bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term dietary exposure to a mixture of phthalates enhances estrogen and beta-catenin signaling pathways, leading to endometrial hyperplasia in mice
Authors: Shukla Ritwik , Kannan Athilakshmi , Laws Mary J. , Johnson Amy Wagoner , Flaws Jodi A. , Bagchi Milan K. , Bagchi Indrani C. 
Published: September 2024

ABSTRACTPhthalates, synthetic chemicals widely utilized as plasticizers and stabilizers in various consumer products, present a significant concern due to their persistent presence in daily human life. While past research predominantly focused on individual phthalates, real-life human exposure typically encompasses complex mixtures of these compounds. The cumulative effects of prolonged exposure to phthalate mixtures on uterine health remain poorly understood. To address this knowledge gap, we conducted studies utilizing adult female mice exposed to a phthalate mixture for 6 and 12 months through ad libitum chow consumption. We previously reported that continuous exposure to this phthalate mixture for 6 months led to uterine fibrosis. In this study, we show that the exposure, when continued beyond 6 months to 1 year, caused fibrotic uteri to display hyperplasia with a significant increase in gland to stroma ratio. Endometrial hyperplasia is commonly caused by unopposed estrogen action, which promotes increased expression of pro-inflammatory cytokines and chemokines and proliferation of the endometrial epithelial cells. Indeed, RNA sequencing analysis revealed a marked upregulation of several estrogen-regulated genes, Wnt ligands that are involved in oncogenic pathways, as well as chemokines, in phthalate-exposed uterine tissues. Consequently, the exposed uteri exhibited increased proliferation of endometrial epithelial cells, and a heightened inflammatory response indicated by extensive homing of macrophages. Further studies revealed a marked enhancement of the Wnt/β-Catenin signaling pathway, potentially contributing to the development of endometrial hyperplasia. Collectively, this study underscores the significance of understanding the exposure to environmental factors in the pathogenesis of endometrial disorders.
TIRTL-seq: Deep, quantitative, and affordable paired TCR repertoire sequencing
Authors: Pogorelyy Mikhail V. , Kirk Allison M. , Adhikari Samir , Minervina Anastasia A. , Sundararaman Balaji , Vegesana Kasi , Brice David C. , Scott Zachary B. ,   SJTRC Study Team, Thomas Paul G. 
Published: September 2024

Abstractɑ/β T cells are key players in adaptive immunity. The specificity of T cells is determined by the sequences of the hypervariable T cell receptor (TCR) ɑ and β chains. Although bulk TCR sequencing offers a cost-effective approach for in-depth TCR repertoire profiling, it does not provide chain pairings, which are essential for determining T cell specificity. In contrast, single-cell TCR sequencing technologies produce paired chain data, but are limited in throughput to thousands of cells and are cost-prohibitive for cohort-scale studies.Here, we presentTIRTL-seq (Throughput-IntensiveRapidTCRLibrarysequencing), a novel approach that generates ready-to-sequence TCR libraries from live cells in less than 7 hours. The protocol is optimized for use with non-contact liquid handlers in an automation-friendly 384-well plate format. Reaction volume miniaturization reduces library preparation costs to <$0.50 per well.The core principle of TIRTL-seq is the parallel generation of hundreds of libraries providing multiple biological replicates from a single sample that allows precise inference of both frequencies of individual clones and TCR chain pairings from well-occurrence patterns. We demonstrate scalability of our approach up to 1 million unique paired ɑβTCR clonotypes corresponding to over 30 million T cells per sample at a cost of less than $2000. For a sample of 10 million cells the cost is ∼$200. We benchmarked TIRTL-seq against state-of-the-art 5’RACE bulk TCR-seq and 10x Genomics Chromium technologies on longitudinal samples. We show that TIRTL-seq is able to quantitatively identify expanding and contracting clonotypes between timepoints while providing accurate TCR chain pairings, including distinct temporal dynamics of SARS-CoV-2-specific and EBV-specific CD8+ T cell responses after infection. While clonal expansion was followed by sharp contraction for SARS-CoV-2 specific TCRs, EBV-specific TCRs remained stable once established.The sequences of both ɑ and β TCR chains are essential for determining T cell specificity. As the field moves towards greater applications in diagnostics and immunotherapy that rely on TCR specificity, we anticipate that our scalable paired TCR sequencing methodology will be instrumental for collecting large paired-chain datasets and ultimately extracting therapeutically relevant information from the TCR repertoire.
Fibroblasts Regulate the Transformation Potential of Human Papillomavirus-positive Keratinocytes
Authors: James Claire D. , Lewis Rachel L. , Witt Austin J. , Carter Christiane , Rais Nabiha M. , Wang Xu , Bristol Molly L. 
Published: September 2024

