bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting Cellular Senescence with Senotherapeutics: Development of New Approaches for Skin Care
Authors: Thompson Elizabeth L. , Pitcher Louise E. , Niedernhofer Laura J. , Robbins Paul D. 
Published: September 2022

Summary:Aging of the skin is evidenced by increased wrinkles, age spots, dryness, and thinning with decreased elasticity. Extrinsic and intrinsic factors including UV, pollution, and inflammation lead to an increase in senescent cells (SnCs) in skin with age that contribute to these observed pathological changes. Cellular senescence is induced by multiple types of damage and stress and is characterized by the irreversible exit from the cell cycle with upregulation of cell cycle-dependent kinase inhibitors p16INK4aand p21CIP1. Most SnCs also developed an inflammatory senescence-associated secretory phenotype (SASP) that drives further pathology through paracrine effects on neighboring cells and endocrine effects on cells at a distance. Recently, compounds able to kill senescent cells specifically, termed senolytics, or suppress the SASP, termed senomorphics, have been developed that have the potential to improve skin aging as well as systemic aging in general. Here, we provide a summary of the evidence for a key role in cellular senescence in driving skin aging. In addition, the evidence for the potential application of senotherapeutics for skin treatments is presented. Overall, topical, and possibly oral senotherapeutic treatments have tremendous potential to eventually become a standard of care for skin aging and related skin disorders.
Diversity, Equity, and Inclusion in the Melanoma Research Community
Authors: Portuallo Marie E. , Lu David Y. , Alicea Gretchen M. , Bolling Joel , Lee Rebecca , McQuade Jennifer , Warner Allison Betof , Davies Michael , Weeraratna Ashani , Villanueva Jessie , Rebecca Vito W. 
Published: September 2022

AbstractLast October, within the 2021 SMR congress, we held the inaugural Diversity in Science Session. The goal of the session was to discuss diversity, equity, and inclusion in the melanoma research community and strategies to promote the advancement of underrepresented melanoma researchers. An international survey was conducted to assess the diversity, equity, and inclusion (DEI) climate among researchers and clinicians within the Society for Melanoma Research (SMR). The findings suggest there are feelings and experiences of inequity, bias, and harassment within the melanoma community that correlate with one’s gender, ethnic/racial group, and/or geographic location. Notably, significant reports of inequity in opportunity, discrimination, and sexual harassment demonstrate there is much work remaining to ensure all scientists in our community experience an academic workplace culture built on mutual respect, fair access, inclusion, and equitable opportunity.
Nature of epigenetic aging from a single-cell perspective
Authors: Tarkhov Andrei E. , Lindstrom-Vautrin Thomas , Zhang Sirui , Ying Kejun , Moqri Mahdi , Zhang Bohan , Tyshkovskiy Alexander , Levy Orr , Gladyshev Vadim N. 
Published: September 2022

AbstractAge-related changes in DNA methylation (DNAm) form the basis for the development of most robust predictors of age, epigenetic clocks, but a clear mechanistic basis for exactly what part of the aging process they quantify is lacking. Here, to clarify the nature of epigenetic aging, we juxtapose the aging dynamics of tissue and single-cell DNAm (scDNAm) with scDNAm changes during early development, and corroborate our analyses with a single-cell RNAseq analysis within the same multi-omics dataset. We show that epigenetic aging involves co-regulated changes, but it is dominated by the stochastic component, and this agrees with transcriptional coordination patterns. We further support the finding of stochastic epigenetic aging by direct tissue and single-cell DNAm analyses and modeling of aging DNAm trajectories with a stochastic process akin to radiocarbon decay. Finally, we describe a single-cell algorithm for the identification of co-regulated and stochastic CpG clusters showing consistent transcriptomic coordination patterns, providing new opportunities for targeting aging and evaluating longevity interventions.
Can genomics and meteorology predict outbreaks of legionellosis in urban settings?
Authors: Timms Verlaine J , Sim Eby , Pey Keenan , Sintchenko Vitali 
Published: September 2022

