cascade. NB organoids established from relapsed PDX tumors retained drug resistance, tumorigenicity, and transcriptional cell states ex vivo. This work sheds light on mechanisms involved in NB chemotherapy response in vivo and ex vivo using a clinically-relevant protocol, and emphasizes the importance of transcriptional cell states in treatment response. Detailed characterization of resistance mechanisms is essential for the development of novel treatment strategies in non-responsive or relapsed high-risk NB.One Sentence SummaryCOJEC chemotherapy treatment of neuroblastoma PDX models uncovers patterns of transcriptional plasticity and chemoresistance.
A Locally Activatable Sensor for Robust Quantification of Organellar Glutathione
Authors: Hübner Sarah , Quargnali Gianluca , Thallmair Sebastian , Rivera-Fuentes Pablo 
Published: April 2022

AbstractGlutathione (GSH) is the main determinant of intracellular redox potential and participates in multiple cellular signaling pathways. Achieving a detailed understanding of intracellular GSH trafficking and regulation depends on the development of tools to map GSH compartmentalization and intra-organelle fluctuations. Herein, we present a new GSH sensing platform, TRaQ-G, for live-cell imaging. This small-molecule/protein hybrid sensor possesses a unique reactivity turn-on mechanism that ensures that the small molecule is only sensitive to GSH in the desired location. Furthermore, TRaQ-G can be fused to a fluorescent protein of choice to give a ratiometric response. Using TRaQ-G-mGold, we demonstrated that the nuclear and cytosolic GSH pools are independently regulated during cell proliferation. We also used this sensor, in combination with roGFP, to quantify redox potential and GSH concentration simultaneously in the endoplasmic reticulum. Finally, by exchanging the fluorescent protein, we created a near-infrared, targetable and quantitative GSH sensor.
Characterization of cell-fate decision landscapes by estimating transcription factor dynamics
Authors: Jiménez Sara , Schreiber Valérie , Mercier Reuben , Gradwohl Gérard , Molina Nacho 
Published: April 2022

AbstractModulation of gene expression during differentiation by transcription factors promotes cell diversity. Despite their role in cell fate decisions, no experimental assays estimate their regulatory activity in a high-throughput manner and at the single-cell resolution. We present FateCompass for identifying lineage-specific transcription factors across differentiation. It uses single-cell transcriptomics data to infer differentiation trajectories and transcription factor activities. We combined a probabilistic framework with RNA velocities or a differentiation potential to estimate transition probabilities and perform stochastic simulations. Also, we learned transcription factor activities using a linear model of gene regulation. Considering dynamic changes and correlations, we identified lineage-specific regulators. We applied FateCompass to an islet cell formation dataset from the mouse embryo, and we found known and novel potential cell-type drivers. Also, when applied to a differentiation protocol dataset towards beta-like cells, we pinpointed undescribed regulators of an off-target population, which were experimentally validated. Thus, as a framework for identifying lineage-specific transcription factors, FateCompass could have implications on hypothesis generation to increase the understanding of the gene regulatory networks driving cell fate choices.HighlightsWe developed FateCompass, a flexible pipeline to estimate transcription factor activities during cell-fate decision using single-cell RNA seq data.FateCompass outlines gene expression stochastic trajectories by infusing the direction of differentiation using RNA velocity or a differentiation potential when RNA velocity fails.Transcription factor dynamics allow the identification of time-specific regulatory interactions.FateCompass predictions revealed known and novel cell-subtype-specific regulators of mouse pancreatic islet cell development.Differential motif analysis predicts lineage-specific regulators of stem cell-derived human β- cells and sheds light on the cellular heterogeneity of β-cell differentiation protocols.Experimental validation supports the proposed GRN controlling SC-EC differentiation predicted by FateCompass.
Evolutionary barriers to horizontal gene transfer in macrophage associated Salmonella
Authors: Bhatia Rama P. , Kirit Hande A. , Lewis Cecil M. , Sankaranarayanan Krithivasan , Bollback Jonathan P. 
Published: April 2022

