bluuebunny/crossref_metadata_2025 huggingface dataset:
A web tool for the exploration of hospital prescription data in England
Authors: Sanderson Theo
Published: December 2023

Medicine prescription data is a valuable resource, with the power to reveal insights into healthcare trends, cost efficiencies, and geographic disparities. In England, primary care prescription data has been openly accessible for analysis for some time through a web tool, providing significant benefits. Since 2020, the National Health Service in England has also released data on secondary care prescriptions, i.e. prescribing within hospitals. This is an important dataset, but until now has been available only in a raw form that requires considerable technical skills to be used for even the analysis of basic trends. I have built a web application that enables anyone to easily analyse trends in this data, which is available at hospitalprescriptions.genomium.org.
Genetic implication of prenatal GABAergic and cholinergic neuron development in susceptibility to schizophrenia
Authors: Cameron Darren , Vinh Ngoc-Nga , Prapaiwongs Parinda , Perry Elizabeth A. , Walters James T. R. , Li Meng , O’Donovan Michael C. , Bray Nicholas J.
Published: December 2023

Background

The ganglionic eminences are fetal-specific structures that give rise to gamma- aminobutyric acid (GABA)- and acetylcholine- releasing neurons of the forebrain. Given evidence for GABAergic and cholinergic disturbances in schizophrenia, as well as an early neurodevelopmental component to the disorder, we tested the potential involvement of developing cells of the ganglionic eminences in mediating genetic risk for the condition.

Study Design

We combined data from a recent large-scale genome-wide association study of schizophrenia with single cell RNA sequencing data from the human ganglionic eminences to test enrichment of schizophrenia risk variation in genes with high expression specificity for particular developing cell populations within these structures. We additionally performed the single nuclei Assay for Transposase-Accessible Chromatin with Sequencing (snATAC-Seq) to map potential regulatory genomic regions operating in individual cell populations of the human ganglionic eminences, using these to additionally test for enrichment of schizophrenia common genetic variant liability and to functionally annotate non-coding variants associated with the disorder.

Study Results

Schizophrenia common variant liability was enriched in genes with high expression specificity for developing neuron populations that are predicted to form dopamine D1 and D2 receptor expressing GABAergic medium spiny neurons of the striatum, cortical somatostatin-positive GABAergic interneurons, calretinin-positive GABAergic neurons and cholinergic neurons. Consistent with these findings, schizophrenia genetic risk was also concentrated in predicted regulatory genomic sequence mapped in developing neuronal populations of the ganglionic eminences.

Conclusions

Our study provides evidence for a role of prenatal GABAergic and cholinergic neuron development in later susceptibility to schizophrenia.
Increased Donor Inhibitory KIR Are Associated with Reduced GVHD and Improved Survival Following HLA Matched Unrelated Donor HCT in Pediatric Acute Leukemia
Authors: Krieger Elizabeth , Qayyum Rehan , Toor Amir
Published: December 2023

Killer immunoglobulin-like receptor (KIR) and KIR-ligand (KIRL) interactions play an important role in natural killer cell-mediated effects after hematopoietic stem cell transplantation (HCT). Previous work has shown that accounting for known KIR-KIRL interactions may identify donors with optimal NK cell-mediated alloreactivity in the adult transplant setting.

Pediatric acute leukemia patients were retrospectively analyzed and KIR-KIRL combinations and maximal inhibitory KIR ligand (IM-KIR) scores determined. Clinical outcomes were examined using a series of graphs depicting clinical events and endpoints.

The graph methodology demonstrated that prognostic variables significant in the occurrence of specific clinical endpoints, remained significant for relevant downstream events. KIR-KIRL combinations were significantly predictive for reduced grade 3-4 aGVHD likelihood, in patients transplanted with increased inhibitory KIR gene content and IM-KIR=5 scores. Improvements were also observed in associated outcomes for both ALL and AML patients, including relapse-free survival, GRFS, and overall survival.

This study demonstrates that NK cell KIR HLA interactions may be relevant to the pediatric acute leukemia transplant setting. Reduction in aGVHD suggests KIR effects may extend beyond NK cells. Moving forward clinical trials utilizing donors with a higher iKIR should be considered for URD HCT in pediatric recipients with acute leukemia to optimize clinical outcomes.
Empirical phenotyping in coupled patient+care systems: Generating low-dimensional categories for hypothesis-driven investigation of mechanically-ventilated patients
Authors: Stroh J.N. , Sottile Peter D. , Wang Yanran , Smith Bradford J. , Bennett Tellen D. , Moss Marc , Albers David J.
Published: December 2023

Background

Analyzing patient data under current mechanical ventilation (MV) management processes is essential to develop hypotheses about improvements and to understand MV consequences over time. How-ever, progress is complicated by the complexity of lung-ventilator system (LVS) interactions, patient-care and patient-ventilator heterogeneity, and a lack of classification schemes for observable behavior.

Method

Ventilator waveform data arise from patient-ventilator interactions within the LVS while care processes manage both patient and ventilator settings. This study develops a computational pipeline that segments these joint waveform data and care settings timeseries to phenotype the data generating process. The modular method supports many methodological choices for representing waveform data and unsuper-vised clustering.