AbstractPersistent human papillomavirus (HPV) infection is necessary but insufficient for viral oncogenesis. Additional contributing co-factors, such as immune evasion and viral integration have been implicated in HPV-induced cancer progression. It is widely accepted that HPV+ keratinocytes require co-culture with fibroblasts to maintain viral episome expression, yet the exact mechanisms for this have yet to be elucidated. Here we present comprehensive RNA sequencing and proteomic analysis demonstrating that fibroblasts not only support the viral life cycle, but reduce HPV+ keratinocyte transformation. Our co-culture models offer novel insights into HPV-related transformation mechanisms.HighlightsFibroblasts support HPV RNA expression and episomal maintenance in HPV+ keratinocytesFibroblasts reduce EMT related expression in HPV+ keratinocytesFibroblasts promote EMT related expression in E6E7+ keratinocytes
Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC
Authors: Jha Anupama , Hristov Borislav , Wang Xiao , Wang Sheng , Greenleaf William J. , Kundaje Anshul , Aiden Erez Lieberman , Bertero Alessandro , Noble William Stafford 
Published: September 2024

AbstractThree-dimensional nuclear DNA architecture comprises well-studied intra-chromosomal (cis) folding and less characterized inter-chromosomal (trans) interfaces. Current predictive models of 3D genome folding can effectively infer pairwisecis-chromatin interactions from the primary DNA sequence but generally ignoretranscontacts. There is an unmet need for robust models oftrans-genome organization that provide insights into their underlying principles and functional relevance. We present TwinC, an interpretable convolutional neural network model that reliably predictstranscontacts measurable through genome-wide chromatin conformation capture (Hi-C). TwinC uses a paired sequence design from replicate Hi-C experiments to learn single base pair relevance intransinteractions across two stretches of DNA. The method achieves high predictive accuracy (AUROC=0.80) on a cross-chromosomal test set from Hi-C experiments in heart tissue. Mechanistically, the neural network learns the importance of compartments, chromatin accessibility, clustered transcription factor binding and G-quadruplexes in formingtranscontacts. In summary, TwinC models and interpretstransgenome architecture, shedding light on this poorly understood aspect of gene regulation.
A Kinetic Scout Approach Accelerates Targeted Protein Degrader Development
Authors: Fan Angela T. , Gadbois Gillian E. , Huang Hai-Tsang , Jiang Jiewei , Sigua Logan H. , Smith Emily R. , Wu Sitong , Dunne-Dombrink Kara , Goyal Pavitra , Tao Andrew J. , Sellers William , Fischer Eric S. , Donovan Katherine A. , Ferguson Fleur M. 
Published: September 2024

AbstractBifunctional molecules such as targeted protein degraders induce proximity to promote gain-of-function pharmacology. These powerful approaches have gained broad traction across academia and the pharmaceutical industry, leading to an intensive focus on strategies that can accelerate their identification and optimization. We and others have previously used chemical proteomics to map degradable target space, and these datasets have been used to develop and train multiparameter models to extend degradability predictions across the proteome. In this study, we now turn our attention to develop generalizable chemistry strategies to accelerate the development of new bifunctional degraders. We implement lysine-targeted reversible-covalent chemistry to rationally tune the binding kinetics at the protein-of-interest across a set of 25 targets. We define an unbiased workflow consisting of global proteomics analysis, IP/MS of ternary complexes and the E-STUB assay, to mechanistically characterize the effects of ligand residence time on targeted protein degradation and formulate hypotheses about the rate-limiting step of degradation for each target. Our key finding is that target residence time is a major determinant of degrader activity, and this can be rapidly and rationally tuned through the synthesis of a minimal number of analogues to accelerate early degrader discovery and optimization efforts.
Clonal dynamics and somatic evolution of haematopoiesis in mouse
Authors: Kapadia Chiraag D. , Williams Nicholas , Dawson Kevin J. , Watson Caroline , Yousefzadeh Matthew J. , Le Duy , Nyamondo Kudzai , Cagan Alex , Waldvogel Sarah , De La Fuente Josephine , Leongamornlert Daniel , Mitchell Emily , Florez Marcus A. , Aguilar Rogelio , Martell Alejandra , Guzman Anna , Harrison David , Niedernhofer Laura J. , King Katherine Y. , Campbell Peter J. , Blundell Jamie , Goodell Margaret A. , Nangalia Jyoti 
Published: September 2024