AbstractLegionella pneumophila is ubiquitous and sporadically infects humans causing Legionnaires disease (LD). Globally, reported cases of LD has risen four-fold from 2000-2014. In 2016, Sydney, Australia was the epicentre of an outbreak caused by L. pneumophila serogroup 1 (Lpsg1). Whole genome sequencing was instrumental in identifying the causal clone which was found in multiple locations across the city. This study examined the epidemiology of Lpsg1 in an urban environment, assessed typing schemes to classify resident clones and investigated the association between local climate variables and LD outbreaks. Of 223 local Lpsg1 isolates, we identified dominant clones with one clone isolated from patients in high frequency during outbreak investigations. The cgMLST scheme was the most reliable in identifying this Lpsg1 clone. While an increase in humidity and rainfall was found to coincide with a rise in LD cases, the incidence of the major L. pneumophila outbreak clone did not link to weather phenomena. These findings demonstrated the role of high resolution typing and weather context assessment in determining source attribution for LD outbreaks in urban settings, particularly when clinical isolates remain scarce.ImportanceWe investigated the genomic and meteorological influences of infections caused by Legionella pneumophila in Sydney, Australia. Our study contributes to a knowledge gap of factors that drive outbreaks of legionellosis compared to sporadic infections in urban settings. In such cases, clinical isolates can be rare and other data is then relied upon to inform decision making around control measures. We found that cgMLST typing offered a robust and scalable approach for high-resolution investigation of Lpsg1 outbreaks. The genomic landscape of Lpsg1 in Sydney was dominated by a single clone which was responsible for multiple clusters of community cases over four decades. While legionellosis incidence peaked in Autumn, this was not linked to the dominant outbreak clone. The synthesis of meteorological data with Lpsg1 genomics can be a part of the risk assessment for legionellosis in urban settings and is relevant for other densely populated areas around the world.
Phenome-wide genetic correlation analysis and genetically-informed causal inference of amyotrophic lateral sclerosis
Authors: D’Antona Salvatore , Pathak Gita A , Koller Dora , Porro Danilo , Cava Claudia , Polimanti Renato 
Published: September 2022

AbstractLeveraging genome-wide association statistics generated from a large study of amyotrophic lateral sclerosis (ALS; 29,612 cases and 122,656 controls) and UK Biobank (UKB; 4,024 phenotypes, up to 361,194 participants), we conducted a phenome-wide genetic correlation analysis of ALS and identified 46 genetically-correlated traits, such as fluid intelligence score (rg = −0.21, p = 1.74×10−6), “spending time in pub or social club” (rg = 0.24, p = 2.77×10−6), non-work related walking (rg = −0.25, p = 1.95×10−6), college education (rg = −0.15, p = 7.08×10−5), “ever diagnosed with panic attacks (rg = 0.39, p = 4.24×10−5), and “self-reported other gastritis including duodenitis” (rg = 0.28, p = 1.4×10−3). To assess the putative directionality of these genetic correlations, we conducted a latent causal variable analysis, identifying significant genetic causality proportions (gĉp) linking ALS to seven traits. While the genetic component of “self-reported other gastritis including duodenitis” showed a positive causal effect on ALS (gĉp = 0.50, p = 1.26×10−29), the genetic liability to ALS is potentially causal for multiple traits, also including a positive effect on “ever being diagnosed with panic attacks” (gĉp = 0.79, p = 5.011×10−15) and inverse effects on “other leisure/social group activities” (gĉp = 0.66, p = 1×10−4) and prospective memory result (gĉp = 0.35, p = 0.005). Our subsequent Mendelian randomization analysis indicated that some of these associations may be due to bi-directional effects. In conclusion, this is the first phenome-wide investigation of ALS polygenic architecture, highlighting the complex pleiotropy linking this disorder with different health domains.
The fitness of an introgressing haplotype
Authors: Dagilis Andrius J. , Matute Daniel R. 
Published: September 2022