Results

Applied to 35 ARDS patients including 8 with COVID-19, typcially 8[6.8] (median[IQR]) phenotypes capture 97[3.1]% of data using naive similarity assumptions on waveform and MV settings data. Individual phenotypes organized around ventilator mode, PEEP, and tidal volume with additional segmentation reflecting waveform behaviors. Few (<10% of) phenotype changes tie to ventilator settings, indicating considerable dynamics in LVS behaviors. Evaluation of phenotype heterogeneity reveals LVS dynamics that cannot be discretized into sub-phenotypes without additional data or alternate assumptions. Suitably normalized individual phenotypes may be aggregated into coherent groupings suitable for analysis of cohort data.

Conclusions

The pipeline is generalizable although empirical output is data- and algorithm-dependent. Further, output phenotypes compactly discretize the data for longitudinal analysis and may be optimized to resolve features of interest for specific applications.
The counterpart congenital overgrowth syndromes Beckwith-Wiedemann Syndrome in human and large offspring syndrome in bovine involve alterations in DNA methylation, transcription, and chromatin configuration
Authors: Li Yahan , Xiao Ping , Boadu Frimpong , Goldkamp Anna K. , Nirgude Snehal , Cheng Jianlin , Hagen Darren E. , Kalish Jennifer M. , Rivera Rocío Melissa
Published: December 2023

Beckwith-Wiedemann Syndrome (BWS, OMIM #130650) is a congenital epigenetic disorder in humans which affects approximately 1 in 10,340 children. The incidence is likely an underestimation as the condition is usually recognized based on observable phenotypes at birth. BWS children have up to a 28% risk of developing tumors and currently, only 80% of patients can be corroborated molecularly (epimutations/variants). It is unknown how the subtypes of this condition are molecularly similar/dissimilar globally, therefore there is a need to deeply characterize the syndrome at the molecular level. Here we characterize the methylome, transcriptome and chromatin configuration of 18 BWS individuals together with the animal model of the condition, the bovine large offspring syndrome (LOS). Sex specific comparisons are performed for a subset of the BWS patients and LOS. Given that this epigenetic overgrowth syndrome has been characterized as a loss-of-imprinting condition, parental allele-specific comparisons were performed using the bovine animal model. In general, the differentially methylated regions (DMRs) detected in BWS and LOS showed significant enrichment for CTCF binding sites. Altered chromosome compartments in BWS and LOS were positively correlated with gene expression changes, and the promoters of differentially expressed genes showed significant enrichment for DMRs, differential topologically associating domains, and differential A/B compartments in some comparisons of BWS subtypes and LOS. We show shared regions of dysregulation between BWS and LOS, including several HOX gene clusters, and also demonstrate that altered DNA methylation differs between the clinically epigenetically identified BWS patients and those identified as having DNA variants (i.e.CDKN1Cmicrodeletion). Lastly, we highlight additional genes and genomic regions that have the potential to serve as targets for biomarker development to improve current molecular methodologies. In summary, our results suggest that genome-wide alternation of chromosome architecture, which is partially caused by DNA methylation changes, also contribute to the development of BWS and LOS.
Levodopa reduces consumption of multiple classes of addictive substances in rats
Authors: Farero Ryan D. , Holtz Nathan A. , Lee Suhjung J. , Kruse Lauren C. , Clark Jeremy J. , Phillips Paul E. M.
Published: December 2023

Dopamine transmission is implicated in aberrant behaviors associated with substance use disorders. Previous research revealed a causal link between excessive drug consumption and the loss of dopamine signaling to stimuli associated with psychostimulant use. The emerging change in dopamine signaling is specific to stimuli associated with the substance rather than the pharmacological properties of the drug itself. Because the change in dopamine signaling was specific to the associated stimuli and not the pharmacological properties of the substance, we examined if treatment with the dopamine precursor, L-DOPA, alters alcohol and opioid self-administration. Therefore, we trained rats to orally self-administer ethanol or the synthetic opioid fentanyl and found that treating animals with L-DOPA significantly reduced consumption of both alcohol and fentanyl. These data suggest dopamine signaling has a vital role in mediating the amount of drug animals will voluntarily take, across multiple classes of drugs. Importantly, these data are preclinical demonstrations of L-DOPA being utilized as a harm reducing treatment in substance use disorders.
‘Are you even listening?’ - EEG-based decoding of absolute auditory attention to natural speech
Authors: Roebben Arnout , Heintz Nicolas , Geirnaert Simon , Francart Tom , Bertrand Alexander
Published: December 2023

Objective

In this study, we use electroencephalography (EEG) recordings to determine whether a subject is actively listening to a presented speech stimulus. More precisely, we aim to discriminate between an active listening condition, and a distractor condition where subjects focus on an unrelated distractor task while being exposed to a speech stimulus. We refer to this task as absolute auditory attention decoding.

Approach

We re-use an existing EEG dataset where the subjects watch a silent movie as a distractor condition, and introduce a new dataset with two distractor conditions (silently reading a text and performing arithmetic exercises). We focus on two EEG features, namely neural envelope tracking (NET) and spectral entropy (SE). Additionally, we investigate whether the detection of such an active listening condition can be combined with a selective auditory attention decoding task, where the goal is to decide to which of multiple competing speakers the subject is attending. The latter is a key task in so-called neuro-steered hearing devices that aim to suppress unattended audio, while preserving the attended speaker.