AbstractHaematopoietic stem cells maintain blood production throughout life. While extensively characterised using the laboratory mouse, little is known about how the population is sustained and evolves with age. We isolated stem cells and progenitors from young and old mice, identifying 221,890 somatic mutations genome-wide in 1845 single cell-derived colonies, and used phylogenetic analysis to infer the ontogeny and population dynamics of the stem cell pool. Mouse stem cells and progenitors accrue ∼45 somatic mutations per year, a rate only about 2-fold greater than human progenitors despite the vastly different organismal sizes and lifespans. Phylogenetic patterns reveal that stem and multipotent progenitor cell pools are both established during embryogenesis, after which they independently self-renew in parallel over life. The stem cell pool grows steadily over the mouse lifespan to approximately 70,000 cells, self-renewing about every six weeks. Aged mice did not display the profound loss of stem cell clonal diversity characteristic of human haematopoietic ageing. However, targeted sequencing revealed small, expanded clones in the context of murine ageing, which were larger and more numerous following haematological perturbations and exhibited a selection landscape similar to humans. Our data illustrate both conserved features of population dynamics of blood and distinct patterns of age-associated somatic evolution in the short-lived mouse.
Improving Structural Plausibility in 3D Molecule Generation via Property-Conditioned Training with Distorted Molecules
Authors: Vost Lucy , Chenthamarakshan Vijil , Das Payel , Deane Charlotte M. 
Published: September 2024

AbstractTraditional drug design methods are costly and time-consuming due to their reliance on trial-and-error processes. As a result, computational methods, including diffusion models, designed for molecule generation tasks have gained significant traction. Despite their potential, they have faced criticism for producing physically implausible outputs. We alleviate this problem by conditionally training a diffusion model capable of generating molecules of varying and controllable levels of structural plausibility. This is achieved by adding distorted molecules to training datasets, and then annotating each molecule with a label representing the extent of its distortion, and hence its quality. By training the model to distinguish between favourable and unfavourable molecular conformations alongside the standard molecule generation training process, we can selectively sample molecules from the high-quality region of learned space, resulting in improvements in the validity of generated molecules. In addition to the standard two datasets used by molecule generation methods (QM9 and GEOM), we also test our method on a druglike dataset derived from ZINC. We use our conditional method with EDM, the first E(3) equivariant diffusion model for molecule generation, as well as two further models—a more recent diffusion model and a flow matching model—which were built off EDM. We demonstrate improvements in validity as assessed by RD-Kit parsability and the PoseBusters test suite; more broadly, though, our findings highlight the effectiveness of conditioning methods on low-quality data to improve the sampling of high-quality data.
Characterizing human CMV-specific CD8+T cells using multi-layer single-cell omics
Authors: Gemünd Ioanna , Bonaguro Lorenzo , Becker Matthias , Müller Sophie , Joos Clemens , De Domenico Elena , Aschenbrenner Anna C , Schultze Joachim L , Moosmann Andreas , Beyer Marc D 
Published: September 2024