AbstractHorizontal gene transfer (HGT) is a powerful evolutionary force facilitating bacterial adaptation and emergence of novel phenotypes. Several factors, including environmental ones, are predicted to restrict HGT, but we lack systematic and experimental data supporting these predictions. Here, we address this gap by measuring the relative fitness of genes horizontally transferred from E. coli to S. enterica in infection relevant environments. We estimated the distribution of fitness effects in each environment and identified dosage-dependent effects across different environments are a significant barrier to HGT. The majority of genes were found to be deleterious. We also found longer genes had stronger negative fitness consequences than shorter ones, showing that gene length can significantly hinder HGT. Furthermore, fitness effects of transferred genes were found to be environmentally dependent. In summary, a substantial fraction of transferred genes had a significant fitness cost on the recipient, with both gene characteristics and the environment acting as evolutionary barriers to HGT.
Potent Human Broadly SARS-CoV-2 Neutralizing IgA and IgG Antibodies Effective Against Omicron BA.1 and BA.2
Authors: Planchais Cyril , Fernández Ignacio , Bruel Timothée , Dias de Melo Guilherme , Prot Matthieu , Beretta Maxime , Guardado-Calvo Pablo , Dufloo Jérémy , Molinos-Albert Luis M. , Backovic Marija , Chiaravalli Jeanne , Giraud Emilie , Vesin Benjamin , Conquet Laurine , Grzelak Ludivine , Planas Delphine , Staropoli Isabelle , Guivel-Benhassine Florence , Boullé Mikaël , Cervantes-Gonzalez Minerva ,   French COVID Cohort Study Group,   CORSER Study Group, Ungeheuer Marie-Noëlle , Charneau Pierre , van der Werf Sylvie , Agou Fabrice , Dimitrov Jordan D. , Simon-Lorière Etienne , Bourhy Hervé , Montagutelli Xavier , Rey Félix A. , Schwartz Olivier , Mouquet Hugo 
Published: April 2022

AbstractMemory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, which can also be prevented by antibody-based interventions. Here, wide SARS-CoV-2 immunoprofiling in COVID-19 convalescents combining serological, cellular and monoclonal antibody explorations, revealed humoral immunity coordination. Detailed characterization of a hundred SARS-CoV-2 spike memory B-cell monoclonal antibodies uncovered diversity in their repertoire and antiviral functions. The latter were influenced by the targeted spike region with strong Fc-dependent effectors to the S2 subunit and potent neutralizers to the receptor binding domain. Amongst those, Cv2.1169 and Cv2.3194 antibodies cross-neutralized SARS-CoV-2 variants of concern including Omicron BA.1 and BA.2. Cv2.1169, isolated from a mucosa-derived IgA memory B cell, demonstrated potency boost as IgA dimers and therapeutic efficacy as IgG antibodies in animal models. Structural data provided mechanistic clues to Cv2.1169 potency and breadth. Thus, potent broadly neutralizing IgA antibodies elicited in mucosal tissues can stem SARS-CoV-2 infection, and Cv2.1169 and Cv2.3194 are prime candidates for COVID-19 prevention and treatment.
Inter-Individual Variability in Dorsal Stream Dynamics During Word Production
Authors: Liégeois-Chauvel C. , Dubarry A.-S. , Wang I. , Chauvel P. , Gonzalez-Martinez J.A. , Alario F.-X. 
Published: April 2022

AbstractThe current standard model of language production involves a sensorimotor dorsal stream connecting areas in the temporo-parietal junction with those in the inferior frontal gyrus and lateral premotor cortex. These regions have been linked to various aspects of word production such as phonological processing or articulatory programming, primarily through neuropsychological and functional imaging group studies. Most if not all the theoretical descriptions of this model imply that the same network should be identifiable across individual speakers. We tested this hypothesis by quantifying the variability of activation observed across individuals within each dorsal stream anatomical region. This estimate was based on electrical activity recorded directly from the cerebral cortex with millisecond accuracy in awake epileptic patients clinically implanted with intracerebral depth electrodes for pre-surgical diagnosis. Each region’s activity was quantified using two different metrics—intra-cerebral evoked related potentials and high gamma activity—at the level of the group, the individual, and the recording contact. Using picture naming task, the two metrics show simultaneous activation of parietal and frontal regions in line with models that posit interactive processing during word retrieval. They also reveal different levels of variability across brain regions and patients except in auditory and motor regions. The independence and non-uniformity of cortical activity according to the two metrics push the current model towards sub-second and sub-region explorations focused on individualized language speech production. Several hypotheses are considered for this within-region heterogeneity.
Olfactory Sensitivity Aligns with Caste Revealing Multipotential Minors and Specialized Soldier Majors in Camponotus floridanus Ants
Authors: Ferguson S.T. , Bakis I. , Edwards N.D. , Zwiebel L.J. 
Published: April 2022