Main results

Contrary to a previous hypothesis of higher SE being related with actively listening rather than passively listening (without any distractors), we find significantly lower SE in the active listening condition compared to the distractor conditions. Nevertheless, the NET is consistently significantly higher when actively listening. Similarly, we show that the accuracy of a selective auditory attention decoding task improves when evaluating the accuracy only on the highest NET segments. However, the reverse is observed when evaluating the accuracy only on the lowest SE segments.

Significance

We conclude that the NET is more reliable for decoding absolute auditory attention as it is consistently higher when actively listening, whereas the relation of the SE between actively and passively listening seems to depend on the nature of the distractor.
Scm6A: A fast and low-cost method for quantifying m6A modifications at the single-cell level
Authors: Li Yueqi , Li Jingyi , Li Wenxing , Liang Shuaiyi , Wei Wudi , Chu Jiemei , Lai Jingzhen , Lin Yao , Chen Hubin , Su Jinming , Hu Xiaopeng , Wang Gang , Meng Jun , Jiang Junjun , Ye Li , An Sanqi
Published: December 2023

It is widely accepted that m6A exhibits significant intercellular specificity, which poses challenges for its detection using existing m6A quantitative methods. In this study, we introduce Scm6A, a machine learning-based approach for single-cell m6A quantification. Scm6A leverages input features derived from the expression levels of m6Atransregulators andcissequence features, and found that Scm6A offers remarkable prediction efficiency and reliability. To further validate the robustness and precision of Scm6A, we applied a winscore-based m6A calculation method to conduct m6A-seq analysis on CD4+and CD8+T-cells isolated through magnetic-activated cell sorting (MACS). Subsequently, we employed Scm6A for analysis on the same samples. Notably, the m6A levels calculated by Scm6A exhibited a significant positive correlation with m6A quantified through m6A-seq in different cells isolated by MACS, providing compelling evidence for Scm6A’s reliability. We also used the scm6A-seq method to validate the reliability of our approach. Additionally, we performed single-cell level m6A analysis on lung cancer tissues as well as blood samples from COVID-19 patients, and demonstrated the landscape and regulatory mechanisms of m6A in different T-cell subtypes from these diseases. In summary, our work has yielded a novel, dependable, and accurate method for single-cell m6A detection. We are confident that Scm6A will have broad applications in the realm of m6A-related research.
Single-cell Total-RNA Profiling Unveils Regulatory Hubs of Transcription Factors
Authors: Niu Yichi , Luo Jiayi , Zong Chenghang
Published: December 2023

Recent development of RNA velocity uses master equations to establish the kinetics of the life cycle of RNAs from nascent RNA to mature RNA to degradation. To feed this kinetic analysis, simultaneous measurement of nascent RNA and mature RNA in single cells is greatly desired. However, the majority of single-cell RNA-seq chemistry only captures mature RNA species to measure gene expressions. Here, we develop a one-step total-RNA chemistry-based scRNA-seq method: snapTotal-seq. We benchmarked this method with multiple single-cell RNA-seq assays in their performance in kinetic analysis of cell cycle by RNA velocity. Next, with LASSO regression between transcription factors, we identified the critical regulatory hubs mediating the cell cycle dynamics. We also applied snapTotal-seq to profile the oncogene-induced senescence and identified the key regulatory hubs governing the entry of senescence. Furthermore, from the comparative analysis of nascent RNA and mature RNA, we identified a significant portion of genes whose expression changes occurred in mature RNA but not to the same degree in nascent RNA, indicating these gene expression changes are mainly controlled by post-transcriptional regulation. Overall, we demonstrate that snapTotal-seq can provide enriched information about gene regulation, especially during the transition between cell states.
NK cells contribute to resistance to anti-PD1 therapy in immune-excluded melanomas
Authors: Landeloos Ewout , Pozniak Joanna , Roda Niccoló , Visscher Amber De , Martinez Asier Antoranz , Herck Yannick Van , Bervoets Greet , Bosisio Francesca , Boecxstaens Veerle , Bassez Ayse , Lambrechts Diether , Matthys Patrick , Bechter Oliver , Marine Jean-Christophe
Published: December 2023

Immune checkpoint blockade (ICB) has become a standard of care in the treatment of metastatic melanoma (MM). Although ICB is particularly successful in some MM patients, more than half do not obtain a durable benefit. Biomarkers that predict response are urgently needed and overcoming intrinsic resistance is key to improving the success of ICB therapy. Using single cell RNA sequencing, we characterized the immune landscape of pre- and early on-treatment biopsies taken from a cohort of MM patients (n>20) exposed to ICB therapy. Our analysis identified >20 immune cell types and confirmed previously described associations between the abundance of various CD8 T cell populations and ICB outcome. Unexpectedly, we found that lack of response was associated with an increased occurrence of a granulysin-expressing (GNLY+) natural killer (NK) cell population. This observation was replicated in other MM cohorts and in a breast cancer cohort in which paired biopsies were also collected pre and early-on ICB therapy. Spatial proteomics revealed that whereas NK cells colocalized with CD8 T cells within the tumour bed in responding lesions, these cells accumulated at the tumour margin in non-responding lesions. Strikingly, depletion of NK cells in an NRAS-driven melanoma mouse model, which exhibits an immune-excluded phenotype and is refractory to ICB, promoted massive immune cell infiltration and tumour clearance upon anti-PD1 exposure. These data highlight a differential immune cell topography between early on-treatment responding and nonresponding MM lesions, which could be exploited to develop a robust stratification biomarker, and unravel an unexpected contribution of NK cells in primary resistance to ICB.
VCD-induced menopause mouse model reveals reprogramming of hepatic metabolism
Authors: Kumari Roshan , Ponte Michael E. , Franczak Edziu , Prom John C. , O’Neil Maura F. , Sardiu Mihaela E. , Lutkewitte Andrew J. , Shankar Kartik , Morris E. Matthew , Thyfault John P.
Published: December 2023