SummaryIn this study we established a comprehensive workflow to collect multi-omics single-cell data using a commercially available micro-well based platform. This included whole transcriptome, cell surface markers (targeted sequencing-based cell surface proteomics), T cell specificities, adaptive immune receptor repertoire (AIRR) profiles and sample multiplexing. With this technique we identified novel paired T cell receptor sequences for three prominent human CMV epitopes. In addition, we review the ability of dCODE dextramers to detect antigen-specific T cells at low frequencies by estimating sensitivities and specificities when used as reagents for single-cell multi-omics.MotivationIn this study, we report the first five-layer multi-omics dataset using the BD Rhapsody single-cell platform for the characterization of human antigen-specific T cells. Modalities include whole transcriptome, T cell receptor (TCR) sequences, T cell antigen specificity measured by dCODE dextramers, surface marker proteins and combinatorial sample multiplexing combining two distinct hashing approaches.
Retinal ganglion cell vulnerability to pathogenic tau in Alzheimer’s disease
Authors: Davis Miyah R. , Robinson Edward , Koronyo Yosef , Salobrar-Garcia Elena , Rentsendorj Altan , Gaire Bhakta P. , Mirzaei Nazanin , Kayed Rakez , Sadun Alfredo A. , Ljubimov Alexander V. , Schneider Lon S. , Hawes Debra , Black Keith L. , Fuchs Dieu-Trang , Koronyo-Hamaoui Maya 
Published: September 2024

AbstractAccumulation of pathological tau isoforms, especially hyperphosphorylated tau at serine 396 (pS396-tau) and tau oligomers, has been demonstrated in the retinas of patients with mild cognitive impairment (MCI) and Alzheimer’s disease (AD). Previous studies have noted a decrease in retinal ganglion cells (RGCs) in AD patients, but the presence and impact of pathological tau isoforms in RGCs and RGC integrity, particularly in early AD stages, have not been explored. To investigate this, we examined retinal superior temporal cross-sections from 25 patients with MCI (due to AD) or AD dementia and 16 cognitively normal (CN) controls, matched for age and gender. We utilized the RGC marker ribonucleic acid binding protein with multiple splicing (RBPMS) and Nissl staining to assess neuronal density in the ganglion cell layer (GCL). Our study found that hypertrophic RGCs containing pS396-tau and T22-positive tau oligomers were more frequently observed in MCI and AD patients compared to CN subjects. Quantitative analyses indicated a decline in RGC integrity, with 46-55% and 55-56% reductions of RBPMS+RGCs (P<0.01) and Nissl+GCL neurons (P<0.01-0.001), respectively, in MCI and AD patients. This decrease in RGC count was accompanied by increases in necroptotic-like morphology and the cleaved caspase-3 apoptotic marker in RGCs of AD patients. Furthermore, there was a 2.1 to 3.1-fold increase (P<0.05-0.0001) in pS396-tau-laden RGCs in MCI and AD patients, with a greater abundance observed in individuals with higher Braak stages (V-VI), more severe clinical dementia ratings (CDR=3), and lower mini-mental state examination (MMSE) scores. Strong correlations were noted between the decline in RGCs and the total amount of retinal pS396-tau and pS396-tau+RGCs, with pS396-tau+RGC counts correlating significantly with brain neurofibrillary tangle scores (r= 0.71, P= 0.0001), Braak stage (r= 0.65, P= 0.0009), and MMSE scores (r= -0.76, P= 0.0004). These findings suggest that retinal tauopathy, characterized by pS396-tau and oligomeric tau in hypertrophic RGCs, is associated with and may contribute to RGC degeneration in AD. Future research should validate these findings in larger cohorts and explore noninvasive retinal imaging techniques that target tau pathology in RGCs to improve AD detection and monitor disease progression.
CCR2 limits inflammatory functions of CD8 TRM cells that impair recognition memory during recovery from WNV encephalitis
Authors: Ai Shenjian , Arutyunov Artem , Liu Joshua , Hill Jeremy D. , Jiang Xiaoping , Klein Robyn S. 
Published: September 2024

AbstractCentral nervous system (CNS) resident memory CD8 T cells (TRM) that express IFN-γ contribute to neurodegenerative processes, including synapse loss, leading to memory impairments. Here, we show that CCR2 signalling in CD8 TRMthat persist within the hippocampus after recovery from CNS infection with West Nile virus (WNV) significantly prevents the development of memory impairments. Using CCR2-deficient mice, we determined that CCR2 expression is not essential for CNS T cell recruitment or virologic control during acute WNV infection. However, transcriptomic analyses of forebrain CCR2+versus CCR2-CD8 TRMduring WNV recovery reveal that CCR2 signalling significantly regulates hippocampal CD8 TRMphenotype and function via extrinsic and intrinsic effects, decreasing the expression of CD103 and granzyme A and IFN-γ, respectively. Consistent with this, WNV-recoveredCd8acreCcr2fl/flmice exhibit decreased recognition memory. Our findings highlight a neuroprotective role for CCR2 in limiting CD8 T cell-mediated neuroinflammation and cognitive deficits, providing insights into potential therapeutic targets for CNS infections.
Vapor pressure deficit dominates the spatiotemporal variations in ecosystem photosynthetic quantum yield
Authors: Yu Liyao , Luo Xiangzhong , Zhao Ruiying , Satriawan Tin W. , Tian Jiaqi 
Published: September 2024