AbstractCamponotus floridanus ant colonies are comprised of a single reproductive queen and thousands of sterile female offspring that consist of two morphologically distinct castes: smaller minors and larger majors. Minors perform most of the tasks within the colony, including brood care and food collection, whereas majors have fewer clear roles and have been hypothesized to act as a specialized solider caste associated with colony defense. The allocation of workers to these different tasks depends on the detection and processing of local information including pheromones and other chemical blends such as cuticular hydrocarbons. We examined the electrophysiological responses to general odorants, cuticular extracts, and a trail pheromone in adult minor and major C. floridanus workers, revealing that the repertoire of social behaviors is positively correlated with olfactory sensitivity. Minors in particular display primarily excitatory responses to olfactory stimuli, whereas major workers respond primarily with inhibitory signals. The notable exception to this paradigm is that both minors and majors display robust, dose-dependent excitatory responses to conspecific, non-nestmate cuticular extracts. Moreover, while both minors and majors actively aggress non-nestmate foes, majors display significantly enhanced capabilities to rapidly subdue and kill opponents. Overall, our data suggest that C. floridanus majors do indeed represent a physiologically and behaviorally specialized soldier caste and support a model in which caste-specific olfactory sensitivity plays an important role in task allocation and the regulation of social behavior in ant colonies.Significance StatementThe detection and odor coding of chemical cues are essential components of the collective behavior observed in eusocial ants. To better understand the interdependent relationship between olfactory sensitivity and the allocation of worker castes to the various tasks critical for the success of the colony, a series of behavioral assessments and an electrophysiological survey of the antennae comprising general odorants, cuticular extracts, and a trail pheromone were undertaken. These studies reveal the behavioral repertoire of minors and majors aligned with profound shifts in olfactory sensitivity and odor coding. Our data support the hypothesis that minors are multipotential workers with broad excitatory sensitivity, and majors are dedicated soldiers with a highly specialized olfactory system for the detection of non-nestmate foes.
Death-seq identifies regulators of cell death and senolytic therapies
Authors: Colville Alex , Liu Jie-Yu , Thomas Samantha , Ishak Heather D. , Zhou Ronghao , Klein Julian D.D. , Morgens David W. , Goshayeshi Armon , Salvi Jayesh S. , Yao David , Spees Kaitlyn , Bassik Michael C. , Rando Thomas A. 
Published: April 2022

SUMMARYSelectively ablating senescent cells (“senolysis”) is an evolving therapeutic approach for age-related diseases. Current senolytics are limited to local administration by potency and side effects. While genetic screens could identify senolytics, current screens are underpowered for identifying genes that regulate cell death due to limitations in screen methodology. Here, we establish Death-seq, a positive selection CRISPR screen optimized to identify enhancers and mechanisms of cell death. Our screens identified synergistic enhancers of cell death induced by the known senolytic ABT-263, a BH3 mimetic. SMAC mimetics, enhancers in our screens, synergize with ABT-199, another BH3 mimetic that is not senolytic alone, clearing senescent cells in models of age-related disease while sparing human platelets, avoiding the thrombocytopenia associated with ABT-263. Death-seq enables the systematic screening of cell death pathways to uncover molecular mechanisms of regulated cell death subroutines and identify drug targets for diverse pathological states such as senescence, cancer, and neurodegeneration.
miRNA upregulate protein and glycan expression via direct activation in proliferating cells
Authors: Jame-Chenarboo Faezeh , Ng Hoi Hei , Macdonald Dawn , Mahal Lara K. 
Published: April 2022

AbstractThe dominant paradigm is that miRNA binding to mRNA represses protein expression. Activation by miRNA has been observed in select circumstances (quiescent cells, mitochondria), but is not thought a feature of miRNA action in actively dividing cells. Herein, we comprehensively map the miRNA regulation of α-2,6-sialyltransferases ST6GAL1 and ST6GAL2 using a high-throughput assay (miRFluR). We find the majority of miRNA targeting ST6GAL1, the main enzyme controlling α-2,6-sialylation, upregulate protein expression. In contrast, those that regulate ST6GAL2 are predominantly downregulatory. We provide evidence that miRNA-mediated upregulation occurs in proliferating cells and is a direct effect. Further, we show that AGO2 and FXR1 are required. Our data expands current understanding of miRNA, providing strong evidence of both upregulatory and downregulatory roles for these non-coding RNA.One-Sentence SummarymiRNA directly activate expression of α-2,6-sialyltransferases and sialylation, expanding miRNA actions in dividing cells.