Menopause adversely impacts systemic energy metabolism and increases the risk of metabolic disease(s) including hepatic steatosis, but the mechanisms are largely unknown. Dosing female mice with vinyl cyclohexene dioxide (VCD) selectively causes follicular atresia in ovaries, leading to a murine menopause-like phenotype. In this study, we treated female C57BL6/J mice with VCD (160mg/kg i.p. for 20 consecutive days followed by verification of the lack of estrous cycling) to investigate changes in body composition, energy expenditure (EE), hepatic mitochondrial function, and hepatic steatosis across different dietary conditions. VCD treatment induced ovarian follicular loss and increased follicle-stimulating hormone (FSH) levels in female mice, mimicking a menopause-like phenotype. VCD treatment did not affect body composition, or EE in mice on a low-fat diet or in response to a short-term (1-week) high-fat, high sucrose diet (HFHS). However, the transition to a HFHS lowered cage activity in VCD mice. A chronic HFHS diet (16 weeks) significantly increased weight gain, fat mass, and hepatic steatosis in VCD-treated mice compared to HFHS-fed controls. In the liver, VCD mice showed suppressed hepatic mitochondrial respiration on LFD, while chronic HFHS diet resulted in compensatory increases in hepatic mitochondrial respiration. Also, liver RNA sequencing revealed that VCD promoted global upregulation of hepatic lipid/cholesterol synthesis pathways. Our findings suggest that the VCD- induced menopause model compromises hepatic mitochondrial function and lipid/cholesterol homeostasis that sets the stage for HFHS diet-induced steatosis while also increasing susceptibility to obesity.
Whole group tracking reveals that relatedness drives consistent subgrouping patterns in white-nosed coatis
Authors: Grout Emily M. , Ortega Josué , Minasandra Pranav , Quin Matthew J. , Crofoot Margaret C. , Strandburg-Peshkin Ariana , Hirsch Ben T.
Published: December 2023

The formation of subgroups can allow group-living animals flexibility to balance the costs and benefits of sociality over time. Subgrouping dynamics emerge from individual decisions about whether and with whom to maintain cohesion, with these decisions potentially influenced by ecological, physiological, and social factors. We GPS-tracked the movements of nearly all members of three wild white-nosed coati (Nasua narica) social groups that differed in their demographic profiles to better understand how these highly social, frugivorous carnivores weight the relative importance of these different factors in their grouping decisions. Quantifying group movements and subgrouping patterns, we found that two of the three groups we tracked exhibited fission-fusion behaviours, with groups splitting into subgroups that persisted over varying timespans from minutes to days. In contrast, the third group remained together across the entire observation period. When groups split, they did not do so randomly; instead, individuals tended to form subgroups with the same individuals consistently over time. Assessing the drivers of subgrouping patterns revealed that subgroup membership was associated with genetic relatedness, but not physiological similarity as quantified by age and sex homophily. Our results demonstrate great variation in subgrouping patterns within a single species, while also highlighting a consistent role of relatedness in driving social preferences when subgroups form.
TurboID mapping reveals exportome of secreted intrinsically disordered proteins in the transforming parasiteTheileria annulata
Authors: Brühlmann Francis , Perry Carmen , Griessen Charlotte , Gunasekera Kapila , Reymond Jean-Louis , Naguleswaran Arunasalam , Rottenberg Sven , Woods Kerry , Olias Philipp
Published: December 2023

Theileria annulatais a tick-transmitted apicomplexan parasite that gained the unique ability among parasitic eukaryotes to transform its host cell, inducing a fatal cancer-like disease in cattle. Understanding the mechanistic interplay driving this transformation between the host cell and malignantTheileriaspecies requires the identification of responsible parasite effector proteins. In this study, we used TurboID-based proximity labelling, which unbiasedly identified secreted effector proteins within host cell compartments. By fusing TurboID to nuclear export or localization signals, we biotinylated proteins in the vicinity of the ligase enzyme in the nucleus or cytoplasm of infected macrophages, followed by mass spectrometry analysis. Our approach revealed with high confidence nine nuclear and four cytosolic candidate effector proteins within the host cell compartments, eight of which had no orthologues in non-transformingT. orientalis. Strikingly, all eight of these proteins are predicted to be highly intrinsically disordered proteins (IDPs). We discovered a novel tandem arrayed protein family, Nuclear Intrinsically Disordered Proteins (NIDP) 1 - 4, featuring diverse functions predicted by conserved protein domains. Particularly, NIDP2 exhibited a biphasic host cell-cycle dependent localization, interacting with the EB1/CD2AP/CLASP1 parasite membrane complex during mitosis and the tumor suppressor Stromal Antigen 2 (STAG2), a cohesion complex subunit, in the host nucleus. In addition to STAG2, numerous NIDP2-associated host nuclear proteins implicated in various cancers were identified, shedding light on the potential role of theT. annulataexported protein family NIDP in host cell transformation and cancer-related pathways.