SummaryThe quantum yield (α) of photosynthesis represents the maximum efficiency of light use as indicated by the initial slope of photosynthetic light response curves. Understandingαis crucial for accurate modeling of photosynthesis and terrestrial carbon cycle. Despite its importance, the spatial and temporal variations inαat large scales remain largely elusive.We leveraged long-term eddy-covariance observations from 90 sites globally and examined the spatiotemporal variations inαdue to climatic drivers, using statistical and machine learning approaches.We found significant spatial variability inαacross and within biomes, primarily driven by atmospheric vapor pressure deficit and soil moisture variations. Meanwhile, the temporal changes inαare mainly driven by the negative effect of vapor pressure deficit, which weakens the positive effects of elevated CO2and leaf area index.Our results highlight the dominant role of vapor pressure deficit in controlling the spatiotemporal variations ofαas well as the unneglectable impacts of soil water content, CO2, and leaf area onα. Those new results provide insights for improving the representation ofαin ecosystem photosynthesis models.
Bolero: a dedicated workflow to decipher Hepatitis B virus transcriptome from long-reads sequencing method coupled to 5’RACE amplification of transcripts
Authors: Grand Xavier , Giraud Guillaume , Rifki Alia , Paturel Alexia , Bousquet Delphine , Roca Suarez Armando Andres , Bourgeois Cyril , Levrero Massimo , Zoulim Fabien , Testoni Barbara 
Published: September 2024

AbstractHepatitis B virus (HBV) represents a major health burden, as it affects close to 290 million people worldwide. Although prophylactic vaccines are available, current therapeutic compounds do not usually achieve HBV eradication due to the persistence of the covalently closed circular (ccc)DNA that serves as viral reservoir. Thus, novel biomarkers that reliably reflect intrahepatic cccDNA transcriptional activity would be highly relevant for the monitoring of infected individuals, as well as the evaluation of new treatments targeting HBV. In this context, the development of 5’ rapid amplification of complementary DNA ends (5’RACE) as a strategy to capture and amplify full-length HBV RNAs, coupled with long-read and full-length sequencing approaches (e.g., Oxford Nanopore Technology), has recently enabled the detailed characterization of these molecules. The analysis of such data requires a dedicated bioinformatics pipeline due to the highly condensed nature of the HBV genome, which is characterized by the production of multiple transcripts and spliced variants that overlap each other. Here, we present Bolero, a computational method and built-in workflow designed to handle HBV sequencing data and evaluate the relative expression of viral RNAs and their spliced variants. The analysis of HBV-infected cell lines demonstrates that our bioinformatics pipeline is efficient for the identification and quantification of individual HBV mRNAs. Thus, Bolero represents a useful tool to study cccDNA transcriptional activity and the heterogeneity of HBV RNA spliced variants.Author summaryTranscriptomic analyses have brought comprehensive insights in the mechanisms controlling gene expression. Moreover, with the recent advances in sequencing technologies and computational methods, researchers can nowadays not only quantify gene expression, but also study alternative splicing, polyadenylation, transcription initiation, and even rare phenomena such as distant gene fusions. However, conventional analysis tools still rely heavily on the assumption of linear genomes with minimal overlap between open reading frames, rendering them insufficient for studying complex viruses such as hepatitis B virus (HBV).Unlike typical linear genomes, HBV genome consists in a circular DNA molecule, which results in an extensive sequence overlap between its transcripts. To tackle these challenges, we developed an innovative approach coupling 5’ rapid amplification of complementary DNA ends (5’RACE) and long-read sequencing to comprehensively explore the HBV transcriptome. Furthermore, we developed Bolero, a computational method designed to handle the peculiarities of HBV sequencing data, which allows a detailed characterization of the HBV transcriptome.