AbstractThe genomic era has made clear that introgression, or the movement of genetic material between species, is a common feature of evolution. Examples of both adaptive and deleterious introgression exist in a variety of systems. What is unclear is how the fitness of an introgressing haplotype changes as species diverge, or as the size of the introgressing haplotype changes. In a simple model, we show that early in the process of divergence, introgression of large haplotypes can be favored more than introgression of individual alleles. The key insight is that alleles from a shared genetic background are likely to have positive epistatic interactions, increasing the fitness of a larger introgressing block. The buildup of incompatibilities between diverging species in the form of deleterious epistasis eventually favors the introgression of small haplotypes as the number of diverged alleles increases, and eventually even single alleles with positive direct effects can be selected against. This model is consistent with observations of a positive relationship between recombination rate and introgression frequency across the genome, however it generates several novel predictions. First, the model suggests that the relationship between recombination rate and introgression may not exist, or may be negative, in recently diverged species pairs. Furthermore, the model suggests that introgression that replaces existing derived variation will always be more deleterious than introgression at sites carrying ancestral variants. These predictions are tested in an example of introgression in D. melanogaster, with some support for both.
Enhanced Complex Stability and Optimal JAK Geometry are Pivotal for a Potent Type III Interferon Response
Authors: Aung Theint , Horvath Curt M. , Mendoza Juan L. 
Published: September 2022

AbstractType I and III Interferons (IFN) constitute the host system’s first line of defense against viral infections. Although the two families use distinct extracellular receptor complexes, an identical pair of Janus kinases (JAK) activates a similar set of signal transducer and activator of transcription (STATs) through a conserved pathway. Consequently, type I and III IFNs are presumed to activate a largely overlapping set of IFN-stimulated genes (ISGs) and elicit similar biological responses. Therapeutically, type III IFNs are attractive alternatives to type I IFNs due to their innate tissue specificity and lower systemic toxicity. However, a major limitation of type III IFNs is the significantly lower potency of their physiological activities compared to type I IFNs. To evaluate the role of receptor geometry in IFN signaling, we engineered cell lines that express wild-type and mutant IFNλ receptors (IFNλR1) with rotated intracellular registers with respect to the associated JAK1. Evaluation of downstream signaling and biological activity of type III IFNs in cells with varied JAK-JAK geometries uncovered variant receptors that result in potentiation of type III IFN signaling and all downstream activities. With the combined use of a high-affinity ligand to stabilize the extracellular receptor complex, we found that the optimization of the intracellular JAK-JAK geometry enhances the type III IFN antiviral and anti-proliferative activities by 2- and 3-logs, respectively. In addition to providing a molecular basis for the observed differences in potency between type I and III IFNs, this work provides deeper insights into broader cytokine signaling mechanisms and novel blueprints for modulating cytokine functions to develop next generation antiviral and anticancer therapeutics.
Spatiotemporally resolved transcriptomics reveals subcellular RNA kinetic landscape
Authors: Ren Jingyi , Zhou Haowen , Zeng Hu , Wang Connie Kangni , Huang Jiahao , Qiu Xiaojie , Maher Kamal , Lin Zuwan , He Yichun , Tang Xin , Li Brian , Liu Jia , Wang Xiao 
Published: September 2022

SummarySpatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and cellular function1. However, the intricate subcellular dynamics of RNA synthesis, decay, export, and translocation remain obscured due to the limitations of existing transcriptomics methods2–8. Here, we report a spatiotemporally resolved RNA mapping method (TEMPOmap) to uncover subcellular RNA profiles across time and space at the single-cell level in heterogeneous cell populations. TEMPOmap integrates pulse-chase metabolic labeling of the transcriptome with highly multiplexed three-dimensional (3D) in situ sequencing to simultaneously profile the age and location of individual RNA molecules. Using TEMPOmap, we constructed the subcellular RNA kinetic landscape of 991 genes in human HeLa cells from upstream transcription to downstream subcellular translocation. Clustering analysis of critical RNA kinetic parameters across single cells revealed kinetic gene clusters whose expression patterns were shaped by multi-step kinetic sculpting. Importantly, these kinetic gene clusters are functionally segregated, suggesting that subcellular RNA kinetics are differentially regulated to serve molecular and cellular functions in cell-cycle dependent manner. Together, these single-cell spatiotemporally resolved transcriptomics measurements provide us the gateway to uncover new gene regulation principles and understand how kinetic strategies enable precise RNA expression in time and space.
Metabolic Stability of the Demyelination PET Tracer [18F]3F4AP and Identification of its Metabolites
Authors: Sun Yang , Ramos-Torres Karla , Brugarolas Pedro 
Published: September 2022