IMPORTANCE

TurboID proximity labelling was used to unveil the secreted proteins ofTheileria annulata, an apicomplexan parasite responsible for a fatal, proliferative disorder in cattle, representing a significant socio-economic burden particularly in north Africa, central Asia, and India. Our investigation has provided important insights into the unique host-parasite interaction, revealing effector proteins characterized by high intrinsically disordered protein (IDP) structures. Remarkably, these proteins are conspicuously absent in non-transformingTheileriaspecies, strongly suggesting their central role in the transformative processes within host cells. In addition, our study identified a novel tandem arrayed protein family, with Nuclear Intrinsically Disordered Protein (NIDP) 2 emerging as a central player interacting with established tumor genes. Significantly, this work represents the first unbiased screening for exported effector proteins inTheileriaand contributes essential insights into the molecular intricacies behind the malignant transformation of immune cells.
Abundant microorganisms in soil are mainly controlled by stochastic processes, while bacteria and fungi differ in rare taxa
Authors: Qian Guo , Gong Lu
Published: December 2023

The assembly mode of microbial communities helps to explain the ecological processes of soil subsurface groups, and abundant and rare microorganisms have their own unique assembly patterns. In this paper, the effect of changing vegetation types on the assembly of bacteria and fungi with different abundances in soil was investigated by iCAMP in the Tianshan Mountains. The results showed that: (i) there were differences in the distribution of rare and abundant microbial communities among different vegetation types: the main trends were forests>shrubs > grasslands, and the α diversity and variability of rare microorganisms were greater than those of abundant taxa; (ii) abundant taxa were mainly affected by stochastic processes (mainly diffusion limitation), whereas among rare microbes, the main controlling process for bacteria was heterogeneous selection and for fungi was diffusion limitation; (ⅲ)soil carbon, nitrogen and temperature were important determinants driving bacterial community structure. Our results deepen the understanding of the various ecological processes involved in microbial community assembly, reveal the effects of environmental factors on abundant and rare microorganisms, and provide evidence for understanding the mechanisms of soil microbial community construction among different vegetation covers in arid zones.

Importance

The study compares the response of different vegetation types to soil microbial community processes in the arid zone and deepens the understanding of the mechanisms of soil microbial community composition at different abundances.
Acidic Sphingomyelinase Interactions with Lysosomal Membranes and Cation Amphiphilic Drugs: a Molecular Dynamics Investigation
Authors: Scrima Simone , Lambrughi Matteo , Maeda Kenji , Jäättelä Marja , Papaleo Elena
Published: December 2023

Lysosomes are pivotal in cellular functions and disease, influencing cancer progression and therapy resistance with Acid Sphingomyelinase (ASM) governing their membrane integrity. Moreover, cation amphiphilic drugs (CADs) are known as ASM inhibitors and have anti-cancer activity, but the structural mechanisms of their interactions with the lysosomal membrane and ASM are poorly explored.

Our study, leveraging all-atom explicit solvent molecular dynamics simulations, delves into the interaction of glycosylated ASM with the lysosomal membrane and the effects of one of the CAD representatives, i.e., ebastine on the membrane and ASM.

Our results confirm the ASM association to the membrane through the saposin domain, previously only showed with coarse grained models. Furthermore, we elucidated the role of specific residues and ASM-induced membrane curvature in lipid recruitment and orientation. Ebastine also interferes with the association of ASM with the membrane at the level of a loop in the catalytic domain engaging in membrane interactions. Our computational approach, applicable to various CADs or membrane compositions, provides insights into ASM and CAD interaction with the membrane, offering a valuable tool for future studies.
Common anesthetic used in preclinical PET imaging inhibits metabolism of the PET tracer [18F]3F4AP
Authors: Ramos-Torres Karla , Sun Yang , Takahashi Kazue , Zhou Yu-Peng , Brugarolas Pedro
Published: December 2023

PET imaging studies in laboratory animals are almost always performed under isoflurane anesthesia to ensure that the subject stays still during the image acquisition. Isoflurane is effective, safe, and easy to use, and it is generally assumed to not have an impact on the imaging results. Motivated by marked differences observed in [18F]3F4AP brain uptake and metabolism between human and nonhuman primate studies, this study investigates the possible effect of isoflurane on [18F]3F4AP metabolism and brain uptake. Isoflurane was found to largely abolish tracer metabolism in mice resulting in a 3.3-fold higher brain uptake in anesthetized mice at 35 min post radiotracer administration, which replicated the observed effect in unanesthetized humans and anesthetized monkeys. This effect is attributed to isoflurane’s interference in the CYP2E1-mediated breakdown of [18F]3F4AP, which was confirmed by reproducing a higher brain uptake and metabolic stability upon treatment with the known CYP2E1 inhibitor disulfiram. These findings underscore the critical need to examine the effect of isoflurane in PET imaging studies before translating tracers to humans that will be scanned without anesthesia.
Prenatal exposure to valproic acid reduces synaptic δ-catenin levels and disrupts ultrasonic vocalization in neonates
Authors: Roh Seung Hyun , Mendez-Vazquez Hadassah , Sathler Matheus F. , Doolittle Michael J. , Zaytseva Anastasiya , Brown Hannah , Sainsbury Morgan , Kim Seonil
Published: December 2023