Abstract[18F]3-fluoro-4-aminopyridine ([18F]3F4AP) is a PET tracer for imaging demyelination based on the multiple sclerosis drug 4-aminopyridine (4AP, dalfampridine). This radiotracer was found to be stable in rodents and nonhuman primates imaged under isoflurane anesthesia. However, recent findings indicate that its stability is greatly decreased in awake humans and mice. Since both 4AP and isoflurane are metabolized primarily by cytochrome P450 enzymes, particularly CYP2E1, we postulated that this enzyme may be responsible for the metabolism of 3F4AP. Here, we investigated the metabolism of [18F]3F4AP by CYP2E1 and identified its metabolites. We also investigated whether deuteration, a common approach to increase the stability of drugs, could improve its stability. Our results demonstrate that CYP2E1 readily metabolizes 3F4AP and its deuterated analogues and that the primary metabolites are 5-hydroxy-3-fluoro-4-aminopyridine and 3-fluoro-4-aminopyridine N-oxide. Although deuteration did not decrease the rate of the CYP2E1 mediated oxidation, our findings explain the diminished in vivo stability of 3F4AP compared to 4AP and further our understanding of when deuteration may improve the metabolic stability of drugs and PET ligands.Significance StatementUnderstanding the metabolic stability of PET tracers is paramount to its application in humans as metabolism, which varies from person to person, can affect the target-to-background signal. This study identified the predominant enzyme that metabolizes the demyelination PET tracer [18F]3F4AP and its metabolites. These findings may allow assessment of whether the radiometabolites can get into the brain and potentially lead to tracers with enhanced stability. Furthermore, this study furthers our understanding of when deuteration can improve metabolic stability.
Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics
Authors: Vuckovic Ziva , Wang Jinan , Pham Vi , Mobbs Jesse I. , Belousoff Matthew J. , Bhattarai Apurba , Burger Wessel A.C. , Thompson Geoff , Yeasmin Mahmuda , Leach Katie , van der Westhuizen Emma T. , Khajehali Elham , Liang Yi-Lynn , Glukhova Alisa , Wootten Denise , Lindsley Craig W. , Tobin Andrew B. , Sexton Patrick M. , Danev Radostin , Valant Celine , Miao Yinglong , Christopoulos Arthur , Thal David M. 
Published: September 2022

AbstractAllosteric modulation of G protein-coupled receptors (GPCRs) is a major paradigm in drug discovery. Despite decades of research, a molecular level understanding of the general principals that govern the myriad pharmacological effects exerted by GPCR allosteric modulators remains limited. The M4muscarinic acetylcholine receptor (M4mAChR) is a well-validated and clinically relevant allosteric drug target for several major psychiatric and cognitive disorders. Here, we present high-resolution cryo-electron microscopy structures of the M4mAChR bound to a cognate Gi1protein and the high affinity agonist, iperoxo, in the absence and presence of two different positive allosteric modulators, LY2033298 or VU0467154. We have also determined the structure of the M4mAChR-Gi1complex bound to its endogenous agonist, acetylcholine (ACh). Structural comparisons, together with molecular dynamics, mutagenesis, and pharmacological validations, have provided in-depth insights into the role of structure and dynamics in orthosteric and allosteric ligand binding, global mechanisms of receptor activation, cooperativity, probe-dependence, and species variability; all key hallmarks underpinning contemporary GPCR drug discovery.
SARS-CoV-2 variants show temperature-dependent enhanced polymerase activity in the upper respiratory tract and high transmissibility
Authors: Kim Se-Mi , Kim Eun-Ha , Casel Mark Anthony B. , Kim Young-Il , Sun Rong , Kwack Mi-Jeong , Yoo Ji-Seung , Yu Min-Ah , Yu Kwang-Min , Jang Seung-Gyu , Rollon Rare , Choi Jeong Ho , Gil JuRyeon , Eun Kiyoung , Kim Hyunggee , Ensser Armin , Hwang Jungwon , Song Min-Suk , Kim Myung Hee , Jung Jae U , Choi Young Ki 
Published: September 2022