Valproic acid (VPA) is an effective and commonly prescribed drug for epilepsy and bipolar disorder. However, children born from mothers treated with VPA during pregnancy exhibit an increased incidence of autism spectrum disorder (ASD). Although VPA may impair brain development at the cellular level, the mechanism of VPA-induced ASD has not been completely addressed. A previous study has found that VPA treatment strongly reduces δ-catenin mRNA levels in cultured human neurons. δ-catenin is important for the control of glutamatergic synapses and is strongly associated with ASD. VPA inhibits dendritic morphogenesis in developing neurons, an effect that is also found in neurons lacking δ-catenin expression. We thus hypothesize that prenatal exposure to VPA significantly reduces δ-catenin levels in the brain, which impairs glutamatergic synapses to cause ASD. Here, we found that prenatal exposure to VPA markedly reduced δ-catenin levels in the brain of mouse pups. VPA treatment also impaired dendritic branching in developing mouse cortical neurons, which was reversed by elevating δ-catenin expression. Prenatal VPA exposure significantly reduced synaptic AMPA receptor levels and postsynaptic density 95 (PSD95) in the brain of mouse pups, indicating dysfunctions in glutamatergic synaptic transmission. VPA exposure also significantly altered ultrasonic vocalization (USV) in newly born pups when they were isolated from their nest. Moreover, VPA-exposed pups show impaired hypothalamic response to isolation, which is required to produce animals’ USVs following isolation from the nest. Therefore, these results suggest that VPA-induced ASD pathology can be mediated by the loss of δ-catenin functions.

Highlights

Prenatal exposure of valproic acid (VPA) in mice significantly reduces synaptic δ-catenin protein and AMPA receptor levels in the pups’ brains.

VPA treatment significantly impairs dendritic branching in cultured cortical neurons, which is reversed by increased δ-catenin expression.

VPA exposed pups exhibit impaired communication such as ultrasonic vocalization.

Neuronal activation linked to ultrasonic vocalization is absent in VPA-exposed pups.

The loss of δ-catenin functions underlies VPA-induced autism spectrum disorder (ASD) in early childhood.
AVENGERS: Analysis of Variant Effects using Next Generation sequencing to EnhanceBRCA2Stratification
Authors: Sahu Sounak , Galloux Melissa , Southon Eileen , Caylor Dylan , Sullivan Teresa , Arnaudi Matteo , Geh Josephine , Chari Raj , Papaleo Elena , Sharan Shyam K.
Published: December 2023

Accurate interpretation of genetic variation is a critical step towards realizing the potential of precision medicine. Sequencing-based genetic tests have uncovered a vast array ofBRCA2sequence variants. Due to limited clinical, familial and/or epidemiological data, thousands of variants are considered to be variants of uncertain significance (VUS). To determine the functional impact of VUSs, here we develop AVENGERS: Analysis of Variant Effects using NGs to Enhance BRCA2 Stratification, utilizing CRISPR-Cas9-based saturation genome editing (SGE) in a humanized-mouse embryonic stem cell line. We have categorized nearly all possible missense single nucleotide variants (SNVs) encompassing the C-terminal DNA binding domain ofBRCA2.We have generated the function scores for 6270 SNVs, covering 95.5% of possible SNVs in exons 15-26 spanning residues 2479-3216, including 1069 unique missense VUS, with 81% functional and 14% found to be nonfunctional. Our classification aligns strongly with pathogenicity data from ClinVar, orthogonal functional assays and computational meta predictors. Our statistical classifier exhibits 92.2% sensitivity and 96% specificity in distinguishing clinically benign and pathogenic variants recorded in ClinVar. Furthermore, we offer proactive evidence for 617 SNVs being non-functional and 3396 SNVs being functional demonstrated by impact on cell growth and response to DNA damaging drugs like cisplatin and olaparib. This classification serves as a valuable resource for interpreting unidentified variants in the population and for physicians and genetic counselors assessingBRCA2VUSs in patients.
A molecular toolkit for heterologous protein secretion across Bacteroides species
Authors: Yeh Yu-Hsuan , Kelly Vince W. , Pour Rahman Rahman , Sirk Shannon J.
Published: December 2023

Bacteroides species are abundant and prevalent stably colonizing members of the human gut microbiota, making them a promising chassis for developing long-term interventions for chronic diseases. Engineering these bacteria as on-site production and delivery vehicles for biologic drugs or diagnostics, however, requires efficient heterologous protein secretion tools, which are currently lacking. To address this limitation, we systematically investigated methods to enable heterologous protein secretion in Bacteroides using both endogenous and exogenous secretion systems. Here, we report a collection of secretion carriers that can export functional proteins across multiple Bacteroides species at high titers. To understand the mechanistic drivers of Bacteroides secretion, we characterized signal peptide sequence features as well as post-secretion extracellular fate and cargo size limit of protein cargo. To increase titers and enable flexible control of protein secretion, we developed a strong, self-contained, inducible expression circuit. Finally, we validated the functionality of our secretion carriers in vivo in a mouse model. This toolkit should enable expanded development of long-term living therapeutic interventions for chronic gastrointestinal disease.
Genetic landscape of anin vivoprotein interactome
Authors: Besse Savandara , Sakaguchi Tatsuya , Gauthier Louis , Sahaf Zahra , Péloquin Olivier , Gonzalez Lidice , Castellanos-Girouard Xavier , Koçatug Nazli , Matta Chloé , Hussin Julie G. , Michnick Stephen W. , Serohijos Adrian W.R.
Published: December 2023

Protein-protein interaction (PPI) networks accurately map environmental perturbations to their molecular consequences in cells, but effects of genome-wide genetic variation on PPIs remain unknown. We hypothesized that PPI networks integrate genetic and environmental effects, potentially defining biochemical mechanisms underlying complex polygenic traits. Here, we measured 61 PPIs in inbred strains ofSaccharomyces cerevisiaewith ∼12,000 single-nucleotide polymorphisms (SNPs) across the genome. Unlike mRNA expression and protein abundance that are primarily affected by SNPs local (in “cis”) to a gene, PPIs are predominantly affected by SNPs far (in “trans”) to the genomic loci of the interacting proteins. However, consistent with the PPI network’s small-world characteristic, these transacting SNPs are in neighboring genes in the network. We likewise discovered SNPs in non-coding RNAs and post-transcriptional regulators (3’ UTRs) with, counterintuitively, larger PPI-modulating effects than SNPs within protein-coding regions. Finally, we inferred known and novel mechanisms of action for yeast and human drugs.

HIGHLIGHTS

Protein-interaction quantitative trait locus (“piQTL”) mapping reveals sensitivity ofin vivoPPIs to polymorphisms across the yeast genome

Trans-piQTLs significantly outnumber and are stronger than cis-piQTLs

SNPs in non-coding RNAs and 3’ UTRs have comparable effects to PPI as SNPs in coding regions

piQTL mapping reveals known and novel mechanism of yeast and human drugs
A high-throughput screening approach to discover potential colorectal cancer chemotherapeutics: Repurposing drugs to disrupt 14-3-3 protein-BAD interactions
Authors: He Siyi , Silva Luis Delgadillo , Rutter Guy A. , Lim Gareth E.
Published: December 2023

Inducing apoptosis in different types of cancer cells is an effective therapeutic strategy. However, the success of existing chemotherapeutics can be compromised by tumor cell resistance and systemic off-target effects. Therefore, the discovery of pro-apoptotic compounds with minimal systemic side-effects is crucial. 14-3-3 proteins are molecular scaffolds that serve as important regulators of cell survival. Our previous study demonstrated that 14-3-3ζ can sequester BAD, a pro-apoptotic member of the BCL-2 protein family, in the cytoplasm and prevent its translocation to mitochondria to inhibit the induction of apoptosis. Despite being a critical mechanism of cell survival, it is unclear whether disrupting 14-3-3 protein:BAD interactions could be harnessed as a chemotherapeutic approach. Herein, we established a BRET-based high-throughput drug screening approach (Z’-score= 0.52) capable of identifying molecules that can disrupt 14-3-3ζBAD interactions. An FDA-approved drug library containing 1971 compounds was used for screening, and the capacity of identified hits to induce cell death was examined in NIH3T3-fibroblasts and colorectal cancer cell lines, HT-29 and Caco-2. Ourin vitroresults suggest that terfenadine, penfluridol, and lomitapide could be potentially repurposed for treating colorectal cancer. Moreover, our screening method demonstrates the feasibility of identifying pro-apoptotic agents that can be applied towards conditions where aberrant cell growth or function are key determinants of disease pathogenesis.
Ecological niche contributes to the persistence of the Western x Glaucous-winged Gull hybrid zone
Authors: Geng Xuewen , Summers Jeremy , Chen Nancy
Published: December 2023

Hybrid zones occur in nature when populations with limited reproductive barriers overlap in space. Many hybrid zones persist over time, and different models have been proposed to explain how selection can maintain hybrid zone stability. More empirical studies are needed to elucidate the role of ecological adaptation in maintaining stable hybrid zones. Here, we investigated the role of exogenous factors in maintaining a hybrid zone between western gulls (Larus occidentalis) and glaucous-winged gulls (L. glaucescens). We used ecological niche models (ENMs) and niche similarity tests to quantify and examine the ecological niches of western gulls, glaucous-winged gulls, and their hybrids. We found evidence of niche divergence between all three groups. Our results best support the bounded superiority model, providing further evidence that exogenous selection favoring hybrids may be an important factor in maintaining this stable hybrid zone.
Metabolic and genomic characterization of two novel butyrate producing Lachnospiraceae isolated from swine feces
Authors: Watkins Hannah R. , Trachsel Julian M. , Bearson Shawn M. D. , Loving Crystal L. , Anderson Christopher L.
Published: December 2023