AbstractWith the convergent global emergence of SARS-CoV-2 variants of concern (VOC), a precise comparison study of viral fitness and transmission characteristics is necessary for the prediction of dominant VOCs and the development of suitable countermeasures. While airway temperature plays important roles in the fitness and transmissibility of respiratory tract viruses, it has not been well studied with SARS-CoV-2. Here we demonstrate that natural temperature differences between the upper (33°C) and lower (37°C) respiratory tract have profound effects on SARS-CoV-2 replication and transmission. Specifically, SARS-COV-2 variants containing the P323L or P323L/G671S mutation in the NSP12 RNA-dependent RNA polymerase (RdRp) exhibited enhanced RdRp enzymatic activity at 33°C compared to 37°C and high transmissibility in ferrets. MicroScale Thermophoresis demonstrated that the NSP12 P323L or P323L/G671S mutation stabilized the NSP12-NSP7-NSP8 complex interaction. Furthermore, reverse genetics-derived SARS-CoV-2 variants containing the NSP12 P323L or P323L/G671S mutation displayed enhanced replication at 33°C, and high transmission in ferrets. This suggests that the evolutionarily forced NSP12 P323L and P323L/G671S mutations of recent SARS-CoV-2 VOC strains are associated with increases of the RdRp complex stability and enzymatic activity, promoting the high transmissibility.
An automated microscopy workflow to study Shigella-neutrophil interactions and antibiotic efficacy in vivo
Authors: Lensen Arthur , Gomes Margarida C. , López-Jiménez Ana Teresa , Mostowy Serge 
Published: September 2022

ABSTRACTShigella are Gram-negative bacterial pathogens responsible for bacillary dysentery (also called shigellosis). The absence of a licensed vaccine and widespread emergence of antibiotic resistance has recently led the WHO to highlight Shigella as a priority pathogen requiring urgent attention. Several infection models have been useful to explore the Shigella infection process, yet we still lack information regarding events taking place in vivo. Here, using a Shigella-zebrafish infection model and high-content microscopy, we develop an automated microscopy workflow to non-invasively study fluorescently labelled bacteria and neutrophils in vivo. We apply our workflow to antibiotic-treated zebrafish and demonstrate that neutrophil recruitment is independent of bacterial burden. Strikingly, we discover that nalidixic acid (a bactericidal antibiotic) can restrict Shigella dissemination from the hindbrain ventricle. We envision that our automated microscopy workflow, applied here to study Shigella-neutrophil interactions and antibiotic efficacy in zebrafish, can be useful to innovate treatments for infection control in humans.SUMMARY STATEMENTWe develop an automated image analysis workflow to enable fast and reliant immune cell counting in Shigella-infected zebrafish larvae, and reveal how antibiotics impact Shigella-neutrophil interactions in vivo.
An analysis of laboratory variability and thresholds for human in vitro ADME/PK methods
Authors: Fagerholm Urban 
Published: September 2022

AbstractIntroductionVarious in vitro methods are used to measure absorption, distribution, metabolism and excretion/pharmacokinetics (ADME/PK) of candidate drugs and predict and decide whether properties are clinically adequate.MethodsObjectives were to evaluate variability within and between laboratories for commonly used human in vitro ADME/PK methods and to explore whether reliable thresholds may be defined. The literature was searched for in vitro data for intrinsic metabolic clearance (hepatocyte CLint), apparent intestinal permeability (Caco-2 Papp), efflux ratio (Caco-2 ER), solubility (S) and BCS-class, and corresponding clinical estimates. In vitro ADME/PK data for three example drugs (atenolol, diclofenac and gemfibrozil) were used to predict human in vivo ADME/PK and investigate whether these would pass a compound selection process.Results and ConclusionsInterlaboratory variability is considerable, especially for fu, S, ER and BCS-classification, and on average about twice as high as intralaboratory variability. Approximate mean interlaboratory variability for CLint, Papp, ER and fu (3- to 3.5-fold) appears to be about 2- to 3-fold higher than corresponding interlaboratory variability. Mean and maximum interlaboratory range for CLint, Papp, ER, fu and S are approximately 5- to 100-fold and 50- to 4500-fold, respectively, with second largest range for fu and largest range for S. For one drug, laboratories produced almost 1000-fold different CLint • fu-values. It appears difficult/impossible to set clear clinically useful thresholds, especially for CLint, ER and S. Poor in vitro-in vivo consistency for S and BCS-classification and large portions of compounds out of reach for Caco-2 and conventional hepatocyte assays are evident. Predictions for reference compounds are consistent with inadequate in vivo ADME/PK. Ways to improve predictions and compound selection are suggested.