Commensal bacteria from the swine gut microbiome that can be isolated have numerous potential applications in the animal production industry, including mitigation of disease, improving performance, and promoting colonization resistance to human foodborne pathogens. Butyrate-producing bacteria are targets for next-generation probiotics and microbiome-engineering strategies because butyrate is a metabolite of central importance in large intestinal homeostasis and may augment colonization resistance to enteric pathogens. However, relatively few butyrate-producers from swine have been cultured and extensively characterized. Here, we describe the substrate utilization, metabolic profiles, and genomic features of two novel species that produce high concentration of butyratein vitro,Roseburia sp.831b andPetralouisia sp.499, isolated from swine feces. The complete genomes illustrated versatility in carbon metabolism and unique carbohydrate-active enzymes not observed in other species ofRoseburiaandPetralouisiathat encode a combination of glycosidic hydrolases and carbohydrate-binding modules involved in starch and pectin utilization.Roseburia sp.831b fermented a broader range and more complex mono- and polysaccharides thanPetralouisia sp.499. Fecal and cecal metagenomes from eight-week-old pigs challenged with Salmonella revealed thatRoseburia sp.831b increased to detectable abundances in the swine hindgut in most animals at ∼63-70 days of age. Additionally, the abundance ofRoseburia sp.831b in fecal metagenomes correlated with fecal butyrate concentrations in the pigs fed a diet supplemented with a prebiotic resistant potato starch. Together, these findings highlight the probiotic potential and ecological niche in the swine gastrointestinal tract for two novel butyrate-producers.

Importance

Antibiotics have been important for swine production and management of enteric pathogens; however, the Veterinary Feed Directive limits the use of medically important in-feed antibiotics for production purposes. As a result, there is a need for alternatives to antibiotics. Butyrate-producing bacteria can improve colonization resistance to human pathogens within the swine gastrointestinal tract by reinforcing the intestinal barrier, increasing mucus production, and reducing local oxygen and pH levels. Here, we demonstrate the versatile substrate utilization and metabolic potential of two novel species isolated from swine that produce high butyrate concentrationsin vitro. These findings will help develop strategies that increase the abundance of these species and other butyrate producers in the swine gut. Further, isolating and characterizing swine butyrate producers is necessary for controlled studies that provide a mechanistic understanding of how this functional group of bacteria promotes swine gut health and colonization resistance to bacteria of public health concern.
50-color phenotyping of the human immune system with in-depth assessment of T cells and dendritic cells
Authors: Konecny Andrew J. , Mage Peter , Tyznik Aaron J. , Prlic Martin , Mair Florian
Published: December 2023

We report the development of an optimized 50-color spectral flow cytometry panel designed for the in-depth analysis of the immune system in human blood and tissues, with the goal of maximizing the amount of information that can be collected using currently available flow cytometry platforms. We established and tested this panel using peripheral blood mononuclear cells (PBMCs), but included CD45 to enable its use for the analysis of human tissue samples. The panel contains lineage markers for all major immune cell subsets, and an extensive set of phenotyping markers focused on the activation and differentiation status of the T cell and dendritic cell (DC) compartment.

We outline the biological insight that can be gained from the simultaneous measurement of such a large number of proteins and propose that this approach provides a unique opportunity for the comprehensive exploration of the immune status in tissue biopsies and other human samples with a limited number of cells. Of note, we tested the panel to be compatible with cell sorting for further downstream applications. Furthermore, to facilitate the wide-spread implementation of such a panel across different cohorts and samples, we established a trimmed-down 45-color version which can be used with different spectral cytometry platforms.

Finally, to generate this panel, we utilized not only existing panel design guidelines, but also developed new metrics to systematically identify the optimal combination of 50 fluorochromes and evaluate fluorochrome-specific resolution in the context of a 50-color unmixing matrix.
BMI and BPH correlate with urinary microbiome diversity and lower urinary tract symptoms in men
Authors: Bowie Kate R. , Garzotto Mark , Orwoll Eric , Karstens Lisa
Published: December 2023

Several studies have identified bacteria and other microbes in the bladder and lower urinary tract in the absence of infection. In women, the urinary microbiome has been associated with lower urinary tract symptoms (LUTS), however, similar studies have not been undertaken in large cohorts of men. Here we examine the urinary microbiome and its association with LUTS in a subset of 500 men aged 65 to 90 years from the Osteoporotic Fractures in Men (MrOS) study. We identified significant associations between benign prostatic hyperplasia (BPH), age, and body mass index (BMI) with several diversity metrics. Our analysis revealed complex relationships between BMI, BPH, LUTS, and alpha diversity which give insight into the intricate dynamics of the urinary microbiome. By beginning to uncover the interrelationships of BPH, BMI, LUTS, and the urinary microbiome, these results can inform future study design to better understand the heterogeneity of the male urinary microbiome.
SpatialPPI: three-dimensional space protein-protein interaction prediction with AlphaFold Multimer
Authors: Hu Wenxing , Ohue Masahito
Published: December 2023

The rapid advancement of protein sequencing technology has resulted in a gap between proteins with identified sequences and those with mapped structures. Although sequence-based predictions offer insights, they can be incomplete due to the absence of structural details. On the other hand, structure-based methods face challenges with newly sequenced proteins. AlphaFold emerges as a potential solution, especially in predicting protein-protein interactions. This research delves into using deep neural networks, specifically analyzing protein complex structures as predicted by AlphaFold Multimer. By transforming atomic coordinates and utilizing sophisticated image processing techniques, the study extracts vital 3D structural details from protein complexes. Recognizing the significance of evaluating residue distances in protein interactions, the study leverages image recognition approaches, notably integrating DenseNet and ResNet within 3D convolutional networks for protein 3D structure analysis. When benchmarked against leading protein-protein interaction prediction methods like SpeedPPI, D-script, DeepTrio, and PEPPI, our proposed method, named SpatialPPI, exhibits notable efficacy, emphasizing the promising role of 3D spatial processing in advancing the realm of structural biology.

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